Problems using Populate Metadata script

Dear all,
Sorry Josh… I’m not so “expert” with this forum :-)… I re-post this message for all the people, after deleting it…
So ! I used the script Populate metadata our Omero database with my dataset containing 3 images, like this :
image
I have taken the four image.csv file from your webpage and modfied it as follow for these 3_images : 3-images.csv (262 Bytes)
The csv conversion done by Excel (indicated in the webpage) seems to be a of problem as the files accepted by the script should contain comas instead of semi-colon. After a modification in a notepad, the script is executed but the images ID are not recognized, apparently, as indicated in the bulk annotations file by -1 bulk_annotations.csv (250 Bytes) . Could you give me complementary indications about the correct way to proceed? Many thanks in advance,
Best regards,
Frédéric

Hi @brau,

have you been running the metadata population script against the project or the dataset? Looking at your example CSV file, there are two mismatches with the screenshot you paster above:

  • the Dataset Name is named Deconvolved rather than Tif
  • the Image Name are not suffixed with .tif in the CSV

Have you tried adjusting these two columns to match exactly the object names in the database to see if it fixes the issue?

Sebastien

H Sebastien,

Many thanks, the problem comes surely from there… :wink:

I will try as soons as I could attach a csv in our database… Because sometimes we have problems (my last try) :

Traceback (most recent call last):

File “/opt/omero/web/venv3/lib64/python3.6/site-packages/django/core/handlers/exception.py”, line 41, in inner
response = get_response(request)

File “/opt/omero/web/venv3/lib64/python3.6/site-packages/django/core/handlers/base.py”, line 187, in _get_response
response = self.process_exception_by_middleware(e, request)

File “/opt/omero/web/venv3/lib64/python3.6/site-packages/django/core/handlers/base.py”, line 185, in _get_response
response = wrapped_callback(request, *callback_args, **callback_kwargs)

File “/opt/omero/web/venv3/lib64/python3.6/site-packages/omeroweb/decorators.py”, line 538, in wrapped
retval = f(request, *args, **kwargs)

File “/opt/omero/web/venv3/lib64/python3.6/site-packages/omeroweb/decorators.py”, line 597, in wrapper
context = f(request, *args, **kwargs)

File “/opt/omero/web/venv3/lib64/python3.6/site-packages/omeroweb/webclient/views.py”, line 2390, in annotate_file
newFileId = manager.createFileAnnotations(fileupload, oids)

File “/opt/omero/web/venv3/lib64/python3.6/site-packages/omeroweb/webclient/controller/container.py”, line 670, in createFileAnnotations
of = self.conn.saveAndReturnFile(newFile, ofid)

File “/opt/omero/web/venv3/lib64/python3.6/site-packages/omeroweb/webclient/webclient_gateway.py”, line 1821, in saveAndReturnFile
raise Exception(msg)

Exception: SHA-1 checksums do not match in file upload: client has 805b16bc0eb0e7090b1ba16caaab4710292faec2 but server has 8246951279b8660ec5359833affb4eff10b86a11

<WSGIRequest: POST ‘/omero-mica/webclient/annotate_file/’>

If anybody from you team could help us (C. Blanchet) about this problem? We are running this 5.6.3 version in proto mode to dispatch it in production this wenesday.

Best,

Frédéric

@will-moore may have more ideas, but could you also try with insight or the CLI?
~Josh

Many thanks Sebastien and Josh. It’s working now.
image
Best regards,
Frédéric

1 Like