def loadCache(obj, user=None):
if isinstance(obj, dict):
if 'applet' in obj:
try:
obj["applet"]["responseDates"] = responseDateList(
obj['applet'].get('_id', '').split('applet/')[-1],
user.get('_id'),
user
)
except:
obj["applet"]["responseDates"] = []
return(obj)
else:
cache = json_util.loads(obj)
if 'applet' in cache:
try:
cache["applet"]["responseDates"] = responseDateList(
cache['applet'].get('_id', '').split('applet/')[-1],
user.get('_id'),
user
)
except:
cache["applet"]["responseDates"] = []
return(
{
k: v for k, v in cache.items() if k!="prov:generatedAtTime"
} if isinstance(cache, dict) else cache
)
def formatLdObject(obj,
mesoPrefix='folder',
user=None,
keepUndefined=False,
dropErrors=False,
refreshCache=False,
responseDates=False):
"""
Function to take a compacted JSON-LD Object within a Girder for Mindlogger
database and return an exapanded JSON-LD Object including an _id.
:param obj: Compacted JSON-LD Object
:type obj: dict or list
:param mesoPrefix: Girder for Mindlogger entity type, defaults to 'folder'
if not provided
:type mesoPrefix: str
:param user: User making the call
:type user: User
:param keepUndefined: Keep undefined properties
:type keepUndefined: bool
:param dropErrors: Return `None` instead of raising an error for illegal
JSON-LD definitions.
:type dropErrors: bool
:param refreshCache: Refresh from Dereferencing URLs?
:type refreshCache: bool
:param responseDates: Include list of ISO date strings of responses
:type responseDates: bool
:returns: Expanded JSON-LD Object (dict or list)
"""
from girderformindlogger.models import pluralize
refreshCache = False if refreshCache is None else refreshCache
try:
if obj is None:
return (None)
if isinstance(obj, dict):
oc = obj.get("cached")
if all([not refreshCache, oc is not None]):
return (loadCache(oc))
if 'meta' not in obj.keys():
return (_fixUpFormat(obj))
mesoPrefix = camelCase(mesoPrefix)
if type(obj) == list:
return (_fixUpFormat([
formatLdObject(o,
mesoPrefix,
refreshCache=refreshCache,
user=user) for o in obj if o is not None
]))
if not type(obj) == dict and not dropErrors:
raise TypeError("JSON-LD must be an Object or Array.")
newObj = obj.get('meta', obj)
newObj = newObj.get(mesoPrefix, newObj)
newObj = expand(newObj, keepUndefined=keepUndefined)
if type(newObj) == list and len(newObj) == 1:
try:
newObj = newObj[0]
except:
raise ValidationException(str(newObj))
if type(newObj) != dict:
newObj = {}
objID = str(obj.get('_id', 'undefined'))
if objID == 'undefined':
raise ResourcePathNotFound()
newObj['_id'] = "/".join([snake_case(mesoPrefix), objID])
if mesoPrefix == 'applet':
protocolUrl = obj.get('meta', {}).get('protocol', obj).get(
'http://schema.org/url',
obj.get('meta', {}).get('protocol', obj).get('url'))
protocol = ProtocolModel().getFromUrl(
protocolUrl,
'protocol',
user,
thread=False,
refreshCache=refreshCache
)[0] if protocolUrl is not None else {}
protocol = formatLdObject(protocol,
'protocol',
user,
refreshCache=refreshCache)
applet = {}
applet['activities'] = protocol.pop('activities', {})
applet['items'] = protocol.pop('items', {})
applet['protocol'] = {
key: protocol.get('protocol', protocol.get('activitySet',
{})).pop(key)
for key in
['@type', '_id', 'http://schema.org/url', 'schema:url', 'url']
if key in list(protocol.get('protocol', {}).keys())
}
applet['applet'] = {
**protocol.pop('protocol', {}),
**obj.get('meta', {}).get(mesoPrefix, {}), '_id':
"/".join([snake_case(mesoPrefix), objID]),
'url':
"#".join(
[obj.get('meta', {}).get('protocol', {}).get("url", "")])
}
createCache(obj, applet, 'applet', user)
