Test [1/132] General test of command line generation Test [2/132] Test nested prefixes with arrays Test [3/132] Test nested command line bindings Test [4/132] Test command line with optional input (missing) Test [5/132] Test command line with optional input (provided) Test [6/132] Test InitialWorkDirRequirement ExpressionEngineRequirement.engineConfig feature v1.0/template-tool.cwl:7:9: JSHINT: exports = module.exports = _; v1.0/template-tool.cwl:7:9: JSHINT: ^ v1.0/template-tool.cwl:7:9: JSHINT: W117: 'exports' is not defined. v1.0/template-tool.cwl:7:9: JSHINT: exports._ = _; v1.0/template-tool.cwl:7:9: JSHINT: ^ v1.0/template-tool.cwl:7:9: JSHINT: W117: 'exports' is not defined. v1.0/template-tool.cwl:7:9: JSHINT: if (typeof module !== 'undefined' && module.exports) { v1.0/template-tool.cwl:7:9: JSHINT: ^ v1.0/template-tool.cwl:7:9: JSHINT: W117: 'module' is not defined. v1.0/template-tool.cwl:7:9: JSHINT: exports = module.exports = _; v1.0/template-tool.cwl:7:9: JSHINT: ^ v1.0/template-tool.cwl:7:9: JSHINT: W117: 'module' is not defined. v1.0/template-tool.cwl:7:9: JSHINT: return setTimeout(function(){ v1.0/template-tool.cwl:7:9: JSHINT: ^ v1.0/template-tool.cwl:7:9: JSHINT: W117: 'setTimeout' is not defined. v1.0/template-tool.cwl:7:9: JSHINT: timeout = setTimeout(later, remaining); v1.0/template-tool.cwl:7:9: JSHINT: ^ v1.0/template-tool.cwl:7:9: JSHINT: W117: 'setTimeout' is not defined. v1.0/template-tool.cwl:7:9: JSHINT: timeout = setTimeout(later, wait - last); v1.0/template-tool.cwl:7:9: JSHINT: ^ v1.0/template-tool.cwl:7:9: JSHINT: W117: 'setTimeout' is not defined. v1.0/template-tool.cwl:7:9: JSHINT: if (!timeout) timeout = setTimeout(later, wait); v1.0/template-tool.cwl:7:9: JSHINT: ^ v1.0/template-tool.cwl:7:9: JSHINT: W117: 'setTimeout' is not defined. v1.0/template-tool.cwl:7:9: JSHINT: clearTimeout(timeout); v1.0/template-tool.cwl:7:9: JSHINT: ^ v1.0/template-tool.cwl:7:9: JSHINT: W117: 'clearTimeout' is not defined. v1.0/template-tool.cwl:7:9: JSHINT: root._ = previousUnderscore; v1.0/template-tool.cwl:7:9: JSHINT: ^ v1.0/template-tool.cwl:7:9: JSHINT: W117: 'previousUnderscore' is not defined. v1.0/template-tool.cwl:7:9: JSHINT: if (typeof define === 'function' && define.amd) { v1.0/template-tool.cwl:7:9: JSHINT: ^ v1.0/template-tool.cwl:7:9: JSHINT: W117: 'define' is not defined. v1.0/template-tool.cwl:7:9: JSHINT: define('underscore', [], function() { v1.0/template-tool.cwl:7:9: JSHINT: ^ v1.0/template-tool.cwl:7:9: JSHINT: W117: 'define' is not defined. v1.0/template-tool.cwl:8:9: JSHINT: var t = function(s) { return _.template(s, {variable: 'data'})({'inputs': inputs}); }; v1.0/template-tool.cwl:8:9: JSHINT: ^ v1.0/template-tool.cwl:8:9: JSHINT: W117: '_' is not defined. Got workflow error Traceback (most recent call last): File "/home/mcrusoe/cwltool/cwltool/executors.py", line 238, in runner my_job.run(my_runtime_context) File "/home/mcrusoe/src/cwl-tes/cwl_tes/tes.py", line 358, in run task = self.create_task_msg() File "/home/mcrusoe/src/cwl-tes/cwl_tes/tes.py", line 265, in create_task_msg input_parameters = self.get_inputs() File "/home/mcrusoe/src/cwl-tes/cwl_tes/tes.py", line 246, in get_inputs self.parse_listing(self.generatefiles["listing"], inputs) File "/home/mcrusoe/src/cwl-tes/cwl_tes/tes.py", line 213, in parse_listing "The TES spec does not allow for writable inputs" cwltool.errors.UnsupportedRequirement: The TES spec does not allow for writable inputs Workflow or tool uses unsupported feature: The TES spec does not allow for writable inputs Test [7/132] Test command execution in Docker with stdout redirection [job cat3-tool.cwl] job error: Error collecting output for parameter 'output_file': v1.0/cat3-tool.cwl:17:21: Did not find output file with glob pattern: '['output.txt']' Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpg5pwzz1x v1.0/cat3-tool.cwl v1.0/cat-job.json Test command execution in Docker with stdout redirection Returned non-zero Test [8/132] Test command execution in Docker with shortcut stdout redirection [job cat3-tool-shortcut.cwl] job error: Error collecting output for parameter 'output_file': test:1:1: Did not find output file with glob pattern: '['4c79f1d6610e0a12ad7033766053d605d74b2373']' Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpvn9x2xbm v1.0/cat3-tool-shortcut.cwl v1.0/cat-job.json Test command execution in Docker with shortcut stdout redirection Returned non-zero Test [9/132] Test command execution in Docker with mediumcut stdout redirection [job cat3-tool-mediumcut.cwl] job error: Error collecting output for parameter 'output_file': test:1:1: Did not find output file with glob pattern: '['cat-out']' Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpiyjlhzfw v1.0/cat3-tool-mediumcut.cwl v1.0/cat-job.json Test command execution in Docker with mediumcut stdout redirection Returned non-zero Test [10/132] Test command line with stderr redirection [job stderr.cwl] job error: Error collecting output for parameter 'output_file': v1.0/stderr.cwl:11:21: Did not find output file with glob pattern: '['error.txt']' Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpcfywnz6t v1.0/stderr.cwl v1.0/empty.json Test command line with stderr redirection Returned non-zero Test [11/132] Test command line with stderr redirection, brief syntax [job stderr-shortcut.cwl] job error: Error collecting output for parameter 'output_file': test:1:1: Did not find output file with glob pattern: '['0f1c620d001b4fcd3281ec99af6b255e6976092b']' Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpg89b1e9t v1.0/stderr-shortcut.cwl v1.0/empty.json Test command line with stderr redirection, brief syntax Returned non-zero Test [12/132] Test command line with stderr redirection, named brief syntax [job stderr-mediumcut.cwl] job error: Error collecting output for parameter 'output_file': test:1:1: Did not find output file with glob pattern: '['std.err']' Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmp1g2noc7e v1.0/stderr-mediumcut.cwl v1.0/empty.json Test command line with stderr redirection, named brief syntax Returned non-zero Test [13/132] Test command execution in Docker with stdin and stdout redirection [job cat4-tool.cwl] job error: Error collecting output for parameter 'output_txt': v1.0/cat4-tool.cwl:14:7: Did not find output file with glob pattern: '['output.txt']' Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmp8sd46kds v1.0/cat4-tool.cwl v1.0/cat-job.json Test command execution in Docker with stdin and stdout redirection Returned non-zero Test [14/132] Test default usage of Any in expressions. Test [15/132] Test explicitly passing null to Any type inputs with default values. Test [16/132] Testing the string 'null' does not trip up an Any with a default value. Test [17/132] Test Any without defaults cannot be unspecified. Workflow error, try again with --debug for more information: Invalid job input record: v1.0/null-expression2-tool.cwl:9:3: Missing required input parameter 'i1' Test [18/132] Test explicitly passing null to Any type without a default value. Workflow error, try again with --debug for more information: Invalid job input record: v1.0/null-expression2-tool.cwl:9:3: Missing required input parameter 'i1' Test [19/132] Testing the string 'null' does not trip up an Any without a default value. Test [20/132] Testing Any type compatibility in outputSource Test [21/132] Test command execution in with stdin and stdout redirection [job cat-tool.cwl] job error: Error collecting output for parameter 'output': v1.0/cat-tool.cwl:12:22: Did not find output file with glob pattern: '['output']' Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmp3zpmsrj1 v1.0/cat-tool.cwl v1.0/cat-job.json Test command execution in with stdin and stdout redirection Returned non-zero Test [22/132] Test ExpressionTool with Javascript engine Unhandled error, try again with --debug for more information: [Errno 2] No such file or directory: 'ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/4fe3b05d-ef80-43d1-b612-0e3d05aa09cd/inputs/number.txt' Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpzooy3xud v1.0/parseInt-tool.cwl v1.0/parseInt-job.json Test ExpressionTool with Javascript engine Returned non-zero Test [23/132] Test outputEval to transform output [job wc2-tool.cwl] job error: Error collecting output for parameter 'output': v1.0/wc2-tool.cwl:15:9: Expression evaluation error: v1.0/wc2-tool.cwl:15:9: Expecting value: line 1 column 1 (char 0) v1.0/wc2-tool.cwl:15:9: script was: v1.0/wc2-tool.cwl:15:9: 01 "use strict"; v1.0/wc2-tool.cwl:15:9: 02 var inputs = { v1.0/wc2-tool.cwl:15:9: 03 "file1": { v1.0/wc2-tool.cwl:15:9: 04 "class": "File", v1.0/wc2-tool.cwl:15:9: 05 "location": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/897b9961-7d0d-47ea-81ea-bdf29dc68193/inputs/whale.txt", v1.0/wc2-tool.cwl:15:9: 06 "size": 1111, v1.0/wc2-tool.cwl:15:9: 07 "basename": "whale.txt", v1.0/wc2-tool.cwl:15:9: 08 "nameroot": "whale", v1.0/wc2-tool.cwl:15:9: 09 "nameext": ".txt", v1.0/wc2-tool.cwl:15:9: 10 "path": "/tmp/tmpr7a26eam/stg7191e96c-8cd3-4950-894b-26dee9a64cd5/whale.txt", v1.0/wc2-tool.cwl:15:9: 11 "dirname": "/tmp/tmpr7a26eam/stg7191e96c-8cd3-4950-894b-26dee9a64cd5" v1.0/wc2-tool.cwl:15:9: 12 } v1.0/wc2-tool.cwl:15:9: 13 }; v1.0/wc2-tool.cwl:15:9: 14 var self = []; v1.0/wc2-tool.cwl:15:9: 15 var runtime = { v1.0/wc2-tool.cwl:15:9: 16 "cores": 1, v1.0/wc2-tool.cwl:15:9: 17 "ram": 1024, v1.0/wc2-tool.cwl:15:9: 18 "tmpdirSize": 1024, v1.0/wc2-tool.cwl:15:9: 19 "outdirSize": 1024, v1.0/wc2-tool.cwl:15:9: 20 "tmpdir": "/tmp/tmpbn0gp63n", v1.0/wc2-tool.cwl:15:9: 21 "outdir": "/tmp/tmpe54z2w9z" v1.0/wc2-tool.cwl:15:9: 22 }; v1.0/wc2-tool.cwl:15:9: 23 (function(){return ((parseInt(self[0].contents)));})() v1.0/wc2-tool.cwl:15:9: stdout was: '' v1.0/wc2-tool.cwl:15:9: stderr was: 'evalmachine.:23 v1.0/wc2-tool.cwl:15:9: (function(){return ((parseInt(self[0].contents)));})() v1.0/wc2-tool.cwl:15:9: ^ v1.0/wc2-tool.cwl:15:9: v1.0/wc2-tool.cwl:15:9: TypeError: Cannot read property 'contents' of undefined v1.0/wc2-tool.cwl:15:9: at evalmachine.:23:39 v1.0/wc2-tool.cwl:15:9: at evalmachine.:23:53 v1.0/wc2-tool.cwl:15:9: at ContextifyScript.Script.runInContext (vm.js:59:29) v1.0/wc2-tool.cwl:15:9: at ContextifyScript.Script.runInNewContext (vm.js:65:15) v1.0/wc2-tool.cwl:15:9: at Object.runInNewContext (vm.js:135:38) v1.0/wc2-tool.cwl:15:9: at Socket. ([eval]:11:57) v1.0/wc2-tool.cwl:15:9: at emitOne (events.js:116:13) v1.0/wc2-tool.cwl:15:9: at Socket.emit (events.js:211:7) v1.0/wc2-tool.cwl:15:9: at addChunk (_stream_readable.js:263:12) v1.0/wc2-tool.cwl:15:9: at readableAddChunk (_stream_readable.js:246:13)' Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmptm8e3bx0 v1.0/wc2-tool.cwl v1.0/wc-job.json Test outputEval to transform output Returned non-zero Test [24/132] Test two step workflow with imported tools [job step1] job error: Error collecting output for parameter 'output': v1.0/wc-tool.cwl:12:22: Did not find output file with glob pattern: '['output']' [step step1] Output is missing expected field file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/count-lines1-wf.cwl#step1/output [step step1] completed permanentFail Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpvs_s4um_ v1.0/count-lines1-wf.cwl v1.0/wc-job.json Test two step workflow with imported tools Returned non-zero Test [25/132] Test two step workflow with inline tools [job step1] job error: Error collecting output for parameter 'wc_output': v1.0/count-lines2-wf.cwl:32:13: Did not find output file with glob pattern: '['output.txt']' [step step1] Output is missing expected field file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/count-lines2-wf.cwl#step1/wc_output [step step1] completed permanentFail Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmp8lc9gx5t v1.0/count-lines2-wf.cwl v1.0/wc-job.json Test two step workflow with inline tools Returned non-zero Test [26/132] Test single step workflow with Scatter step [job step1_2] job error: Error collecting output for parameter 'output': v1.0/wc2-tool.cwl:15:9: Expression evaluation error: v1.0/wc2-tool.cwl:15:9: Expecting value: line 1 column 1 (char 0) v1.0/wc2-tool.cwl:15:9: script was: v1.0/wc2-tool.cwl:15:9: 01 "use strict"; v1.0/wc2-tool.cwl:15:9: 02 var inputs = { v1.0/wc2-tool.cwl:15:9: 03 "file1": { v1.0/wc2-tool.cwl:15:9: 04 "class": "File", v1.0/wc2-tool.cwl:15:9: 05 "location": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/7abd94a4-9605-4a4b-b75b-d3d873befe61/inputs/hello.txt", v1.0/wc2-tool.cwl:15:9: 06 "size": 13, v1.0/wc2-tool.cwl:15:9: 07 "basename": "hello.txt", v1.0/wc2-tool.cwl:15:9: 08 "nameroot": "hello", v1.0/wc2-tool.cwl:15:9: 09 "nameext": ".txt", v1.0/wc2-tool.cwl:15:9: 10 "path": "/tmp/tmpfjlcjjyx/stgc797319c-ab6f-41c1-ad59-3905a391a1ef/hello.txt", v1.0/wc2-tool.cwl:15:9: 11 "dirname": "/tmp/tmpfjlcjjyx/stgc797319c-ab6f-41c1-ad59-3905a391a1ef" v1.0/wc2-tool.cwl:15:9: 12 } v1.0/wc2-tool.cwl:15:9: 13 }; v1.0/wc2-tool.cwl:15:9: 14 var self = []; v1.0/wc2-tool.cwl:15:9: 15 var runtime = { v1.0/wc2-tool.cwl:15:9: 16 "cores": 1, v1.0/wc2-tool.cwl:15:9: 17 "ram": 1024, v1.0/wc2-tool.cwl:15:9: 18 "tmpdirSize": 1024, v1.0/wc2-tool.cwl:15:9: 19 "outdirSize": 1024, v1.0/wc2-tool.cwl:15:9: 20 "tmpdir": "/tmp/tmp159xy041", v1.0/wc2-tool.cwl:15:9: 21 "outdir": "/tmp/tmpac61c4sj" v1.0/wc2-tool.cwl:15:9: 22 }; v1.0/wc2-tool.cwl:15:9: 23 (function(){return ((parseInt(self[0].contents)));})() v1.0/wc2-tool.cwl:15:9: stdout was: '' v1.0/wc2-tool.cwl:15:9: stderr was: 'evalmachine.:23 v1.0/wc2-tool.cwl:15:9: (function(){return ((parseInt(self[0].contents)));})() v1.0/wc2-tool.cwl:15:9: ^ v1.0/wc2-tool.cwl:15:9: v1.0/wc2-tool.cwl:15:9: TypeError: Cannot read property 'contents' of undefined v1.0/wc2-tool.cwl:15:9: at evalmachine.:23:39 v1.0/wc2-tool.cwl:15:9: at evalmachine.:23:53 v1.0/wc2-tool.cwl:15:9: at ContextifyScript.Script.runInContext (vm.js:59:29) v1.0/wc2-tool.cwl:15:9: at ContextifyScript.Script.runInNewContext (vm.js:65:15) v1.0/wc2-tool.cwl:15:9: at Object.runInNewContext (vm.js:135:38) v1.0/wc2-tool.cwl:15:9: at Socket. ([eval]:11:57) v1.0/wc2-tool.cwl:15:9: at emitOne (events.js:116:13) v1.0/wc2-tool.cwl:15:9: at Socket.emit (events.js:211:7) v1.0/wc2-tool.cwl:15:9: at addChunk (_stream_readable.js:263:12) v1.0/wc2-tool.cwl:15:9: at readableAddChunk (_stream_readable.js:246:13)' [job step1] job error: Error collecting output for parameter 'output': v1.0/wc2-tool.cwl:15:9: Expression evaluation error: v1.0/wc2-tool.cwl:15:9: Expecting value: line 1 column 1 (char 0) v1.0/wc2-tool.cwl:15:9: script was: v1.0/wc2-tool.cwl:15:9: 01 "use strict"; v1.0/wc2-tool.cwl:15:9: 02 var inputs = { v1.0/wc2-tool.cwl:15:9: 03 "file1": { v1.0/wc2-tool.cwl:15:9: 04 "class": "File", v1.0/wc2-tool.cwl:15:9: 05 "location": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/7abd94a4-9605-4a4b-b75b-d3d873befe61/inputs/whale.txt", v1.0/wc2-tool.cwl:15:9: 06 "size": 1111, v1.0/wc2-tool.cwl:15:9: 07 "basename": "whale.txt", v1.0/wc2-tool.cwl:15:9: 08 "nameroot": "whale", v1.0/wc2-tool.cwl:15:9: 09 "nameext": ".txt", v1.0/wc2-tool.cwl:15:9: 10 "path": "/tmp/tmpsepb1ywx/stgb4065630-be6e-4769-a27d-be8e61b6aede/whale.txt", v1.0/wc2-tool.cwl:15:9: 11 "dirname": "/tmp/tmpsepb1ywx/stgb4065630-be6e-4769-a27d-be8e61b6aede" v1.0/wc2-tool.cwl:15:9: 12 } v1.0/wc2-tool.cwl:15:9: 13 }; v1.0/wc2-tool.cwl:15:9: 14 var self = []; v1.0/wc2-tool.cwl:15:9: 15 var runtime = { v1.0/wc2-tool.cwl:15:9: 16 "cores": 1, v1.0/wc2-tool.cwl:15:9: 17 "ram": 1024, v1.0/wc2-tool.cwl:15:9: 18 "tmpdirSize": 1024, v1.0/wc2-tool.cwl:15:9: 19 "outdirSize": 1024, v1.0/wc2-tool.cwl:15:9: 20 "tmpdir": "/tmp/tmpfy7xez35", v1.0/wc2-tool.cwl:15:9: 21 "outdir": "/tmp/tmpifma8x5x" v1.0/wc2-tool.cwl:15:9: 22 }; v1.0/wc2-tool.cwl:15:9: 23 (function(){return ((parseInt(self[0].contents)));})() v1.0/wc2-tool.cwl:15:9: stdout was: '' v1.0/wc2-tool.cwl:15:9: stderr was: 'evalmachine.:23 v1.0/wc2-tool.cwl:15:9: (function(){return ((parseInt(self[0].contents)));})() v1.0/wc2-tool.cwl:15:9: ^ v1.0/wc2-tool.cwl:15:9: v1.0/wc2-tool.cwl:15:9: TypeError: Cannot read property 'contents' of undefined v1.0/wc2-tool.cwl:15:9: at evalmachine.:23:39 v1.0/wc2-tool.cwl:15:9: at evalmachine.:23:53 v1.0/wc2-tool.cwl:15:9: at ContextifyScript.Script.runInContext (vm.js:59:29) v1.0/wc2-tool.cwl:15:9: at ContextifyScript.Script.runInNewContext (vm.js:65:15) v1.0/wc2-tool.cwl:15:9: at Object.runInNewContext (vm.js:135:38) v1.0/wc2-tool.cwl:15:9: at Socket. ([eval]:11:57) v1.0/wc2-tool.cwl:15:9: at emitOne (events.js:116:13) v1.0/wc2-tool.cwl:15:9: at Socket.emit (events.js:211:7) v1.0/wc2-tool.cwl:15:9: at addChunk (_stream_readable.js:263:12) v1.0/wc2-tool.cwl:15:9: at readableAddChunk (_stream_readable.js:246:13)' [step step1] completed permanentFail Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpn08qc3h9 v1.0/count-lines3-wf.cwl v1.0/count-lines3-job.json Test single step workflow with Scatter step Returned non-zero Test [27/132] Test single step workflow with Scatter step and two data links connected to same input, default merge behavior [job step1] job error: Error collecting output for parameter 'output': v1.0/wc2-tool.cwl:15:9: Expression evaluation error: v1.0/wc2-tool.cwl:15:9: Expecting value: line 1 column 1 (char 0) v1.0/wc2-tool.cwl:15:9: script was: v1.0/wc2-tool.cwl:15:9: 01 "use strict"; v1.0/wc2-tool.cwl:15:9: 02 var inputs = { v1.0/wc2-tool.cwl:15:9: 03 "file1": { v1.0/wc2-tool.cwl:15:9: 04 "class": "File", v1.0/wc2-tool.cwl:15:9: 05 "location": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/36cb954e-5000-4ba4-bf51-c0f29ccc3905/inputs/whale.txt", v1.0/wc2-tool.cwl:15:9: 06 "size": 1111, v1.0/wc2-tool.cwl:15:9: 07 "basename": "whale.txt", v1.0/wc2-tool.cwl:15:9: 08 "nameroot": "whale", v1.0/wc2-tool.cwl:15:9: 09 "nameext": ".txt", v1.0/wc2-tool.cwl:15:9: 10 "path": "/tmp/tmpkjelj52d/stg4006d749-54bc-4fdb-b4f4-1f0b723ccd95/whale.txt", v1.0/wc2-tool.cwl:15:9: 11 "dirname": "/tmp/tmpkjelj52d/stg4006d749-54bc-4fdb-b4f4-1f0b723ccd95" v1.0/wc2-tool.cwl:15:9: 12 } v1.0/wc2-tool.cwl:15:9: 13 }; v1.0/wc2-tool.cwl:15:9: 14 var self = []; v1.0/wc2-tool.cwl:15:9: 15 var runtime = { v1.0/wc2-tool.cwl:15:9: 16 "cores": 1, v1.0/wc2-tool.cwl:15:9: 17 "ram": 1024, v1.0/wc2-tool.cwl:15:9: 18 "tmpdirSize": 1024, v1.0/wc2-tool.cwl:15:9: 19 "outdirSize": 1024, v1.0/wc2-tool.cwl:15:9: 20 "tmpdir": "/tmp/tmprvdyx74n", v1.0/wc2-tool.cwl:15:9: 21 "outdir": "/tmp/tmp9nu9zc5_" v1.0/wc2-tool.cwl:15:9: 22 }; v1.0/wc2-tool.cwl:15:9: 23 (function(){return ((parseInt(self[0].contents)));})() v1.0/wc2-tool.cwl:15:9: stdout was: '' v1.0/wc2-tool.cwl:15:9: stderr was: 'evalmachine.:23 v1.0/wc2-tool.cwl:15:9: (function(){return ((parseInt(self[0].contents)));})() v1.0/wc2-tool.cwl:15:9: ^ v1.0/wc2-tool.cwl:15:9: v1.0/wc2-tool.cwl:15:9: TypeError: Cannot read property 'contents' of undefined v1.0/wc2-tool.cwl:15:9: at evalmachine.:23:39 v1.0/wc2-tool.cwl:15:9: at evalmachine.:23:53 v1.0/wc2-tool.cwl:15:9: at ContextifyScript.Script.runInContext (vm.js:59:29) v1.0/wc2-tool.cwl:15:9: at ContextifyScript.Script.runInNewContext (vm.js:65:15) v1.0/wc2-tool.cwl:15:9: at Object.runInNewContext (vm.js:135:38) v1.0/wc2-tool.cwl:15:9: at Socket. ([eval]:11:57) v1.0/wc2-tool.cwl:15:9: at emitOne (events.js:116:13) v1.0/wc2-tool.cwl:15:9: at Socket.emit (events.js:211:7) v1.0/wc2-tool.cwl:15:9: at addChunk (_stream_readable.js:263:12) v1.0/wc2-tool.cwl:15:9: at readableAddChunk (_stream_readable.js:246:13)' [job step1_2] job error: Error collecting output for parameter 'output': v1.0/wc2-tool.cwl:15:9: Expression evaluation error: v1.0/wc2-tool.cwl:15:9: Expecting value: line 1 column 1 (char 0) v1.0/wc2-tool.cwl:15:9: script was: v1.0/wc2-tool.cwl:15:9: 01 "use strict"; v1.0/wc2-tool.cwl:15:9: 02 var inputs = { v1.0/wc2-tool.cwl:15:9: 03 "file1": { v1.0/wc2-tool.cwl:15:9: 04 "class": "File", v1.0/wc2-tool.cwl:15:9: 05 "location": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/36cb954e-5000-4ba4-bf51-c0f29ccc3905/inputs/hello.txt", v1.0/wc2-tool.cwl:15:9: 06 "size": 13, v1.0/wc2-tool.cwl:15:9: 07 "basename": "hello.txt", v1.0/wc2-tool.cwl:15:9: 08 "nameroot": "hello", v1.0/wc2-tool.cwl:15:9: 09 "nameext": ".txt", v1.0/wc2-tool.cwl:15:9: 10 "path": "/tmp/tmp7gkvy6zh/stg8d1e6f08-3a06-4d12-93fa-76d2cd342ca8/hello.txt", v1.0/wc2-tool.cwl:15:9: 11 "dirname": "/tmp/tmp7gkvy6zh/stg8d1e6f08-3a06-4d12-93fa-76d2cd342ca8" v1.0/wc2-tool.cwl:15:9: 12 } v1.0/wc2-tool.cwl:15:9: 13 }; v1.0/wc2-tool.cwl:15:9: 14 var self = []; v1.0/wc2-tool.cwl:15:9: 15 var runtime = { v1.0/wc2-tool.cwl:15:9: 16 "cores": 1, v1.0/wc2-tool.cwl:15:9: 17 "ram": 1024, v1.0/wc2-tool.cwl:15:9: 18 "tmpdirSize": 1024, v1.0/wc2-tool.cwl:15:9: 19 "outdirSize": 1024, v1.0/wc2-tool.cwl:15:9: 20 "tmpdir": "/tmp/tmpz7xfev6v", v1.0/wc2-tool.cwl:15:9: 21 "outdir": "/tmp/tmphdkmqiqq" v1.0/wc2-tool.cwl:15:9: 22 }; v1.0/wc2-tool.cwl:15:9: 23 (function(){return ((parseInt(self[0].contents)));})() v1.0/wc2-tool.cwl:15:9: stdout was: '' v1.0/wc2-tool.cwl:15:9: stderr was: 'evalmachine.:23 v1.0/wc2-tool.cwl:15:9: (function(){return ((parseInt(self[0].contents)));})() v1.0/wc2-tool.cwl:15:9: ^ v1.0/wc2-tool.cwl:15:9: v1.0/wc2-tool.cwl:15:9: TypeError: Cannot read property 'contents' of undefined v1.0/wc2-tool.cwl:15:9: at evalmachine.:23:39 v1.0/wc2-tool.cwl:15:9: at evalmachine.:23:53 v1.0/wc2-tool.cwl:15:9: at ContextifyScript.Script.runInContext (vm.js:59:29) v1.0/wc2-tool.cwl:15:9: at ContextifyScript.Script.runInNewContext (vm.js:65:15) v1.0/wc2-tool.cwl:15:9: at Object.runInNewContext (vm.js:135:38) v1.0/wc2-tool.cwl:15:9: at Socket. ([eval]:11:57) v1.0/wc2-tool.cwl:15:9: at emitOne (events.js:116:13) v1.0/wc2-tool.cwl:15:9: at Socket.emit (events.js:211:7) v1.0/wc2-tool.cwl:15:9: at addChunk (_stream_readable.js:263:12) v1.0/wc2-tool.cwl:15:9: at readableAddChunk (_stream_readable.js:246:13)' [step step1] completed permanentFail Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmp03n2ixk9 v1.0/count-lines4-wf.cwl v1.0/count-lines4-job.json Test single step workflow with Scatter step and two data links connected to same input, default merge behavior Returned non-zero Test [28/132] Test single step workflow with Scatter step and two data links connected to same input, nested merge behavior FTP upload, file whale.txt already exists FTP upload, file hello.txt already exists [job step1] job error: Error collecting output for parameter 'output': v1.0/wc3-tool.cwl:18:9: Expression evaluation error: v1.0/wc3-tool.cwl:18:9: Expecting value: line 1 column 1 (char 0) v1.0/wc3-tool.cwl:18:9: script was: v1.0/wc3-tool.cwl:18:9: 01 "use strict"; v1.0/wc3-tool.cwl:18:9: 02 var inputs = { v1.0/wc3-tool.cwl:18:9: 03 "file1": [ v1.0/wc3-tool.cwl:18:9: 04 { v1.0/wc3-tool.cwl:18:9: 05 "class": "File", v1.0/wc3-tool.cwl:18:9: 06 "location": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/441431ef-5ae7-4f8f-912d-2f75856ff2d1/inputs/whale.txt", v1.0/wc3-tool.cwl:18:9: 07 "size": 1111, v1.0/wc3-tool.cwl:18:9: 08 "basename": "whale.txt", v1.0/wc3-tool.cwl:18:9: 09 "nameroot": "whale", v1.0/wc3-tool.cwl:18:9: 10 "nameext": ".txt", v1.0/wc3-tool.cwl:18:9: 11 "path": "/tmp/tmpszmnfb1n/stg785db3ad-f32d-46ce-8473-14829f4cd724/whale.txt", v1.0/wc3-tool.cwl:18:9: 12 "dirname": "/tmp/tmpszmnfb1n/stg785db3ad-f32d-46ce-8473-14829f4cd724" v1.0/wc3-tool.cwl:18:9: 13 }, v1.0/wc3-tool.cwl:18:9: 14 { v1.0/wc3-tool.cwl:18:9: 15 "class": "File", v1.0/wc3-tool.cwl:18:9: 16 "location": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/441431ef-5ae7-4f8f-912d-2f75856ff2d1/inputs/whale.txt", v1.0/wc3-tool.cwl:18:9: 17 "size": 1111, v1.0/wc3-tool.cwl:18:9: 18 "basename": "whale.txt", v1.0/wc3-tool.cwl:18:9: 19 "nameroot": "whale", v1.0/wc3-tool.cwl:18:9: 20 "nameext": ".txt", v1.0/wc3-tool.cwl:18:9: 21 "path": "/tmp/tmpszmnfb1n/stg785db3ad-f32d-46ce-8473-14829f4cd724/whale.txt", v1.0/wc3-tool.cwl:18:9: 22 "dirname": "/tmp/tmpszmnfb1n/stg785db3ad-f32d-46ce-8473-14829f4cd724" v1.0/wc3-tool.cwl:18:9: 23 } v1.0/wc3-tool.cwl:18:9: 24 ] v1.0/wc3-tool.cwl:18:9: 25 }; v1.0/wc3-tool.cwl:18:9: 26 var self = []; v1.0/wc3-tool.cwl:18:9: 27 var runtime = { v1.0/wc3-tool.cwl:18:9: 28 "cores": 1, v1.0/wc3-tool.cwl:18:9: 29 "ram": 1024, v1.0/wc3-tool.cwl:18:9: 30 "tmpdirSize": 1024, v1.0/wc3-tool.cwl:18:9: 31 "outdirSize": 1024, v1.0/wc3-tool.cwl:18:9: 32 "tmpdir": "/tmp/tmpyiyjqjrs", v1.0/wc3-tool.cwl:18:9: 33 "outdir": "/tmp/tmpqwkirbq2" v1.0/wc3-tool.cwl:18:9: 34 }; v1.0/wc3-tool.cwl:18:9: 35 (function(){ v1.0/wc3-tool.cwl:18:9: 36 var s = self[0].contents.split(/\r?\n/); v1.0/wc3-tool.cwl:18:9: 37 return parseInt(s[s.length-2]); v1.0/wc3-tool.cwl:18:9: 38 })() v1.0/wc3-tool.cwl:18:9: stdout was: '' v1.0/wc3-tool.cwl:18:9: stderr was: 'evalmachine.:36 v1.0/wc3-tool.cwl:18:9: var s = self[0].contents.split(/\r?\n/); v1.0/wc3-tool.cwl:18:9: ^ v1.0/wc3-tool.cwl:18:9: v1.0/wc3-tool.cwl:18:9: TypeError: Cannot read property 'contents' of undefined v1.0/wc3-tool.cwl:18:9: at evalmachine.:36:19 v1.0/wc3-tool.cwl:18:9: at evalmachine.:38:3 v1.0/wc3-tool.cwl:18:9: at ContextifyScript.Script.runInContext (vm.js:59:29) v1.0/wc3-tool.cwl:18:9: at ContextifyScript.Script.runInNewContext (vm.js:65:15) v1.0/wc3-tool.cwl:18:9: at Object.runInNewContext (vm.js:135:38) v1.0/wc3-tool.cwl:18:9: at Socket. ([eval]:11:57) v1.0/wc3-tool.cwl:18:9: at emitOne (events.js:116:13) v1.0/wc3-tool.cwl:18:9: at Socket.emit (events.js:211:7) v1.0/wc3-tool.cwl:18:9: at addChunk (_stream_readable.js:263:12) v1.0/wc3-tool.cwl:18:9: at readableAddChunk (_stream_readable.js:246:13)' [job step1_2] job error: Error collecting output for parameter 'output': v1.0/wc3-tool.cwl:18:9: Expression evaluation error: v1.0/wc3-tool.cwl:18:9: Expecting value: line 1 column 1 (char 0) v1.0/wc3-tool.cwl:18:9: script was: v1.0/wc3-tool.cwl:18:9: 01 "use strict"; v1.0/wc3-tool.cwl:18:9: 02 var inputs = { v1.0/wc3-tool.cwl:18:9: 03 "file1": [ v1.0/wc3-tool.cwl:18:9: 04 { v1.0/wc3-tool.cwl:18:9: 05 "class": "File", v1.0/wc3-tool.cwl:18:9: 06 "location": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/441431ef-5ae7-4f8f-912d-2f75856ff2d1/inputs/hello.txt", v1.0/wc3-tool.cwl:18:9: 07 "size": 13, v1.0/wc3-tool.cwl:18:9: 08 "basename": "hello.txt", v1.0/wc3-tool.cwl:18:9: 09 "nameroot": "hello", v1.0/wc3-tool.cwl:18:9: 10 "nameext": ".txt", v1.0/wc3-tool.cwl:18:9: 11 "path": "/tmp/tmp83dpztvw/stg8023475b-1eb9-4f83-96bc-7dddf6047724/hello.txt", v1.0/wc3-tool.cwl:18:9: 12 "dirname": "/tmp/tmp83dpztvw/stg8023475b-1eb9-4f83-96bc-7dddf6047724" v1.0/wc3-tool.cwl:18:9: 13 }, v1.0/wc3-tool.cwl:18:9: 14 { v1.0/wc3-tool.cwl:18:9: 15 "class": "File", v1.0/wc3-tool.cwl:18:9: 16 "location": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/441431ef-5ae7-4f8f-912d-2f75856ff2d1/inputs/hello.txt", v1.0/wc3-tool.cwl:18:9: 17 "size": 13, v1.0/wc3-tool.cwl:18:9: 18 "basename": "hello.txt", v1.0/wc3-tool.cwl:18:9: 19 "nameroot": "hello", v1.0/wc3-tool.cwl:18:9: 20 "nameext": ".txt", v1.0/wc3-tool.cwl:18:9: 21 "path": "/tmp/tmp83dpztvw/stg8023475b-1eb9-4f83-96bc-7dddf6047724/hello.txt", v1.0/wc3-tool.cwl:18:9: 22 "dirname": "/tmp/tmp83dpztvw/stg8023475b-1eb9-4f83-96bc-7dddf6047724" v1.0/wc3-tool.cwl:18:9: 23 } v1.0/wc3-tool.cwl:18:9: 24 ] v1.0/wc3-tool.cwl:18:9: 25 }; v1.0/wc3-tool.cwl:18:9: 26 var self = []; v1.0/wc3-tool.cwl:18:9: 27 var runtime = { v1.0/wc3-tool.cwl:18:9: 28 "cores": 1, v1.0/wc3-tool.cwl:18:9: 29 "ram": 1024, v1.0/wc3-tool.cwl:18:9: 30 "tmpdirSize": 1024, v1.0/wc3-tool.cwl:18:9: 31 "outdirSize": 1024, v1.0/wc3-tool.cwl:18:9: 32 "tmpdir": "/tmp/tmp54ephyxd", v1.0/wc3-tool.cwl:18:9: 33 "outdir": "/tmp/tmp_o5tzu87" v1.0/wc3-tool.cwl:18:9: 34 }; v1.0/wc3-tool.cwl:18:9: 35 (function(){ v1.0/wc3-tool.cwl:18:9: 36 var s = self[0].contents.split(/\r?\n/); v1.0/wc3-tool.cwl:18:9: 37 return parseInt(s[s.length-2]); v1.0/wc3-tool.cwl:18:9: 38 })() v1.0/wc3-tool.cwl:18:9: stdout was: '' v1.0/wc3-tool.cwl:18:9: stderr was: 'evalmachine.:36 v1.0/wc3-tool.cwl:18:9: var s = self[0].contents.split(/\r?\n/); v1.0/wc3-tool.cwl:18:9: ^ v1.0/wc3-tool.cwl:18:9: v1.0/wc3-tool.cwl:18:9: TypeError: Cannot read property 'contents' of undefined v1.0/wc3-tool.cwl:18:9: at evalmachine.:36:19 v1.0/wc3-tool.cwl:18:9: at evalmachine.:38:3 v1.0/wc3-tool.cwl:18:9: at ContextifyScript.Script.runInContext (vm.js:59:29) v1.0/wc3-tool.cwl:18:9: at ContextifyScript.Script.runInNewContext (vm.js:65:15) v1.0/wc3-tool.cwl:18:9: at Object.runInNewContext (vm.js:135:38) v1.0/wc3-tool.cwl:18:9: at Socket. ([eval]:11:57) v1.0/wc3-tool.cwl:18:9: at emitOne (events.js:116:13) v1.0/wc3-tool.cwl:18:9: at Socket.emit (events.js:211:7) v1.0/wc3-tool.cwl:18:9: at addChunk (_stream_readable.js:263:12) v1.0/wc3-tool.cwl:18:9: at readableAddChunk (_stream_readable.js:246:13)' [step step1] completed permanentFail Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpo_hjq83n v1.0/count-lines6-wf.cwl v1.0/count-lines6-job.json Test single step workflow with Scatter step and two data links connected to same input, nested merge behavior Returned non-zero Test [29/132] Test single step workflow with Scatter step and two data links connected to same input, flattened merge behavior FTP upload, file whale.txt already exists FTP upload, file hello.txt already exists [job step1] job error: Error collecting output for parameter 'output': v1.0/wc3-tool.cwl:18:9: Expression evaluation error: v1.0/wc3-tool.cwl:18:9: Expecting value: line 1 column 1 (char 0) v1.0/wc3-tool.cwl:18:9: script was: v1.0/wc3-tool.cwl:18:9: 01 "use strict"; v1.0/wc3-tool.cwl:18:9: 02 var inputs = { v1.0/wc3-tool.cwl:18:9: 03 "file1": [ v1.0/wc3-tool.cwl:18:9: 04 { v1.0/wc3-tool.cwl:18:9: 05 "class": "File", v1.0/wc3-tool.cwl:18:9: 06 "location": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/b84cca34-40c8-4057-bc53-669ca3fcae02/inputs/whale.txt", v1.0/wc3-tool.cwl:18:9: 07 "size": 1111, v1.0/wc3-tool.cwl:18:9: 08 "basename": "whale.txt", v1.0/wc3-tool.cwl:18:9: 09 "nameroot": "whale", v1.0/wc3-tool.cwl:18:9: 10 "nameext": ".txt", v1.0/wc3-tool.cwl:18:9: 11 "path": "/tmp/tmp2jqurluc/stg021bb3b1-316a-4d83-b2c0-bf417d21cbd1/whale.txt", v1.0/wc3-tool.cwl:18:9: 12 "dirname": "/tmp/tmp2jqurluc/stg021bb3b1-316a-4d83-b2c0-bf417d21cbd1" v1.0/wc3-tool.cwl:18:9: 13 }, v1.0/wc3-tool.cwl:18:9: 14 { v1.0/wc3-tool.cwl:18:9: 15 "class": "File", v1.0/wc3-tool.cwl:18:9: 16 "location": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/b84cca34-40c8-4057-bc53-669ca3fcae02/inputs/whale.txt", v1.0/wc3-tool.cwl:18:9: 17 "size": 1111, v1.0/wc3-tool.cwl:18:9: 18 "basename": "whale.txt", v1.0/wc3-tool.cwl:18:9: 19 "nameroot": "whale", v1.0/wc3-tool.cwl:18:9: 20 "nameext": ".txt", v1.0/wc3-tool.cwl:18:9: 21 "path": "/tmp/tmp2jqurluc/stg021bb3b1-316a-4d83-b2c0-bf417d21cbd1/whale.txt", v1.0/wc3-tool.cwl:18:9: 22 "dirname": "/tmp/tmp2jqurluc/stg021bb3b1-316a-4d83-b2c0-bf417d21cbd1" v1.0/wc3-tool.cwl:18:9: 23 }, v1.0/wc3-tool.cwl:18:9: 24 { v1.0/wc3-tool.cwl:18:9: 25 "class": "File", v1.0/wc3-tool.cwl:18:9: 26 "location": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/b84cca34-40c8-4057-bc53-669ca3fcae02/inputs/hello.txt", v1.0/wc3-tool.cwl:18:9: 27 "size": 13, v1.0/wc3-tool.cwl:18:9: 28 "basename": "hello.txt", v1.0/wc3-tool.cwl:18:9: 29 "nameroot": "hello", v1.0/wc3-tool.cwl:18:9: 30 "nameext": ".txt", v1.0/wc3-tool.cwl:18:9: 31 "path": "/tmp/tmp2jqurluc/stgd952970c-2de9-4d6d-8f08-47505ebbbe8c/hello.txt", v1.0/wc3-tool.cwl:18:9: 32 "dirname": "/tmp/tmp2jqurluc/stgd952970c-2de9-4d6d-8f08-47505ebbbe8c" v1.0/wc3-tool.cwl:18:9: 33 }, v1.0/wc3-tool.cwl:18:9: 34 { v1.0/wc3-tool.cwl:18:9: 35 "class": "File", v1.0/wc3-tool.cwl:18:9: 36 "location": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/b84cca34-40c8-4057-bc53-669ca3fcae02/inputs/hello.txt", v1.0/wc3-tool.cwl:18:9: 37 "size": 13, v1.0/wc3-tool.cwl:18:9: 38 "basename": "hello.txt", v1.0/wc3-tool.cwl:18:9: 39 "nameroot": "hello", v1.0/wc3-tool.cwl:18:9: 40 "nameext": ".txt", v1.0/wc3-tool.cwl:18:9: 41 "path": "/tmp/tmp2jqurluc/stgd952970c-2de9-4d6d-8f08-47505ebbbe8c/hello.txt", v1.0/wc3-tool.cwl:18:9: 42 "dirname": "/tmp/tmp2jqurluc/stgd952970c-2de9-4d6d-8f08-47505ebbbe8c" v1.0/wc3-tool.cwl:18:9: 43 } v1.0/wc3-tool.cwl:18:9: 44 ] v1.0/wc3-tool.cwl:18:9: 45 }; v1.0/wc3-tool.cwl:18:9: 46 var self = []; v1.0/wc3-tool.cwl:18:9: 47 var runtime = { v1.0/wc3-tool.cwl:18:9: 48 "cores": 1, v1.0/wc3-tool.cwl:18:9: 49 "ram": 1024, v1.0/wc3-tool.cwl:18:9: 50 "tmpdirSize": 1024, v1.0/wc3-tool.cwl:18:9: 51 "outdirSize": 1024, v1.0/wc3-tool.cwl:18:9: 52 "tmpdir": "/tmp/tmpdgr77oa6", v1.0/wc3-tool.cwl:18:9: 53 "outdir": "/tmp/tmp3hi4pfcj" v1.0/wc3-tool.cwl:18:9: 54 }; v1.0/wc3-tool.cwl:18:9: 55 (function(){ v1.0/wc3-tool.cwl:18:9: 56 var s = self[0].contents.split(/\r?\n/); v1.0/wc3-tool.cwl:18:9: 57 return parseInt(s[s.length-2]); v1.0/wc3-tool.cwl:18:9: 58 })() v1.0/wc3-tool.cwl:18:9: stdout was: '' v1.0/wc3-tool.cwl:18:9: stderr was: 'evalmachine.:56 v1.0/wc3-tool.cwl:18:9: var s = self[0].contents.split(/\r?\n/); v1.0/wc3-tool.cwl:18:9: ^ v1.0/wc3-tool.cwl:18:9: v1.0/wc3-tool.cwl:18:9: TypeError: Cannot read property 'contents' of undefined v1.0/wc3-tool.cwl:18:9: at evalmachine.:56:19 v1.0/wc3-tool.cwl:18:9: at evalmachine.:58:3 v1.0/wc3-tool.cwl:18:9: at ContextifyScript.Script.runInContext (vm.js:59:29) v1.0/wc3-tool.cwl:18:9: at ContextifyScript.Script.runInNewContext (vm.js:65:15) v1.0/wc3-tool.cwl:18:9: at Object.runInNewContext (vm.js:135:38) v1.0/wc3-tool.cwl:18:9: at Socket. ([eval]:11:57) v1.0/wc3-tool.cwl:18:9: at emitOne (events.js:116:13) v1.0/wc3-tool.cwl:18:9: at Socket.emit (events.js:211:7) v1.0/wc3-tool.cwl:18:9: at addChunk (_stream_readable.js:263:12) v1.0/wc3-tool.cwl:18:9: at readableAddChunk (_stream_readable.js:246:13)' [step step1] Output is missing expected field file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/count-lines7-wf.cwl#step1/output [step step1] completed permanentFail Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpg1sct_vj v1.0/count-lines7-wf.cwl v1.0/count-lines6-job.json Test single step workflow with Scatter step and two data links connected to same input, flattened merge behavior Returned non-zero Test [30/132] Test that no MultipleInputFeatureRequirement is necessary when workflow step source is a single-item list FTP upload, file whale.txt already exists FTP upload, file hello.txt already exists [job step1] job error: Error collecting output for parameter 'output': v1.0/wc3-tool.cwl:18:9: Expression evaluation error: v1.0/wc3-tool.cwl:18:9: Expecting value: line 1 column 1 (char 0) v1.0/wc3-tool.cwl:18:9: script was: v1.0/wc3-tool.cwl:18:9: 01 "use strict"; v1.0/wc3-tool.cwl:18:9: 02 var inputs = { v1.0/wc3-tool.cwl:18:9: 03 "file1": [ v1.0/wc3-tool.cwl:18:9: 04 { v1.0/wc3-tool.cwl:18:9: 05 "class": "File", v1.0/wc3-tool.cwl:18:9: 06 "location": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/f8ae82b2-ae2d-4d3b-a5cb-7ddae0fd6204/inputs/whale.txt", v1.0/wc3-tool.cwl:18:9: 07 "size": 1111, v1.0/wc3-tool.cwl:18:9: 08 "basename": "whale.txt", v1.0/wc3-tool.cwl:18:9: 09 "nameroot": "whale", v1.0/wc3-tool.cwl:18:9: 10 "nameext": ".txt", v1.0/wc3-tool.cwl:18:9: 11 "path": "/tmp/tmpxa0pzfq1/stgf9b7b4aa-6bc4-4647-bf30-c66367e373f4/whale.txt", v1.0/wc3-tool.cwl:18:9: 12 "dirname": "/tmp/tmpxa0pzfq1/stgf9b7b4aa-6bc4-4647-bf30-c66367e373f4" v1.0/wc3-tool.cwl:18:9: 13 }, v1.0/wc3-tool.cwl:18:9: 14 { v1.0/wc3-tool.cwl:18:9: 15 "class": "File", v1.0/wc3-tool.cwl:18:9: 16 "location": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/f8ae82b2-ae2d-4d3b-a5cb-7ddae0fd6204/inputs/whale.txt", v1.0/wc3-tool.cwl:18:9: 17 "size": 1111, v1.0/wc3-tool.cwl:18:9: 18 "basename": "whale.txt", v1.0/wc3-tool.cwl:18:9: 19 "nameroot": "whale", v1.0/wc3-tool.cwl:18:9: 20 "nameext": ".txt", v1.0/wc3-tool.cwl:18:9: 21 "path": "/tmp/tmpxa0pzfq1/stgf9b7b4aa-6bc4-4647-bf30-c66367e373f4/whale.txt", v1.0/wc3-tool.cwl:18:9: 22 "dirname": "/tmp/tmpxa0pzfq1/stgf9b7b4aa-6bc4-4647-bf30-c66367e373f4" v1.0/wc3-tool.cwl:18:9: 23 } v1.0/wc3-tool.cwl:18:9: 24 ] v1.0/wc3-tool.cwl:18:9: 25 }; v1.0/wc3-tool.cwl:18:9: 26 var self = []; v1.0/wc3-tool.cwl:18:9: 27 var runtime = { v1.0/wc3-tool.cwl:18:9: 28 "cores": 1, v1.0/wc3-tool.cwl:18:9: 29 "ram": 1024, v1.0/wc3-tool.cwl:18:9: 30 "tmpdirSize": 1024, v1.0/wc3-tool.cwl:18:9: 31 "outdirSize": 1024, v1.0/wc3-tool.cwl:18:9: 32 "tmpdir": "/tmp/tmpjnz9qcip", v1.0/wc3-tool.cwl:18:9: 33 "outdir": "/tmp/tmpya_lyzvn" v1.0/wc3-tool.cwl:18:9: 34 }; v1.0/wc3-tool.cwl:18:9: 35 (function(){ v1.0/wc3-tool.cwl:18:9: 36 var s = self[0].contents.split(/\r?\n/); v1.0/wc3-tool.cwl:18:9: 37 return parseInt(s[s.length-2]); v1.0/wc3-tool.cwl:18:9: 38 })() v1.0/wc3-tool.cwl:18:9: stdout was: '' v1.0/wc3-tool.cwl:18:9: stderr was: 'evalmachine.:36 v1.0/wc3-tool.cwl:18:9: var s = self[0].contents.split(/\r?