diff --git a/pybis/src/python/pybis/pybis.py b/pybis/src/python/pybis/pybis.py
index c6aa9b38588bc53aa3fc7d51f6a1be02aa5769fd..468969b282a705deeeb558ee5816db4ad88ce4b4 100644
--- a/pybis/src/python/pybis/pybis.py
+++ b/pybis/src/python/pybis/pybis.py
@@ -86,6 +86,8 @@ import errno
import requests
import urllib3
+import logging
+import sys
# import the various openBIS entities
@@ -101,6 +103,8 @@ LOG_DEBUG = 7
DEBUG_LEVEL = LOG_NONE
+def now():
+ return time.time_ns() // 1000000
def get_search_type_for_entity(entity, operator=None):
"""Returns a dictionary containing the correct search criteria type
@@ -2034,6 +2038,7 @@ class Openbis:
attrs=None,
props=None,
where=None,
+ thingsFetchOptions={"withDataFrame": True, "withObjects": True},
**properties,
):
"""Returns a DataFrame of all samples for a given space/project/experiment (or any combination)
@@ -2068,6 +2073,10 @@ class Openbis:
b) property is not defined for this sampleType
"""
+ logger = logging.getLogger('get_samples')
+ logger.setLevel(logging.DEBUG)
+ logger.addHandler(logging.StreamHandler(sys.stdout))
+
if collection is not None:
experiment = collection
@@ -2150,27 +2159,39 @@ class Openbis:
fetchopts,
],
}
+
+ time1 = now()
+ logger.debug("get_samples posting request")
resp = self._post_request(self.as_v3, request)
- samples = []
+ time2 = now()
+
+ logger.debug(f"get_samples got response. Delay: {time2 - time1}")
parse_jackson(resp)
- for obj in resp["objects"]:
- sample = Sample(
- openbis_obj=self,
- type=self.get_sample_type(obj["type"]["code"]),
- data=obj,
- )
- samples.append(sample)
- return self._sample_list_for_response(
- response=resp["objects"],
- attrs=attrs,
- props=props,
- start_with=start_with,
- count=count,
- totalCount=resp["totalCount"],
- objects=samples,
- )
+ time3 = now()
+
+ response = resp["objects"]
+ # samples = range(len(objects))
+ logger.debug(f"get_samples got JSON. Delay: {time3 - time2}")
+
+ objects = None
+ if thingsFetchOptions["withObjects"]:
+ objects = list(map(lambda obj: Sample(openbis_obj=self, type=self.get_sample_type(obj["type"]["code"]),
+ data=obj), response))
+
+ time4 = now()
+
+ logger.debug(f"get_samples after result mapping. Delay: {time4 - time3}")
+
+ result = self._sample_list_for_response(response=response, thingsFetchOptions=thingsFetchOptions,
+ attrs=attrs, props=props, start_with=start_with, count=count,
+ totalCount=resp["totalCount"], objects=objects, parsed=True)
+
+ time5 = now()
+
+ logger.debug(f"get_samples computed final result. Delay: {time5 - time4}")
+ return result
get_objects = get_samples # Alias
@@ -2534,7 +2555,6 @@ class Openbis:
)
fetchopts["kind"] = kind
raise NotImplementedError("you cannot search for dataSet kinds yet")
-
request = {
"method": "searchDataSets",
"params": [
@@ -2749,7 +2769,11 @@ 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
@@ -2771,7 +2795,11 @@ 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
@@ -3330,7 +3358,6 @@ class Openbis:
"code"
]
obj["creationDate"] = format_timestamp(obj["creationDate"])
-
return objects
def get_semantic_annotations(self):
@@ -3466,7 +3493,6 @@ class Openbis:
def new_plugin(self, name, pluginType, **kwargs):
"""Creates a new Plugin in openBIS.
-
name -- name of the plugin
description --
pluginType -- DYNAMIC_PROPERTY, MANAGED_PROPERTY, ENTITY_VALIDATION
@@ -4195,7 +4221,13 @@ class Openbis:
)
def get_sample(
- self, sample_ident, only_data=False, withAttachments=False, props=None, **kvals
+ self,
+ sample_ident,
+ only_data=False,
+ withAttachments=False,
+ props=None,
+ thingsFetchOptions={"withDataFrame": True, "withObjects": True},
+ **kvals
):
"""Retrieve metadata for the sample.
