def root_create():
"""
/
PUT POST PATCH
Register a program.
The content of the request is a JSON containing the information
describing a program. Authorization for registering programs is
limited to administrative users.
: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": "program",
"name": "CGCI",
"dbgap_accession_number": "phs000178"
}
"""
auth.admin_auth()
message = None
node_id = None
doc = parse.parse_request_json()
if not isinstance(doc, dict):
raise UserError('Root endpoint only supports single documents')
if doc.get('type') != 'program':
raise UserError("Invalid type in key type='{}'".format(
doc.get('type')))
phsid = doc.get('dbgap_accession_number')
program = doc.get('name')
if not program:
raise UserError("No program specified in key 'name'")
with current_app.db.session_scope(can_inherit=False) as session:
node = (current_app.db.nodes(
models.Program).props(name=program).scalar())
if node:
message = 'Program already exists.'
node_id = node.node_id
else:
node_id = str(uuid.uuid5(PROGRAM_SEED, program.encode('utf-8')))
session.add(
models.Program( # pylint: disable=not-callable
node_id,
name=program,
dbgap_accession_number=phsid))
message = 'Program registered.'
return flask.jsonify({
'id': node_id,
'name': program,
'message': message,
})
def root_create():
"""
Register a program.
The content of the request is a JSON containing the information
describing a program. Authorization for registering programs is
limited to administrative users.
Summary:
Create a program
Tags:
program
Args:
body (schema_program): input body
Responses:
200: Registered successfully.
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": "program",
"name": "CGCI",
"dbgap_accession_number": "phs000178"
}
"""
message = None
node_id = None
doc = parse.parse_request_json()
if not isinstance(doc, dict):
raise UserError(
"The program creation endpoint only supports single documents (dict). Received data of type {}"
.format(type(doc)))
if doc.get("type") != "program":
raise UserError("Invalid type in key type='{}'".format(
doc.get("type")))
phsid = doc.get("dbgap_accession_number")
program = doc.get("name")
if not program:
raise UserError("No program specified in key 'name'")
# create the resource in sheepdog DB
with current_app.db.session_scope(can_inherit=False) as session:
node = current_app.db.nodes(
models.Program).props(name=program).scalar()
if node:
message = "Program is updated!"
node_id = node.node_id
node.props["dbgap_accession_number"] = phsid
else:
node_id = str(uuid.uuid5(PROGRAM_SEED, program))
session.add(
models.Program( # pylint: disable=not-callable
node_id,
name=program,
dbgap_accession_number=phsid))
message = "Program registered."
# create the resource in arborist
auth.create_resource(phsid)
return flask.jsonify({"id": node_id, "name": program, "message": message})
def create_program():
"""
Register a program.
The content of the request is a JSON containing the information
describing a program. Authorization for registering programs is
limited to administrative users.
Summary:
Create a program
Tags:
program
Args:
body (schema_program): input body
Responses:
200: Registered successfully.
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": "program",
"name": "CGCI",
"dbgap_accession_number": "phs000178"
}
"""
input_doc = flask.request.get_data().decode("utf-8")
content_type = flask.request.headers.get("Content-Type", "").lower()
errors = None
if content_type == "text/csv":
doc, errors = utils.transforms.CSVToJSONConverter().convert(input_doc)
elif content_type in ["text/tab-separated-values", "text/tsv"]:
doc, errors = utils.transforms.TSVToJSONConverter().convert(input_doc)
else:
doc = utils.parse.parse_request_json()
if errors:
raise UserError("Unable to parse doc '{}': {}".format(
input_doc, errors))
if isinstance(doc, list) and len(doc) == 1:
# handle TSV/CSV submissions that are parsed as lists of 1 element
doc = doc[0]
if not isinstance(doc, dict):
raise UserError(
"The program creation endpoint only supports single documents (dict). Received data of type {}: {}"
.format(type(doc), doc))
if doc.get("type") != "program":
raise UserError("Invalid type in key type='{}'".format(
doc.get("type")))
phsid = doc.get("dbgap_accession_number")
program = doc.get("name")
if not program:
raise UserError("No program specified in key 'name'")
# create the resource in sheepdog DB
message = None
node_id = None
with current_app.db.session_scope(can_inherit=False) as session:
node = current_app.db.nodes(
models.Program).props(name=program).scalar()
if node:
message = "Program is updated!"
node_id = node.node_id
node.props["dbgap_accession_number"] = phsid
else:
node_id = str(uuid.uuid5(PROGRAM_SEED, program))
session.add(
models.Program( # pylint: disable=not-callable
node_id,
name=program,
dbgap_accession_number=phsid))
message = "Program registered."
# create the resource in arborist
auth.create_resource(phsid)
return flask.jsonify({"id": node_id, "name": program, "message": message})