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 handle_log_record(self, id, params):
user = self.getCurrentUser()
if not self._model.load(id, user=user, level=AccessType.ADMIN):
raise RestException('Cluster not found.', code=404)
return self._model.append_to_log(user, id, getBodyJson())
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 update(self, id, params):
user = self.getCurrentUser()
body = getBodyJson()
job = self._model.load(id, user=user, level=AccessType.WRITE)
if not job:
raise RestException('Job not found.', code=404)
if 'status' in body:
job['status'] = body['status']
if 'queueJobId' in body:
job['queueJobId'] = body['queueJobId']
if 'output' in body:
job['output'] = body['output']
if 'timings' in body:
if 'timings' in job:
job['timings'].update(body['timings'])
else:
job['timings'] = body['timings']
if 'dir' in body:
job['dir'] = body['dir']
job = self._model.update_job(user, job)
# Don't return the access object
del job['access']
# Don't return the log
del job['log']
return job
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, 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 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(self, simulation, params):
immutable = [
'projectId', 'folderId', 'access', 'userId', '_id', 'updated',
'created'
]
updates = getBodyJson()
for p in updates:
if p in immutable:
raise RestException('\'%s\' is an immutable property' % p, 400)
user = getCurrentUser()
name = updates.get('name')
description = updates.get('description')
active = updates.get('active')
disabled = updates.get('disabled')
status = updates.get('status')
metadata = updates.get('metadata')
steps = updates.get('steps')
return self._model.update(user,
simulation,
name=name,
metadata=metadata,
description=description,
active=active,
disabled=disabled,
status=status,
steps=steps)
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()
# Default ec2 cluster
cluster_type = 'ec2'
if 'type' in body:
if not ClusterType.is_valid_type(body['type']):
raise RestException('Invalid cluster type.', code=400)
cluster_type = body['type']
if cluster_type == ClusterType.EC2:
cluster = self._create_ec2(params, body)
elif cluster_type == ClusterType.ANSIBLE:
cluster = self._create_ansible(params, body)
elif cluster_type == ClusterType.TRADITIONAL:
cluster = self._create_traditional(params, body)
elif cluster_type == ClusterType.NEWT:
cluster = self._create_newt(params, body)
else:
raise RestException('Invalid cluster type.', code=400)
cherrypy.response.status = 201
cherrypy.response.headers['Location'] = '/clusters/%s' % cluster['_id']
return self._model.filter(cluster, self.getCurrentUser())
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 create_file(self, assetstore, params):
params = getBodyJson()
self.requireParams(('name', 'itemId', 'size', 'path'), params)
name = params['name']
item_id = params['itemId']
size = int(params['size'])
path = params['path']
user = self.getCurrentUser()
mime_type = params.get('mimeType')
item = self.model('item').load(id=item_id,
user=user,
level=AccessType.WRITE,
exc=True)
file = self.model('file').createFile(name=name,
creator=user,
item=item,
reuseExisting=True,
assetstore=assetstore,
mimeType=mime_type,
size=size)
file['path'] = path
file['imported'] = True
self.model('file').save(file)
return self.model('file').filter(file)
def create(self, params):
body = getBodyJson()
# Default ec2 cluster
cluster_type = 'ec2'
if 'type' in body:
if not ClusterType.is_valid_type(body['type']):
raise RestException('Invalid cluster type.', code=400)
cluster_type = body['type']
if cluster_type == ClusterType.EC2:
cluster = self._create_ec2(params, body)
elif cluster_type == ClusterType.ANSIBLE:
cluster = self._create_ansible(params, body)
elif cluster_type == ClusterType.TRADITIONAL:
cluster = self._create_traditional(params, body)
elif cluster_type == ClusterType.NEWT:
cluster = self._create_newt(params, body)
else:
raise RestException('Invalid cluster type.', code=400)
cherrypy.response.status = 201
cherrypy.response.headers['Location'] = '/clusters/%s' % cluster['_id']