if responseDates:
try:
applet["applet"]["responseDates"] = responseDateList(
obj.get('_id'), user.get('_id'), user)
except:
applet["applet"]["responseDates"] = []
return (applet)
elif mesoPrefix == 'protocol':
protocol = {'protocol': newObj, 'activities': {}, "items": {}}
activitiesNow = set()
itemsNow = set()
try:
protocol = componentImport(newObj,
deepcopy(protocol),
user,
refreshCache=refreshCache)
except:
print("636")
protocol = componentImport(newObj,
deepcopy(protocol),
user,
refreshCache=True)
newActivities = [
a for a in protocol.get('activities', {}).keys()
if a not in activitiesNow
]
newItems = [
i for i in protocol.get('items', {}).keys()
if i not in itemsNow
]
while (any([len(newActivities), len(newItems)])):
activitiesNow = set(protocol.get('activities', {}).keys())
itemsNow = set(protocol.get('items', {}).keys())
for activityURL in newActivities:
activity = protocol['activities'][activityURL]
activity = activity.get('meta',
{}).get('activity', activity)
try:
protocol = componentImport(deepcopy(activity),
deepcopy(protocol),
user,
refreshCache=refreshCache)
except:
print("670")
protocol = componentImport(deepcopy(activity),
deepcopy(protocol),
user,
refreshCache=True)
for itemURL in newItems:
activity = protocol['items'][itemURL]
activity = activity.get('meta', {}).get('screen', activity)
try:
protocol = componentImport(deepcopy(activity),
deepcopy(protocol),
user,
refreshCache=refreshCache)
except:
print("691")
protocol = componentImport(deepcopy(activity),
deepcopy(protocol),
user,
refreshCache=True)
newActivities = list(
set(protocol.get('activities', {}).keys()) - activitiesNow)
newItems = list(
set(protocol.get('items', {}).keys()) - itemsNow)
return (_fixUpFormat(protocol))
else:
return (_fixUpFormat(newObj))
except:
if refreshCache == False:
return (_fixUpFormat(
formatLdObject(obj,
mesoPrefix,
user,
keepUndefined,
dropErrors,
refreshCache=False,
responseDates=responseDates)))
import sys, traceback
print(sys.exc_info())
print(traceback.print_tb(sys.exc_info()[2]))
def formatLdObject(obj,
mesoPrefix='folder',
user=None,
keepUndefined=False,
dropErrors=False,
refreshCache=False,
responseDates=False):
"""
Function to take a compacted JSON-LD Object within a Girder for Mindlogger
database and return an exapanded JSON-LD Object including an _id.
:param obj: Compacted JSON-LD Object
:type obj: dict or list
:param mesoPrefix: Girder for Mindlogger entity type, defaults to 'folder'
if not provided
:type mesoPrefix: str
:param user: User making the call
:type user: User
:param keepUndefined: Keep undefined properties
:type keepUndefined: bool
:param dropErrors: Return `None` instead of raising an error for illegal
JSON-LD definitions.
:type dropErrors: bool
:param refreshCache: Refresh from Dereferencing URLs?
:type refreshCache: bool
:param responseDates: Include list of ISO date strings of responses
:type responseDates: bool
:returns: Expanded JSON-LD Object (dict or list)
"""
from girderformindlogger.models import pluralize
refreshCache = False if refreshCache is None else refreshCache
try:
if obj is None:
return (None)
if isinstance(obj, dict):
oc = obj.get("cached")
if all([not refreshCache, oc is not None]):
return (loadCache(oc))
if 'meta' not in obj.keys():
return (_fixUpFormat(obj))
mesoPrefix = camelCase(mesoPrefix)
if type(obj) == list:
return (_fixUpFormat([
formatLdObject(o,
mesoPrefix,
refreshCache=refreshCache,
user=user) for o in obj if o is not None
]))
if not type(obj) == dict and not dropErrors:
raise TypeError("JSON-LD must be an Object or Array.")
