get_idr_annotations.py

import omero
from omero.gateway import BlitzGateway
from omero.sys import ParametersI
from omero.rtypes import rint
import requests

USERNAME = "root"
PASSWORD = "omero"
conn = BlitzGateway(USERNAME, PASSWORD, host="localhost", port=4064)
conn.connect()

idr_well_ids = [67137, 67066, 67069, 67070, 67073, 67074, 67075, 67077, 67079, 67080, 67081, 67082, 67084, 67085, 67086, 67089, 67090, 67093, 67094, 67095, 67096, 67097, 67098, 67099, 67105, 67106, 67109, 67110, 67111, 67112, 67113, 67114, 67115, 67116, 67117, 67118, 67119, 67120, 67123, 67124, 67125, 67126, 67127, 67128, 67132, 67133, 67134, 67135, 67138, 67140, 67141, 67143, 67144, 67146, 67147, 67148, 67150, 67154, 67155, 67156]

session = requests.Session()

base_url = "http://idr.openmicroscopy.org/webclient/api/annotations/?type=map"
ns = "openmicroscopy.org/mapr/gene"

# dataset_image_ids = [4406, 4407, 4415, 4416, 4417, 4418, 72484, 72489, 72497, 73397, 73398, 73399, 73400, 73842]

imageIds = range(1, 780)

def get_well_image_ids(conn, plate_id, field_id=0):
    """Get list of [wellId, imageId] for Plate"""
    
    # conn.SERVICE_OPTS.setOmeroGroup('-1')
    query_service = conn.getQueryService()
    params = ParametersI()
    params.addId(plate_id)
    params.add('wsidx', rint(field_id))
    query = "select well.id, img.id "\
            "from Well well "\
            "join well.wellSamples ws "\
            "join ws.image img "\
            "where well.plate.id = :id "\
            "and index(ws) = :wsidx"
    p = query_service.projection(query, params, conn.SERVICE_OPTS)
    img_ids = []
    for i in p:
        well_id = i[0].val
        img_id = i[1].val
        img_ids.append([well_id, img_id])
    return img_ids


# well_img_ids = get_well_image_ids(conn, 103, 0)
# print imageIds

for idr_id, img_id in zip(idr_well_ids, imageIds):
	url = base_url + "&well=%s" % idr_id
	map_anns = session.get(url).json()['annotations']

	for ann in map_anns:
		if ann['ns'] == ns:
			key_value_data = ann['values']
			map_ann = omero.gateway.MapAnnotationWrapper(conn)
			map_ann.setValue(key_value_data)
			map_ann.setNs(ns)
			map_ann.save()
			# w = conn.getObject('Well', well_img_id[0])
			# w.linkAnnotation(map_ann)
			i = conn.getObject('Image', img_id)
			i.linkAnnotation(map_ann)

idr_get_original.py

import omero
from omero.gateway import BlitzGateway
from omero.sys import ParametersI
from omero.rtypes import rint
import requests

USERNAME = "username"
PASSWORD = "secret"
conn = BlitzGateway(USERNAME, PASSWORD, host="localhost", port=4064)
conn.connect()

idr_well_ids = [67137, 67066, 67069, 67070, 67073, 67074, 67075, 67077, 67079, 67080, 67081, 67082, 67084, 67085, 67086, 67089, 67090, 67093, 67094, 67095, 67096, 67097, 67098, 67099, 67105, 67106, 67109, 67110, 67111, 67112, 67113, 67114, 67115, 67116, 67117, 67118, 67119, 67120, 67123, 67124, 67125, 67126, 67127, 67128, 67132, 67133, 67134, 67135, 67138, 67140, 67141, 67143, 67144, 67146, 67147, 67148, 67150, 67154, 67155, 67156]

session = requests.Session()

base_url = "http://idr.openmicroscopy.org/webclient/api/annotations/?type=map"
ns = "openmicroscopy.org/mapr/gene"

# dataset_image_ids = [4406, 4407, 4415, 4416, 4417, 4418, 72484, 72489, 72497, 73397, 73398, 73399, 73400, 73842]

def get_well_image_ids(conn, plate_id, field_id=0):
    """Get list of [wellId, imageId] for Plate"""
    
    # conn.SERVICE_OPTS.setOmeroGroup('-1')
    query_service = conn.getQueryService()
    params = ParametersI()
    params.addId(plate_id)
    params.add('wsidx', rint(field_id))
    query = "select well.id, img.id "\
            "from Well well "\
            "join well.wellSamples ws "\
            "join ws.image img "\
            "where well.plate.id = :id "\
            "and index(ws) = :wsidx"
    p = query_service.projection(query, params, conn.SERVICE_OPTS)
    img_ids = []
    for i in p:
        well_id = i[0].val
        img_id = i[1].val
        img_ids.append([well_id, img_id])
    return img_ids


well_img_ids = get_well_image_ids(conn, 103, 0)

print well_img_ids

for idr_id, well_img_id in zip(idr_well_ids, well_img_ids):
	url = base_url + "&well=%s" % idr_id
	map_anns = session.get(url).json()['annotations']

	for ann in map_anns:
		if ann['ns'] == ns:
			key_value_data = ann['values']
			map_ann = omero.gateway.MapAnnotationWrapper(conn)
			map_ann.setValue(key_value_data)
			map_ann.setNs(ns)
			map_ann.save()
			w = conn.getObject('Well', well_img_id[0])
			w.linkAnnotation(map_ann)
			i = conn.getObject('Image', well_img_id[1])
			i.linkAnnotation(map_ann)