From fce3d680ef63fbea314990322d9f4227215d338c Mon Sep 17 00:00:00 2001
From: Swen Vermeul <swen@ethz.ch>
Date: Wed, 10 Aug 2016 15:11:22 +0200
Subject: [PATCH] added sample_types
---
src/python/PyBis/pybis/pybis.py | 115 +++++++++++++++-----------------
1 file changed, 53 insertions(+), 62 deletions(-)
diff --git a/src/python/PyBis/pybis/pybis.py b/src/python/PyBis/pybis/pybis.py
index a1fce5b78ee..ee183a7aaa4 100644
--- a/src/python/PyBis/pybis/pybis.py
+++ b/src/python/PyBis/pybis/pybis.py
@@ -34,6 +34,7 @@ search_for_type = {
"project": "as.dto.project.search.ProjectSearchCriteria",
"experiment": "as.dto.experiment.search.ExperimentSearchCriteria",
"code": "as.dto.common.search.CodeSearchCriteria",
+ "sample_type":"as.dto.sample.search.SampleTypeSearchCriteria",
}
@@ -48,6 +49,16 @@ def extract_identifier(ident):
return str(ident)
return ident['identifier']
+def extract_permid(permid):
+ if not isinstance(permid, dict):
+ return str(permid)
+ return permid['permId']
+
+def extract_nested_permid(permid):
+ if not isinstance(permid, dict):
+ return str(permid)
+ return permid['permId']['permId']
+
def extract_nested_identifier(ident):
if not isinstance(ident, dict):
return str(ident)
@@ -58,6 +69,24 @@ def extract_person(person):
return str(person)
return "%s %s <%s>" % (person['firstName'], person['lastName'], person['email'])
+def _criteria_for_code(code, object_type):
+ criteria = {
+ "criteria": [
+ {
+ "fieldName": "code",
+ "fieldType": "ATTRIBUTE",
+ "fieldValue": {
+ "value": code,
+ "@type": "as.dto.common.search.StringEqualToValue"
+ },
+ "@type": "as.dto.common.search.CodeSearchCriteria"
+ }
+ ],
+ "@type": search_for_type[object_type],
+ "operator": "AND"
+ }
+ return criteria
+
class Openbis:
"""Interface for communicating with openBIS. A current version of openBIS is needed (at
least version 16.05).
@@ -267,6 +296,8 @@ class Openbis:
def get_space(self, spaceId):
""" Returns a Space object for a given identifier (spaceId).
"""
+
+ spaceId = str(spaceId).upper()
request = {
"method": "getSpaces",
"params": [
@@ -289,42 +320,27 @@ class Openbis:
"jsonrpc": "2.0"
}
resp = self._post_request(self.as_v3, request)
+ if len(resp) == 0:
+ raise ValueError("No such space: %s" % spaceId)
return Space(self, resp[spaceId])
- def _criteria_for_code(self, code, object_type):
- criteria = {
- "criteria": [
- {
- "fieldName": "code",
- "fieldType": "ATTRIBUTE",
- "fieldValue": {
- "value": code,
- "@type": "as.dto.common.search.StringEqualToValue"
- },
- "@type": "as.dto.common.search.CodeSearchCriteria"
- }
- ],
- "@type": search_for_type[object_type],
- "operator": "AND"
- }
- return criteria
-
-
- def get_samples(self, space=None, project=None, experiment=None):
+ def get_samples(self, space=None, project=None, experiment=None, sample_type=None):
""" Get a list of all samples for a given space/project/experiment (or any combination)
"""
sub_criteria = []
if space:
- sub_criteria.append(self._criteria_for_code(space, 'space'))
+ sub_criteria.append(_criteria_for_code(space, 'space'))
if project:
- exp_crit = self._criteria_for_code(experiment, 'experiment')
- proj_crit = self._criteria_for_code(project, 'project')
+ exp_crit = _criteria_for_code(experiment, 'experiment')
