def set_workflow_status(workflow_id_or_name): # noqa
r"""Set workflow status.
---
put:
summary: Set workflow status.
description: >-
This resource sets the status of workflow.
operationId: set_workflow_status
produces:
- application/json
parameters:
- name: user
in: query
description: Required. UUID of workflow owner.
required: true
type: string
- name: workflow_id_or_name
in: path
description: Required. Workflow UUID or name.
required: true
type: string
- name: status
in: query
description: Required. New status.
required: true
type: string
enum:
- start
- stop
- deleted
- name: parameters
in: body
description: >-
Optional. Additional input parameters and operational options for
workflow execution. Possible parameters are `CACHE=on/off`, passed
to disable caching of results in serial workflows,
`all_runs=True/False` deletes all runs of a given workflow
if status is set to deleted, `workspace=True/False` which deletes
the workspace of a workflow and finally `hard_delete=True` which
removes completely the workflow data from the database and the
workspace from the shared filesystem.
required: false
schema:
type: object
properties:
CACHE:
type: string
all_runs:
type: boolean
workspace:
type: boolean
hard_delete:
type: boolean
responses:
200:
description: >-
Request succeeded. Info about workflow, including the status is
returned.
schema:
type: object
properties:
message:
type: string
workflow_id:
type: string
workflow_name:
type: string
status:
type: string
user:
type: string
examples:
application/json:
{
"message": "Workflow successfully launched",
"workflow_id": "256b25f4-4cfb-4684-b7a8-73872ef455a1",
"workflow_name": "mytest-1",
"status": "running",
"user": "******"
}
400:
description: >-
Request failed. The incoming data specification seems malformed.
examples:
application/json:
{
"message": "Malformed request."
}
403:
description: >-
Request failed. User is not allowed to access workflow.
examples:
application/json:
{
"message": "User 00000000-0000-0000-0000-000000000000
is not allowed to access workflow
256b25f4-4cfb-4684-b7a8-73872ef455a1"
}
404:
description: >-
Request failed. Either User or Workflow does not exist.
examples:
application/json:
{
"message": "User 00000000-0000-0000-0000-000000000000 does not
exist"
}
application/json:
{
"message": "Workflow 256b25f4-4cfb-4684-b7a8-73872ef455a1
does not exist"
}
409:
description: >-
Request failed. The workflow could not be started due to a
conflict.
examples:
application/json:
{
"message": "Workflow 256b25f4-4cfb-4684-b7a8-73872ef455a1
could not be started because it is already
running."
}
500:
description: >-
Request failed. Internal controller error.
501:
description: >-
Request failed. The specified status change is not implemented.
examples:
application/json:
{
"message": "Status resume is not supported yet."
}
502:
description: >-
Request failed. Connection to a third party system has failed.
examples:
application/json:
{
"message": "Connection to database timed out, please retry."
}
"""
try:
user_uuid = request.args["user"]
workflow = _get_workflow_with_uuid_or_name(workflow_id_or_name,
user_uuid)
status = request.args.get("status")
if not (status in STATUSES):
return (
jsonify({
"message":
"Status {0} is not one of: {1}".format(
status, ", ".join(STATUSES))
}),
400,
)
if not str(workflow.owner_id) == user_uuid:
return (
jsonify({
"message":
"User {} is not allowed to access workflow {}".format(
user_uuid, workflow_id_or_name)
}),
403,
)
parameters = {}
if request.json:
parameters = request.json
if status == START:
start_workflow(workflow, parameters)
return (
jsonify({
"message": "Workflow successfully launched",
"workflow_id": str(workflow.id_),
"workflow_name": get_workflow_name(workflow),
"status": workflow.status.name,
"user": str(workflow.owner_id),
}),
200,
)
elif status == DELETED:
all_runs = True if request.json.get("all_runs") else False
hard_delete = True if request.json.get("hard_delete") else False
workspace = True if hard_delete or request.json.get(
"workspace") else False
return delete_workflow(workflow, all_runs, hard_delete, workspace)
if status == STOP:
stop_workflow(workflow)
return (
jsonify({
"message": "Workflow successfully stopped",
"workflow_id": workflow.id_,
"workflow_name": get_workflow_name(workflow),
"status": workflow.status.name,
"user": str(workflow.owner_id),
}),
200,
)
else:
raise NotImplementedError(
"Status {} is not supported yet".format(status))
except ValueError:
return (
jsonify({
"message":
"REANA_WORKON is set to {0}, but "
"that workflow does not exist. "
"Please set your REANA_WORKON environment "
"variable appropriately.".format(workflow_id_or_name)
}),
404,
)
except REANAWorkflowControllerError as e:
return jsonify({"message": str(e)}), 409
except REANAWorkflowStatusError as e:
return jsonify({"message": str(e)}), 404
except KeyError as e:
return jsonify({"message": str(e)}), 400
except NotImplementedError as e:
return jsonify({"message": str(e)}), 501
except REANAExternalCallError as e:
return jsonify({"message": str(e)}), 502
except Exception as e:
return jsonify({"message": str(e)}), 500
def get_workflow_logs(workflow_id_or_name): # noqa
r"""Get workflow logs from a workflow engine.
