def removeUser(request):
userid = request.unauthenticated_userid
userToRemove = request.params['couserName']
hubName = request.params['hubName']
Hubs.removeUserFromHub(hubName, userid, userToRemove)
url = request.route_url('myHubs')
return HTTPFound(location=url)
def addUser(request):
newUser = request.params['userEmail']
hubName = request.params['hubName']
owner = request.params['owner']
Hubs.addUserToHub(hubName, owner, newUser)
url = request.route_url('myHubs')
return HTTPFound(location=url)
def getProblems(data, txn=None):
if 'genome' not in data:
data['genome'] = getGenome(data, txn=txn)
problems = db.Problems(data['genome'])
problemsInBounds = problems.getInBounds(data['ref'], data['start'],
data['end'])
if problemsInBounds is None:
problemsPath = os.path.join(cfg.jbrowsePath, cfg.dataPath, 'genomes',
data['genome'], 'problems.bed')
if not os.path.exists(problemsPath):
location = Hubs.generateProblems(data['genome'], problemsPath)
if not location == problemsPath:
raise Exception
problemsDf = pd.read_csv(problemsPath, sep='\t', header=None)
problemsDf.columns = problemColumns
problems.put(problemsDf, txn=txn)
problemsIsInBounds = problemsDf.apply(db.checkInBounds,
axis=1,
args=(data['ref'], data['start'],
data['end']))
return problemsDf[problemsIsInBounds].to_dict('records')
else:
return problemsInBounds.to_dict('records')
def isPublic(request):
query = request.matchdict
hubName = query['hub']
user = query['user']
chkpublic = "chkpublic" in request.params.keys()
hub = db.HubInfo(user, hubName).get()
hub['isPublic'] = chkpublic
db.HubInfo(user, hubName).put(hub)
if chkpublic:
Hubs.addUserToHub(hubName, user, 'Public')
elif 'Public' in hub['users']:
Hubs.removeUserFromHub(hubName, user, 'Public')
url = request.route_url('myHubs')
return HTTPFound(location=url)
def uploadHubUrl(request):
user = request.authenticated_userid
if 'POST' == request.method:
# TODO: Implement user authentication (and maybe an anonymous user
if not request.json_body['args']['hubUrl']:
return
url = request.json_body['args']['hubUrl']
hubName = ""
if request.json_body['args']['hubName']:
hubName = request.json_body['args']['hubName']
return Hubs.parseHub({'user': user, 'url': url, 'hubName': hubName})
return
def myHubs(request):
userid = request.authenticated_userid
everyKey = db.HubInfo.keysWhichMatch(db.HubInfo)
hubInfos = Hubs.getHubInfos(everyKey, userid)
labels = {}
usersdict = {}
permissions = {}
for hubName in hubInfos:
currHubInfo = hubInfos[hubName]
owner = currHubInfo['owner']
usersdict[hubName] = currHubInfo[
'users'] if 'users' in currHubInfo.keys() else []
everyLabelKey = db.Labels.keysWhichMatch(owner, hubName)
num_labels = 0
for key in everyLabelKey:
if key[0] == userid or userid in hubInfos[key[1]]['users']:
num_labels += db.Labels(*key).get().shape[0]
labels[hubName] = num_labels
# get each co users permissions
for couser in usersdict[hubName]:
permissions[(hubName,
couser)] = db.Permissions(owner, hubName,
couser).get()
return {
"user": userid,
"hubInfos": hubInfos,
"usersdict": usersdict,
"permissions": permissions,
"labels": labels
}
def hubInfo(request):
query = request.matchdict
return Hubs.getHubInfo(query['user'], query['hub'])