+ proj_crit = _criteria_for_code(project, 'project')
exp_crit['criteria'] = []
exp_crit['criteria'].append(proj_crit)
sub_criteria.append(exp_crit)
if experiment:
- sub_criteria.append(self._criteria_for_code(experiment, 'experiment'))
+ sub_criteria.append(_criteria_for_code(experiment, 'experiment'))
+ if sample_type:
+ sub_criteria.append(_criteria_for_code(sample_type, 'sample_type'))
criteria = {
"criteria": sub_criteria,
@@ -348,7 +364,10 @@ class Openbis:
"experiment": {
"@type": "as.dto.experiment.fetchoptions.ExperimentFetchOptions"
},
- "@type": "as.dto.sample.fetchoptions.SampleFetchOptions"
+ "type": {
+ "@type": "as.dto.sample.fetchoptions.SampleTypeFetchOptions"
+ },
+ "@type": "as.dto.sample.fetchoptions.SampleFetchOptions",
}
request = {
@@ -367,7 +386,7 @@ class Openbis:
cache = {}
for obj in objects:
for key in obj.keys():
- if key in ('registrator','modifier','project','experiment','space'):
+ if key in ('registrator','modifier','project','experiment','space','type'):
if isinstance(obj[key], dict):
cache[ obj[key]['@id'] ] = obj[key]
else:
@@ -384,8 +403,9 @@ class Openbis:
samples['modifier'] = samples['modifier'].map(extract_person)
samples['identifier'] = samples['identifier'].map(extract_identifier)
samples['experiment'] = samples['experiment'].map(extract_nested_identifier)
+ samples['type'] = samples['type'].map(extract_nested_permid)
- return samples[['code', 'identifier', 'experiment', 'registrator', 'registrationDate', 'modifier', 'modificationDate']]
+ return samples[['code', 'identifier', 'experiment', 'type', 'registrator', 'registrationDate', 'modifier', 'modificationDate']]
else:
raise ValueError("No samples found!")
@@ -395,9 +415,9 @@ class Openbis:
sub_criteria = []
if space:
- sub_criteria.append(self._criteria_for_code(space, 'space'))
+ sub_criteria.append(_criteria_for_code(space, 'space'))
if project:
- sub_criteria.append(self._criteria_for_code(project, 'project'))
+ sub_criteria.append(_criteria_for_code(project, 'project'))
criteria = {
"criteria": sub_criteria,
@@ -464,7 +484,7 @@ class Openbis:
sub_criteria = []
if space:
- sub_criteria.append(self._criteria_for_code(space, 'space'))
+ sub_criteria.append(_criteria_for_code(space, 'space'))
criteria = {
"criteria": sub_criteria,
@@ -1231,37 +1251,8 @@ class Space(dict):
self.openbis = openbis_obj
self.code = self.code
- def get_samples(self):
+ def get_samples(self, *args, **kwargs):
""" Lists all samples in a given space. A pandas DataFrame object is returned.
"""
- fields = ['spaceCode','permId', 'identifier','experimentIdentifierOrNull']
- request = {
- "method": "searchForSamples",
- "params": [
- self.openbis.token,
- {
- "matchClauses": [
- {
- "@type": "AttributeMatchClause",
- "fieldType": "ATTRIBUTE",
- "attribute": "SPACE",
- "desiredValue": self.code,
- }
- ],
- "subCriterias": [],
- "operator": "MATCH_ALL_CLAUSES"
- },
- [
- "PROPERTIES",
- "PARENTS"
- ]
- ],
- "id": "1",
- "jsonrpc": "2.0"
- }
- resp = self.openbis._post_request(self.openbis.as_v1, request)
- if resp is not None and len(resp) > 0:
- datasets = DataFrame(resp)[fields]
- return datasets
- else:
- return None
+
+ return self.openbis.get_samples(space=self.code, *args, **kwargs)
--
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