omero-metadata installation issue

[sbesson]

Tried to test omero-py and a decoupled library like omero-metadata together, I found that the installation order seems to matter with 5.5.dev2.

This can be reproduced using two virtual environments

sbesson@ls30630:~ $ virtualenv /tmp/venv1
New python executable in /tmp/venv1/bin/python2.7
Also creating executable in /tmp/venv1/bin/python
Installing setuptools, pip, wheel...done.
sbesson@ls30630:~ $ virtualenv /tmp/venv2
New python executable in /tmp/venv2/bin/python2.7
Also creating executable in /tmp/venv2/bin/python
Installing setuptools, pip, wheel...done.
sbesson@ls30630:~ $ /tmp/venv1/bin/pip install omero-py==5.5dev2 omero-metadata==0.4.0
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support
Collecting omero-py==5.5dev2
  Downloading https://files.pythonhosted.org/packages/ca/98/9085cec1c281b531537cf856404b88df38d67ea1c565cfc07d6131ea22da/omero-py-5.5.dev2.tar.gz (2.3MB)
     |████████████████████████████████| 2.4MB 1.5MB/s 
Collecting omero-metadata==0.4.0
  Downloading https://files.pythonhosted.org/packages/b3/84/a29d4fef46c564ca9988984c376e82b2297ef51a3e57da3b3936e4d9e78d/omero-metadata-0.4.0.tar.gz
Collecting zeroc-ice<3.7,>=3.6.4 (from omero-py==5.5dev2)
  Downloading https://files.pythonhosted.org/packages/1e/65/43c3ad2412467c731ee3c23bce03fad7e2b79df31301e27cc7b1b454554b/zeroc-ice-3.6.5.tar.gz (1.2MB)
     |████████████████████████████████| 1.2MB 12.4MB/s 
Building wheels for collected packages: omero-py, omero-metadata, zeroc-ice
  Building wheel for omero-py (setup.py) ... done
  Created wheel for omero-py: filename=omero_py-5.5.dev2-cp27-none-any.whl size=2786752 sha256=f129a7145496b2db504736fa401cdc74a3140705e3e9ce290305c4330ad9797c
  Stored in directory: /Users/sbesson/Library/Caches/pip/wheels/ef/33/d5/14b3e1771b18731097588668583c68e02375767a3f606c4887
  Building wheel for omero-metadata (setup.py) ... done
  Created wheel for omero-metadata: filename=omero_metadata-0.4.0-cp27-none-any.whl size=25739 sha256=e7df430d48219b0d08b1b6c6db2d6253433a95a9c6072f9681b6e994ab4fb818
  Stored in directory: /Users/sbesson/Library/Caches/pip/wheels/97/ed/f6/790aa61a63dd768a7a53874688e3124195424b9ec9eeab3eb0
  Building wheel for zeroc-ice (setup.py) ... done
  Created wheel for zeroc-ice: filename=zeroc_ice-3.6.5-cp27-cp27m-macosx_10_13_x86_64.whl size=2925471 sha256=3a5f1c4d3200c9ecfd2045fe9d1c8f56a8a53cdb8e802bff8e596c39896cb6ae
  Stored in directory: /Users/sbesson/Library/Caches/pip/wheels/d5/20/93/a2f791674372ad8e5664cdd8c3a0c128ae00a5b3a5c7cee538
Successfully built omero-py omero-metadata zeroc-ice
Installing collected packages: zeroc-ice, omero-py, omero-metadata
Successfully installed omero-metadata-0.4.0 omero-py-5.5.dev2 zeroc-ice-3.6.5
sbesson@ls30630:~ $ /tmp/venv2/bin/pip install omero-metadata==0.4.0 omero-py==5.5dev2 
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support
Collecting omero-metadata==0.4.0
Collecting omero-py==5.5dev2
Collecting zeroc-ice<3.7,>=3.6.4 (from omero-py==5.5dev2)
Installing collected packages: omero-metadata, zeroc-ice, omero-py
Successfully installed omero-metadata-0.4.0 omero-py-5.5.dev2 zeroc-ice-3.6.5

