diff --git a/pybis/src/python/pybis/pybis.py b/pybis/src/python/pybis/pybis.py
index 31d5940a5143ad728ee5fc3351bf0ff319eef307..9ce2c225adb1884119ab17486212a681e5a65960 100644
--- a/pybis/src/python/pybis/pybis.py
+++ b/pybis/src/python/pybis/pybis.py
@@ -103,9 +103,11 @@ LOG_DEBUG = 7
DEBUG_LEVEL = LOG_NONE
+
def now():
return time.time()
+
def get_search_type_for_entity(entity, operator=None):
"""Returns a dictionary containing the correct search criteria type
for a given entity.
@@ -267,7 +269,15 @@ def _list_update(ids=None, entity=None, action="Add"):
if not isinstance(ids, list):
ids = [ids]
- items = list(map(lambda id: {"code": id, "@type": "as.dto.{}.id.{}Code".format(entity.lower(), entity)}, ids))
+ items = list(
+ map(
+ lambda id: {
+ "code": id,
+ "@type": "as.dto.{}.id.{}Code".format(entity.lower(), entity),
+ },
+ ids,
+ )
+ )
list_update = {
"actions": [
@@ -379,7 +389,9 @@ def _gen_search_criteria(req):
sreq = {}
for key, val in req.items():
if key == "criteria":
- sreq["criteria"] = list(map(lambda item: _gen_search_criteria(item), req["criteria"]))
+ sreq["criteria"] = list(
+ map(lambda item: _gen_search_criteria(item), req["criteria"])
+ )
elif key == "code":
sreq["criteria"] = [
_common_search("as.dto.common.search.CodeSearchCriteria", val.upper())
@@ -426,15 +438,20 @@ def _subcriteria_for_tags(tags):
if not isinstance(tags, list):
tags = [tags]
- criteria = list(map(lambda tag: {
- "fieldName": "code",
- "fieldType": "ATTRIBUTE",
- "fieldValue": {
- "value": tag,
- "@type": "as.dto.common.search.StringEqualToValue",
- },
- "@type": "as.dto.common.search.CodeSearchCriteria",
- }, tags))
+ criteria = list(
+ map(
+ lambda tag: {
+ "fieldName": "code",
+ "fieldType": "ATTRIBUTE",
+ "fieldValue": {
+ "value": tag,
+ "@type": "as.dto.common.search.StringEqualToValue",
+ },
+ "@type": "as.dto.common.search.CodeSearchCriteria",
+ },
+ tags,
+ )
+ )
return {
"@type": "as.dto.tag.search.TagSearchCriteria",
@@ -716,15 +733,20 @@ def _subcriteria_for_identifier(ids, entity, parents_or_children="", operator="A
if not isinstance(ids, list):
ids = [ids]
- criteria = list(map(lambda id: {
- "@type": "as.dto.common.search.IdentifierSearchCriteria",
- "fieldValue": {
- "value": id,
- "@type": "as.dto.common.search.StringEqualToValue",
- },
- "fieldType": "ATTRIBUTE",
- "fieldName": "identifier",
- }, ids))
+ criteria = list(
+ map(
+ lambda id: {
+ "@type": "as.dto.common.search.IdentifierSearchCriteria",
+ "fieldValue": {
+ "value": id,
+ "@type": "as.dto.common.search.StringEqualToValue",
+ },
+ "fieldType": "ATTRIBUTE",
+ "fieldName": "identifier",
+ },
+ ids,
+ )
+ )
search_type = get_type_for_entity(entity, "search", parents_or_children)
return {"criteria": criteria, **search_type, "operator": operator}
@@ -734,15 +756,20 @@ def _subcriteria_for_permid(permids, entity, parents_or_children="", operator="A
if not isinstance(permids, list):
permids = [permids]
- criteria = list(map(lambda permid: {
- "@type": "as.dto.common.search.PermIdSearchCriteria",
- "fieldValue": {
- "value": permid,
- "@type": "as.dto.common.search.StringEqualToValue",
- },
- "fieldType": "ATTRIBUTE",
- "fieldName": "perm_id",
- }, permids))
+ criteria = list(
+ map(
+ lambda permid: {
+ "@type": "as.dto.common.search.PermIdSearchCriteria",
+ "fieldValue": {
+ "value": permid,
+ "@type": "as.dto.common.search.StringEqualToValue",
+ },
+ "fieldType": "ATTRIBUTE",
+ "fieldName": "perm_id",
+ },
+ permids,
+ )
+ )
search_type = get_type_for_entity(entity, "search", parents_or_children)
return {"criteria": criteria, **search_type, "operator": operator}
@@ -752,15 +779,20 @@ def _subcriteria_for_permid_new(codes, entity, parents_or_children="", operator=
if not isinstance(codes, list):
codes = [codes]
- criteria = list(map(lambda code: {
- "@type": "as.dto.common.search.PermIdSearchCriteria",
- "fieldValue": {
