def reloadAndUpdateCache(self, applet, editor):
from girderformindlogger.models.protocol import Protocol
protocolUrl = applet.get('meta', {}).get('protocol', applet).get(
'http://schema.org/url',
applet.get('meta', {}).get('protocol', applet).get('url'))
if protocolUrl is not None:
protocol = Protocol().getFromUrl(protocolUrl,
'protocol',
editor,
thread=False,
refreshCache=True)
protocol = protocol[0].get('protocol', protocol[0])
if protocol.get('_id'):
self.update({'_id': ObjectId(applet['_id'])},
{'$set': {
'meta.protocol._id': protocol['_id']
}})
if 'meta' in applet and 'protocol' in applet['meta']:
applet['meta']['protocol']['_id'] = protocol['_id']
from girderformindlogger.utility import jsonld_expander
jsonld_expander.formatLdObject(applet,
'applet',
editor,
refreshCache=False,
responseDates=False)
def createAppletFromUrl(self,
name,
protocolUrl,
user=None,
roles=None,
constraints=None,
sendEmail=True):
from girderformindlogger.models.protocol import Protocol
# get a protocol from a URL
protocol = Protocol().getFromUrl(protocolUrl,
'protocol',
user,
thread=False,
refreshCache=True)
protocol = protocol[0].get('protocol', protocol[0])
displayName = Protocol().preferredName(protocol)
name = name if name is not None and len(name) else displayName
if len(displayName) == 0:
displayName = name if len(name) else "activity"
applet = self.createApplet(
name=name,
protocol={
'_id':
'protocol/{}'.format(str(protocol.get('_id')).split('/')[-1]),
'url':
protocol.get('meta', {}).get('protocol',
{}).get('url', protocolUrl)
},
user=user,
roles=roles,
constraints=constraints,
displayName=displayName)
emailMessage = "Your applet, {}, has been successfully created. The " \
"applet's ID is {}".format(
name,
str(applet.get('applet', applet).get('_id')
)
)
if sendEmail and 'email' in user:
from girderformindlogger.utility.mail_utils import sendMail
sendMail(subject=name, text=emailMessage, to=[user['email']])
print(emailMessage)
def createAppletFromUrl(self,
name,
protocolUrl,
user=None,
roles=None,
constraints=None,
email='',
sendEmail=True):
from girderformindlogger.models.protocol import Protocol
from girderformindlogger.utility import mail_utils
# we have cases to show manager's email to users
if mail_utils.validateEmailAddress(email):
user['email'] = email
user['email_encrypted'] = False
UserModel().save(user)
# get a protocol from a URL
protocol = Protocol().getFromUrl(protocolUrl,
'protocol',
user,
thread=False,
refreshCache=True)
protocol = protocol[0].get('protocol', protocol[0])
displayName = Protocol().preferredName(protocol)
name = name if name is not None and len(name) else displayName
appletName = '{}/'.format(protocolUrl)
applet = self.createApplet(
name=name,
protocol={
'_id':
'protocol/{}'.format(str(protocol.get('_id')).split('/')[-1]),
'url':
protocol.get('meta', {}).get('protocol',
{}).get('url', protocolUrl)
},
user=user,
roles=roles,
constraints=constraints,
appletName=appletName)
def getOldVersions(responses, applet):
IRIs = {}
insertedIRI = {}
for IRI in responses:
IRIs[IRI] = []
for response in responses[IRI]:
if 'version' not in response:
continue
identifier = '{}/{}'.format(IRI, response['version'])
if identifier not in insertedIRI:
IRIs[IRI].append(response['version'])
insertedIRI[identifier] = True
return Protocol().getHistoryDataFromItemIRIs(
applet.get('meta', {}).get('protocol',
{}).get('_id', '').split('/')[-1], IRIs)
def createAppletFromProtocolData(self,
name,
protocol,
user=None,
roles=None,
constraints=None,
email='',
sendEmail=True):
from girderformindlogger.models.protocol import Protocol
from girderformindlogger.utility import mail_utils
# we have cases to show manager's email to users
if mail_utils.validateEmailAddress(email):
user['email'] = email
user['email_encrypted'] = False
UserModel().save(user)
# get a protocol from single json file
protocol = Protocol().createProtocol(protocol, user)
protocol = protocol.get('protocol', protocol)
displayName = Protocol().preferredName(protocol)
name = name if name is not None and len(name) else displayName
appletName = '{}/'.format(protocol.get('@id'))
applet = self.createApplet(
name=name,
protocol={
'_id':
'protocol/{}'.format(str(protocol.get('_id')).split('/')[-1])
},
user=user,
roles=roles,
constraints=constraints,
appletName=appletName)
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 htmlInvitation(
self,
invitation,
invitee=None,
fullDoc=False,
includeLink=True
):
"""
Returns an HTML document rendering the invitation.
