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 upload(self, args):
client = self.ctx.conn(args)
obj_ids = []
for local_file in args.file:
if not path(local_file).exists():
self.ctx.die(500, "File: %s does not exist" % local_file)
for local_file in args.file:
omero_format = UNKNOWN
if args.mimetype:
omero_format = args.mimetype
elif (mimetypes.guess_type(local_file) != (None, None)):
omero_format = mimetypes.guess_type(local_file)[0]
if args.data_dir:
obj = upload_ln_s(client, local_file, args.data_dir,
omero_format)
obj_id = obj.id
else:
obj = client.upload(local_file, type=omero_format)
obj_id = obj.id.val
if args.wrap:
fa = FileAnnotationI()
fa.setFile(OriginalFileI(obj_id, False))
if args.namespace:
fa.setNs(rstring(args.namespace))
fa = client.sf.getUpdateService().saveAndReturnObject(fa)
obj_ids.append(fa.id.val)
else:
obj_ids.append(obj_id)
self.ctx.set("last.upload.id", obj_id)
obj_ids = self._order_and_range_ids(obj_ids)
if args.wrap:
self.ctx.out("FileAnnotation:%s" % obj_ids)
else:
self.ctx.out("OriginalFile:%s" % obj_ids)
def upload_and_link(conn, attachment, project):
fo = upload_ln_s(conn.c, attachment, OMERO_DATA_DIR, MIMETYPE)
fa = FileAnnotationI()
fa.setFile(fo._obj)
fa.setNs(omero.rtypes.rstring(NAMESPACE))
fa = conn.getUpdateService().saveAndReturnObject(fa)
fa = omero.gateway.FileAnnotationWrapper(conn, fa)
project.linkAnnotation(fa)
def upload_csv_to_omero(ctx,
file,
tablename,
target_id,
target_type="Project"):
"""Upload the CSV file and attach it to the specified object"""
print file
print file.name
svc = gateway.getFacility(DataManagerFacility)
file_size = os.path.getsize(file.name)
original_file = OriginalFileI()
original_file.setName(rstring(tablename))
original_file.setPath(rstring(file.name))
original_file.setSize(rlong(file_size))
checksum_algorithm = ChecksumAlgorithmI()
checksum_algorithm.setValue(rstring(ChecksumAlgorithmSHA1160.value))
original_file.setHasher(checksum_algorithm)
original_file.setMimetype(rstring("text/csv"))
original_file = svc.saveAndReturnObject(ctx, original_file)
store = gateway.getRawFileService(ctx)
# Open file and read stream
store.setFileId(original_file.getId().getValue())
print original_file.getId().getValue()
try:
store.setFileId(original_file.getId().getValue())
with open(file.name, 'rb') as stream:
buf = 10000
for pos in range(0, long(file_size), buf):
block = None
if file_size - pos < buf:
block_size = file_size - pos
else:
block_size = buf
stream.seek(pos)
block = stream.read(block_size)
store.write(block, pos, block_size)
original_file = store.save()
finally:
store.close()
# create the file annotation
namespace = "training.demo"
fa = FileAnnotationI()
fa.setFile(original_file)
fa.setNs(rstring(namespace))
if target_type == "Project":
target_obj = ProjectData(ProjectI(target_id, False))
elif target_type == "Dataset":
target_obj = DatasetData(DatasetI(target_id, False))
elif target_type == "Image":
target_obj = ImageData(ImageI(target_id, False))
svc.attachAnnotation(ctx, FileAnnotationData(fa), target_obj)
def upload_and_link(conn, target, attachment):
print("upload_and_link", attachment)
attachment = os.path.join(FILESETS_DIR, attachment)
fo = upload_ln_s(conn.c, attachment, OMERO_DATA_DIR, MIMETYPE)
fa = FileAnnotationI()
fa.setFile(fo._obj)
fa.setNs(omero.rtypes.rstring(NAMESPACE))
fa = conn.getUpdateService().saveAndReturnObject(fa)
fa = omero.gateway.FileAnnotationWrapper(conn, fa)
target.linkAnnotation(fa)
def upload_and_link(conn, attachment, image):
fa = image.getAnnotation(ns=NAMESPACE)
if fa is not None:
log.warning("Found file annotation. Skipping upload")
return
log.info("Uploading and linking %s to %s" % (attachment, image.getName()))
fo = upload_ln_s(conn.c, attachment, OMERO_DATA_DIR, MIMETYPE)
fa = FileAnnotationI()
fa.setFile(fo._obj)
fa.setNs(omero.rtypes.rstring(NAMESPACE))
fa = conn.getUpdateService().saveAndReturnObject(fa)
fa = omero.gateway.FileAnnotationWrapper(conn, fa)
image.linkAnnotation(fa)
def make_file_annotation(self,
name=None,
binary=None,
format=None,
client=None,
ns=None):
"""
Creates a new DatasetI instance and returns the persisted object.
