From cd39fd5585377a918010d6836ca3bc409013af70 Mon Sep 17 00:00:00 2001
From: Swen Vermeul <swen@ethz.ch>
Date: Mon, 9 Jan 2017 17:28:00 +0100
Subject: [PATCH] added Project with nice overview
---
src/python/PyBis/pybis/pybis.py | 143 +++++++++++++++++++++-----------
1 file changed, 96 insertions(+), 47 deletions(-)
diff --git a/src/python/PyBis/pybis/pybis.py b/src/python/PyBis/pybis/pybis.py
index c209ac72755..955c29b72f2 100644
--- a/src/python/PyBis/pybis/pybis.py
+++ b/src/python/PyBis/pybis/pybis.py
@@ -32,10 +32,10 @@ from queue import Queue
DROPBOX_PLUGIN = "jupyter-uploader-api"
-def _definitions(what):
+def _definitions(entity):
entities = {
"Sample": {
- "attrs": "code permId identifier type parents children attachments space project experiment container components tags ".split(),
+ "attrs": "code permId identifier type parents children attachments space experiment container components tags ".split(),
"ids2type": {
'parentIds': { 'permId': { '@type': 'as.dto.sample.id.SamplePermId' } },
'childIds': { 'permId': { '@type': 'as.dto.sample.id.SamplePermId' } },
@@ -51,7 +51,7 @@ def _definitions(what):
"identifier": "experimentId",
},
"Project": {
- "attrs": "code permId identifier type space tags samples attachments".split(),
+ "attrs": "code description permId identifier space attachments".split(),
"multi": "tags".split(),
"identifier": "projectId",
},
@@ -70,12 +70,12 @@ def _definitions(what):
"sample" : "sampleId",
"experiment" : "experimentId",
"space" : "spaceId",
+ "project" : "projectId",
"container" : "containerId",
"component" : "componentId",
"components" : "componentIds",
"parents" : "parentIds",
"children" : "childIds",
- "project" : "projectId",
"tags" : "tagIds",
},
"ids2type": {
@@ -85,7 +85,7 @@ def _definitions(what):
'tagIds': { 'code': { '@type': 'as.dto.tag.id.TagCode' } },
},
}
- return entities[what]
+ return entities[entity]
search_criteria = {
@@ -225,18 +225,18 @@ def is_permid(ident):
else:
return False
-def search_request_for_identifier(ident, entity_type):
+def search_request_for_identifier(ident, entity):
search_request = {}
if is_identifier(ident):
search_request = {
"identifier": ident.upper(),
- "@type": "as.dto.{}.id.{}Identifier".format(entity_type.lower(), entity_type.capitalize())
+ "@type": "as.dto.{}.id.{}Identifier".format(entity.lower(), entity.capitalize())
}
else:
search_request = {
"permId": ident,
- "@type": "as.dto.{}.id.{}PermId".format(entity_type.lower(), entity_type.capitalize())
+ "@type": "as.dto.{}.id.{}PermId".format(entity.lower(), entity.capitalize())
}
return search_request
@@ -444,10 +444,10 @@ def _criteria_for_code(code):
"@type": "as.dto.common.search.CodeSearchCriteria"
}
-def _subcriteria_for_type(code, entity_type):
+def _subcriteria_for_type(code, entity):
return {
- "@type": "as.dto.{}.search.{}TypeSearchCriteria".format(entity_type.lower(), entity_type),
+ "@type": "as.dto.{}.search.{}TypeSearchCriteria".format(entity.lower(), entity),
"criteria": [
{
"@type": "as.dto.common.search.CodeSearchCriteria",
@@ -559,7 +559,7 @@ def _subcriteria_for_properties(prop, val):
}
}
-def _subcriteria_for_permid(permids, entity_type, parents_or_children=''):
+def _subcriteria_for_permid(permids, entity, parents_or_children=''):
if not isinstance(permids, list):
permids = [permids]
@@ -579,7 +579,7 @@ def _subcriteria_for_permid(permids, entity_type, parents_or_children=''):
criteria = {
"criteria": criterias,
"@type": "as.dto.{}.search.{}{}SearchCriteria".format(
- entity_type.lower(), entity_type, parents_or_children
+ entity.lower(), entity, parents_or_children
),
"operator": "OR"
}
@@ -1244,13 +1244,13 @@ class Openbis:
self._post_request(self.as_v3, request)
- def delete_entity(self, what, permid, reason):
+ def delete_entity(self, entity, permid, reason):
"""Deletes Spaces, Projects, Experiments, Samples and DataSets
"""
- entity_type = "as.dto.{}.id.{}PermId".format(what.lower(), what.capitalize())
+ entity_type = "as.dto.{}.id.{}PermId".format(entity.lower(), entity.capitalize())
request = {
- "method": "delete" + what.capitalize() + 's',
+ "method": "delete" + entity.capitalize() + 's',
"params": [
self.token,
[
@@ -1261,7 +1261,7 @@ class Openbis:
],
{
"reason": reason,
- "@type": "as.dto.{}.delete.{}DeletionOptions".format(what.lower(), what.capitalize())
+ "@type": "as.dto.{}.delete.{}DeletionOptions".format(entity.lower(), entity.capitalize())
}
]
}
@@ -1319,9 +1319,11 @@ class Openbis:
def get_project(self, projectId):
- request = self._create_get_request('getProjects', 'project', projectId, ['attachments'])
+ request = self._create_get_request(
+ 'getProjects', 'project', projectId, ['space', 'registrator', 'attachments']
+ )
resp = self._post_request(self.as_v3, request)
- return resp
+ return Project(self, resp[projectId])
def get_projects(self, space=None):
@@ -1378,12 +1380,12 @@ class Openbis:
raise ValueError("No projects found!")