:param invitation: Invitation to render
:type invitation: dict
:param invitee: Invited user
:type invitee: dict or None
:returns: html document
"""
from girderformindlogger.models.applet import Applet
from girderformindlogger.models.profile import Profile
from girderformindlogger.models.protocol import Protocol
from girderformindlogger.models.token import Token
from girderformindlogger.models.user import User
from girderformindlogger.exceptions import GirderException
from girderformindlogger.api.rest import getApiUrl
from girderformindlogger.utility import context as contextUtil, \
mail_utils
accept = (
"To accept or decline, visit <a href=\"{u}\">{u}</a>".format(
u="https://web.mindlogger.org/#/invitation/{}".format(str(
invitation['_id']
))
)
) if includeLink else ""
applet = Applet().load(ObjectId(invitation['appletId']), force=True)
appletName = applet.get(
'displayName',
'a new applet'
)
try:
skin = contextUtil.getSkin()
except:
skin = {}
instanceName = skin.get("name", "MindLogger")
role = invitation.get("role", "user")
try:
coordinator = Profile().coordinatorProfile(
applet['_id'],
invitation["invitedBy"]
)
except:
coordinator = None
displayProfile = Profile().displayProfileFields(invitation, invitee)
description = applet.get('meta', {}).get(
'applet',
{}
).get(
"schema:desciription",
Protocol().load(
applet['meta']['protocol']['_id'].split('protocol/')[-1],
force=True
).get('meta', {}).get('protocol') if 'protocol' in applet.get(
'meta',
{}
) else {}
).get("schema:description", "")
managers = mail_utils.htmlUserList(
Applet().listUsers(applet, 'manager', force=True)
)
coordinators = mail_utils.htmlUserList(
Applet().listUsers(applet, 'coordinator', force=True)
)
reviewers = mail_utils.htmlUserList(
Applet().listUsers(applet, 'reviewer', force=True)
)
body = """
{greeting}ou were invited {byCoordinator}to be {role} of <b>{appletName}</b>{instanceName}.
<br/>
Below are the users that have access to your data:
{reviewers}
{managers}
{coordinators}
<br/>
{accept}
""".format(
accept=accept,
appletName=appletName,
byCoordinator="by {} ({}) ".format(
coordinator.get("displayName", "an anonymous entity"),
"<a href=\"mailto:{email}\">{email}</a>".format(
email=coordinator["email"]
) if "email" in coordinator and coordinator["email"] is not None else "email not available"
) if isinstance(coordinator, dict) else "",
coordinators="<h3>Users who can change this applet's settings, "
"but who cannot change who can see your data: </h3>{}"
"".format(
coordinators if len(
coordinators
) else "<ul><li>None</li></ul>"
),
greeting="Welcome to MindLogger! Y",
instanceName=" on {}".format(
instanceName
) if instanceName is not None and len(instanceName) else "",
managers="<h3>Users who can change this applet's settings, "
" including who can access your data: </h3>{}"
"".format(
managers if len(managers) else "<ul><li>None</li></ul>"
),
reviewers="<h3>Users who can see your data for this "
"applet: </h3>{}"
"".format(
reviewers if len(reviewers) else "<ul><li>None</li></ul>"
),
role="an editor" if role=="editor" else "a {}".format(role)
).strip()
return(body if not fullDoc else """
<!DOCTYPE html>
<html>
<head>
<meta charset="UTF-8">
<title>Invitation to {appletName} on {instanceName}</title>
</head>
<body>
{body}
</body>
</html>
""".format(
appletName=appletName,
instanceName=instanceName,
body=body
).strip())
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 htmlInvitation(self,
invitation,
invitee=None,
fullDoc=False,
includeLink=True):
"""
Returns an HTML document rendering the invitation.
