def find(self,
project,
composite,
sample,
runId,
fitted=False,
offset=0,
limit=None,
sort=None):
query = {
'sampleId': sample['_id'],
'runId': {
'$in': [None, ObjectId(runId)]
}
}
cursor = TimeSeriesModel().find(query=query,
offset=offset,
sort=sort,
user=getCurrentUser())
timeseries = list(TimeSeriesModel().filterResultsByPermission(
cursor=cursor,
user=getCurrentUser(),
level=AccessType.READ,
limit=limit,
offset=offset))
if fitted and False:
for t in timeseries:
t['data'] = make_models(t['data'], (1, 3), 0.15)
return timeseries
def validate(self):
profile_id = parse('profileId').find(self.volume)[0].value
profile = self.model('aws', 'cumulus').load(profile_id,
user=getCurrentUser())
if not profile:
raise ValidationException('Invalid profile id')
valid_fs = ['ext2', 'ext3', 'ext4']
if 'fs' in self.volume and self.volume['fs'] not in valid_fs:
raise ValidationException('Unsupported file system type', 'fs')
try:
int(self.volume['size'])
except ValueError:
raise ValidationException('size number in an integer', 'size')
# Name should be unique
user = getCurrentUser()
query = {
'name': self.volume['name'],
'userId': user['_id']
}
if '_id' in self.volume:
query['_id'] = {'$ne': self.volume['_id']}
volume = self.model('volume', 'cumulus').findOne(query)
if volume:
raise ValidationException('A volume with that name already exists',
'name')
return self.volume
def nearestNeighbors(self, item, limit, params):
limit = int(limit)
desc_set = self.descriptorSetFromItem(item)
nn_index = self.nearestNeighborIndex(item, getCurrentUser(), desc_set)
if nn_index is None:
raise RestException('Nearest neighbor index could not be found.')
try:
smqtk_uuid = item['meta']['smqtk_uuid']
descriptor = desc_set.get_descriptor(smqtk_uuid)
except KeyError:
raise RestException(
'Unable to retrieve image descriptor for querying object.')
neighbors, dists = nn_index.nn(descriptor, limit)
uuid_dist = dict(zip([x.uuid() for x in neighbors], dists))
smqtkFolder = ModelImporter.model('folder').load(item['folderId'],
user=getCurrentUser())
items = list(
ModelImporter.model('folder').childItems(
smqtkFolder,
filters={
'meta.smqtk_uuid': {
'$in': [x.uuid() for x in neighbors]
}
}))
for item in items:
item['smqtk_distance'] = uuid_dist[item['meta']['smqtk_uuid']]
return items
def nearestNeighbors(self, item, limit, params):
limit = int(limit)
desc_index = self.descriptorIndexFromItem(item)
nn_index = self.nearestNeighborIndex(item, getCurrentUser(), desc_index)
if nn_index is None:
raise RestException('Nearest neighbor index could not be found.')
try:
smqtk_uuid = item['meta']['smqtk_uuid']
descriptor = desc_index.get_descriptor(smqtk_uuid)
except KeyError:
raise RestException('Unable to retrieve image descriptor for querying object.')
neighbors, dists = nn_index.nn(descriptor, limit)
uuid_dist = dict(zip([x.uuid() for x in neighbors], dists))
smqtkFolder = ModelImporter.model('folder').load(item['folderId'], user=getCurrentUser())
items = list(ModelImporter.model('folder').childItems(smqtkFolder, filters={'meta.smqtk_uuid': {
'$in': [x.uuid() for x in neighbors]
}}))
for item in items:
item['smqtk_distance'] = uuid_dist[item['meta']['smqtk_uuid']]
return items
def find_samples(project,
composite,
runId=None,
platemapId=None,
elements=None,
offset=0,
limit=None,
sort=None):
platemap = PlateMapModel().load(ObjectId(platemapId),
level=AccessType.READ,
user=getCurrentUser())
and_exp = [{'$eq': ['$plateId', platemap['plateId']]}]
match_samples = {
'$match': {
'$expr': {
'$and': and_exp
},
}
}
if elements is not None:
and_exp.append({'$setIsSubset': ['$composition.elements', elements]})
lookup_fom_match = {'$expr': {'$and': [{'$eq': ["$sampleId", "$$id"]}]}}
if runId is not None:
lookup_fom_match['$expr']['$and'].append(
{'$eq': ['$runId', ObjectId(runId)]})
lookup_fom = {
'$lookup': {
'from':
'edp.fom',
'let': {
'id': '$_id'
},
'pipeline': [{
'$match': lookup_fom_match
}, {
'$project': {
'sampleId': 0
}
}],
'as':
'fom'
}
}
exclude_empty = {"$match": {"fom": {"$ne": []}}}
pipeline = [match_samples, lookup_fom, exclude_empty]
cursor = SampleModel().collection.aggregate(pipeline)
return list(SampleModel().filterResultsByPermission(cursor=cursor,
user=getCurrentUser(),
level=AccessType.READ,
limit=limit,
offset=offset))
def search(self, params):
limit, offset, sort = parse_pagination_params(params)
query_string = params.get('q')
formula = params.get('formula')
cactus = params.get('cactus')
if query_string is None and formula is None and cactus is None:
raise RestException(
'Either \'q\', \'formula\' or \'cactus\' is required.')