\n/); v1.0/wc3-tool.cwl:18:9: ^ v1.0/wc3-tool.cwl:18:9: v1.0/wc3-tool.cwl:18:9: TypeError: Cannot read property 'contents' of undefined v1.0/wc3-tool.cwl:18:9: at evalmachine.:36:19 v1.0/wc3-tool.cwl:18:9: at evalmachine.:38:3 v1.0/wc3-tool.cwl:18:9: at ContextifyScript.Script.runInContext (vm.js:59:29) v1.0/wc3-tool.cwl:18:9: at ContextifyScript.Script.runInNewContext (vm.js:65:15) v1.0/wc3-tool.cwl:18:9: at Object.runInNewContext (vm.js:135:38) v1.0/wc3-tool.cwl:18:9: at Socket. ([eval]:11:57) v1.0/wc3-tool.cwl:18:9: at emitOne (events.js:116:13) v1.0/wc3-tool.cwl:18:9: at Socket.emit (events.js:211:7) v1.0/wc3-tool.cwl:18:9: at addChunk (_stream_readable.js:263:12) v1.0/wc3-tool.cwl:18:9: at readableAddChunk (_stream_readable.js:246:13)' [step step1] Output is missing expected field file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/count-lines13-wf.cwl#step1/output [step step1] completed permanentFail Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpxsildqlv v1.0/count-lines13-wf.cwl v1.0/count-lines6-job.json Test that no MultipleInputFeatureRequirement is necessary when workflow step source is a single-item list Returned non-zero Test [31/132] Test workflow with default value for input parameter (missing) [job step1] job error: Error collecting output for parameter 'output': v1.0/wc2-tool.cwl:15:9: Expression evaluation error: v1.0/wc2-tool.cwl:15:9: Expecting value: line 1 column 1 (char 0) v1.0/wc2-tool.cwl:15:9: script was: v1.0/wc2-tool.cwl:15:9: 01 "use strict"; v1.0/wc2-tool.cwl:15:9: 02 var inputs = { v1.0/wc2-tool.cwl:15:9: 03 "file1": { v1.0/wc2-tool.cwl:15:9: 04 "class": "File", v1.0/wc2-tool.cwl:15:9: 05 "location": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/c9dda64e-89e7-4716-af22-b7607e56c178/inputs/hello.txt", v1.0/wc2-tool.cwl:15:9: 06 "size": 13, v1.0/wc2-tool.cwl:15:9: 07 "basename": "hello.txt", v1.0/wc2-tool.cwl:15:9: 08 "nameroot": "hello", v1.0/wc2-tool.cwl:15:9: 09 "nameext": ".txt", v1.0/wc2-tool.cwl:15:9: 10 "path": "/tmp/tmp6x4e3urk/stgdd9a3c85-5ef3-4727-baea-fad8f57e4f1a/hello.txt", v1.0/wc2-tool.cwl:15:9: 11 "dirname": "/tmp/tmp6x4e3urk/stgdd9a3c85-5ef3-4727-baea-fad8f57e4f1a" v1.0/wc2-tool.cwl:15:9: 12 } v1.0/wc2-tool.cwl:15:9: 13 }; v1.0/wc2-tool.cwl:15:9: 14 var self = []; v1.0/wc2-tool.cwl:15:9: 15 var runtime = { v1.0/wc2-tool.cwl:15:9: 16 "cores": 1, v1.0/wc2-tool.cwl:15:9: 17 "ram": 1024, v1.0/wc2-tool.cwl:15:9: 18 "tmpdirSize": 1024, v1.0/wc2-tool.cwl:15:9: 19 "outdirSize": 1024, v1.0/wc2-tool.cwl:15:9: 20 "tmpdir": "/tmp/tmpxmhbh63e", v1.0/wc2-tool.cwl:15:9: 21 "outdir": "/tmp/tmpefi347do" v1.0/wc2-tool.cwl:15:9: 22 }; v1.0/wc2-tool.cwl:15:9: 23 (function(){return ((parseInt(self[0].contents)));})() v1.0/wc2-tool.cwl:15:9: stdout was: '' v1.0/wc2-tool.cwl:15:9: stderr was: 'evalmachine.:23 v1.0/wc2-tool.cwl:15:9: (function(){return ((parseInt(self[0].contents)));})() v1.0/wc2-tool.cwl:15:9: ^ v1.0/wc2-tool.cwl:15:9: v1.0/wc2-tool.cwl:15:9: TypeError: Cannot read property 'contents' of undefined v1.0/wc2-tool.cwl:15:9: at evalmachine.:23:39 v1.0/wc2-tool.cwl:15:9: at evalmachine.:23:53 v1.0/wc2-tool.cwl:15:9: at ContextifyScript.Script.runInContext (vm.js:59:29) v1.0/wc2-tool.cwl:15:9: at ContextifyScript.Script.runInNewContext (vm.js:65:15) v1.0/wc2-tool.cwl:15:9: at Object.runInNewContext (vm.js:135:38) v1.0/wc2-tool.cwl:15:9: at Socket. ([eval]:11:57) v1.0/wc2-tool.cwl:15:9: at emitOne (events.js:116:13) v1.0/wc2-tool.cwl:15:9: at Socket.emit (events.js:211:7) v1.0/wc2-tool.cwl:15:9: at addChunk (_stream_readable.js:263:12) v1.0/wc2-tool.cwl:15:9: at readableAddChunk (_stream_readable.js:246:13)' [step step1] Output is missing expected field file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/count-lines5-wf.cwl#step1/output [step step1] completed permanentFail Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpzli3uzf3 v1.0/count-lines5-wf.cwl v1.0/empty.json Test workflow with default value for input parameter (missing) Returned non-zero Test [32/132] Test workflow with default value for input parameter (provided) [job step1] job error: Error collecting output for parameter 'output': v1.0/wc2-tool.cwl:15:9: Expression evaluation error: v1.0/wc2-tool.cwl:15:9: Expecting value: line 1 column 1 (char 0) v1.0/wc2-tool.cwl:15:9: script was: v1.0/wc2-tool.cwl:15:9: 01 "use strict"; v1.0/wc2-tool.cwl:15:9: 02 var inputs = { v1.0/wc2-tool.cwl:15:9: 03 "file1": { v1.0/wc2-tool.cwl:15:9: 04 "class": "File", v1.0/wc2-tool.cwl:15:9: 05 "location": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/dba22692-2b24-43e3-8bd6-a1a0b32309df/inputs/whale.txt", v1.0/wc2-tool.cwl:15:9: 06 "size": 1111, v1.0/wc2-tool.cwl:15:9: 07 "basename": "whale.txt", v1.0/wc2-tool.cwl:15:9: 08 "nameroot": "whale", v1.0/wc2-tool.cwl:15:9: 09 "nameext": ".txt", v1.0/wc2-tool.cwl:15:9: 10 "path": "/tmp/tmpfhzayxg_/stg03aabe02-b6da-4f2f-a3f5-17057cded067/whale.txt", v1.0/wc2-tool.cwl:15:9: 11 "dirname": "/tmp/tmpfhzayxg_/stg03aabe02-b6da-4f2f-a3f5-17057cded067" v1.0/wc2-tool.cwl:15:9: 12 } v1.0/wc2-tool.cwl:15:9: 13 }; v1.0/wc2-tool.cwl:15:9: 14 var self = []; v1.0/wc2-tool.cwl:15:9: 15 var runtime = { v1.0/wc2-tool.cwl:15:9: 16 "cores": 1, v1.0/wc2-tool.cwl:15:9: 17 "ram": 1024, v1.0/wc2-tool.cwl:15:9: 18 "tmpdirSize": 1024, v1.0/wc2-tool.cwl:15:9: 19 "outdirSize": 1024, v1.0/wc2-tool.cwl:15:9: 20 "tmpdir": "/tmp/tmpiap_sil9", v1.0/wc2-tool.cwl:15:9: 21 "outdir": "/tmp/tmp2p6ga0bo" v1.0/wc2-tool.cwl:15:9: 22 }; v1.0/wc2-tool.cwl:15:9: 23 (function(){return ((parseInt(self[0].contents)));})() v1.0/wc2-tool.cwl:15:9: stdout was: '' v1.0/wc2-tool.cwl:15:9: stderr was: 'evalmachine.:23 v1.0/wc2-tool.cwl:15:9: (function(){return ((parseInt(self[0].contents)));})() v1.0/wc2-tool.cwl:15:9: ^ v1.0/wc2-tool.cwl:15:9: v1.0/wc2-tool.cwl:15:9: TypeError: Cannot read property 'contents' of undefined v1.0/wc2-tool.cwl:15:9: at evalmachine.:23:39 v1.0/wc2-tool.cwl:15:9: at evalmachine.:23:53 v1.0/wc2-tool.cwl:15:9: at ContextifyScript.Script.runInContext (vm.js:59:29) v1.0/wc2-tool.cwl:15:9: at ContextifyScript.Script.runInNewContext (vm.js:65:15) v1.0/wc2-tool.cwl:15:9: at Object.runInNewContext (vm.js:135:38) v1.0/wc2-tool.cwl:15:9: at Socket. ([eval]:11:57) v1.0/wc2-tool.cwl:15:9: at emitOne (events.js:116:13) v1.0/wc2-tool.cwl:15:9: at Socket.emit (events.js:211:7) v1.0/wc2-tool.cwl:15:9: at addChunk (_stream_readable.js:263:12) v1.0/wc2-tool.cwl:15:9: at readableAddChunk (_stream_readable.js:246:13)' [step step1] Output is missing expected field file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/count-lines5-wf.cwl#step1/output [step step1] completed permanentFail Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpo5o6984d v1.0/count-lines5-wf.cwl v1.0/wc-job.json Test workflow with default value for input parameter (provided) Returned non-zero Test [33/132] Test that workflow defaults override tool defaults [job step1] job error: Error collecting output for parameter 'out': v1.0/echo-tool-default.cwl:17:7: Expression evaluation error: v1.0/echo-tool-default.cwl:17:7: Syntax error in parameter reference 'self[0].contents': self list index 0 out of range. This could be due to using Javascript code without specifying InlineJavascriptRequirement. [step step1] Output is missing expected field file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/echo-wf-default.cwl#step1/out [step step1] completed permanentFail Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmph2s2wcgb v1.0/echo-wf-default.cwl v1.0/empty.json Test that workflow defaults override tool defaults Returned non-zero Test [34/132] Test EnvVarRequirement [job env-tool1.cwl] job error: Error collecting output for parameter 'out': v1.0/env-tool1.cwl:9:7: Did not find output file with glob pattern: '['out']' Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpx0660np7 v1.0/env-tool1.cwl v1.0/env-job.json Test EnvVarRequirement Returned non-zero Test [35/132] Test workflow scatter with single scatter parameter [job step1_3] job error: Error collecting output for parameter 'echo_out': v1.0/scatter-wf1.cwl:32:13: Expression evaluation error: v1.0/scatter-wf1.cwl:32:13: Syntax error in parameter reference 'self[0].contents': self list index 0 out of range. This could be due to using Javascript code without specifying InlineJavascriptRequirement. [job step1] job error: Error collecting output for parameter 'echo_out': v1.0/scatter-wf1.cwl:32:13: Expression evaluation error: v1.0/scatter-wf1.cwl:32:13: Syntax error in parameter reference 'self[0].contents': self list index 0 out of range. This could be due to using Javascript code without specifying InlineJavascriptRequirement. [job step1_2] job error: Error collecting output for parameter 'echo_out': v1.0/scatter-wf1.cwl:32:13: Expression evaluation error: v1.0/scatter-wf1.cwl:32:13: Syntax error in parameter reference 'self[0].contents': self list index 0 out of range. This could be due to using Javascript code without specifying InlineJavascriptRequirement. [job step1_4] job error: Error collecting output for parameter 'echo_out': v1.0/scatter-wf1.cwl:32:13: Expression evaluation error: v1.0/scatter-wf1.cwl:32:13: Syntax error in parameter reference 'self[0].contents': self list index 0 out of range. This could be due to using Javascript code without specifying InlineJavascriptRequirement. [step step1] completed permanentFail Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmphheb04aw v1.0/scatter-wf1.cwl v1.0/scatter-job1.json Test workflow scatter with single scatter parameter Returned non-zero Test [36/132] Test workflow scatter with two scatter parameters and nested_crossproduct join method [job step1_2] job error: Error collecting output for parameter 'echo_out': v1.0/scatter-wf2.cwl:46:13: Expression evaluation error: v1.0/scatter-wf2.cwl:46:13: Syntax error in parameter reference 'self[0].contents': self list index 0 out of range. This could be due to using Javascript code without specifying InlineJavascriptRequirement. [job step1] job error: Error collecting output for parameter 'echo_out': v1.0/scatter-wf2.cwl:46:13: Expression evaluation error: v1.0/scatter-wf2.cwl:46:13: Syntax error in parameter reference 'self[0].contents': self list index 0 out of range. This could be due to using Javascript code without specifying InlineJavascriptRequirement. [job step1_3] job error: Error collecting output for parameter 'echo_out': v1.0/scatter-wf2.cwl:46:13: Expression evaluation error: v1.0/scatter-wf2.cwl:46:13: Syntax error in parameter reference 'self[0].contents': self list index 0 out of range. This could be due to using Javascript code without specifying InlineJavascriptRequirement. [job step1_4] job error: Error collecting output for parameter 'echo_out': v1.0/scatter-wf2.cwl:46:13: Expression evaluation error: v1.0/scatter-wf2.cwl:46:13: Syntax error in parameter reference 'self[0].contents': self list index 0 out of range. This could be due to using Javascript code without specifying InlineJavascriptRequirement. [step step1] completed permanentFail Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpf9hmvic5 v1.0/scatter-wf2.cwl v1.0/scatter-job2.json Test workflow scatter with two scatter parameters and nested_crossproduct join method Returned non-zero Test [37/132] Test workflow scatter with two scatter parameters and flat_crossproduct join method [job step1_4] job error: Error collecting output for parameter 'echo_out': v1.0/scatter-wf3.cwl:21:9: Expression evaluation error: v1.0/scatter-wf3.cwl:21:9: Syntax error in parameter reference 'self[0].contents': self list index 0 out of range. This could be due to using Javascript code without specifying InlineJavascriptRequirement. [job step1_2] job error: Error collecting output for parameter 'echo_out': v1.0/scatter-wf3.cwl:21:9: Expression evaluation error: v1.0/scatter-wf3.cwl:21:9: Syntax error in parameter reference 'self[0].contents': self list index 0 out of range. This could be due to using Javascript code without specifying InlineJavascriptRequirement. [job step1_3] job error: Error collecting output for parameter 'echo_out': v1.0/scatter-wf3.cwl:21:9: Expression evaluation error: v1.0/scatter-wf3.cwl:21:9: Syntax error in parameter reference 'self[0].contents': self list index 0 out of range. This could be due to using Javascript code without specifying InlineJavascriptRequirement. [job step1] job error: Error collecting output for parameter 'echo_out': v1.0/scatter-wf3.cwl:21:9: Expression evaluation error: v1.0/scatter-wf3.cwl:21:9: Syntax error in parameter reference 'self[0].contents': self list index 0 out of range. This could be due to using Javascript code without specifying InlineJavascriptRequirement. [step step1] completed permanentFail Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpfx8xz2rg 'v1.0/scatter-wf3.cwl#main' v1.0/scatter-job2.json Test workflow scatter with two scatter parameters and flat_crossproduct join method Returned non-zero Test [38/132] Test workflow scatter with two scatter parameters and dotproduct join method [job step1_2] job error: Error collecting output for parameter 'echo_out': v1.0/scatter-wf4.cwl:19:9: Expression evaluation error: v1.0/scatter-wf4.cwl:19:9: Syntax error in parameter reference 'self[0].contents': self list index 0 out of range. This could be due to using Javascript code without specifying InlineJavascriptRequirement. [job step1] job error: Error collecting output for parameter 'echo_out': v1.0/scatter-wf4.cwl:19:9: Expression evaluation error: v1.0/scatter-wf4.cwl:19:9: Syntax error in parameter reference 'self[0].contents': self list index 0 out of range. This could be due to using Javascript code without specifying InlineJavascriptRequirement. [step step1] completed permanentFail Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmp7pa91zq4 'v1.0/scatter-wf4.cwl#main' v1.0/scatter-job2.json Test workflow scatter with two scatter parameters and dotproduct join method Returned non-zero Test [39/132] Test workflow scatter with single empty list parameter [job step step1] Notice: scattering over empty input in 'echo_in'. All outputs will be empty. Test [40/132] Test workflow scatter with two scatter parameters and nested_crossproduct join method with second list empty [job step step1] Notice: scattering over empty input in 'echo_in2'. All outputs will be empty. Test [41/132] Test workflow scatter with two scatter parameters and nested_crossproduct join method with first list empty [job step step1] Notice: scattering over empty input in 'echo_in1'. All outputs will be empty. Test [42/132] Test workflow scatter with two scatter parameters, one of which is empty and flat_crossproduct join method [job step step1] Notice: scattering over empty input in 'echo_in2'. All outputs will be empty. Test [43/132] Test workflow scatter with two empty scatter parameters and dotproduct join method [job step step1] Notice: scattering over empty input in 'echo_in1', 'echo_in2'. All outputs will be empty. Test [44/132] Test Any type input parameter [job echo-tool.cwl] job error: Error collecting output for parameter 'out': v1.0/echo-tool.cwl:15:7: Expression evaluation error: v1.0/echo-tool.cwl:15:7: Syntax error in parameter reference 'self[0].contents': self list index 0 out of range. This could be due to using Javascript code without specifying InlineJavascriptRequirement. Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpgy61dpm9 v1.0/echo-tool.cwl v1.0/env-job.json Test Any type input parameter Returned non-zero Test [45/132] Test nested workflow [job step1] job error: Error collecting output for parameter 'output': v1.0/wc-tool.cwl:12:22: Did not find output file with glob pattern: '['output']' [step step1_2] Output is missing expected field file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/count-lines1-wf.cwl#step1/output [step step1_2] completed permanentFail [step step1] completed permanentFail Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpav6r_7g5 v1.0/count-lines8-wf.cwl v1.0/wc-job.json Test nested workflow Returned non-zero Test [46/132] Test requirement priority [job step1] job error: Error collecting output for parameter 'out': v1.0/env-tool1.cwl:9:7: Did not find output file with glob pattern: '['out']' [step step1] Output is missing expected field file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/env-wf1.cwl#step1/out [step step1] completed permanentFail Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmp6xf16znp v1.0/env-wf1.cwl v1.0/env-job.json Test requirement priority Returned non-zero Test [47/132] Test requirements override hints [job step1] job error: Error collecting output for parameter 'out': v1.0/env-tool2.cwl:9:7: Did not find output file with glob pattern: '['out']' [step step1] Output is missing expected field file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/env-wf2.cwl#step1/out [step step1] completed permanentFail Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmp5cgvbv36 v1.0/env-wf2.cwl v1.0/env-job.json Test requirements override hints Returned non-zero Test [48/132] Test requirements on workflow steps [job step1] job error: Error collecting output for parameter 'out': v1.0/env-tool2.cwl:9:7: Did not find output file with glob pattern: '['out']' [step step1] Output is missing expected field file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/env-wf3.cwl#step1/out [step step1] completed permanentFail Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmp7ipd_16e v1.0/env-wf3.cwl v1.0/env-job.json Test requirements on workflow steps Returned non-zero Test [49/132] Test default value on step input parameter unprocessed File CommentedMap([('class', 'File'), ('location', 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/whale.txt'), ('size', 1111), ('basename', 'whale.txt'), ('nameroot', 'whale'), ('nameext', '.txt')]) [job step1] task id: task-e47882cd [job step1] logs: [TaskLog(start_time=datetime.datetime(2018, 8, 25, 14, 18, 12, tzinfo=tzutc()), end_time=datetime.datetime(2018, 8, 25, 14, 24, 11, tzinfo=tzutc()), metadata={'USER_ID': 'anonymousUser'}, logs=None, outputs=None, system_logs=['08/25/2018 02:18:19 DEBUG: Starting taskmaster\n08/25/2018 02:18:19 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:18:19 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:18:19 DEBUG: dirname of /tmp/tmp9lm3u5z8/stgdb384ff1-0069-42b5-a770-d622f30ef3cb/whale.txtis: /tmp/tmp9lm3u5z8/stgdb384ff1-0069-42b5-a770-d622f30ef3cb\n08/25/2018 02:18:19 DEBUG: appending task-volume at path /tmp/tmp9lm3u5z8/stgdb384ff1-0069-42b5-a770-d622f30ef3cb with subPath: dir0\n08/25/2018 02:18:19 DEBUG: dirname of /var/spool/cwl/outputis: /var/spool/cwl\n08/25/2018 02:18:19 DEBUG: appending task-volume at path /var/spool/cwl with subPath: dir1\n08/25/2018 02:18:19 DEBUG: [{\'mountPath\': u\'/tmp/tmp9lm3u5z8/stgdb384ff1-0069-42b5-a770-d622f30ef3cb\', \'subPath\': \'dir0\', \'name\': \'task-volume\'}, {\'mountPath\': u\'/var/spool/cwl\', \'subPath\': \'dir1\', \'name\': \'task-volume\'}]\n08/25/2018 02:18:19 DEBUG: \n08/25/2018 02:18:19 DEBUG: {\'kind\': \'Job\', \'spec\': {\'template\': {\'spec\': {\'restartPolicy\': \'Never\', \'volumes\': [{\'name\': \'task-volume\', \'persistentVolumeClaim\': {\'claimName\': u\'task-e47882cd-pvc\'}}], \'containers\': [{\'name\': \'filer\', \'image\': \'eu.gcr.io/tes-wes/filer:v0.4\', \'args\': [\'inputs\', \'$(JSON_INPUT)\', \'-d\'], \'volumeMounts\': [{\'mountPath\': u\'/tmp/tmp9lm3u5z8/stgdb384ff1-0069-42b5-a770-d622f30ef3cb\', \'subPath\': \'dir0\', \'name\': \'task-volume\'}, {\'mountPath\': u\'/var/spool/cwl\', \'subPath\': \'dir1\', \'name\': \'task-volume\'}], \'env\': [{\'name\': \'JSON_INPUT\', \'value\': \'{"outputs": [{"url": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/f8342a83-e5ed-4cb7-a82a-c70be91f9a9a/output", "path": "/var/spool/cwl/output", "type": "FILE", "name": "stdout"}, {"url": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/f8342a83-e5ed-4cb7-a82a-c70be91f9a9a/", "path": "/var/spool/cwl", "type": "DIRECTORY", "name": "workdir"}], "executors": [{"kind": "Job", "spec": {"template": {"spec": {"restartPolicy": "Never", "containers": [{"name": "task-e47882cd-ex-00", "image": "python:2.7", "workingDir": "/var/spool/cwl", "command": ["/bin/sh", "-c", "wc -l < /tmp/tmp9lm3u5z8/stgdb384ff1-0069-42b5-a770-d622f30ef3cb/whale.txt > /var/spool/cwl/output"], "env": [{"name": "HOME", "value": "/tmp/tmpnkly9q2r"}, {"name": "TMPDIR", "value": "/tmp/tmpw024i7vd"}], "resources": {}}]}, "metadata": {"name": "task-e47882cd-ex-00"}}}, "apiVersion": "batch/v1", "metadata": {"labels": {"taskmaster-name": "task-e47882cd", "executor-no": "0", "job-type": "executor", "creator-user-id": "anonymousUser"}, "annotations": {"tes-task-name": "step1"}, "name": "task-e47882cd-ex-00"}}], "resources": {"disk_gb": 0.1}, "volumes": [], "inputs": [{"url": "file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/whale.txt", "path": "/tmp/tmp9lm3u5z8/stgdb384ff1-0069-42b5-a770-d622f30ef3cb/whale.txt", "type": "FILE", "name": "file1", "description": "cwl_input:file1"}]}\'}, {\'name\': \'TESK_FTP_USERNAME\', \'value\': \'redacted_username\'}, {\'name\': \'TESK_FTP_PASSWORD\', \'value\': \'redacted_password\'}], \'imagePullPolicy\': \'Always\'}]}, \'metadata\': {\'name\': u\'task-e47882cd-filer\'}}}, \'apiVersion\': \'batch/v1\', \'metadata\': {\'name\': u\'task-e47882cd-inputs-filer\'}}\n08/25/2018 02:18:19 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:18:19 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:18:24 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:18:24 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:18:29 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:18:29 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:18:34 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:18:34 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:18:39 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:18:39 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:18:44 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:18:44 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:18:49 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:18:49 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:18:54 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:18:54 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:18:59 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:18:59 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:19:04 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:19:04 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:19:09 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:19:09 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:19:14 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:19:14 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:19:19 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:19:19 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:19:24 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:19:24 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:19:29 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:19:29 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:19:34 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:19:34 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:19:39 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:19:39 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:19:44 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:19:44 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:19:49 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:19:49 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:19:54 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:19:54 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:19:59 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:19:59 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:20:04 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:20:04 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:20:09 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:20:09 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:20:14 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:20:14 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:20:19 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:20:19 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:20:24 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:20:24 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:20:29 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:20:29 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:20:34 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:20:34 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:20:39 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:20:39 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:20:44 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:20:44 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:20:49 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:20:49 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:20:54 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:20:54 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:20:59 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:20:59 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:21:04 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:21:04 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:21:09 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:21:09 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:21:14 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:21:15 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:21:20 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:21:20 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:21:25 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:21:25 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:21:30 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:21:30 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:21:35 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:21:35 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:21:40 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:21:40 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:21:45 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:21:45 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:21:50 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:21:50 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:21:55 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:21:55 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:22:00 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:22:00 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:22:05 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:22:05 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:22:10 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:22:10 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:22:15 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:22:15 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:22:20 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:22:20 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:22:25 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:22:25 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:22:30 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:22:30 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:22:35 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:22:35 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:22:40 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:22:40 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:22:45 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:22:45 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:22:50 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:22:50 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:22:55 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:22:55 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:23:00 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:23:00 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:23:05 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:23:05 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:23:10 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:23:10 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:23:15 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:23:15 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:23:20 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:23:20 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:23:25 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:23:25 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:23:30 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:23:30 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:23:35 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:23:35 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:23:40 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:23:40 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:23:45 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:23:45 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:23:50 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:23:50 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:23:55 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:23:55 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:24:00 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:24:00 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:24:05 DEBUG: Got label: "b3581a44-a871-11e8-916e-fa163e364743"\n\n08/25/2018 02:24:05 DEBUG: Got label: "task-e47882cd"\n08/25/2018 02:24:10 ERROR: Cancelling taskmaster: Got status Failed\n'])] [job step1] job error: Error collecting output for parameter 'output': v1.0/wc-tool.cwl:12:22: Did not find output file with glob pattern: '['output']' [step step1] Output is missing expected field file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/count-lines9-wf.cwl#step1/output [step step1] completed permanentFail Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpea3dxbdy v1.0/count-lines9-wf.cwl v1.0/empty.json Test default value on step input parameter Returned non-zero Test [50/132] Test use default value on step input parameter with empty source Workflow checker warning: v1.0/count-lines11-wf.cwl:6:3: Source 'file1' of type ["null", "File"] may be incompatible v1.0/count-lines11-wf.cwl:17:7: with sink 'file1' of type "File" unprocessed File CommentedMap([('class', 'File'), ('location', 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/whale.txt'), ('size', 1111), ('basename', 'whale.txt'), ('nameroot', 'whale'), ('nameext', '.txt')]) [job step1] task id: task-273ec8f7 [job step1] logs: [TaskLog(start_time=datetime.datetime(2018, 8, 25, 14, 24, 18, tzinfo=tzutc()), end_time=datetime.datetime(2018, 8, 25, 14, 31, 37, tzinfo=tzutc()), metadata={'USER_ID': 'anonymousUser'}, logs=None, outputs=None, system_logs=['08/25/2018 02:24:24 DEBUG: Starting taskmaster\n08/25/2018 02:24:24 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:24:24 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:24:25 DEBUG: dirname of /tmp/tmpxyybdvi9/stg59fa2e50-d6e1-46e7-9388-199ade0e48d3/whale.txtis: /tmp/tmpxyybdvi9/stg59fa2e50-d6e1-46e7-9388-199ade0e48d3\n08/25/2018 02:24:25 DEBUG: appending task-volume at path /tmp/tmpxyybdvi9/stg59fa2e50-d6e1-46e7-9388-199ade0e48d3 with subPath: dir0\n08/25/2018 02:24:25 DEBUG: dirname of /var/spool/cwl/outputis: /var/spool/cwl\n08/25/2018 02:24:25 DEBUG: appending task-volume at path /var/spool/cwl with subPath: dir1\n08/25/2018 02:24:25 DEBUG: [{\'mountPath\': u\'/tmp/tmpxyybdvi9/stg59fa2e50-d6e1-46e7-9388-199ade0e48d3\', \'subPath\': \'dir0\', \'name\': \'task-volume\'}, {\'mountPath\': u\'/var/spool/cwl\', \'subPath\': \'dir1\', \'name\': \'task-volume\'}]\n08/25/2018 02:24:25 DEBUG: \n08/25/2018 02:24:25 DEBUG: {\'kind\': \'Job\', \'spec\': {\'template\': {\'spec\': {\'restartPolicy\': \'Never\', \'volumes\': [{\'name\': \'task-volume\', \'persistentVolumeClaim\': {\'claimName\': u\'task-273ec8f7-pvc\'}}], \'containers\': [{\'name\': \'filer\', \'image\': \'eu.gcr.io/tes-wes/filer:v0.4\', \'args\': [\'inputs\', \'$(JSON_INPUT)\', \'-d\'], \'volumeMounts\': [{\'mountPath\': u\'/tmp/tmpxyybdvi9/stg59fa2e50-d6e1-46e7-9388-199ade0e48d3\', \'subPath\': \'dir0\', \'name\': \'task-volume\'}, {\'mountPath\': u\'/var/spool/cwl\', \'subPath\': \'dir1\', \'name\': \'task-volume\'}], \'env\': [{\'name\': \'JSON_INPUT\', \'value\': \'{"outputs": [{"url": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/6c95bdc6-3e80-4f04-91c2-cafb6751f37b/output", "path": "/var/spool/cwl/output", "type": "FILE", "name": "stdout"}, {"url": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/6c95bdc6-3e80-4f04-91c2-cafb6751f37b/", "path": "/var/spool/cwl", "type": "DIRECTORY", "name": "workdir"}], "executors": [{"kind": "Job", "spec": {"template": {"spec": {"restartPolicy": "Never", "containers": [{"name": "task-273ec8f7-ex-00", "image": "python:2.7", "workingDir": "/var/spool/cwl", "command": ["/bin/sh", "-c", "wc -l < /tmp/tmpxyybdvi9/stg59fa2e50-d6e1-46e7-9388-199ade0e48d3/whale.txt > /var/spool/cwl/output"], "env": [{"name": "HOME", "value": "/tmp/tmpz9ybtdge"}, {"name": "TMPDIR", "value": "/tmp/tmpfl54u2lk"}], "resources": {}}]}, "metadata": {"name": "task-273ec8f7-ex-00"}}}, "apiVersion": "batch/v1", "metadata": {"labels": {"taskmaster-name": "task-273ec8f7", "executor-no": "0", "job-type": "executor", "creator-user-id": "anonymousUser"}, "annotations": {"tes-task-name": "step1"}, "name": "task-273ec8f7-ex-00"}}], "resources": {"disk_gb": 0.1}, "volumes": [], "inputs": [{"url": "file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/whale.txt", "path": "/tmp/tmpxyybdvi9/stg59fa2e50-d6e1-46e7-9388-199ade0e48d3/whale.txt", "type": "FILE", "name": "file1", "description": "cwl_input:file1"}]}\'}, {\'name\': \'TESK_FTP_USERNAME\', \'value\': \'redacted_username\'}, {\'name\': \'TESK_FTP_PASSWORD\', \'value\': \'redacted_password\'}], \'imagePullPolicy\': \'Always\'}]}, \'metadata\': {\'name\': u\'task-273ec8f7-filer\'}}}, \'apiVersion\': \'batch/v1\', \'metadata\': {\'name\': u\'task-273ec8f7-inputs-filer\'}}\n08/25/2018 02:24:25 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:24:25 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:24:30 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:24:30 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:24:35 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:24:35 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:24:40 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:24:40 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:24:45 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:24:45 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:24:50 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:24:50 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:24:55 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:24:55 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:25:00 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:25:00 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:25:05 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:25:05 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:25:10 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:25:10 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:25:15 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:25:15 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:25:20 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:25:20 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:25:25 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:25:25 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:25:30 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:25:30 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:25:35 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:25:35 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:25:40 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:25:40 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:25:45 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:25:45 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:25:50 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:25:50 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:25:55 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:25:55 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:26:00 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:26:00 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:26:05 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:26:05 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:26:10 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:26:10 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:26:15 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:26:15 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:26:20 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:26:20 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:26:25 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:26:25 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:26:30 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:26:30 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:26:35 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:26:35 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:26:40 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:26:40 