- def _create_get_request(self, method_name, entity_type, permids, options):
+ def _create_get_request(self, method_name, entity, permids, options):
if not isinstance(permids, list):
permids = [permids]
- type = "as.dto.{}.id.{}".format(entity_type.lower(), entity_type.capitalize())
+ type = "as.dto.{}.id.{}".format(entity.lower(), entity.capitalize())
search_params = []
for permid in permids:
# decide if we got a permId or an identifier
@@ -1519,7 +1521,7 @@ class Openbis:
raise ValueError("No such dataSet type: {}".format(type))
- def _get_types_of(self, method_name, entity_type, type=None, additional_attributes=[]):
+ def _get_types_of(self, method_name, entity, type=None, additional_attributes=[]):
""" Returns a list of all available experiment types
"""
@@ -1530,14 +1532,14 @@ class Openbis:
if type is not None:
search_request = _gen_search_request({
- entity_type.lower(): entity_type + "Type",
+ entity.lower(): entity + "Type",
"operator": "AND",
"code": type
})
fetch_options = {
"@type": "as.dto.{}.fetchoptions.{}TypeFetchOptions".format(
- entity_type.lower(), entity_type
+ entity.lower(), entity
)
}
fetch_options['propertyAssignments'] = fetch_option['propertyAssignments']
@@ -1555,7 +1557,7 @@ class Openbis:
if len(resp['objects']) >= 1:
types = DataFrame(resp['objects'])
types['modificationDate'] = types['modificationDate'].map(format_timestamp)
- return Things(self, entity_type.lower()+'_type', types[attributes])
+ return Things(self, entity.lower()+'_type', types[attributes])
return types[attributes]
else:
@@ -1684,7 +1686,6 @@ class Openbis:
"params": [
self.token,
[ {
- "@id": 0,
"code": name,
"description": description,
"@type": "as.dto.space.create.SpaceCreation"
@@ -2237,13 +2238,14 @@ class AttrHolder():
- tags
"""
- def __init__(self, openbis_obj, type):
+ def __init__(self, openbis_obj, entity, type=None):
self.__dict__['_openbis'] = openbis_obj
- self.__dict__['_type_obj'] = type
+ self.__dict__['_entity'] = entity
+
+ if type is not None:
+ self.__dict__['_type_obj'] = type
- entity_type = type.data['@type'].split('.')[2].capitalize()
- self.__dict__['_entity_type'] = entity_type
- self.__dict__['_allowed_attrs'] = _definitions(entity_type)['attrs']
+ self.__dict__['_allowed_attrs'] = _definitions(entity)['attrs']
self.__dict__['_identifier'] = None
self.__dict__['_is_new'] = True
@@ -2255,34 +2257,39 @@ class AttrHolder():
"container","components","attachments"]:
self.__dict__['_'+attr] = data.get(attr, None)
- if attr in ["space"]:
+ elif attr in ["space"]:
d = data.get(attr, None)
if d is not None:
d = d['permId']
self.__dict__['_'+attr] = d
- if attr in ["experiment", "project"]:
+ elif attr in ["experiment", "project"]:
d = data.get(attr, None)
if d is not None:
d = d['identifier']
self.__dict__['_'+attr] = d
- if attr in ["parents","children","samples"]:
+ elif attr in ["parents","children","samples"]:
self.__dict__['_'+attr] = []
for item in data[attr]:
self.__dict__['_'+attr].append(item['identifier'])
- if attr in ["tags"]:
+ elif attr in ["tags"]:
self.__dict__['_'+attr] = []
for item in data[attr]:
self.__dict__['_'+attr].append({
"code": item['code'],
"@type": "as.dto.tag.id.TagCode"
})
+ elif attr in ["attachments"]:
+ pass
+
+ else:
+ self.__dict__['_'+attr] = data.get(attr, None)
def _all_attrs(self):
- defs = _definitions(self._entity_type)
+ defs = _definitions(self._entity)
attr2ids = _definitions('attr2ids')
ids2type = _definitions('ids2type')
@@ -2390,7 +2397,7 @@ class AttrHolder():
objs = []
for val in value:
# fetch objects in openBIS, make sure they actually exists
- obj = getattr(self._openbis, 'get_'+self._entity_type.lower())(val)
+ obj = getattr(self._openbis, 'get_'+self._entity.lower())(val)
objs.append(obj)
self.__dict__['_'+name] = {
"@type": "as.dto.common.update.IdListUpdateValue",
@@ -2409,7 +2416,18 @@ class AttrHolder():
self.__dict__['_tags'] = tags
- elif name in ["space", "project", "experiment"]:
+ elif name in ["experiment"]:
+ # fetch object in openBIS, make sure it actually exists
+ obj = getattr(self._openbis, "get_"+name)(value)
+ self.__dict__['_'+name] = obj.data['identifier']