---
get:
summary: Returns logs of a specific workflow from a workflow engine.
description: >-
This resource is expecting a workflow UUID and a filename to return
its outputs.
operationId: get_workflow_logs
produces:
- application/json
parameters:
- name: user
in: query
description: Required. UUID of workflow owner.
required: true
type: string
- name: workflow_id_or_name
in: path
description: Required. Workflow UUID or name.
required: true
type: string
- name: steps
in: body
description: Steps of a workflow.
required: false
schema:
type: array
description: List of step names to get logs for.
items:
type: string
description: Step name.
responses:
200:
description: >-
Request succeeded. Info about workflow, including the status is
returned.
schema:
type: object
properties:
workflow_id:
type: string
workflow_name:
type: string
logs:
type: string
user:
type: string
examples:
application/json:
{
"workflow_id": "256b25f4-4cfb-4684-b7a8-73872ef455a1",
"workflow_name": "mytest-1",
"logs": "{'workflow_logs': string,
'job_logs': {
'256b25f4-4cfb-4684-b7a8-73872ef455a2': string,
'256b25f4-4cfb-4684-b7a8-73872ef455a3': string,
},
'engine_specific': object,
}",
"user": "******"
}
400:
description: >-
Request failed. The incoming data specification seems malformed.
404:
description: >-
Request failed. User does not exist.
examples:
application/json:
{
"message": "User 00000000-0000-0000-0000-000000000000 does not
exist"
}
500:
description: >-
Request failed. Internal controller error.
examples:
application/json:
{
"message": "Internal workflow controller error."
}
"""
try:
user_uuid = request.args["user"]
workflow = _get_workflow_with_uuid_or_name(workflow_id_or_name,
user_uuid)
if not str(workflow.owner_id) == user_uuid:
return (
jsonify({
"message":
"User {} is not allowed to access workflow {}".format(
user_uuid, workflow_id_or_name)
}),
403,
)
steps = None
if request.json:
steps = request.json
if steps:
workflow_logs = {
"workflow_logs": None,
"job_logs": build_workflow_logs(workflow, steps),
"engine_specific": None,
}
else:
workflow_logs = {
"workflow_logs": workflow.logs,
"job_logs": build_workflow_logs(workflow),
"engine_specific": workflow.engine_specific,
}
return (
jsonify({
"workflow_id": workflow.id_,
"workflow_name": get_workflow_name(workflow),
"logs": json.dumps(workflow_logs),
"user": user_uuid,
}),
200,
)
except ValueError:
return (
jsonify({
"message":
"REANA_WORKON is set to {0}, but "
"that workflow does not exist. "
"Please set your REANA_WORKON environment "
"variable appropriately.".format(workflow_id_or_name)
}),
404,
)
except KeyError as e:
return jsonify({"message": str(e)}), 400
except Exception as e:
return jsonify({"message": str(e)}), 500
def get_workflow_diff(workflow_id_or_name_a, workflow_id_or_name_b): # noqa
r"""Get differences between two workflows.