:param invitation: Invitation to render
:type invitation: dict
:param invitee: Invited user
:type invitee: dict or None
:returns: html document
"""
from girderformindlogger.models.applet import Applet
from girderformindlogger.models.profile import Profile
from girderformindlogger.models.protocol import Protocol
from girderformindlogger.models.token import Token
from girderformindlogger.models.user import User
from girderformindlogger.exceptions import GirderException
from girderformindlogger.api.rest import getApiUrl
from girderformindlogger.utility import context as contextUtil, \
mail_utils
web_url = os.getenv('WEB_URI') or 'localhost:8082'
accept = ("To accept or decline, visit <a href=\"{u}\">{u}</a>".format(
u=f"https://{web_url}/#/invitation/{str(invitation['_id'])}")
) if includeLink else ""
applet = Applet().load(ObjectId(invitation['appletId']), force=True)
appletName = applet['meta']['applet'].get(
'displayName', applet.get('displayName', 'new applet'))
try:
skin = contextUtil.getSkin()
except:
skin = {}
instanceName = skin.get("name", "MindLogger")
role = invitation.get("role", "user")
try:
coordinator = Profile().coordinatorProfile(applet['_id'],
invitation["invitedBy"])
except:
coordinator = None
displayProfile = Profile().displayProfileFields(invitation, invitee)
description = applet.get('meta', {}).get('applet', {}).get(
"schema:description",
Protocol().load(
applet['meta']['protocol']['_id'].split('protocol/')[-1],
force=True).get('meta', {}).get('protocol') if 'protocol'
in applet.get('meta', {}) else {}).get("schema:description", "")
managers = mail_utils.htmlUserList(Applet().listUsers(applet,
'manager',
force=True))
coordinators = mail_utils.htmlUserList(Applet().listUsers(
applet, 'coordinator', force=True))
reviewers = mail_utils.htmlUserList(Applet().listUsers(applet,
'reviewer',
force=True))
body = mail_utils.renderTemplate(
f'welcome{"Owner" if role == "owner" else ""}.{invitation.get("lang", "en")}.mako',
{
'accept':
accept,
'appletName':
appletName,
'byCoordinator':
"by {} ({}) ".format(
coordinator.get("displayName", "an anonymous entity"),
"<a href=\"mailto:{email}\">{email}</a>".format(
email=coordinator["email"]) if "email" in coordinator
and coordinator["email"] is not None
else "email not available") if isinstance(
coordinator, dict) else "",
'coordinators':
"{}".format(coordinators if len(coordinators) else
"<ul><li>None</li></ul>"),
'instanceName':
" on {}".format(instanceName)
if instanceName is not None and len(instanceName) else "",
'managers':
"{}".format(
managers if len(managers) else "<ul><li>None</li></ul>"),
'reviewers':
"{}".format(
reviewers if len(reviewers) else "<ul><li>None</li></ul>"),
'role':
"an editor" if role == "editor" else "a {}".format(role),
'url':
f'https://{web_url}/#/invitation/{str(invitation["_id"])}'
})
return (body if not fullDoc else """
<!DOCTYPE html>
<html>
<head>
<meta charset="UTF-8">
<title>Invitation to {appletName} on {instanceName}</title>
</head>
<body>
{body}
</body>
</html>
""".format(appletName=appletName, instanceName=instanceName,
body=body).strip())