From 8b2f27f63114fa478a8d0ffd85a5591dcf3a9863 Mon Sep 17 00:00:00 2001
From: vermeul <swen@ethz.ch>
Date: Tue, 4 Dec 2018 00:58:19 +0100
Subject: [PATCH] added start_with and count to Things object
---
pybis/src/python/pybis/pybis.py | 188 +++++++++++++++++++++++++-------
1 file changed, 148 insertions(+), 40 deletions(-)
diff --git a/pybis/src/python/pybis/pybis.py b/pybis/src/python/pybis/pybis.py
index 6521ff9c2bf..b74948d6b23 100644
--- a/pybis/src/python/pybis/pybis.py
+++ b/pybis/src/python/pybis/pybis.py
@@ -1018,12 +1018,14 @@ class Openbis:
roles['space'] = roles['space'].map(extract_code)
roles['project'] = roles['project'].map(extract_code)
- p = Things(
- self, entity='role_assignment',
+ return Things(
+ openbis_obj = self,
+ entity='role_assignment',
df=roles[attrs],
- identifier_name='techId'
+ identifier_name='techId',
+ start_with = start_with,
+ count = count,
)
- return p
def get_role_assignment(self, techId, only_data=False):
""" Fetches one assigned role by its techId.
@@ -1101,7 +1103,7 @@ class Openbis:
request = {
"method": "createRoleAssignments",
"params": [
- self.token,
+ self.token,
[
{
"role": role,
@@ -1172,7 +1174,14 @@ class Openbis:
groups['users'] = groups['users'].map(extract_userId)
groups['registrationDate'] = groups['registrationDate'].map(format_timestamp)
groups['modificationDate'] = groups['modificationDate'].map(format_timestamp)
- return Things(self, entity='group', df=groups[attrs], identifier_name='permId')
+ return Things(
+ openbis_obj = self,
+ entity='group',
+ df=groups[attrs],
+ identifier_name='permId',
+ start_with = start_with,
+ count = count,
+ )
def get_persons(self, start_with=None, count=None, **search_args):
@@ -1208,7 +1217,12 @@ class Openbis:
persons['space'] = persons['space'].map(extract_nested_permid)
return Things(
- self, entity='person', df=persons[attrs], identifier_name='permId'
+ openbis_obj = self,
+ entity='person',
+ df=persons[attrs],
+ identifier_name='permId',
+ start_with = start_with,
+ count = count,
)
@@ -1279,7 +1293,13 @@ class Openbis:
spaces = DataFrame(resp['objects'])
spaces['registrationDate'] = spaces['registrationDate'].map(format_timestamp)
spaces['modificationDate'] = spaces['modificationDate'].map(format_timestamp)
- return Things(self, 'space', spaces[attrs])
+ return Things(
+ openbis_obj = self,
+ entity = 'space',
+ df = spaces[attrs],
+ start_with = start_with,
+ count = count,
+ )
def get_space(self, code, only_data=False):
@@ -1314,7 +1334,8 @@ class Openbis:
def get_samples(
- self, identifier=None, code=None, permId=None, space=None, project=None, experiment=None, type=None,
+ self, identifier=None, code=None, permId=None,
+ space=None, project=None, experiment=None, type=None,
start_with=None, count=None,
withParents=None, withChildren=None, tags=None, props=None, **properties
):
@@ -1400,14 +1421,19 @@ class Openbis:
}
resp = self._post_request(self.as_v3, request)
- return self._sample_list_for_response(response=resp['objects'], props=props)
+ return self._sample_list_for_response(
+ response=resp['objects'],
+ props=props,
+ start_with=start_with,
+ count=count,
+ )
get_objects = get_samples # Alias
def get_experiments(
- self, code=None, permId=None, type=None, space=None, project=None,
+ self, code=None, permId=None, type=None, space=None, project=None,
start_with=None, count=None,
tags=None, is_finished=None, props=None, **properties
):
@@ -1486,11 +1512,18 @@ class Openbis:
experiments[prop.upper()] = experiments['properties'].map(lambda x: x.get(prop.upper(), ''))
attrs.append(prop.upper())
- return Things(self, 'experiment', experiments[attrs], 'identifier')
+ return Things(
+ openbis_obj = self,
+ entity = 'experiment',
+ df = experiments[attrs],
+ identifier_name ='identifier',
+ start_with = start_with,
+ count = count,
+ )
def get_datasets(
- self, code=None, type=None, withParents=None, withChildren=None,
+ self, code=None, type=None, withParents=None, withChildren=None,
start_with=None, count=None,
status=None, sample=None, experiment=None, project=None,
tags=None, props=None, **properties
@@ -1548,7 +1581,12 @@ class Openbis:
}
resp = self._post_request(self.as_v3, request)
- return self._dataset_list_for_response(response=resp['objects'], props=props)
+ return self._dataset_list_for_response(
+ response=resp['objects'],
+ props=props,
+ start_with=start_with,
+ count=count,
+ )
def get_experiment(self, expId, withAttachments=False, only_data=False):
@@ -1595,12 +1633,12 @@ class Openbis:
""" Creates a new experiment of a given experiment type.
