From 67ec278dcd3e60f79cd481a010e0f62bfdcfc858 Mon Sep 17 00:00:00 2001
From: vermeul <swen@ethz.ch>
Date: Fri, 2 Mar 2018 13:49:29 +0100
Subject: [PATCH] no longer errors when searching for entities (empty DataSet
instead). Searching for groups allows code search
---
src/python/PyBis/pybis/dataset.py | 7 +-
src/python/PyBis/pybis/group.py | 1 +
src/python/PyBis/pybis/pybis.py | 189 ++++++++++++++----------------
3 files changed, 96 insertions(+), 101 deletions(-)
diff --git a/src/python/PyBis/pybis/dataset.py b/src/python/PyBis/pybis/dataset.py
index 5e506a25e4d..403629e635c 100644
--- a/src/python/PyBis/pybis/dataset.py
+++ b/src/python/PyBis/pybis/dataset.py
@@ -53,8 +53,7 @@ class DataSet(OpenBisObject):
'add_attachment()', 'get_attachments()', 'download_attachments()',
"get_files(start_folder='/')", 'file_list',
'download(files=None, destination=None, wait_until_finished=True)',
- 'status', 'archive()', 'unarchive()',
- 'data'
+ 'status', 'archive()', 'unarchive()'
]
def __setattr__(self, name, value):
@@ -166,6 +165,7 @@ class DataSet(OpenBisObject):
queue.join()
if VERBOSE: print("Files downloaded to: %s" % os.path.join(destination, self.permId))
+ return destination
@property
def folder(self):
@@ -261,6 +261,8 @@ class DataSet(OpenBisObject):
experiment_identifier = self.experiment.identifier
parentIds = self.parents
+ if parentIds is None:
+ parentIds = []
dataset_type = self.type.code
properties = self.props.all_nonempty()
@@ -308,7 +310,6 @@ class DataSet(OpenBisObject):
# activate the ingestion plugin, as soon as the data is uploaded
request = self._generate_plugin_request(dss=datastores['code'][0])
- print(json.dumps(request))
resp = self.openbis._post_request(self.openbis.reg_v1, request)
if resp['rows'][0][0]['value'] == 'OK':
diff --git a/src/python/PyBis/pybis/group.py b/src/python/PyBis/pybis/group.py
index 129ab01e3ef..df022d398d6 100644
--- a/src/python/PyBis/pybis/group.py
+++ b/src/python/PyBis/pybis/group.py
@@ -1,6 +1,7 @@
from .attribute import AttrHolder
from .openbis_object import OpenBisObject
from .utils import VERBOSE
+from pandas import DataFrame
class Group(OpenBisObject):
""" Managing openBIS authorization groups
diff --git a/src/python/PyBis/pybis/pybis.py b/src/python/PyBis/pybis/pybis.py
index 594fa6df90e..084cf1d5d89 100644
--- a/src/python/PyBis/pybis/pybis.py
+++ b/src/python/PyBis/pybis/pybis.py
@@ -1106,11 +1106,11 @@ class Openbis:
"""
criteria = []
- for search_arg in ['code', 'description', 'registrator']:
+ for search_arg in ['code']:
+ # unfortunately, there aren't many search possibilities yet...
if search_arg in search_args:
- pass
- #sub_crit = get_search_type_for_entity(search_arg)
- #criteria.append(sub_crit)
+ if search_arg == 'code':
+ criteria.append(_criteria_for_code(search_args[search_arg]))
search_criteria = get_search_type_for_entity('authorizationGroup')
search_criteria['criteria'] = criteria
@@ -1128,25 +1128,21 @@ class Openbis:
],
}
resp = self._post_request(self.as_v3, request)
- if len(resp['objects']) == 0:
- raise ValueError("No groups found!")
-
- objects = resp['objects']
- parse_jackson(objects)
- groups = DataFrame(objects)
+ attrs = ['permId', 'code', 'description', 'users', 'registrator', 'registrationDate', 'modificationDate']
+ if len(resp['objects']) == 0:
+ groups = DataFrame(columns=attrs)
+ else:
+ objects = resp['objects']
+ parse_jackson(objects)
+ groups = DataFrame(objects)
- groups['permId'] = groups['permId'].map(extract_permid)
- groups['registrator'] = groups['registrator'].map(extract_person)
- groups['users'] = groups['users'].map(extract_userId)
- groups['registrationDate'] = groups['registrationDate'].map(format_timestamp)
- groups['modificationDate'] = groups['modificationDate'].map(format_timestamp)
- p = Things(
- self, entity='group',
- df=groups[['permId', 'code', 'description', 'users', 'registrator', 'registrationDate', 'modificationDate']],
- identifier_name='permId'
- )
- return p
+ groups['permId'] = groups['permId'].map(extract_permid)
+ groups['registrator'] = groups['registrator'].map(extract_person)
+ 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')
def get_persons(self, **search_args):
@@ -1166,22 +1162,23 @@ class Openbis:
],
}
resp = self._post_request(self.as_v3, request)
+
+ attrs = ['permId', 'userId', 'firstName', 'lastName', 'email', 'space', 'registrationDate', 'active']
if len(resp['objects']) == 0:
- raise ValueError("No persons found!")
