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Cloud ObjectStore #4352
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538ef00
Also load yaml sample files. cc @jmchilton, is this ok?
hexylena 3e8919c
correct name to type
hexylena 5563ecc
fix import order
hexylena 00ee109
fix css class
hexylena 4c36b5a
not a useful test in this location
hexylena a2b0206
Remove unneeded messages.mako.
jmchilton 4146123
rebuild client
hexylena 6d7d4e9
Merge pull request #4305 from erasche/bug-report-actions
jmchilton fcd06a9
Merge pull request #4408 from erasche/grt-pardir
jmchilton e3de5e2
Merge pull request #4329 from glormph/collection_list_sort
jmchilton bcdf2c8
Merge pull request #4254 from ffinfo/vcf_gz_datatype
jmchilton 583765c
Merge branch 'dev' into revise_grid_forms
guerler be19b36
Merge branch 'revise_grid_forms' into admin_grid_roles
guerler b38ccbc
Merge branch 'admin_grid_roles' into admin_grid_groups
guerler ad2f39c
Fix lint
guerler 6a7cc34
Bring Galaxy, reports, and shed run scripts in sync.
jmchilton 72e5a00
Centralize launching server for reports and tool shed.
jmchilton 1bdb99b
Update galaxy.util.properties to allow YAML.
jmchilton 8189a1f
Scripts to manage configuration infrastructure.
jmchilton 7973a91
Add uwsgi_schema.yml.
jmchilton 90e899d
Update tool shed to use newer configuration schema.
jmchilton 102566d
Update Galaxy Reports to use newer configuration schema.
jmchilton 50d426e
Add reports documentation to ``doc/``.
jmchilton 4945f55
Makefile shortcuts for configuration script.
jmchilton ef46a60
Add required dependency on uwsgi.
jmchilton 8191fd4
Add pykwalify as dependency for the new config validation stuff.
jmchilton ffe295e
Fix Python 3 linting problem with test_config_manage.py.
jmchilton 1ce93cc
Pin version of uWSGI to freshly released 2.0.15 available on wheels.g…
jmchilton 539a62f
Fix ORM scripts for #3179.
jmchilton 98ca8ce
Update config overhaul branch for introduction of galaxy.web.stack pa…
jmchilton 23db89b
Merge remote-tracking branch 'jmchilton/dev' into install_workflow_an…
jmchilton 7dd3ddc
Require admin for new import_tools function in workflows API.
jmchilton 6353704
Merge pull request #4039 from VJalili/patch-11
jmchilton e49ba40
Generalize allow_library_path_paste to allow_path_paste.
jmchilton f97efa6
Remove unused dataset_info in parameters.grouping.
jmchilton 33acc1f
Merge branch 'admin_grid_groups' into admin_grid_toolversion
guerler ba3249a
Add missing chemical formats to datatypes_conf.xml.sample
nsoranzo 61d172f
Update pin for flake8-docstrings
nsoranzo a249dc0
Use container-based infrastructure (sudo: false) in TravisCI
nsoranzo ef2c32a
Fix lint
guerler 600b0aa
Merge pull request #4377 from guerler/revise_grid_forms
martenson 33c794d
Merge pull request #4385 from guerler/admin_grid_roles
jmchilton 10285b8
Tweak Excel format phrasing based on review from @nsoranzo.
jmchilton fbde34f
Add EDAM format for excel.xls datatype.
jmchilton cca00ea
Merge pull request #4404 from jmchilton/allow_path_paste
martenson c6e45e7
Merge pull request #4410 from jmchilton/excel97
bgruening 331851b
Merge pull request #3179 from jmchilton/web_config_overhaul_0
bgruening 7a1fbd3
Fix bug in upload HTML checker.
jmchilton 59aa118
Add configuration option to disable upload content checking.
jmchilton 53b0b25
Better error reporting in test/base/populators.py.
jmchilton bee6af1
Allow API tests to work with admin users (not just admin keys).
jmchilton fec1eab
Add ability to arbitrarily not decompress files on upload via API.
jmchilton fc861cd
Merge pull request #3064 from manabuishii/install_workflow_and_tools
jmchilton 06ca789
Configuration tests for the last few upload enhancements.