if query_string is not None:
try:
mongo_query = query.to_mongo_query(query_string)
except query.InvalidQuery:
raise RestException('Invalid query', 400)
fields = ['inchikey', 'smiles', 'properties', 'name']
cursor = MoleculeModel().find(query=mongo_query,
fields=fields,
limit=limit,
offset=offset,
sort=sort)
mols = [x for x in cursor]
num_matches = cursor.collection.count_documents(mongo_query)
return search_results_dict(mols, num_matches, limit, offset, sort)
elif formula:
# Search using formula
return MoleculeModel().findmol(params)
elif cactus:
if getCurrentUser() is None:
raise RestException('Must be logged in to search with cactus.')
# Disable cert verification for now
# TODO Ensure we have the right root certs so this just works.
r = requests.get(
'https://cactus.nci.nih.gov/chemical/structure/%s/file?format=sdf'
% cactus,
verify=False)
if r.status_code == 404:
return []
else:
r.raise_for_status()
sdf_data = r.content.decode('utf8')
provenance = 'cactus: ' + cactus
mol = create_molecule(sdf_data,
'sdf',
getCurrentUser(),
True,
provenance=provenance)
return search_results_dict([mol], 1, limit, offset, sort)
def create_calc(self, params):
body = getBodyJson()
if 'cjson' not in body and ('fileId' not in body
or 'format' not in body):
raise RestException('Either cjson or fileId is required.')
user = getCurrentUser()
cjson = body.get('cjson')
props = body.get('properties', {})
molecule_id = body.get('moleculeId', None)
geometry_id = body.get('geometryId', None)
public = body.get('public', True)
notebooks = body.get('notebooks', [])
image = body.get('image')
input_parameters = body.get('input', {}).get('parameters')
if input_parameters is None:
input_parameters = body.get('inputParameters', {})
file_id = None
file_format = body.get('format', 'cjson')
if 'fileId' in body:
file = File().load(body['fileId'], user=getCurrentUser())
file_id = file['_id']
cjson = self._file_to_cjson(file, file_format)
if molecule_id is None:
mol = create_molecule(json.dumps(cjson),
'cjson',
user,
public,
parameters=input_parameters)
molecule_id = mol['_id']
calc = CalculationModel().create_cjson(
user,
cjson,
props,
molecule_id,
geometry_id=geometry_id,
image=image,
input_parameters=input_parameters,
file_id=file_id,
notebooks=notebooks,
public=public)
cherrypy.response.status = 201
cherrypy.response.headers['Location'] \
= '/calculations/%s' % (str(calc['_id']))
return CalculationModel().filter(calc, user)
def ingest_calc(self, calculation, body, detectBonds=None):
self.requireParams(['fileId', 'format'], body)
file = File().load(body['fileId'], user=getCurrentUser())
cjson = self._file_to_cjson(file, body['format'])
calc_props = calculation['properties']
# The calculation is no longer pending
if 'pending' in calc_props:
del calc_props['pending']
# Add bonds if they were not there already
if detectBonds is None:
detectBonds = False
bonds = cjson.get('bonds')
if bonds is None and detectBonds:
new_cjson = openbabel.autodetect_bonds(cjson)
if new_cjson.get('bonds') is not None:
cjson['bonds'] = new_cjson['bonds']
calculation['properties'] = calc_props
calculation['cjson'] = cjson
calculation['fileId'] = file['_id']
image = body.get('image')
if image is not None:
calculation['image'] = image
code = body.get('code')
if code is not None:
calculation['code'] = code
scratch_folder_id = body.get('scratchFolderId')
if scratch_folder_id is not None:
calculation['scratchFolderId'] = scratch_folder_id
# If this was a geometry optimization, create a geometry from it
task = parse('input.parameters.task').find(calculation)
if task and task[0].value == 'optimize':
moleculeId = calculation.get('moleculeId')
provenanceType = 'calculation'
provenanceId = calculation.get('_id')
# The cjson will be whitelisted
geometry = GeometryModel().create(getCurrentUser(), moleculeId,
cjson, provenanceType,
provenanceId)
calculation['optimizedGeometryId'] = geometry.get('_id')
return CalculationModel().save(calculation)
def detach(self, volume, params):
profile_id = parse('profileId').find(volume)[0].value
profile, secret_key = _get_profile(profile_id)
girder_callback_info = {
'girder_api_url': cumulus.config.girder.baseUrl,
'girder_token': get_task_token()['_id']
}
log_write_url = '%s/volumes/%s/log' % (cumulus.config.girder.baseUrl,
volume['_id'])
p = CloudProvider(dict(secretAccessKey=secret_key, **profile))
aws_volume = p.get_volume(volume)
if aws_volume is None or aws_volume['state'] != VolumeState.INUSE:
