From cc56a7dd2b97228f826268c5fcc1fec7b85d3606 Mon Sep 17 00:00:00 2001
From: vermeul <swen@ethz.ch>
Date: Mon, 1 Oct 2018 00:15:18 +0200
Subject: [PATCH] better handling of tags, sample.container
---
pybis/src/python/pybis/dataset.py | 8 ++--
pybis/src/python/pybis/pybis.py | 69 +++++++++++++++++++++----------
pybis/src/python/pybis/sample.py | 13 +++---
3 files changed, 60 insertions(+), 30 deletions(-)
diff --git a/pybis/src/python/pybis/dataset.py b/pybis/src/python/pybis/dataset.py
index f90c837efb8..e1aff9ace2a 100755
--- a/pybis/src/python/pybis/dataset.py
+++ b/pybis/src/python/pybis/dataset.py
@@ -67,10 +67,10 @@ class DataSet(OpenBisObject):
def __dir__(self):
return [
'props',
- 'get_parents()', 'add_parents()', 'del_parents()',
- 'get_children()', 'add_children()', 'del_children()',
- 'get_containers()', 'add_containers()', 'del_containers()',
- 'get_components()', 'add_components()', 'del_components()',
+ 'get_parents()', 'get_children()', 'get_components()', 'get_containers()',
+ 'add_parents()', 'add_children()', 'add_components()', 'add_containers()',
+ 'del_parents()', 'del_children()', 'del_components()', 'del_containers()',
+ 'set_parents()', 'set_children()', 'set_components()', 'set_containers()',
'sample',
'experiment',
'physicalData',
diff --git a/pybis/src/python/pybis/pybis.py b/pybis/src/python/pybis/pybis.py
index e20e2817fb9..c786c63c3af 100644
--- a/pybis/src/python/pybis/pybis.py
+++ b/pybis/src/python/pybis/pybis.py
@@ -131,6 +131,19 @@ def _type_for_id(ident, entity):
"@type": "as.dto.sample.id.SamplePermId"
}
"""
+ # Tags have strange permIds...
+ if entity.lower() == 'tag':
+ if '/' in ident:
+ return {
+ "permId": ident,
+ "@type" : "as.dto.tag.id.TagPermId"
+ }
+ else:
+ return {
+ "code": ident,
+ "@type": "as.dto.tag.id.TagCode"
+ }
+
entities = {
"sample" : "Sample",
"dataset" : "DataSet",
@@ -2029,49 +2042,63 @@ class Openbis:
}
resp = self._post_request(self.as_v3, request)
- attrs = ['permId', 'code', 'description', 'owner', 'private', 'registrationDate']
- if len(resp['objects']) == 0:
- tags = DataFrame(columns = attrs)
- else:
- objects = resp['objects']
- parse_jackson(resp)
- tags = DataFrame(objects)
- 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)
- tags['owner'] = tags['owner'].map(extract_person)
-
- return Things(self, 'tag', tags[attrs], 'permId')
+ return self._tag_list_for_response(response=resp['objects'])
def get_tag(self, permId, only_data=False):
""" Returns a specific tag
"""
- fetchopts = {}
+ just_one = True
+ identifiers = []
+ if isinstance(permId, list):
+ just_one = False
+ for ident in permId:
+ identifiers.append(_type_for_id(ident, 'tag'))
+ else:
+ identifiers.append(_type_for_id(permId, 'tag'))
+
+ fetchopts = fetch_option['tag']
+ for option in ['owner']:
+ fetchopts[option] = fetch_option[option]
request = {
"method": "getTags",
"params": [
self.token,
- [{
- "permId": permId,
- "@type": "as.dto.tag.id.TagPermId"
- }],
+ identifiers,
fetchopts
],
}
resp = self._post_request(self.as_v3, request)
- if resp is None or len(resp) == 0:
- raise ValueError('no such tag: ' + permId)
- else:
+ if just_one:
+ if len(resp) == 0:
+ raise ValueError('no such tag found: {}'.format(permId))
+
parse_jackson(resp)
for permId in resp:
if only_data:
return resp[permId]
else:
return Tag(self, data=resp[permId])
+ else:
+ return self._tag_list_for_response(response=list(resp.values()))
+
+ def _tag_list_for_response(self, response):
+
+ parse_jackson(response)
+ attrs = ['permId', 'code', 'description', 'owner', 'private', 'registrationDate']
+ if len(response) == 0:
+ tags = DataFrame(columns = attrs)
+ else:
+ tags = DataFrame(response)
+ 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)
+ tags['owner'] = tags['owner'].map(extract_person)
+
+ return Things(self, 'tag', tags[attrs], 'permId')
def search_semantic_annotations(self, permId=None, entityType=None, propertyType=None, only_data = False):
diff --git a/pybis/src/python/pybis/sample.py b/pybis/src/python/pybis/sample.py
index ca8aee02d69..63fcdb5371a 100644
--- a/pybis/src/python/pybis/sample.py
+++ b/pybis/src/python/pybis/sample.py
@@ -64,8 +64,10 @@ class Sample(OpenBisObject):
'get_parents()', 'get_children()', 'get_components()',
'add_parents()', 'add_children()', 'add_components()',
'del_parents()', 'del_children()', 'del_components()',
- 'get_datasets()', 'get_experiment()', 'get_container()',
- 'space', 'project', 'experiment', 'tags',
+ 'set_parents()', 'set_children()', 'set_components()',
+ 'get_datasets()',
+ 'get_experiment()',
+ 'space', 'project', 'experiment', 'container', 'tags',
'set_tags()', 'add_tags()', 'del_tags()',
'add_attachment()', 'get_attachments()', 'download_attachments()',
'save()', 'delete()'
@@ -138,15 +140,16 @@ class Sample(OpenBisObject):
def get_projects(self, **kwargs):
return self.openbis.get_project(withSamples=[self.permId], **kwargs)
- def get_experiment(self):
+ @property
+ def experiment(self):
try:
return self.openbis.get_experiment(self._experiment['identifier'])
except Exception:
pass
@property
- def experiment(self):
+ def container(self):
try:
- return self.openbis.get_experiment(self._experiment['identifier'])
+ return self.openbis.get_sample(self._container['identifier'])
except Exception:
pass
--
GitLab