jmchilton 5f1b7d5
Show verison button in workflow editor and trigger on_change
mvdbeek 25e05b6
Do postchange action only when modifiying tool versions in the workfl…
mvdbeek 5afe490
Fix qunit test
mvdbeek 36ce911
Keep spacing consistent (thx @nsoranzo)
mvdbeek 526e98e
Reset outputs when changing tool versions in wf-editor
mvdbeek db2ea85
Now thing are mostly working -- input and output connections are corr…
mvdbeek ea1f4f8
Fix the occasional loading of the wrong workflow. Turns out that some…
mvdbeek bc95f5e
Now adding/removing datasets and multiple version switches work fine,…
mvdbeek 92fedc0
Fix logic for adding and removing outputs
mvdbeek 1c286b1
Remove extra newlines
mvdbeek 2e95026
Remove unused old_version variable
mvdbeek 31c423a
Fix typo and remove leftover comment (thanks @nsoranzo)
mvdbeek df91881
Remove unused workflow outputs
mvdbeek d0b06a3
Don't cast tool_version to string if tool_version is None-type
mvdbeek 73f4141
Add static JS
mvdbeek f849c7e
Merge pull request #4417 from jmchilton/upload_enhance
bgruening 6ad6fd9
Rebuild tool_version_cache on DetachedInstanceError
mvdbeek 8e192db
Merge pull request #4397 from jmchilton/api_test_enhancement
mvdbeek e594152
Merge pull request #4394 from jmchilton/subworkflow_loading_fix
mvdbeek 0f5ad34
Merge pull request #4413 from nsoranzo/release_17.01_really_add_datat…
mvdbeek 4faf496
Merge branch 'release_17.01' into release_17.05
nsoranzo 9cbabef
Merge branch 'release_17.05' into dev
nsoranzo 4dd5030
Update conda channel order to sync with Bioconda
nsoranzo 420e7a4
Remove _ensure_conda_context() function
nsoranzo cdbac05
Override channel list on the command line instead of modifying condarc
nsoranzo eccdc8c
Removed unreached message line
guerler fd5f42d
Merge branch 'dev' into admin_grid_groups
guerler 68555f5
some unicoding
hexylena 7f78ee7
Merge pull request #4420 from mvdbeek/fix_wrong_tool_version_cast
jmchilton 8721da8
Merge pull request #4426 from erasche/local-runner-unicode
jmchilton 44548f8
Merge pull request #4409 from nsoranzo/fix_conda_channel_order
jmchilton 07a3049
Merge branch 'release_17.05' into dev
nsoranzo aa7be28
Merge branch 'dev' into switch_versions_in_workflows
martenson 27be249
Merge pull request #4373 from mvdbeek/switch_versions_in_workflows
martenson 462b7de
Merge pull request #4427 from nsoranzo/merge_release_17.05
dannon e72948c
Merge branch 'dev' into admin_grid_groups
guerler b726c33
Merge branch 'admin_grid_groups' into admin_grid_toolversion
guerler a078ee0
Move form augmentation to form handler
guerler 5cebb08
Add support for the MEME psp format
gregvonkuster 4bddd61
Merge pull request #4405 from guerler/admin_grid_groups
martenson 9dfee37
Optionally allow to show or hide select all
guerler a1897bd
Hide select all for role and group selectors
guerler d6f6a78
Use 'Save' as default title for configuration forms
guerler 4688eef
Fix user id decoding, fix optional array handling
guerler 96cad03
Fix label for default quotas
guerler 09c4b10
Break connection in workflow editor if necessary
mvdbeek 246489a
Fix messages
guerler f9e8892
Catch user input error for auto created roles and groups
guerler bebc5ff
Move decode id to correct location
guerler f1e13ce
More messages to validate inputs
guerler 86cdaaf
Add validation messages if resource ids are not correct
guerler 522ca9e
Fix private role validation
guerler 2073151
Merge branch 'dev' into admin_grid_toolversion
guerler abe8117
Fix
guerler 8eb487e
Merge pull request #4431 from mvdbeek/break_connections
jmchilton 8063701
fix XML error
bgruening 338abee
Separate input augmentation helpers from form views, augment inputs f…
guerler b6f0600
Merge pull request #4387 from jmchilton/tool_unit_test_cleanup
bgruening 7af41d4
Simplify form wrapper calling
guerler c5a9149
Merge pull request #4432 from guerler/fix_role_association_check
dannon 7dae650
Change Psp to MemePsp and misc fixes per initial review
gregvonkuster 7ef9b4c
Remove spurious null check.
43ddd47
Add missing `var` declarations.
48b835c
Remove an unused variable.
8950d44
Move two variable definitions to combine them with their declarations.
57c6284
Run `make client`.