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:26:45 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:26:45 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:26:50 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:26:50 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:26:55 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:26:55 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:27:00 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:27:00 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:27:05 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:27:05 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:27:10 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:27:10 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:27:15 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:27:15 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:27:20 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:27:20 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:27:25 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:27:25 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:27:30 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:27:30 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:27:35 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:27:35 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:27:40 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:27:40 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:27:45 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:27:45 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:27:50 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:27:50 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:27:55 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:27:55 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:28:00 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:28:00 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:28:05 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:28:05 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:28:10 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:28:10 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:28:15 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:28:15 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:28:20 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:28:20 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:28:25 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:28:25 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:28:30 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:28:30 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:28:35 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:28:35 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:28:40 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:28:40 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:28:45 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:28:45 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:28:50 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:28:50 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:28:55 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:28:55 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:29:00 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:29:00 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:29:05 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:29:05 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:29:10 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:29:10 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:29:15 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:29:15 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:29:20 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:29:20 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:29:25 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:29:25 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:29:30 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:29:30 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:29:35 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:29:35 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:29:40 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:29:40 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:29:45 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:29:45 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:29:50 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:29:50 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:29:55 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:29:55 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:30:00 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:30:00 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:30:05 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:30:05 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:30:10 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:30:10 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:30:15 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:30:15 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:30:20 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:30:20 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:30:25 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:30:25 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:30:30 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:30:30 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:30:35 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:30:35 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:30:40 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:30:40 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:30:45 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:30:45 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:30:50 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:30:50 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:30:55 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:30:55 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:31:00 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:31:00 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:31:05 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:31:05 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:31:10 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:31:10 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:31:15 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:31:15 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:31:20 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:31:20 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:31:25 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:31:25 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:31:30 DEBUG: Got label: "8d1dbc53-a872-11e8-916e-fa163e364743"\n\n08/25/2018 02:31:30 DEBUG: Got label: "task-273ec8f7"\n08/25/2018 02:31:36 ERROR: Cancelling taskmaster: Got status Failed\n'])] [job step1] job error: Error collecting output for parameter 'output': v1.0/wc-tool.cwl:12:22: Did not find output file with glob pattern: '['output']' [step step1] Output is missing expected field file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/count-lines11-wf.cwl#step1/output [step step1] completed permanentFail Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmp8hmwi5nr v1.0/count-lines11-wf.cwl v1.0/empty.json Test use default value on step input parameter with empty source Returned non-zero Test [51/132] Test use default value on step input parameter with null source Workflow checker warning: v1.0/count-lines11-wf.cwl:6:3: Source 'file1' of type ["null", "File"] may be incompatible v1.0/count-lines11-wf.cwl:17:7: with sink 'file1' of type "File" unprocessed File CommentedMap([('class', 'File'), ('location', 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/whale.txt'), ('size', 1111), ('basename', 'whale.txt'), ('nameroot', 'whale'), ('nameext', '.txt')]) Test timed out: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpp8uamalr v1.0/count-lines11-wf.cwl v1.0/file1-null.json Test use default value on step input parameter with null source Terminating lingering process Test [52/132] Test default value on step input parameter overridden by provided source Workflow checker warning: v1.0/count-lines11-wf.cwl:6:3: Source 'file1' of type ["null", "File"] may be incompatible v1.0/count-lines11-wf.cwl:17:7: with sink 'file1' of type "File" [job step1] job error: Error collecting output for parameter 'output': v1.0/wc-tool.cwl:12:22: Did not find output file with glob pattern: '['output']' [step step1] Output is missing expected field file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/count-lines11-wf.cwl#step1/output [step step1] completed permanentFail Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpb_pc98up v1.0/count-lines11-wf.cwl v1.0/cat-job.json Test default value on step input parameter overridden by provided source Returned non-zero Test [53/132] Test simple workflow [job rev] task id: task-6905e80f [job rev] logs: [TaskLog(start_time=datetime.datetime(2018, 8, 25, 14, 44, 9, tzinfo=tzutc()), end_time=None, metadata={'USER_ID': 'anonymousUser'}, logs=None, outputs=None, system_logs=['08/25/2018 02:45:52 DEBUG: Starting taskmaster\n08/25/2018 02:45:52 DEBUG: Got label: "534bd65f-a875-11e8-916e-fa163e364743"\n\n08/25/2018 02:45:52 DEBUG: Got label: "task-6905e80f"\nTraceback (most recent call last):\n File "/usr/bin/taskmaster.py", line 214, in \n main(sys.argv)\n File "/usr/bin/taskmaster.py", line 185, in main\n run_task(data, args.filer_version)\n File "/usr/bin/taskmaster.py", line 117, in run_task\n pvc = init_pvc(data, filer)\n File "/usr/bin/taskmaster.py", line 83, in init_pvc\n pvc = PVC(pvc_name, pvc_size, args.namespace)\n File "/usr/bin/pvc.py", line 19, in __init__\n self.cv1.create_namespaced_persistent_volume_claim(self.namespace, self.spec)\n File "/usr/lib/python2.7/site-packages/kubernetes/client/apis/core_v1_api.py", line 5950, in create_namespaced_persistent_volume_claim\n (data) = self.create_namespaced_persistent_volume_claim_with_http_info(namespace, body, **kwargs)\n File "/usr/lib/python2.7/site-packages/kubernetes/client/apis/core_v1_api.py", line 6035, in create_namespaced_persistent_volume_claim_with_http_info\n collection_formats=collection_formats)\n File "/usr/lib/python2.7/site-packages/kubernetes/client/api_client.py", line 321, in call_api\n _return_http_data_only, collection_formats, _preload_content, _request_timeout)\n File "/usr/lib/python2.7/site-packages/kubernetes/client/api_client.py", line 155, in __call_api\n _request_timeout=_request_timeout)\n File "/usr/lib/python2.7/site-packages/kubernetes/client/api_client.py", line 364, in request\n body=body)\n File "/usr/lib/python2.7/site-packages/kubernetes/client/rest.py", line 266, in POST\n body=body)\n File "/usr/lib/python2.7/site-packages/kubernetes/client/rest.py", line 222, in request\n raise ApiException(http_resp=r)\nkubernetes.client.rest.ApiException: (409)\nReason: Conflict\nHTTP response headers: HTTPHeaderDict({\'Date\': \'Sat, 25 Aug 2018 14:45:52 GMT\', \'Content-Length\': \'248\', \'Content-Type\': \'application/json\'})\nHTTP response body: {"kind":"Status","apiVersion":"v1","metadata":{},"status":"Failure","message":"persistentvolumeclaims \\"task-6905e80f-pvc\\" already exists","reason":"AlreadyExists","details":{"name":"task-6905e80f-pvc","kind":"persistentvolumeclaims"},"code":409}\n\n\n'])] [job rev] job error: Error collecting output for parameter 'output': v1.0/revtool.cwl:30:7: Did not find output file with glob pattern: '['output.txt']' [step rev] Output is missing expected field file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/revsort.cwl#rev/output [step rev] completed permanentFail Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpgl4q6sd7 v1.0/revsort.cwl v1.0/revsort-job.json Test simple workflow Returned non-zero Test [54/132] Test unknown hints are ignored. v1.0/cat5-tool.cwl:10:3: checking item v1.0/cat5-tool.cwl:10:3: Field `class` contains undefined reference to `http://example.com/BlibberBlubberFakeRequirement` [job cat5-tool.cwl] job error: Error collecting output for parameter 'output_file': v1.0/cat5-tool.cwl:21:21: Did not find output file with glob pattern: '['output.txt']' Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmp7dhtcf7p v1.0/cat5-tool.cwl v1.0/cat-job.json Test unknown hints are ignored. Returned non-zero Test [55/132] Test InitialWorkDirRequirement linking input files and capturing secondaryFiles on input and output. Also tests the use of a variety of parameter references and expressions in the secondaryFiles field. Workflow checker warning: v1.0/search.cwl:108:9: Sink 'file' v1.0/search.cwl:57:7: expects secondaryFiles: ['.idx1', '^.idx2', '$(self.basename).idx3', '${ return self.basename+".idx4"; }', '$(self.nameroot).idx6$(self.nameext)', '${ return [self.basename+".idx7"]; }', '_idx8'] but v1.0/search.cwl:103:13: source 'result' has secondaryFiles ['.idx1', '^.idx2', '$(self.basename).idx3', '${ return self.basename+".idx4"; }', '$({"path": self.path+".idx5", "class": "File"})', '$(self.nameroot).idx6$(self.nameext)', '${ return [self.basename+".idx7", inputs.secondfile]; }', '_idx8']. To fix, add secondaryFiles: ['.idx1', '^.idx2', '$(self.basename).idx3', '${ return self.basename+".idx4"; }', '$(self.nameroot).idx6$(self.nameext)', '${ return [self.basename+".idx7"]; }', '_idx8'] to definition of 'result'. unprocessed File CommentedMap([('class', 'File'), ('location', 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/index.py'), ('size', 1031), ('basename', 'index.py'), ('nameroot', 'index'), ('nameext', '.py')]) Got workflow error Traceback (most recent call last): File "/home/mcrusoe/cwltool/cwltool/executors.py", line 238, in runner my_job.run(my_runtime_context) File "/home/mcrusoe/src/cwl-tes/cwl_tes/tes.py", line 358, in run task = self.create_task_msg() File "/home/mcrusoe/src/cwl-tes/cwl_tes/tes.py", line 265, in create_task_msg input_parameters = self.get_inputs() File "/home/mcrusoe/src/cwl-tes/cwl_tes/tes.py", line 246, in get_inputs self.parse_listing(self.generatefiles["listing"], inputs) File "/home/mcrusoe/src/cwl-tes/cwl_tes/tes.py", line 213, in parse_listing "The TES spec does not allow for writable inputs" cwltool.errors.UnsupportedRequirement: The TES spec does not allow for writable inputs Workflow or tool uses unsupported feature: The TES spec does not allow for writable inputs Test [56/132] Test InitialWorkDirRequirement with expression in filename. Got workflow error Traceback (most recent call last): File "/home/mcrusoe/cwltool/cwltool/executors.py", line 238, in runner my_job.run(my_runtime_context) File "/home/mcrusoe/src/cwl-tes/cwl_tes/tes.py", line 358, in run task = self.create_task_msg() File "/home/mcrusoe/src/cwl-tes/cwl_tes/tes.py", line 265, in create_task_msg input_parameters = self.get_inputs() File "/home/mcrusoe/src/cwl-tes/cwl_tes/tes.py", line 246, in get_inputs self.parse_listing(self.generatefiles["listing"], inputs) File "/home/mcrusoe/src/cwl-tes/cwl_tes/tes.py", line 213, in parse_listing "The TES spec does not allow for writable inputs" cwltool.errors.UnsupportedRequirement: The TES spec does not allow for writable inputs Workflow or tool uses unsupported feature: The TES spec does not allow for writable inputs Test [57/132] Test if trailing newline is present in file entry in InitialWorkDir Got workflow error Traceback (most recent call last): File "/home/mcrusoe/cwltool/cwltool/executors.py", line 238, in runner my_job.run(my_runtime_context) File "/home/mcrusoe/src/cwl-tes/cwl_tes/tes.py", line 358, in run task = self.create_task_msg() File "/home/mcrusoe/src/cwl-tes/cwl_tes/tes.py", line 265, in create_task_msg input_parameters = self.get_inputs() File "/home/mcrusoe/src/cwl-tes/cwl_tes/tes.py", line 246, in get_inputs self.parse_listing(self.generatefiles["listing"], inputs) File "/home/mcrusoe/src/cwl-tes/cwl_tes/tes.py", line 213, in parse_listing "The TES spec does not allow for writable inputs" cwltool.errors.UnsupportedRequirement: The TES spec does not allow for writable inputs Workflow or tool uses unsupported feature: The TES spec does not allow for writable inputs Test [58/132] Test inline expressions [job wc4-tool.cwl] job error: Error collecting output for parameter 'output': v1.0/wc4-tool.cwl:17:9: Expression evaluation error: v1.0/wc4-tool.cwl:17:9: Expecting value: line 1 column 1 (char 0) v1.0/wc4-tool.cwl:17:9: script was: v1.0/wc4-tool.cwl:17:9: 01 "use strict"; v1.0/wc4-tool.cwl:17:9: 02 var inputs = { v1.0/wc4-tool.cwl:17:9: 03 "file1": { v1.0/wc4-tool.cwl:17:9: 04 "class": "File", v1.0/wc4-tool.cwl:17:9: 05 "location": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/03e2a8f2-5186-498b-85aa-b769955eea5f/inputs/whale.txt", v1.0/wc4-tool.cwl:17:9: 06 "size": 1111, v1.0/wc4-tool.cwl:17:9: 07 "basename": "whale.txt", v1.0/wc4-tool.cwl:17:9: 08 "nameroot": "whale", v1.0/wc4-tool.cwl:17:9: 09 "nameext": ".txt", v1.0/wc4-tool.cwl:17:9: 10 "path": "/tmp/tmptivv4uv2/stg567d64fc-ef3b-430f-859c-feb3e4b4371b/whale.txt", v1.0/wc4-tool.cwl:17:9: 11 "dirname": "/tmp/tmptivv4uv2/stg567d64fc-ef3b-430f-859c-feb3e4b4371b" v1.0/wc4-tool.cwl:17:9: 12 } v1.0/wc4-tool.cwl:17:9: 13 }; v1.0/wc4-tool.cwl:17:9: 14 var self = []; v1.0/wc4-tool.cwl:17:9: 15 var runtime = { v1.0/wc4-tool.cwl:17:9: 16 "cores": 1, v1.0/wc4-tool.cwl:17:9: 17 "ram": 1024, v1.0/wc4-tool.cwl:17:9: 18 "tmpdirSize": 1024, v1.0/wc4-tool.cwl:17:9: 19 "outdirSize": 1024, v1.0/wc4-tool.cwl:17:9: 20 "tmpdir": "/tmp/tmpci2ygy7f", v1.0/wc4-tool.cwl:17:9: 21 "outdir": "/tmp/tmplme_nvab" v1.0/wc4-tool.cwl:17:9: 22 }; v1.0/wc4-tool.cwl:17:9: 23 (function(){ v1.0/wc4-tool.cwl:17:9: 24 var s = self[0].contents.split(/\r?\n/); v1.0/wc4-tool.cwl:17:9: 25 return parseInt(s[s.length-2]); v1.0/wc4-tool.cwl:17:9: 26 })() v1.0/wc4-tool.cwl:17:9: stdout was: '' v1.0/wc4-tool.cwl:17:9: stderr was: 'evalmachine.:24 v1.0/wc4-tool.cwl:17:9: var s = self[0].contents.split(/\r?\n/); v1.0/wc4-tool.cwl:17:9: ^ v1.0/wc4-tool.cwl:17:9: v1.0/wc4-tool.cwl:17:9: TypeError: Cannot read property 'contents' of undefined v1.0/wc4-tool.cwl:17:9: at evalmachine.:24:19 v1.0/wc4-tool.cwl:17:9: at evalmachine.:26:3 v1.0/wc4-tool.cwl:17:9: at ContextifyScript.Script.runInContext (vm.js:59:29) v1.0/wc4-tool.cwl:17:9: at ContextifyScript.Script.runInNewContext (vm.js:65:15) v1.0/wc4-tool.cwl:17:9: at Object.runInNewContext (vm.js:135:38) v1.0/wc4-tool.cwl:17:9: at Socket. ([eval]:11:57) v1.0/wc4-tool.cwl:17:9: at emitOne (events.js:116:13) v1.0/wc4-tool.cwl:17:9: at Socket.emit (events.js:211:7) v1.0/wc4-tool.cwl:17:9: at addChunk (_stream_readable.js:263:12) v1.0/wc4-tool.cwl:17:9: at readableAddChunk (_stream_readable.js:246:13)' Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpdqr5wiyp v1.0/wc4-tool.cwl v1.0/wc-job.json Test inline expressions Returned non-zero Test [59/132] Test SchemaDefRequirement definition used in tool parameter [job schemadef-tool.cwl] job error: Error collecting output for parameter 'output': v1.0/schemadef-tool.cwl:18:9: Did not find output file with glob pattern: '['output.txt']' Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpff2x7_4r v1.0/schemadef-tool.cwl v1.0/schemadef-job.json Test SchemaDefRequirement definition used in tool parameter Returned non-zero Test [60/132] Test SchemaDefRequirement definition used in workflow parameter [job step1] job error: Error collecting output for parameter 'output': v1.0/schemadef-tool.cwl:18:9: Did not find output file with glob pattern: '['output.txt']' [step step1] Output is missing expected field file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/schemadef-wf.cwl#step1/output [step step1] completed permanentFail Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpkxesk_fb v1.0/schemadef-wf.cwl v1.0/schemadef-job.json Test SchemaDefRequirement definition used in workflow parameter Returned non-zero Test [61/132] Test parameter evaluation, no support for JS expressions Test [62/132] Test parameter evaluation, with support for JS expressions Test [63/132] Test metadata Expecting value: line 1 column 1 (char 0) Test [64/132] Test simple format checking. [job formattest.cwl] job error: Error collecting output for parameter 'output': v1.0/formattest.cwl:16:7: Did not find output file with glob pattern: '['output.txt']' Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpnyuh1cd0 v1.0/formattest.cwl v1.0/formattest-job.json Test simple format checking. Returned non-zero Test [65/132] Test format checking against ontology using subclassOf. [job formattest2.cwl] job error: Error collecting output for parameter 'output': v1.0/formattest2.cwl:22:7: Did not find output file with glob pattern: '['output.txt']' Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpb5tr_gpf v1.0/formattest2.cwl v1.0/formattest2-job.json Test format checking against ontology using subclassOf. Returned non-zero Test [66/132] Test format checking against ontology using equivalentClass. [job formattest3.cwl] job error: Error collecting output for parameter 'output': v1.0/formattest3.cwl:24:7: Did not find output file with glob pattern: '['output.txt']' Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmppqm5mbaf v1.0/formattest3.cwl v1.0/formattest2-job.json Test format checking against ontology using equivalentClass. Returned non-zero Test [67/132] Test optional output file and optional secondaryFile on output. [job optional-output.cwl] job error: Error collecting output for parameter 'output_file': v1.0/optional-output.cwl:18:7: Did not find output file with glob pattern: '['output.txt']' Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpvaq9bxl4 v1.0/optional-output.cwl v1.0/cat-job.json Test optional output file and optional secondaryFile on output. Returned non-zero Test [68/132] Test that valueFrom is ignored when the parameter is null [job vf-concat.cwl] job error: Error collecting output for parameter 'out': v1.0/vf-concat.cwl:18:7: Expression evaluation error: v1.0/vf-concat.cwl:18:7: Expecting value: line 1 column 1 (char 0) v1.0/vf-concat.cwl:18:7: script was: v1.0/vf-concat.cwl:18:7: 01 "use strict"; v1.0/vf-concat.cwl:18:7: 02 var inputs = { v1.0/vf-concat.cwl:18:7: 03 "file1": null v1.0/vf-concat.cwl:18:7: 04 }; v1.0/vf-concat.cwl:18:7: 05 var self = []; v1.0/vf-concat.cwl:18:7: 06 var runtime = { v1.0/vf-concat.cwl:18:7: 07 "cores": 1, v1.0/vf-concat.cwl:18:7: 08 "ram": 1024, v1.0/vf-concat.cwl:18:7: 09 "tmpdirSize": 1024, v1.0/vf-concat.cwl:18:7: 10 "outdirSize": 1024, v1.0/vf-concat.cwl:18:7: 11 "tmpdir": "/tmp/tmpmei03hqv", v1.0/vf-concat.cwl:18:7: 12 "outdir": "/tmp/tmpkf2y6g5y" v1.0/vf-concat.cwl:18:7: 13 }; v1.0/vf-concat.cwl:18:7: 14 (function(){return ((self[0].contents));})() v1.0/vf-concat.cwl:18:7: stdout was: '' v1.0/vf-concat.cwl:18:7: stderr was: 'evalmachine.:14 v1.0/vf-concat.cwl:18:7: (function(){return ((self[0].contents));})() v1.0/vf-concat.cwl:18:7: ^ v1.0/vf-concat.cwl:18:7: v1.0/vf-concat.cwl:18:7: TypeError: Cannot read property 'contents' of undefined v1.0/vf-concat.cwl:18:7: at evalmachine.:14:30 v1.0/vf-concat.cwl:18:7: at evalmachine.:14:43 v1.0/vf-concat.cwl:18:7: at ContextifyScript.Script.runInContext (vm.js:59:29) v1.0/vf-concat.cwl:18:7: at ContextifyScript.Script.runInNewContext (vm.js:65:15) v1.0/vf-concat.cwl:18:7: at Object.runInNewContext (vm.js:135:38) v1.0/vf-concat.cwl:18:7: at Socket. ([eval]:11:57) v1.0/vf-concat.cwl:18:7: at emitOne (events.js:116:13) v1.0/vf-concat.cwl:18:7: at Socket.emit (events.js:211:7) v1.0/vf-concat.cwl:18:7: at addChunk (_stream_readable.js:263:12) v1.0/vf-concat.cwl:18:7: at readableAddChunk (_stream_readable.js:246:13)' Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpjtez29r9 v1.0/vf-concat.cwl v1.0/empty.json Test that valueFrom is ignored when the parameter is null Returned non-zero Test [69/132] Test that second expression in concatenated valueFrom is not ignored [job vf-concat.cwl] job error: Error collecting output for parameter 'out': v1.0/vf-concat.cwl:18:7: Expression evaluation error: v1.0/vf-concat.cwl:18:7: Expecting value: line 1 column 1 (char 0) v1.0/vf-concat.cwl:18:7: script was: v1.0/vf-concat.cwl:18:7: 01 "use strict"; v1.0/vf-concat.cwl:18:7: 02 var inputs = { v1.0/vf-concat.cwl:18:7: 03 "file1": { v1.0/vf-concat.cwl:18:7: 04 "class": "File", v1.0/vf-concat.cwl:18:7: 05 "location": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/e5c3f257-b9ff-4866-94b8-2dfe359dacea/inputs/hello.txt", v1.0/vf-concat.cwl:18:7: 06 "size": 13, v1.0/vf-concat.cwl:18:7: 07 "basename": "hello.txt", v1.0/vf-concat.cwl:18:7: 08 "nameroot": "hello", v1.0/vf-concat.cwl:18:7: 09 "nameext": ".txt", v1.0/vf-concat.cwl:18:7: 10 "path": "/tmp/tmpgmr3xjpp/stgc38ce55f-ed68-4fec-ae60-ef6e2578b0d7/hello.txt", v1.0/vf-concat.cwl:18:7: 11 "dirname": "/tmp/tmpgmr3xjpp/stgc38ce55f-ed68-4fec-ae60-ef6e2578b0d7" v1.0/vf-concat.cwl:18:7: 12 } v1.0/vf-concat.cwl:18:7: 13 }; v1.0/vf-concat.cwl:18:7: 14 var self = []; v1.0/vf-concat.cwl:18:7: 15 var runtime = { v1.0/vf-concat.cwl:18:7: 16 "cores": 1, v1.0/vf-concat.cwl:18:7: 17 "ram": 1024, v1.0/vf-concat.cwl:18:7: 18 "tmpdirSize": 1024, v1.0/vf-concat.cwl:18:7: 19 "outdirSize": 1024, v1.0/vf-concat.cwl:18:7: 20 "tmpdir": "/tmp/tmpsww9keeq", v1.0/vf-concat.cwl:18:7: 21 "outdir": "/tmp/tmpnhfrcjll" v1.0/vf-concat.cwl:18:7: 22 }; v1.0/vf-concat.cwl:18:7: 23 (function(){return ((self[0].contents));})() v1.0/vf-concat.cwl:18:7: stdout was: '' v1.0/vf-concat.cwl:18:7: stderr was: 'evalmachine.:23 v1.0/vf-concat.cwl:18:7: (function(){return ((self[0].contents));})() v1.0/vf-concat.cwl:18:7: ^ v1.0/vf-concat.cwl:18:7: v1.0/vf-concat.cwl:18:7: TypeError: Cannot read property 'contents' of undefined v1.0/vf-concat.cwl:18:7: at evalmachine.:23:30 v1.0/vf-concat.cwl:18:7: at evalmachine.:23:43 v1.0/vf-concat.cwl:18:7: at ContextifyScript.Script.runInContext (vm.js:59:29) v1.0/vf-concat.cwl:18:7: at ContextifyScript.Script.runInNewContext (vm.js:65:15) v1.0/vf-concat.cwl:18:7: at Object.runInNewContext (vm.js:135:38) v1.0/vf-concat.cwl:18:7: at Socket. ([eval]:11:57) v1.0/vf-concat.cwl:18:7: at emitOne (events.js:116:13) v1.0/vf-concat.cwl:18:7: at Socket.emit (events.js:211:7) v1.0/vf-concat.cwl:18:7: at addChunk (_stream_readable.js:263:12) v1.0/vf-concat.cwl:18:7: at readableAddChunk (_stream_readable.js:246:13)' Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpqznqeira v1.0/vf-concat.cwl v1.0/cat-job.json Test that second expression in concatenated valueFrom is not ignored Returned non-zero Test [70/132] Test valueFrom on workflow step. [job step1] job error: Error collecting output for parameter 'output': v1.0/wc-tool.cwl:12:22: Did not find output file with glob pattern: '['output']' [step step1] Output is missing expected field file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/step-valuefrom-wf.cwl#step1/output [step step1] completed permanentFail Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmp0rf3akm2 v1.0/step-valuefrom-wf.cwl v1.0/step-valuefrom-wf.json Test valueFrom on workflow step. Returned non-zero Test [71/132] Test valueFrom on workflow step with multiple sources [job step1] job error: Error collecting output for parameter 'echo_out': v1.0/step-valuefrom2-wf.cwl:33:13: Expression evaluation error: v1.0/step-valuefrom2-wf.cwl:33:13: Expecting value: line 1 column 1 (char 0) v1.0/step-valuefrom2-wf.cwl:33:13: script was: v1.0/step-valuefrom2-wf.cwl:33:13: 01 "use strict"; v1.0/step-valuefrom2-wf.cwl:33:13: 02 var inputs = { v1.0/step-valuefrom2-wf.cwl:33:13: 03 "c": 3 v1.0/step-valuefrom2-wf.cwl:33:13: 04 }; v1.0/step-valuefrom2-wf.cwl:33:13: 05 var self = []; v1.0/step-valuefrom2-wf.cwl:33:13: 06 var runtime = { v1.0/step-valuefrom2-wf.cwl:33:13: 07 "cores": 1, v1.0/step-valuefrom2-wf.cwl:33:13: 08 "ram": 1024, v1.0/step-valuefrom2-wf.cwl:33:13: 09 "tmpdirSize": 1024, v1.0/step-valuefrom2-wf.cwl:33:13: 10 "outdirSize": 1024, v1.0/step-valuefrom2-wf.cwl:33:13: 11 "tmpdir": "/tmp/tmpcbqgxj2r", v1.0/step-valuefrom2-wf.cwl:33:13: 12 "outdir": "/tmp/tmp4xsqotc8" v1.0/step-valuefrom2-wf.cwl:33:13: 13 }; v1.0/step-valuefrom2-wf.cwl:33:13: 14 (function(){return ((self[0].contents));})() v1.0/step-valuefrom2-wf.cwl:33:13: stdout was: '' v1.0/step-valuefrom2-wf.cwl:33:13: stderr was: 'evalmachine.:14 v1.0/step-valuefrom2-wf.cwl:33:13: (function(){return ((self[0].contents));})() v1.0/step-valuefrom2-wf.cwl:33:13: ^ v1.0/step-valuefrom2-wf.cwl:33:13: v1.0/step-valuefrom2-wf.cwl:33:13: TypeError: Cannot read property 'contents' of undefined v1.0/step-valuefrom2-wf.cwl:33:13: at evalmachine.:14:30 v1.0/step-valuefrom2-wf.cwl:33:13: at evalmachine.:14:43 v1.0/step-valuefrom2-wf.cwl:33:13: at ContextifyScript.Script.runInContext (vm.js:59:29) v1.0/step-valuefrom2-wf.cwl:33:13: at ContextifyScript.Script.runInNewContext (vm.js:65:15) v1.0/step-valuefrom2-wf.cwl:33:13: at Object.runInNewContext (vm.js:135:38) v1.0/step-valuefrom2-wf.cwl:33:13: at Socket. ([eval]:11:57) v1.0/step-valuefrom2-wf.cwl:33:13: at emitOne (events.js:116:13) v1.0/step-valuefrom2-wf.cwl:33:13: at Socket.emit (events.js:211:7) v1.0/step-valuefrom2-wf.cwl:33:13: at addChunk (_stream_readable.js:263:12) v1.0/step-valuefrom2-wf.cwl:33:13: at readableAddChunk (_stream_readable.js:246:13)' [step step1] Output is missing expected field file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/step-valuefrom2-wf.cwl#step1/echo_out [step step1] completed permanentFail Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpkpn7654z v1.0/step-valuefrom2-wf.cwl v1.0/step-valuefrom-job.json Test valueFrom on workflow step with multiple sources Returned non-zero Test [72/132] Test valueFrom on workflow step referencing other inputs Workflow checker warning: v1.0/step-valuefrom3-wf.cwl:37:7: 'a' is not an input parameter of CommentedMap([('id', 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/step-valuefrom3-wf.cwl#step1/echo'), ('class', 'CommandLineTool'), ('inputs', [CommentedMap([('type', 'int'), ('inputBinding', CommentedMap()), ('id', 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/step-valuefrom3-wf.cwl#step1/echo/c')])]), ('outputs', [CommentedMap([('type', 'string'), ('outputBinding', CommentedMap([('glob', 'step1_out'), ('loadContents', True), ('outputEval', '$(self[0].contents)')])), ('id', 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/step-valuefrom3-wf.cwl#step1/echo/echo_out')])]), ('baseCommand', 'echo'), ('stdout', 'step1_out')]), expected c v1.0/step-valuefrom3-wf.cwl:38:7: 'b' is not an input parameter of CommentedMap([('id', 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/step-valuefrom3-wf.cwl#step1/echo'), ('class', 'CommandLineTool'), ('inputs', [CommentedMap([('type', 'int'), ('inputBinding', CommentedMap()), ('id', 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/step-valuefrom3-wf.cwl#step1/echo/c')])]), ('outputs', [CommentedMap([('type', 'string'), ('outputBinding', CommentedMap([('glob', 'step1_out'), ('loadContents', True), ('outputEval', '$(self[0].contents)')])), ('id', 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/step-valuefrom3-wf.cwl#step1/echo/echo_out')])]), ('baseCommand', 'echo'), ('stdout', 'step1_out')]), expected c [job step1] job error: Error collecting output for parameter 'echo_out': v1.0/step-valuefrom3-wf.cwl:32:13: Expression evaluation error: v1.0/step-valuefrom3-wf.cwl:32:13: Expecting value: line 1 column 1 (char 0) v1.0/step-valuefrom3-wf.cwl:32:13: script was: v1.0/step-valuefrom3-wf.cwl:32:13: 01 "use strict"; v1.0/step-valuefrom3-wf.cwl:32:13: 02 var inputs = { v1.0/step-valuefrom3-wf.cwl:32:13: 03 "c": 3 v1.0/step-valuefrom3-wf.cwl:32:13: 04 }; v1.0/step-valuefrom3-wf.cwl:32:13: 05 var self = []; v1.0/step-valuefrom3-wf.cwl:32:13: 06 var runtime = { v1.0/step-valuefrom3-wf.cwl:32:13: 07 "cores": 1, v1.0/step-valuefrom3-wf.cwl:32:13: 08 "ram": 1024, v1.0/step-valuefrom3-wf.cwl:32:13: 09 "tmpdirSize": 1024, v1.0/step-valuefrom3-wf.cwl:32:13: 10 "outdirSize": 1024, v1.0/step-valuefrom3-wf.cwl:32:13: 11 "tmpdir": "/tmp/tmpo8k4j15g", v1.0/step-valuefrom3-wf.cwl:32:13: 12 "outdir": "/tmp/tmpntb5znl4" v1.0/step-valuefrom3-wf.cwl:32:13: 13 }; v1.0/step-valuefrom3-wf.cwl:32:13: 14 (function(){return ((self[0].contents));})() v1.0/step-valuefrom3-wf.cwl:32:13: stdout was: '' v1.0/step-valuefrom3-wf.cwl:32:13: stderr was: 'evalmachine.:14 v1.0/step-valuefrom3-wf.cwl:32:13: (function(){return ((self[0].contents));})() v1.0/step-valuefrom3-wf.cwl:32:13: ^ v1.0/step-valuefrom3-wf.cwl:32:13: v1.0/step-valuefrom3-wf.cwl:32:13: TypeError: Cannot read property 'contents' of undefined v1.0/step-valuefrom3-wf.cwl:32:13: at evalmachine.:14:30 v1.0/step-valuefrom3-wf.cwl:32:13: at evalmachine.:14:43 v1.0/step-valuefrom3-wf.cwl:32:13: at ContextifyScript.Script.runInContext (vm.js:59:29) v1.0/step-valuefrom3-wf.cwl:32:13: at ContextifyScript.Script.runInNewContext (vm.js:65:15) v1.0/step-valuefrom3-wf.cwl:32:13: at Object.runInNewContext (vm.js:135:38) v1.0/step-valuefrom3-wf.cwl:32:13: at Socket. ([eval]:11:57) v1.0/step-valuefrom3-wf.cwl:32:13: at emitOne (events.js:116:13) v1.0/step-valuefrom3-wf.cwl:32:13: at Socket.emit (events.js:211:7) v1.0/step-valuefrom3-wf.cwl:32:13: at addChunk (_stream_readable.js:263:12) v1.0/step-valuefrom3-wf.cwl:32:13: at readableAddChunk (_stream_readable.js:246:13)' [step step1] Output is missing expected field file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/step-valuefrom3-wf.cwl#step1/echo_out [step step1] completed permanentFail Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpz0r47q2v v1.0/step-valuefrom3-wf.cwl v1.0/step-valuefrom-job.json Test valueFrom on workflow step referencing other inputs Returned non-zero Test [73/132] Test record type output binding. [job record-output.cwl] job error: Error collecting output for parameter 'orec': v1.0/record-output.cwl:28:11: Did not find output file with glob pattern: '['foo']' Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpgmlfcqh2 v1.0/record-output.cwl v1.0/record-output-job.json Test record type output binding. Returned non-zero Test [74/132] Test support for reading cwl.output.json when running in a Docker container and just 'path' is provided. [job test-cwl-out.cwl] job error: File or stream is not seekable. Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmp_h0w22gk v1.0/test-cwl-out.cwl v1.0/empty.json Test support for reading cwl.output.json when running in a Docker container and just 'path' is provided. Returned non-zero Test [75/132] Test support for reading cwl.output.json when running in a Docker container and just 'location' is provided. [job test-cwl-out2.cwl] job error: File or stream is not seekable. Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpchr5_7un v1.0/test-cwl-out2.cwl v1.0/empty.json Test support for reading cwl.output.json when running in a Docker container and just 'location' is provided. Returned non-zero Test [76/132] Test support for returning multiple glob patterns from expression Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpo7nvgnso v1.0/glob-expr-list.cwl v1.0/abc.json Test support for returning multiple glob patterns from expression Compare failure expected: { "files": [ { "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", "class": "File", "location": "a", "size": 0 }, { "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", "class": "File", "location": "b", "size": 0 }, { "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", "class": "File", "location": "c", "size": 0 } ] } got: { "files": [] } caused by: failed comparison for key 'files': expected: [ { "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", "class": "File", "location": "a", "size": 0 }, { "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", "class": "File", "location": "b", "size": 0 }, { "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", "class": "File", "location": "c", "size": 0 } ] got: [] caused by: lengths don't match Test [77/132] Test workflow scatter with single scatter parameter and two valueFrom on step input (first and current el) [job step1] job error: Error collecting output for parameter 'echo_out': v1.0/scatter-valuefrom-wf1.cwl:53:13: Expression evaluation error: v1.0/scatter-valuefrom-wf1.cwl:53:13: Syntax error in parameter reference 'self[0].contents': self list index 0 out of range. This could be due to using Javascript code without specifying InlineJavascriptRequirement. [job step1_3] job error: Error collecting output for parameter 'echo_out': v1.0/scatter-valuefrom-wf1.cwl:53:13: Expression evaluation error: v1.0/scatter-valuefrom-wf1.cwl:53:13: Syntax error in parameter reference 'self[0].contents': self list index 0 out of range. This could be due to using Javascript code without specifying InlineJavascriptRequirement. [job step1_4] job error: Error collecting output for parameter 'echo_out': v1.0/scatter-valuefrom-wf1.cwl:53:13: Expression evaluation error: v1.0/scatter-valuefrom-wf1.cwl:53:13: Syntax error in parameter reference 'self[0].contents': self list index 0 out of range. This could be due to using Javascript code without specifying InlineJavascriptRequirement. [job step1_2] job error: Error collecting output for parameter 'echo_out': v1.0/scatter-valuefrom-wf1.cwl:53:13: Expression evaluation error: v1.0/scatter-valuefrom-wf1.cwl:53:13: Syntax error in parameter reference 'self[0].contents': self list index 0 out of range. This could be due to using Javascript code without specifying InlineJavascriptRequirement. [step step1] completed permanentFail Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmptf7cafkm v1.0/scatter-valuefrom-wf1.cwl v1.0/scatter-valuefrom-job1.json Test workflow scatter with single scatter parameter and two valueFrom on step input (first and current el) Returned non-zero Test [78/132] Test workflow scatter with two scatter parameters and nested_crossproduct join method and valueFrom on step input [job step1_4] job error: Error collecting output for parameter 'echo_out': v1.0/scatter-valuefrom-wf2.cwl:68:13: Expression evaluation error: v1.0/scatter-valuefrom-wf2.cwl:68:13: Syntax error in parameter reference 'self[0].contents': self list index 0 out of range. This could be due to using Javascript code without specifying InlineJavascriptRequirement. [job step1_3] job error: Error collecting output for parameter 'echo_out': v1.0/scatter-valuefrom-wf2.cwl:68:13: Expression evaluation error: v1.0/scatter-valuefrom-wf2.cwl:68:13: Syntax error in parameter reference 'self[0].contents': self list index 0 out of range. This could be due to using Javascript code without specifying InlineJavascriptRequirement. [job step1_2] job error: Error collecting output for parameter 'echo_out': v1.0/scatter-valuefrom-wf2.cwl:68:13: Expression evaluation error: v1.0/scatter-valuefrom-wf2.cwl:68:13: Syntax error in parameter reference 'self[0].contents': self list index 0 out of range. This could be due to using Javascript code without specifying InlineJavascriptRequirement. [job step1] job error: Error collecting output for parameter 'echo_out': v1.0/scatter-valuefrom-wf2.cwl:68:13: Expression evaluation error: v1.0/scatter-valuefrom-wf2.cwl:68:13: Syntax error in parameter reference 'self[0].contents': self list index 0 out of range. This could be due to using Javascript code without specifying InlineJavascriptRequirement. [step step1] completed permanentFail Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpxhydp6l6 v1.0/scatter-valuefrom-wf2.cwl v1.0/scatter-valuefrom-job2.json Test workflow scatter with two scatter parameters and nested_crossproduct join method and valueFrom on step input Returned non-zero Test [79/132] Test workflow scatter with two scatter parameters and flat_crossproduct join method and valueFrom on step input [job step1_2] job error: Error collecting output for parameter 'echo_out': v1.0/scatter-valuefrom-wf3.cwl:27:9: Expression evaluation error: v1.0/scatter-valuefrom-wf3.cwl:27:9: Syntax error in parameter reference 'self[0].contents': self list index 0 out of range. This could be due to using Javascript code without specifying InlineJavascriptRequirement. [job step1_3] job error: Error collecting output for parameter 'echo_out': v1.0/scatter-valuefrom-wf3.cwl:27:9: Expression evaluation error: v1.0/scatter-valuefrom-wf3.cwl:27:9: Syntax error in parameter reference 'self[0].contents': self list index 0 out of range. This could be due to using Javascript code without specifying InlineJavascriptRequirement. [job step1] job error: Error collecting output for parameter 'echo_out': v1.0/scatter-valuefrom-wf3.cwl:27:9: Expression evaluation error: v1.0/scatter-valuefrom-wf3.cwl:27:9: Syntax error in parameter reference 'self[0].contents': self list index 0 out of range. This could be due to using Javascript code without specifying InlineJavascriptRequirement. [job step1_4] job error: Error collecting output for parameter 'echo_out': v1.0/scatter-valuefrom-wf3.cwl:27:9: Expression evaluation error: v1.0/scatter-valuefrom-wf3.cwl:27:9: Syntax error in parameter reference 'self[0].contents': self list index 0 out of range. This could be due to using Javascript code without specifying InlineJavascriptRequirement. [step step1] completed permanentFail Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpadwwo7zy 'v1.0/scatter-valuefrom-wf3.cwl#main' v1.0/scatter-valuefrom-job2.json Test workflow scatter with two scatter parameters and flat_crossproduct join method and valueFrom on step input Returned non-zero Test [80/132] Test workflow scatter with two scatter parameters and dotproduct join method and valueFrom on step input [job step1] job error: Error collecting output for parameter 'echo_out': v1.0/scatter-valuefrom-wf4.cwl:25:9: Expression evaluation error: v1.0/scatter-valuefrom-wf4.cwl:25:9: Syntax error in parameter reference 'self[0].contents': self list index 0 out of range. This could be due to using Javascript code without specifying InlineJavascriptRequirement. [job step1_2] job error: Error collecting output for parameter 'echo_out': v1.0/scatter-valuefrom-wf4.cwl:25:9: Expression evaluation error: v1.0/scatter-valuefrom-wf4.cwl:25:9: Syntax error in parameter reference 'self[0].contents': self list index 0 out of range. This could be due to using Javascript code without specifying InlineJavascriptRequirement. [step step1] completed permanentFail Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmp1jpv8k9a 'v1.0/scatter-valuefrom-wf4.cwl#main' v1.0/scatter-valuefrom-job2.json Test workflow scatter with two scatter parameters and dotproduct join method and valueFrom on step input Returned non-zero Test [81/132] Test workflow scatter with single scatter parameter and two valueFrom on step input (current el twice) [job step1] job error: Error collecting output for parameter 'echo_out': v1.0/scatter-valuefrom-wf5.cwl:53:13: Expression evaluation error: v1.0/scatter-valuefrom-wf5.cwl:53:13: Syntax error in parameter reference 'self[0].contents': self list index 0 out of range. This could be due to using Javascript code without specifying InlineJavascriptRequirement. [job step1_2] job error: Error collecting output for parameter 'echo_out': v1.0/scatter-valuefrom-wf5.cwl:53:13: Expression evaluation error: v1.0/scatter-valuefrom-wf5.cwl:53:13: Syntax error in parameter reference 'self[0].contents': self list index 0 out of range. This could be due to using Javascript code without specifying InlineJavascriptRequirement. [job step1_4] job error: Error collecting output for parameter 'echo_out': v1.0/scatter-valuefrom-wf5.cwl:53:13: Expression evaluation error: v1.0/scatter-valuefrom-wf5.cwl:53:13: Syntax error in parameter reference 'self[0].contents': self list index 0 out of range. This could be due to using Javascript code without specifying InlineJavascriptRequirement. [job step1_3] job error: Error collecting output for parameter 'echo_out': v1.0/scatter-valuefrom-wf5.cwl:53:13: Expression evaluation error: v1.0/scatter-valuefrom-wf5.cwl:53:13: Syntax error in parameter reference 'self[0].contents': self list index 0 out of range. This could be due to using Javascript code without specifying InlineJavascriptRequirement. [step step1] completed permanentFail Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpctracbse v1.0/scatter-valuefrom-wf5.cwl v1.0/scatter-valuefrom-job1.json Test workflow scatter with single scatter parameter and two valueFrom on step input (current el twice) Returned non-zero Test [82/132] Test valueFrom eval on scattered input parameter [job step1_2] job error: Error collecting output for parameter 'out_message': test:1:1: Did not find output file with glob pattern: '['76673db4efd058ac0a85911ee245d3d6cf7a6be8']' [job step1] task id: task-65ff61e5 [job step1] logs: [TaskLog(start_time=datetime.datetime(2018, 8, 25, 15, 43, 55, tzinfo=tzutc()), end_time=None, metadata={'USER_ID': 'anonymousUser'}, logs=None, outputs=None, system_logs=['08/25/2018 03:47:21 DEBUG: Starting taskmaster\n08/25/2018 03:47:21 DEBUG: Got label: "ac603a41-a87d-11e8-916e-fa163e364743"\n\n08/25/2018 03:47:21 DEBUG: Got label: "task-65ff61e5"\nTraceback (most recent call last):\n File "/usr/bin/taskmaster.py", line 214, in \n main(sys.argv)\n File "/usr/bin/taskmaster.py", line 185, in main\n run_task(data, args.filer_version)\n File "/usr/bin/taskmaster.py", line 117, in run_task\n pvc = init_pvc(data, filer)\n File "/usr/bin/taskmaster.py", line 83, in init_pvc\n pvc = PVC(pvc_name, pvc_size, args.namespace)\n File "/usr/bin/pvc.py", line 19, in __init__\n self.cv1.create_namespaced_persistent_volume_claim(self.namespace, self.spec)\n File "/usr/lib/python2.7/site-packages/kubernetes/client/apis/core_v1_api.py", line 5950, in create_namespaced_persistent_volume_claim\n (data) = self.create_namespaced_persistent_volume_claim_with_http_info(namespace, body, **kwargs)\n File "/usr/lib/python2.7/site-packages/kubernetes/client/apis/core_v1_api.py", line 6035, in create_namespaced_persistent_volume_claim_with_http_info\n collection_formats=collection_formats)\n File "/usr/lib/python2.7/site-packages/kubernetes/client/api_client.py", line 321, in call_api\n _return_http_data_only, collection_formats, _preload_content, _request_timeout)\n File "/usr/lib/python2.7/site-packages/kubernetes/client/api_client.py", line 155, in __call_api\n _request_timeout=_request_timeout)\n File "/usr/lib/python2.7/site-packages/kubernetes/client/api_client.py", line 364, in request\n body=body)\n File "/usr/lib/python2.7/site-packages/kubernetes/client/rest.py", line 266, in POST\n body=body)\n File "/usr/lib/python2.7/site-packages/kubernetes/client/rest.py", line 222, in request\n raise ApiException(http_resp=r)\nkubernetes.client.rest.ApiException: (409)\nReason: Conflict\nHTTP response headers: HTTPHeaderDict({\'Date\': \'Sat, 25 Aug 2018 15:47:21 GMT\', \'Content-Length\': \'248\', \'Content-Type\': \'application/json\'})\nHTTP response body: {"kind":"Status","apiVersion":"v1","metadata":{},"status":"Failure","message":"persistentvolumeclaims \\"task-65ff61e5-pvc\\" already exists","reason":"AlreadyExists","details":{"name":"task-65ff61e5-pvc","kind":"persistentvolumeclaims"},"code":409}\n\n\n'])] [job step1] job error: Error collecting output for parameter 'out_message': test:1:1: Did not find output file with glob pattern: '['76673db4efd058ac0a85911ee245d3d6cf7a6be8']' [step step1] completed permanentFail Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpo_05otce v1.0/scatter-valuefrom-wf6.cwl v1.0/scatter-valuefrom-job3.json Test valueFrom eval on scattered input parameter Returned non-zero Test [83/132] Test workflow two input files with same name. [job echo_1] job error: Error collecting output for parameter 'fileout': v1.0/conflict-wf.cwl:14:9: Did not find output file with glob pattern: '['out.txt']' [step echo_1] Output is missing expected field file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/conflict-wf.cwl#collision/echo_1/fileout [step echo_1] completed permanentFail [job echo_2] job error: Error collecting output for parameter 'fileout': v1.0/conflict-wf.cwl:14:9: Did not find output file with glob pattern: '['out.txt']' [step echo_2] Output is missing expected field file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/conflict-wf.cwl#collision/echo_2/fileout [step echo_2] completed permanentFail Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpi1zkivrc 'v1.0/conflict-wf.cwl#collision' v1.0/conflict-job.json Test workflow two input files with same name. Returned non-zero Test [84/132] Test directory input with parameter reference a file:// based Directory slipped through: CommentedMap([('class', 'Directory'), ('location', 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir'), ('basename', 'testdir'), ('listing', [{'class': 'File', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/b', 'basename': 'b'}, {'class': 'Directory', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/c', 'basename': 'c', 'listing': [{'class': 'File', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/c/d', 'basename': 'd'}]}, {'class': 'File', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/a', 'basename': 'a'}])]) unprocessed File {'class': 'File', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/b', 'basename': 'b'} a file:// based Directory slipped through: {'class': 'Directory', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/c', 'basename': 'c', 'listing': [{'class': 'File', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/c/d', 'basename': 'd'}]} unprocessed File {'class': 'File', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/c/d', 'basename': 'd'} unprocessed File {'class': 'File', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/a', 'basename': 'a'} [job dir.cwl] task id: task-848f1856 [job dir.cwl] logs: [TaskLog(start_time=datetime.datetime(2018, 8, 25, 15, 52, 49, tzinfo=tzutc()), end_time=datetime.datetime(2018, 8, 25, 15, 58, 29, tzinfo=tzutc()), metadata={'USER_ID': 'anonymousUser'}, logs=None, outputs=None, system_logs=['08/25/2018 03:52:52 DEBUG: Starting taskmaster\n08/25/2018 03:52:52 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:52:52 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:52:52 DEBUG: appending task-volume at path /tmp/tmptqdarju7/stg3ca77c07-39d5-4aee-af26-a89e724d7837/testdir with subPath: dir0\n08/25/2018 03:52:52 DEBUG: dirname of /var/spool/cwl/output.txtis: /var/spool/cwl\n08/25/2018 03:52:52 DEBUG: appending task-volume at path /var/spool/cwl with subPath: dir1\n08/25/2018 03:52:52 DEBUG: [{\'mountPath\': u\'/tmp/tmptqdarju7/stg3ca77c07-39d5-4aee-af26-a89e724d7837/testdir\', \'subPath\': \'dir0\', \'name\': \'task-volume\'}, {\'mountPath\': u\'/var/spool/cwl\', \'subPath\': \'dir1\', \'name\': \'task-volume\'}]\n08/25/2018 03:52:52 DEBUG: \n08/25/2018 03:52:52 DEBUG: {\'kind\': \'Job\', \'spec\': {\'template\': {\'spec\': {\'restartPolicy\': \'Never\', \'volumes\': [{\'name\': \'task-volume\', \'persistentVolumeClaim\': {\'claimName\': u\'task-848f1856-pvc\'}}], \'containers\': [{\'name\': \'filer\', \'image\': \'eu.gcr.io/tes-wes/filer:v0.4\', \'args\': [\'inputs\', \'$(JSON_INPUT)\', \'-d\'], \'volumeMounts\': [{\'mountPath\': u\'/tmp/tmptqdarju7/stg3ca77c07-39d5-4aee-af26-a89e724d7837/testdir\', \'subPath\': \'dir0\', \'name\': \'task-volume\'}, {\'mountPath\': u\'/var/spool/cwl\', \'subPath\': \'dir1\', \'name\': \'task-volume\'}], \'env\': [{\'name\': \'JSON_INPUT\', \'value\': \'{"outputs": [{"url": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/fadd992f-26ca-49e9-bb06-800849358add/output.txt", "path": "/var/spool/cwl/output.txt", "type": "FILE", "name": "stdout"}, {"url": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/fadd992f-26ca-49e9-bb06-800849358add/", "path": "/var/spool/cwl", "type": "DIRECTORY", "name": "workdir"}], "executors": [{"kind": "Job", "spec": {"template": {"spec": {"restartPolicy": "Never", "containers": [{"name": "task-848f1856-ex-00", "image": "python:2.7", "workingDir": "/var/spool/cwl", "command": ["/bin/sh", "-c", "/bin/sh -c \\\'\\\'\\\\"\\\'\\\\"\\\'cd\\\'\\\\"\\\'\\\\"\\\' \\\'\\\\"\\\'\\\\"\\\'/tmp/tmptqdarju7/stg3ca77c07-39d5-4aee-af26-a89e724d7837/testdir\\\'\\\\"\\\'\\\\"\\\' && \\\'\\\\"\\\'\\\\"\\\'find\\\'\\\\"\\\'\\\\"\\\' \\\'\\\\"\\\'\\\\"\\\'.\\\'\\\\"\\\'\\\\"\\\' | \\\'\\\\"\\\'\\\\"\\\'sort\\\'\\\\"\\\'\\\\"\\\'\\\' > /var/spool/cwl/output.txt"], "env": [{"name": "HOME", "value": "/tmp/tmpcs2_j4hr"}, {"name": "TMPDIR", "value": "/tmp/tmpc9z6c6z5"}], "resources": {}}]}, "metadata": {"name": "task-848f1856-ex-00"}}}, "apiVersion": "batch/v1", "metadata": {"labels": {"taskmaster-name": "task-848f1856", "executor-no": "0", "job-type": "executor", "creator-user-id": "anonymousUser"}, "annotations": {"tes-task-name": "dir.cwl"}, "name": "task-848f1856-ex-00"}}], "resources": {"disk_gb": 0.1}, "volumes": [], "inputs": [{"url": "file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir", "path": "/tmp/tmptqdarju7/stg3ca77c07-39d5-4aee-af26-a89e724d7837/testdir", "type": "DIRECTORY", "name": "indir", "description": "cwl_input:indir"}]}\'}, {\'name\': \'TESK_FTP_USERNAME\', \'value\': \'redacted_username\'}, {\'name\': \'TESK_FTP_PASSWORD\', \'value\': \'redacted_password\'}], \'imagePullPolicy\': \'Always\'}]}, \'metadata\': {\'name\': u\'task-848f1856-filer\'}}}, \'apiVersion\': \'batch/v1\', \'metadata\': {\'name\': u\'task-848f1856-inputs-filer\'}}\n08/25/2018 03:52:52 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:52:52 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:52:57 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:52:57 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:53:02 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:53:02 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:53:07 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:53:07 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:53:12 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:53:12 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:53:17 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:53:17 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:53:22 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:53:22 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:53:27 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:53:27 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:53:32 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:53:32 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:53:37 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:53:37 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:53:43 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:53:43 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:53:48 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:53:48 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:53:53 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:53:53 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:53:58 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:53:58 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:54:03 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:54:03 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:54:08 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:54:08 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:54:13 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:54:13 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:54:18 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:54:18 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:54:23 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:54:23 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:54:28 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:54:28 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:54:33 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:54:33 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:54:38 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:54:38 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:54:43 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:54:43 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:54:48 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:54:48 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:54:53 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:54:53 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:54:58 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:54:58 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:55:03 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:55:03 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:55:08 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:55:08 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:55:13 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:55:13 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:55:18 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:55:18 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:55:23 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:55:23 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:55:28 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:55:28 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:55:33 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:55:33 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:55:38 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:55:38 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:55:43 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:55:43 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:55:48 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:55:48 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:55:53 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:55:53 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:55:58 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:55:58 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:56:03 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:56:03 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:56:08 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:56:08 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:56:13 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:56:13 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:56:18 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:56:18 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:56:23 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:56:23 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:56:28 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:56:28 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:56:33 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:56:33 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:56:38 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:56:38 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:56:43 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:56:43 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:56:48 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:56:48 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:56:53 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:56:53 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:56:58 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:56:58 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:57:03 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:57:03 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:57:08 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:57:08 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:57:13 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:57:13 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:57:18 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:57:18 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:57:23 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:57:23 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:57:28 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:57:28 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:57:33 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:57:33 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:57:38 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:57:38 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:57:43 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:57:43 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:57:48 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:57:48 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:57:53 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:57:53 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:57:58 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:57:58 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:58:03 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:58:03 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:58:08 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:58:08 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:58:13 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:58:13 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:58:18 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:58:18 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:58:23 DEBUG: Got label: "eb0a86e8-a87e-11e8-916e-fa163e364743"\n\n08/25/2018 03:58:23 DEBUG: Got label: "task-848f1856"\n08/25/2018 03:58:28 ERROR: Cancelling taskmaster: Got status Failed\n'])] [job dir.cwl] job error: Error collecting output for parameter 'outlist': v1.0/dir.cwl:11:7: Did not find output file with glob pattern: '['output.txt']' Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpf42lngjh v1.0/dir.cwl v1.0/dir-job.yml Test directory input with parameter reference Returned non-zero Test [85/132] Test directory input in Docker a file:// based Directory slipped through: CommentedMap([('class', 'Directory'), ('location', 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir'), ('basename', 'testdir'), ('listing', [{'class': 'File', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/b', 'basename': 'b'}, {'class': 'Directory', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/c', 'basename': 'c', 'listing': [{'class': 'File', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/c/d', 'basename': 'd'}]}, {'class': 'File', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/a', 'basename': 'a'}])]) unprocessed File {'class': 'File', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/b', 'basename': 'b'} a file:// based Directory slipped through: {'class': 'Directory', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/c', 'basename': 'c', 'listing': [{'class': 'File', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/c/d', 'basename': 'd'}]} unprocessed File {'class': 'File', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/c/d', 'basename': 'd'} unprocessed File {'class': 'File', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/a', 'basename': 'a'} [job dir2.cwl] task id: task-d32d193c [job dir2.cwl] logs: [TaskLog(start_time=datetime.datetime(2018, 8, 25, 15, 58, 34, tzinfo=tzutc()), end_time=datetime.datetime(2018, 8, 25, 16, 5, 44, tzinfo=tzutc()), metadata={'USER_ID': 'anonymousUser'}, logs=None, outputs=None, system_logs=['08/25/2018 03:58:37 DEBUG: Starting taskmaster\n08/25/2018 03:58:37 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 03:58:37 DEBUG: Got label: "task-d32d193c"\n08/25/2018 03:58:37 DEBUG: appending task-volume at path /var/lib/cwl/stgc60dac4b-bf2c-4309-9080-6a26ef4e2987/testdir with subPath: dir0\n08/25/2018 03:58:37 DEBUG: dirname of /var/spool/cwl/output.txtis: /var/spool/cwl\n08/25/2018 03:58:37 DEBUG: appending task-volume at path /var/spool/cwl with subPath: dir1\n08/25/2018 03:58:37 DEBUG: [{\'mountPath\': u\'/var/lib/cwl/stgc60dac4b-bf2c-4309-9080-6a26ef4e2987/testdir\', \'subPath\': \'dir0\', \'name\': \'task-volume\'}, {\'mountPath\': u\'/var/spool/cwl\', \'subPath\': \'dir1\', \'name\': \'task-volume\'}]\n08/25/2018 03:58:37 DEBUG: \n08/25/2018 03:58:37 DEBUG: {\'kind\': \'Job\', \'spec\': {\'template\': {\'spec\': {\'restartPolicy\': \'Never\', \'volumes\': [{\'name\': \'task-volume\', \'persistentVolumeClaim\': {\'claimName\': u\'task-d32d193c-pvc\'}}], \'containers\': [{\'name\': \'filer\', \'image\': \'eu.gcr.io/tes-wes/filer:v0.4\', \'args\': [\'inputs\', \'$(JSON_INPUT)\', \'-d\'], \'volumeMounts\': [{\'mountPath\': u\'/var/lib/cwl/stgc60dac4b-bf2c-4309-9080-6a26ef4e2987/testdir\', \'subPath\': \'dir0\', \'name\': \'task-volume\'}, {\'mountPath\': u\'/var/spool/cwl\', \'subPath\': \'dir1\', \'name\': \'task-volume\'}], \'env\': [{\'name\': \'JSON_INPUT\', \'value\': \'{"outputs": [{"url": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/56d2b3bf-a6e0-4058-ab6b-1e5e181c29b0/output.txt", "path": "/var/spool/cwl/output.txt", "type": "FILE", "name": "stdout"}, {"url": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/56d2b3bf-a6e0-4058-ab6b-1e5e181c29b0/", "path": "/var/spool/cwl", "type": "DIRECTORY", "name": "workdir"}], "executors": [{"kind": "Job", "spec": {"template": {"spec": {"restartPolicy": "Never", "containers": [{"name": "task-d32d193c-ex-00", "image": "debian:stretch-slim", "workingDir": "/var/spool/cwl", "command": ["/bin/sh", "-c", "/bin/sh -c \\\'\\\'\\\\"\\\'\\\\"\\\'cd\\\'\\\\"\\\'\\\\"\\\' \\\'\\\\"\\\'\\\\"\\\'/var/lib/cwl/stgc60dac4b-bf2c-4309-9080-6a26ef4e2987/testdir\\\'\\\\"\\\'\\\\"\\\' && \\\'\\\\"\\\'\\\\"\\\'find\\\'\\\\"\\\'\\\\"\\\' \\\'\\\\"\\\'\\\\"\\\'.\\\'\\\\"\\\'\\\\"\\\' | \\\'\\\\"\\\'\\\\"\\\'sort\\\'\\\\"\\\'\\\\"\\\'\\\' > /var/spool/cwl/output.txt"], "env": [{"name": "HOME", "value": "/tmp/tmpqjczebsd"}, {"name": "TMPDIR", "value": "/tmp/tmpvll8zpmv"}], "resources": {}}]}, "metadata": {"name": "task-d32d193c-ex-00"}}}, "apiVersion": "batch/v1", "metadata": {"labels": {"taskmaster-name": "task-d32d193c", "executor-no": "0", "job-type": "executor", "creator-user-id": "anonymousUser"}, "annotations": {"tes-task-name": "dir2.cwl"}, "name": "task-d32d193c-ex-00"}}], "resources": {"disk_gb": 0.1}, "volumes": [], "inputs": [{"url": "file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir", "path": "/var/lib/cwl/stgc60dac4b-bf2c-4309-9080-6a26ef4e2987/testdir", "type": "DIRECTORY", "name": "indir", "description": "cwl_input:indir"}]}\'}, {\'name\': \'TESK_FTP_USERNAME\', \'value\': \'redacted_username\'}, {\'name\': \'TESK_FTP_PASSWORD\', \'value\': \'redacted_password\'}], \'imagePullPolicy\': \'Always\'}]}, \'metadata\': {\'name\': u\'task-d32d193c-filer\'}}}, \'apiVersion\': \'batch/v1\', \'metadata\': {\'name\': u\'task-d32d193c-inputs-filer\'}}\n08/25/2018 03:58:37 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 03:58:37 DEBUG: Got label: "task-d32d193c"\n08/25/2018 03:58:42 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 03:58:42 DEBUG: Got label: "task-d32d193c"\n08/25/2018 03:58:47 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 03:58:47 DEBUG: Got label: "task-d32d193c"\n08/25/2018 03:58:52 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 03:58:52 DEBUG: Got label: "task-d32d193c"\n08/25/2018 03:58:57 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 03:58:57 DEBUG: Got label: "task-d32d193c"\n08/25/2018 03:59:02 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 03:59:02 DEBUG: Got label: "task-d32d193c"\n08/25/2018 03:59:07 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 03:59:07 DEBUG: Got label: "task-d32d193c"\n08/25/2018 03:59:12 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 03:59:12 DEBUG: Got label: "task-d32d193c"\n08/25/2018 03:59:17 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 03:59:17 DEBUG: Got label: "task-d32d193c"\n08/25/2018 03:59:22 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 03:59:22 DEBUG: Got label: "task-d32d193c"\n08/25/2018 03:59:27 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 03:59:27 DEBUG: Got label: "task-d32d193c"\n08/25/2018 03:59:32 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 03:59:32 DEBUG: Got label: "task-d32d193c"\n08/25/2018 03:59:37 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 03:59:37 DEBUG: Got label: "task-d32d193c"\n08/25/2018 03:59:42 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 03:59:42 DEBUG: Got label: "task-d32d193c"\n08/25/2018 03:59:47 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 03:59:47 DEBUG: Got label: "task-d32d193c"\n08/25/2018 03:59:52 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 03:59:52 DEBUG: Got label: "task-d32d193c"\n08/25/2018 03:59:57 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 03:59:57 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:00:02 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:00:02 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:00:07 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:00:07 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:00:12 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:00:12 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:00:17 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:00:17 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:00:22 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:00:22 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:00:27 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:00:27 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:00:32 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:00:32 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:00:37 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:00:37 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:00:42 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:00:42 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:00:47 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:00:47 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:00:52 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:00:52 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:00:57 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:00:57 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:01:02 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:01:02 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:01:07 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:01:07 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:01:12 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:01:12 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:01:17 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:01:17 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:01:22 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:01:22 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:01:27 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:01:27 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:01:32 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:01:32 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:01:37 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:01:37 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:01:42 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:01:42 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:01:48 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:01:48 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:01:53 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:01:53 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:01:58 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:01:58 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:02:03 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:02:03 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:02:08 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:02:08 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:02:13 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:02:13 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:02:18 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:02:18 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:02:23 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:02:23 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:02:28 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:02:28 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:02:33 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:02:33 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:02:38 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:02:38 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:02:43 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:02:43 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:02:48 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:02:48 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:02:53 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:02:53 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:02:58 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:02:58 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:03:03 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:03:03 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:03:08 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:03:08 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:03:13 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:03:13 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:03:18 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:03:18 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:03:23 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:03:23 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:03:28 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:03:28 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:03:33 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:03:33 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:03:38 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:03:38 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:03:43 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:03:43 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:03:48 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:03:48 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:03:53 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:03:53 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:03:58 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:03:58 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:04:03 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:04:03 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:04:08 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:04:08 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:04:13 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:04:13 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:04:18 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:04:18 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:04:23 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:04:23 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:04:28 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:04:28 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:04:33 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:04:33 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:04:38 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:04:38 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:04:43 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:04:43 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:04:48 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:04:48 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:04:53 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:04:53 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:04:58 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:04:58 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:05:03 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:05:03 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:05:08 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:05:08 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:05:13 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:05:13 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:05:18 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:05:18 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:05:23 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:05:23 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:05:28 DEBUG: Got label: "b89c4fa6-a87f-11e8-916e-fa163e364743"\n\n08/25/2018 04:05:28 DEBUG: Got label: "task-d32d193c"\n08/25/2018 04:05:33 ERROR: Cancelling taskmaster: Got status Failed\n'])] [job dir2.cwl] job error: Error collecting output for parameter 'outlist': v1.0/dir2.cwl:13:7: Did not find output file with glob pattern: '['output.txt']' Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmp8c8acv7l v1.0/dir2.cwl v1.0/dir-job.yml Test directory input in Docker Returned non-zero Test [86/132] Test directory output [job dir3.cwl] job error: Error collecting output for parameter 'outdir': v1.0/dir3.cwl:13:7: Did not find output file with glob pattern: '['.']' Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpf3gl2nue v1.0/dir3.cwl v1.0/dir3-job.yml Test directory output Returned non-zero Test [87/132] Test directories in secondaryFiles a file:// based Directory slipped through: CommentedMap([('class', 'Directory'), ('basename', 'xtestdir'), ('location', 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir')]) [job dir4.cwl] task id: task-1c127f88 [job dir4.cwl] logs: [TaskLog(start_time=datetime.datetime(2018, 8, 25, 16, 7, 1, tzinfo=tzutc()), end_time=datetime.datetime(2018, 8, 25, 16, 13, 16, tzinfo=tzutc()), metadata={'USER_ID': 'anonymousUser'}, logs=None, outputs=None, system_logs=['08/25/2018 04:07:04 DEBUG: Starting taskmaster\n08/25/2018 04:07:04 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:07:04 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:07:04 DEBUG: dirname of /tmp/tmpbs3f45mz/stg0737d130-ae84-4aec-aad3-98d5dff5741f/hello.taris: /tmp/tmpbs3f45mz/stg0737d130-ae84-4aec-aad3-98d5dff5741f\n08/25/2018 04:07:04 DEBUG: appending task-volume at path /tmp/tmpbs3f45mz/stg0737d130-ae84-4aec-aad3-98d5dff5741f with subPath: dir0\n08/25/2018 04:07:04 DEBUG: dirname of /tmp/tmpbs3f45mz/stg0737d130-ae84-4aec-aad3-98d5dff5741f/index.pyis: /tmp/tmpbs3f45mz/stg0737d130-ae84-4aec-aad3-98d5dff5741f\n08/25/2018 04:07:04 DEBUG: appending task-volume at path /tmp/tmpbs3f45mz/stg0737d130-ae84-4aec-aad3-98d5dff5741f/xtestdir with subPath: dir1\n08/25/2018 04:07:04 DEBUG: dirname of /var/spool/cwl/output.txtis: /var/spool/cwl\n08/25/2018 04:07:04 DEBUG: appending task-volume at path /var/spool/cwl with subPath: dir2\n08/25/2018 04:07:04 DEBUG: [{\'mountPath\': u\'/tmp/tmpbs3f45mz/stg0737d130-ae84-4aec-aad3-98d5dff5741f\', \'subPath\': \'dir0\', \'name\': \'task-volume\'}, {\'mountPath\': u\'/tmp/tmpbs3f45mz/stg0737d130-ae84-4aec-aad3-98d5dff5741f/xtestdir\', \'subPath\': \'dir1\', \'name\': \'task-volume\'}, {\'mountPath\': u\'/var/spool/cwl\', \'subPath\': \'dir2\', \'name\': \'task-volume\'}]\n08/25/2018 04:07:04 DEBUG: \n08/25/2018 04:07:04 DEBUG: {\'kind\': \'Job\', \'spec\': {\'template\': {\'spec\': {\'restartPolicy\': \'Never\', \'volumes\': [{\'name\': \'task-volume\', \'persistentVolumeClaim\': {\'claimName\': u\'task-1c127f88-pvc\'}}], \'containers\': [{\'name\': \'filer\', \'image\': \'eu.gcr.io/tes-wes/filer:v0.4\', \'args\': [\'inputs\', \'$(JSON_INPUT)\', \'-d\'], \'volumeMounts\': [{\'mountPath\': u\'/tmp/tmpbs3f45mz/stg0737d130-ae84-4aec-aad3-98d5dff5741f\', \'subPath\': \'dir0\', \'name\': \'task-volume\'}, {\'mountPath\': u\'/tmp/tmpbs3f45mz/stg0737d130-ae84-4aec-aad3-98d5dff5741f/xtestdir\', \'subPath\': \'dir1\', \'name\': \'task-volume\'}, {\'mountPath\': u\'/var/spool/cwl\', \'subPath\': \'dir2\', \'name\': \'task-volume\'}], \'env\': [{\'name\': \'JSON_INPUT\', \'value\': \'{"outputs": [{"url": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/80ca76e9-d39d-40f8-bdaf-85a3b4caa2d8/output.txt", "path": "/var/spool/cwl/output.txt", "type": "FILE", "name": "stdout"}, {"url": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/80ca76e9-d39d-40f8-bdaf-85a3b4caa2d8/", "path": "/var/spool/cwl", "type": "DIRECTORY", "name": "workdir"}], "executors": [{"kind": "Job", "spec": {"template": {"spec": {"restartPolicy": "Never", "containers": [{"name": "task-1c127f88-ex-00", "image": "python:2.7", "workingDir": "/var/spool/cwl", "command": ["/bin/sh", "-c", "/bin/sh -c \\\'\\\'\\\\"\\\'\\\\"\\\'cd\\\'\\\\"\\\'\\\\"\\\' \\\'\\\\"\\\'\\\\"\\\'/tmp/tmpbs3f45mz/stg0737d130-ae84-4aec-aad3-98d5dff5741f/xtestdir\\\'\\\\"\\\'\\\\"\\\' && \\\'\\\\"\\\'\\\\"\\\'find\\\'\\\\"\\\'\\\\"\\\' \\\'\\\\"\\\'\\\\"\\\'.\\\'\\\\"\\\'\\\\"\\\' | \\\'\\\\"\\\'\\\\"\\\'sort\\\'\\\\"\\\'\\\\"\\\'\\\' > /var/spool/cwl/output.txt"], "env": [{"name": "HOME", "value": "/tmp/tmpa05aln29"}, {"name": "TMPDIR", "value": "/tmp/tmp_va5vzva"}], "resources": {}}]}, "metadata": {"name": "task-1c127f88-ex-00"}}}, "apiVersion": "batch/v1", "metadata": {"labels": {"taskmaster-name": "task-1c127f88", "executor-no": "0", "job-type": "executor", "creator-user-id": "anonymousUser"}, "annotations": {"tes-task-name": "dir4.cwl"}, "name": "task-1c127f88-ex-00"}}], "resources": {"disk_gb": 0.1}, "volumes": [], "inputs": [{"url": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/80ca76e9-d39d-40f8-bdaf-85a3b4caa2d8/inputs/hello.tar", "path": "/tmp/tmpbs3f45mz/stg0737d130-ae84-4aec-aad3-98d5dff5741f/hello.tar", "type": "FILE", "name": "inf", "description": "cwl_input:inf"}, {"url": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/80ca76e9-d39d-40f8-bdaf-85a3b4caa2d8/inputs/index.py", "path": "/tmp/tmpbs3f45mz/stg0737d130-ae84-4aec-aad3-98d5dff5741f/index.py", "type": "FILE", "name": "index.py", "description": "cwl_input:index.py"}, {"url": "file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir", "path": "/tmp/tmpbs3f45mz/stg0737d130-ae84-4aec-aad3-98d5dff5741f/xtestdir", "type": "DIRECTORY", "name": "xtestdir", "description": "cwl_input:xtestdir"}]}\'}, {\'name\': \'TESK_FTP_USERNAME\', \'value\': \'redacted_username\'}, {\'name\': \'TESK_FTP_PASSWORD\', \'value\': \'redacted_password\'}], \'imagePullPolicy\': \'Always\'}]}, \'metadata\': {\'name\': u\'task-1c127f88-filer\'}}}, \'apiVersion\': \'batch/v1\', \'metadata\': {\'name\': u\'task-1c127f88-inputs-filer\'}}\n08/25/2018 04:07:04 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:07:04 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:07:09 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:07:09 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:07:14 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:07:14 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:07:19 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:07:19 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:07:24 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:07:24 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:07:29 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:07:29 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:07:34 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:07:34 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:07:39 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:07:39 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:07:44 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:07:44 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:07:49 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:07:49 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:07:54 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:07:54 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:07:59 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:07:59 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:08:04 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:08:04 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:08:09 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:08:09 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:08:14 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:08:14 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:08:19 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:08:19 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:08:24 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:08:24 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:08:29 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:08:29 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:08:34 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:08:34 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:08:39 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:08:39 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:08:44 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:08:44 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:08:49 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:08:49 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:08:54 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:08:54 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:08:59 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:08:59 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:09:04 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:09:04 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:09:09 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:09:09 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:09:14 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:09:14 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:09:19 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:09:19 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:09:24 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:09:24 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:09:29 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:09:29 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:09:34 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:09:34 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:09:39 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:09:39 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:09:44 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:09:44 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:09:49 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:09:49 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:09:54 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:09:54 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:09:59 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:09:59 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:10:04 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:10:04 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:10:09 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:10:09 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:10:14 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:10:14 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:10:19 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:10:19 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:10:24 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:10:24 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:10:29 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:10:29 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:10:34 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:10:34 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:10:39 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:10:39 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:10:44 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:10:44 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:10:49 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:10:49 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:10:54 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:10:54 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:10:59 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:10:59 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:11:04 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:11:04 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:11:09 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:11:09 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:11:14 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:11:14 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:11:19 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:11:19 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:11:24 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:11:24 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:11:29 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:11:29 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:11:34 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:11:34 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:11:39 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:11:39 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:11:44 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:11:44 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:11:49 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:11:49 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:11:54 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:11:54 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:11:59 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:11:59 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:12:04 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:12:04 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:12:09 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:12:09 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:12:14 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:12:14 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:12:19 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:12:19 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:12:24 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:12:24 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:12:29 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:12:29 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:12:34 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:12:34 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:12:40 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:12:40 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:12:45 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:12:45 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:12:50 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:12:50 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:12:55 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:12:55 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:13:00 DEBUG: Got label: "e6a1fbaf-a880-11e8-916e-fa163e364743"\n\n08/25/2018 04:13:00 DEBUG: Got label: "task-1c127f88"\n08/25/2018 04:13:05 ERROR: Cancelling taskmaster: Got status Failed\n'])] [job dir4.cwl] job error: Error collecting output for parameter 'outlist': v1.0/dir4.cwl:11:7: Did not find output file with glob pattern: '['output.txt']' Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpccc6efrv v1.0/dir4.cwl v1.0/dir4-job.yml Test directories in secondaryFiles Returned non-zero Test [88/132] Test dynamic initial work dir a file:// based Directory slipped through: CommentedMap([('class', 'Directory'), ('location', 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir'), ('basename', 'testdir'), ('listing', [{'class': 'File', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/b', 'basename': 'b'}, {'class': 'Directory', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/c', 'basename': 'c', 'listing': [{'class': 'File', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/c/d', 'basename': 'd'}]}, {'class': 'File', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/a', 'basename': 'a'}])]) unprocessed File {'class': 'File', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/b', 'basename': 'b'} a file:// based Directory slipped through: {'class': 'Directory', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/c', 'basename': 'c', 'listing': [{'class': 'File', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/c/d', 'basename': 'd'}]} unprocessed File {'class': 'File', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/c/d', 'basename': 'd'} unprocessed File {'class': 'File', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/a', 'basename': 'a'} [job dir5.cwl] task id: task-1bb19357 [job dir5.cwl] logs: [TaskLog(start_time=datetime.datetime(2018, 8, 25, 16, 13, 22, tzinfo=tzutc()), end_time=datetime.datetime(2018, 8, 25, 16, 19, 21, tzinfo=tzutc()), metadata={'USER_ID': 'anonymousUser'}, logs=None, outputs=None, system_logs=['08/25/2018 04:13:25 DEBUG: Starting taskmaster\n08/25/2018 04:13:25 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:13:25 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:13:25 DEBUG: appending task-volume at path /tmp/tmppu9mngc_/stge01c9c1c-8118-4adb-8d36-ff240008c207/testdir with subPath: dir0\n08/25/2018 04:13:25 DEBUG: dirname of /var/spool/cwl/bis: /var/spool/cwl\n08/25/2018 04:13:25 DEBUG: appending task-volume at path /var/spool/cwl with subPath: dir1\n08/25/2018 04:13:25 DEBUG: appending task-volume at path /var/spool/cwl/c with subPath: dir2\n08/25/2018 04:13:25 DEBUG: dirname of /var/spool/cwl/ais: /var/spool/cwl\n08/25/2018 04:13:25 DEBUG: dirname of /var/spool/cwl/output.txtis: /var/spool/cwl\n08/25/2018 04:13:25 DEBUG: [{\'mountPath\': u\'/tmp/tmppu9mngc_/stge01c9c1c-8118-4adb-8d36-ff240008c207/testdir\', \'subPath\': \'dir0\', \'name\': \'task-volume\'}, {\'mountPath\': u\'/var/spool/cwl\', \'subPath\': \'dir1\', \'name\': \'task-volume\'}, {\'mountPath\': u\'/var/spool/cwl/c\', \'subPath\': \'dir2\', \'name\': \'task-volume\'}]\n08/25/2018 04:13:25 DEBUG: \n08/25/2018 04:13:25 DEBUG: {\'kind\': \'Job\', \'spec\': {\'template\': {\'spec\': {\'restartPolicy\': \'Never\', \'volumes\': [{\'name\': \'task-volume\', \'persistentVolumeClaim\': {\'claimName\': u\'task-1bb19357-pvc\'}}], \'containers\': [{\'name\': \'filer\', \'image\': \'eu.gcr.io/tes-wes/filer:v0.4\', \'args\': [\'inputs\', \'$(JSON_INPUT)\', \'-d\'], \'volumeMounts\': [{\'mountPath\': u\'/tmp/tmppu9mngc_/stge01c9c1c-8118-4adb-8d36-ff240008c207/testdir\', \'subPath\': \'dir0\', \'name\': \'task-volume\'}, {\'mountPath\': u\'/var/spool/cwl\', \'subPath\': \'dir1\', \'name\': \'task-volume\'}, {\'mountPath\': u\'/var/spool/cwl/c\', \'subPath\': \'dir2\', \'name\': \'task-volume\'}], \'env\': [{\'name\': \'JSON_INPUT\', \'value\': \'{"outputs": [{"url": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/d2e74295-3b32-46ab-b468-e29683c8cd45/output.txt", "path": "/var/spool/cwl/output.txt", "type": "FILE", "name": "stdout"}, {"url": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/d2e74295-3b32-46ab-b468-e29683c8cd45/", "path": "/var/spool/cwl", "type": "DIRECTORY", "name": "workdir"}], "executors": [{"kind": "Job", "spec": {"template": {"spec": {"restartPolicy": "Never", "containers": [{"name": "task-1bb19357-ex-00", "image": "python:2.7", "workingDir": "/var/spool/cwl", "command": ["/bin/sh", "-c", "/bin/sh -c \\\'\\\'\\\\"\\\'\\\\"\\\'find\\\'\\\\"\\\'\\\\"\\\' \\\'\\\\"\\\'\\\\"\\\'-L\\\'\\\\"\\\'\\\\"\\\' \\\'\\\\"\\\'\\\\"\\\'.\\\'\\\\"\\\'\\\\"\\\' ! \\\'\\\\"\\\'\\\\"\\\'-path\\\'\\\\"\\\'\\\\"\\\' \\\'\\\\"\\\'\\\\"\\\'*.txt\\\'\\\\"\\\'\\\\"\\\' | \\\'\\\\"\\\'\\\\"\\\'sort\\\'\\\\"\\\'\\\\"\\\'\\\' > /var/spool/cwl/output.txt"], "env": [{"name": "HOME", "value": "/tmp/tmpnke66f6q"}, {"name": "TMPDIR", "value": "/tmp/tmpwkb53024"}], "resources": {}}]}, "metadata": {"name": "task-1bb19357-ex-00"}}}, "apiVersion": "batch/v1", "metadata": {"labels": {"taskmaster-name": "task-1bb19357", "executor-no": "0", "job-type": "executor", "creator-user-id": "anonymousUser"}, "annotations": {"tes-task-name": "dir5.cwl"}, "name": "task-1bb19357-ex-00"}}], "resources": {"disk_gb": 0.1}, "volumes": [], "inputs": [{"url": "file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir", "path": "/tmp/tmppu9mngc_/stge01c9c1c-8118-4adb-8d36-ff240008c207/testdir", "type": "DIRECTORY", "name": "indir", "description": "cwl_input:indir"}, {"url": "file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/b", "path": "/var/spool/cwl/b", "type": "FILE", "name": "b", "description": "InitialWorkDirRequirement:cwl_input:b"}, {"url": "file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/c", "path": "/var/spool/cwl/c", "type": "DIRECTORY", "name": "c", "description": "InitialWorkDirRequirement:cwl_input:c"}, {"url": "file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/a", "path": "/var/spool/cwl/a", "type": "FILE", "name": "a", "description": "InitialWorkDirRequirement:cwl_input:a"}]}\'}, {\'name\': \'TESK_FTP_USERNAME\', \'value\': \'redacted_username\'}, {\'name\': \'TESK_FTP_PASSWORD\', \'value\': \'redacted_password\'}], \'imagePullPolicy\': \'Always\'}]}, \'metadata\': {\'name\': u\'task-1bb19357-filer\'}}}, \'apiVersion\': \'batch/v1\', \'metadata\': {\'name\': u\'task-1bb19357-inputs-filer\'}}\n08/25/2018 04:13:25 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:13:25 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:13:30 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:13:30 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:13:35 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:13:35 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:13:40 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:13:40 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:13:45 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:13:45 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:13:50 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:13:50 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:13:55 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:13:55 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:14:00 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:14:00 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:14:05 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:14:05 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:14:10 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:14:10 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:14:15 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:14:15 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:14:20 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:14:20 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:14:25 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:14:25 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:14:30 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:14:30 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:14:35 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:14:35 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:14:40 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:14:40 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:14:45 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:14:45 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:14:50 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:14:50 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:14:55 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:14:55 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:15:00 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:15:00 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:15:05 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:15:05 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:15:10 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:15:10 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:15:15 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:15:15 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:15:20 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:15:20 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:15:25 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:15:25 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:15:30 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:15:30 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:15:35 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:15:35 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:15:40 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:15:40 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:15:45 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:15:45 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:15:50 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:15:50 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:15:55 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:15:55 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:16:00 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:16:00 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:16:05 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:16:05 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:16:10 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:16:10 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:16:15 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:16:15 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:16:20 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:16:20 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:16:25 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:16:25 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:16:30 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:16:30 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:16:35 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:16:35 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:16:40 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:16:40 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:16:45 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:16:45 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:16:50 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:16:50 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:16:55 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:16:55 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:17:00 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:17:00 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:17:05 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:17:05 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:17:10 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:17:10 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:17:15 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:17:15 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:17:20 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:17:20 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:17:25 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:17:25 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:17:30 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:17:30 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:17:35 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:17:35 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:17:40 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:17:40 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:17:45 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:17:45 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:17:50 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:17:50 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:17:55 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:17:55 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:18:00 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:18:00 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:18:05 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:18:05 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:18:10 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:18:10 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:18:15 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:18:15 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:18:20 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:18:20 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:18:25 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:18:25 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:18:30 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:18:30 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:18:35 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:18:35 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:18:40 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:18:40 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:18:45 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:18:45 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:18:50 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:18:50 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:18:55 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:18:55 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:19:00 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:19:00 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:19:05 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:19:05 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:19:10 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:19:10 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:19:15 DEBUG: Got label: "c98ef3e6-a881-11e8-916e-fa163e364743"\n\n08/25/2018 04:19:15 DEBUG: Got label: "task-1bb19357"\n08/25/2018 04:19:21 ERROR: Cancelling taskmaster: Got status Failed\n'])] [job dir5.cwl] job error: Error collecting output for parameter 'outlist': v1.0/dir5.cwl:13:7: Did not find output file with glob pattern: '['output.txt']' Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpbzmugy8e v1.0/dir5.cwl v1.0/dir-job.yml Test dynamic initial work dir Returned non-zero Test [89/132] Test writable staged files. Got workflow error Traceback (most recent call last): File "/home/mcrusoe/cwltool/cwltool/executors.py", line 238, in runner my_job.run(my_runtime_context) File "/home/mcrusoe/src/cwl-tes/cwl_tes/tes.py", line 358, in run task = self.create_task_msg() File "/home/mcrusoe/src/cwl-tes/cwl_tes/tes.py", line 265, in create_task_msg input_parameters = self.get_inputs() File "/home/mcrusoe/src/cwl-tes/cwl_tes/tes.py", line 246, in get_inputs self.parse_listing(self.generatefiles["listing"], inputs) File "/home/mcrusoe/src/cwl-tes/cwl_tes/tes.py", line 213, in parse_listing "The TES spec does not allow for writable inputs" cwltool.errors.UnsupportedRequirement: The TES spec does not allow for writable inputs Workflow or tool uses unsupported feature: The TES spec does not allow for writable inputs Test [90/132] Test file literal as input [job cat3-tool.cwl] job error: Error collecting output for parameter 'output_file': v1.0/cat3-tool.cwl:17:21: Did not find output file with glob pattern: '['output.txt']' Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmp7ikx92ra v1.0/cat3-tool.cwl v1.0/file-literal.yml Test file literal as input Returned non-zero Test [91/132] Test expression in InitialWorkDir listing [job linkfile.cwl] task id: task-0b110ac9 [job linkfile.cwl] logs: [TaskLog(start_time=datetime.datetime(2018, 8, 25, 16, 20, 41, tzinfo=tzutc()), end_time=datetime.datetime(2018, 8, 25, 16, 27, 31, tzinfo=tzutc()), metadata={'USER_ID': 'anonymousUser'}, logs=None, outputs=None, system_logs=['08/25/2018 04:20:44 DEBUG: Starting taskmaster\n08/25/2018 04:20:44 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:20:44 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:20:44 DEBUG: dirname of /tmp/tmp_qeocl9p/Hello.javais: /tmp/tmp_qeocl9p\n08/25/2018 04:20:44 DEBUG: appending task-volume at path /tmp/tmp_qeocl9p with subPath: dir0\n08/25/2018 04:20:44 DEBUG: dirname of /var/spool/cwl/Hello.javais: /var/spool/cwl\n08/25/2018 04:20:44 DEBUG: appending task-volume at path /var/spool/cwl with subPath: dir1\n08/25/2018 04:20:44 DEBUG: [{\'mountPath\': u\'/tmp/tmp_qeocl9p\', \'subPath\': \'dir0\', \'name\': \'task-volume\'}, {\'mountPath\': u\'/var/spool/cwl\', \'subPath\': \'dir1\', \'name\': \'task-volume\'}]\n08/25/2018 04:20:44 DEBUG: \n08/25/2018 04:20:44 DEBUG: {\'kind\': \'Job\', \'spec\': {\'template\': {\'spec\': {\'restartPolicy\': \'Never\', \'volumes\': [{\'name\': \'task-volume\', \'persistentVolumeClaim\': {\'claimName\': u\'task-0b110ac9-pvc\'}}], \'containers\': [{\'name\': \'filer\', \'image\': \'eu.gcr.io/tes-wes/filer:v0.4\', \'args\': [\'inputs\', \'$(JSON_INPUT)\', \'-d\'], \'volumeMounts\': [{\'mountPath\': u\'/tmp/tmp_qeocl9p\', \'subPath\': \'dir0\', \'name\': \'task-volume\'}, {\'mountPath\': u\'/var/spool/cwl\', \'subPath\': \'dir1\', \'name\': \'task-volume\'}], \'env\': [{\'name\': \'JSON_INPUT\', \'value\': \'{"outputs": [{"url": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/99b379c3-c665-482e-beb3-818a860572ed/", "path": "/var/spool/cwl", "type": "DIRECTORY", "name": "workdir"}], "executors": [{"kind": "Job", "spec": {"template": {"spec": {"restartPolicy": "Never", "containers": [{"name": "task-0b110ac9-ex-00", "image": "python:2.7", "workingDir": "/var/spool/cwl", "command": ["touch", "Hello.class"], "env": [{"name": "HOME", "value": "/tmp/tmp_qeocl9p"}, {"name": "TMPDIR", "value": "/tmp/tmpx42yh41f"}], "resources": {}}]}, "metadata": {"name": "task-0b110ac9-ex-00"}}}, "apiVersion": "batch/v1", "metadata": {"labels": {"taskmaster-name": "task-0b110ac9", "executor-no": "0", "job-type": "executor", "creator-user-id": "anonymousUser"}, "annotations": {"tes-task-name": "linkfile.cwl"}, "name": "task-0b110ac9-ex-00"}}], "resources": {"disk_gb": 0.1}, "volumes": [], "inputs": [{"url": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/99b379c3-c665-482e-beb3-818a860572ed/inputs/Hello.java", "path": "/tmp/tmp_qeocl9p/Hello.java", "type": "FILE", "name": "src", "description": "cwl_input:src"}, {"url": "file://ftp%3A//ftp-private.ebi.ac.uk/upload/cwl_conf004/99b379c3-c665-482e-beb3-818a860572ed/inputs/Hello.java", "path": "/var/spool/cwl/Hello.java", "type": "FILE", "name": "Hello.java", "description": "InitialWorkDirRequirement:cwl_input:Hello.java"}]}\'}, {\'name\': \'TESK_FTP_USERNAME\', \'value\': \'redacted_username\'}, {\'name\': \'TESK_FTP_PASSWORD\', \'value\': \'redacted_password\'}], \'imagePullPolicy\': \'Always\'}]}, \'metadata\': {\'name\': u\'task-0b110ac9-filer\'}}}, \'apiVersion\': \'batch/v1\', \'metadata\': {\'name\': u\'task-0b110ac9-inputs-filer\'}}\n08/25/2018 04:20:44 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:20:44 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:20:49 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:20:49 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:20:54 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:20:54 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:20:59 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:20:59 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:21:04 