The first environment successfully loads the metadata plugin while the second fails to discover it:

sbesson@ls30630:~ $ /tmp/venv1/bin/omero metadata
ERROR:omero.gateway:No Pillow installed, line plots and split channel will fail!
usage: /tmp/venv1/bin/omero metadata [-h] [-C] [-s SERVER] [-p PORT]
                                     [-g GROUP] [-u USER] [-w PASSWORD]
                                     [-k KEY] [--sudo ADMINUSER] [-q]
                                     <subcommand> ...
/tmp/venv1/bin/omero metadata: error: too few arguments
sbesson@ls30630:~ $ /tmp/venv2/bin/omero metadata
ERROR:omero.gateway:No Pillow installed, line plots and split channel will fail!
usage: /tmp/venv2/bin/omero [-h] [-v] [-d DEBUG] [--path PATH] [-C]
                            [-s SERVER] [-p PORT] [-g GROUP] [-u USER]
                            [-w PASSWORD] [-k KEY] [--sudo ADMINUSER] [-q]
                            <subcommand> ...
/tmp/venv2/bin/omero: error: argument <subcommand>: invalid choice: 'metadata'

choose from:
	admin, chgrp, chown, config, db, delete, download, errors, export, 
	fs, group, help, hql, import, ldap, load, login, logout, node, 
	obj, perf, quit, script, search, server, sessions, shell, tag, 
	testengine, upload, user, version

Running diff -r -x '*.pyc' /tmp/venv1/ /tmp/venv2/ reveals that both plugins are indeed competing to write under lib/python2.7/site-packages/omero/plugins/metadata.py.

[sbesson]

Retested following the release of omero-py 5.6.dev7 with

FROM centos:7

RUN yum install -y python3
RUN useradd -ms /bin/bash omero

USER omero
WORKDIR /tmp
RUN python3 -m venv venv1 && venv1/bin/pip install https://github.com/ome/zeroc-ice-py-centos7/releases/download/0.2.1/zeroc_ice-3.6.5-cp36-cp36m-linux_x86_64.whl && venv1/bin/pip install --pre omero-py
RUN python3 -m venv venv2 && venv2/bin/pip install https://github.com/ome/zeroc-ice-py-centos7/releases/download/0.2.1/zeroc_ice-3.6.5-cp36-cp36m-linux_x86_64.whl && venv2/bin/pip install --pre omero-metadata

As expected, the first virtual environment requires OMERO_DEV_PLUGINS set to consume the deprecated metadata plugin while the second environment uses the omero-metadata plugin

[omero@7961ec8becd5 tmp]$ venv1/bin/omero metadata populate Dataset:1 --file foo
usage: venv1/bin/omero [-h] [-v] [-d DEBUG] [--path PATH] [-C] [-s SERVER]
                       [-p PORT] [-g GROUP] [-u USER] [-w PASSWORD] [-k KEY]
                       [--sudo ADMINUSER] [-q]
                       <subcommand> ...
venv1/bin/omero: error: argument <subcommand>: invalid choice: 'metadata'

choose from:
	admin, chgrp, chown, config, db, delete, download, errors, export, 
	fs, group, help, hql, import, ldap, load, login, logout, node, 
	obj, perf, quit, script, search, server, sessions, shell, tag, 
	testengine, upload, user, version
[omero@7961ec8becd5 tmp]$ OMERO_DEV_PLUGINS=1 venv1/bin/omero metadata populate Dataset:1 --file foo
This plugin is deprecated as of OMERO 5.4.8. Use the plugin available from https://pypi.org/project/omero-metadata/ instead.
Server: [localhost:4064]^CCancelled
[omero@7961ec8becd5 tmp]$ venv2/bin/omero metadata populate Dataset:1 --file foo
Server: [localhost:4064]^CCancelled