---
get:
summary: Get diff between two workflows.
description: >-
This resource shows the differences between
the assets of two workflows.
Resource is expecting two workflow UUIDs or names.
operationId: get_workflow_diff
produces:
- application/json
parameters:
- name: user
in: query
description: Required. UUID of workflow owner.
required: true
type: string
- name: workflow_id_or_name_a
in: path
description: Required. Analysis UUID or name of the first workflow.
required: true
type: string
- name: workflow_id_or_name_b
in: path
description: Required. Analysis UUID or name of the second workflow.
required: true
type: string
- name: brief
in: query
description: Optional flag. If set, file contents are examined.
required: false
type: boolean
default: false
- name: context_lines
in: query
description: Optional parameter. Sets number of context lines
for workspace diff output.
required: false
type: string
default: '5'
responses:
200:
description: >-
Request succeeded. Info about a workflow, including the status is
returned.
schema:
type: object
properties:
reana_specification:
type: string
workspace_listing:
type: string
examples:
application/json:
{
"reana_specification":
["- nevents: 100000\n+ nevents: 200000"],
"workspace_listing": {"Only in workspace a: code"}
}
400:
description: >-
Request failed. The incoming payload seems malformed.
examples:
application/json:
{
"message": "Malformed request."
}
403:
description: >-
Request failed. User is not allowed to access workflow.
examples:
application/json:
{
"message": "User 00000000-0000-0000-0000-000000000000
is not allowed to access workflow
256b25f4-4cfb-4684-b7a8-73872ef455a1"
}
404:
description: >-
Request failed. Either user or workflow does not exist.
examples:
application/json:
{
"message": "Workflow 256b25f4-4cfb-4684-b7a8-73872ef455a1 does
not exist."
}
500:
description: >-
Request failed. Internal controller error.
"""
try:
user_uuid = request.args["user"]
brief = json.loads(request.args.get("brief", "false").lower())
context_lines = request.args.get("context_lines", 5)
workflow_a_exists = False
workflow_a = _get_workflow_with_uuid_or_name(workflow_id_or_name_a,
user_uuid)
workflow_a_exists = True
workflow_b = _get_workflow_with_uuid_or_name(workflow_id_or_name_b,
user_uuid)
if not workflow_id_or_name_a or not workflow_id_or_name_b:
raise ValueError("Workflow id or name is not supplied")
specification_diff = get_specification_diff(workflow_a, workflow_b)
try:
workspace_diff = get_workspace_diff(workflow_a, workflow_b, brief,
context_lines)
except ValueError as e:
workspace_diff = str(e)
response = {
"reana_specification": json.dumps(specification_diff),
"workspace_listing": json.dumps(workspace_diff),
}
return jsonify(response)
except REANAWorkflowControllerError as e:
return jsonify({"message": str(e)}), 409
except ValueError as e:
wrong_workflow = (workflow_id_or_name_b
if workflow_a_exists else workflow_id_or_name_a)
return (
jsonify({
"message":
"Workflow {0} does not exist.".format(wrong_workflow)
}),
404,
)
except KeyError as e:
return jsonify({"message": str(e)}), 400
except ValueError as e:
return jsonify({"message": str(e)}), 400
except json.JSONDecodeError:
return jsonify({"message":
"Your request contains not valid JSON."}), 400
except Exception as e:
return jsonify({"message": str(e)}), 500
def get_workflow_status(workflow_id_or_name): # noqa
r"""Get workflow status.
---
get:
summary: Get workflow status.
description: >-
This resource reports the status of workflow.
operationId: get_workflow_status
produces:
- application/json
parameters:
- name: user
in: query
description: Required. UUID of workflow owner.
required: true
type: string
- name: workflow_id_or_name
in: path
description: Required. Workflow UUID or name.
required: true
type: string
responses:
200:
description: >-
Request succeeded. Info about workflow, including the status is
returned.
schema:
type: object
properties:
id:
type: string
name:
type: string
created:
type: string
status:
type: string
user:
type: string
logs:
type: string
progress:
type: object
examples:
application/json:
{
"id": "256b25f4-4cfb-4684-b7a8-73872ef455a1",
"name": "mytest-1",
"created": "2018-06-13T09:47:35.66097",
"status": "running",
"user": "******"
}
400:
description: >-
Request failed. The incoming data specification seems malformed.
examples:
application/json:
{
"message": "Malformed request."
