Generating OMERO.Figures in Python using json templates

[jstitlow]

Sharing a Python function (modified from code written by wmoore and carandraug) to generate OMERO.Figures in Python using json text files as a template. It's useful for iterating Figure generation over a whole dataset.

Also posting to ask if it is possible to delete OMERO.Figures in CLI using the Figure ID. While testing the code below I accidentally generated several blank Figures, which for some reason can't be deleted from the Figure GUI.

Thanks!
j

Code: Select all

def make_figure(data):   # where data is a json.txt file

    # convert json.txt to a json dict
    figure_json = json.load(data)

    # generate OMERO figure and save with new ID
    name = figure_json['figureName']
    description = {'name': name}
    file_ann = conn.createFileAnnfromLocalFile(figure_fpath,
        origFilePathAndName=name, mimetype='application/json',
        ns='omero.web.figure.json', desc=description)


[jstitlow]

Presumably the Figures live in OMERO as FileAnnotations..?

They appear to be deleted when I ran this:

Code: Select all

FigureIDs = [2115475, 2115470]
conn.deleteObjects("FileAnnotation", FigureIDs)


[jmoore]

Josh,

Indeed:

Code: Select all

[jamoore@ome-demoserver ~]$ omero hql -q "select fa from FileAnnotation fa where fa.id = 3062"
# | Class           | Id   | ns                    | description                                             | file                | details
---+-----------------+------+-----------------------+---------------------------------------------------------+---------------------+-----------------
0 | FileAnnotationI | 3062 | omero.web.figure.json | {"name": "Figure_2018-9-13_13:46:29", "imageId": 24256} | OriginalFileI:68299 | owner=0;group=0
(1 row)


[jamoore@ome-demoserver ~]$ omero -q delete --report FileAnnotation:3062
omero.cmd.Delete2 FileAnnotation:3062 ok
Steps: 6
Elapsed time: 0.118 secs.
Flags: []
Deleted objects
  FileAnnotation:3062
  OriginalFile:68299


All the best,
~Josh.