def get_history(conn, type, id):
""" Get history information of ReceptorLight object based on the type.
@param conn OMERO gateway
@param type ReceptorLight Object Type
@param id Unique id of the ReceptorLight Object
"""
rlService = utilities.get_receptor_light_service(conn)
metadata_json_data = get_metadata_json(type)
rl_function_name = get_rl_function_name(type)
rlobject = getattr(rlService, rl_function_name)(id)
versions = [rlobject]
parent_ids_list = get_all_parents_of_rlobject(rlService, rl_function_name,
rlobject, versions)
rlobject_versions = []
if not parent_ids_list:
parent_ids_list = versions
for rlobject in parent_ids_list:
if rlobject:
history = {}
history['name'] = rlobject.getName().getValue()
history['id'] = rlobject.getUId().getValue()
history['creation_time'] = rlobject.getCreationDateTime().getValue(
)
history['ownername'] = utilities.get_experimenter_name(
conn,
rlobject.getOwnerId().getValue())
rlobject_versions.append(history)
return rlobject_versions
def get_sections_from_model(conn, type):
rlService = utilities.get_receptor_light_service(conn)
model_type = 'Rl' + str(type)
if type == 'RestrictionEnzyme':
model_type += 's'
sections = rlService.uihelpGetSectionsOfType(model_type)
return sections
def get_all_exp_materials(conn, type, *args, **kwargs):
""" Get ReceptorLight object list based on the type.
@param conn OMERO gateway
@param type ReceptorLight Object Type
"""
if 'status' in kwargs:
status = int(kwargs.get('status', -1))
rlService = utilities.get_receptor_light_service(conn)
exp_material_type = type + 's'
rl_function_name = get_rl_function_name(exp_material_type)
rlobjects = getattr(rlService, rl_function_name)()
exp_materials = []
for rlobject in rlobjects:
if rlobject.getStatus().getValue() == status:
exp_material = {}
exp_material['name'] = rlobject.getName().getValue()
exp_material['id'] = rlobject.getUId().getValue()
exp_material['originalid'] = rlobject.getOriginalObjectId(
).getValue()
exp_material['access_right'] = getAccessRights(rlobject, conn)
exp_material['ownername'] = utilities.get_experimenter_name(
conn,
rlobject.getOwnerId().getValue())
exp_material['status'] = rlobject.getStatus().getValue()
if type == 'Experiment':
exp_material['datasetId'] = rlobject.getDatasetId().getValue()
exp_materials.append(exp_material)
return exp_materials
def get_json_from_server(conn, type):
""" Get ReceptorLight object data in json based on the type.
@param conn OMERO gateway
@param type ReceptorLight Object Type
@param id Unique id of the ReceptorLight Object
"""
rlService = utilities.get_receptor_light_service(conn)
model_type = 'Rl' + str(type)
if type == 'RestrictionEnzyme':
model_type += 's'
experiment_sections = rlService.uihelpGetSectionsOfType(model_type)
rl_function_name = get_rl_function_name(type)
experiment_object = {}
for section in experiment_sections:
experiment_object[section] = []
for element in rlService.uihelpGetElementsOfSections(
model_type, section):
elem_info = rlService.uihelpGetElementInfo(model_type, element)
e = {}
e['key'] = element
e['name'] = elem_info.getUiName().getValue()
e['help'] = elem_info.getUiHelp().getValue()
e['index'] = elem_info.getIndex().getValue()
e['isVisible'] = elem_info.getIsVisible().getValue()
experiment_object[section].append(e)
return experiment_object
def delete_rl_object(conn, type, id):
""" Delete ReceptorLight object based on the type.
@param conn OMERO gateway
@param type ReceptorLight Object Type
@param id Unique id of the ReceptorLight Object
"""
rlService = utilities.get_receptor_light_service(conn)
rl_function_name = delete_rl_function_name(type)
delete_used_materials(conn, id)
return getattr(rlService, rl_function_name)(id)
def get_rl_object(conn, type, id):
""" Get ReceptorLight object based on the type.
