def create_figure_file(conn, figure_json, figure_name):
"""Create Figure FileAnnotation from json data."""
if len(figure_json['panels']) == 0:
raise Exception('No Panels')
first_img_id = figure_json['panels'][0]['imageId']
# we store json in description field...
description = {}
description['name'] = figure_name
description['imageId'] = first_img_id
# Try to set Group context to the same as first image
conn.SERVICE_OPTS.setOmeroGroup('-1')
i = conn.getObject("Image", first_img_id)
gid = i.getDetails().getGroup().getId()
conn.SERVICE_OPTS.setOmeroGroup(gid)
json_bytes = json.dumps(figure_json).encode('utf-8')
file_size = len(json_bytes)
f = BytesIO()
try:
f.write(json_bytes)
update = conn.getUpdateService()
orig_file = conn.createOriginalFileFromFileObj(
f, '', figure_name, file_size, mimetype="application/json")
finally:
f.close()
fa = FileAnnotationI()
fa.setFile(OriginalFileI(orig_file.getId(), False))
fa.setNs(rstring(JSON_FILEANN_NS))
desc = json.dumps(description)
fa.setDescription(rstring(desc))
fa = update.saveAndReturnObject(fa, conn.SERVICE_OPTS)
return fa.getId().getValue()
def save_web_figure(conn, json_data):
"""
Saves 'figureJSON' in POST as an original file. If 'fileId' is specified
in POST, then we update that file. Otherwise create a new one with
name 'figureName' from POST.
"""
image_ids = []
first_img_id = None
try:
for panel in json_data['panels']:
image_ids.append(panel['imageId'])
if len(image_ids) > 0:
first_img_id = int(image_ids[0])
# remove duplicates
image_ids = list(set(image_ids))
# pretty-print json
figure_json = json.dumps(json_data,
sort_keys=True,
indent=2,
separators=(',', ': '))
except Exception:
pass
# See https://github.com/will-moore/figure/issues/16
figure_json = figure_json.encode('utf8')
if 'figureName' in json_data and len(json_data['figureName']) > 0:
figure_name = json_data['figureName']
else:
print("No figure name found")
return
# we store json in description field...
description = {}
if first_img_id is not None:
# We duplicate the figure name here for quicker access when
# listing files
# (use this instead of file name because it supports unicode)
description['name'] = figure_name
description['imageId'] = first_img_id
if 'baseUrl' in panel:
description['baseUrl'] = panel['baseUrl']
desc = json.dumps(description)
# Create new file
# Try to set Group context to the same as first image
curr_gid = conn.SERVICE_OPTS.getOmeroGroup()
i = None
if first_img_id:
i = conn.getObject("Image", first_img_id)
if i is not None:
gid = i.getDetails().getGroup().getId()
conn.SERVICE_OPTS.setOmeroGroup(gid)
else:
# Don't leave as -1
conn.SERVICE_OPTS.setOmeroGroup(curr_gid)
file_size = len(figure_json)
f = BytesIO()
f.write(figure_json)
orig_file = conn.createOriginalFileFromFileObj(f,
'',
figure_name,
file_size,
mimetype="application/json")
fa = FileAnnotationI()
fa.setFile(OriginalFileI(orig_file.getId(), False))
fa.setNs(wrap(JSON_FILEANN_NS))
fa.setDescription(wrap(desc))
update = conn.getUpdateService()
fa = update.saveAndReturnObject(fa, conn.SERVICE_OPTS)
ann_id = fa.getId().getValue()
return ann_id
