csv_tsv_to_map_annotation.py

import csv
import omero
from omero.gateway import BlitzGateway, TagAnnotationWrapper, MapAnnotationWrapper

conn = BlitzGateway("username", "password", host='localhost', port=4064)
conn.connect()

DATASET = 25403
NAMESPACE = "map.annotation.from.csv"

dataset = conn.getObject('Dataset', DATASET)
# make a dict of name: image
images = {}
for image in dataset.listChildren():
    images[image.getName()] = image

# open the file in universal-newline mode
with open('/Users/wmoore/Documents/biology-data/Zegami-Oxford/zegami_epic.txt', 'rU') as tsvfile:
    # from https://medium.com/@adds68/parsing-tsv-file-with-csv-in-python-662d6347b0cd
    reader = csv.DictReader(tsvfile, dialect='excel-tab')
    # print dir(reader)
    print reader.fieldnames
    for row in reader:
        name = row['image']
        image = images.get(name)
        if image is None:
            continue
        print "\n", name
        # Create a Map annotation and link to image:
        key_value_data = [[field, row[field]] for field in reader.fieldnames]
        map_ann = MapAnnotationWrapper(conn)
        map_ann.setNs(NAMESPACE)
        map_ann.setValue(key_value_data)
        map_ann.save()
        image.linkAnnotation(map_ann)
        
        # Set Description to link to the figure
        figure_url = row['OMERO.Figure link']
        image.setDescription(figure_url)
        image.save()

        # Find or create a Tag from "Gene" and link to Image
        gene = row['Gene']
        tags = list(conn.getObjects("TagAnnotation", attributes={'textValue': gene}))
        if len(tags) > 0:
            try:
                image.linkAnnotation(tags[0])
            except omero.ValidationException:
                # Tag already on Image
                pass
        else:
            tag = TagAnnotationWrapper(conn)
            tag.setValue(gene)
            tag.save()
            image.linkAnnotation(tag)

print "Done"
conn.close()