@param conn OMERO gateway
@param type ReceptorLight Object Type
@param id Unique id of the ReceptorLight Object
"""
rlService = utilities.get_receptor_light_service(conn)
rl_function_name = get_rl_function_name(type)
rlobject = getattr(rlService, rl_function_name)(id)
return rlobject
def get_all_experimentids_of_login_user(conn, type, *args, **kwargs):
current_user_id = conn.getUser().getId()
rlService = utilities.get_receptor_light_service(conn)
exp_material_type = type + 's'
rl_function_name = get_rl_function_name(exp_material_type)
rlobjects = getattr(rlService, rl_function_name)()
rl_obj_ids = []
for rlobject in rlobjects:
if rlobject.getOwnerId().getValue() == current_user_id:
rl_obj_ids.append(rlobject.getUId().getValue())
return rl_obj_ids
def delete_used_materials(conn, source_id):
rlService = utilities.get_receptor_light_service(conn)
used_materials = rlService.getUsedMaterialsBySourceId(source_id)
for used_material in used_materials:
used_material_id = used_material.getUId().getValue()
if used_material.getTargetType().getValue() == 'RlFileInformation':
fileId = used_material.getTargetID().getValue()
fileService = utilities.get_receptor_light_file_service(conn)
fileService.deleteFile(int(fileId))
rlService.deleteUsedMaterial(int(used_material_id))
def execute_proposal_action(conn, input_type, input_id, action_id):
rlService = utilities.get_receptor_light_service(conn)
rlobject = get_rl_object(conn, input_type, input_id)
if int(action_id) == 1:
rlobject.setStatus(omero.rtypes.rint(4))
elif int(action_id) == 2:
rlobject.setStatus(omero.rtypes.rint(8))
current_user_id = conn.getUser().getId()
rlobject.setOwnerId(omero.rtypes.rint(current_user_id))
current_user_group_id = conn.getGroupFromContext().getId()
rlobject.setOwnerGroupId(omero.rtypes.rint(current_user_group_id))
save_rl_fn_name = save_rl_function_name(input_type)
getattr(rlService, save_rl_fn_name)(rlobject)
def get_experiment_id_from_dataset(conn, datasetId):
""" Get experiment id from the dataset with ReceptorLight Service
@param rlService ReceptorLight Service
@param datasetId Dataset Id to which the experiment belongs
@type datasetId Integer
"""
rlService = utilities.get_receptor_light_service(conn)
exp = rlService.getExperimentByDatasetId(datasetId)
if exp:
if int(exp.getStatus().getValue()) == 1:
return int(exp.getUId().getValue())
else:
return None
def get_options(conn, type):
""" Get options of ReceptorLight object
@param conn OMERO gateway
@param type ReceptorLight Object Type
"""
rlService = utilities.get_receptor_light_service(conn)
exp_material_type = type + 's'
rl_function_name = get_rl_function_name(exp_material_type)
rlobjects = getattr(rlService, rl_function_name)()
exp_materials = {}
for rlobject in rlobjects:
exp_materials[
rlobject.getUId().getValue()] = rlobject.getName().getValue()
return exp_materials
def get_fieldsets_of_type(conn, type):
rlService = utilities.get_receptor_light_service(conn)
model_type = 'Rl' + str(type)
if type == 'RestrictionEnzyme':
model_type += 's'
experiment_sections = rlService.uihelpGetSectionsOfType(model_type)
fieldsets = []
for section in experiment_sections:
fields = []
for element in rlService.uihelpGetElementsOfSections(
model_type, section):
elem_info = rlService.uihelpGetElementInfo(model_type, element)
if elem_info.getIsVisible().getValue():
fields.append(element)
fieldset_values = {"fields": tuple(fields), "classes": ['collapse']}
fieldsets.append((section, fieldset_values))
fieldsets = tuple(fieldsets)
return fieldsets
def add_to_used_material(conn, source_id, source_type, target_id, target_type,
used_in_step):
rlService = utilities.get_receptor_light_service(conn)
used_material = rlService.createUsedMaterial()
source_type = get_used_material_type(source_type)
used_material.setSourceID(omero.rtypes.rint(source_id))
st = used_material.getSourceType()
st.setValue(omero.rtypes.rstring(source_type))
used_material.setSourceType(st)
used_material.setTargetID(omero.rtypes.rint(target_id))
tt = used_material.getTargetType()
tt.setValue(omero.rtypes.rstring(target_type))
used_material.setTargetType(tt)
used_material.setUsedIn(omero.rtypes.rstring(used_in_step))
return rlService.saveUsedMaterial(used_material)
def get_proposals_on_mine(conn, type, *args, **kwargs):
""" Get ReceptorLight object list based on the type.