+
+ # mark attribute as modified, if it's an existing entity
+ if self.__dict__['_is_new']:
+ pass
+ else:
+ self.__dict__['_'+name]['isModified'] = True
+
+ elif name in ["space"]:
# fetch object in openBIS, make sure it actually exists
obj = getattr(self._openbis, "get_"+name)(value)
self.__dict__['_'+name] = obj['permId']
@@ -2420,11 +2438,23 @@ class AttrHolder():
else:
self.__dict__['_'+name]['isModified'] = True
+ elif name in ["project"]:
+ # fetch object in openBIS, make sure it actually exists
+ obj = getattr(self._openbis, "get_"+name)(value)
+ self.__dict__['_'+name] = obj['identifier']
+
+ # mark attribute as modified, if it's an existing entity
+ if self.__dict__['_is_new']:
+ pass
+ else:
+ self.__dict__['_'+name]['isModified'] = True
+
+
elif name in ["identifier", "project"]:
raise KeyError("you can not modify the {}".format(name))
elif name == "code":
if self.__dict__['_type_obj'].data['autoGeneratedCode']:
- raise KeyError("for this {}Type you can not set a code".format(self.__dict__['_entity_type']))
+ raise KeyError("for this {}Type you can not set a code".format(self.__dict__['_entity']))
else:
self.__dict__['_code'] = value
else:
@@ -2435,11 +2465,11 @@ class AttrHolder():
def get_parents(self):
# e.g. self._openbis.get_samples(withChildren=self.identifier)
- return getattr(self._openbis, 'get_'+self._entity_type.lower()+'s')(withChildren=self.identifier)
+ return getattr(self._openbis, 'get_'+self._entity.lower()+'s')(withChildren=self.identifier)
def get_children(self):
# e.g. self._openbis.get_samples(withParents=self.identifier)
- return getattr(self._openbis, 'get_'+self._entity_type.lower()+'s')(withParents=self.identifier)
+ return getattr(self._openbis, 'get_'+self._entity.lower()+'s')(withParents=self.identifier)
@property
def set_tags(self, tags):
@@ -2477,7 +2507,7 @@ class AttrHolder():
html += "<tr> <td>{}</td> <td>{}</td> </tr>".format(
attr, nvl(getattr(self, attr, ''),'')
)
- if 'attachments' in self._allowed_attrs:
+ if 'attachments' in self._allowed_attrs and self._attachments is not None:
html += "<tr><td>attachments</td><td>"
html += "<br/>".join(att['fileName'] for att in self._attachments)
html += "</td></tr>"
@@ -2497,7 +2527,7 @@ class Sample():
self.__dict__['openbis'] = openbis_obj
self.__dict__['type'] = type
self.__dict__['p'] = PropertyHolder(openbis_obj, type)
- self.__dict__['a'] = AttrHolder(openbis_obj, type)
+ self.__dict__['a'] = AttrHolder(openbis_obj, 'Sample', type)
if data is not None:
self._set_data(data)
@@ -2634,9 +2664,9 @@ class Things():
"""
- def __init__(self, openbis_obj, what, df, identifier_name='code'):
+ def __init__(self, openbis_obj, entity, df, identifier_name='code'):
self.openbis = openbis_obj
- self.what = what
+ self.entity = entity
self.df = df
self.identifier_name = identifier_name
@@ -2657,8 +2687,8 @@ class Things():
row = self.df[self.df[self.identifier_name]==key.upper()]
if row is not None:
- # invoke the openbis.get_what() method
- return getattr(self.openbis, 'get_'+self.what)(row[self.identifier_name].values[0])
+ # invoke the openbis.get_entity() method
+ return getattr(self.openbis, 'get_'+self.entity)(row[self.identifier_name].values[0])
class Experiment():
@@ -2669,7 +2699,7 @@ class Experiment():
self.__dict__['openbis'] = openbis_obj
self.__dict__['type'] = type
self.__dict__['p'] = PropertyHolder(openbis_obj, type)
- self.__dict__['a'] = AttrHolder(openbis_obj, type)
+ self.__dict__['a'] = AttrHolder(openbis_obj, 'Experiment', type)
if data is not None:
self._set_data(data)
@@ -2870,3 +2900,22 @@ class Attachments:
if row is not None:
self._download()
+
+class Project:
+
+ def __init__(self, openbis_obj, data=None, **kwargs):
+ self.__dict__['openbis'] = openbis_obj
+ self.__dict__['type'] = type
+ self.__dict__['a'] = AttrHolder(openbis_obj, 'Project')
+
+ if data is not None:
+ self.a(data)
+ self.__dict__['data'] = data
+
+ if kwargs is not None:
+ for key in kwargs:
+ setattr(self, key, kwargs[key])
+
+ def _repr_html_(self):
+ html = self.a._repr_html_()
+ return html
--
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