TRIAL OMERO.web requirements

[atarkowska]

What this PR does

This PR improve requirement files and help deploying OMERO.web using virtualenv.

This PR is self tested by CI-JOB https://ci.openmicroscopy.org/job/WEB-DEV-trial-deploy/

Testing this PR

$ mkdir test
$ cd test
$ virtualenv venvweb
$ source venvweb/bin/activate
(venvweb) $ pip install omego 
(venvweb) $ omego download --ice 3.6 --branch OMERO-DEV-merge-build py
(venvweb) $ mv OMERO.py[currentversion] OMERO.py
(venvweb) $ pip install -r OMERO.py/share/web/requirements-py27-trial.txt

(venvweb) $ pip install git+git://github.com/aleksandra-tarkowska/figure.git@pip_installer
(venvweb) $ OMERO.py/bin/omero config append omero.web.apps '"figure"'
(venvweb) $ OMERO.py/bin/omero config append omero.web.ui.top_links '["Figure", "figure_index", {"title": "Open Figure in new tab", "target": "figure"}]' 

(venvweb) $ pip install git+git://github.com/aleksandra-tarkowska/weberror.git@pip_installer
(venvweb) $ OMERO.py/bin/omero config append omero.web.apps '"weberror"'

(venvweb) $ OMERO.py/bin/omero web start

then generate nginx config and reload. Web should operate as normal

Full doc in http://www.openmicroscopy.org/site/support/omero5.3-staging/sysadmins/unix/install-web/install-web-trial.html

Check also walkthrough http://www.openmicroscopy.org/site/support/omero5.3-staging/sysadmins/unix/install-web.html

To install webapp follow ome/omero-figure#168 (comment)

---

For more details see omeroweb-install in https://github.com/ome/omeroweb-install and travis https://travis-ci.org/ome/omeroweb-install/builds

[joshmoore]

Ready for rebase. Do you want to try omero-marshal and PyYAML here or do that in a follow-up?

[atarkowska]

sure I will add them too

[joshmoore]

See also https://trello.com/c/6ffKXuPH/101-add-omero-marshal-to-requirements-file

[atarkowska]

@joshmoore rebased due to windows removal #4782

omero-marshall added

[jburel]

With a potential (likely) 5.2.6, opportunity to indicate that Apache is "deprecated".
https://trello.com/c/s3Dp1Zs5/4-apache-deprecation

[joshmoore]

What needs to happen to bring this out of breaking?

[atarkowska]

If no objections I could start moving https://ci.openmicroscopy.org/view/Web/job/WEB-DEV-trial-deploy/ to existing spider web

[atarkowska]

@joshmoore @jburel @sbesson my apology but I think I got a bit confused with what I would like to go into m4. Initially this PR would be good to have in m4 as the doc PR ome/omero-documentation#1516 was already merged. Initial discussion diverted directly to drop TRIAL, that I personally wasn't after. We can decide in the next iteration if we wish to drop trial or not, but at the moment I would keep it as it is and get that in for m4, if no objections. Sorry for the confusion

[atarkowska]

apache changes removed, handled in PR #4825 to simplify rebasing for 5.2.6

[atarkowska]

This is now on merge https://cowfish.openmicroscopy.org/webtrial/

[ximenesuk]

Does the testing scenario require Ice 3.6?

[ximenesuk]

It looks like it does, in which case I am going to have to pass on testing this.

[atarkowska]

@ximenesuk sorry I don;t understand your comment. You need to pip install IcePy in virtualenv in isolation. This doesnt matter what is already installed on the machine. THAT IS THE WHOLE PURPOSE of that PR! IT is enough to follow listed commands in the description.

[ximenesuk]

@aleksandra-tarkowska

...
(venweb)ls30778:test colin$ OMERO.py/bin/omero config append omero.web.apps '"figure"'
Traceback (most recent call last):
  File "OMERO.py/bin/omero", line 97, in <module>
    import omero.cli
  File "/Users/colin/Work/test/OMERO.py/lib/python/omero/__init__.py", line 43, in <module>
    raise Exception(msg)
Exception:

        ERROR: Ice version mismatch!

        Your OMERO code has been compiled using Ice version 3.6.2
        but you seem to have Ice version 3.5.1 installed. If you need
        help understanding this issue, please send this error message
        to the OME community:

        http://www.openmicroscopy.org/site/community

        Debugging Info:
        --------------
        VERSION=5.3.0-m3-210-be6b074-ice36-b425
        PYTHONPATH=/Users/colin/Work/test/OMERO.py/lib/python:/Users/colin/Work/test/OMERO.py/var/lib:/Users/colin/Work/test/OMERO.py/bin:/Users/colin/Work/repos/openmicroscopy/dist/lib/python:/usr/local/opt/zeroc-ice35/lib/python2.7/site-packages:/Users/colin/Work/repos/openmicroscopy/components/tests/python:/Users/colin/Work/test/venweb/lib/python27.zip:/Users/colin/Work/test/venweb/lib/python2.7:/Users/colin/Work/test/venweb/lib/python2.7/plat-darwin:/Users/colin/Work/test/venweb/lib/python2.7/plat-mac:/Users/colin/Work/test/venweb/lib/python2.7/plat-mac/lib-scriptpackages:/Users/colin/Work/test/venweb/Extras/lib/python:/Users/colin/Work/test/venweb/lib/python2.7/lib-tk:/Users/colin/Work/test/venweb/lib/python2.7/lib-old:/Users/colin/Work/test/venweb/lib/python2.7/lib-dynload:/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7:/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-darwin:/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-tk:/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac:/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac/lib-scriptpackages:/Users/colin/Work/test/venweb/lib/python2.7/site-packages:/Users/colin/Work/test/OMERO.py/lib/fallback

All commands prior to this one were copied and pasted from the scenario.