newObj = obj.get('meta', obj)
newObj = newObj.get(mesoPrefix, newObj)
if not obj.get('loadedFromSingleFile', False):
newObj = expand(newObj, keepUndefined=keepUndefined)
if type(newObj) == list and len(newObj) == 1:
try:
newObj = newObj[0]
except:
raise ValidationException(str(newObj))
if type(newObj) != dict:
newObj = {}
objID = str(obj.get('_id', 'undefined'))
if objID == 'undefined':
raise ResourcePathNotFound('unable to load object')
newObj['_id'] = "/".join([snake_case(mesoPrefix), objID])
if mesoPrefix == 'applet':
protocolUrl = obj.get('meta', {}).get('protocol', obj).get(
'http://schema.org/url',
obj.get('meta', {}).get('protocol', obj).get('url'))
# get protocol data from id
protocol = None
protocolId = obj.get('meta', {}).get('protocol',
{}).get('_id',
'').split('/')[-1]
if protocolId:
cache = ProtocolModel().getCache(protocolId)
if cache:
protocol = loadCache(cache)
if protocolUrl is not None and not protocol:
# get protocol from url
protocol = ProtocolModel().getFromUrl(
protocolUrl,
'protocol',
user,
thread=False,
refreshCache=refreshCache)[0]
# format protocol data
protocol = formatLdObject(protocol,
'protocol',
user,
refreshCache=refreshCache)
applet = {}
applet['activities'] = protocol.pop('activities', {})
applet['items'] = protocol.pop('items', {})
applet['protocol'] = {
key: protocol.get('protocol', protocol.get('activitySet',
{})).pop(key)
for key in
['@type', '_id', 'http://schema.org/url', 'schema:url', 'url']
if key in list(protocol.get('protocol', {}).keys())
}
applet['applet'] = {
**protocol.pop('protocol', {}),
**obj.get('meta', {}).get(mesoPrefix, {}), '_id':
"/".join([snake_case(mesoPrefix), objID]),
'url':
"#".join(
[obj.get('meta', {}).get('protocol', {}).get("url", "")])
}
if 'appletName' in obj and obj['appletName']:
suffix = obj['appletName'].split('/')[-1]
inserted = False
candidates = ['prefLabel', 'altLabel']
for candidate in candidates:
for key in applet['applet']:
if not inserted and str(key).endswith(
candidate) and len(
applet['applet'][key]) and len(
applet['applet'][key][0].get(
'@value', '')):
if len(suffix):
applet['applet'][key][0]['@value'] += (' ' +
suffix)
if not len(applet['applet']
['url']): # for development
applet['applet'][key][0][
'@value'] += ' ( single-file )'
AppletModel().update({'_id': obj['_id']}, {
'$set': {
'displayName':
applet['applet'][key][0]['@value']
}
})
inserted = True
createCache(obj, applet, 'applet', user)
if responseDates:
try:
applet["applet"]["responseDates"] = responseDateList(
obj.get('_id'), user.get('_id'), user)
except:
applet["applet"]["responseDates"] = []
return (applet)
elif mesoPrefix == 'protocol':
protocol = {'protocol': newObj, 'activities': {}, "items": {}}
if obj.get('loadedFromSingleFile', False):
activities = list(ActivityModel().find({
'meta.protocolId':
'{}/{}'.format(MODELS()['protocol']().name, obj['_id'])
}))
items = list(ScreenModel().find({
'meta.protocolId':
'{}/{}'.format(MODELS()['protocol']().name, obj['_id'])
}))
for activity in activities:
formatted = formatLdObject(activity, 'activity', user)
protocol['activities'][formatted['@id']] = formatted
for item in items:
formatted = formatLdObject(item, 'screen', user)
protocol['items'][formatted['@id']] = formatted
else:
try:
protocol = componentImport(newObj,
deepcopy(protocol),
user,
refreshCache=refreshCache)
except:
print("636")