return self._model.filter(cluster, self.getCurrentUser())
def move_files(params):
def load_file(file):
return ModelImporter.model('file').load(file['_id'],
user=getCurrentUser())
files = list(map(load_file, getBodyJson()))
total_size = sum([file['size'] for file in files])
move_files_to_assetstore(files, total_size)
def handle_log_record(self, id, params):
user = self.getCurrentUser()
if not self._model.load(id, user=user, level=AccessType.ADMIN):
raise RestException('Cluster not found.', code=404)
return self._model.append_to_log(
user, id, getBodyJson())
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):
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 _loadJsonBody(self, name, info):
val = None
if cherrypy.request.body.length == 0 and info['required']:
raise RestException('JSON parameter %s must be passed in request body.' % name)
elif cherrypy.request.body.length > 0:
val = getBodyJson()
self._validateJsonType(name, info, val)
return val
def _loadJsonBody(self, name, info):
val = None
if cherrypy.request.body.length == 0 and info['required']:
raise RestException('JSON parameter %s must be passed in request body.' % name)
elif cherrypy.request.body.length > 0:
val = getBodyJson()
self._validateJsonType(name, info, val)
return val
def refine(self, params):
params = getBodyJson()
r = requests.put(self.search_url + '/refine', data={
'sid': params['sid'],
'pos_uuids': json.dumps(params['pos_uuids']),
'neg_uuids': json.dumps(params['neg_uuids'])
})
return r.json()
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 refine(self, params):
params = getBodyJson()
r = requests.put(self.search_url + '/refine',
data={
'sid': params['sid'],
'pos_uuids': json.dumps(params['pos_uuids']),
'neg_uuids': json.dumps(params['neg_uuids'])
})
return r.json()
def clone(self, simulation, params):
props = getBodyJson()
self.requireParams(('name', ), props)
user = getCurrentUser()
cloned = self._model.clone(user, simulation, props['name'])
cherrypy.response.status = 201
cherrypy.response.headers['Location'] = '/simulations/%s' \
% cloned['_id']
return cloned
def create_simulation(self, project, params):
simulation = getBodyJson()
user = getCurrentUser()
simulation = self.model('simulation', 'hpccloud').create(
user, project, simulation)
cherrypy.response.status = 201
cherrypy.response.headers['Location'] = '/simulations/%s' \
% simulation['_id']
return simulation
def create_task(self, taskflow, params):
user = getCurrentUser()
task = getBodyJson()
self.requireParams(['celeryTaskId'], task)
task = self.model('task', 'taskflow').create(user, taskflow, task)
cherrypy.response.status = 201
cherrypy.response.headers['Location'] = '/tasks/%s' % task['_id']
return task
def clone(self, simulation, params):
props = getBodyJson()
self.requireParams(('name', ), props)
user = getCurrentUser()
cloned = self._model.clone(user, simulation, props['name'])
cherrypy.response.status = 201
cherrypy.response.headers['Location'] = '/simulations/%s' \
% cloned['_id']
return cloned
def create_simulation(self, project, params):
simulation = getBodyJson()
user = getCurrentUser()
simulation = self.model('simulation',
'hpccloud').create(user, project, simulation)
cherrypy.response.status = 201
cherrypy.response.headers['Location'] = '/simulations/%s' \
% simulation['_id']
return simulation
def update_profile(user, profile, params):
body = getBodyJson()
properties = [
'accessKeyId', 'secretAccessKey', 'status', 'errorMessage',
'publicIPs', 'cloudProvider'
]
for prop in properties:
if prop in body:
profile[prop] = body[prop]
ModelImporter.model('aws',
'cumulus').update_aws_profile(getCurrentUser(),
profile)
def create(self, params):
user = self.getCurrentUser()
body = getBodyJson()
self.requireParams(['name'], body)
if 'commands' not in body and 'scriptId' not in body:
raise RestException('command or scriptId must be provided',
code=400)
if 'scriptId' in body:
script = ModelImporter.model('script',
'cumulus').load(body['scriptId'],
user=user,
level=AccessType.READ)
if not script:
raise RestException('Script not found', 400)
del body['scriptId']
body['commands'] = script['commands']