raise RestException('This volume is not attached '
'to a cluster', 400)
if 'clusterId' not in volume:
raise RestException('clusterId is not set on this volume!', 400)
try:
volume['path']
except KeyError:
raise RestException('path is not set on this volume!', 400)
cluster = ModelImporter.model('cluster',
'cumulus').load(volume['clusterId'],
user=getCurrentUser(),
level=AccessType.ADMIN)
master = p.get_master_instance(cluster['_id'])
if master['state'] != InstanceState.RUNNING:
raise RestException('Master instance is not running!', 400)
user = getCurrentUser()
cluster = ModelImporter.model('cluster',
'cumulus').filter(cluster,
user,
passphrase=False)
cumulus.ansible.tasks.volume.detach_volume\
.delay(profile, cluster, master,
self._model.filter(volume, user),
secret_key, log_write_url, girder_callback_info)
volume['status'] = VolumeState.DETACHING
volume = self._model.update_volume(user, volume)
return self._model.filter(volume, user)
def _loadModel(self, name, info, id, model):
if info['force']:
doc = model.load(id, force=True, **info['kwargs'])
elif info['level'] is not None:
doc = model.load(id=id, level=info['level'], user=getCurrentUser(), **info['kwargs'])
else:
doc = model.load(id, **info['kwargs'])
if doc is None and info['exc']:
raise RestException('Invalid %s id (%s).' % (model.name, str(id)))
if info['requiredFlags']:
model.requireAccessFlags(doc, user=getCurrentUser(), flags=info['requiredFlags'])
return doc
def _loadModel(self, name, info, id, model):
if info['force']:
doc = model.load(id, force=True, **info['kwargs'])
elif info['level'] is not None:
doc = model.load(id=id, level=info['level'], user=getCurrentUser(), **info['kwargs'])
else:
doc = model.load(id, **info['kwargs'])
if doc is None and info['exc']:
raise RestException('Invalid %s id (%s).' % (model.name, str(id)))
if info['requiredFlags']:
model.requireAccessFlags(doc, user=getCurrentUser(), flags=info['requiredFlags'])
return doc
def create(self, **kwargs):
model = {}
for prop in self.create_props:
prop_value = kwargs.get(prop['name'], prop.get('default'))
if prop_value is not None:
if prop.get('type') == 'file':
file = File().load(prop_value,
user=getCurrentUser(),
level=AccessType.READ)
if file is None:
raise ValidationException('File doesn\'t exists: %s' %
prop_value)
if not isinstance(prop_value, ObjectId):
prop_value = ObjectId(prop_value)
elif prop.get('type') == ObjectId:
if isinstance(prop_value, list):
prop_value = [ObjectId(x) for x in prop_value]
else:
prop_value = ObjectId(prop_value)
elif prop.get('type') == 'timestamp':
prop_value = parseTimestamp(prop_value)
model[prop['name']] = prop_value
self.setPublic(model, public=kwargs.get('public', False))
user = kwargs.get('user')
self.setUserAccess(model, user=user, level=AccessType.ADMIN)
model['owner'] = user['_id']
if edp_group() is not None:
self.setGroupAccess(model, edp_group(), AccessType.ADMIN)
saved_model = self.save(model)
# Now spawn thumbnail jobs if the model contains any image
for prop in self.create_props:
prop_value = kwargs.get(prop['name'], prop.get('default'))
if prop_value is not None and prop.get('type') == 'file':
file = File().load(prop_value,
user=getCurrentUser(),
level=AccessType.READ)
mime_type = file.get('mimeType', '')
if mime_type is not None and mime_type.startswith('image/'):
self._create_thumbnail(file, saved_model, prop['name'],
user)
return saved_model
def find_id(self, id, params):
cal = self._model.load(id,
level=AccessType.READ,
user=getCurrentUser())
if not cal:
raise RestException('Calculation not found.', code=404)
return cal
def provision(self):
self.status = ClusterStatus.PROVISIONING
base_url = getApiUrl()
log_write_url = '%s/clusters/%s/log' % (base_url, self.cluster['_id'])
girder_token = get_task_token()['_id']
profile, secret_key = _get_profile(self.cluster['profileId'])
playbook = get_property(
'config.provision.spec', self.cluster,
default=self.DEFAULT_PLAYBOOK)
playbook_params = get_property(
'config.provision.params', self.cluster, default={})
provision_ssh_user = get_property(
'config.provision.ssh.user', self.cluster, default='ubuntu')
playbook_params['cluster_state'] = ClusterStatus.RUNNING
playbook_params['ansible_ssh_user'] = provision_ssh_user
cumulus.ansible.tasks.cluster.provision_cluster \
.delay(playbook,
self._model.filter(self.cluster, getCurrentUser(), passphrase=False),
profile, secret_key, playbook_params,
girder_token, log_write_url, ClusterStatus.RUNNING)
return self.cluster