Get metadata for the sample and any directly connected parents of the sample to allow access
@@ -4258,9 +4290,149 @@ class Openbis:
else:
return self._sample_list_for_response(
response=list(resp.values()),
+ thingsFetchOptions=thingsFetchOptions,
props=props,
)
+ def _sample_list_for_response(
+ self,
+ response,
+ thingsFetchOptions,
+ attrs=None,
+ props=None,
+ start_with=None,
+ count=None,
+ totalCount=0,
+ objects=None,
+ parsed=False,
+ ):
+ """returns a Things object, containing a DataFrame plus additional information"""
+
+ def extract_attribute(attribute_to_extract):
+ def return_attribute(obj):
+ if obj is None:
+ return ""
+ return obj.get(attribute_to_extract, "")
+
+ return return_attribute
+
+ logger = logging.getLogger('_sample_list_for_response')
+ logger.setLevel(logging.DEBUG)
+ logger.addHandler(logging.StreamHandler(sys.stdout))
+
+ time1 = now()
+
+ logger.debug("_sample_list_for_response before parsing JSON")
+ if not parsed:
+ parse_jackson(response)
+
+ time2 = now()
+
+ logger.debug(f"_sample_list_for_response got response. Delay: {time2 - time1}")
+
+ dataFrame = None
+ if thingsFetchOptions["withDataFrame"]:
+ if attrs is None:
+ attrs = []
+ default_attrs = [
+ "identifier",
+ "permId",
+ "type",
+ "registrator",
+ "registrationDate",
+ "modifier",
+ "modificationDate",
+ ]
+ display_attrs = default_attrs + attrs
+
+ if props is None:
+ props = []
+ else:
+ if isinstance(props, str):
+ props = [props]
+
+ if len(response) == 0:
+ for prop in props:
+ if prop == "*":
+ continue
+ display_attrs.append(prop)
+ samples = DataFrame(columns=display_attrs)
+ else:
+ time3 = now()
+ logger.debug(f"_sample_list_for_response computing attributes. Delay: {time3 - time2}")
+
+ samples = DataFrame(response)
+ for attr in attrs:
+ if "." in attr:
+ entity, attribute_to_extract = attr.split(".")
+ samples[attr] = samples[entity].map(
+ extract_attribute(attribute_to_extract)
+ )
+ # if no dot supplied, just display the code of the space, project or experiment
+ elif attr in ["project", "experiment"]:
+ samples[attr] = samples[attr].map(extract_nested_identifier)
+ elif attr in ["space"]:
+ samples[attr] = samples[attr].map(extract_code)
+
+ samples["registrationDate"] = samples["registrationDate"].map(
+ format_timestamp
+ )
+ samples["modificationDate"] = samples["modificationDate"].map(
+ format_timestamp
+ )
+ 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)
+ for column in ["parents", "children", "components"]:
+ if column in samples:
+ samples[column] = samples[column].map(extract_identifiers)
+ samples["permId"] = samples["permId"].map(extract_permid)
+ samples["type"] = samples["type"].map(extract_nested_permid)
+
+ time4 = now()
+ logger.debug(f"_sample_list_for_response computed attributes. Delay: {time4 - time3}")
+
+ for prop in props:
+ if prop == "*":
+ # include all properties in dataFrame.
+ # expand the dataFrame by adding new columns
+ columns = []
+ for i, sample in enumerate(response):
+ for prop_name, val in sample.get("properties", {}).items():
+ samples.loc[i, prop_name.upper()] = val
+ columns.append(prop_name.upper())
+
+ display_attrs += set(columns)
+ continue
+ else:
+ # property name is provided
+ for i, sample in enumerate(response):
+ if "properties" in sample:
+ properties = sample["properties"]
+ 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}")
+
+ dataFrame = samples[display_attrs]
+
+ time6 = now()
+ logger.debug("_sample_list_for_response computing result.")
+
+ result = Things(openbis_obj=self, entity="sample",
+ df=dataFrame,
+ identifier_name="identifier", start_with=start_with,
+ count=count, totalCount=totalCount, objects=objects, response=response)
+
+ time7 = now()
+ logger.debug(f"_sample_list_for_response computed result. Delay: {time7 - time6}")
+ return result
+
@staticmethod
def decode_attribute(entity, attribute):
params = {}
@@ -4328,118 +4500,6 @@ class Openbis:
return params
- def _sample_list_for_response(
- self,
- response,
- attrs=None,
- props=None,
- start_with=None,
- count=None,
- totalCount=0,
- objects=None,
- ):
- """returns a Things object, containing a DataFrame plus additional information"""
-
- def extract_attribute(attribute_to_extract):
- def return_attribute(obj):
- if obj is None:
- return ""
- return obj.get(attribute_to_extract, "")
-
- return return_attribute
-
- parse_jackson(response)
-
- if attrs is None:
- attrs = []
- default_attrs = [
- "identifier",
- "permId",
- "type",
- "registrator",
- "registrationDate",
- "modifier",
- "modificationDate",
- ]
- display_attrs = default_attrs + attrs
-
- if props is None:
- props = []
- else:
- if isinstance(props, str):
- props = [props]
-
- if len(response) == 0:
- for prop in props:
- if prop == "*":
- continue
- display_attrs.append(prop)
- samples = DataFrame(columns=display_attrs)
- else:
- samples = DataFrame(response)
- for attr in attrs:
- if "." in attr:
- entity, attribute_to_extract = attr.split(".")