- "value": code,
- "@type": "as.dto.common.search.StringEqualToValue",
- },
- "fieldType": "ATTRIBUTE",
- "fieldName": "perm_id",
- }, codes))
+ criteria = list(
+ map(
+ lambda code: {
+ "@type": "as.dto.common.search.PermIdSearchCriteria",
+ "fieldValue": {
+ "value": code,
+ "@type": "as.dto.common.search.StringEqualToValue",
+ },
+ "fieldType": "ATTRIBUTE",
+ "fieldName": "perm_id",
+ },
+ codes,
+ )
+ )
search_type = get_type_for_entity(entity, "search", parents_or_children)
return {"criteria": criteria, **search_type, "operator": operator}
@@ -770,15 +802,20 @@ def _subcriteria_for_code_new(codes, entity, parents_or_children="", operator="A
if not isinstance(codes, list):
codes = [codes]
- criteria = list(map(lambda code: {
- "@type": "as.dto.common.search.CodeSearchCriteria",
- "fieldValue": {
- "value": code,
- "@type": "as.dto.common.search.StringEqualToValue",
- },
- "fieldType": "ATTRIBUTE",
- "fieldName": "code",
- }, codes))
+ criteria = list(
+ map(
+ lambda code: {
+ "@type": "as.dto.common.search.CodeSearchCriteria",
+ "fieldValue": {
+ "value": code,
+ "@type": "as.dto.common.search.StringEqualToValue",
+ },
+ "fieldType": "ATTRIBUTE",
+ "fieldName": "code",
+ },
+ codes,
+ )
+ )
search_type = get_type_for_entity(entity, "search", parents_or_children)
return {"criteria": criteria, **search_type, "operator": operator}
@@ -1667,7 +1704,7 @@ class Openbis:
count=count,
totalCount=resp.get("totalCount"),
response=resp,
- df_initializer=create_data_frame
+ df_initializer=create_data_frame,
)
def get_role_assignment(self, techId, only_data=False):
@@ -1835,7 +1872,7 @@ class Openbis:
count=count,
totalCount=resp.get("totalCount"),
response=resp,
- df_initializer=create_data_frame
+ df_initializer=create_data_frame,
)
def get_persons(self, start_with=None, count=None, **search_args):
@@ -1886,7 +1923,7 @@ class Openbis:
count=count,
totalCount=resp.get("totalCount"),
response=resp,
- df_initializer=create_data_frame
+ df_initializer=create_data_frame,
)
get_users = get_persons # Alias
@@ -1965,7 +2002,7 @@ class Openbis:
count=count,
totalCount=resp.get("totalCount"),
response=resp,
- df_initializer=create_data_frame
+ df_initializer=create_data_frame,
)
def get_space(self, code, only_data=False, use_cache=True):
@@ -2059,8 +2096,8 @@ class Openbis:
b) property is not defined for this sampleType
"""
- logger = logging.getLogger('get_samples')
- logger.setLevel(logging.DEBUG)
+ logger = logging.getLogger("get_samples")
+ logger.setLevel(logging.CRITICAL)
logger.addHandler(logging.StreamHandler(sys.stdout))
if collection is not None:
@@ -2164,8 +2201,15 @@ class Openbis:
logger.debug(f"get_samples after result mapping. Delay: {time4 - time3}")
- result = self._sample_list_for_response(response=response, attrs=attrs, props=props, start_with=start_with,
- count=count, totalCount=resp["totalCount"], parsed=True)
+ result = self._sample_list_for_response(
+ response=response,
+ attrs=attrs,
+ props=props,
+ start_with=start_with,
+ count=count,
+ totalCount=resp["totalCount"],
+ parsed=True,
+ )
time5 = now()
@@ -2275,9 +2319,16 @@ class Openbis:
else:
properties = {**where, **properties}
if properties is not None:
- sub_criteria.extend(list(map(
- lambda prop: _subcriteria_for_properties(prop, properties[prop], entity="experiment"), properties
- )))
+ sub_criteria.extend(
+ list(
+ map(
+ lambda prop: _subcriteria_for_properties(
+ prop, properties[prop], entity="experiment"
+ ),
+ properties,
+ )
+ )
+ )
search_criteria = get_search_type_for_entity("experiment")
search_criteria["criteria"] = sub_criteria
@@ -2343,7 +2394,9 @@ class Openbis:
for attr in attrs:
# if no dot supplied, just display the code of the space, project or experiment
if attr in ["project"]:
- experiments[attr] = experiments[attr].map(extract_nested_identifier)
+ experiments[attr] = experiments[attr].map(