+ persons = DataFrame(columns=attrs)
+ else:
+ objects = resp['objects']
+ parse_jackson(objects)
- objects = resp['objects']
- parse_jackson(objects)
+ persons = DataFrame(resp['objects'])
+ persons['permId'] = persons['permId'].map(extract_permid)
+ persons['registrationDate'] = persons['registrationDate'].map(format_timestamp)
+ persons['space'] = persons['space'].map(extract_nested_permid)
- persons = DataFrame(resp['objects'])
- persons['permId'] = persons['permId'].map(extract_permid)
- persons['registrationDate'] = persons['registrationDate'].map(format_timestamp)
- persons['space'] = persons['space'].map(extract_nested_permid)
- p = Things(
- self, entity='person',
- df=persons[['permId', 'userId', 'firstName', 'lastName', 'email', 'space', 'registrationDate', 'active']],
- identifier_name='permId'
+ return Things(
+ self, entity='person', df=persons[attrs], identifier_name='permId'
)
- return p
+
get_users = get_persons # Alias
@@ -1240,18 +1237,16 @@ class Openbis:
],
}
resp = self._post_request(self.as_v3, request)
- if resp is not None:
+
+ attrs = ['code', 'description', 'registrationDate', 'modificationDate']
+ if len(resp['objects']) == 0:
+ spaces = DataFrame(columns=attrs)
+ else:
spaces = DataFrame(resp['objects'])
spaces['registrationDate'] = spaces['registrationDate'].map(format_timestamp)
spaces['modificationDate'] = spaces['modificationDate'].map(format_timestamp)
- sp = Things(
- self,
- 'space',
- spaces[['code', 'description', 'registrationDate', 'modificationDate']]
- )
- return sp
- else:
- raise ValueError("No spaces found!")
+ return Things(self, 'space', spaces[attrs])
+
def get_space(self, code, only_data=False):
""" Returns a Space object for a given identifier.
@@ -1356,8 +1351,8 @@ class Openbis:
fetchopts,
],
}
-
resp = self._post_request(self.as_v3, request)
+
attrs = ['identifier', 'permId', 'experiment', 'sample_type',
'registrator', 'registrationDate', 'modifier', 'modificationDate']
if len(resp['objects']) == 0:
@@ -1381,8 +1376,7 @@ class Openbis:
samples[prop.upper()] = samples['properties'].map(lambda x: x.get(prop.upper(), ''))
attrs.append(prop.upper())
- ss = samples[attrs]
- return Things(self, 'sample', ss, 'identifier')
+ return Things(self, 'sample', samples[attrs], 'identifier')
get_objects = get_samples # Alias
@@ -1436,32 +1430,31 @@ class Openbis:
],
}
resp = self._post_request(self.as_v3, request)
- if len(resp['objects']) == 0:
- raise ValueError("No experiments found!")
-
- objects = resp['objects']
- parse_jackson(objects)
-
- experiments = DataFrame(objects)
- experiments['registrationDate'] = experiments['registrationDate'].map(format_timestamp)
- experiments['modificationDate'] = experiments['modificationDate'].map(format_timestamp)
- experiments['project'] = experiments['project'].map(extract_code)
- experiments['registrator'] = experiments['registrator'].map(extract_person)
- experiments['modifier'] = experiments['modifier'].map(extract_person)
- experiments['identifier'] = experiments['identifier'].map(extract_identifier)
- experiments['permId'] = experiments['permId'].map(extract_permid)
- experiments['type'] = experiments['type'].map(extract_code)
-
attrs = ['identifier', 'permId', 'project', 'type',
'registrator', 'registrationDate', 'modifier', 'modificationDate']
+ if len(resp['objects']) == 0:
+ experiments = DataFrame(columns=attrs)
+ else:
+ objects = resp['objects']
+ parse_jackson(objects)
+
+ experiments = DataFrame(objects)
+ experiments['registrationDate'] = experiments['registrationDate'].map(format_timestamp)
+ experiments['modificationDate'] = experiments['modificationDate'].map(format_timestamp)
+ experiments['project'] = experiments['project'].map(extract_code)
+ experiments['registrator'] = experiments['registrator'].map(extract_person)
+ experiments['modifier'] = experiments['modifier'].map(extract_person)
+ experiments['identifier'] = experiments['identifier'].map(extract_identifier)
+ experiments['permId'] = experiments['permId'].map(extract_permid)
+ experiments['type'] = experiments['type'].map(extract_code)
if props is not None:
for prop in props:
experiments[prop.upper()] = experiments['properties'].map(lambda x: x.get(prop.upper(), ''))
attrs.append(prop.upper())
- exps = experiments[attrs]
- return Things(self, 'experiment', exps, 'identifier')
+ return Things(self, 'experiment', experiments[attrs], 'identifier')
+
def get_datasets(self,
code=None, type=None, withParents=None, withChildren=None, status=None,
@@ -1517,23 +1510,24 @@ class Openbis:
],
}
resp = self._post_request(self.as_v3, request)
+
+ attrs = ['permId', 'properties', 'type', 'experiment', 'sample', 'registrationDate', 'modificationDate', 'location']
+
if len(resp['objects']) == 0:
- raise ValueError("no datasets found!")