- samples[attr] = samples[entity].map(
- extract_attribute(attribute_to_extract)
- )
-
- for attr in attrs:
- # if no dot supplied, just display the code of the space, project or experiment
- if attr in ["project", "experiment"]:
- samples[attr] = samples[attr].map(extract_nested_identifier)
- if attr in ["space"]:
- samples[attr] = samples[attr].map(extract_code)
-
- samples["registrationDate"] = samples["registrationDate"].map(
- format_timestamp
- )
- samples["modificationDate"] = samples["modificationDate"].map(
- format_timestamp
- )
- 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)
- for column in ["parents", "children", "components"]:
- if column in samples:
- samples[column] = samples[column].map(extract_identifiers)
- samples["permId"] = samples["permId"].map(extract_permid)
- samples["type"] = samples["type"].map(extract_nested_permid)
-
- for prop in props:
- if prop == "*":
- # include all properties in dataFrame.
- # expand the dataFrame by adding new columns
- columns = []
- for i, sample in enumerate(response):
- for prop_name, val in sample.get("properties", {}).items():
- samples.loc[i, prop_name.upper()] = val
- columns.append(prop_name.upper())
-
- display_attrs += set(columns)
- continue
-
- else:
- # property name is provided
- for i, sample in enumerate(response):
- val = sample.get("properties", {}).get(prop, "") or sample.get(
- "properties", {}
- ).get(prop.upper(), "")
- samples.loc[i, prop.upper()] = val
- display_attrs.append(prop.upper())
-
- return Things(
- openbis_obj=self,
- entity="sample",
- df=samples[display_attrs],
- identifier_name="identifier",
- start_with=start_with,
- count=count,
- totalCount=totalCount,
- objects=objects,
- )
-
get_object = get_sample # Alias
def get_external_data_management_systems(
diff --git a/pybis/src/python/pybis/sample.py b/pybis/src/python/pybis/sample.py
index 1bedb35909553a60ecbf577fb831527767011ad1..7ae6c8ab428e84fed135520ee5ca04230a8738a2 100644
--- a/pybis/src/python/pybis/sample.py
+++ b/pybis/src/python/pybis/sample.py
@@ -1,6 +1,6 @@
from .property import PropertyHolder
from .attribute import AttrHolder
-from .openbis_object import OpenBisObject
+from .openbis_object import OpenBisObject
from .definitions import openbis_definitions
from .utils import VERBOSE
@@ -23,11 +23,13 @@ class Sample(
if data is not None:
self._set_data(data)
+ # TODO: Why are we using getattr() and setattr() here? They are considerably slower.
if project is not None:
- setattr(self, 'project', project)
+ self.project = project
if props is not None:
for key in props:
+ # self.p[key] = props[key]
setattr(self.p, key, props[key])
if kwargs is not None:
@@ -36,10 +38,10 @@ class Sample(
if 'experiment' in kwargs:
try:
- experiment = getattr(self, 'experiment')
+ experiment = self.experiment
if not 'space' in kwargs:
project = experiment.project
- setattr(self.a, 'space', project.space)
+ self.a.space = project.space
except Exception:
pass
@@ -77,10 +79,10 @@ class Sample(
return [
'type',
'get_parents()', 'get_children()', 'get_components()',
- 'add_parents()', 'add_children()', 'add_components()',
+ 'add_parents()', 'add_children()', 'add_components()',
'del_parents()', 'del_children()', 'del_components()',
'set_parents()', 'set_children()', 'set_components()',
- 'get_datasets()',
+ 'get_datasets()',
'space', 'project', 'experiment', 'container', 'tags',
'set_tags()', 'add_tags()', 'del_tags()',
'add_attachment()', 'get_attachments()', 'download_attachments()',
diff --git a/pybis/src/python/pybis/things.py b/pybis/src/python/pybis/things.py
index 51497d3a6c97089031a84696370e556aebbb2212..166a330191d69df69b77e3ee9b4d7c43ec3d6cc7 100644
--- a/pybis/src/python/pybis/things.py
+++ b/pybis/src/python/pybis/things.py
@@ -16,18 +16,19 @@ class Things():
Because the order of the elements cannot be ensured, you should choose the identifier instead:
openbis.get_samples()['/SOME_SPACE/SAMPLE_CODE']
- Of course, if you know the identifier already, you would rather do:
+ Of course, if you know the identifier already, you would rather do:
openbis.get_sample('/SOME_SPACE/SAMPLE_CODE')
-
-
+
+
"""
def __init__(
self, openbis_obj, entity, df,
- identifier_name='code', additional_identifier=None,
+ identifier_name='code', additional_identifier=None,
start_with=None, count=None, totalCount=None,
single_item_method=None,
- objects=None
+ objects=None,
+ response=None
):
self.openbis = openbis_obj
self.entity = entity
@@ -39,6 +40,7 @@ class Things():
self.totalCount=totalCount
self.single_item_method=single_item_method
self.objects=objects
+ self.response = response
def __repr__(self):
return tabulate(self.df, headers=list(self.df))
diff --git a/pybis/src/python/pybis/utils.py b/pybis/src/python/pybis/utils.py
index ad917f5e46e7507fce048517d3169dd1685fa548..6ebd6cf72451a6f9f34424bf3c813c60b98a58c0 100644
--- a/pybis/src/python/pybis/utils.py
+++ b/pybis/src/python/pybis/utils.py
@@ -16,14 +16,14 @@ def parse_jackson(input_json):
Any further findings only carry this reference id.