if 'onTerminate' in body and 'scriptId' in body['onTerminate']:
script = ModelImporter.model('script', 'cumulus') \
.load(body['onTerminate']['scriptId'], user=user,
level=AccessType.READ)
if not script:
raise RestException('onTerminate script not found', 400)
del body['onTerminate']['scriptId']
body['onTerminate']['commands'] = script['commands']
if 'input' in body:
if not isinstance(body['input'], list):
raise RestException('input must be a list', 400)
for i in body['input']:
if i['path'] == body['name']:
raise RestException('input can\'t be the same as job name',
400)
if 'output' in body:
if not isinstance(body['output'], list):
raise RestException('output must be a list', 400)
job = self._model.create(user, body)
cherrypy.response.status = 201
cherrypy.response.headers['Location'] = '/jobs/%s' % job['_id']
return self._clean(job)
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 update(self, task, params):
immutable = ['access', '_id', 'celeryTaskId', 'log']
user = getCurrentUser()
updates = getBodyJson()
if not updates:
raise RestException('A body must be provided', code=400)
for p in updates:
if p in immutable:
raise RestException('\'%s\' is an immutable property' % p, 400)
status = updates.get('status')
return self._model.update_task(user, task, status=status)
def create(self, params):
user = self.getCurrentUser()
body = getBodyJson()
self.requireParams(['name'], body)
if 'commands' not in body and 'scriptId' not in body:
raise RestException('command or scriptId must be provided',
code=400)
if 'scriptId' in body:
script = self.model('script', 'cumulus').load(body['scriptId'],
user=user,
level=AccessType.READ)
if not script:
raise RestException('Script not found', 400)
del body['scriptId']
body['commands'] = script['commands']
if 'onTerminate' in body and 'scriptId' in body['onTerminate']:
script = self.model('script', 'cumulus') \
.load(body['onTerminate']['scriptId'], user=user,
level=AccessType.READ)
if not script:
raise RestException('onTerminate script not found', 400)
del body['onTerminate']['scriptId']
body['onTerminate']['commands'] = script['commands']
if 'input' in body:
if not isinstance(body['input'], list):
raise RestException('input must be a list', 400)
for i in body['input']:
if i['path'] == body['name']:
raise RestException('input can\'t be the same as job name',
400)
if 'output' in body:
if not isinstance(body['output'], list):
raise RestException('output must be a list', 400)
job = self._model.create(user, body)
cherrypy.response.status = 201
cherrypy.response.headers['Location'] = '/jobs/%s' % job['_id']
return self._clean(job)
def append_to_log(self, id, params):
user = self.getCurrentUser()
job = self._model.load(id, user=user, level=AccessType.WRITE)
if not job:
raise RestException('Job not found.', code=404)
body = getBodyJson()
if not body:
raise RestException('Log entry must be provided', code=400)
return self._model.append_to_log(user, id, body)
def append_to_log(self, id, params):
user = self.getCurrentUser()
job = self._model.load(id, user=user, level=AccessType.WRITE)
if not job:
raise RestException('Job not found.', code=404)
body = getBodyJson()
if not body:
raise RestException('Log entry must be provided', code=400)
return self._model.append_to_log(user, id, body)
def update(self, task, params):
immutable = ['access', '_id', 'celeryTaskId', 'log']
user = getCurrentUser()
updates = getBodyJson()
if not updates:
raise RestException('A body must be provided', code=400)
for p in updates:
if p in immutable:
raise RestException('\'%s\' is an immutable property' % p, 400)
status = updates.get('status')
return self._model.update_task(user, task, status=status)
def create_assetstore(self, params):
"""Create a new SFTP assetstore."""
params = getBodyJson()
self.requireParams(('name', 'host', 'user'), params)
return self.model('assetstore').save({
'type': AssetstoreType.SFTP,
'name': params.get('name'),
'sftp': {
'host': params.get('host'),
'user': params.get('user'),
'authKey': params.get('authKey')
}
})
def create_assetstore(self, params):
"""Create a new SFTP assetstore."""
