def handle_single_transaction(role, program, project, **tx_kwargs):
"""
Main entry point for single file transactions.
This function multiplexes on the content-type to call the appropriate
transaction handler.
"""
doc = flask.request.get_data().decode("utf-8")
content_type = flask.request.headers.get("Content-Type", "").lower()
if content_type == "text/csv":
doc_format = "csv"
data, errors = utils.transforms.CSVToJSONConverter().convert(doc)
elif content_type in ["text/tab-separated-values", "text/tsv"]:
doc_format = "tsv"
data, errors = utils.transforms.TSVToJSONConverter().convert(doc)
else:
doc_format = "json"
data = utils.parse.parse_request_json()
errors = None
# TODO: use errors value?
name = flask.request.headers.get("X-Document-Name", None)
doc_args = [name, doc_format, doc, data]
is_async = tx_kwargs.pop("is_async", utils.is_flag_set(FLAG_IS_ASYNC))
db_driver = tx_kwargs.pop("db_driver", flask.current_app.db)
transaction = UploadTransaction(
program=program,
project=project,
role=role,
logger=flask.current_app.logger,
flask_config=flask.current_app.config,
index_client=flask.current_app.index_client,
external_proxies=utils.get_external_proxies(),
db_driver=db_driver,
**tx_kwargs)
if is_async:
session = transaction.db_driver.session_scope(can_inherit=False)
with session, transaction:
response = {
"code": 200,
"message": "Transaction submitted.",
"transaction_id": transaction.transaction_id,
}
flask.current_app.async_pool.schedule(single_transaction_worker,
transaction, *doc_args)
# create the resource in arborist
auth.create_resource(program, project, doc_args[3])
return flask.jsonify(response)
else:
response, code = single_transaction_worker(transaction, *doc_args)
# create the resource in arborist
auth.create_resource(program, project, doc_args[3])
return flask.jsonify(response), code
def handle_single_transaction(role, program, project, **tx_kwargs):
"""
Main entry point for single file transactions.
This function multiplexes on the content-type to call the appropriate
transaction handler.
"""
doc = flask.request.get_data()
content_type = flask.request.headers.get('Content-Type', '').lower()
if content_type == 'text/csv':
doc_format = 'csv'
data, errors = utils.transforms.CSVToJSONConverter().convert(doc)
elif content_type in ['text/tab-separated-values', 'text/tsv']:
doc_format = 'tsv'
data, errors = utils.transforms.TSVToJSONConverter().convert(doc)
else:
doc_format = 'json'
data = utils.parse.parse_request_json()
errors = None
# TODO: use errors value?
name = flask.request.headers.get('X-Document-Name', None)
doc_args = [name, doc_format, doc, data]
is_async = tx_kwargs.pop('is_async', utils.is_flag_set(FLAG_IS_ASYNC))
db_driver = tx_kwargs.pop('db_driver', flask.current_app.db)
transaction = UploadTransaction(program=program,
project=project,
role=role,
user=flask.g.user,
logger=flask.current_app.logger,
flask_config=flask.current_app.config,
signpost=flask.current_app.signpost,
external_proxies=utils.get_external_proxies(),
db_driver=db_driver,
**tx_kwargs)
if is_async:
session = transaction.db_driver.session_scope(can_inherit=False)
with session, transaction:
response = {
"code": 200,
"message": "Transaction submitted.",
"transaction_id": transaction.transaction_id,
}
flask.current_app.async_pool.schedule(
single_transaction_worker, transaction, *doc_args
)
return flask.jsonify(response)
else:
response, code = single_transaction_worker(transaction, *doc_args)
return flask.jsonify(response), code
def _single_transaction(role, program, project, *doc_args, **tx_kwargs):
"""
Create and execute a single (not bulk) transaction.
Most non-bulk variations of upload actions (based on content-type,
etc.) should wrap this function.
Return:
Tuple[flask.Response, int]: (API response json, status code)
"""
is_async = tx_kwargs.pop('is_async', utils.is_flag_set(FLAG_IS_ASYNC))
db_driver = tx_kwargs.pop('db_driver', flask.current_app.db)
transaction = UploadTransaction(
program=program,
project=project,
role=role,
user=flask.g.user,
logger=flask.current_app.logger,
signpost=flask.current_app.signpost,
flask_config=flask.current_app.config,
db_driver=db_driver,
external_proxies=utils.get_external_proxies(),
**tx_kwargs
)
if is_async:
session = transaction.db_driver.session_scope(can_inherit=False)
with session, transaction:
response = {
"code": 200,
"message": "Transaction submitted.",
"transaction_id": transaction.transaction_id,
}
flask.current_app.async_pool.schedule(
single_transaction_worker, transaction, *doc_args
)
return flask.jsonify(response)
else:
response, code = single_transaction_worker(transaction, *doc_args)
return flask.jsonify(response), code
def create_project(program):
"""
Register a project.
The content of the request is a JSON containing the information describing
a project. Authorization for registering projects is limited to
administrative users.
Summary:
Create a project
Tags:
project
Args:
program (str): |program_id|
body (schema_project): input body
Responses:
200: Registered successfully.
400: User error.
404: Program not found.
403: Unauthorized request.
:reqheader Content-Type: |reqheader_Content-Type|
:reqheader Accept: |reqheader_Accept|
:reqheader X-Auth-Token: |reqheader_X-Auth-Token|
:resheader Content-Type: |resheader_Content-Type|
Example:
.. code-block:: http
POST /v0/submission/CGCI/ HTTP/1.1
Host: example.com
Content-Type: application/json
X-Auth-Token: MIIDKgYJKoZIhvcNAQcC...
