table download #3
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Re-opening to activate travis |
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This was referenced Aug 28, 2019
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Not sure if this was closed on purpose or accident, but ome/openmicroscopy#6055 has been updated to only include the integration tests. They will initial fail until this is re-opened and green. Note: I used |
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Closing to allow #54 in (conflicting) |
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plate_grid will have to be updated when modifications are made to the returned output |
manics
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$ curl -sSL https://patch-diff.githubusercontent.com/raw/ome/openmicroscopy/pull/5994.diff | sed -e 's%/components/tools/OmeroPy/%/%g' -e 's%/components/tools/OmeroWeb/%/%g' -e 's%etc/templates/web/%omeroweb/templates/%g' -e 's%/test/unit/clitest/%/test/unit/%g' -e 's%/src/%/%g' | git apply --reject Checking patch omero/plugins/web.py... error: while searching for: import traceback from datetime import datetime from omero.cli import DiagnosticsControl from omero.cli import CLI import platform error: patch failed: omero/plugins/web.py:10 Hunk ome#2 succeeded at 276 (offset 1 line). error: while searching for: "Web template configuration requires" "wsgi or wsgi-tcp.") template_file = "%s.conf.template" % server c = file(self._get_web_templates_dir() / template_file).read() self.ctx.out(c % d) def syncmedia(self, args): self.collectstatic() error: patch failed: omero/plugins/web.py:301 Checking patch test/unit/reference_templates/nginx-development-withoptions.conf... Checking patch test/unit/reference_templates/nginx-development.conf... Checking patch test/unit/reference_templates/nginx-location-withoptions.conf... Checking patch test/unit/reference_templates/nginx-location.conf... Checking patch test/unit/reference_templates/nginx-withoptions.conf... Checking patch test/unit/reference_templates/nginx.conf... Checking patch omeroweb/templates/nginx-development.conf.template... Checking patch omeroweb/templates/nginx-location.conf.template... Checking patch omeroweb/templates/nginx.conf.j2... Checking patch omeroweb/templates/nginx.conf.template... Applying patch omero/plugins/web.py with 2 rejects... Rejected hunk ome#1. Hunk ome#2 applied cleanly. Rejected hunk ome#3. Applied patch test/unit/reference_templates/nginx-development-withoptions.conf cleanly. Applied patch test/unit/reference_templates/nginx-development.conf cleanly. Applied patch test/unit/reference_templates/nginx-location-withoptions.conf cleanly. Applied patch test/unit/reference_templates/nginx-location.conf cleanly. Applied patch test/unit/reference_templates/nginx-withoptions.conf cleanly. Applied patch test/unit/reference_templates/nginx.conf cleanly. Applied patch omeroweb/templates/nginx-development.conf.template cleanly. Applied patch omeroweb/templates/nginx-location.conf.template cleanly. Applied patch omeroweb/templates/nginx.conf.j2 cleanly. Applied patch omeroweb/templates/nginx.conf.template cleanly.
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Tests passing on py-3 at https://py3-ci.openmicroscopy.org/jenkins/job/OMERO-test-integration/96/testReport/OmeroWeb.test.integration.test_table/TestOmeroTables/ Needs py3 UI testing to match earlier testing on ome/openmicroscopy#6055 |
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Ported from ome/openmicroscopy#6055
NB: Integration tests remain in that PR, so should be merged at the same time.
In several training workshops, explaining what an OMERO.table is and what data is contains is made difficult because it is very hard to show a table. Even when downloaded, it is not easy see the contents of a table since it's an HDF file.
For users of tables, inspecting the data they contain for trouble-shooting purposes etc is also hard. It is only possible to see the data for a single object/row at a time.
This allows users to view an OMERO.table file as an html table and to download it as a CSV.
Testing this PR
openmicroscopy.org/omero/bulk_annotationsnamespace (you can find objects annotated with this namespace by searching for 'bulk'. E.g. http://web-dev-merge.openmicroscopy.org/webclient/search/?search_query=bulk (user-3)NB: the default action of clicking the OMERO.table annotation itself to download the HDF file remains the same.