+ extract_nested_identifier
+ )
if attr in ["space"]:
experiments[attr] = experiments[attr].map(extract_code)
@@ -2354,7 +2407,9 @@ class Openbis:
format_timestamp
)
experiments["project"] = experiments["project"].map(extract_code)
- experiments["registrator"] = experiments["registrator"].map(extract_person)
+ experiments["registrator"] = experiments["registrator"].map(
+ extract_person
+ )
experiments["modifier"] = experiments["modifier"].map(extract_person)
experiments["identifier"] = experiments["identifier"].map(
extract_identifier
@@ -2368,7 +2423,9 @@ class Openbis:
# expand the dataFrame by adding new columns
columns = []
for i, experiment in enumerate(response):
- for prop_name, val in experiment.get("properties", {}).items():
+ for prop_name, val in experiment.get(
+ "properties", {}
+ ).items():
experiments.loc[i, prop_name.upper()] = val
columns.append(prop_name.upper())
@@ -2394,7 +2451,7 @@ class Openbis:
attrs=attrs,
props=props,
response=resp,
- df_initializer=create_data_frame
+ df_initializer=create_data_frame,
)
get_collections = get_experiments # Alias
@@ -2497,9 +2554,16 @@ class Openbis:
properties = {**where, **properties}
if properties is not None:
- sub_criteria.extend(list(map(
- lambda prop: _subcriteria_for_properties(prop, properties[prop], entity="dataset"), properties
- )))
+ sub_criteria.extend(
+ list(
+ map(
+ lambda prop: _subcriteria_for_properties(
+ prop, properties[prop], entity="dataset"
+ ),
+ properties,
+ )
+ )
+ )
search_criteria = get_search_type_for_entity("dataset")
search_criteria["criteria"] = sub_criteria
@@ -2562,7 +2626,7 @@ class Openbis:
count=count,
totalCount=resp["totalCount"],
objects=datasets,
- parsed=True
+ parsed=True,
)
def get_experiment(
@@ -2749,11 +2813,7 @@ class Openbis:
if only_data:
return resp[projectId]
- project = Project(
- openbis_obj=self,
- type=None,
- data=resp[projectId]
- )
+ project = Project(openbis_obj=self, type=None, data=resp[projectId])
if self.use_cache:
self._object_cache(entity="project", code=projectId, value=project)
return project
@@ -2775,11 +2835,7 @@ class Openbis:
if only_data:
return resp["objects"][0]
- project = Project(
- openbis_obj=self,
- type=None,
- data=resp["objects"][0]
- )
+ project = Project(openbis_obj=self, type=None, data=resp["objects"][0])
if self.use_cache:
self._object_cache(entity="project", code=projectId, value=project)
return project
@@ -2860,7 +2916,7 @@ class Openbis:
count=count,
totalCount=resp.get("totalCount"),
response=resp,
- df_initializer=create_data_frame
+ df_initializer=create_data_frame,
)
def _create_get_request(self, method_name, entity, permids, options, foType):
@@ -2963,8 +3019,12 @@ class Openbis:
terms["vocabularyCode"] = terms["permId"].map(
extract_attr("vocabularyCode")
)
- terms["registrationDate"] = terms["registrationDate"].map(format_timestamp)
- terms["modificationDate"] = terms["modificationDate"].map(format_timestamp)
+ terms["registrationDate"] = terms["registrationDate"].map(
+ format_timestamp
+ )
+ terms["modificationDate"] = terms["modificationDate"].map(
+ format_timestamp
+ )
return terms[attrs]
things = Things(
@@ -2976,7 +3036,7 @@ class Openbis:
count=count,
totalCount=resp.get("totalCount"),
response=resp,
- df_initializer=create_data_frame
+ df_initializer=create_data_frame,
)
if (
self.use_cache
@@ -3061,8 +3121,12 @@ class Openbis:
else:
parse_jackson(response)
vocs = DataFrame(objects)
- vocs["registrationDate"] = vocs["registrationDate"].map(format_timestamp)
- vocs["modificationDate"] = vocs["modificationDate"].map(format_timestamp)
+ vocs["registrationDate"] = vocs["registrationDate"].map(
+ format_timestamp
+ )
+ vocs["modificationDate"] = vocs["modificationDate"].map(
+ format_timestamp
+ )
vocs["registrator"] = vocs["registrator"].map(extract_person)
return vocs[attrs]
@@ -3074,7 +3138,7 @@ class Openbis:
count=count,
