omero admin diagnostics: move OMERO.py version as part of the output #339

sbesson · 2022-10-12T16:11:30Z

The historical behavior of the omero admin diagnostics is to output a title line of type OMERO Diagnostics (plugin) version. Since OMERO 5.6.0 and the decoupling of OMERO.py from OMERO.server, this leads to ambiguity as this will display the OMERO.py version but will typically be executed on a server environment.

This commit proposes to strip the version from the command title and instead report the versions of OMERO.py and OMERO.server as separate entries under the report.

To test this PR, run omero admin diagnostics on OMERO.server ideally with and without this change and compare the output

sbesson · 2022-10-12T16:24:24Z

While this PR immediately helps clarifying a confusion reported several few times, this work is partly related to phase 4 ome/omero-certificates#26 as it adds an API for the discovery of properties stored under etc/omero.properties

sbesson · 2022-11-10T10:37:24Z

Now included in the daily builds and should be ready for review - see e.g. https://merge-ci.openmicroscopy.org/jenkins/job/OMERO-server/1402/console

10:29:16 + omero admin diagnostics
10:29:18 
10:29:18 ================================================================================
10:29:18 OMERO Diagnostics (admin)
10:29:18 ================================================================================
10:29:18         
10:29:18 Commands:   java -version                  1.8.0     (/home/omero/tools/hudson.model.JDK/JDK8/bin/java -- 2 others)
10:29:18 Commands:   python -V                      3.6.8     (/home/omero/workspace/OMERO-server/.venv3/bin/python -- 2 others)
10:29:18 Commands:   icegridnode --version          3.6.4     (/usr/bin/icegridnode)
10:29:18 Commands:   icegridadmin --version         3.6.4     (/usr/bin/icegridadmin)
10:29:18 Commands:   psql --version                 9.4.22    (/usr/bin/psql)
10:29:18 Commands:   openssl version                1.0.2     (/usr/bin/openssl)
10:29:18 
10:29:18 Component:  OMERO.py                       5.12.2.dev0
10:29:18 Component:  OMERO.server                   5.6.3-293-301773d-ice36-b1371
10:29:18 
10:29:18 Server:     icegridnode                    running
10:29:18 Server:     Blitz-0                        active (pid = 18268, enabled)
10:29:18 Server:     DropBox                        active (pid = 18277, enabled)

pwalczysko · 2022-11-16T15:44:50Z

Comparing the

omero admin diagnostics on merge-ci vs latest-ci, I can see two changes

Change 1 (vanishing of the version of the diagnostics itself - pretty confusing number, good riddance imho)
latest

OMERO Diagnostics (admin) 5.12.2.dev0

merge

OMERO Diagnostics (admin)

Change 2
merge has 2 additional lines

Component:  OMERO.py                       5.12.2.dev0
Component:  OMERO.server                   5.6.3-294-25a351b-ice36-b1378

which make sense when looking at https://merge-ci.openmicroscopy.org/jenkins/job/OMERO-python-superbuild-build/ and https://merge-ci.openmicroscopy.org/jenkins/job/OMERO-build/ (just slightly surprising that on merge-ci is the version number so low, not 5.6.5, but I guess this is another issue)

lgtm

jburel · 2022-11-16T20:59:36Z

src/omero/plugins/admin.py

@@ -1112,6 +1117,16 @@ def _glacier2_icessl_xml(self, config_props):
        return ['<property name="%s" value="%s"/>' % kv
                for kv in list(glacier2_icessl.items())]

+    def get_omero_server_version(self):
+        """Returns the value of omero.version stored in omero.properties"""
+        omero_props_file = old_div(self._get_etc_dir(), "omero.properties")


the usage of old_div gives me trouble during the API generation in some cases. Any reason not to use os.path.join

👍 sounds good

I think the usage of old_div comes from my copying the implementation in

omero-py/src/omero/plugins/admin.py

Lines 1094 to 1095 in d23ae9f

def _get_omero_properties(self):

omero_props_file = old_div(self._get_etc_dir(), "omero.properties")

.