}
403:
description: >-
Request failed. User is not allowed to access workflow.
examples:
application/json:
{
"message": "User 00000000-0000-0000-0000-000000000000
is not allowed to access workflow
256b25f4-4cfb-4684-b7a8-73872ef455a1"
}
404:
description: >-
Request failed. Either User or Workflow does not exist.
examples:
application/json:
{
"message": "User 00000000-0000-0000-0000-000000000000 does not
exist"
}
application/json:
{
"message": "Workflow 256b25f4-4cfb-4684-b7a8-73872ef455a1
does not exist"
}
500:
description: >-
Request failed. Internal controller error.
"""
try:
user_uuid = request.args["user"]
workflow = _get_workflow_with_uuid_or_name(workflow_id_or_name,
user_uuid)
workflow_logs = build_workflow_logs(workflow)
if not str(workflow.owner_id) == user_uuid:
return (
jsonify({
"message":
"User {} is not allowed to access workflow {}".format(
user_uuid, workflow_id_or_name)
}),
403,
)
return (
jsonify({
"id": workflow.id_,
"name": get_workflow_name(workflow),
"created": workflow.created.strftime(WORKFLOW_TIME_FORMAT),
"status": workflow.status.name,
"progress": get_workflow_progress(workflow),
"user": user_uuid,
"logs": json.dumps(workflow_logs),
}),
200,
)
except ValueError:
return (
jsonify({
"message":
"REANA_WORKON is set to {0}, but "
"that workflow does not exist. "
"Please set your REANA_WORKON environment "
"variable appropriately.".format(workflow_id_or_name)
}),
404,
)
except KeyError as e:
return jsonify({"message": str(e)}), 400
except Exception as e:
return jsonify({"message": str(e)}), 500
def move_files(workflow_id_or_name): # noqa
r"""Move files within workspace.
---
put:
summary: Move files within workspace.
description: >-
This resource moves files within the workspace. Resource is expecting
a workflow UUID.
operationId: move_files
consumes:
- application/json
produces:
- application/json
parameters:
- name: workflow_id_or_name
in: path
description: Required. Analysis UUID or name.
required: true
type: string
- name: source
in: query
description: Required. Source file(s).
required: true
type: string
- name: target
in: query
description: Required. Target file(s).
required: true
type: string
- name: user
in: query
description: Required. UUID of workflow owner..
required: true
type: string
responses:
200:
description: >-
Request succeeded. Message about successfully moved files is
returned.
schema:
type: object
properties:
message:
type: string
workflow_id:
type: string
workflow_name:
type: string
examples:
application/json:
{
"message": "Files were successfully moved",
"workflow_id": "256b25f4-4cfb-4684-b7a8-73872ef455a1",
"workflow_name": "mytest.1",
}
400:
description: >-
Request failed. The incoming payload seems malformed.
examples:
application/json:
{
"message": "Malformed request."
}
403:
description: >-
Request failed. User is not allowed to access workflow.
examples:
application/json:
{
"message": "User 00000000-0000-0000-0000-000000000000
is not allowed to access workflow
256b25f4-4cfb-4684-b7a8-73872ef455a1"
}
404:
description: >-
Request failed. Either User or Workflow does not exist.
examples:
application/json:
{
"message": "Workflow 256b25f4-4cfb-4684-b7a8-73872ef455a1
does not exist"
}
500:
description: >-
Request failed. Internal controller error.