[atarkowska]

Why your PYTHONPATh contains /Users/colin/Work/repos/openmicroscopy/dist/lib/python:/usr/local/opt/zeroc-ice35/lib/python2.7/site-packages? Cowfish has globally installed Ice 3.5 and https://ci.openmicroscopy.org/job/WEB-DEV-trial-deploy/ runs without any issues.

Sorry I don;t know what you have set up on your machine, but I trust cowfish is pretty much a good representation of server env

Please provide what is in your PYTHONPATH, PATH, version of virtualenv and pip

[ximenesuk]

My PYTHONPATH contains that because it does. I will retest in a fresh terminal with the path unset.

[mtbc]

Something to note in docs though? Not everybody may be doing this on a pristine machine.

[ximenesuk]

With PYTHONPATH unset locally the scenario runs okay without any problem. I have not tested the steps below the scenario as I don't have nginx installed.

The docs look okay though I don't follow the config adjustment at http://www.openmicroscopy.org/site/support/omero5.3-staging/sysadmins/unix/install-web/install-web-trial.html#nginx-configuration Is this mean to be something that has to be adjusted in the generated file? Or elsewhere? Maybe this makes much more sense to someone familiar with nginx?

This PR may need more rigorous testing from someone more familiar with deploying web servers.

[atarkowska]

Please provide what is in your PYTHONPATH, PATH, version of virtualenv and pip

Without answering my question above it is hard to say how the env look like.

Cowfish gives a flavour of real server and has Ice3.5 installed globally, we are running multiple integration servers

$ ls -al /opt/hudson/workspace/ | grep OMERO
drwxrwxr-x  4 hudson hudson 4096 Sep 12 05:06 OMERO-DEV-breaking-integration-Python27
drwxrwxr-x  5 hudson hudson 4096 Sep  6 11:52 OMERO-DEV-merge-docs-autogen-omeroweb
drwxrwxr-x  4 hudson hudson 4096 Sep 12 03:45 OMERO-DEV-merge-integration-Python27
drwxrwxr-x  4 hudson hudson 4096 Sep 12 04:29 OMERO-DEV-Python27-merge-deploy

and Trial job is run in isolation

+ virtualenv /opt/hudson/workspace/WEB-DEV-trial-deploy/trial-venv
New python executable in /opt/hudson/workspace/WEB-DEV-trial-deploy/trial-venv/bin/python
Installing Setuptools..............................................................................................................................................................................................................................done.
Installing Pip.....................................................................................................................................................................................................................................................................................................................................done.
+ source /opt/hudson/workspace/WEB-DEV-trial-deploy/trial-venv/bin/activate
...
++ VIRTUAL_ENV=/opt/hudson/workspace/WEB-DEV-trial-deploy/trial-venv
++ export VIRTUAL_ENV
++ _OLD_VIRTUAL_PATH=/opt/cmake/bin:/usr/local/bin:/usr/bin:/opt/texlive/2015/bin/x86_64-linux/
++ PATH=/opt/hudson/workspace/WEB-DEV-trial-deploy/trial-venv/bin:/opt/cmake/bin:/usr/local/bin:/usr/bin:/opt/texlive/2015/bin/x86_64-linux/

all the paths are set correctly.

[atarkowska]

@mtbc would be good to know whether export $PATH=/path/to/OMERO.server/bin:$PATH or any other manual manipulations affect virtualenv that we could put in the doc. At the moment I am not sure.

[ximenesuk]

@aleksandra-tarkowska

ls30778:~ colin$ echo $PATH
/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/usr/local/bin:/usr/local/sbin:/Users/colin/bin:/Users/colin/Work/repos/openmicroscopy/dist/bin
ls30778:~ colin$ echo $PYTHONPATH
/Users/colin/Work/repos/openmicroscopy/dist/lib/python:/usr/local/opt/zeroc-ice35/lib/python2.7/site-packages/:/Users/colin/Work/repos/openmicroscopy/components/tests/python
ls30778:~ colin$ virtualenv --version
12.1.1
ls30778:~ colin$ pip --version
pip 8.1.2 from /Library/Python/2.7/site-packages (python 2.7)

[atarkowska]

@jburel https://trello.com/c/WkSDITRL/187-rfe-omero-added-to-path

[jburel]

@aleksandra-tarkowska Thanks for the card.

merging