Closed will-moore closed 4 years ago
./omero/figure_scripts/Thumbnail_Figure.py:100:5: E722 do not use bare except'
Travis now failing with more flake8s from python3 since omero-test-infra
is now py3.
./omero/util_scripts/Dataset_To_Plate.py:40:5: F821 undefined name 'long'
./omero/figure_scripts/ROI_Split_Figure.py:56:5: F821 undefined name 'long'
./omero/import_scripts/Populate_Metadata.py:35:5: F821 undefined name 'long'
Travis is failing with importing fake images in integration tests:
out, err = popen.communicate()
rc = popen.wait()
if rc != 0:
raise Exception("import failed: [%r] %s\n%s\n%s" % (
> args, rc, out, err))
E Exception: import failed: [['/opt/omero/server/venv3/bin/python', './bin/omero', '-s', 'localhost', '-k', 'cbf3400c-b7e4-40a9-b038-c1d11335ecbe', '-p', '4064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/opt/omero/server/omero/tmp/omero_omero-server/969/import_fake_file_08w9va1yv&&plates=1&plateAcqs=1&plateCols=1&plateRows=1&fields=2.fake')]] 102
E b''
E b"Cannot get JAR files from '/opt/omero/server/venv3/lib/lib/client' (No such file or directory)\n"
This is likely the same issue @sbesson saw with OMERODIR in https://github.com/ome/omero-test-infra/pull/44#issuecomment-553877422
Conflicting PR. Removed from build OMERO-python-superbuild-push#71. See the console output for more details. Possible conflicts:
--conflicts
travis now working again. Failed with:
E Traceback (most recent call last):
E File "./script", line 672, in <module>
E run_script()
E File "./script", line 555, in run_script
E ckeys.sort()
E AttributeError: 'dict_keys' object has no attribute 'sort'
Conflicting PR. Removed from build OMERO-python-superbuild-push#75. See the console output for more details. Possible conflicts:
--conflicts Conflict resolved in build OMERO-python-superbuild-push#76. See the console output for more details.
Make Movie ... from the figure scripts still errors on py3-ci
...
Traceback (most recent call last): File "./script", line 74, in from cStringIO import StringIO ModuleNotFoundError: No module named 'cStringIO' --------------------------------- }
Those last commits should fix Batch_ROI_Export
script and Make_Movie
script, except that mencoder
is not installed on py3-ci or merge-ci.
Given that at least two open scripts PRs are currently blocked on the fixes included in this PR, if no huge blocker is found during testing, I am in favor of getting this merged. Issues reported during the functional testing can be captured as issues and prioritized before general availability release if needed.
Make Movie - I guess there is some progress here, as the error has changed (tested on py3-ci). Nevertheless, still unable to test the whole workflow.
sh: mencoder: command not found
mencoder installed via:
[jamoore@idr1-slot2 py3-ci]$ git diff server/Dockerfile
diff --git a/server/Dockerfile b/server/Dockerfile
index b579538..461728e 100644
--- a/server/Dockerfile
+++ b/server/Dockerfile
@@ -66,6 +66,11 @@ RUN /py3/bin/pip install scc
ENV VIRTUAL_ENV=/py3
ENV PATH="$VIRTUAL_ENV/bin:$PATH"
+# Install mencoder
+# See https://github.com/ome/prod-playbooks/blob/7d8e59ced0b47a224d6be02907d913c392ef9379/ome-dundeeomero.yml#L48
+RUN yum install -y http://li.nux.ro/download/nux/dextop/el7/x86_64/nux-dextop-release-0-5.el7.nux.noarch.rpm
+RUN yum install -y mencoder
On py3-ci, figure_scripts > Movie ROI Figure crashes immediately when selected the menu item (the first dialog does not materialize)
Not sure this is the right place to report, but see below @joshmoore @will-moore - I have a memory of that particualr script already working on py3-ci ...
File "/home/omero/workspace/OMERO-web/OMERO.web/lib/python/omero_api_IScript_ice.py", line 842, in getParams
return _M_omero.api.IScript._op_getParams.invoke(self, ((scriptID, ), _ctx))
omero.ValidationException: exception ::omero::ValidationException
{
serverStackTrace =
serverExceptionClass =
message = Can't find params for 5504!
No stdout.
stderr is in file 7719:
---------------------------------
Traceback (most recent call last):
File "/home/omero/workspace/OMERO-server/OMERO.server/lib/python/omero/util/image_utils.py", line 30, in <module>
from PIL import Image, ImageDraw, ImageFont # see ticket:2597
ModuleNotFoundError: No module named 'PIL'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "./script", line 37, in <module>
import omero.util.image_utils as image_utils
File "/home/omero/workspace/OMERO-server/OMERO.server/lib/python/omero/util/image_utils.py", line 32, in <module>
import Image
ModuleNotFoundError: No module named 'Image'
---------------------------------
Make Movie
crashes too, with the empty "Send Feedback" dialog.
Definitely, we are in much worse state on py3-ci now in comparison with yesterday
Retest after job rerun:
Re https://github.com/ome/scripts/pull/159#issuecomment-559042079 - Movie ROI Figure now fully passes.
Re: https://github.com/ome/scripts/pull/159#issuecomment-559043402 - the Make Movie as well as the other two "figure" scripts work now without any errors.
The only problem remaining here is that Make Movie (the one started from RHP) is producing black movies only (2 very different images tested). some output is produced such as
[mjpeg @ 0x7ff5fe9665a0]AVFrame.format is not set
[mjpeg @ 0x7ff5fe9665a0]AVFrame.width or height is not set
...
for every plane of the image in question.
That last commit should fix the black Make_Movie frames.
Yes, the Make Movie is fixed now in py3-ci .
user-2 on https://py3-ci.openmicroscopy.org/web/webclient/?show=well-2102 is working without a problem.
user-3 on https://py3-ci.openmicroscopy.org/web/webclient/?show=image-2970 produces a movie which has a strange blinking effects - they cannot be seen if the image is played inside OMERO in iviewer - I would suspect this is because the frames coming into the avi movie are not in correct order, which might be connected to the fact that this is a multi-z (and multi-t of course) image.
@pwalczysko : i.e. good to merge?
Good to merge
Thanks @pwalczysko. Merging to fix the Travis on #160 and #163
Fixes figure scripts for python 3.
To test:
This ports some code from
image_util
to fix it in the script itself.paint_thumbnail_grid
isn't used by any other code and could be deprecated/removed fromimage_utils.py