"""
try:
user_uuid = request.args["user"]
workflow = _get_workflow_with_uuid_or_name(workflow_id_or_name, user_uuid)
source = request.args["source"]
target = request.args["target"]
if workflow.status == "running":
return (
jsonify({"message": "Workflow is running, files can not be " "moved"}),
400,
)
if not str(workflow.owner_id) == user_uuid:
return (
jsonify(
{
"message": "User {} is not allowed to access workflow {}".format(
user_uuid, workflow_id_or_name
)
}
),
403,
)
mv_files(source, target, workflow)
message = "File(s) {} were successfully moved".format(source)
return (
jsonify(
{
"message": message,
"workflow_id": workflow.id_,
"workflow_name": get_workflow_name(workflow),
}
),
200,
)
except ValueError:
return (
jsonify(
{
"message": "REANA_WORKON is set to {0}, but "
"that workflow does not exist. "
"Please set your REANA_WORKON environment "
"variable appropriately.".format(workflow_id_or_name)
}
),
404,
)
except REANAWorkflowControllerError as e:
return jsonify({"message": str(e)}), 409
except KeyError as e:
return jsonify({"message": str(e)}), 400
except NotImplementedError as e:
return jsonify({"message": str(e)}), 501
except Exception as e:
return jsonify({"message": str(e)}), 500
def get_workflow_parameters(workflow_id_or_name): # noqa
r"""Get workflow input parameters.
---
get:
summary: Get workflow parameters.
description: >-
This resource reports the input parameters of workflow.
operationId: get_workflow_parameters
produces:
- application/json
parameters:
- name: user
in: query
description: Required. UUID of workflow owner.
required: true
type: string
- name: workflow_id_or_name
in: path
description: Required. Workflow UUID or name.
required: true
type: string
responses:
200:
description: >-
Request succeeded. Workflow input parameters, including the status
are returned.
schema:
type: object
properties:
id:
type: string
name:
type: string
type:
type: string
parameters:
type: object
examples:
application/json:
{
'id': 'dd4e93cf-e6d0-4714-a601-301ed97eec60',
'name': 'workflow.24',
'type': 'serial',
'parameters': {'helloworld': 'code/helloworld.py',
'inputfile': 'data/names.txt',
'outputfile': 'results/greetings.txt',
'sleeptime': 2}
}
400:
description: >-
Request failed. The incoming data specification seems malformed.
examples:
application/json:
{
"message": "Malformed request."
}
403:
description: >-
Request failed. User is not allowed to access workflow.
examples:
application/json:
{
"message": "User 00000000-0000-0000-0000-000000000000
is not allowed to access workflow
256b25f4-4cfb-4684-b7a8-73872ef455a1"
}
404:
description: >-
Request failed. Either User or Workflow does not exist.
examples:
application/json:
{
"message": "User 00000000-0000-0000-0000-000000000000 does not
exist"
}
application/json:
{
"message": "Workflow 256b25f4-4cfb-4684-b7a8-73872ef455a1
does not exist"
}
500:
description: >-
Request failed. Internal controller error.
"""
try:
user_uuid = request.args["user"]
workflow = _get_workflow_with_uuid_or_name(workflow_id_or_name,
user_uuid)
if not str(workflow.owner_id) == user_uuid:
return (
jsonify({
"message":
"User {} is not allowed to access workflow {}".format(
user_uuid, workflow_id_or_name)
}),
403,
)
workflow_parameters = workflow.get_input_parameters()
return (
jsonify({
"id": workflow.id_,
"name": get_workflow_name(workflow),
"type": workflow.reana_specification["workflow"]["type"],
"parameters": workflow_parameters,
}),
200,
)
except ValueError:
return (
jsonify({
"message":
"REANA_WORKON is set to {0}, but "
"that workflow does not exist. "
"Please set your REANA_WORKON environment "
"variable appropriately.".format(workflow_id_or_name)
}),
404,
)
except KeyError as e:
return jsonify({"message": str(e)}), 400
except Exception as e:
return jsonify({"message": str(e)}), 500
def get_files(workflow_id_or_name, paginate=None): # noqa
r"""List all files contained in a workspace.