+ datasets = DataFrame(columns=attrs)
+ else:
+ objects = resp['objects']
+ parse_jackson(objects)
- objects = resp['objects']
- parse_jackson(objects)
+ datasets = DataFrame(objects)
+ datasets['registrationDate'] = datasets['registrationDate'].map(format_timestamp)
+ datasets['modificationDate'] = datasets['modificationDate'].map(format_timestamp)
+ datasets['experiment'] = datasets['experiment'].map(extract_nested_identifier)
+ datasets['sample'] = datasets['sample'].map(extract_nested_identifier)
+ datasets['type'] = datasets['type'].map(extract_code)
+ datasets['permId'] = datasets['code']
+ datasets['location'] = datasets['physicalData'].map(lambda x: x.get('location') if x else '')
- datasets = DataFrame(objects)
- datasets['registrationDate'] = datasets['registrationDate'].map(format_timestamp)
- datasets['modificationDate'] = datasets['modificationDate'].map(format_timestamp)
- datasets['experiment'] = datasets['experiment'].map(extract_nested_identifier)
- datasets['sample'] = datasets['sample'].map(extract_nested_identifier)
- datasets['type'] = datasets['type'].map(extract_code)
- datasets['permId'] = datasets['code']
- datasets['location'] = datasets['physicalData'].map(lambda x: x.get('location') if x else '')
-
- attrs = ['permId', 'properties', 'type', 'experiment', 'sample', 'registrationDate', 'modificationDate',
- 'location']
if props is not None:
for prop in props:
datasets[prop.upper()] = datasets['properties'].map(lambda x: x.get(prop.upper(), ''))
@@ -1541,6 +1535,7 @@ class Openbis:
return Things(self, 'dataset', datasets[attrs], 'permId')
+
def get_experiment(self, expId, withAttachments=False, only_data=False):
""" Returns an experiment object for a given identifier (expId).
"""
@@ -1830,29 +1825,27 @@ class Openbis:
fetchopts,
],
}
-
resp = self._post_request(self.as_v3, request)
- objects = resp['objects']
- if len(objects) == 0:
- raise ValueError("No projects found!")
-
- parse_jackson(objects)
- projects = DataFrame(objects)
- if len(projects) is 0:
- raise ValueError("No projects found!")
-
- projects['registrationDate'] = projects['registrationDate'].map(format_timestamp)
- projects['modificationDate'] = projects['modificationDate'].map(format_timestamp)
- projects['leader'] = projects['leader'].map(extract_person)
- projects['registrator'] = projects['registrator'].map(extract_person)
- projects['modifier'] = projects['modifier'].map(extract_person)
- projects['permId'] = projects['permId'].map(extract_permid)
- projects['identifier'] = projects['identifier'].map(extract_identifier)
-
- pros = projects[['identifier', 'permId', 'leader', 'registrator', 'registrationDate',
- 'modifier', 'modificationDate']]
- return Things(self, 'project', pros, 'identifier')
+ attrs = ['identifier', 'permId', 'leader', 'registrator', 'registrationDate', 'modifier', 'modificationDate']
+ if len(resp['objects']) == 0:
+ projects = DataFrame(columns=attrs)
+ else:
+ objects = resp['objects']
+ parse_jackson(objects)
+
+ projects = DataFrame(objects)
+
+ projects['registrationDate'] = projects['registrationDate'].map(format_timestamp)
+ projects['modificationDate'] = projects['modificationDate'].map(format_timestamp)
+ projects['leader'] = projects['leader'].map(extract_person)
+ projects['registrator'] = projects['registrator'].map(extract_person)
+ projects['modifier'] = projects['modifier'].map(extract_person)
+ projects['permId'] = projects['permId'].map(extract_permid)
+ projects['identifier'] = projects['identifier'].map(extract_identifier)
+
+ return Things(self, 'project', projects[attrs], 'identifier')
+
def _create_get_request(self, method_name, entity, permids, options):
--
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