params = getBodyJson()
self.requireParams(('name', 'host', 'user'), params)
return self.model('assetstore').save({
'type': AssetstoreType.SFTP,
'name': params.get('name'),
'sftp': {
'host': params.get('host'),
'user': params.get('user'),
'authKey': params.get('authKey')
}
})
def update(self, project, params):
immutable = ['type', 'steps', 'folderId', 'access', 'userId', '_id',
'created', 'updated']
updates = getBodyJson()
for p in updates:
if p in immutable:
raise RestException('\'%s\' is an immutable property' % p, 400)
user = getCurrentUser()
name = updates.get('name')
metadata = updates.get('metadata')
description = updates.get('description')
return self._model.update(user, project, name=name, metadata=metadata,
description=description)
def update(self, taskflow, params):
user = self.getCurrentUser()
immutable = [
'access', '_id', 'taskFlowClass', 'log', 'activeTaskCount'
]
updates = getBodyJson()
if not updates:
raise RestException('A body must be provided', code=400)
for p in updates:
if p in immutable:
raise RestException('\'%s\' is an immutable property' % p, 400)
taskflow = self._model.update_taskflow(user, taskflow, updates)
return taskflow
def start(self, taskflow, params):
user = self.getCurrentUser()
try:
params = getBodyJson()
except RestException:
params = {}
constructor = load_class(taskflow['taskFlowClass'])
token = self.model('token').createToken(user=user, days=7)
workflow = constructor(id=str(taskflow['_id']),
girder_token=token['_id'],
girder_api_url=cumulus.config.girder.baseUrl)
workflow.start(**params)
def update(self, id, params):
body = getBodyJson()
user = self.getCurrentUser()
cluster = self._model.load(id, user=user, level=AccessType.WRITE)
if not cluster:
raise RestException('Cluster not found.', code=404)
if 'assetstoreId' in body:
cluster['assetstoreId'] = body['assetstoreId']
if 'status' in body:
if ClusterStatus.valid(body['status']):
cluster['status'] = body['status']
else:
raise RestException('%s is not a valid cluster status' %
body['status'],
code=400)
if 'timings' in body:
if 'timings' in cluster:
cluster['timings'].update(body['timings'])
else:
cluster['timings'] = body['timings']
if 'config' in body:
# Need to check we aren't try to update immutable fields
immutable_paths = ['_id', 'ssh.user']
for path in immutable_paths:
if parse(path).find(body['config']):
raise RestException("The '%s' field can't be updated" %
path)
update_dict(cluster['config'], body['config'])
cluster = self._model.update_cluster(user, cluster)
# Now do any updates the adapter provides
adapter = get_cluster_adapter(cluster)
try:
adapter.update(body)
# Skip adapter.update if update not defined for this adapter
except (NotImplementedError, ValidationException):
pass
return self._model.filter(cluster, user)
def update(self, id, params):
body = getBodyJson()
user = self.getCurrentUser()
cluster = self._model.load(id, user=user, level=AccessType.WRITE)
if not cluster:
raise RestException('Cluster not found.', code=404)
if 'assetstoreId' in body:
cluster['assetstoreId'] = body['assetstoreId']
if 'status' in body:
if ClusterStatus.valid(body['status']):
cluster['status'] = body['status']
else:
raise RestException('%s is not a valid cluster status' %
body['status'], code=400)
if 'timings' in body:
if 'timings' in cluster:
cluster['timings'].update(body['timings'])
else:
cluster['timings'] = body['timings']
if 'config' in body:
# Need to check we aren't try to update immutable fields
immutable_paths = ['_id', 'ssh.user']
for path in immutable_paths:
if parse(path).find(body['config']):
raise RestException("The '%s' field can't be updated"
% path)
update_dict(cluster['config'], body['config'])
cluster = self._model.update_cluster(user, cluster)
# Now do any updates the adapter provides
adapter = get_cluster_adapter(cluster)
try:
adapter.update(body)
# Skip adapter.update if update not defined for this adapter
except (NotImplementedError, ValidationException):
pass
return self._model.filter(cluster, user)
def share(self, project, params):
body = getBodyJson()
user = getCurrentUser()
# Validate we have been given a value body
try:
ref_resolver = jsonschema.RefResolver.from_schema(
schema.definitions)
jsonschema.validate(body, schema.project['definitions']['share'],
resolver=ref_resolver)
except jsonschema.ValidationError as ve:
raise RestException(ve.message, 400)
users = body.get('users', [])
groups = body.get('groups', [])
return self._model.share(user, project, users, groups)
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': 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 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 = ModelImporter.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, log_write_url, girder_callback_info)
volume['status'] = VolumeState.ATTACHING
volume = self._model.update_volume(getCurrentUser(), volume)
return self._model.filter(volume, getCurrentUser())
def share(self, project, params):
body = getBodyJson()
user = getCurrentUser()
# Validate we have been given a value body
try:
ref_resolver = jsonschema.RefResolver.from_schema(
schema.definitions)