def append_to_log(self, id, params):
user = getCurrentUser()
if not self._model.load(id, user=user, level=AccessType.ADMIN):
raise RestException('Volume not found.', code=404)
return self._model.append_to_log(user, id, getBodyJson())
def create(self, params):
body = getBodyJson()
self.requireParams(['name', 'type', 'size', 'profileId'], body)
if not VolumeType.is_valid_type(body['type']):
raise RestException('Invalid volume type.', code=400)
profile_id = parse('profileId').find(body)
if not profile_id:
raise RestException('A profile id must be provided', 400)
profile_id = profile_id[0].value
profile, secret_key = _get_profile(profile_id)
if not profile:
raise RestException('Invalid profile', 400)
if 'zone' in body:
zone = body['zone']
else:
zone = profile['availabilityZone']
volume = self._create_ebs(body, zone)
cherrypy.response.status = 201
cherrypy.response.headers['Location'] = '/volumes/%s' % volume['_id']
return self._model.filter(volume, getCurrentUser())
def find_calc(self,
moleculeId=None,
geometryId=None,
imageName=None,
inputParameters=None,
inputGeometryHash=None,
name=None,
inchi=None,
inchikey=None,
smiles=None,
formula=None,
creatorId=None,
pending=None,
limit=None,
offset=None,
sort=None):
return CalculationModel().findcal(
molecule_id=moleculeId,
geometry_id=geometryId,
image_name=imageName,
input_parameters=inputParameters,
input_geometry_hash=inputGeometryHash,
name=name,
inchi=inchi,
inchikey=inchikey,
smiles=smiles,
formula=formula,
creator_id=creatorId,
pending=pending,
limit=limit,
offset=offset,
sort=sort,
user=getCurrentUser())
def get_all(self, params):
user = getCurrentUser()
limit, offset, _ = self.getPagingParameters(params)
cursor = self._model.find(limit=limit, offset=offset)
return list(self._model.filterResultsByPermission(cursor=cursor,
user=user, level=AccessType.READ))
def ingest_calc(self, calculation, body, detectBonds=None):
self.requireParams(['fileId', 'format'], body)
file = File().load(body['fileId'], user=getCurrentUser())
cjson = self._file_to_cjson(file, body['format'])
calc_props = calculation['properties']
# The calculation is no longer pending
if 'pending' in calc_props:
del calc_props['pending']
# Add bonds if they were not there already
if detectBonds is None:
detectBonds = False
bonds = cjson.get('bonds')
if bonds is None and detectBonds:
new_cjson = openbabel.autodetect_bonds(cjson)
if new_cjson.get('bonds') is not None:
cjson['bonds'] = new_cjson['bonds']
calculation['properties'] = calc_props
calculation['cjson'] = cjson
calculation['fileId'] = file['_id']
image = body.get('image')
if image is not None:
calculation['image'] = image
scratch_folder_id = body.get('scratchFolderId')
if scratch_folder_id is not None:
calculation['scratchFolderId'] = scratch_folder_id
return CalculationModel().save(calculation)
def delete(self, id, params):
user = getCurrentUser()
cal = self._model.load(id, level=AccessType.READ, user=user)
if not cal:
raise RestException('Calculation not found.', code=404)
return self._model.remove(cal, user)
def validate(self, cluster):
if not cluster['name']:
raise ValidationException('Name must not be empty.', 'name')
if not cluster['type']:
raise ValidationException('Type must not be empty.', 'type')
scheduler_type = parse('config.scheduler.type').find(cluster)
if scheduler_type:
scheduler_type = scheduler_type[0].value
else:
scheduler_type = QueueType.SGE
config = cluster.setdefault('config', {})
scheduler = config.setdefault('scheduler', {})
scheduler['type'] = scheduler_type
if not queue.is_valid_type(scheduler_type):
raise ValidationException('Unsupported scheduler.', 'type')
# If inserting, ensure no other clusters have the same name field amd
# type
if '_id' not in cluster:
query = {
'name': cluster['name'],
'userId': getCurrentUser()['_id'],
'type': cluster['type']
}
if self.findOne(query):
raise ValidationException('A cluster with that name already '
'exists', 'name')
adapter = get_cluster_adapter(cluster)
return adapter.validate()
def start(self, *args, **kwargs):
user = getCurrentUser()
cluster = kwargs.get('cluster')
image = kwargs.get('image')
container = kwargs.get('container')
if cluster is None:
raise Exception('Unable to extract cluster.')
if '_id' not in cluster and 'name' not in cluster:
raise Exception('Unable to extract cluster.')
if image is None:
raise Exception('Unable to extract the image name.')
if container is None:
raise Exception('Unable to extract container type.')