@param conn OMERO gateway
@param type ReceptorLight Object Type
"""
if 'status' in kwargs:
status = int(kwargs.get('status', -1))
if 'flag' in kwargs:
flag = int(kwargs.get('flag', -1))
current_user_id = conn.getUser().getId()
rlService = utilities.get_receptor_light_service(conn)
exp_material_type = type + 's'
rl_function_name = get_rl_function_name(exp_material_type)
rlobjects = getattr(rlService, rl_function_name)()
exp_materials = []
login_user_exp_ids = get_all_experimentids_of_login_user(
conn, type, *args, **kwargs)
for rlobject in rlobjects:
if rlobject.getOriginalObjectId().getValue(
) in login_user_exp_ids and rlobject.getStatus().getValue() in (2, 4,
8):
exp_material = {}
exp_material['name'] = rlobject.getName().getValue()
exp_material['id'] = rlobject.getUId().getValue()
exp_material['originalid'] = rlobject.getOriginalObjectId(
).getValue()
exp_material['access_right'] = getAccessRights(rlobject, conn)
exp_material['ownername'] = utilities.get_experimenter_name(
conn,
rlobject.getOwnerId().getValue())
exp_material['status'] = rlobject.getStatus().getValue()
if exp_material['status'] == 2:
exp_material['status_text'] = 'Proposed'
elif exp_material['status'] == 4:
exp_material['status_text'] = 'Accepted'
elif exp_material['status'] == 8:
exp_material['status_text'] = 'Rejected'
if type == 'Experiment':
exp_material['datasetId'] = rlobject.getDatasetId().getValue()
exp_materials.append(exp_material)
return exp_materials
def get_all_exp_materials_choices(conn):
""" Get options of ReceptorLight object
@param conn OMERO gateway
"""
rlService = utilities.get_receptor_light_service(conn)
exp_material_types = [
'Proteins', 'Plasmids', 'Vectors', 'Dnas', 'Rnas',
'ChemicalSubstances', 'Solutions', 'FluorescentProteins',
'RestrictionEnzymes', 'Oligonucleotides', 'Sops'
]
all_exp_materials_choices = {}
for exp_material_type in exp_material_types:
rl_function_name = get_rl_function_name(exp_material_type)
rlobjects = getattr(rlService, rl_function_name)()
exp_materials = {}
for rlobject in rlobjects:
if rlobject.getStatus().getValue() == 1:
exp_materials[rlobject.getUId().getValue()] = rlobject.getName(
).getValue()
all_exp_materials_choices[exp_material_type[:-1]] = exp_materials
return all_exp_materials_choices
def create_new_from_parent_rlobject(conn, type, rlobject, *args, **kwargs):
if 'rl_obj_name' in kwargs:
rl_obj_name = str(kwargs.get('rl_obj_name', ''))
if rl_obj_name == '':
rl_obj_name = rlobject.getName().getValue()
rlService = utilities.get_receptor_light_service(conn)
create_rl_object_fn = get_create_rl_object_fn(type)
new_rlobject = getattr(rlService, create_rl_object_fn)(rl_obj_name)
new_rlobject_id = new_rlobject.getUId().getValue()
new_rlobject_creation_time = new_rlobject.getCreationDateTime().getValue()
new_rlobject_owner_id = new_rlobject.getOwnerId().getValue()
new_rlobject_owner_group_id = new_rlobject.getOwnerGroupId().getValue()
rl_object_keys = getattr(rlService, 'getMemberNames')(new_rlobject)
if rlobject:
rl_object_id = rlobject.getUId().getValue()
for rl_obj_key in rl_object_keys:
set_fn = 'set' + rl_obj_key
get_fn = 'get' + rl_obj_key
rlobject_value = getattr(rlobject, get_fn)()
getattr(new_rlobject, set_fn)(rlobject_value)
new_rlobject.setUId(omero.rtypes.rint(new_rlobject_id))
new_rlobject.setCreationDateTime(
omero.rtypes.rstring(new_rlobject_creation_time))
new_rlobject.setOwnerId(omero.rtypes.rint(new_rlobject_owner_id))
new_rlobject.setOwnerGroupId(
omero.rtypes.rint(new_rlobject_owner_group_id))
used_materials = rlService.getUsedMaterialsBySourceId(rl_object_id)
for used_material in used_materials:
source_id = new_rlobject_id