3026bf5
Remove strange import - no idea from where it originated
gregvonkuster 1b7f25e
Merge pull request #4421 from xiemaisi/fix-lgtm-alerts
dannon c72f43d
Avoid adding `(imported from API)` to workflows
chambm 9ef13a1
Remove `(imported from API)` suffix from test
chambm 03a3d34
Remove `(imported from API)` suffix from test
chambm 73d6bd0
Restore build model bypass
guerler 1fc4bb1
Merge branch 'dev' into improve_form_modules
guerler a0217cb
Attempt to customize build model
guerler fdcd469
Remove unfilterable columns from group and quota search grids
guerler 2c4cf68
Merge branch 'dev' into admin_grid_toolversion
martenson 0458334
Merge pull request #4411 from guerler/admin_grid_toolversion
martenson 25bd717
Remove print of non-existent attribute 'content'
chambm 5b64e6d
Decouple model building
guerler 2b94fa3
Fix MemePsp sniff entry
gregvonkuster 3c4e892
Hide initial tool version message
guerler 8b43348
Move workflow tool form model rebuilding to workflow forms
guerler 192c4b1
Properly update workflow tool module
guerler 6d87448
Add optional initial model caller
guerler 4098672
Remove form dom removal through workflow manager
guerler 0092600
Merge branch 'dev' into improve_form_modules
guerler d8925d7
Fix message style
guerler 1b69b9a
Merge pull request #4439 from chambm/patch-2
bgruening 008a1d8
Merge pull request #4434 from chambm/patch-1
bgruening 5799fbc
change file_ext to be inline with memexml and co
bgruening 9a5016f
Update CloudBridge to its current latest
VJalili 21b44bf
Fix all E201 and E202 style errors
nsoranzo a353b2e
Fix E127 errors introduced by previous commit
nsoranzo a8d7b2d
Fix more indentation errors
nsoranzo a85ee59
Merge pull request #4440 from nsoranzo/fix_E201_E202
jmchilton 03df496
Fix API tests broken in #4434
nsoranzo 56c1f25
Fix help text style
guerler b8f11df
Improve error message for unknown module types when encountered.
jmchilton 2131370
Print warning if any input connections are unused during workflow exe…
jmchilton 7bf7f39
Cleanup a couple things in #4396 caught by @nsoranzo.
jmchilton 35ab745
Merge pull request #4445 from nsoranzo/followup_on_4434
dannon cca1f9e
Merge pull request #4430 from gregvonkuster/psp_format
dannon df442ea
Fix E201 errors (spaces in parens) in new memepsp datatype
dannon 7ef099f
Merge pull request #4446 from dannon/memepsp_formatting
nsoranzo 5a91370
Fix title
guerler 7bab16e
Preserve advanced search visibility
guerler ee4c8e2
Fix filters
guerler 114997d
Prevent search tag duplication
guerler 0fa287f
Add autopep8 script to help rebasing branches after #4440.
jmchilton 1e1c549
added missing parameter to function ensure_installed
bernt-matthias a1b8a54
ensure_installed is now iterative instead of recursive
bernt-matthias 349c9c8
version with no repetition at all
bernt-matthias a765472
Set timeout for aquiring lock to 5min
bernt-matthias 748539a
Merge pull request #4450 from mvdbeek/fix_file_lock_error
dannon 685b9de
Merge remote-tracking branch 'origin/release_17.01' into release_17.05
mvdbeek 8c225ec
Merge branch 'release_17.05' into dev
nsoranzo 68e8abc
Merge pull request #4447 from jmchilton/autopep8
dannon 706741f
Merge pull request #4449 from guerler/fix_grid_search
martenson 2596012
Merge branch 'dev' into improve_form_modules
guerler 517f248
Overhaul of tool provided job metadata.
jmchilton 72e361b
Allow discovering datasets directly from galaxy.json...
jmchilton 6563e38
Allow discovering dataset collections in galaxy.json in a nested fash…
jmchilton 39d4411
Move determining tool provided metadata style to tool parser.
jmchilton a8bec7a
Allow override of provided metadata location.
jmchilton 1e1df67
Variety of fixes for #4437.
jmchilton 4e17c8e
Add Cloud configuration to object_store_conf.xml.sample
VJalili 2489499
possibility to don't uppercase env variables
xgaia cff9292
Uniform indentation of multiline if conditionals
nsoranzo d2d1f85
Fix import order and Python3 compatibility for lib/galaxy/util/pastes…
nsoranzo 784e6f5
Merge pull request #4396 from jmchilton/workflow_warnings
nsoranzo 4e75635
Use log.warning() instead of deprecated warn()
nsoranzo e32ad28
Remove container config log message from cleanup scripts logs
nsoranzo bd88524
Fix import order and Python3 compatibility
nsoranzo b459399
Merge pull request #4454 from xgaia/interactive_environment
hexylena 8d132b2
More detailed sentry reports
hexylena dd89a9c
Merge pull request #4437 from jmchilton/galaxy_json_rev
mvdbeek e987b9b
swap id to username
hexylena 30562c0
don't uppercase envoverride
xgaia e492494
Merge pull request #4456 from nsoranzo/logging_fixes
jmchilton 9c6fd67
Merge pull request #4455 from nsoranzo/multiline_if_conditionals
dannon cd22de1
Merge pull request #4457 from erasche/sentry-extra-info
jmchilton 7f50a8a
Merge pull request #4438 from guerler/improve_form_modules
dannon dd27c1e
Client rebuild, @guerler and I were trying to figure out what changed…
dannon 2630183
Merge pull request #4464 from dannon/rebuild_000
martenson 1342c2b
Integrated File Browsing and Workflow support for GenomeSpace
nuwang e39901e
Moved back some code to wrapper and added back data type sniffing.