cluster_id = parse('cluster._id').find(kwargs)
if cluster_id:
cluster_id = cluster_id[0].value
model = ModelImporter.model('cluster', 'cumulus')
cluster = model.load(cluster_id, user=user, level=AccessType.ADMIN)
super(ContainerPullTaskFlow,
self).start(start.s(user, cluster, image, container), *args,
**kwargs)
def get_task_folder():
folder = Setting().get(PluginSettings.SLICER_CLI_WEB_TASK_FOLDER)
if not folder:
return None
return Folder().load(folder,
level=AccessType.WRITE,
user=getCurrentUser())
def createSession(self, params):
smqtkFolder = params['smqtkFolder']
sessionsFolder = getCreateSessionsFolder()
# Get the folder with images in it, since this is what's used for computing
# what descriptor index table to use
dataFolderId = ModelImporter.model('folder').load(ObjectId(smqtkFolder), user=getCurrentUser())
dataFolderId = str(dataFolderId['parentId'])
# Create session named after its id
session = ModelImporter.model('item').createItem('placeholder_name',
getCurrentUser(), sessionsFolder)
session['name'] = str(session['_id'])
ModelImporter.model('item').save(session)
sessionId = str(session['_id'])
ModelImporter.model('item').setMetadata(session, {
'smqtk_folder_id': smqtkFolder,
'data_folder_id': dataFolderId,
'pos_uuids': [],
'neg_uuids': []
})
# already registered in the controller, return
if self.controller.has_session_uuid(sessionId):
return session
iqrs = IqrSession(self.positive_seed_neighbors, session_uid=sessionId)
with self.controller:
with iqrs: # because classifier maps locked by session
self.controller.add_session(iqrs)
self.session_classifiers[sessionId] = None
self.session_classifier_dirty[sessionId] = True
return session
def create_profile(self, userId, name, profile_type, access_key_id,
secret_access_key, region_name, availability_zone,
public_ips):
user = getCurrentUser()
profile = {
'name': name,
'cloudProvider': profile_type,
'accessKeyId': access_key_id,
'secretAccessKey': secret_access_key,
'regionName': region_name,
'availabilityZone': availability_zone,
'userId': userId,
'status': 'creating',
'publicIPs': public_ips
}
profile = self.setUserAccess(profile, user, level=AccessType.ADMIN,
save=False)
group = {
'_id': ObjectId(self.get_group_id())
}
profile = self.setGroupAccess(profile, group, level=AccessType.ADMIN)
return self.save(profile)
def attach_complete(self, volume, cluster, params):
user = getCurrentUser()
path = getBodyJson().get('path', None)
if path is not None:
cluster.setdefault('volumes', [])
cluster['volumes'].append(volume['_id'])
cluster['volumes'] = list(set(cluster['volumes']))
volume['status'] = VolumeState.INUSE
volume['path'] = path
# TODO: removing msg should be refactored into
# a general purpose 'update_status' function
# on the volume model. This way msg only referes
# to the current status.
try:
del volume['msg']
except KeyError:
pass
# Add cluster id to volume
volume['clusterId'] = cluster['_id']
self.model('cluster', 'cumulus').save(cluster)
self._model.update_volume(user, volume)
else:
volume['status'] = VolumeState.ERROR
volume['msg'] = 'Volume path was not communicated on complete'
self._model.update_volume(user, volume)
def find_id(self, id, params):
mol = self._model.load(id,
level=AccessType.READ,
user=getCurrentUser())
if not mol:
raise RestException('Molecule not found.', code=404)
return self._clean(mol)
def provision(self):
self.status = ClusterStatus.PROVISIONING
base_url = cumulus.config.girder.baseUrl
log_write_url = '%s/clusters/%s/log' % (base_url, self.cluster['_id'])
girder_token = get_task_token()['_id']
profile, secret_key = _get_profile(self.cluster['profileId'])
playbook = get_property('config.provision.spec',
self.cluster,
default=self.DEFAULT_PLAYBOOK)
playbook_params = get_property('config.provision.params',
self.cluster,
default={})
provision_ssh_user = get_property('config.provision.ssh.user',
self.cluster,
default='ubuntu')
playbook_params['cluster_state'] = ClusterStatus.RUNNING
playbook_params['ansible_ssh_user'] = provision_ssh_user
cumulus.ansible.tasks.cluster.provision_cluster \
.delay(playbook,
self._model.filter(self.cluster, getCurrentUser(), passphrase=False),
profile, secret_key, playbook_params,
girder_token, log_write_url, ClusterStatus.RUNNING)
return self.cluster
def create(self, params):
body = getBodyJson()
self.requireParams(['name', 'type', 'size', 'profileId'], body)
if not VolumeType.is_valid_type(body['type']):
raise RestException('Invalid volume type.', code=400)
profile_id = parse('profileId').find(body)
if not profile_id:
raise RestException('A profile id must be provided', 400)
profile_id = profile_id[0].value
profile, secret_key = _get_profile(profile_id)
if not profile:
raise RestException('Invalid profile', 400)
if 'zone' in body:
zone = body['zone']
else:
zone = profile['availabilityZone']
volume = self._create_ebs(body, zone)
cherrypy.response.status = 201
cherrypy.response.headers['Location'] = '/volumes/%s' % volume['_id']