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:21:04 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:21:09 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:21:09 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:21:14 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:21:14 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:21:19 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:21:19 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:21:24 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:21:24 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:21:29 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:21:29 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:21:34 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:21:34 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:21:39 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:21:39 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:21:44 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:21:44 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:21:49 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:21:49 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:21:54 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:21:54 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:21:59 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:21:59 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:22:04 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:22:04 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:22:09 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:22:09 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:22:14 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:22:14 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:22:19 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:22:19 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:22:24 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:22:24 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:22:29 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:22:29 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:22:34 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:22:34 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:22:39 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:22:39 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:22:44 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:22:44 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:22:49 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:22:49 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:22:54 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:22:54 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:22:59 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:22:59 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:23:04 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:23:04 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:23:09 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:23:09 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:23:14 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:23:14 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:23:19 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:23:19 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:23:24 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:23:24 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:23:29 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:23:29 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:23:34 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:23:34 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:23:39 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:23:39 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:23:44 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:23:44 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:23:49 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:23:49 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:23:54 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:23:54 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:23:59 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:23:59 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:24:04 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:24:04 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:24:09 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:24:09 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:24:14 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:24:14 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:24:19 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:24:19 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:24:24 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:24:24 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:24:29 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:24:29 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:24:34 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:24:34 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:24:39 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:24:39 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:24:44 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:24:44 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:24:49 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:24:49 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:24:54 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:24:54 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:24:59 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:24:59 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:25:04 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:25:04 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:25:09 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:25:09 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:25:14 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:25:14 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:25:19 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:25:19 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:25:24 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:25:24 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:25:29 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:25:29 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:25:34 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:25:34 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:25:39 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:25:39 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:25:44 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:25:44 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:25:49 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:25:49 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:25:54 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:25:54 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:25:59 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:25:59 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:26:04 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:26:04 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:26:09 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:26:09 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:26:14 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:26:14 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:26:19 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:26:19 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:26:24 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:26:24 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:26:29 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:26:29 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:26:34 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:26:34 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:26:39 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:26:39 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:26:44 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:26:44 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:26:49 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:26:49 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:26:54 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:26:54 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:26:59 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:26:59 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:27:04 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:27:04 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:27:09 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:27:09 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:27:14 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:27:14 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:27:19 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:27:19 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:27:24 DEBUG: Got label: "cf300992-a882-11e8-916e-fa163e364743"\n\n08/25/2018 04:27:24 DEBUG: Got label: "task-0b110ac9"\n08/25/2018 04:27:30 ERROR: Cancelling taskmaster: Got status Failed\n'])] [job linkfile.cwl] job error: Error collecting output for parameter 'classfile': v1.0/linkfile.cwl:22:7: Did not find output file with glob pattern: '['*.class']' Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmp161nsvm8 v1.0/linkfile.cwl v1.0/arguments-job.yml Test expression in InitialWorkDir listing Returned non-zero Test [92/132] Test nameroot/nameext expression in arguments, stdout [job nameroot.cwl] job error: Error collecting output for parameter 'b': test:1:1: Did not find output file with glob pattern: '['whale.xtx']' Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpz0j0euel v1.0/nameroot.cwl v1.0/wc-job.json Test nameroot/nameext expression in arguments, stdout Returned non-zero Test [93/132] Test directory input with inputBinding a file:// based Directory slipped through: CommentedMap([('class', 'Directory'), ('location', 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir'), ('basename', 'testdir'), ('listing', [{'class': 'File', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/b', 'basename': 'b'}, {'class': 'Directory', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/c', 'basename': 'c', 'listing': [{'class': 'File', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/c/d', 'basename': 'd'}]}, {'class': 'File', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/a', 'basename': 'a'}])]) unprocessed File {'class': 'File', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/b', 'basename': 'b'} a file:// based Directory slipped through: {'class': 'Directory', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/c', 'basename': 'c', 'listing': [{'class': 'File', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/c/d', 'basename': 'd'}]} unprocessed File {'class': 'File', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/c/d', 'basename': 'd'} unprocessed File {'class': 'File', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/a', 'basename': 'a'} [job dir6.cwl] task id: task-ccaad1c4 [job dir6.cwl] logs: [TaskLog(start_time=datetime.datetime(2018, 8, 25, 16, 29, 4, tzinfo=tzutc()), end_time=datetime.datetime(2018, 8, 25, 16, 35, 19, tzinfo=tzutc()), metadata={'USER_ID': 'anonymousUser'}, logs=None, outputs=None, system_logs=['08/25/2018 04:29:07 DEBUG: Starting taskmaster\n08/25/2018 04:29:07 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:29:07 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:29:07 DEBUG: appending task-volume at path /tmp/tmpo7sx_7jh/stg11ce993a-1dfd-4891-8d8b-7f64b0cef851/testdir with subPath: dir0\n08/25/2018 04:29:07 DEBUG: dirname of /var/spool/cwl/output.txtis: /var/spool/cwl\n08/25/2018 04:29:07 DEBUG: appending task-volume at path /var/spool/cwl with subPath: dir1\n08/25/2018 04:29:07 DEBUG: [{\'mountPath\': u\'/tmp/tmpo7sx_7jh/stg11ce993a-1dfd-4891-8d8b-7f64b0cef851/testdir\', \'subPath\': \'dir0\', \'name\': \'task-volume\'}, {\'mountPath\': u\'/var/spool/cwl\', \'subPath\': \'dir1\', \'name\': \'task-volume\'}]\n08/25/2018 04:29:07 DEBUG: \n08/25/2018 04:29:07 DEBUG: {\'kind\': \'Job\', \'spec\': {\'template\': {\'spec\': {\'restartPolicy\': \'Never\', \'volumes\': [{\'name\': \'task-volume\', \'persistentVolumeClaim\': {\'claimName\': u\'task-ccaad1c4-pvc\'}}], \'containers\': [{\'name\': \'filer\', \'image\': \'eu.gcr.io/tes-wes/filer:v0.4\', \'args\': [\'inputs\', \'$(JSON_INPUT)\', \'-d\'], \'volumeMounts\': [{\'mountPath\': u\'/tmp/tmpo7sx_7jh/stg11ce993a-1dfd-4891-8d8b-7f64b0cef851/testdir\', \'subPath\': \'dir0\', \'name\': \'task-volume\'}, {\'mountPath\': u\'/var/spool/cwl\', \'subPath\': \'dir1\', \'name\': \'task-volume\'}], \'env\': [{\'name\': \'JSON_INPUT\', \'value\': \'{"outputs": [{"url": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/cc5936e9-39ef-4e4d-b21a-cb736eb16885/output.txt", "path": "/var/spool/cwl/output.txt", "type": "FILE", "name": "stdout"}, {"url": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/cc5936e9-39ef-4e4d-b21a-cb736eb16885/", "path": "/var/spool/cwl", "type": "DIRECTORY", "name": "workdir"}], "executors": [{"kind": "Job", "spec": {"template": {"spec": {"restartPolicy": "Never", "containers": [{"name": "task-ccaad1c4-ex-00", "image": "python:2.7", "workingDir": "/var/spool/cwl", "command": ["/bin/sh", "-c", "/bin/sh -c \\\'\\\'\\\\"\\\'\\\\"\\\'cd\\\'\\\\"\\\'\\\\"\\\' \\\'\\\\"\\\'\\\\"\\\'/tmp/tmpo7sx_7jh/stg11ce993a-1dfd-4891-8d8b-7f64b0cef851/testdir\\\'\\\\"\\\'\\\\"\\\' && \\\'\\\\"\\\'\\\\"\\\'find\\\'\\\\"\\\'\\\\"\\\' \\\'\\\\"\\\'\\\\"\\\'.\\\'\\\\"\\\'\\\\"\\\' | \\\'\\\\"\\\'\\\\"\\\'sort\\\'\\\\"\\\'\\\\"\\\'\\\' > /var/spool/cwl/output.txt"], "env": [{"name": "HOME", "value": "/tmp/tmpr8qcxygi"}, {"name": "TMPDIR", "value": "/tmp/tmprf_d5321"}], "resources": {}}]}, "metadata": {"name": "task-ccaad1c4-ex-00"}}}, "apiVersion": "batch/v1", "metadata": {"labels": {"taskmaster-name": "task-ccaad1c4", "executor-no": "0", "job-type": "executor", "creator-user-id": "anonymousUser"}, "annotations": {"tes-task-name": "dir6.cwl"}, "name": "task-ccaad1c4-ex-00"}}], "resources": {"disk_gb": 0.1}, "volumes": [], "inputs": [{"url": "file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir", "path": "/tmp/tmpo7sx_7jh/stg11ce993a-1dfd-4891-8d8b-7f64b0cef851/testdir", "type": "DIRECTORY", "name": "indir", "description": "cwl_input:indir"}]}\'}, {\'name\': \'TESK_FTP_USERNAME\', \'value\': \'redacted_username\'}, {\'name\': \'TESK_FTP_PASSWORD\', \'value\': \'redacted_password\'}], \'imagePullPolicy\': \'Always\'}]}, \'metadata\': {\'name\': u\'task-ccaad1c4-filer\'}}}, \'apiVersion\': \'batch/v1\', \'metadata\': {\'name\': u\'task-ccaad1c4-inputs-filer\'}}\n08/25/2018 04:29:07 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:29:07 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:29:12 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:29:12 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:29:17 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:29:17 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:29:22 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:29:22 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:29:27 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:29:27 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:29:32 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:29:32 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:29:37 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:29:37 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:29:42 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:29:42 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:29:47 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:29:47 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:29:52 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:29:52 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:29:57 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:29:57 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:30:03 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:30:03 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:30:08 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:30:08 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:30:13 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:30:13 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:30:18 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:30:18 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:30:23 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:30:23 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:30:28 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:30:28 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:30:33 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:30:33 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:30:38 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:30:38 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:30:43 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:30:43 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:30:48 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:30:48 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:30:53 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:30:53 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:30:58 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:30:58 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:31:03 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:31:03 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:31:08 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:31:08 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:31:13 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:31:13 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:31:18 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:31:18 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:31:23 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:31:23 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:31:28 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:31:28 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:31:33 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:31:33 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:31:38 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:31:38 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:31:43 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:31:43 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:31:48 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:31:48 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:31:53 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:31:53 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:31:58 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:31:58 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:32:03 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:32:03 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:32:08 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:32:08 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:32:13 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:32:13 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:32:18 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:32:18 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:32:23 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:32:23 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:32:28 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:32:28 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:32:33 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:32:33 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:32:38 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:32:38 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:32:43 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:32:43 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:32:48 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:32:48 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:32:53 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:32:53 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:32:58 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:32:58 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:33:03 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:33:03 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:33:08 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:33:08 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:33:13 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:33:13 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:33:18 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:33:18 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:33:23 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:33:23 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:33:28 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:33:28 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:33:33 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:33:33 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:33:38 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:33:38 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:33:43 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:33:43 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:33:48 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:33:48 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:33:53 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:33:53 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:33:58 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:33:58 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:34:03 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:34:03 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:34:08 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:34:08 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:34:13 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:34:13 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:34:18 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:34:18 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:34:23 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:34:23 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:34:28 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:34:28 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:34:33 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:34:33 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:34:38 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:34:38 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:34:43 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:34:43 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:34:48 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:34:48 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:34:53 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:34:53 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:34:58 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:34:58 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:35:03 DEBUG: Got label: "fb5ccc0d-a883-11e8-916e-fa163e364743"\n\n08/25/2018 04:35:03 DEBUG: Got label: "task-ccaad1c4"\n08/25/2018 04:35:08 ERROR: Cancelling taskmaster: Got status Failed\n'])] [job dir6.cwl] job error: Error collecting output for parameter 'outlist': v1.0/dir6.cwl:15:7: Did not find output file with glob pattern: '['output.txt']' Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmp583uy5jw v1.0/dir6.cwl v1.0/dir-job.yml Test directory input with inputBinding Returned non-zero Test [94/132] Test command line generation of array-of-arrays [job nested-array.cwl] job error: Error collecting output for parameter 'echo': test:1:1: Did not find output file with glob pattern: '['echo.txt']' Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmp7podjd73 v1.0/nested-array.cwl v1.0/nested-array-job.yml Test command line generation of array-of-arrays Returned non-zero Test [95/132] Test $HOME and $TMPDIR are set correctly Expecting value: line 1 column 1 (char 0) Test [96/132] Test $HOME and $TMPDIR are set correctly in Docker [job envvar2.cwl] task id: task-55ddb5cd [job envvar2.cwl] logs: [TaskLog(start_time=datetime.datetime(2018, 8, 25, 16, 37, 12, tzinfo=tzutc()), end_time=datetime.datetime(2018, 8, 25, 16, 44, 32, tzinfo=tzutc()), metadata={'USER_ID': 'anonymousUser'}, logs=[ExecutorLog(start_time=datetime.datetime(2018, 8, 25, 16, 37, 30, tzinfo=tzutc()), end_time=None, stdout='HOME=/tmp/tmp5uzid5bt TMPDIR=/tmp/tmpt9i61ovj\n', stderr=None, exit_code=1)], outputs=None, system_logs=['08/25/2018 04:37:15 DEBUG: Starting taskmaster\n08/25/2018 04:37:15 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:37:15 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:37:15 DEBUG: appending task-volume at path /var/spool/cwl with subPath: dir0\n08/25/2018 04:37:15 DEBUG: [{\'mountPath\': u\'/var/spool/cwl\', \'subPath\': \'dir0\', \'name\': \'task-volume\'}]\n08/25/2018 04:37:15 DEBUG: \n08/25/2018 04:37:15 DEBUG: {\'kind\': \'Job\', \'spec\': {\'template\': {\'spec\': {\'restartPolicy\': \'Never\', \'volumes\': [{\'name\': \'task-volume\', \'persistentVolumeClaim\': {\'claimName\': u\'task-55ddb5cd-pvc\'}}], \'containers\': [{\'name\': \'filer\', \'image\': \'eu.gcr.io/tes-wes/filer:v0.4\', \'args\': [\'inputs\', \'$(JSON_INPUT)\', \'-d\'], \'volumeMounts\': [{\'mountPath\': u\'/var/spool/cwl\', \'subPath\': \'dir0\', \'name\': \'task-volume\'}], \'env\': [{\'name\': \'JSON_INPUT\', \'value\': \'{"outputs": [{"url": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/7865d816-1697-4f2a-b05a-ee3031816a8b/", "path": "/var/spool/cwl", "type": "DIRECTORY", "name": "workdir"}], "executors": [{"kind": "Job", "spec": {"template": {"spec": {"restartPolicy": "Never", "containers": [{"name": "task-55ddb5cd-ex-00", "image": "debian:stretch-slim", "workingDir": "/var/spool/cwl", "command": ["/bin/sh", "-c", "\\\'echo\\\' \\\\"HOME=$HOME\\\\" \\\\"TMPDIR=$TMPDIR\\\\" && \\\'test\\\' \\\\"$HOME\\\\" \\\'=\\\' \\\'/var/spool/cwl\\\' \\\'-a\\\' \\\\"$TMPDIR\\\\" \\\'=\\\' \\\'/tmp\\\'"], "env": [{"name": "HOME", "value": "/tmp/tmp5uzid5bt"}, {"name": "TMPDIR", "value": "/tmp/tmpt9i61ovj"}], "resources": {}}]}, "metadata": {"name": "task-55ddb5cd-ex-00"}}}, "apiVersion": "batch/v1", "metadata": {"labels": {"taskmaster-name": "task-55ddb5cd", "executor-no": "0", "job-type": "executor", "creator-user-id": "anonymousUser"}, "annotations": {"tes-task-name": "envvar2.cwl"}, "name": "task-55ddb5cd-ex-00"}}], "resources": {"disk_gb": 0.1}, "volumes": [], "inputs": []}\'}, {\'name\': \'TESK_FTP_USERNAME\', \'value\': \'redacted_username\'}, {\'name\': \'TESK_FTP_PASSWORD\', \'value\': \'redacted_password\'}], \'imagePullPolicy\': \'Always\'}]}, \'metadata\': {\'name\': u\'task-55ddb5cd-filer\'}}}, \'apiVersion\': \'batch/v1\', \'metadata\': {\'name\': u\'task-55ddb5cd-inputs-filer\'}}\n08/25/2018 04:37:15 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:37:15 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:37:20 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:37:20 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:37:25 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:37:25 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:37:30 DEBUG: Created job: task-55ddb5cd-ex-00\n08/25/2018 04:37:30 DEBUG: Job spec: {u\'kind\': u\'Job\', u\'spec\': {u\'template\': {u\'spec\': {u\'restartPolicy\': u\'Never\', \'volumes\': [{\'name\': \'task-volume\', \'persistentVolumeClaim\': {\'readonly\': False, \'claimName\': u\'task-55ddb5cd-pvc\'}}], u\'containers\': [{u\'name\': u\'task-55ddb5cd-ex-00\', \'volumeMounts\': [{\'mountPath\': u\'/var/spool/cwl\', \'subPath\': \'dir0\', \'name\': \'task-volume\'}], u\'image\': u\'debian:stretch-slim\', u\'workingDir\': u\'/var/spool/cwl\', u\'command\': [u\'/bin/sh\', u\'-c\', u\'\\\'echo\\\' "HOME=$HOME" "TMPDIR=$TMPDIR" && \\\'test\\\' "$HOME" \\\'=\\\' \\\'/var/spool/cwl\\\' \\\'-a\\\' "$TMPDIR" \\\'=\\\' \\\'/tmp\\\'\'], u\'env\': [{u\'name\': u\'HOME\', u\'value\': u\'/tmp/tmp5uzid5bt\'}, {u\'name\': u\'TMPDIR\', u\'value\': u\'/tmp/tmpt9i61ovj\'}], u\'resources\': {}}]}, u\'metadata\': {u\'name\': u\'task-55ddb5cd-ex-00\'}}}, u\'apiVersion\': u\'batch/v1\', u\'metadata\': {u\'labels\': {u\'taskmaster-name\': u\'task-55ddb5cd\', u\'executor-no\': u\'0\', u\'job-type\': u\'executor\', u\'creator-user-id\': u\'anonymousUser\'}, u\'annotations\': {u\'tes-task-name\': u\'envvar2.cwl\'}, u\'name\': u\'task-55ddb5cd-ex-00\'}}\n08/25/2018 04:37:30 DEBUG: {u\'kind\': u\'Job\', u\'spec\': {u\'template\': {u\'spec\': {u\'restartPolicy\': u\'Never\', \'volumes\': [{\'name\': \'task-volume\', \'persistentVolumeClaim\': {\'readonly\': False, \'claimName\': u\'task-55ddb5cd-pvc\'}}], u\'containers\': [{u\'name\': u\'task-55ddb5cd-ex-00\', \'volumeMounts\': [{\'mountPath\': u\'/var/spool/cwl\', \'subPath\': \'dir0\', \'name\': \'task-volume\'}], u\'image\': u\'debian:stretch-slim\', u\'workingDir\': u\'/var/spool/cwl\', u\'command\': [u\'/bin/sh\', u\'-c\', u\'\\\'echo\\\' "HOME=$HOME" "TMPDIR=$TMPDIR" && \\\'test\\\' "$HOME" \\\'=\\\' \\\'/var/spool/cwl\\\' \\\'-a\\\' "$TMPDIR" \\\'=\\\' \\\'/tmp\\\'\'], u\'env\': [{u\'name\': u\'HOME\', u\'value\': u\'/tmp/tmp5uzid5bt\'}, {u\'name\': u\'TMPDIR\', u\'value\': u\'/tmp/tmpt9i61ovj\'}], u\'resources\': {}}]}, u\'metadata\': {u\'name\': u\'task-55ddb5cd-ex-00\'}}}, u\'apiVersion\': u\'batch/v1\', u\'metadata\': {u\'labels\': {u\'taskmaster-name\': u\'task-55ddb5cd\', u\'executor-no\': u\'0\', u\'job-type\': u\'executor\', u\'creator-user-id\': u\'anonymousUser\'}, u\'annotations\': {u\'tes-task-name\': u\'envvar2.cwl\'}, u\'name\': u\'task-55ddb5cd-ex-00\'}}\n08/25/2018 04:37:31 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:37:31 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:37:36 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:37:36 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:37:41 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:37:41 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:37:46 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:37:46 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:37:51 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:37:51 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:37:56 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:37:56 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:38:01 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:38:01 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:38:06 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:38:06 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:38:11 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:38:11 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:38:16 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:38:16 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:38:21 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:38:21 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:38:26 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:38:26 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:38:31 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:38:31 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:38:36 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:38:36 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:38:41 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:38:41 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:38:46 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:38:46 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:38:51 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:38:51 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:38:56 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:38:56 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:39:01 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:39:01 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:39:06 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:39:06 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:39:11 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:39:11 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:39:16 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:39:16 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:39:21 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:39:21 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:39:26 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:39:26 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:39:31 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:39:31 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:39:36 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:39:36 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:39:41 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:39:41 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:39:46 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:39:46 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:39:51 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:39:51 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:39:56 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:39:56 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:40:01 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:40:01 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:40:06 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:40:06 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:40:11 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:40:11 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:40:16 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:40:16 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:40:21 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:40:21 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:40:26 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:40:26 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:40:31 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:40:31 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:40:36 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:40:36 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:40:41 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:40:41 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:40:46 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:40:46 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:40:51 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:40:51 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:40:56 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:40:56 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:41:01 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:41:01 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:41:06 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:41:06 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:41:11 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:41:11 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:41:16 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:41:16 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:41:21 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:41:21 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:41:26 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:41:26 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:41:31 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:41:31 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:41:36 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:41:36 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:41:41 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:41:41 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:41:46 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:41:46 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:41:51 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:41:51 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:41:56 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:41:56 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:42:01 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:42:01 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:42:06 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:42:06 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:42:11 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:42:11 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:42:16 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:42:16 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:42:21 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:42:21 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:42:26 