---
get:
summary: Returns the workspace file list.
description: >-
This resource retrieves the file list of a workspace, given
its workflow UUID.
operationId: get_files
produces:
- multipart/form-data
parameters:
- name: user
in: query
description: Required. UUID of workflow owner.
required: true
type: string
- name: workflow_id_or_name
in: path
description: Required. Workflow UUID or name.
required: true
type: string
- name: file_name
in: query
description: File name(s) (glob) to list.
required: false
type: string
- name: page
in: query
description: Results page number (pagination).
required: false
type: integer
- name: size
in: query
description: Number of results per page (pagination).
required: false
type: integer
- name: search
in: query
description: Filter workflow workspace files.
required: false
type: string
responses:
200:
description: >-
Requests succeeded. The list of code|input|output files has been
retrieved.
schema:
type: object
properties:
total:
type: integer
items:
type: array
items:
type: object
properties:
name:
type: string
last-modified:
type: string
size:
type: object
properties:
raw:
type: number
human_readable:
type: string
400:
description: >-
Request failed. The incoming data specification seems malformed.
404:
description: >-
Request failed. Workflow does not exist.
examples:
application/json:
{
"message": "Workflow 256b25f4-4cfb-4684-b7a8-73872ef455a1 does
not exist."
}
500:
description: >-
Request failed. Internal controller error.
examples:
application/json:
{
"message": "Internal workflow controller error."
}
"""
try:
user_uuid = request.args["user"]
search = request.args.get("search")
user = User.query.filter(User.id_ == user_uuid).first()
if not user:
return jsonify({"message": "User {} does not exist".format(user)}), 404
workflow = _get_workflow_with_uuid_or_name(workflow_id_or_name, user_uuid)
file_name = request.args.get("file_name")
if search:
search = json.loads(search)
if file_name:
file_list = list_files_recursive_wildcard(
workflow.workspace_path, file_name, search=search
)
else:
file_list = list_directory_files(workflow.workspace_path, search=search)
pagination_dict = paginate(file_list)
return jsonify(pagination_dict), 200
except ValueError:
return (
jsonify(
{
"message": "REANA_WORKON is set to {0}, but "
"that workflow does not exist. "
"Please set your REANA_WORKON environment "
"variable appropriately.".format(workflow_id_or_name)
}
),
404,
)
except KeyError:
return jsonify({"message": "Malformed request."}), 400
except CreateFailed:
return jsonify({"message": "Workspace does not exist."}), 404
except Exception as e:
return jsonify({"message": str(e)}), 500
def upload_file(workflow_id_or_name):
r"""Upload file to workspace.
---
post:
summary: Adds a file to the workspace.
description: >-
This resource is expecting a workflow UUID and a file to place in the
workspace.
operationId: upload_file
consumes:
- application/octet-stream
produces:
- application/json
parameters:
- name: user
in: query
description: Required. UUID of workflow owner.
required: true
type: string
- name: workflow_id_or_name
in: path
description: Required. Workflow UUID or name.
required: true
type: string
- name: file
in: body
description: Required. File to add to the workspace.
required: true
schema:
type: string
- name: file_name
in: query
description: Required. File name.
required: true
type: string
responses:
200:
description: >-
Request succeeded. The file has been added to the workspace.
schema:
type: object
properties:
message:
type: string
examples:
application/json:
{
"message": "`file_name` has been successfully uploaded.",
}
400:
description: >-
Request failed. The incoming data specification seems malformed
404:
description: >-
Request failed. Workflow does not exist.
schema:
type: object
properties:
message:
type: string
examples:
application/json:
{
"message": "Workflow cdcf48b1-c2f3-4693-8230-b066e088c6ac does
not exist",
}
500:
description: >-
Request failed. Internal controller error.
