Update filetable.py example to make it work

examples/filetable.py

@@ -1,94 +1,158 @@
 #!/usr/bin/env python
 
+from argparse import ArgumentParser, HelpFormatter
 import csv
 from glob import glob
 import os
 import tempfile
+import textwrap
 
 import firefly_client
 
-def filetable_to_firefly(ffclient, topdir, pattern, recursive=True):
+
+# From https://stackoverflow.com/a/64102901
+class RawFormatter(HelpFormatter):
+    def _fill_text(self, text, width, indent):
+        return "\n".join(
+            [
+                textwrap.fill(line, width)
+                for line in textwrap.indent(textwrap.dedent(text), indent).splitlines()
+            ]
+        )
+
+
+def filetable_to_firefly(
+    ffclient, topdir, pattern, path_prefix="", recursive=True, sort=False
+):
     """Upload table of files matching a pattern to a FireflyClient
 
     Parameters:
     -----------
     ffclient: firefly_client.FireflyClient
         Instance of FireflyClient connected to a Firefly server
 
-    topdir: 'str'
+    topdir: "str"
         pathname for directory to search
 
-    pattern: 'str'
-        filename pattern to search for, e.g. '*.fits'
+    pattern: "str"
+        filename pattern to search for, e.g. "*.fits"
+
+    path_prefix: "str"
+        string to prepend to each file path after "file://"
+        for example, specify "/external" for Firefly-in-Docker
+        (default="")
 
     recursive: `bool`
         Search all subdirectories recursively (default=True)
 
+    sort: `bool`
+        Sort the file paths (default=False)
+
     Returns:
     --------
-    tbl_val: 'str'
+    tbl_val: "str"
         Descriptor of table that was uploaded to the Firefly server
 
     metadict: `dict`
         Dictionary of metadata items
 
     """
-    filelist = glob(topdir+'/**/' + pattern, recursive=recursive)
-    metadict = {'datasource': 'path'}
-    with tempfile.NamedTemporaryFile(mode='w+t',
-                                     delete=False,
-                                     suffix='.csv') as fd:
+    filelist = glob(topdir + "/**/" + pattern, recursive=recursive)
+    if sort:
+        filelist = sorted(filelist)
+    metadict = {"datasource": "path"}
+    with tempfile.NamedTemporaryFile(mode="w+t", delete=False, suffix=".csv") as fd:
         csv_writer = csv.writer(fd)
-        csv_writer.writerow(['number','name','path'])
+        csv_writer.writerow(["number", "name", "path"])
         for i, path in enumerate(filelist):
-            csv_writer.writerow([i, os.path.basename(path),
-                                 'file://'+path])
+            # Docker Firefly allows uploads from /external
+            csv_writer.writerow(
+                [i, os.path.basename(path), "file://" + path_prefix + path]
+            )
 
     tbl_val = ffclient.upload_file(fd.name)
     os.remove(fd.name)
-    return(tbl_val, metadict)
+    return (tbl_val, metadict)
 
 
 # Sample application
 def main():
-    import argparse
-    parser = argparse.ArgumentParser(description="""
-        Display a table of files in a Firefly window
-        """)
-    parser.add_argument('topdir', help='top-level directory to search')
-    parser.add_argument('pattern', help='filename pattern for search')
-    parser.add_argument('--norecursion', help='do not recursively search topdir',
-                        action='store_true')
-    parser.add_argument('--host', help='host address for Firefly',
-                        default='localhost')
-    parser.add_argument('--port', help='port for Firefly', default='8080')
-    parser.add_argument('--base', help='base.for Firefly', default='firefly')
-    parser.add_argument('--channel', help='channel name for websocket',
-                        default=None)
-    parser.add_argument('--printurl', help='print browser url instead of' +
-                        ' attempting to launch browser', action='store_true')
+    parser = ArgumentParser(
+        description="""
+        Display a table of files in a Firefly window.
+
+        Note that you must be running a Firefly server that is
+        local to the data.
+        """,
+        epilog="""
+        If running Firefly via Docker, note that you can mount your
+        disk area onto /external.
+
+        Sample command for running the Firefly server:
+            docker run -p 8090:8080  -e "MAX_JVM_SIZE=64G"  \\
+            -e "LOG_FILE_TO_CONSOLE=firefly.log" --rm --name ncmds_firefly \\
+            -v /neoswork:/external/neoswork ipac/firefly:latest
+        """,
+        formatter_class=RawFormatter,
+    )
+    parser.add_argument("topdir", help="top-level directory to search")
+    parser.add_argument("pattern", help="filename pattern for search")
+    parser.add_argument(
+        "--path_prefix",
+        help=textwrap.dedent(
+            """string to prepend to file paths,
+        e.g. specify '/external' for Firefly-in-Docker"""
+        ),
+        default="",
+    )
+    parser.add_argument(
+        "--norecursion", help="do not recursively search topdir", action="store_true"
+    )
+    parser.add_argument("--sort", help="sort the file paths", action="store_true")
+    parser.add_argument(
+        "--firefly_url", help="URL for Firefly server", default=os.getenv("FIREFLY_URL")
+    )
+    parser.add_argument("--channel", help="channel name for websocket", default=None)
+    parser.add_argument(
+        "--printurl",
+        help="print browser url instead of" + " attempting to launch browser",
+        action="store_true",
+    )
 
     args = parser.parse_args()
     topdir = args.topdir
     pattern = args.pattern
-    host = args.host
-    port = args.port
-    basedir = args.base
+    firefly_url = args.firefly_url
     channel = args.channel
     printurl = args.printurl
+    launch_browser = False if printurl else True
     recursion = not args.norecursion
+    sort = args.sort
+    path_prefix = args.path_prefix
+
+    fc = firefly_client.FireflyClient.make_client(
+        url=firefly_url,
+        channel_override=channel,
+        html_file="slate.html",
+        launch_browser=launch_browser,
+    )
+    if printurl:
+        print("Firefly URL is {}".format(fc.get_firefly_url()))
+
+    print("Searching for files...", end="")
+    tbl_val, metainfo = filetable_to_firefly(
+        fc, topdir, pattern, path_prefix=path_prefix, recursive=recursion, sort=sort
+    )
+    print("done.")
 
-    fc = FireflyClient.make_client(url='{}:{}'.format(host, port), channel_override=channel, html_file='slate.html')
     if printurl:
-        print('Firefly url is {}'.format(fc.get_firefly_url()))
+        input("Press Enter after you have opened the Firefly URL printed above...")
 
-    tbl_val, metainfo = filetable_to_firefly(fc, topdir, pattern,
-                                             recursive=recursion)
-    r = fc.add_cell(0, 0, 1, 2, 'tables', 'main')
+    r = fc.add_cell(0, 0, 1, 2, "tables", "main")
     fc.show_table(tbl_val, meta=metainfo)
-    r = fc.add_cell(0, 1, 1, 2, 'tableImageMeta', 'image-meta')
-    fc.show_image_metadata(viewer_id=r['cell_id'])
+    r = fc.add_cell(0, 1, 1, 2, "tableImageMeta", "image-meta")
+    fc.show_image_metadata(viewer_id=r["cell_id"])
 
-if __name__ == '__main__':
-    main()
 
+if __name__ == "__main__":
+    main()