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Scripts for using Pychrm in OMERO
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Choose a namespace for release #19

Open manics opened 10 years ago

manics commented 10 years ago

Currently Pychrm objects are stored in the namespace /classifier/testing/pychrm/...., see e.g. https://github.com/manics/omero-pychrm/blob/de46941d7fee1729ec92072b9d7959bd2c9e5468/OmeroPychrm/PychrmStorage.py#L40

We should decide on a final string to use /classifier/pychrm/....? Something else? Note this will be a breaking change (all existing attached tables will have to be deleted and recalculated, unless all namespaces are converted.

/cc @colettace

joshmoore commented 10 years ago

Any thoughts on this? For reference, from the production DB:

omero=# select distinct ns from annotation order by ns;
                                            ns                                            
------------------------------------------------------------------------------------------

 com.glencoesoftware.journal_bridge:fileset_uuid
 com.glencoesoftware.journal_bridge:imgdefrdef
 com.glencoesoftware.journal_bridge:origfilepath
 com.glencoesoftware.journal_bridge:part
 hms-tracking
 lccb.analysis
 omero.web.figure.json
 ome.share.comment/
 ome-xml.org:additions:post2010-06:objective
 ome-xml.org:additions:post2010-06:spim:positions
 ome-xml.org:additions:post2010-06:spim:set
 openmicroscopy.org/omero/bulk_annotations
 openmicroscopy.org/omero/editor/experiment
 openmicroscopy.org/omero/editor/protocol
 openmicroscopy.org/omero/experimenter/photo
 openmicroscopy.org/omero/import/companionFile
 openmicroscopy.org/omero/importer/archived
 openmicroscopy.org/omero/insight/rating
 openmicroscopy.org/omero/insight/tagset
 openmicroscopy.org/omero/measurement
 openmicroscopy.org/omero/movie
 openmicroscopy.org/omero/ome_tiff
 openmicroscopy.org/omero/scripts/results/created/omero/export_scripts/Batch_Image_Export
 openmicroscopy.org/omero/scripts/results/created/omero/export_scripts/Make_Movie
 openmicroscopy.org/omero/scripts/results/created/omero/figure_scripts/Movie_Figure
 openmicroscopy.org/omero/scripts/results/created/omero/figure_scripts/ROI_Split_Figure
 openmicroscopy.org/omero/scripts/results/created/omero/figure_scripts/Split_View_Figure
 openmicroscopy.org/omero/scripts/results/created/omero/figure_scripts/Thumbnail_Figure
 sample.ome-xml.org:spim-sample-custom-system

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manics commented 10 years ago

origin based hierarchy (wndcharm/classifier/..., this is also used by searcher: direct.edu.cmu.cs.compbio.omepslid:...) vs semantic (analysis/machinelearning/classifier/wndcharm/...)

It depends on our future plans, the former is consistent with the rest of OMERO, the latter is better for auto-discovery but that's a long way off, and chances are it'll change anyway.

manics commented 10 years ago

I spoke to @colettace yesterday, no real preference so unless someone intends to come up with a standard namespace format for OMERO I'll just go with /classifier/pychrm/...