This function is used to dereference the output.
"""
- interesting=['tags', 'registrator', 'modifier', 'owner', 'type',
- 'parents', 'children', 'containers', # 'container',
+ interesting=['tags', 'registrator', 'modifier', 'owner', 'type',
+ 'parents', 'children', 'containers', # 'container',
'properties', 'experiment', 'sample',
'project', 'space', 'propertyType', 'entityType', 'propertyType', 'propertyAssignment',
'externalDms', 'roleAssignments', 'user', 'users', 'authorizationGroup', 'vocabulary',
'validationPlugin', 'dataSetPermId', 'dataStore'
]
- found = {}
+ found = {}
def build_cache(graph):
if isinstance(graph, list):
for item in graph:
@@ -45,15 +45,17 @@ def parse_jackson(input_json):
build_cache(value)
elif isinstance(value, list):
build_cache(value)
-
- def deref_graph(graph):
+
+ def deref_graph(graph):
if isinstance(graph, list):
for i, list_item in enumerate(graph):
if isinstance(list_item, int):
- try:
- graph[i] = found[list_item]
- except KeyError:
- pass
+ # try: # TODO: use "if list_item in found" with found.get()
+ # graph[i] = found[list_item]
+ # except KeyError:
+ # pass
+ if list_item in found:
+ graph[i] = found.get(list_item)
else:
deref_graph(list_item)
elif isinstance(graph, dict) and len(graph) > 0:
@@ -63,7 +65,6 @@ def parse_jackson(input_json):
deref_graph(value)
elif isinstance(value, int):
graph[key] = found.get(value)
-
elif isinstance(value, list):
for i, list_item in enumerate(value):
if isinstance(list_item, int):
@@ -189,9 +190,9 @@ def extract_identifiers(items):
return []
try:
return [
- data['identifier']['identifier']
- if 'identifier' in data
- else data['permId']['permId']
+ data['identifier']['identifier']
+ if 'identifier' in data
+ else data['permId']['permId']
for data in items
]
except TypeError:
@@ -206,8 +207,8 @@ def extract_nested_identifier(ident):
def extract_nested_permid(permid):
if not isinstance(permid, dict):
return '' if permid is None else str(permid)
- return '' if permid['permId']['permId'] is None else permid['permId']['permId']
-
+ return '' if permid['permId']['permId'] is None else permid['permId']['permId']
+
def extract_nested_permids(items):
if not isinstance(items, list):
return []
diff --git a/pybis/src/python/tests/conftest.py b/pybis/src/python/tests/conftest.py
index 4bddb2c2294b6141ef0329da15c6a1c21e8186d8..edeaf72291fbd921c1a49128438e1929451636e6 100644
--- a/pybis/src/python/tests/conftest.py
+++ b/pybis/src/python/tests/conftest.py
@@ -4,12 +4,10 @@ import time
import pytest
from pybis import Openbis
-
openbis_url = "https://localhost:8443"
admin_username = "admin"
admin_password = "changeit"
-
@pytest.fixture(scope="module")
def openbis_instance():
instance = Openbis(
@@ -28,6 +26,7 @@ def other_openbis_instance():
instance = Openbis(
url=openbis_url,
verify_certificates=False,
+
)
print("\nLOGGING IN...")
instance.login(admin_username, admin_password)
@@ -41,6 +40,7 @@ def space():
o = Openbis(
url=openbis_url,
verify_certificates=False,
+
)
o.login(admin_username, admin_password)