jsonschema.validate(body,
schema.project['definitions']['share'],
resolver=ref_resolver)
except jsonschema.ValidationError as ve:
raise RestException(ve.message, 400)
users = body.get('users', [])
groups = body.get('groups', [])
return self._model.share(user, project, users, groups)
def patch(self, volume, params):
body = getBodyJson()
if not volume:
raise RestException('Volume not found.', code=404)
if 'ec2' in body:
if 'ec2' not in volume:
volume['ec2'] = {}
volume['ec2'].update(body['ec2'])
mutable = ['status', 'msg', 'path']
for k in mutable:
if k in body:
volume[k] = body[k]
user = getCurrentUser()
volume = self._model.update_volume(user, volume)
return self._model.filter(volume, user)
def patch(self, volume, params):
body = getBodyJson()
if not volume:
raise RestException('Volume not found.', code=404)
if 'ec2' in body:
if 'ec2' not in volume:
volume['ec2'] = {}
volume['ec2'].update(body['ec2'])
mutable = ['status', 'msg', 'path']
for k in mutable:
if k in body:
volume[k] = body[k]
user = getCurrentUser()
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 update(self, simulation, params):
immutable = ['projectId', 'folderId', 'access', 'userId', '_id',
'steps', 'updated', 'created']
updates = getBodyJson()
for p in updates:
if p in immutable:
raise RestException('\'%s\' is an immutable property' % p, 400)
user = getCurrentUser()
name = updates.get('name')
description = updates.get('description')
active = updates.get('active')
disabled = updates.get('disabled')
status = updates.get('status')
metadata = updates.get('metadata')
return self._model.update(user, simulation, name=name,
metadata=metadata, description=description,
active=active, disabled=disabled,
status=status)
def update(self, project, params):
immutable = [
'type', 'steps', 'folderId', 'access', 'userId', '_id', 'created',
'updated'
]
updates = getBodyJson()
for p in updates:
if p in immutable:
raise RestException('\'%s\' is an immutable property' % p, 400)
user = getCurrentUser()
name = updates.get('name')
metadata = updates.get('metadata')
description = updates.get('description')
return self._model.update(user,
project,
name=name,
metadata=metadata,
description=description)
def create(self, params):
user = self.getCurrentUser()
taskflow = getBodyJson()
self.requireParams(['taskFlowClass'], taskflow)
# Check that we can load the class
try:
load_class(taskflow['taskFlowClass'])
except Exception as ex:
msg = 'Unable to load taskflow class: %s (%s)' % \
(taskflow['taskFlowClass'], ex)
logger.exception(msg)
traceback.print_exc()
raise RestException(msg, 400)
taskflow = self._model.create(user, taskflow)
cherrypy.response.status = 201
cherrypy.response.headers['Location'] = '/taskflows/%s' % \
taskflow['_id']
return taskflow
def create_file(self, assetstore, params):
params = getBodyJson()
self.requireParams(('name', 'itemId', 'size', 'path'), params)
name = params['name']
item_id = params['itemId']
size = int(params['size'])
path = params['path']
user = self.getCurrentUser()
mime_type = params.get('mimeType')
item = self.model('item').load(id=item_id, user=user,
level=AccessType.WRITE, exc=True)
file = self.model('file').createFile(
name=name, creator=user, item=item, reuseExisting=True,
assetstore=assetstore, mimeType=mime_type, size=size)
file['path'] = path
file['imported'] = True
self.model('file').save(file)
return self.model('file').filter(file)
def add_entry(self, params):
body = getBodyJson()
if "key" not in body:
raise RestException("key is required", code=400)
if "host" not in body:
raise RestException("host is required", code=400)
if "port" not in body:
raise RestException("port is required", code=400)
key = body["key"]
host = body["host"]
port = body["port"]
with LockFile(self._proxy_file_path):
db = None
try:
db = dbm.open(self._proxy_file_path, "c")
# Encode the slash
db[key] = "%s:%s" % (host, port)
finally:
if db:
db.close()
def add_entry(self, params):
body = getBodyJson()
if 'key' not in body:
raise RestException('key is required', code=400)
if 'host' not in body:
raise RestException('host is required', code=400)
if 'port' not in body:
raise RestException('port is required', code=400)
key = body['key']
host = body['host']
port = body['port']
with LockFile(self._proxy_file_path):
db = None
try:
db = dbm.open(self._proxy_file_path, 'c')
# Encode the slash
db[key] = '%s:%s' % (host, port)
finally:
if db:
db.close()
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)
public = body.get('public', False)
notebooks = body.get('notebooks', [])
image = body.get('image')
input_parameters = body.get('input', {}).get('parameters')
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)
molecule_id = mol['_id']
calc = CalculationModel().create_cjson(user, cjson, props, molecule_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 update_properties(self, calculation, params):
props = getBodyJson()
calculation['properties'] = props
calculation = self._model.save(calculation)
return calculation
def create(self, params):
params = getBodyJson()
self.requireParams(('name', 'machine'), params)
return create_assetstore(params)