return self._model.filter(volume, getCurrentUser())
def update_step(self, simulation, stepName, updates, params):
user = getCurrentUser()
immutable = ['type', 'folderId']
if stepName not in simulation.get('steps', {}):
raise RestException(
'Simulation %s doesn\'t contain step %s' %
(simulation['_id'], stepName), 400)
for p in updates:
if p in immutable:
raise RestException('\'%s\' is an immutable property' % p, 400)
try:
ref_resolver = jsonschema.RefResolver.from_schema(
schema.definitions)
jsonschema.validate(updates,
schema.definitions['stepUpdate'],
resolver=ref_resolver)
except jsonschema.ValidationError as ve:
raise RestException(ve.message, 400)
status = updates.get('status')
metadata = updates.get('metadata')
export = updates.get('export')
view = updates.get('view')
return self._model.update_step(user, simulation, stepName, status,
metadata, export, view)
def update_step(self, simulation, stepName, params):
user = getCurrentUser()
immutable = ['type', 'folderId']
updates = getBodyJson()
if stepName not in simulation.get('steps', {}):
raise RestException('Simulation %s doesn\'t contain step %s' %
(simulation['_id'], stepName), 400)
for p in updates:
if p in immutable:
raise RestException('\'%s\' is an immutable property' % p, 400)
try:
ref_resolver = jsonschema.RefResolver.from_schema(
schema.definitions)
jsonschema.validate(
updates, schema.definitions['stepUpdate'],
resolver=ref_resolver)
except jsonschema.ValidationError as ve:
raise RestException(ve.message, 400)
status = updates.get('status')
metadata = updates.get('metadata')
export = updates.get('export')
view = updates.get('view')
return self._model.update_step(
user, simulation, stepName, status, metadata, export, view)
def validate(self, project):
"""
Validate using jsonschema
"""
try:
ref_resolver = jsonschema.RefResolver.from_schema(
schema.definitions)
jsonschema.validate(project, schema.project, resolver=ref_resolver)
except jsonschema.ValidationError as ve:
raise ValidationException(ve.message)
# Ensure unique name for the project
user = getCurrentUser()
q = {
'name': project['name'],
'userId': user['_id']
}
if '_id' in project:
q['_id'] = {'$ne': project['_id']}
duplicate = self.findOne(q, fields=['_id'])
if duplicate is not None:
raise ValidationException('A project with that name already '
'exists.', 'name')
return project
def delete(self, id, params):
user = getCurrentUser()
cal = self._model.load(id, level=AccessType.READ, user=user)
if not cal:
raise RestException('Calculation not found.', code=404)
return self._model.remove(cal, user)
def ingest_calc(self, calculation, body, detectBonds=None):
self.requireParams(['fileId', 'format'], body)
file = File().load(body['fileId'], user=getCurrentUser())
cjson = self._file_to_cjson(file, body['format'])
calc_props = calculation['properties']
# The calculation is no longer pending
if 'pending' in calc_props:
del calc_props['pending']
# Add bonds if they were not there already
if detectBonds is None:
detectBonds = False
bonds = cjson.get('bonds')
if bonds is None and detectBonds:
new_cjson = openbabel.autodetect_bonds(cjson)
if new_cjson.get('bonds') is not None:
cjson['bonds'] = new_cjson['bonds']
calculation['properties'] = calc_props
calculation['cjson'] = cjson
calculation['fileId'] = file['_id']
image = body.get('image')
if image is not None:
calculation['image'] = image
scratch_folder_id = body.get('scratchFolderId')
if scratch_folder_id is not None:
calculation['scratchFolderId'] = scratch_folder_id
return CalculationModel().save(calculation)
def create_profile(user, params):
body = getBodyJson()
requireParams([
'name', 'accessKeyId', 'secretAccessKey', 'regionName',
'availabilityZone'
], body)
profile_type = 'ec2' if 'cloudProvider' not in body.keys() \
else body['cloudProvider']
model = ModelImporter.model('aws', 'cumulus')
profile = model.create_profile(user['_id'], body['name'], profile_type,
body['accessKeyId'],
body['secretAccessKey'], body['regionName'],
body['availabilityZone'],
body.get('publicIPs', False))
# Now fire of a task to create a key pair for this profile
try:
cumulus.aws.ec2.tasks.key.generate_key_pair.delay(
_filter(profile),
get_task_token()['_id'])
cherrypy.response.status = 201
cherrypy.response.headers['Location'] \
= '/user/%s/aws/profile/%s' % (str(user['_id']),
str(profile['_id']))
return model.filter(profile, getCurrentUser())
except Exception:
# Remove profile if error occurs fire of task
model.remove(profile)
raise
def start(self, *args, **kwargs):
user = getCurrentUser()
input_ = kwargs.get('input')
cluster = kwargs.get('cluster')
image = kwargs.get('image')
run_parameters = kwargs.get('runParameters')
if input_ is None:
raise Exception('Unable to extract input.')
if '_id' not in cluster and 'name' not in cluster:
raise Exception('Unable to extract cluster.')
if image is None:
raise Exception('Unable to extract the docker image name.')