Accept: application/json
.. code-block:: JavaScript
{
"type": "project",
"code": "BLGSP",
"disease_type": "Burkitt Lymphoma",
"name": "Burkitt Lymphoma Genome Sequencing Project",
"primary_site": "Lymph Nodes",
"dbgap_accession_number": "phs000527",
"state": "active"
}
"""
auth.current_user.require_admin()
doc = utils.parse.parse_request_json()
if not isinstance(doc, dict):
raise UserError("Program endpoint only supports single documents")
if doc.get("type") and doc.get("type") not in ["project"]:
raise UserError(
"Invalid post to program endpoint with type='{}'".format(
doc.get("type")))
# Parse project.code
project = doc.get("code")
if not project:
raise UserError("No project specified in key 'code'")
project = project.encode("utf-8")
# Parse dbgap accession number.
phsid = doc.get("dbgap_accession_number")
if not phsid:
raise UserError("No dbGaP accesion number specified.")
# Create base JSON document.
base_doc = utils.parse.parse_request_json()
with flask.current_app.db.session_scope() as session:
program_node = utils.lookup_program(flask.current_app.db, program)
if not program_node:
raise NotFoundError("Program {} is not registered".format(program))
# Look up project node.
node = utils.lookup_project(flask.current_app.db, program, project)
if not node:
# Create a new project node
node_uuid = str(uuid.uuid5(PROJECT_SEED, project.encode("utf-8")))
if flask.current_app.db.nodes(
models.Project).ids(node_uuid).first():
raise UserError(
"ERROR: Project {} already exists in DB".format(project))
node = models.Project(node_uuid) # pylint: disable=not-callable
node.programs = [program_node]
action = "create"
node.props["state"] = "open"
else:
action = "update"
# silently drop system_properties
base_doc.pop("type", None)
base_doc.pop("state", None)
base_doc.pop("released", None)
node.props.update(base_doc)
doc = dict(
{
"type": "project",
"programs": {
"id": program_node.node_id
}
}, **base_doc)
# Create transaction
transaction_args = dict(
program=program,
project=project,
role=ROLES["UPDATE"],
flask_config=flask.current_app.config,
)
with UploadTransaction(**transaction_args) as trans:
node = session.merge(node)
session.commit()
entity = UploadEntityFactory.create(
trans, doc=None, config=flask.current_app.config)
entity.action = action
entity.doc = doc
entity.entity_type = "project"
entity.unique_keys = node._secondary_keys_dicts
entity.node = node
entity.entity_id = entity.node.node_id
trans.entities = [entity]
return flask.jsonify(trans.json)
def create_project(program):
"""
Register a project.
The content of the request is a JSON containing the information describing
a project. Authorization for registering projects is limited to
administrative users.
Args:
program (str): |program_id|
:reqheader Content-Type: |reqheader_Content-Type|
:reqheader Accept: |reqheader_Accept|
:reqheader X-Auth-Token: |reqheader_X-Auth-Token|
:resheader Content-Type: |resheader_Content-Type|
:statuscode 200: Registered successfully.
:statuscode 404: Program not found.
:statuscode 403: Unauthorized request.
Example:
.. code-block:: http
POST /v0/submission/CGCI/ HTTP/1.1
Host: example.com
Content-Type: application/json
X-Auth-Token: MIIDKgYJKoZIhvcNAQcC...
Accept: application/json
.. code-block:: JavaScript
{
"type": "project",
"code": "BLGSP",
"disease_type": "Burkitt Lymphoma",
"name": "Burkitt Lymphoma Genome Sequencing Project",
"primary_site": "Lymph Nodes",
"dbgap_accession_number": "phs000527",
"state": "active"
}
"""
auth.admin_auth()
doc = utils.parse.parse_request_json()
if not isinstance(doc, dict):
raise UserError('Program endpoint only supports single documents')
if doc.get('type') and doc.get('type') not in ['project']:
raise UserError(
"Invalid post to program endpoint with type='{}'".format(
doc.get('type')))
# Parse project.code
project = doc.get('code')
if not project:
raise UserError("No project specified in key 'code'")
project = project.encode('utf-8')
# Parse dbgap accession number.
phsid = doc.get('dbgap_accession_number')
if not phsid:
raise UserError("No dbGaP accesion number specified.")
# Create base JSON document.
base_doc = utils.parse.parse_request_json()
with flask.current_app.db.session_scope() as session:
program_node = utils.lookup_program(flask.current_app.db, program)
if not program_node:
raise NotFoundError('Program {} is not registered'.format(program))
# Look up project node.
node = utils.lookup_project(flask.current_app.db, program, project)
if not node:
# Create a new project node
node_uuid = str(uuid.uuid5(PROJECT_SEED, project.encode('utf-8')))
node = models.Project(node_uuid) # pylint: disable=not-callable
node.programs = [program_node]
action = 'create'
node.props['state'] = 'open'
else:
action = 'update'
# silently drop system_properties
base_doc.pop('type', None)
base_doc.pop('state', None)
base_doc.pop('released', None)
node.props.update(base_doc)
doc = dict(
{
'type': 'project',
'programs': {
'id': program_node.node_id
},
}, **base_doc)
# Create transaction
transaction_args = dict(program=program,
project=project,
role=ROLES['UPDATE'],
flask_config=flask.current_app.config)
with UploadTransaction(**transaction_args) as trans:
node = session.merge(node)
session.commit()
entity = UploadEntityFactory.create(
trans, doc=None, config=flask.current_app.config)
entity.action = action
entity.doc = doc
entity.entity_type = 'project'
entity.unique_keys = node._secondary_keys_dicts
entity.node = node
entity.entity_id = entity.node.node_id
trans.entities = [entity]
return flask.jsonify(trans.json)