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:42:26 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:42:31 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:42:31 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:42:36 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:42:36 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:42:41 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:42:41 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:42:46 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:42:46 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:42:51 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:42:51 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:42:56 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:42:56 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:43:01 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:43:01 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:43:06 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:43:06 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:43:11 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:43:11 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:43:16 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:43:16 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:43:21 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:43:21 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:43:26 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:43:26 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:43:31 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:43:31 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:43:36 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:43:36 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:43:41 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:43:41 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:43:46 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:43:46 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:43:51 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:43:51 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:43:56 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:43:56 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:44:01 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:44:01 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:44:06 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:44:06 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:44:11 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:44:11 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:44:16 DEBUG: Got label: "1e6db477-a885-11e8-916e-fa163e364743"\n\n08/25/2018 04:44:16 DEBUG: Got label: "task-55ddb5cd"\n08/25/2018 04:44:21 ERROR: Cancelling taskmaster: Got status Failed\n'])] Expecting value: line 1 column 1 (char 0) Test [97/132] Test that expressionLib requirement of individual tool step overrides expressionLib of workflow. [job tool] job error: Error collecting output for parameter 'out': test:1:1: Did not find output file with glob pattern: '['whatever.txt']' [step tool] Output is missing expected field file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/js-expr-req-wf.cwl#wf/tool/out [step tool] completed permanentFail Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmp83ozxm94 'v1.0/js-expr-req-wf.cwl#wf' v1.0/empty.json Test that expressionLib requirement of individual tool step overrides expressionLib of workflow. Returned non-zero Test [98/132] Test output of InitialWorkDir [job initialworkdirrequirement-docker-out.cwl] task id: task-0699184e [job initialworkdirrequirement-docker-out.cwl] logs: [TaskLog(start_time=datetime.datetime(2018, 8, 25, 16, 45, 42, tzinfo=tzutc()), end_time=datetime.datetime(2018, 8, 25, 16, 52, 42, tzinfo=tzutc()), metadata={'USER_ID': 'anonymousUser'}, logs=None, outputs=None, system_logs=['08/25/2018 04:45:45 DEBUG: Starting taskmaster\n08/25/2018 04:45:45 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:45:45 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:45:45 DEBUG: dirname of /var/spool/cwl/ref.fastais: /var/spool/cwl\n08/25/2018 04:45:45 DEBUG: appending task-volume at path /var/spool/cwl with subPath: dir0\n08/25/2018 04:45:45 DEBUG: dirname of /var/spool/cwl/ref.fastais: /var/spool/cwl\n08/25/2018 04:45:45 DEBUG: [{\'mountPath\': u\'/var/spool/cwl\', \'subPath\': \'dir0\', \'name\': \'task-volume\'}]\n08/25/2018 04:45:45 DEBUG: \n08/25/2018 04:45:45 DEBUG: {\'kind\': \'Job\', \'spec\': {\'template\': {\'spec\': {\'restartPolicy\': \'Never\', \'volumes\': [{\'name\': \'task-volume\', \'persistentVolumeClaim\': {\'claimName\': u\'task-0699184e-pvc\'}}], \'containers\': [{\'name\': \'filer\', \'image\': \'eu.gcr.io/tes-wes/filer:v0.4\', \'args\': [\'inputs\', \'$(JSON_INPUT)\', \'-d\'], \'volumeMounts\': [{\'mountPath\': u\'/var/spool/cwl\', \'subPath\': \'dir0\', \'name\': \'task-volume\'}], \'env\': [{\'name\': \'JSON_INPUT\', \'value\': \'{"outputs": [{"url": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/5fe9e32e-32bf-469f-8b88-5bfd1c0360b6/", "path": "/var/spool/cwl", "type": "DIRECTORY", "name": "workdir"}], "executors": [{"kind": "Job", "spec": {"template": {"spec": {"restartPolicy": "Never", "containers": [{"name": "task-0699184e-ex-00", "image": "debian:stretch-slim", "workingDir": "/var/spool/cwl", "command": ["touch", "ref.fasta.fai"], "env": [{"name": "HOME", "value": "/tmp/tmp68pkgjo1"}, {"name": "TMPDIR", "value": "/tmp/tmp_7sfmj0b"}], "resources": {}}]}, "metadata": {"name": "task-0699184e-ex-00"}}}, "apiVersion": "batch/v1", "metadata": {"labels": {"taskmaster-name": "task-0699184e", "executor-no": "0", "job-type": "executor", "creator-user-id": "anonymousUser"}, "annotations": {"tes-task-name": "initialworkdirrequirement-docker-out.cwl"}, "name": "task-0699184e-ex-00"}}], "resources": {"disk_gb": 0.1}, "volumes": [], "inputs": [{"url": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/5fe9e32e-32bf-469f-8b88-5bfd1c0360b6/inputs/ref.fasta", "path": "/var/spool/cwl/ref.fasta", "type": "FILE", "name": "INPUT", "description": "cwl_input:INPUT"}, {"url": "file://ftp%3A//ftp-private.ebi.ac.uk/upload/cwl_conf004/5fe9e32e-32bf-469f-8b88-5bfd1c0360b6/inputs/ref.fasta", "path": "/var/spool/cwl/ref.fasta", "type": "FILE", "name": "ref.fasta", "description": "InitialWorkDirRequirement:cwl_input:ref.fasta"}]}\'}, {\'name\': \'TESK_FTP_USERNAME\', \'value\': \'redacted_username\'}, {\'name\': \'TESK_FTP_PASSWORD\', \'value\': \'redacted_password\'}], \'imagePullPolicy\': \'Always\'}]}, \'metadata\': {\'name\': u\'task-0699184e-filer\'}}}, \'apiVersion\': \'batch/v1\', \'metadata\': {\'name\': u\'task-0699184e-inputs-filer\'}}\n08/25/2018 04:45:45 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:45:45 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:45:50 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:45:50 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:45:55 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:45:55 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:46:00 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:46:00 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:46:05 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:46:05 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:46:10 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:46:10 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:46:15 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:46:15 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:46:20 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:46:20 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:46:25 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:46:25 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:46:30 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:46:30 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:46:35 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:46:35 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:46:40 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:46:40 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:46:45 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:46:45 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:46:50 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:46:50 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:46:55 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:46:55 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:47:00 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:47:00 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:47:05 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:47:05 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:47:10 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:47:10 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:47:15 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:47:15 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:47:20 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:47:20 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:47:25 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:47:25 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:47:30 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:47:30 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:47:35 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:47:35 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:47:40 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:47:40 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:47:45 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:47:45 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:47:50 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:47:50 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:47:55 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:47:55 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:48:00 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:48:00 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:48:05 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:48:05 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:48:10 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:48:10 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:48:15 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:48:15 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:48:20 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:48:20 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:48:25 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:48:25 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:48:30 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:48:30 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:48:35 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:48:35 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:48:40 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:48:40 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:48:46 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:48:46 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:48:51 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:48:51 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:48:56 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:48:56 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:49:01 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:49:01 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:49:06 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:49:06 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:49:11 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:49:11 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:49:16 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:49:16 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:49:21 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:49:21 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:49:26 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:49:26 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:49:31 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:49:31 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:49:36 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:49:36 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:49:41 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:49:41 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:49:46 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:49:46 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:49:51 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:49:51 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:49:56 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:49:56 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:50:01 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:50:01 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:50:06 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:50:06 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:50:11 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:50:11 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:50:16 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:50:16 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:50:21 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:50:21 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:50:26 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:50:26 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:50:31 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:50:31 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:50:36 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:50:36 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:50:41 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:50:41 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:50:46 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:50:46 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:50:51 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:50:51 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:50:56 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:50:56 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:51:01 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:51:01 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:51:06 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:51:06 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:51:11 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:51:11 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:51:16 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:51:16 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:51:21 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:51:21 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:51:26 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:51:26 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:51:31 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:51:31 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:51:36 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:51:36 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:51:41 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:51:41 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:51:46 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:51:46 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:51:51 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:51:51 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:51:56 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:51:56 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:52:01 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:52:01 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:52:06 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:52:06 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:52:11 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:52:11 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:52:16 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:52:16 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:52:21 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:52:21 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:52:26 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:52:26 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:52:31 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:52:31 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:52:36 DEBUG: Got label: "4e34cc8f-a886-11e8-916e-fa163e364743"\n\n08/25/2018 04:52:36 DEBUG: Got label: "task-0699184e"\n08/25/2018 04:52:41 ERROR: Cancelling taskmaster: Got status Failed\n'])] [job initialworkdirrequirement-docker-out.cwl] job error: Error collecting output for parameter 'OUTPUT': v1.0/initialworkdirrequirement-docker-out.cwl:22:7: Did not find output file with glob pattern: '['ref.fasta']' Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmp1na_p3y8 v1.0/initialworkdirrequirement-docker-out.cwl v1.0/initialworkdirrequirement-docker-out-job.json Test output of InitialWorkDir Returned non-zero Test [99/132] Test embedded subworkflow [job step1] job error: Error collecting output for parameter 'output': v1.0/wc-tool.cwl:12:22: Did not find output file with glob pattern: '['output']' [step step1] Output is missing expected field file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/count-lines10-wf.cwl#step0/d40adc82-7d0d-4c16-ad32-b1edfd7707c5/step1/output [step step1] completed permanentFail [step step0] completed permanentFail Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpsussi74h v1.0/count-lines10-wf.cwl v1.0/wc-job.json Test embedded subworkflow Returned non-zero Test [100/132] Test secondaryFiles on array of files. [job docker-array-secondaryfiles.cwl] task id: task-9fe2f1e5 [job docker-array-secondaryfiles.cwl] logs: [TaskLog(start_time=datetime.datetime(2018, 8, 25, 16, 54, 28, tzinfo=tzutc()), end_time=datetime.datetime(2018, 8, 25, 17, 1, 28, tzinfo=tzutc()), metadata={'USER_ID': 'anonymousUser'}, logs=None, outputs=None, system_logs=['08/25/2018 04:54:31 DEBUG: Starting taskmaster\n08/25/2018 04:54:31 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:54:31 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:54:31 DEBUG: dirname of /var/lib/cwl/stgc7b06787-c985-42ee-808e-767b194789fb/ref.fastais: /var/lib/cwl/stgc7b06787-c985-42ee-808e-767b194789fb\n08/25/2018 04:54:31 DEBUG: appending task-volume at path /var/lib/cwl/stgc7b06787-c985-42ee-808e-767b194789fb with subPath: dir0\n08/25/2018 04:54:31 DEBUG: dirname of /var/lib/cwl/stgc7b06787-c985-42ee-808e-767b194789fb/ref.fasta.faiis: /var/lib/cwl/stgc7b06787-c985-42ee-808e-767b194789fb\n08/25/2018 04:54:31 DEBUG: dirname of /var/lib/cwl/stg735e262b-1422-4186-9191-d29623b4d41d/ref2.fastais: /var/lib/cwl/stg735e262b-1422-4186-9191-d29623b4d41d\n08/25/2018 04:54:31 DEBUG: appending task-volume at path /var/lib/cwl/stg735e262b-1422-4186-9191-d29623b4d41d with subPath: dir1\n08/25/2018 04:54:31 DEBUG: dirname of /var/lib/cwl/stg735e262b-1422-4186-9191-d29623b4d41d/ref2.fasta.faiis: /var/lib/cwl/stg735e262b-1422-4186-9191-d29623b4d41d\n08/25/2018 04:54:31 DEBUG: appending task-volume at path /var/spool/cwl with subPath: dir2\n08/25/2018 04:54:31 DEBUG: [{\'mountPath\': u\'/var/lib/cwl/stgc7b06787-c985-42ee-808e-767b194789fb\', \'subPath\': \'dir0\', \'name\': \'task-volume\'}, {\'mountPath\': u\'/var/lib/cwl/stg735e262b-1422-4186-9191-d29623b4d41d\', \'subPath\': \'dir1\', \'name\': \'task-volume\'}, {\'mountPath\': u\'/var/spool/cwl\', \'subPath\': \'dir2\', \'name\': \'task-volume\'}]\n08/25/2018 04:54:31 DEBUG: \n08/25/2018 04:54:31 DEBUG: {\'kind\': \'Job\', \'spec\': {\'template\': {\'spec\': {\'restartPolicy\': \'Never\', \'volumes\': [{\'name\': \'task-volume\', \'persistentVolumeClaim\': {\'claimName\': u\'task-9fe2f1e5-pvc\'}}], \'containers\': [{\'name\': \'filer\', \'image\': \'eu.gcr.io/tes-wes/filer:v0.4\', \'args\': [\'inputs\', \'$(JSON_INPUT)\', \'-d\'], \'volumeMounts\': [{\'mountPath\': u\'/var/lib/cwl/stgc7b06787-c985-42ee-808e-767b194789fb\', \'subPath\': \'dir0\', \'name\': \'task-volume\'}, {\'mountPath\': u\'/var/lib/cwl/stg735e262b-1422-4186-9191-d29623b4d41d\', \'subPath\': \'dir1\', \'name\': \'task-volume\'}, {\'mountPath\': u\'/var/spool/cwl\', \'subPath\': \'dir2\', \'name\': \'task-volume\'}], \'env\': [{\'name\': \'JSON_INPUT\', \'value\': \'{"outputs": [{"url": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/716d46fe-623e-4854-ade8-33a421612c19/", "path": "/var/spool/cwl", "type": "DIRECTORY", "name": "workdir"}], "executors": [{"kind": "Job", "spec": {"template": {"spec": {"restartPolicy": "Never", "containers": [{"name": "task-9fe2f1e5-ex-00", "image": "debian:stretch-slim", "workingDir": "/var/spool/cwl", "command": ["/bin/sh", "-c", " cat /var/lib/cwl/stgc7b06787-c985-42ee-808e-767b194789fb/ref.fasta.fai >> fai.list && cat /var/lib/cwl/stg735e262b-1422-4186-9191-d29623b4d41d/ref2.fasta.fai >> fai.list "], "env": [{"name": "HOME", "value": "/tmp/tmpgmpacv9q"}, {"name": "TMPDIR", "value": "/tmp/tmpsrl99tfw"}], "resources": {}}]}, "metadata": {"name": "task-9fe2f1e5-ex-00"}}}, "apiVersion": "batch/v1", "metadata": {"labels": {"taskmaster-name": "task-9fe2f1e5", "executor-no": "0", "job-type": "executor", "creator-user-id": "anonymousUser"}, "annotations": {"tes-task-name": "docker-array-secondaryfiles.cwl"}, "name": "task-9fe2f1e5-ex-00"}}], "resources": {"disk_gb": 0.1}, "volumes": [], "inputs": [{"url": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/716d46fe-623e-4854-ade8-33a421612c19/inputs/ref.fasta", "path": "/var/lib/cwl/stgc7b06787-c985-42ee-808e-767b194789fb/ref.fasta", "type": "FILE", "name": "fasta_path[0]", "description": "cwl_input:fasta_path[0]"}, {"url": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/716d46fe-623e-4854-ade8-33a421612c19/inputs/ref.fasta.fai", "path": "/var/lib/cwl/stgc7b06787-c985-42ee-808e-767b194789fb/ref.fasta.fai", "type": "FILE", "name": "ref.fasta.fai", "description": "cwl_input:ref.fasta.fai"}, {"url": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/716d46fe-623e-4854-ade8-33a421612c19/inputs/ref2.fasta", "path": "/var/lib/cwl/stg735e262b-1422-4186-9191-d29623b4d41d/ref2.fasta", "type": "FILE", "name": "fasta_path[1]", "description": "cwl_input:fasta_path[1]"}, {"url": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/716d46fe-623e-4854-ade8-33a421612c19/inputs/ref2.fasta.fai", "path": "/var/lib/cwl/stg735e262b-1422-4186-9191-d29623b4d41d/ref2.fasta.fai", "type": "FILE", "name": "ref2.fasta.fai", "description": "cwl_input:ref2.fasta.fai"}]}\'}, {\'name\': \'TESK_FTP_USERNAME\', \'value\': \'redacted_username\'}, {\'name\': \'TESK_FTP_PASSWORD\', \'value\': \'redacted_password\'}], \'imagePullPolicy\': \'Always\'}]}, \'metadata\': {\'name\': u\'task-9fe2f1e5-filer\'}}}, \'apiVersion\': \'batch/v1\', \'metadata\': {\'name\': u\'task-9fe2f1e5-inputs-filer\'}}\n08/25/2018 04:54:31 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:54:31 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:54:36 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:54:36 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:54:41 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:54:41 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:54:46 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:54:46 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:54:51 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:54:51 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:54:56 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:54:56 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:55:01 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:55:01 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:55:06 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:55:06 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:55:11 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:55:11 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:55:16 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:55:16 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:55:21 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:55:21 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:55:26 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:55:26 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:55:31 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:55:31 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:55:36 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:55:36 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:55:41 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:55:41 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:55:46 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:55:46 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:55:51 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:55:51 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:55:56 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:55:56 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:56:01 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:56:01 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:56:06 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:56:06 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:56:11 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:56:11 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:56:16 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:56:16 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:56:21 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:56:21 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:56:26 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:56:26 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:56:31 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:56:31 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:56:36 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:56:36 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:56:41 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:56:41 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:56:46 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:56:46 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:56:51 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:56:51 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:56:56 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:56:56 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:57:01 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:57:01 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:57:06 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:57:06 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:57:11 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:57:11 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:57:16 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:57:16 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:57:21 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:57:21 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:57:26 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:57:26 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:57:31 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:57:31 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:57:36 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:57:36 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:57:41 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:57:41 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:57:46 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:57:46 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:57:51 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:57:51 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:57:56 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:57:56 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:58:01 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:58:01 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:58:06 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:58:06 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:58:11 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:58:11 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:58:16 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:58:16 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:58:22 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:58:22 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:58:27 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:58:27 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:58:32 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:58:32 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:58:37 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:58:37 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:58:42 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:58:42 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:58:47 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:58:47 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:58:52 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:58:52 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:58:57 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:58:57 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:59:02 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:59:02 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:59:07 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:59:07 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:59:12 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:59:12 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:59:17 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:59:17 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:59:22 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:59:22 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:59:27 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:59:27 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:59:32 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:59:32 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:59:37 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:59:37 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:59:42 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:59:42 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:59:47 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:59:47 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:59:52 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:59:52 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 04:59:57 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 04:59:57 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 05:00:02 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 05:00:02 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 05:00:07 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 05:00:07 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 05:00:12 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 05:00:12 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 05:00:17 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 05:00:17 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 05:00:22 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 05:00:22 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 05:00:27 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 05:00:27 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 05:00:32 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 05:00:32 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 05:00:37 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 05:00:37 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 05:00:42 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 05:00:42 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 05:00:47 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 05:00:47 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 05:00:52 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 05:00:52 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 05:00:57 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 05:00:57 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 05:01:02 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 05:01:02 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 05:01:07 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 05:01:07 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 05:01:12 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 05:01:12 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 05:01:17 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 05:01:17 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 05:01:22 DEBUG: Got label: "879e3ede-a887-11e8-916e-fa163e364743"\n\n08/25/2018 05:01:22 DEBUG: Got label: "task-9fe2f1e5"\n08/25/2018 05:01:27 ERROR: Cancelling taskmaster: Got status Failed\n'])] [job docker-array-secondaryfiles.cwl] job error: Error collecting output for parameter 'bai_list': v1.0/docker-array-secondaryfiles.cwl:25:7: Did not find output file with glob pattern: '['fai.list']' Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpmypzskea v1.0/docker-array-secondaryfiles.cwl v1.0/docker-array-secondaryfiles-job.json Test secondaryFiles on array of files. Returned non-zero Test [101/132] Test directory literal output created by ExpressionTool Input object failed validation: [Errno 2] No such file or directory: 'ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/74236ac5-56d3-4772-a792-751c4bf9fd1c/inputs/hello.txt' Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpbmp25urn v1.0/dir7.cwl v1.0/dir7.yml Test directory literal output created by ExpressionTool Returned non-zero Test [102/132] Test file literal output created by ExpressionTool Test [103/132] Test dockerOutputDirectory [job docker-output-dir.cwl] job error: Error collecting output for parameter 'thing': v1.0/docker-output-dir.cwl:12:7: Did not find output file with glob pattern: '['thing']' Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpk1bcz7mr v1.0/docker-output-dir.cwl v1.0/empty.json Test dockerOutputDirectory Returned non-zero Test [104/132] Test hints with $import [job imported-hint.cwl] job error: Error collecting output for parameter 'out': test:1:1: Did not find output file with glob pattern: '['out']' Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpa9jp5pak v1.0/imported-hint.cwl v1.0/empty.json Test hints with $import Returned non-zero Test [105/132] Test warning instead of error when default path is not found v1.0/default_path.cwl:8:7: Field `path` contains undefined reference to `file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/default.txt` Expecting value: line 1 column 1 (char 0) Test [106/132] Test InlineJavascriptRequirement with multiple expressions in the same tool Test [107/132] Test if a writable input directory is recursively copied and writable a file:// based Directory slipped through: CommentedMap([('class', 'Directory'), ('location', 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir'), ('basename', 'testdir'), ('listing', [{'class': 'File', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/b', 'basename': 'b'}, {'class': 'Directory', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/c', 'basename': 'c', 'listing': [{'class': 'File', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/c/d', 'basename': 'd'}]}, {'class': 'File', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/a', 'basename': 'a'}])]) unprocessed File {'class': 'File', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/b', 'basename': 'b'} a file:// based Directory slipped through: {'class': 'Directory', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/c', 'basename': 'c', 'listing': [{'class': 'File', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/c/d', 'basename': 'd'}]} unprocessed File {'class': 'File', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/c/d', 'basename': 'd'} unprocessed File {'class': 'File', 'location': 'file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/testdir/a', 'basename': 'a'} Got workflow error Traceback (most recent call last): File "/home/mcrusoe/cwltool/cwltool/executors.py", line 238, in runner my_job.run(my_runtime_context) File "/home/mcrusoe/src/cwl-tes/cwl_tes/tes.py", line 358, in run task = self.create_task_msg() File "/home/mcrusoe/src/cwl-tes/cwl_tes/tes.py", line 265, in create_task_msg input_parameters = self.get_inputs() File "/home/mcrusoe/src/cwl-tes/cwl_tes/tes.py", line 246, in get_inputs self.parse_listing(self.generatefiles["listing"], inputs) File "/home/mcrusoe/src/cwl-tes/cwl_tes/tes.py", line 213, in parse_listing "The TES spec does not allow for writable inputs" cwltool.errors.UnsupportedRequirement: The TES spec does not allow for writable inputs Workflow or tool uses unsupported feature: The TES spec does not allow for writable inputs Test [108/132] Test