nuwang ad1b613
Added support for pushing multiple files from GenomeSpace to Galaxy.
nuwang b04ccbe
Fixed genomespace_importer.xml command block
Slugger70 cb1b086
Fixed pylint errors
nuwang 46c04dc
Fix incorrect reference when determining file type through file ext
nuwang 678d575
Improved recognition of compressed files
nuwang ae6ae8f
Added new config setting for GenomeSpace UI URL
nuwang 517fd23
Fixed typo in exporter help text
nuwang b73e21b
Formatting and linting fixes for GenomeSpace tool
nuwang b995e55
Fixed alignment of buttons in Genomespace Importer
nuwang 46dc4a2
Fixed template formatting according to review comments
nuwang 3e8bf3c
Moved genomespace token to environment variable
nuwang 52b26f4
Registered genomespace_importer as a tool needing Galaxy's python env
nuwang 3240197
Rebuilt galaxy client files
nuwang fd51a61
Merge pull request #1814 from gvlproject/genomespace_workflows
martenson 912da2f
Fix checking WorkflowInvocation for published workflows
mvdbeek 413233e
Correctly raise Exception if invocation not found
mvdbeek 0a4203e
Fix test to use invocation_id instead of history_id
mvdbeek 80e264d
Check ownership of invocation, instead of stored_workflow
mvdbeek 2d16470
Allow admin user to view workflow invocation (thx @nsoranzo)
mvdbeek cff306b
Only skip check_security checks if check_ownership and check_accessib…
mvdbeek 64f8e74
Fix subworkflow tests
mvdbeek 0e46888
Show up to 15 histories by default in saved histories menu
mvdbeek a9d5c7c
Show tag if < 3 tags on history
mvdbeek 2346c0a
Merge pull request #4467 from mvdbeek/saved_history_tags
martenson e3b3457
Merge pull request #4465 from mvdbeek/workflow_invocation_security_check
jmchilton 092ad6d
Fix quota function name
guerler 63d1d42
Merge pull request #4469 from guerler/fix_quota_api
nsoranzo a6632f3
replace exclamation with a clock icon
martenson 27bd713
Merge pull request #4485 from martenson/remove-exclamation
dannon 351ac64
Rebase.
VJalili f51add2
Removed white spaces.
VJalili 4546ff7
Merge remote-tracking branch 'origin/CloudObjectStore' into CloudObje…
VJalili a834381
Merge pull request #4458 from xgaia/interactive_environment
hexylena 4b9d720
Added CloudBridge to the requirements list.
VJalili 6cae07e
Added CloudBridge to the dependencies check.
VJalili d69807f
(1) Added Cloud to ObjectStore; (2) updated CloudBridge dependencies.
VJalili 7e74613
- Updated `Cloud` to account for changes in `CloudBridge` interface.
VJalili 1565fca
Reverted the changes on package versions, as these changes are
VJalili 2a7a9bd
Changed boto import style.
VJalili 8da60dc
Updated CloudBridge to its current latest version.
VJalili b256e8b
Commented on boto import, and removed a `use_reduced_redundancy` config.
VJalili 916d8b1
Removed boto import, and replaced all S3-specific exception catches with
VJalili 8742eb2
Consolidated two upload methods, i.e., upload from file and string,
VJalili 36d49aa
Removed a S3-related comment, and swapped an if/else condition.
VJalili 4e8e20f
Removed a comment section.
VJalili 7bb5d21
Changed indentation of two lines.
VJalili e1ac03d
Update CloudBridge to its current latest
VJalili 7df7ed2
Add Cloud configuration to object_store_conf.xml.sample
VJalili d1e5c41
Removed white spaces.
VJalili d3d0abe
Merge branch 'CloudObjectStore' of https://github.com/VJalili/galaxy …
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Any reason not to go with the latest current release (0.3.2)?
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No specific reason, I updated to the current latest version (also see starforge PR #138).