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July 26, 2016 09:03
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Using http://docs.python-requests.org/ to access OMERO via json api. For OMERO 5.2.x and earlier. See discussion at https://www.openmicroscopy.org/community/viewtopic.php?f=6&t=8077
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import requests | |
session = requests.Session() | |
BASE_URL = "https://test.openmicroscopy.org/omero/" | |
# BASE_URL = "http://localhost:4080/" | |
login_url = BASE_URL + "webclient/login/" | |
r = session.get(login_url) | |
token = r.cookies['csrftoken'] | |
# Add token and referer to session header | |
session.headers.update({'X-CSRFToken': token, | |
'Referer': login_url}) | |
# Login with username, password and server | |
payload = {'username': 'will', | |
'password': 'ome', | |
'server': 1} | |
r = session.post(login_url, data=payload) | |
projectId = None | |
datasetId = None | |
imageId = None | |
# list Projects | |
projects_url = BASE_URL + "webgateway/proj/list/" | |
r = session.get(projects_url) | |
projects = r.json() | |
for p in projects: | |
print p['id'], p['name'] | |
if p['name'] == 'DVs': | |
projectId = p['id'] | |
# list Datasets in Project | |
datasets_url = BASE_URL + "webgateway/proj/%s/children/" % projectId | |
r = session.get(datasets_url) | |
datasets = r.json() | |
for d in datasets: | |
if d['name'] == 'dv': | |
datasetId = d['id'] | |
# list Images in Dataset | |
images_url = BASE_URL + "webgateway/dataset/%s/children/" % datasetId | |
r = session.get(images_url) | |
images = r.json() | |
for i in images: | |
if i['name'] == 'test.dv': | |
imageId = i['id'] | |
# Get image data | |
image_url = BASE_URL + "webgateway/imgData/%s/" % imageId | |
r = session.get(image_url) | |
print r.json() | |
# Log out | |
logout_url = BASE_URL + "webclient/logout/" | |
r = session.post(logout_url) | |
print 'logout', r.status_code |
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