protocol = componentImport(newObj,
deepcopy(protocol),
user,
refreshCache=True)
newActivities = protocol.get('activities', {}).keys()
newItems = protocol.get('items', {}).keys()
while (any([len(newActivities), len(newItems)])):
activitiesNow = set(protocol.get('activities', {}).keys())
itemsNow = set(protocol.get('items', {}).keys())
for activityURL in newActivities:
activity = protocol['activities'][activityURL]
activity = activity.get('meta',
{}).get('activity', activity)
try:
protocol = componentImport(
deepcopy(activity),
deepcopy(protocol),
user,
refreshCache=refreshCache)
except:
print("670")
protocol = componentImport(deepcopy(activity),
deepcopy(protocol),
user,
refreshCache=True)
for itemURL in newItems:
activity = protocol['items'][itemURL]
activity = activity.get('meta',
{}).get('screen', activity)
try:
protocol = componentImport(
deepcopy(activity),
deepcopy(protocol),
user,
refreshCache=refreshCache)
except:
print("691")
protocol = componentImport(deepcopy(activity),
deepcopy(protocol),
user,
refreshCache=True)
newActivities = list(
set(protocol.get('activities', {}).keys()) -
activitiesNow)
newItems = list(
set(protocol.get('items', {}).keys()) - itemsNow)
formatted = _fixUpFormat(protocol)
createCache(obj, formatted, 'protocol')
return formatted
else:
return (_fixUpFormat(newObj))
except:
if refreshCache == False:
return (_fixUpFormat(
formatLdObject(obj,
mesoPrefix,
user,
keepUndefined,
dropErrors,
refreshCache=True,
responseDates=responseDates)))
import sys, traceback
print(sys.exc_info())
print(traceback.print_tb(sys.exc_info()[2]))
def getOwnApplets(
self,
role,
ids_only=False,
unexpanded=False,
refreshCache=False
):
from bson.objectid import ObjectId
from girderformindlogger.utility.jsonld_expander import loadCache
from girderformindlogger.utility.response import responseDateList
reviewer = self.getCurrentUser()
if reviewer is None:
raise AccessException("You must be logged in to get user applets.")
role = role.lower()
if role not in USER_ROLES.keys():
raise RestException(
'Invalid user role.',
'role'
)
applet_ids = reviewer.get('applets', {}).get(role, [])
if ids_only:
return applet_ids
applets = [AppletModel().load(ObjectId(applet_id), AccessType.READ) for applet_id in applet_ids]
if unexpanded:
return([{
'applet': AppletModel().unexpanded(applet)
} for applet in applets])
try:
result = []
for applet in applets:
if applet.get('cached'):
formatted = {
**jsonld_expander.formatLdObject(
applet,
'applet',
reviewer,
refreshCache=refreshCache,
responseDates=False
),
"users": AppletModel().getAppletUsers(applet, reviewer),
"groups": AppletModel().getAppletGroups(
applet,
arrayOfObjects=True
)
} if role in ["coordinator", "manager"] else {
**jsonld_expander.formatLdObject(
applet,
'applet',
reviewer,
refreshCache=refreshCache,
responseDates=(role=="user")
),
"groups": [
group for group in AppletModel().getAppletGroups(applet).get(
role
) if ObjectId(
group
) in [
*reviewer.get('groups', []),
*reviewer.get('formerGroups', []),
*[invite['groupId'] for invite in [
*reviewer.get('groupInvites', []),
*reviewer.get('declinedInvites', [])
]]
]
]
}
try:
formatted["applet"]["responseDates"] = responseDateList(
applet.get('_id'),
reviewer.get('_id'),
reviewer
)
except:
formatted["applet"]["responseDates"] = []
result.append(formatted)
return(result)
except:
import sys, traceback
print(sys.exc_info())
return([])