def addApplet(new_user, protocolUrl):
"""
adds an applet for the user, where the user becomes a manager for it.
inputs
------
new_user: a user oject (from testCreateUser)
protocolURL: String, a valid URL to an activity set.
returns
-------
applet response object
"""
currentUser = authenticate(new_user)
# TODO: create an activity-set that JUST for testing.
# make sure it has all the weird qualities that can break
userAppletsToStart = AppletModel().getAppletsForUser('manager',
currentUser,
active=True)
userApplets = userAppletsToStart.copy()
# for now, lets do the mindlogger demo
protocol = ProtocolModel().getFromUrl(protocolUrl, 'protocol',
currentUser)[0]
randomAS = np.random.randint(1000000)
ar = AppletModel().createAppletFromUrl(
name="testProtocol{}".format(randomAS),
protocolUrl=protocolUrl,
user=currentUser,
sendEmail=False)
while len(userApplets) == len(userAppletsToStart):
nightyNight(sleepInterval)
userApplets = AppletModel().getAppletsForUser('manager',
currentUser,
active=True)
ar = jsonld_expander.loadCache(userApplets[-1]['cached'])
assert jsonld_expander.reprolibCanonize(
ar['protocol']['url']
) == jsonld_expander.reprolibCanonize(protocolUrl), \
'the URLS do not match! {} {}'.format(
ar['protocol']['url'],
protocolUrl
)
assert ar['applet']['_id'], 'there is no ID!'
assert getAppletById(new_user,
ar) is not None, 'something wrong with getAppletById'
return ar
def unexpanded(self, applet):
from girderformindlogger.utility.jsonld_expander import loadCache
return ({
**(loadCache(applet.get('cached', {})).get('applet') if isinstance(
applet, dict) and 'cached' in applet else {
'_id': "applet/{}".format(str(applet.get('_id'))),
**applet.get('meta', {}).get('applet', {})
})
})
def smartImport(IRI, user=None, refreshCache=False, modelType=None):
from girderformindlogger.constants import MODELS
from girderformindlogger.utility.jsonld_expander import loadCache, \
reprolibCanonize
MODELS = MODELS()
mt1 = "screen" if modelType in [None, "external JSON-LD document"
] else modelType
model, modelType = MODELS[mt1]().getFromUrl(IRI,
user=user,
refreshCache=refreshCache,
thread=False)
return ((modelType, loadCache(model.get('cached',
model)), reprolibCanonize(IRI)))
def getGroupInvites(self):
pending = self.getCurrentUser().get("groupInvites")
output = []
userfields = ['firstName', '_id', 'email', 'gravatar_baseUrl', 'login']
for p in pending:
groupId = p.get('groupId')
applets = list(AppletModel().find(
query={"roles.user.groups.id": groupId},
fields=[
'cached.applet.skos:prefLabel',
'cached.applet.schema:description',
'cached.applet.schema:image', 'roles'
]))
for applet in applets:
for role in ['manager', 'reviewer']:
applet[''.join([role, 's'])] = [{
('image' if userKey == 'gravatar_baseUrl' else
userKey): user.get(userKey)
for userKey in user.keys()
} for user in list(UserModel().find(query={
"groups": {
"$in": [
group.get('id')
for group in applet.get('roles', {}).get(
role, {}).get('groups', [])
]
}
},
fields=userfields))]
appletC = jsonld_expander.loadCache(
applet.get('cached')) if 'cached' in applet else applet
output.append({
'_id':
groupId,
'applets': [{
'name':
appletC.get('applet', {}).get('skos:prefLabel', ''),
'image':
appletC.get('applet', {}).get('schema:image', ''),
'description':
appletC.get('applet', {}).get('schema:description',
''),
'managers':
applet.get('managers'),
'reviewers':
applet.get('reviewers')
} for applet in applets]
})
return (output)
def updateRelationship(self, applet, relationship):
"""
:param applet: Applet to update
:type applet: dict
:param relationship: Relationship to apply
:type relationship: str
:returns: updated Applet
"""
from bson.json_util import dumps
from girderformindlogger.utility.jsonld_expander import loadCache
if not isinstance(relationship, str):
raise TypeError("Applet relationship must be defined as a string.")
if 'meta' not in applet:
applet['meta'] = {'applet': {}}
if 'applet' not in applet['meta']:
applet['meta']['applet'] = {}
applet['meta']['applet']['informantRelationship'] = relationship
if 'cached' in applet:
applet['cached'] = loadCache(applet['cached'])
if 'applet' in applet['cached']:
applet['cached']['applet']['informantRelationship'] = relationship
applet['cached'] = dumps(applet['cached'])
return (self.save(applet, validate=False))
def getHistoryDataFromItemIRIs(self, protocolId, IRIGroup):
from girderformindlogger.models.item import Item as ItemModel
from girderformindlogger.utility import jsonld_expander
protocol = self.load(protocolId, force=True)
items = {}
activities = {}
itemReferences = {}
result = {
'items': items,
'activities': activities,
'itemReferences': itemReferences
}
if 'historyId' not in protocol.get('meta', {}):
return result
historyFolder = FolderModel().load(protocol['meta']['historyId'],
force=True)
if 'referenceId' not in historyFolder.get('meta', {}):
return result
referencesFolder = FolderModel().load(
historyFolder['meta']['referenceId'], force=True)
itemModel = ItemModel()
for IRI in IRIGroup:
reference = itemModel.findOne({
'folderId': referencesFolder['_id'],
'meta.identifier': IRI
})
if not reference:
continue
history = reference['meta']['history']
for version in IRIGroup[IRI]:
if version not in itemReferences:
itemReferences[version] = {}
inserted = False
for i in range(0, len(history)):
if self.compareVersions(version,
history[i]['version']) <= 0:
if not history[i].get('reference', None):
continue
if history[i]['reference'] not in items:
(modelType,
referenceId) = history[i]['reference'].split('/')
model = MODELS()[modelType]().findOne(
{'_id': ObjectId(referenceId)})
items[history[i]
['reference']] = jsonld_expander.loadCache(
model['cached'])
activityId = str(model['meta']['activityId'])
if activityId not in activities:
activities[
activityId] = jsonld_expander.loadCache(
FolderModel().load(
activityId, force=True)['cached'])
if history[i]['reference']:
itemReferences[version][IRI] = history[i][
'reference']
inserted = True
break
if not inserted:
itemReferences[version][
IRI] = None # this is same as latest version
return result