Mapr annotations (rebased onto metadata53) #5222
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Currently this assumes a single top-level default group
DeleteMapAnnotationContext modified to delete all configured namespaces if a config file is provided.
This partially reverts joshmoore@0e784ba which was a hack to modify the appearance of map annotations on wells vs images in plates in combination with https://github.com/openmicroscopy/openmicroscopy/pull/4038/files
Merged
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--rebased-from #4775 |
This was referenced Apr 11, 2017
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This is the same as gh-4775 but rebased onto metadata53.
What this PR does
Implements the grouping of MapAnnotations in separate namespaces required for https://trello.com/c/VVUqCeZC/467-populate-map-annotations
The processing of existing bulkmap configuration files is unchanged.
New support is added for a
groupcolumn type in the configuration file, which must containgroupnameindicating the namespace for the MapAnnotation andcolumnsindicating the columns to be converted into the MapAnnotation. Seetest/integration/metadata/bulk_to_map_annotation_context_ns.csvtest/integration/metadata/bulk_to_map_annotation_context_ns2.ymlFor examples.
Currently this implements deduplication of MapAnnotations within a single invocation only. This means if existing MapAnnotations are already present
omero metadata populatemay create a duplicate.Testing this PR
Import a plate:
bioformats/tools/mkfake -rows 2 -columns 3 test-plate.fakeomero import test-plate.fakeAdd a bulk annotation to the plate:
omero metadata populate --file openmicroscopy/components/tools/OmeroPy/test/integration/metadata/bulk_to_map_annotation_context_ns.csv Plate:IDCopy the bulk-map-annotation config file
components/tools/OmeroPy/test/integration/metadata/bulk_to_map_annotation_context_ns2.ymland add the following at the end:This is a hack to get annotations on wells to display in the webclient.
Convert to MapAnnotations:
omero metadata populate --context bulkmap --cfg bulk_to_map_annotation_context_ns2.yml Plate:IDThe table data should be formatted as described by
bulk_to_map_annotation_context_ns.ymli.e. some key-value pairs should go into a MapAnnotation with a custom namespace, the remainder should go into the bulk-annotations namespace
# Related reading - https://trello.com/c/VVUqCeZC/467-populate-map-annotations - https://github.com/eleanorwilliams/idr-metadata/pull/17 - https://github.com/eleanorwilliams/idr-metadata/pull/18 ## Edits - **Only** map annotations with a primary key defined are de-duplicated