totalCount=resp.get("totalCount"),
response=resp,
- df_initializer=create_data_frame
+ df_initializer=create_data_frame,
)
def get_vocabulary(self, code, only_data=False, use_cache=True):
@@ -3201,7 +3265,9 @@ class Openbis:
tags = DataFrame(columns=attrs)
else:
tags = DataFrame(response)
- tags["registrationDate"] = tags["registrationDate"].map(format_timestamp)
+ tags["registrationDate"] = tags["registrationDate"].map(
+ format_timestamp
+ )
tags["permId"] = tags["permId"].map(extract_permid)
tags["description"] = tags["description"].map(
lambda x: "" if x is None else x
@@ -3215,7 +3281,7 @@ class Openbis:
identifier_name="permId",
totalCount=totalCount,
response=response,
- df_initializer=create_data_frame
+ df_initializer=create_data_frame,
)
def search_semantic_annotations(
@@ -3304,7 +3370,7 @@ class Openbis:
entity="semantic_annotation",
identifier_name="permId",
response=objects,
- df_initializer=create_data_frame
+ df_initializer=create_data_frame,
)
def _search_semantic_annotations(self, criteria):
@@ -3387,7 +3453,7 @@ class Openbis:
entity="semantic_annotation",
identifier_name="permId",
response=objects,
- df_initializer=create_data_frame
+ df_initializer=create_data_frame,
)
def get_semantic_annotation(self, permId, only_data=False):
@@ -3464,7 +3530,7 @@ class Openbis:
count=count,
totalCount=resp.get("totalCount"),
response=resp,
- df_initializer=create_data_frame
+ df_initializer=create_data_frame,
)
def get_plugin(self, permId, only_data=False, with_script=True):
@@ -3543,6 +3609,9 @@ class Openbis:
- materialTypes (deprecated)
"""
+ if isinstance(vocabulary, Vocabulary):
+ vocabulary = vocabulary.code
+
return PropertyType(
openbis_obj=self,
code=code,
@@ -3650,6 +3719,7 @@ class Openbis:
self, objects, start_with=None, count=None, totalCount=None
):
"""takes a list of objects and returns a Things object"""
+
def create_data_frame(attrs, props, response):
attrs = openbis_definitions("propertyType")["attrs"]
if len(response) == 0:
@@ -3672,7 +3742,7 @@ class Openbis:
count=count,
totalCount=totalCount,
response=objects,
- df_initializer=create_data_frame
+ df_initializer=create_data_frame,
)
def get_material_types(self, type=None, start_with=None, count=None):
@@ -3807,7 +3877,7 @@ class Openbis:
count=count,
totalCount=resp.get("totalCount"),
response=resp,
- df_initializer=create_data_frame
+ df_initializer=create_data_frame,
)
def get_entity_type(
@@ -3945,7 +4015,9 @@ class Openbis:
else:
parse_jackson(objects)
types = DataFrame(objects)
- types["modificationDate"] = types["modificationDate"].map(format_timestamp)
+ types["modificationDate"] = types["modificationDate"].map(
+ format_timestamp
+ )
return types[attrs]
return Things(
@@ -3955,7 +4027,7 @@ class Openbis:
count=count,
totalCount=resp.get("totalCount"),
response=resp,
- df_initializer=create_data_frame
+ df_initializer=create_data_frame,
)
def _get_attributes(
@@ -4087,7 +4159,7 @@ class Openbis:
count=None,
totalCount=0,
objects=None,
- parsed=False
+ parsed=False,
):
"""returns a Things object, containing a DataFrame plus some additional information"""
@@ -4164,7 +4236,9 @@ class Openbis:
datasets = DataFrame(response)
for attr in attrs:
if "project" in attr:
- datasets[attr] = datasets["experiment"].map(extract_project(attr))
+ datasets[attr] = datasets["experiment"].map(
+ extract_project(attr)
+ )
elif "space" in attr:
datasets[attr] = datasets["experiment"].map(extract_space(attr))
elif "." in attr:
@@ -4242,16 +4316,11 @@ class Openbis:
props=props,
response=response,
df_initializer=create_data_frame,
- objects_initializer=create_objects
+ objects_initializer=create_objects,
)
def get_sample(
- self,
- sample_ident,
- only_data=False,
- withAttachments=False,
- props=None,
- **kvals
+ self, sample_ident, only_data=False, withAttachments=False, props=None, **kvals
):
"""Retrieve metadata for the sample.