source_type = used_material.getSourceType().getValue().getValue()
target_id = used_material.getTargetID().getValue()
target_type = used_material.getTargetType().getValue().getValue()
used_in_step = used_material.getUsedIn().getValue()
add_to_used_material(conn, source_id, source_type, target_id,
target_type, used_in_step)
return new_rlobject
def get_difference_of_rlobjects(conn, type, id1, id2):
rlService = utilities.get_receptor_light_service(conn)
model_type = 'Rl' + str(type)
if type == 'RestrictionEnzyme':
model_type += 's'
metadata_json_data = get_metadata_json(type)
rl_function_name = get_rl_function_name(type)
rlobject1 = getattr(rlService, rl_function_name)(id1)
rlobject2 = getattr(rlService, rl_function_name)(id2)
experiment_object = {}
for section in metadata_json_data:
experiment_object[section] = []
for data in metadata_json_data[section]:
e = {}
e['key'] = data['key']
e['name'] = data['name']
e['help'] = data['help']
e['index'] = data['index']
e['isVisible'] = data['isVisible']
e['uiType'] = data['uiType']
if data['uiType'] == 'weblink' and 'linkType' in data:
e['linkType'] = data['linkType']
method_name = 'get' + data['key']
val1 = getattr(rlobject1, method_name)()
val2 = getattr(rlobject2, method_name)()
e['value1'] = get_element_value(conn, val1, data)
e['value2'] = get_element_value(conn, val2, data)
if hasattr(val1, '__class__'):
value = val1.__class__
e['type'] = str(value)
experiment_object[section].append(e)
return experiment_object
def get_json(conn, type, id):
""" Get ReceptorLight object data in json based on the type.
@param conn OMERO gateway
@param type ReceptorLight Object Type
@param id Unique id of the ReceptorLight Object
"""
rlService = utilities.get_receptor_light_service(conn)
model_type = 'Rl' + str(type)
if type == 'RestrictionEnzyme':
model_type += 's'
metadata_json_data = get_metadata_json(type)
rl_function_name = get_rl_function_name(type)
rlobject = getattr(rlService, rl_function_name)(id)
experiment_object = {}
for section in metadata_json_data:
experiment_object[section] = []
for data in metadata_json_data[section]:
e = {}
e['key'] = data['key']
e['name'] = data['name']
e['help'] = data['help']
e['index'] = data['index']
e['isVisible'] = data['isVisible']
e['uiType'] = data['uiType']
if 'unit' in data:
e['unit'] = data['unit']
if data['uiType'] == 'weblink' and 'linkType' in data:
e['linkType'] = data['linkType']
method_name = 'get' + data['key']
val = getattr(rlobject, method_name)()
if hasattr(val, 'getValue'):
value = val.getValue()
# if data['key'] == 'ContactPerson':
# if isinstance(value, int):
# e['value'] = utilities.get_experimenter_name(conn, value)
# else:
# e['value'] = value
if data['uiType'] == 'file':
fileService = utilities.get_receptor_light_file_service(
conn)
if value:
fileInfo = fileService.getFileInformation(int(value))
if fileInfo:
e['value'] = str(fileInfo.getName().getValue())
e['fileId'] = int(value)
else:
e['value'] = value if value else None
if hasattr(val, 'copyValues'):
val_list = val.copyValues()
if data['uiType'] == 'multiplefiles':
fileService = utilities.get_receptor_light_file_service(
conn)
e['value'] = {}
for v in val_list:
if v:
fileInfo = fileService.getFileInformation(
int(v.getValue().getValue()))
if fileInfo:
e['value'][int(
v.getValue().getValue())] = (str(
fileInfo.getName().getValue()))
if hasattr(val, '__class__'):
value = val.__class__
e['type'] = str(value)
experiment_object[section].append(e)
return experiment_object
def save_rl_object(conn, type, changed_dict, form_data, *args, **kwargs):
""" Save information of ReceptorLight object based on the type.