"""
return Experiment(
- openbis_obj = self,
- type = self.get_experiment_type(type),
+ openbis_obj = self,
+ type = self.get_experiment_type(type),
project = project,
data = None,
props = props,
- code = code,
+ code = code,
**kwargs
)
@@ -1692,7 +1730,7 @@ class Openbis:
"""
entity_type = "as.dto.{}.id.{}{}{}".format(
- entity.lower(), entity,
+ entity.lower(), entity,
id_name[0].upper(), id_name[1:]
)
request = {
@@ -1851,7 +1889,14 @@ class Openbis:
projects['permId'] = projects['permId'].map(extract_permid)
projects['identifier'] = projects['identifier'].map(extract_identifier)
- return Things(self, 'project', projects[attrs], 'identifier')
+ return Things(
+ openbis_obj = self,
+ entity = 'project',
+ df = projects[attrs],
+ identifier_name = 'identifier',
+ start_with = start_with,
+ count = count,
+ )
def _create_get_request(self, method_name, entity, permids, options):
@@ -1924,14 +1969,21 @@ class Openbis:
terms['registrationDate'] = terms['registrationDate'].map(format_timestamp)
terms['modificationDate'] = terms['modificationDate'].map(format_timestamp)
- return Things(self, 'term', terms[attrs],
- identifier_name='code', additional_identifier='vocabularyCode')
+ return Things(
+ openbis_obj = self,
+ entity = 'term',
+ df = terms[attrs],
+ identifier_name='code',
+ additional_identifier='vocabularyCode',
+ start_with = start_with,
+ count = count,
+ )
def new_term(self, code, vocabularyCode, label=None, description=None):
return VocabularyTerm(
- self, data=None,
- code=code, vocabularyCode=vocabularyCode,
+ self, data=None,
+ code=code, vocabularyCode=vocabularyCode,
label=label, description=description
)
@@ -2032,7 +2084,14 @@ class Openbis:
vocs['modificationDate'] = vocs['modificationDate'].map(format_timestamp)
vocs['registrator'] = vocs['registrator'].map(extract_person)
- return Things(self, 'vocabulary', vocs[attrs], 'code')
+ return Things(
+ openbis_obj = self,
+ entity = 'vocabulary',
+ df = vocs[attrs],
+ identifier_name = 'code',
+ start_with = start_with,
+ count = count,
+ )
def get_vocabulary(self, code, only_data=False):
@@ -2128,7 +2187,12 @@ class Openbis:
tags['description'] = tags['description'].map(lambda x: '' if x is None else x)
tags['owner'] = tags['owner'].map(extract_person)
- return Things(self, 'tag', tags[attrs], 'permId')
+ return Things(
+ openbis_obj = self,
+ entity = 'tag',
+ df = tags[attrs],
+ identifier_name ='permId',
+ )
def search_semantic_annotations(self, permId=None, entityType=None, propertyType=None, only_data = False):
@@ -2189,7 +2253,14 @@ class Openbis:
else:
annotations = DataFrame(objects)
- return Things(self, 'semantic_annotation', annotations[attrs], 'permId')
+ return Things(
+ openbis_obj = self,
+ entity = 'semantic_annotation',
+ df = annotations[attrs],
+ identifier_name = 'permId',
+ start_with = start_with,
+ count = count,
+ )
def _search_semantic_annotations(self, criteria):
@@ -2244,7 +2315,14 @@ class Openbis:
annotations = DataFrame(columns=attrs)
else:
annotations = DataFrame(objects)
- return Things(self, 'semantic_annotation', annotations[attrs], 'permId')
+ return Things(
+ openbis_obj = self,
+ entity = 'semantic_annotation',
+ df = annotations[attrs],
+ identifier_name = 'permId',
+ start_with = start_with,
+ count = count,
+ )
def get_semantic_annotation(self, permId, only_data = False):
objects = self.search_semantic_annotations(permId=permId, only_data=True)
@@ -2291,7 +2369,14 @@ class Openbis:
plugins['description'] = plugins['description'].map(lambda x: '' if x is None else x)
plugins['entityKinds'] = plugins['entityKinds'].map(lambda x: '' if x is None else x)
- return Things(self, 'plugin', plugins[attrs], 'name')
+ return Things(
+ openbis_obj = self,
+ entity = 'plugin',
+ df = plugins[attrs],
+ identifier_name = 'name',
+ start_with = start_with,
+ count = count,
+ )
def get_plugin(self, permId, only_data=False, with_script=True):