Get metadata for the sample and any directly connected parents of the sample to allow access
@@ -4312,7 +4381,9 @@ class Openbis:
data=resp[sample_ident],
)
else:
- return self._sample_list_for_response(response=list(resp.values()), props=props, parsed=False)
+ return self._sample_list_for_response(
+ response=list(resp.values()), props=props, parsed=False
+ )
def _sample_list_for_response(
self,
@@ -4324,8 +4395,9 @@ class Openbis:
totalCount=0,
parsed=False,
):
- logger = logging.getLogger('_sample_list_for_response')
- logger.setLevel(logging.DEBUG)
+ logger = logging.getLogger("_sample_list_for_response")
+ logger.setLevel(logging.CRITICAL)
+ logger.disabled = True
logger.addHandler(logging.StreamHandler(sys.stdout))
time1 = now()
@@ -4352,8 +4424,8 @@ class Openbis:
return return_attribute
- logger = logging.getLogger('create_data_frame')
- logger.setLevel(logging.DEBUG)
+ logger = logging.getLogger("create_data_frame")
+ logger.setLevel(logging.CRITICAL)
logger.addHandler(logging.StreamHandler(sys.stdout))
time2 = now()
@@ -4383,7 +4455,9 @@ class Openbis:
samples = DataFrame(columns=display_attrs)
else:
time3 = now()
- logger.debug(f"createDataFrame computing attributes. Delay: {time3 - time2}")
+ logger.debug(
+ f"createDataFrame computing attributes. Delay: {time3 - time2}"
+ )
samples = DataFrame(response)
for attr in attrs:
@@ -4407,7 +4481,9 @@ class Openbis:
samples["registrator"] = samples["registrator"].map(extract_person)
samples["modifier"] = samples["modifier"].map(extract_person)
samples["identifier"] = samples["identifier"].map(extract_identifier)
- samples["container"] = samples["container"].map(extract_nested_identifier)
+ samples["container"] = samples["container"].map(
+ extract_nested_identifier
+ )
for column in ["parents", "children", "components"]:
if column in samples:
samples[column] = samples[column].map(extract_identifiers)
@@ -4415,7 +4491,9 @@ class Openbis:
samples["type"] = samples["type"].map(extract_nested_permid)
time4 = now()
- logger.debug(f"_sample_list_for_response computed attributes. Delay: {time4 - time3}")
+ logger.debug(
+ f"_sample_list_for_response computed attributes. Delay: {time4 - time3}"
+ )
for prop in props:
if prop == "*":
@@ -4434,32 +4512,50 @@ class Openbis:
for i, sample in enumerate(response):
if "properties" in sample:
properties = sample["properties"]
- val = properties.get(prop, "") or properties.get(prop.upper(), "")
+ val = properties.get(prop, "") or properties.get(
+ prop.upper(), ""
+ )
samples.loc[i, prop.upper()] = val
else:
samples.loc[i, prop.upper()] = ""
display_attrs.append(prop.upper())
time5 = now()
- logger.debug(f"_sample_list_for_response computed properties. Delay: {time5 - time4}")
+ logger.debug(
+ f"_sample_list_for_response computed properties. Delay: {time5 - time4}"
+ )
return samples[display_attrs]
def create_objects(response):
- return list(map(lambda obj: Sample(openbis_obj=self, type=self.get_sample_type(obj["type"]["code"]),
- data=obj), response))
-
- result = Things(openbis_obj=self, entity="sample",
- identifier_name="identifier", start_with=start_with,
- count=count, totalCount=totalCount,
- response=response,
- df_initializer=create_data_frame,
- objects_initializer=create_objects,
- attrs=attrs,
- props=props
- )
+ return list(
+ map(
+ lambda obj: Sample(
+ openbis_obj=self,
+ type=self.get_sample_type(obj["type"]["code"]),
+ data=obj,
+ ),
+ response,
+ )
+ )
+
+ result = Things(
+ openbis_obj=self,
+ entity="sample",
+ identifier_name="identifier",
+ start_with=start_with,
+ count=count,
+ totalCount=totalCount,
+ response=response,
+ df_initializer=create_data_frame,
+ objects_initializer=create_objects,
+ attrs=attrs,
+ props=props,
+ )
time7 = now()
- logger.debug(f"_sample_list_for_response computed result. Delay: {time7 - time6}")
+ logger.debug(
+ f"_sample_list_for_response computed result. Delay: {time7 - time6}"
+ )
return result
@staticmethod
@@ -4569,7 +4665,7 @@ class Openbis:
count=count,
totalCount=response.get("totalCount"),
response=response,
- df_initializer=create_data_frame
+ df_initializer=create_data_frame,
)
def get_external_data_management_system(self, permId, only_data=False):