bin/omero entrypoint

[manics]

Closes https://github.com/ome/omero-py/pull/219

Converts bin/omero into an entrypoint (cross-platform, so *.bat files are no longer needed).

Testing: omero CLI should work as before.

There are probably loads of other cleanups that could be done such as removing the path detection (sys.path.append(vlb)) now that OMERODIR is required for anything server side, but I've tried to keep the changes minimal for now.

bin/omero was renamed to src/omero/main.py, it looks like a new file because I had to wrap most of the script in a main() function but it's mostly indentation and flake8 fixes.

Could do with someone testing this on Windows

[joshmoore]

================ 1171 passed, 154 skipped, 1 xfailed in 33.78s ================
4564___________________________________ summary ___________________________________
4565  py37-win: commands succeeded

So tests are certainly running on travis. It'd be good to review that bin/omero tests are skipped on Windows, though.

[joshmoore]

Changes (with ignore whitespace) all look good.

[dominikl]

Testing on Windows10 VM.

C:\Users\IEUser\omero-py>omero --help
Traceback (most recent call last):
  File "C:\Users\IEUser\AppData\Local\Programs\Python\Python38\Scripts\omero-script.py", line 11, in <module>
    load_entry_point('omero-py==5.7.2.dev0', 'console_scripts', 'omero')()
  File "c:\users\ieuser\appdata\local\programs\python\python38\lib\site-packages\omero\main.py", line 69, in main
    exe = readlink()
  File "c:\users\ieuser\appdata\local\programs\python\python38\lib\site-packages\omero\main.py", line 52, in readlink
    while stat.S_ISLNK(os.lstat(file)[stat.ST_MODE]):
FileNotFoundError: [WinError 2] The system cannot find the file specified: 'C:\\Users\\IEUser\\AppData\\Local\\Programs\\Python\\Python38\\Scripts\\omero'

[manics]

Looks like bin/omero was found and executed but it's now failing in readlink() during the path detection:

def readlink(file=sys.argv[0]):
    """
    Resolve symlinks and similar. This is useful to allow
    linking this file under /usr/bin/, for example.
    """
    import stat

    file = sys.argv[0]
    while stat.S_ISLNK(os.lstat(file)[stat.ST_MODE]):   #### Failing on this line
        target = os.readlink(file)
        if target[0] != "/":
            file = os.path.join(os.path.dirname(file), target)
        else:
            file = target

    file = os.path.abspath(file)
    return file

    exe = readlink()
    top = os.path.join(exe, os.pardir, os.pardir)

    #
    # This list needs to be kept in line with omero.cli.CLI._env
    #
    top = os.path.normpath(top)
    var = os.path.join(top, "var")
    vlb = os.path.join(var, "lib")
    sys.path.append(vlb)

@joshmoore Is it safe to remove, on the assumption that OMERODIR will be set for anything requiring that path?

[joshmoore]

@joshmoore Is it safe to remove,

It's similar to OMERO_HOME in that it will be the removal of a little known feature, but a removal nonetheless.

[manics]

If I'm reading the code correctly, assuming exe = /path/to/venv/bin/omero:

• top = /path/to/venv
• vlb = /path/to/venv/var/lib

What's the expected use of /path/to/venv/var/lib ?

[joshmoore]

Dim memory of a place to put libs for scripts?

[manics]

This is now working on Windows, I've tested it in a VM with omero login wss://idr.openmicroscopy.org/omero-ws

There are still loads of other warnings/errors since Windows isn't (yet) properly supported by omero-py.

[dominikl]

👍

C:\Users\IEUser\omero-py>omero login
Server: [localhost:4064]demo.openmicroscopy.org
Username: [IEUser]dlindner
Password:
Created session for dlindner@demo.openmicroscopy.org:4064. Idle timeout: 10 min. Current group: 2018-02

[snoopycrimecop]

Conflicting PR. Removed from build OMERO-python-superbuild-push#365. See the console output for more details. Possible conflicts:

• PR #114 manics 'First attempt at adding optional packages'
  • setup.py
• PR #219 carandraug 'setup.py: do not install Windows batch scripts on non-Windows systems.'
  • setup.py
• Upstream changes
  • setup.py

--conflicts

[snoopycrimecop]

Conflicting PR. Removed from build OMERO-python-superbuild-push#366. See the console output for more details. Possible conflicts:

• PR #114 manics 'First attempt at adding optional packages'
  • setup.py
• PR #219 carandraug 'setup.py: do not install Windows batch scripts on non-Windows systems.'
  • setup.py
• Upstream changes
  • setup.py

--conflicts Conflict resolved in build OMERO-python-superbuild-push#369. See the console output for more details.