Only perform header detection when --file is specified

[sbesson]

This PR attempts to fix a regression introduced as part of #67 which was primarily tested with the omero metadata populate command

To reproduce, run a workflow composed of a table population followed by a bulk annotation -> map annotation population, for instance as described with https://omero-guides.readthedocs.io/en/latest/upload/docs/metadata.html.

With the current release of omero-metadata 0.11.1, the second step should fail with and error of type

$ omero metadata populate --context bulkmap --cfg simple-annotation-bulkmap-config.yml Dataset:601
Using session for import.user@localhost:4064. Idle timeout: 10 min. Current group: Demo Group
Traceback (most recent call last):
  File "/opt/omero/OMERO.venv/bin/omero", line 8, in <module>
    sys.exit(main())
  File "/opt/omero/OMERO.venv/lib/python3.8/site-packages/omero/main.py", line 126, in main
    rv = omero.cli.argv()
  File "/opt/omero/OMERO.venv/lib/python3.8/site-packages/omero/cli.py", line 1787, in argv
    cli.invoke(args[1:])
  File "/opt/omero/OMERO.venv/lib/python3.8/site-packages/omero/cli.py", line 1225, in invoke
    stop = self.onecmd(line, previous_args)
  File "/opt/omero/OMERO.venv/lib/python3.8/site-packages/omero/cli.py", line 1302, in onecmd
    self.execute(line, previous_args)
  File "/opt/omero/OMERO.venv/lib/python3.8/site-packages/omero/cli.py", line 1384, in execute
    args.func(args)
  File "/opt/omero/OMERO.venv/lib/python3.8/site-packages/omero_metadata/cli.py", line 578, in populate
    first_row = pd.read_csv(args.file, nrows=1, header=None)
  File "/opt/omero/OMERO.venv/lib/python3.8/site-packages/pandas/util/_decorators.py", line 211, in wrapper
    return func(*args, **kwargs)
  File "/opt/omero/OMERO.venv/lib/python3.8/site-packages/pandas/util/_decorators.py", line 331, in wrapper
    return func(*args, **kwargs)
  File "/opt/omero/OMERO.venv/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 950, in read_csv
    return _read(filepath_or_buffer, kwds)
  File "/opt/omero/OMERO.venv/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 605, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
  File "/opt/omero/OMERO.venv/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 1442, in __init__
    self._engine = self._make_engine(f, self.engine)
  File "/opt/omero/OMERO.venv/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 1735, in _make_engine
    self.handles = get_handle(
  File "/opt/omero/OMERO.venv/lib/python3.8/site-packages/pandas/io/common.py", line 713, in get_handle
    ioargs = _get_filepath_or_buffer(
  File "/opt/omero/OMERO.venv/lib/python3.8/site-packages/pandas/io/common.py", line 451, in _get_filepath_or_buffer
    raise ValueError(msg)
ValueError: Invalid file path or buffer object type: <class 'NoneType'>

With this PR included, both population steps should successfully complete.

Given the regression, I would propose to schedule this in an upcoming patch release 0.11.2 (possibly together with #79)

[muhanadz]

Thank you for opening the PR Seb. Changes are necessary and probably overlooked/missed in the previous PR. Tested and, as detailed in the description, this PR fixes ValueError: Invalid file path or buffer object type: <class 'NoneType'> exception as a result of running the bulk annotation workflow.

I agree with the including this in a 0.11.2 patch release.

[pwalczysko]

Confirming the error with 0.11.2, see below

omero metadata populate --context bulkmap --cfg ~/Downloads/simple-annotation-bulkmap-config.yml --batch 100 Dataset:117 
Using session for user-1@localhost:4064. Idle timeout: 10 min. Current group: group1
Traceback (most recent call last):
  File "/Users/pwalczysko/opt/anaconda3/envs/cli/bin/omero", line 10, in <module>
    sys.exit(main())
  File "/Users/pwalczysko/opt/anaconda3/envs/cli/lib/python3.8/site-packages/omero/main.py", line 126, in main
    rv = omero.cli.argv()
  File "/Users/pwalczysko/opt/anaconda3/envs/cli/lib/python3.8/site-packages/omero/cli.py", line 1787, in argv
    cli.invoke(args[1:])
  File "/Users/pwalczysko/opt/anaconda3/envs/cli/lib/python3.8/site-packages/omero/cli.py", line 1225, in invoke
    stop = self.onecmd(line, previous_args)
  File "/Users/pwalczysko/opt/anaconda3/envs/cli/lib/python3.8/site-packages/omero/cli.py", line 1302, in onecmd
    self.execute(line, previous_args)
  File "/Users/pwalczysko/opt/anaconda3/envs/cli/lib/python3.8/site-packages/omero/cli.py", line 1384, in execute
    args.func(args)
  File "/Users/pwalczysko/opt/anaconda3/envs/cli/lib/python3.8/site-packages/omero_metadata/cli.py", line 578, in populate
    first_row = pd.read_csv(args.file, nrows=1, header=None)
  File "/Users/pwalczysko/opt/anaconda3/envs/cli/lib/python3.8/site-packages/pandas/util/_decorators.py", line 211, in wrapper
    return func(*args, **kwargs)
  File "/Users/pwalczysko/opt/anaconda3/envs/cli/lib/python3.8/site-packages/pandas/util/_decorators.py", line 331, in wrapper
    return func(*args, **kwargs)
  File "/Users/pwalczysko/opt/anaconda3/envs/cli/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 950, in read_csv
    return _read(filepath_or_buffer, kwds)
  File "/Users/pwalczysko/opt/anaconda3/envs/cli/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 605, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
  File "/Users/pwalczysko/opt/anaconda3/envs/cli/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 1442, in __init__
    self._engine = self._make_engine(f, self.engine)
  File "/Users/pwalczysko/opt/anaconda3/envs/cli/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 1735, in _make_engine
    self.handles = get_handle(
  File "/Users/pwalczysko/opt/anaconda3/envs/cli/lib/python3.8/site-packages/pandas/io/common.py", line 713, in get_handle
    ioargs = _get_filepath_or_buffer(
  File "/Users/pwalczysko/opt/anaconda3/envs/cli/lib/python3.8/site-packages/pandas/io/common.py", line 451, in _get_filepath_or_buffer
    raise ValueError(msg)
ValueError: Invalid file path or buffer object type: <class 'NoneType'>

[pwalczysko]

With this PR, I get

omero metadata populate --context bulkmap --cfg ~/Downloads/simple-annotation-bulkmap-config.yml --batch 100 Dataset:117
Using session for user-1@localhost:4064. Idle timeout: 10 min. Current group: group1
INFO:omero_metadata.populate:Created/linked 100 MapAnnotations (total 100)
INFO:omero_metadata.populate:Created/linked 65 MapAnnotations (total 165)

and indeed, the MapAnnotations are created as expected:

LGTM

[sbesson]

Pushed another commit with the changelog entry if we are happy with an immediate 0.11.2 @jburel @joshmoore

[jburel]

sorry for dropping that one.
Looks good

[sbesson]

@jburel do you have any timeline for making a release of this plugin (and/or would you like me to do it)? I think it would be valuable to upgrade the version of the plugin deployed on prod114 so that we can test the whole annotation workflow with the new pandas functionality on the next studies. /cc @dominikl

[jburel]

@sbesson your suggestion to deploy the plugin on prod114 makes sense.
If you can take care of the release, that will be great