@param conn OMERO gateway
@param type ReceptorLight Object Type
@param changed_dict Changed information
@param form_data the Form data
@param args Args
@param kwargs Request Args
"""
try:
save_rl_fn_name = save_rl_function_name(type)
rlService = utilities.get_receptor_light_service(conn)
parent_rlobject_id = None
new_rlobject_id = None
rlobject = None
action = ''
root_folder_id = -1
if 'action' in kwargs:
action = str(kwargs.get('action', ''))
if 'input_name' in kwargs:
rl_obj_name = str(kwargs.get('input_name', ''))
if 'id' in kwargs:
input_id = int(kwargs.get('id', -1))
if input_id != -1:
rlobject = get_rl_object(conn, type, input_id)
parent_rlobject_id = rlobject.getUId()
if type == 'Experiment':
root_folder_id = rlobject.getRootFolderId().getValue()
parent_datasetId = rlobject.getDatasetId().getValue()
if action == '':
rlobject.setStatus(omero.rtypes.rint(0))
getattr(rlService, save_rl_fn_name)(rlobject)
if 'files' in kwargs:
rl_files = kwargs.get('files', '')
new_rlobject = create_new_from_parent_rlobject(conn,
type,
rlobject,
rl_obj_name=rl_obj_name)
new_rlobject_id = new_rlobject.getUId().getValue()
if type == 'Experiment':
if input_id == -1:
root_folder_id = getCreateRootFolder(conn, new_rlobject_id)
new_rlobject.setRootFolderId(omero.rtypes.rint(root_folder_id))
getattr(rlService, save_rl_fn_name)(new_rlobject)
new_rlobject = save_rlobject_types(conn,
new_rlobject_id,
type,
changed_dict,
root_folder_id=root_folder_id,
files=rl_files)
if input_id != -1 and type == 'Experiment':
new_rlobject.setDatasetId(omero.rtypes.rint(parent_datasetId))
if parent_rlobject_id:
new_rlobject.setOriginalObjectId(parent_rlobject_id)
if action == 'propose':
new_rlobject.setStatus(omero.rtypes.rint(2))
else:
new_rlobject.setStatus(omero.rtypes.rint(1))
getattr(rlService, save_rl_fn_name)(new_rlobject)
return 1
except Exception as e:
logging.info("Exception:(%s)", e)
if new_rlobject_id:
delete_rl_object(conn, type, new_rlobject_id)
if rlobject:
rlobject.setStatus(omero.rtypes.rint(1))
getattr(rlService, save_rl_fn_name)(rlobject)
return 0
def save_rlobject_types(conn, new_rlobject_id, type, changed_dict, *args,
**kwargs):
if 'files' in kwargs:
rl_files = kwargs.get('files', '')
if 'root_folder_id' in kwargs:
root_folder_id = int(kwargs.get('root_folder_id', -1))
metadata_json_data = get_metadata_json(type)
rlService = utilities.get_receptor_light_service(conn)
new_rlobject = get_rl_object(conn, type, new_rlobject_id)
for key, value in changed_dict.items():
for categories in metadata_json_data:
for data in metadata_json_data[categories]:
if data['key'] == key:
if value:
if data['uiType'] == 'file':
for filename, file in rl_files.iteritems():
if filename == data['key'] and rl_files[
filename]:
if type == 'Experiment':
omero_value_object = save_file_information(
conn,
rl_files[filename],
data['key'],
root_folder_id=root_folder_id,
input_id=new_rlobject_id,
input_type=type)
else:
omero_value_object = save_file_information(
conn,
rl_files[filename],
data['key'],
input_id=new_rlobject_id,
input_type=type)
elif data['uiType'] == 'multiplefiles':
if type == 'Experiment':
omero_value_object = save_multiple_files(
conn,
rl_files,
data['key'],
root_folder_id=root_folder_id,
input_id=new_rlobject_id,
input_type=type)
else:
omero_value_object = save_multiple_files(
conn,
rl_files,
data['key'],
input_id=new_rlobject_id,
input_type=type)
elif data['uiType'] == 'richText':
if type == 'Experiment':
omero_value_object = save_richText(
conn,
rl_files,
value,
data['key'],
root_folder_id=root_folder_id,
input_id=new_rlobject_id,
input_type=type)
else:
omero_value_object = save_richText(
conn,
rl_files,
value,
data['key'],
input_id=new_rlobject_id,
input_type=type)
else:
omero_value_object = convert_value_to_omero_value(
value, data['type'], data['uiType'],
data['key'], conn)
function_name = convert_type_to_function(data['type'])
try:
if data['type'] == 'omero.rtypes.RDoubleI':
set_fn = 'set' + data['key']
getattr(new_rlobject,
set_fn)(omero_value_object)
else:
new_rlobject = getattr(rlService,
function_name)(
new_rlobject, key,
omero_value_object)
except Exception as e:
logging.info("Exception:(%s)", e)
return 0
return new_rlobject