And the old_div usage there itself comes the application of futurize across the code (3e17e99) which substituted division operators and path separators alike. I think in that case os.path.join is appropriate and I'll push a commit for testing appropriately but this might require a wider review.

sbesson · 2022-11-17T12:11:56Z

/home/docs/checkouts/readthedocs.org/user_builds/omero-py/checkouts/339/CHANGELOG.md:109: ERROR: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/omero-py/checkouts/339/CHANGELOG.md:115: ERROR: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/omero-py/checkouts/339/CHANGELOG.md:116: WARNING: Block quote ends without a blank line; unexpected unindent.

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/omero-py/envs/339/lib/python3.7/site-packages/sphinx/cmd/build.py", line 281, in build_main
    app.build(args.force_all, args.filenames)
  File "/home/docs/checkouts/readthedocs.org/user_builds/omero-py/envs/339/lib/python3.7/site-packages/sphinx/application.py", line 347, in build
    self.builder.build_update()
  File "/home/docs/checkouts/readthedocs.org/user_builds/omero-py/envs/339/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 312, in build_update
    len(to_build))
  File "/home/docs/checkouts/readthedocs.org/user_builds/omero-py/envs/339/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 326, in build
    updated_docnames = set(self.read())
  File "/home/docs/checkouts/readthedocs.org/user_builds/omero-py/envs/339/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 437, in read
    self.env.doc2path(self.config.root_doc))
sphinx.errors.SphinxError: root file /home/docs/checkouts/readthedocs.org/user_builds/omero-py/checkouts/339/index.rst not found

Sphinx error:
root file /home/docs/checkouts/readthedocs.org/user_builds/omero-py/checkouts/339/index.rst not found

is that a new error? related to #348 ?

jburel · 2022-11-17T13:18:53Z

This is new but strangely enough it only happens on this PR. Not directly related to #348. I will check
#349 was green

jburel · 2022-11-17T14:29:15Z

I suspect the problem was due to #350
This should hopefully sort the error only seen on this PR

The historical behavior of the `omero admin diagnostics` is to output a title line of type `OMERO Diagnostics (plugin) version`. Since OMERO 5.6.0 and the decoupling of OMERO.py from OMERO.server, this leads to ambiguity as this will display the OMERO.py version but will typically be executed on a server environment. This commit proposes to strip the version from the command title and instead report the versions of OMERO.py and OMERO.server as separate entries under the report.

jburel · 2022-11-17T15:29:01Z

rtd build is now green

jburel · 2022-11-18T09:01:09Z

@pwalczysko are you okay to redo the functional testing after the last round of adjustments?

pwalczysko · 2022-11-18T11:03:14Z

@pwalczysko are you okay to redo the functional testing after the last round of adjustments?

No changes in functionality detected, works as before.

jburel · 2022-11-18T11:03:44Z

thanks @pwalczysko

sbesson marked this pull request as draft October 12, 2022 16:24

sbesson marked this pull request as ready for review November 10, 2022 08:31

sbesson marked this pull request as draft November 10, 2022 08:42

sbesson marked this pull request as ready for review November 10, 2022 08:48

sbesson force-pushed the diagnostics_versions branch from a3e3993 to 3861fce Compare November 10, 2022 10:17

sbesson requested review from jburel and pwalczysko November 10, 2022 10:37

pwalczysko approved these changes Nov 16, 2022

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jburel reviewed Nov 16, 2022

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sbesson closed this Nov 17, 2022

sbesson reopened this Nov 17, 2022

jburel closed this Nov 17, 2022

jburel reopened this Nov 17, 2022

sbesson requested a review from jburel November 17, 2022 12:11

sbesson added 2 commits November 17, 2022 15:25

Use os.path.join for computing path to properties file

895da20

jburel force-pushed the diagnostics_versions branch from 9a8c63b to 895da20 Compare November 17, 2022 15:26

pwalczysko approved these changes Nov 18, 2022

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jburel approved these changes Nov 18, 2022

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jburel merged commit 77680f1 into ome:master Nov 18, 2022

sbesson deleted the diagnostics_versions branch December 2, 2022 08:58

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omero admin diagnostics: move OMERO.py version as part of the output #339

omero admin diagnostics: move OMERO.py version as part of the output #339

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jburel commented Nov 18, 2022

	def _get_omero_properties(self):
	omero_props_file = old_div(self._get_etc_dir(), "omero.properties")

omero admin diagnostics: move OMERO.py version as part of the output #339

omero admin diagnostics: move OMERO.py version as part of the output #339

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