that missing parameters are null (not undefined) in expression [job null-defined.cwl] job error: Error collecting output for parameter 'out': v1.0/null-defined.cwl:13:7: Expression evaluation error: v1.0/null-defined.cwl:13:7: Expecting value: line 1 column 1 (char 0) v1.0/null-defined.cwl:13:7: script was: v1.0/null-defined.cwl:13:7: 01 "use strict"; v1.0/null-defined.cwl:13:7: 02 var inputs = { v1.0/null-defined.cwl:13:7: 03 "file1": null v1.0/null-defined.cwl:13:7: 04 }; v1.0/null-defined.cwl:13:7: 05 var self = []; v1.0/null-defined.cwl:13:7: 06 var runtime = { v1.0/null-defined.cwl:13:7: 07 "cores": 1, v1.0/null-defined.cwl:13:7: 08 "ram": 1024, v1.0/null-defined.cwl:13:7: 09 "tmpdirSize": 1024, v1.0/null-defined.cwl:13:7: 10 "outdirSize": 1024, v1.0/null-defined.cwl:13:7: 11 "tmpdir": "/tmp/tmpmrqot46p", v1.0/null-defined.cwl:13:7: 12 "outdir": "/tmp/tmpyrzuhez_" v1.0/null-defined.cwl:13:7: 13 }; v1.0/null-defined.cwl:13:7: 14 (function(){return ((self[0].contents));})() v1.0/null-defined.cwl:13:7: stdout was: '' v1.0/null-defined.cwl:13:7: stderr was: 'evalmachine.:14 v1.0/null-defined.cwl:13:7: (function(){return ((self[0].contents));})() v1.0/null-defined.cwl:13:7: ^ v1.0/null-defined.cwl:13:7: v1.0/null-defined.cwl:13:7: TypeError: Cannot read property 'contents' of undefined v1.0/null-defined.cwl:13:7: at evalmachine.:14:30 v1.0/null-defined.cwl:13:7: at evalmachine.:14:43 v1.0/null-defined.cwl:13:7: at ContextifyScript.Script.runInContext (vm.js:59:29) v1.0/null-defined.cwl:13:7: at ContextifyScript.Script.runInNewContext (vm.js:65:15) v1.0/null-defined.cwl:13:7: at Object.runInNewContext (vm.js:135:38) v1.0/null-defined.cwl:13:7: at Socket. ([eval]:11:57) v1.0/null-defined.cwl:13:7: at emitOne (events.js:116:13) v1.0/null-defined.cwl:13:7: at Socket.emit (events.js:211:7) v1.0/null-defined.cwl:13:7: at addChunk (_stream_readable.js:263:12) v1.0/null-defined.cwl:13:7: at readableAddChunk (_stream_readable.js:246:13)' Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpujiztmam v1.0/null-defined.cwl v1.0/empty.json Test that missing parameters are null (not undefined) in expression Returned non-zero Test [109/132] Test that provided parameter is not null in expression [job null-defined.cwl] job error: Error collecting output for parameter 'out': v1.0/null-defined.cwl:13:7: Expression evaluation error: v1.0/null-defined.cwl:13:7: Expecting value: line 1 column 1 (char 0) v1.0/null-defined.cwl:13:7: script was: v1.0/null-defined.cwl:13:7: 01 "use strict"; v1.0/null-defined.cwl:13:7: 02 var inputs = { v1.0/null-defined.cwl:13:7: 03 "file1": { v1.0/null-defined.cwl:13:7: 04 "class": "File", v1.0/null-defined.cwl:13:7: 05 "location": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/a02b712b-9433-4f4a-89c8-478ac003536a/inputs/hello.txt", v1.0/null-defined.cwl:13:7: 06 "size": 13, v1.0/null-defined.cwl:13:7: 07 "basename": "hello.txt", v1.0/null-defined.cwl:13:7: 08 "nameroot": "hello", v1.0/null-defined.cwl:13:7: 09 "nameext": ".txt", v1.0/null-defined.cwl:13:7: 10 "path": "/tmp/tmp3iiuc3p0/stg1ca0f704-9f14-43dd-b2f3-0b4eb490e482/hello.txt", v1.0/null-defined.cwl:13:7: 11 "dirname": "/tmp/tmp3iiuc3p0/stg1ca0f704-9f14-43dd-b2f3-0b4eb490e482" v1.0/null-defined.cwl:13:7: 12 } v1.0/null-defined.cwl:13:7: 13 }; v1.0/null-defined.cwl:13:7: 14 var self = []; v1.0/null-defined.cwl:13:7: 15 var runtime = { v1.0/null-defined.cwl:13:7: 16 "cores": 1, v1.0/null-defined.cwl:13:7: 17 "ram": 1024, v1.0/null-defined.cwl:13:7: 18 "tmpdirSize": 1024, v1.0/null-defined.cwl:13:7: 19 "outdirSize": 1024, v1.0/null-defined.cwl:13:7: 20 "tmpdir": "/tmp/tmpzw0xmoxr", v1.0/null-defined.cwl:13:7: 21 "outdir": "/tmp/tmpve5lurvs" v1.0/null-defined.cwl:13:7: 22 }; v1.0/null-defined.cwl:13:7: 23 (function(){return ((self[0].contents));})() v1.0/null-defined.cwl:13:7: stdout was: '' v1.0/null-defined.cwl:13:7: stderr was: 'evalmachine.:23 v1.0/null-defined.cwl:13:7: (function(){return ((self[0].contents));})() v1.0/null-defined.cwl:13:7: ^ v1.0/null-defined.cwl:13:7: v1.0/null-defined.cwl:13:7: TypeError: Cannot read property 'contents' of undefined v1.0/null-defined.cwl:13:7: at evalmachine.:23:30 v1.0/null-defined.cwl:13:7: at evalmachine.:23:43 v1.0/null-defined.cwl:13:7: at ContextifyScript.Script.runInContext (vm.js:59:29) v1.0/null-defined.cwl:13:7: at ContextifyScript.Script.runInNewContext (vm.js:65:15) v1.0/null-defined.cwl:13:7: at Object.runInNewContext (vm.js:135:38) v1.0/null-defined.cwl:13:7: at Socket. ([eval]:11:57) v1.0/null-defined.cwl:13:7: at emitOne (events.js:116:13) v1.0/null-defined.cwl:13:7: at Socket.emit (events.js:211:7) v1.0/null-defined.cwl:13:7: at addChunk (_stream_readable.js:263:12) v1.0/null-defined.cwl:13:7: at readableAddChunk (_stream_readable.js:246:13)' Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpu52j_uay v1.0/null-defined.cwl v1.0/cat-job.json Test that provided parameter is not null in expression Returned non-zero Test [110/132] Test compound workflow document [job rev] job error: Error collecting output for parameter 'output': v1.0/revsort-packed.cwl:82:25: Did not find output file with glob pattern: '['output.txt']' [step rev] Output is missing expected field file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/revsort-packed.cwl#main/rev/output [step rev] completed permanentFail Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpit4u732j 'v1.0/revsort-packed.cwl#main' v1.0/revsort-job.json Test compound workflow document Returned non-zero Test [111/132] Test that nameroot and nameext are generated from basename at execution time by the runner Workflow checker warning: v1.0/basename-fields-test.cwl:22:7: 'tool' is not an input parameter of file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/echo-file-tool.cwl, expected in v1.0/basename-fields-test.cwl:29:7: 'tool' is not an input parameter of file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/echo-file-tool.cwl, expected in [job ext] job error: Error collecting output for parameter 'out': test:1:1: Did not find output file with glob pattern: '['aba27f9cbc36ea202101e1fe244defb8ec8a81c4']' [step ext] Output is missing expected field file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/basename-fields-test.cwl#ext/out [step ext] completed permanentFail [job root] job error: Error collecting output for parameter 'out': test:1:1: Did not find output file with glob pattern: '['aba27f9cbc36ea202101e1fe244defb8ec8a81c4']' [step root] Output is missing expected field file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/basename-fields-test.cwl#root/out [step root] completed permanentFail Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmp8bqx40cg v1.0/basename-fields-test.cwl v1.0/basename-fields-job.yml Test that nameroot and nameext are generated from basename at execution time by the runner Returned non-zero Test [112/132] Test that file path in $(inputs) for initialworkdir is in $(outdir). Got workflow error Traceback (most recent call last): File "/home/mcrusoe/cwltool/cwltool/executors.py", line 238, in runner my_job.run(my_runtime_context) File "/home/mcrusoe/src/cwl-tes/cwl_tes/tes.py", line 358, in run task = self.create_task_msg() File "/home/mcrusoe/src/cwl-tes/cwl_tes/tes.py", line 265, in create_task_msg input_parameters = self.get_inputs() File "/home/mcrusoe/src/cwl-tes/cwl_tes/tes.py", line 246, in get_inputs self.parse_listing(self.generatefiles["listing"], inputs) File "/home/mcrusoe/src/cwl-tes/cwl_tes/tes.py", line 213, in parse_listing "The TES spec does not allow for writable inputs" cwltool.errors.UnsupportedRequirement: The TES spec does not allow for writable inputs Workflow or tool uses unsupported feature: The TES spec does not allow for writable inputs Test [113/132] Test single step workflow with Scatter step and two data links connected to same input, flattened merge behavior. Workflow inputs are set as list FTP upload, file whale.txt already exists FTP upload, file hello.txt already exists [job step1] job error: Error collecting output for parameter 'output': v1.0/wc3-tool.cwl:18:9: Expression evaluation error: v1.0/wc3-tool.cwl:18:9: Expecting value: line 1 column 1 (char 0) v1.0/wc3-tool.cwl:18:9: script was: v1.0/wc3-tool.cwl:18:9: 01 "use strict"; v1.0/wc3-tool.cwl:18:9: 02 var inputs = { v1.0/wc3-tool.cwl:18:9: 03 "file1": [ v1.0/wc3-tool.cwl:18:9: 04 { v1.0/wc3-tool.cwl:18:9: 05 "class": "File", v1.0/wc3-tool.cwl:18:9: 06 "location": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/fda2fe22-93a4-440e-aae3-fac3bc318d9b/inputs/whale.txt", v1.0/wc3-tool.cwl:18:9: 07 "size": 1111, v1.0/wc3-tool.cwl:18:9: 08 "basename": "whale.txt", v1.0/wc3-tool.cwl:18:9: 09 "nameroot": "whale", v1.0/wc3-tool.cwl:18:9: 10 "nameext": ".txt", v1.0/wc3-tool.cwl:18:9: 11 "path": "/tmp/tmpg57s35fo/stg9cc0f3b9-aff4-4148-87ce-f45ee780a4d7/whale.txt", v1.0/wc3-tool.cwl:18:9: 12 "dirname": "/tmp/tmpg57s35fo/stg9cc0f3b9-aff4-4148-87ce-f45ee780a4d7" v1.0/wc3-tool.cwl:18:9: 13 }, v1.0/wc3-tool.cwl:18:9: 14 { v1.0/wc3-tool.cwl:18:9: 15 "class": "File", v1.0/wc3-tool.cwl:18:9: 16 "location": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/fda2fe22-93a4-440e-aae3-fac3bc318d9b/inputs/whale.txt", v1.0/wc3-tool.cwl:18:9: 17 "size": 1111, v1.0/wc3-tool.cwl:18:9: 18 "basename": "whale.txt", v1.0/wc3-tool.cwl:18:9: 19 "nameroot": "whale", v1.0/wc3-tool.cwl:18:9: 20 "nameext": ".txt", v1.0/wc3-tool.cwl:18:9: 21 "path": "/tmp/tmpg57s35fo/stg9cc0f3b9-aff4-4148-87ce-f45ee780a4d7/whale.txt", v1.0/wc3-tool.cwl:18:9: 22 "dirname": "/tmp/tmpg57s35fo/stg9cc0f3b9-aff4-4148-87ce-f45ee780a4d7" v1.0/wc3-tool.cwl:18:9: 23 }, v1.0/wc3-tool.cwl:18:9: 24 { v1.0/wc3-tool.cwl:18:9: 25 "class": "File", v1.0/wc3-tool.cwl:18:9: 26 "location": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/fda2fe22-93a4-440e-aae3-fac3bc318d9b/inputs/hello.txt", v1.0/wc3-tool.cwl:18:9: 27 "size": 13, v1.0/wc3-tool.cwl:18:9: 28 "basename": "hello.txt", v1.0/wc3-tool.cwl:18:9: 29 "nameroot": "hello", v1.0/wc3-tool.cwl:18:9: 30 "nameext": ".txt", v1.0/wc3-tool.cwl:18:9: 31 "path": "/tmp/tmpg57s35fo/stg06dc60b0-91ac-4b22-a6d7-a266fd4703ff/hello.txt", v1.0/wc3-tool.cwl:18:9: 32 "dirname": "/tmp/tmpg57s35fo/stg06dc60b0-91ac-4b22-a6d7-a266fd4703ff" v1.0/wc3-tool.cwl:18:9: 33 }, v1.0/wc3-tool.cwl:18:9: 34 { v1.0/wc3-tool.cwl:18:9: 35 "class": "File", v1.0/wc3-tool.cwl:18:9: 36 "location": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/fda2fe22-93a4-440e-aae3-fac3bc318d9b/inputs/hello.txt", v1.0/wc3-tool.cwl:18:9: 37 "size": 13, v1.0/wc3-tool.cwl:18:9: 38 "basename": "hello.txt", v1.0/wc3-tool.cwl:18:9: 39 "nameroot": "hello", v1.0/wc3-tool.cwl:18:9: 40 "nameext": ".txt", v1.0/wc3-tool.cwl:18:9: 41 "path": "/tmp/tmpg57s35fo/stg06dc60b0-91ac-4b22-a6d7-a266fd4703ff/hello.txt", v1.0/wc3-tool.cwl:18:9: 42 "dirname": "/tmp/tmpg57s35fo/stg06dc60b0-91ac-4b22-a6d7-a266fd4703ff" v1.0/wc3-tool.cwl:18:9: 43 } v1.0/wc3-tool.cwl:18:9: 44 ] v1.0/wc3-tool.cwl:18:9: 45 }; v1.0/wc3-tool.cwl:18:9: 46 var self = []; v1.0/wc3-tool.cwl:18:9: 47 var runtime = { v1.0/wc3-tool.cwl:18:9: 48 "cores": 1, v1.0/wc3-tool.cwl:18:9: 49 "ram": 1024, v1.0/wc3-tool.cwl:18:9: 50 "tmpdirSize": 1024, v1.0/wc3-tool.cwl:18:9: 51 "outdirSize": 1024, v1.0/wc3-tool.cwl:18:9: 52 "tmpdir": "/tmp/tmp_dzltknl", v1.0/wc3-tool.cwl:18:9: 53 "outdir": "/tmp/tmprzjf58g5" v1.0/wc3-tool.cwl:18:9: 54 }; v1.0/wc3-tool.cwl:18:9: 55 (function(){ v1.0/wc3-tool.cwl:18:9: 56 var s = self[0].contents.split(/\r?\n/); v1.0/wc3-tool.cwl:18:9: 57 return parseInt(s[s.length-2]); v1.0/wc3-tool.cwl:18:9: 58 })() v1.0/wc3-tool.cwl:18:9: stdout was: '' v1.0/wc3-tool.cwl:18:9: stderr was: 'evalmachine.:56 v1.0/wc3-tool.cwl:18:9: var s = self[0].contents.split(/\r?\n/); v1.0/wc3-tool.cwl:18:9: ^ v1.0/wc3-tool.cwl:18:9: v1.0/wc3-tool.cwl:18:9: TypeError: Cannot read property 'contents' of undefined v1.0/wc3-tool.cwl:18:9: at evalmachine.:56:19 v1.0/wc3-tool.cwl:18:9: at evalmachine.:58:3 v1.0/wc3-tool.cwl:18:9: at ContextifyScript.Script.runInContext (vm.js:59:29) v1.0/wc3-tool.cwl:18:9: at ContextifyScript.Script.runInNewContext (vm.js:65:15) v1.0/wc3-tool.cwl:18:9: at Object.runInNewContext (vm.js:135:38) v1.0/wc3-tool.cwl:18:9: at Socket. ([eval]:11:57) v1.0/wc3-tool.cwl:18:9: at emitOne (events.js:116:13) v1.0/wc3-tool.cwl:18:9: at Socket.emit (events.js:211:7) v1.0/wc3-tool.cwl:18:9: at addChunk (_stream_readable.js:263:12) v1.0/wc3-tool.cwl:18:9: at readableAddChunk (_stream_readable.js:246:13)' [step step1] Output is missing expected field file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/count-lines12-wf.cwl#step1/output [step step1] completed permanentFail Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmp3iymjfnz v1.0/count-lines12-wf.cwl v1.0/count-lines6-job.json Test single step workflow with Scatter step and two data links connected to same input, flattened merge behavior. Workflow inputs are set as list Returned non-zero Test [114/132] Test step input with multiple sources with multiple types Test [115/132] Test that shell directives are not interpreted. [job shellchar.cwl] job error: Error collecting output for parameter 'stderr_file': test:1:1: Did not find output file with glob pattern: '['610915d8ae4d6257bbde18ced59a50ca748db5bf']' Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpmne1gpmu v1.0/shellchar.cwl v1.0/empty.json Test that shell directives are not interpreted. Returned non-zero Test [116/132] Test that shell directives are quoted. [job shellchar2.cwl] job error: Error collecting output for parameter 'stderr_file': test:1:1: Did not find output file with glob pattern: '['cbfb8289c9bf6320a60cc06b82b100d5b44cc78e']' Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmp1yare8n5 v1.0/shellchar2.cwl v1.0/empty.json Test that shell directives are quoted. Returned non-zero Test [117/132] Test empty writable dir with InitialWorkDirRequirement Got workflow error Traceback (most recent call last): File "/home/mcrusoe/cwltool/cwltool/executors.py", line 238, in runner my_job.run(my_runtime_context) File "/home/mcrusoe/src/cwl-tes/cwl_tes/tes.py", line 358, in run task = self.create_task_msg() File "/home/mcrusoe/src/cwl-tes/cwl_tes/tes.py", line 265, in create_task_msg input_parameters = self.get_inputs() File "/home/mcrusoe/src/cwl-tes/cwl_tes/tes.py", line 246, in get_inputs self.parse_listing(self.generatefiles["listing"], inputs) File "/home/mcrusoe/src/cwl-tes/cwl_tes/tes.py", line 213, in parse_listing "The TES spec does not allow for writable inputs" cwltool.errors.UnsupportedRequirement: The TES spec does not allow for writable inputs Workflow or tool uses unsupported feature: The TES spec does not allow for writable inputs Test [118/132] Test empty writable dir with InitialWorkDirRequirement inside Docker Got workflow error Traceback (most recent call last): File "/home/mcrusoe/cwltool/cwltool/executors.py", line 238, in runner my_job.run(my_runtime_context) File "/home/mcrusoe/src/cwl-tes/cwl_tes/tes.py", line 358, in run task = self.create_task_msg() File "/home/mcrusoe/src/cwl-tes/cwl_tes/tes.py", line 265, in create_task_msg input_parameters = self.get_inputs() File "/home/mcrusoe/src/cwl-tes/cwl_tes/tes.py", line 246, in get_inputs self.parse_listing(self.generatefiles["listing"], inputs) File "/home/mcrusoe/src/cwl-tes/cwl_tes/tes.py", line 213, in parse_listing "The TES spec does not allow for writable inputs" cwltool.errors.UnsupportedRequirement: The TES spec does not allow for writable inputs Workflow or tool uses unsupported feature: The TES spec does not allow for writable inputs Test [119/132] Test dynamic resource reqs referencing inputs Got workflow error Traceback (most recent call last): File "/home/mcrusoe/cwltool/cwltool/executors.py", line 238, in runner my_job.run(my_runtime_context) File "/home/mcrusoe/src/cwl-tes/cwl_tes/tes.py", line 358, in run task = self.create_task_msg() File "/home/mcrusoe/src/cwl-tes/cwl_tes/tes.py", line 308, in create_task_msg "cwl-tes does not yet support dynamic resource " cwltool.errors.UnsupportedRequirement: cwl-tes does not yet support dynamic resource requests Workflow or tool uses unsupported feature: cwl-tes does not yet support dynamic resource requests Test [120/132] Test file literal as input without Docker [job cat3-nodocker.cwl] job error: Error collecting output for parameter 'output_file': v1.0/cat3-nodocker.cwl:14:21: Did not find output file with glob pattern: '['output.txt']' Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpsafr2v89 v1.0/cat3-nodocker.cwl v1.0/file-literal.yml Test file literal as input without Docker Returned non-zero Test [121/132] Test that OutputBinding.glob is sorted as specified by POSIX Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpfe17usf4 v1.0/glob_test.cwl v1.0/empty.json Test that OutputBinding.glob is sorted as specified by POSIX Compare failure expected: { "letters": [ { "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", "class": "File", "location": "a", "size": 0 }, { "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", "class": "File", "location": "b", "size": 0 }, { "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", "class": "File", "location": "c", "size": 0 }, { "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", "class": "File", "location": "w", "size": 0 }, { "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", "class": "File", "location": "x", "size": 0 }, { "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", "class": "File", "location": "y", "size": 0 }, { "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", "class": "File", "location": "z", "size": 0 } ] } got: { "letters": [] } caused by: failed comparison for key 'letters': expected: [ { "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", "class": "File", "location": "a", "size": 0 }, { "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", "class": "File", "location": "b", "size": 0 }, { "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", "class": "File", "location": "c", "size": 0 }, { "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", "class": "File", "location": "w", "size": 0 }, { "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", "class": "File", "location": "x", "size": 0 }, { "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", "class": "File", "location": "y", "size": 0 }, { "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", "class": "File", "location": "z", "size": 0 } ] got: [] caused by: lengths don't match Test [122/132] Test InitialWorkDirRequirement with a nested directory structure from another step [job first] job error: Error collecting output for parameter 'deep_dir': v1.0/iwdr_with_nested_dirs.cwl:20:28: Did not find output file with glob pattern: '['deeply']' [step first] Output is missing expected field file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/iwdr_with_nested_dirs.cwl#first/deep_dir [step first] completed permanentFail Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmp4ry_kuju v1.0/iwdr_with_nested_dirs.cwl v1.0/empty.json Test InitialWorkDirRequirement with a nested directory structure from another step Returned non-zero Test [123/132] Test that boolean flags do not appear on command line if inputBinding is empty and not null Test [124/132] Test that expression engine does not fail to evaluate reference to self with unprovided input Test [125/132] Test successCodes [job exit-success.cwl] task id: task-05c548b2 [job exit-success.cwl] logs: [TaskLog(start_time=datetime.datetime(2018, 8, 25, 17, 23, 22, tzinfo=tzutc()), end_time=datetime.datetime(2018, 8, 25, 17, 29, 47, tzinfo=tzutc()), metadata={'USER_ID': 'anonymousUser'}, logs=[ExecutorLog(start_time=datetime.datetime(2018, 8, 25, 17, 23, 40, tzinfo=tzutc()), end_time=None, stdout=None, stderr=None, exit_code=1)], outputs=None, system_logs=['08/25/2018 05:23:25 DEBUG: Starting taskmaster\n08/25/2018 05:23:25 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:23:25 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:23:25 DEBUG: appending task-volume at path /var/spool/cwl with subPath: dir0\n08/25/2018 05:23:25 DEBUG: [{\'mountPath\': u\'/var/spool/cwl\', \'subPath\': \'dir0\', \'name\': \'task-volume\'}]\n08/25/2018 05:23:25 DEBUG: \n08/25/2018 05:23:25 DEBUG: {\'kind\': \'Job\', \'spec\': {\'template\': {\'spec\': {\'restartPolicy\': \'Never\', \'volumes\': [{\'name\': \'task-volume\', \'persistentVolumeClaim\': {\'claimName\': u\'task-05c548b2-pvc\'}}], \'containers\': [{\'name\': \'filer\', \'image\': \'eu.gcr.io/tes-wes/filer:v0.4\', \'args\': [\'inputs\', \'$(JSON_INPUT)\', \'-d\'], \'volumeMounts\': [{\'mountPath\': u\'/var/spool/cwl\', \'subPath\': \'dir0\', \'name\': \'task-volume\'}], \'env\': [{\'name\': \'JSON_INPUT\', \'value\': \'{"outputs": [{"url": "ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004/ba3a6041-607d-4d55-8b9c-784f7fe3b737/", "path": "/var/spool/cwl", "type": "DIRECTORY", "name": "workdir"}], "executors": [{"kind": "Job", "spec": {"template": {"spec": {"restartPolicy": "Never", "containers": [{"name": "task-05c548b2-ex-00", "image": "python:2.7", "workingDir": "/var/spool/cwl", "command": ["false"], "env": [{"name": "HOME", "value": "/tmp/tmpk6fvqpmy"}, {"name": "TMPDIR", "value": "/tmp/tmp_rlzzyxn"}], "resources": {}}]}, "metadata": {"name": "task-05c548b2-ex-00"}}}, "apiVersion": "batch/v1", "metadata": {"labels": {"taskmaster-name": "task-05c548b2", "executor-no": "0", "job-type": "executor", "creator-user-id": "anonymousUser"}, "annotations": {"tes-task-name": "exit-success.cwl"}, "name": "task-05c548b2-ex-00"}}], "resources": {"disk_gb": 0.1}, "volumes": [], "inputs": []}\'}, {\'name\': \'TESK_FTP_USERNAME\', \'value\': \'redacted_username\'}, {\'name\': \'TESK_FTP_PASSWORD\', \'value\': \'redacted_password\'}], \'imagePullPolicy\': \'Always\'}]}, \'metadata\': {\'name\': u\'task-05c548b2-filer\'}}}, \'apiVersion\': \'batch/v1\', \'metadata\': {\'name\': u\'task-05c548b2-inputs-filer\'}}\n08/25/2018 05:23:25 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:23:25 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:23:30 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:23:30 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:23:35 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:23:35 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:23:40 DEBUG: Created job: task-05c548b2-ex-00\n08/25/2018 05:23:40 DEBUG: Job spec: {u\'kind\': u\'Job\', u\'spec\': {u\'template\': {u\'spec\': {u\'restartPolicy\': u\'Never\', \'volumes\': [{\'name\': \'task-volume\', \'persistentVolumeClaim\': {\'readonly\': False, \'claimName\': u\'task-05c548b2-pvc\'}}], u\'containers\': [{u\'name\': u\'task-05c548b2-ex-00\', \'volumeMounts\': [{\'mountPath\': u\'/var/spool/cwl\', \'subPath\': \'dir0\', \'name\': \'task-volume\'}], u\'image\': u\'python:2.7\', u\'workingDir\': u\'/var/spool/cwl\', u\'command\': [u\'false\'], u\'env\': [{u\'name\': u\'HOME\', u\'value\': u\'/tmp/tmpk6fvqpmy\'}, {u\'name\': u\'TMPDIR\', u\'value\': u\'/tmp/tmp_rlzzyxn\'}], u\'resources\': {}}]}, u\'metadata\': {u\'name\': u\'task-05c548b2-ex-00\'}}}, u\'apiVersion\': u\'batch/v1\', u\'metadata\': {u\'labels\': {u\'taskmaster-name\': u\'task-05c548b2\', u\'executor-no\': u\'0\', u\'job-type\': u\'executor\', u\'creator-user-id\': u\'anonymousUser\'}, u\'annotations\': {u\'tes-task-name\': u\'exit-success.cwl\'}, u\'name\': u\'task-05c548b2-ex-00\'}}\n08/25/2018 05:23:40 DEBUG: {u\'kind\': u\'Job\', u\'spec\': {u\'template\': {u\'spec\': {u\'restartPolicy\': u\'Never\', \'volumes\': [{\'name\': \'task-volume\', \'persistentVolumeClaim\': {\'readonly\': False, \'claimName\': u\'task-05c548b2-pvc\'}}], u\'containers\': [{u\'name\': u\'task-05c548b2-ex-00\', \'volumeMounts\': [{\'mountPath\': u\'/var/spool/cwl\', \'subPath\': \'dir0\', \'name\': \'task-volume\'}], u\'image\': u\'python:2.7\', u\'workingDir\': u\'/var/spool/cwl\', u\'command\': [u\'false\'], u\'env\': [{u\'name\': u\'HOME\', u\'value\': u\'/tmp/tmpk6fvqpmy\'}, {u\'name\': u\'TMPDIR\', u\'value\': u\'/tmp/tmp_rlzzyxn\'}], u\'resources\': {}}]}, u\'metadata\': {u\'name\': u\'task-05c548b2-ex-00\'}}}, u\'apiVersion\': u\'batch/v1\', u\'metadata\': {u\'labels\': {u\'taskmaster-name\': u\'task-05c548b2\', u\'executor-no\': u\'0\', u\'job-type\': u\'executor\', u\'creator-user-id\': u\'anonymousUser\'}, u\'annotations\': {u\'tes-task-name\': u\'exit-success.cwl\'}, u\'name\': u\'task-05c548b2-ex-00\'}}\n08/25/2018 05:23:40 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:23:40 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:23:45 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:23:45 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:23:50 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:23:50 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:23:55 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:23:55 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:24:00 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:24:00 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:24:05 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:24:05 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:24:10 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:24:10 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:24:15 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:24:15 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:24:20 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:24:20 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:24:25 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:24:25 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:24:30 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:24:30 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:24:35 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:24:35 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:24:40 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:24:40 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:24:45 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:24:45 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:24:50 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:24:50 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:24:55 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:24:55 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:25:00 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:25:00 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:25:06 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:25:06 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:25:11 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:25:11 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:25:16 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:25:16 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:25:21 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:25:21 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:25:26 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:25:26 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:25:31 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:25:31 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:25:36 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:25:36 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:25:41 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:25:41 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:25:46 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:25:46 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:25:51 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:25:51 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:25:56 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:25:56 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:26:01 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:26:01 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:26:06 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:26:06 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:26:11 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:26:11 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:26:16 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:26:16 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:26:21 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:26:21 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:26:26 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:26:26 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:26:31 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:26:31 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:26:36 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:26:36 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:26:41 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:26:41 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:26:46 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:26:46 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:26:51 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:26:51 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:26:56 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:26:56 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:27:01 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:27:01 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:27:06 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:27:06 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:27:11 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:27:11 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:27:16 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:27:16 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:27:21 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:27:21 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:27:26 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:27:26 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:27:31 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:27:31 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:27:36 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:27:36 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:27:41 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:27:41 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:27:46 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:27:46 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:27:51 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:27:51 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:27:56 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:27:56 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:28:01 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:28:01 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:28:06 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:28:06 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:28:11 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:28:11 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:28:16 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:28:16 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:28:21 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:28:21 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:28:26 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:28:26 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:28:31 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:28:31 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:28:36 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:28:36 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:28:41 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:28:41 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:28:46 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:28:46 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:28:51 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:28:51 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:28:56 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:28:56 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:29:01 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:29:01 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:29:06 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:29:06 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:29:11 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:29:11 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:29:16 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:29:16 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:29:21 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:29:21 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:29:26 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:29:26 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:29:31 DEBUG: Got label: "9140739f-a88b-11e8-916e-fa163e364743"\n\n08/25/2018 05:29:31 DEBUG: Got label: "task-05c548b2"\n08/25/2018 05:29:36 ERROR: Cancelling taskmaster: Got status Failed\n'])] Expecting value: line 1 column 1 (char 0) Test [126/132] Test simple workflow with a dynamic resource requirement Got workflow error Traceback (most recent call last): File "/home/mcrusoe/cwltool/cwltool/executors.py", line 238, in runner my_job.run(my_runtime_context) File "/home/mcrusoe/src/cwl-tes/cwl_tes/tes.py", line 358, in run task = self.create_task_msg() File "/home/mcrusoe/src/cwl-tes/cwl_tes/tes.py", line 308, in create_task_msg "cwl-tes does not yet support dynamic resource " cwltool.errors.UnsupportedRequirement: cwl-tes does not yet support dynamic resource requests Workflow or tool uses unsupported feature: cwl-tes does not yet support dynamic resource requests Test [127/132] Test that empty array input does not add anything to command line Test [128/132] Test that ResourceRequirement on a step level redefines requirement on the workflow level Got workflow error Traceback (most recent call last): File "/home/mcrusoe/cwltool/cwltool/executors.py", line 238, in runner my_job.run(my_runtime_context) File "/home/mcrusoe/src/cwl-tes/cwl_tes/tes.py", line 358, in run task = self.create_task_msg() File "/home/mcrusoe/src/cwl-tes/cwl_tes/tes.py", line 308, in create_task_msg "cwl-tes does not yet support dynamic resource " cwltool.errors.UnsupportedRequirement: cwl-tes does not yet support dynamic resource requests Workflow or tool uses unsupported feature: cwl-tes does not yet support dynamic resource requests Test [129/132] Test valueFrom with constant value overriding provided array inputs Test [130/132] Test dynamic resource reqs referencing the size of Files inside a Directory Got workflow error Traceback (most recent call last): File "/home/mcrusoe/cwltool/cwltool/executors.py", line 238, in runner my_job.run(my_runtime_context) File "/home/mcrusoe/src/cwl-tes/cwl_tes/tes.py", line 358, in run task = self.create_task_msg() File "/home/mcrusoe/src/cwl-tes/cwl_tes/tes.py", line 308, in create_task_msg "cwl-tes does not yet support dynamic resource " cwltool.errors.UnsupportedRequirement: cwl-tes does not yet support dynamic resource requests Workflow or tool uses unsupported feature: cwl-tes does not yet support dynamic resource requests Test [131/132] Test that it is not an error to connect a parameter to a workflow step, even if the parameter doesn't appear in the `run` process inputs. Workflow checker warning: v1.0/pass-unconnected.cwl:18:7: 'in2' is not an input parameter of file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/echo-tool.cwl, expected in [job step1] job error: Error collecting output for parameter 'out': v1.0/echo-tool.cwl:15:7: Expression evaluation error: v1.0/echo-tool.cwl:15:7: Syntax error in parameter reference 'self[0].contents': self list index 0 out of range. This could be due to using Javascript code without specifying InlineJavascriptRequirement. [step step1] Output is missing expected field file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/pass-unconnected.cwl#step1/out [step step1] completed permanentFail Final process status is permanentFail Test failed: cwl-tes --tes=https://tes-dev.tsi.ebi.ac.uk --quiet --remote-storage-url ftp://ftp-private.ebi.ac.uk/upload/cwl_conf004 --outdir=/tmp/tmpf7ocafbw v1.0/pass-unconnected.cwl v1.0/empty.json Test that it is not an error to connect a parameter to a workflow step, even if the parameter doesn't appear in the `run` process inputs. Returned non-zero Test [132/132] Test that parameters that don't appear in the `run` process inputs are not present in the input object used to run the tool. Workflow checker warning: v1.0/fail-unconnected.cwl:18:7: 'in2' is not an input parameter of file:///home/mcrusoe/common-workflow-language/v1.0/v1.0/fail-unspecified-input.cwl, expected in Exception on step 'step1' [step step1] Cannot make job: v1.0/fail-unspecified-input.cwl:13:33: Expression evaluation error: v1.0/fail-unspecified-input.cwl:13:33: Syntax error in parameter reference 'inputs.in2': inputs does not contain key 'in2'. This could be due to using Javascript code without specifying InlineJavascriptRequirement. Final process status is permanentFail 32 tests passed, 87 failures, 13 unsupported features