if run_parameters is None:
run_parameters = {}
cluster_id = parse('cluster._id').find(kwargs)
if cluster_id:
cluster_id = cluster_id[0].value
model = ModelImporter.model('cluster', 'cumulus')
cluster = model.load(cluster_id, user=user, level=AccessType.ADMIN)
cluster = model.filter(cluster, user, passphrase=False)
super(OpenChemistryTaskFlow,
self).start(start.s(input_, cluster, image, run_parameters),
*args, **kwargs)
def get_twitter(user):
# Either twitterPublic must be true or the user has admin level access
if user.get('twitterPublic') is not True:
if User().getAccessLevel(user, getCurrentUser()) != AccessType.ADMIN:
return None
return user.get('twitter')
def deleteProcessedVideo(self, id, params):
user = getCurrentUser()
itemModel = self.model('item')
fileModel = self.model('file')
item = itemModel.load(id, user=user, level=AccessType.READ)
itemVideoData = item.get('video', {})
fileIdList = itemVideoData.get('createdFiles', [])
for f in fileIdList:
theFile = fileModel.load(f, level=AccessType.WRITE, user=user)
if theFile:
fileModel.remove(theFile)
itemVideoData['createdFiles'] = []
itemVideoData.pop('jobId', None)
itemVideoData = item.get('video', {})
jobId = itemVideoData.get('jobId')
item['video'] = itemVideoData
itemModel.save(item)
return {
'message': 'Processed video data deleted.',
'itemId': id,
'originalJobId': jobId,
'removedFiles': fileIdList
}
def validate(self, cluster):
if not cluster['name']:
raise ValidationException('Name must not be empty.', 'name')
if not cluster['type']:
raise ValidationException('Type must not be empty.', 'type')
scheduler_type = parse('config.scheduler.type').find(cluster)
if scheduler_type:
scheduler_type = scheduler_type[0].value
else:
scheduler_type = QueueType.SGE
config = cluster.setdefault('config', {})
scheduler = config.setdefault('scheduler', {})
scheduler['type'] = scheduler_type
if not queue.is_valid_type(scheduler_type):
raise ValidationException('Unsupported scheduler.', 'type')
# If inserting, ensure no other clusters have the same name field amd
# type
if '_id' not in cluster:
query = {
'name': cluster['name'],
'userId': getCurrentUser()['_id'],
'type': cluster['type']
}
if self.findOne(query):
raise ValidationException('A cluster with that name already '
'exists', 'name')
adapter = get_cluster_adapter(cluster)
return adapter.validate()
def downloadFile(self,
file,
offset=0,
headers=True,
endByte=None,
**kwargs):
if 'path' not in file:
raise Exception('Missing path property')
full_path = file['path']
url = '%s/file/%s/%s?view=read' % (self.newt_base_url, self.machine,
full_path)
if headers:
raise cherrypy.HTTPRedirect(url)
else:
session_id = parse('newt.sessionId').find(getCurrentUser())
if len(session_id) > 0:
session_id = session_id[0].value
if session_id is None:
raise GirderException('Missing NEWT session id')
def stream():
cookies = dict(newt_sessionid=session_id)
r = requests.get(url, cookies=cookies, stream=True)
for chunk in r.iter_content(chunk_size=BUF_LEN):
if chunk:
yield chunk
return stream
def get_geometry_format(self, moleculeId, id, output_format):
if output_format not in Molecule.output_formats:
raise RestException('Format not supported.')
if output_format in Molecule.output_formats_2d:
# It's just smiles or inchi, call the general end point
return self.get_format(moleculeId, output_format, None)
user = getCurrentUser()
geometry = GeometryModel().load(id, level=AccessType.READ, user=user)
if not geometry:
raise RestException('Geometry not found.', code=404)
data = json.dumps(geometry['cjson'])
if output_format != 'cjson':
data = avogadro.convert_str(data, 'cjson', output_format)
def stream():
cherrypy.response.headers['Content-Type'] = (
Molecule.mime_types[output_format])
yield data
return stream
def validate(self, project):
"""
Validate using jsonschema
"""
try:
ref_resolver = jsonschema.RefResolver.from_schema(
schema.definitions)
jsonschema.validate(project, schema.project, resolver=ref_resolver)
except jsonschema.ValidationError as ve:
raise ValidationException(ve.message)
# Ensure unique name for the project
user = getCurrentUser()
q = {
'name': project['name'],
'userId': user['_id']
}
if '_id' in project:
q['_id'] = {'$ne': project['_id']}
duplicate = self.findOne(q, fields=['_id'])
if duplicate is not None:
raise ValidationException('A project with that name already '
'exists.', 'name')
return project
def onGetItem(event):
itemResponse = event.info['returnVal']
# Hide the 'originalFilename' metadata on Images from non-site admins
if 'originalFilename' in itemResponse.get('meta', {}):
currentUser = getCurrentUser()
if not (currentUser and currentUser['admin']):
del itemResponse['meta']['originalFilename']
def _create_ebs(self, body, zone):
user = getCurrentUser()
name = body['name']
size = body['size']
fs = body.get('fs', None)
profileId = body['profileId']
return self._model.create_ebs(user, profileId, name, zone, size, fs)
def append_to_log(self, id, params):
user = getCurrentUser()
if not self._model.load(id, user=user, level=AccessType.ADMIN):
raise RestException('Volume not found.', code=404)
return self._model.append_to_log(
user, id, getBodyJson())
def submit_job(self, job):
log_url = '%s/jobs/%s/log' % (getApiUrl(), job['_id'])
girder_token = get_task_token(self.cluster)['_id']
cumulus.tasks.job.submit(
girder_token,
self._model.filter(self.cluster, getCurrentUser(), passphrase=False),
job, log_url)
def session_id(self, params):
user = getCurrentUser()
user = self.model('user').load(user['_id'], fields=['newt'], force=True)
return {
'sessionId': user.get('newt', {}).get('sessionId')
}
def start(self, request_body):
log_write_url = '%s/clusters/%s/log' % (getApiUrl(),
self.cluster['_id'])
girder_token = get_task_token(self.cluster)['_id']
cumulus.tasks.cluster.test_connection \
.delay(
self._model.filter(self.cluster, getCurrentUser(), passphrase=False),
log_write_url=log_write_url, girder_token=girder_token)
def create(self, params):
project = getBodyJson()
project = self.model('project', 'hpccloud').create(getCurrentUser(),
project)
cherrypy.response.status = 201
cherrypy.response.headers['Location'] = '/projects/%s' % project['_id']
return project
def challengeSaved(event):
"""
After a challenge is saved, we want to update the Assets folder permissions
to be the same as the challenge.