If no name has been provided, a UUID string shall be used.
:param name: the name of the project
:param client: The client to use to create the object
:param ns: The namespace for the annotation
"""
if client is None:
client = self.client
update = client.sf.getUpdateService()
# file
if format is None:
format = "application/octet-stream"
if binary is None:
binary = "12345678910"
if name is None:
name = str(self.uuid())
oFile = OriginalFileI()
oFile.setName(rstring(name))
oFile.setPath(rstring(str(self.uuid())))
oFile.setSize(rlong(len(binary)))
oFile.hasher = ChecksumAlgorithmI()
oFile.hasher.value = rstring("SHA1-160")
oFile.setMimetype(rstring(str(format)))
oFile = update.saveAndReturnObject(oFile)
# save binary
store = client.sf.createRawFileStore()
store.setFileId(oFile.id.val)
store.write(binary, 0, 0)
oFile = store.save() # See ticket:1501
store.close()
fa = FileAnnotationI()
fa.setFile(oFile)
if ns is not None:
fa.setNs(rstring(ns))
return update.saveAndReturnObject(fa)
def make_file_annotation(self, name=None, binary=None, format=None, client=None, ns=None):
"""
Creates a new DatasetI instance and returns the persisted object.
If no name has been provided, a UUID string shall be used.
:param name: the name of the project
:param client: The client to use to create the object
:param ns: The namespace for the annotation
"""
if client is None:
client = self.client
update = client.sf.getUpdateService()
# file
if format is None:
format = "application/octet-stream"
if binary is None:
binary = "12345678910"
if name is None:
name = str(self.uuid())
oFile = OriginalFileI()
oFile.setName(rstring(name))
oFile.setPath(rstring(str(self.uuid())))
oFile.setSize(rlong(len(binary)))
oFile.hasher = ChecksumAlgorithmI()
oFile.hasher.value = rstring("SHA1-160")
oFile.setMimetype(rstring(str(format)))
oFile = update.saveAndReturnObject(oFile)
# save binary
store = client.sf.createRawFileStore()
store.setFileId(oFile.id.val)
store.write(binary, 0, 0)
oFile = store.save() # See ticket:1501
store.close()
fa = FileAnnotationI()
fa.setFile(oFile)
if ns is not None:
fa.setNs(rstring(ns))
return update.saveAndReturnObject(fa)
def save_microscope(request, conn=None, **kwargs):
body_json = json.loads(request.body)
microscope_json = body_json['microscope']
file_name = microscope_json["Name"]
project = conn.getObject("Project", attributes={'name': PROJECT_NAME})
curr_gid = conn.SERVICE_OPTS.getOmeroGroup()
if project is not None:
gid = project.getDetails().getGroup().getId()
conn.SERVICE_OPTS.setOmeroGroup(gid)
else:
# TODO: create Project
conn.SERVICE_OPTS.setOmeroGroup(curr_gid)
update = conn.getUpdateService()
file_data = json.dumps(microscope_json)
file_size = len(file_data)
f = BytesIO()
f.write(file_data.encode("utf-8"))
orig_file = conn.createOriginalFileFromFileObj(f,
'',
file_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))
fa = update.saveAndReturnObject(fa, conn.SERVICE_OPTS)
file_id = fa.getId().getValue()
if project is not None:
fa_wrapper = FileAnnotationWrapper(conn, fa)
project.linkAnnotation(fa_wrapper)
return JsonResponse({'file_id': file_id})
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