@@ -2419,7 +2504,7 @@ class Openbis:
""" Returns a list (DataFrame object) of all currently available dataset types
"""
return self._get_types_of(
- "searchDataSetTypes", "DataSet", type,
+ "searchDataSetTypes", "DataSet", type,
optional_attributes=['kind'],
start_with=start_with,
count=count,
@@ -2432,7 +2517,7 @@ class Openbis:
raise ValueError("No such dataSet type: {}".format(type))
def _get_types_of(
- self, method_name, entity, type_name=None,
+ self, method_name, entity, type_name=None,
start_with=None, count=None,
additional_attributes=None, optional_attributes=None
):
@@ -2486,7 +2571,13 @@ class Openbis:
parse_jackson(objects)
types = DataFrame(objects)
types['modificationDate'] = types['modificationDate'].map(format_timestamp)
- return Things(self, entity.lower() + '_type', types[attrs])
+ return Things(
+ openbis_obj = self,
+ entity = entity.lower() + '_type',
+ df = types[attrs],
+ start_with = start_with,
+ count = count,
+ )
def _get_attributes(self, type_name, types, additional_attributes, optional_attributes):
@@ -2579,7 +2670,7 @@ class Openbis:
return resp[permId]
else:
return DataSet(
- openbis_obj = self,
+ openbis_obj = self,
type = self.get_dataset_type(resp[permId]["type"]["code"]),
data = resp[permId]
)
@@ -2587,12 +2678,12 @@ class Openbis:
return self._dataset_list_for_response(response=list(resp.values()), props=props)
- def _dataset_list_for_response(self, response, props=None):
+ def _dataset_list_for_response(self, response, props=None, start_with=None, count=None):
"""returns a Things object, containing a DataFrame plus some additional information
"""
parse_jackson(response)
- attrs = ['permId', 'type', 'experiment', 'sample',
+ attrs = ['permId', 'type', 'experiment', 'sample',
'registrationDate', 'modificationDate',
'location', 'status', 'presentInArchive', 'size',
'properties'
@@ -2619,7 +2710,14 @@ class Openbis:
datasets[prop.upper()] = datasets['properties'].map(lambda x: x.get(prop.upper(), ''))
attrs.append(prop.upper())
- return Things(self, 'dataset', datasets[attrs], 'permId')
+ return Things(
+ openbis_obj = self,
+ entity = 'dataset',
+ df = datasets[attrs],
+ identifier_name = 'permId',
+ start_with=start_with,
+ count=count,
+ )
def get_sample(self, sample_ident, only_data=False, withAttachments=False, props=None):
@@ -2682,9 +2780,12 @@ class Openbis:
data = resp[sample_ident]
)
else:
- return self._sample_list_for_response(response=list(resp.values()), props=props)
+ return self._sample_list_for_response(
+ response=list(resp.values()),
+ props=props,
+ )
- def _sample_list_for_response(self, response, props=None):
+ def _sample_list_for_response(self, response, props=None, start_with=None, count=None):
"""returns a Things object, containing a DataFrame plus some additional information
"""
@@ -2711,7 +2812,14 @@ class Openbis:
samples[prop.upper()] = samples['properties'].map(lambda x: x.get(prop.upper(), ''))
attrs.append(prop.upper())
- return Things(self, 'sample', samples[attrs], 'identifier')
+ return Things(
+ openbis_obj = self,
+ entity = 'sample',
+ df = samples[attrs],
+ identifier_name = 'identifier',
+ start_with=start_with,
+ count=count,
+ )
get_object = get_sample # Alias
@@ -2872,7 +2980,7 @@ class Openbis:
def new_semantic_annotation(self, entityType=None, propertyType=None, **kwargs):
""" Note: not functional yet. """
return SemanticAnnotation(
- openbis_obj=self, isNew=True,
+ openbis_obj=self, isNew=True,
entityType=entityType, propertyType=propertyType, **kwargs
)
@@ -2954,7 +3062,7 @@ class ServerInformation():
def __init__(self, info):
self._info = info
self.attrs = [
- 'api_version', 'archiving_configured', 'authentication_service',
+ 'api_version', 'archiving_configured', 'authentication_service',
'enabled_technologies', 'project_samples_enabled'
]
--
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