"""
challenge = event.info
folder = getAssetsFolder(challenge, getCurrentUser(), False)
Folder().copyAccessPolicies(
challenge, folder, save=True)
def find_id(self, id, params):
mol = MoleculeModel().load(id, level=AccessType.READ, user=getCurrentUser())
if not mol:
raise RestException('Molecule not found.', code=404)
cjson = True
cjsonParam = params.get('cjson')
if cjsonParam is not None:
cjson = cjsonParam.lower() == 'true'
return self._clean(mol, cjson)
def handle(self, record):
user = getCurrentUser()
Record().save({
'type': record.msg,
'details': record.details,
'ip': cherrypy.request.remote.ip,
'userId': user and user['_id'],
'when': datetime.datetime.utcnow()
}, triggerEvents=False)
def detach(self, volume, params):
profile_id = parse('profileId').find(volume)[0].value
profile, secret_key = _get_profile(profile_id)
girder_callback_info = {
'girder_api_url': getApiUrl(),
'girder_token': get_task_token()['_id']}
p = CloudProvider(dict(secretAccessKey=secret_key, **profile))
aws_volume = p.get_volume(volume)
if aws_volume is None or aws_volume['state'] != VolumeState.INUSE:
raise RestException('This volume is not attached '
'to a cluster',
400)
if 'clusterId' not in volume:
raise RestException('clusterId is not set on this volume!', 400)
try:
volume['path']
except KeyError:
raise RestException('path is not set on this volume!', 400)
cluster = self.model('cluster', 'cumulus').load(volume['clusterId'],
user=getCurrentUser(),
level=AccessType.ADMIN)
master = p.get_master_instance(cluster['_id'])
if master['state'] != InstanceState.RUNNING:
raise RestException('Master instance is not running!',
400)
user = getCurrentUser()
cluster = self.model('cluster', 'cumulus').filter(
cluster, user, passphrase=False)
cumulus.ansible.tasks.volume.detach_volume\
.delay(profile, cluster, master,
self._model.filter(volume, user),
secret_key, girder_callback_info)
volume['status'] = VolumeState.DETACHING
volume = self._model.update_volume(user, volume)
return self._model.filter(volume, user)
def attach(self, volume, cluster, params):
body = getBodyJson()
self.requireParams(['path'], body)
path = body['path']
profile_id = parse('profileId').find(volume)[0].value
profile, secret_key = _get_profile(profile_id)
girder_callback_info = {
'girder_api_url': getApiUrl(),
'girder_token': get_task_token()['_id']}
p = CloudProvider(dict(secretAccessKey=secret_key, **profile))
aws_volume = p.get_volume(volume)
# If volume exists it needs to be available to be attached. If
# it doesn't exist it will be created as part of the attach
# playbook.
if aws_volume is not None and \
aws_volume['state'] != VolumeState.AVAILABLE:
raise RestException('This volume is not available to attach '
'to a cluster',
400)
master = p.get_master_instance(cluster['_id'])
if master['state'] != InstanceState.RUNNING:
raise RestException('Master instance is not running!',
400)
cluster = self.model('cluster', 'cumulus').filter(
cluster, getCurrentUser(), passphrase=False)
cumulus.ansible.tasks.volume.attach_volume\
.delay(profile, cluster, master,
self._model.filter(volume, getCurrentUser()), path,
secret_key, girder_callback_info)
volume['status'] = VolumeState.ATTACHING
volume = self._model.update_volume(getCurrentUser(), volume)
return self._model.filter(volume, getCurrentUser())
def create(self, body):
self.requireParams(['fileId'], body)
file = File().load(body['fileId'], user=getCurrentUser())
with File().open(file) as f:
experiment_data = json.load(f)
if 'experiment' not in experiment_data:
raise RestException('Invalid experiment file.')
return self._process_experimental(experiment_data)
def start(self, request_body):
if self.cluster['status'] == ClusterStatus.CREATING:
raise RestException('Cluster is not ready to start.', code=400)
log_write_url = '%s/clusters/%s/log' % (getApiUrl(),
self.cluster['_id'])
girder_token = get_task_token()['_id']
cumulus.tasks.cluster.test_connection \
.delay(self._model.filter(self.cluster, getCurrentUser(), passphrase=False),
log_write_url=log_write_url,
girder_token=girder_token)
def createSession(self, params):
sessionsFolder = getCreateSessionsFolder()
sessionId = requests.post(self.search_url + '/session').json()['sid']
item = ModelImporter.model('item').createItem(name=sessionId,
creator=getCurrentUser(),
folder=sessionsFolder)
ModelImporter.model('item').setMetadata(item, {
'sid': sessionId
})
return item
def log(self, id, params):
user = getCurrentUser()
offset = 0
if 'offset' in params:
offset = int(params['offset'])
if not self._model.load(id, user=user, level=AccessType.READ):
raise RestException('Volume not found.', code=404)
log_records = self._model.log_records(user, id, offset)
return {'log': log_records}