"""
try:
if not ("application/octet-stream" in request.headers.get("Content-Type")):
return (
jsonify(
{
"message": f"Wrong Content-Type "
f'{request.headers.get("Content-Type")} '
f"use application/octet-stream"
}
),
400,
)
user_uuid = request.args["user"]
full_file_name = request.args["file_name"]
if not full_file_name:
raise ValueError("The file transferred needs to have name.")
workflow = _get_workflow_with_uuid_or_name(workflow_id_or_name, user_uuid)
filename = full_file_name.split("/")[-1]
# Remove starting '/' in path
if full_file_name[0] == "/":
full_file_name = full_file_name[1:]
elif ".." in full_file_name.split("/"):
raise REANAUploadPathError('Path cannot contain "..".')
absolute_workspace_path = workflow.workspace_path
if len(full_file_name.split("/")) > 1:
dirs = full_file_name.split("/")[:-1]
absolute_workspace_path = os.path.join(
workflow.workspace_path, "/".join(dirs)
)
if not os.path.exists(absolute_workspace_path):
os.makedirs(absolute_workspace_path)
absolute_file_path = os.path.join(absolute_workspace_path, filename)
FileStorage(request.stream).save(absolute_file_path, buffer_size=32768)
# update user and workflow resource disk quota
store_workflow_disk_quota(workflow, bytes_to_sum=request.content_length)
update_users_disk_quota(workflow.owner, bytes_to_sum=request.content_length)
return (
jsonify(
{"message": "{} has been successfully uploaded.".format(full_file_name)}
),
200,
)
except ValueError:
return (
jsonify(
{
"message": "REANA_WORKON is set to {0}, but "
"that workflow does not exist. "
"Please set your REANA_WORKON environment"
"variable appropriately.".format(workflow_id_or_name)
}
),
404,
)
except KeyError as e:
return jsonify({"message": str(e)}), 400
except Exception as e:
return jsonify({"message": str(e)}), 500
def download_file(workflow_id_or_name, file_name): # noqa
r"""Download a file from the workspace.
---
get:
summary: Returns the requested file.
description: >-
This resource is expecting a workflow UUID and a filename existing
inside the workspace to return its content.
operationId: download_file
produces:
- multipart/form-data
parameters:
- name: user
in: query
description: Required. UUID of workflow owner.
required: true
type: string
- name: workflow_id_or_name
in: path
description: Required. Workflow UUID or name
required: true
type: string
- name: file_name
in: path
description: Required. Name (or path) of the file to be downloaded.
required: true
type: string
- name: preview
in: query
description: >-
Optional flag to return a previewable response of the file
(corresponding mime-type).
required: false
type: boolean
responses:
200:
description: >-
Requests succeeded. The file has been downloaded.
schema:
type: file
400:
description: >-
Request failed. The incoming data specification seems malformed.
404:
description: >-
Request failed. `file_name` does not exist.
examples:
application/json:
{
"message": "input.csv does not exist"
}
500:
description: >-
Request failed. Internal controller error.
examples:
application/json:
{
"message": "Internal workflow controller error."
}
"""
try:
user_uuid = request.args["user"]
user = User.query.filter(User.id_ == user_uuid).first()
if not user:
return jsonify({"message": "User {} does not exist".format(user)}), 404
workflow = _get_workflow_with_uuid_or_name(workflow_id_or_name, user_uuid)
workflow_name = workflow.get_full_workflow_name()
return download_files_recursive_wildcard(
workflow_name, workflow.workspace_path, file_name
)
except ValueError:
return (
jsonify(
{
"message": "REANA_WORKON is set to {0}, but "
"that workflow does not exist. "
"Please set your REANA_WORKON environment "
"variable appropriately.".format(workflow_id_or_name)
}
),
404,
)
except KeyError:
return jsonify({"message": "Malformed request."}), 400
except NotFound:
return jsonify({"message": "{0} does not exist.".format(file_name)}), 404
except Exception as e:
return jsonify({"message": str(e)}), 500
def delete_file(workflow_id_or_name, file_name): # noqa
r"""Delete a file from the workspace.
---
delete:
summary: Delete the specified file.
description: >-
This resource is expecting a workflow UUID and a filename existing
inside the workspace to be deleted.
operationId: delete_file
produces:
- application/json
parameters:
- name: user
in: query
description: Required. UUID of workflow owner.
required: true
type: string
- name: workflow_id_or_name
in: path
description: Required. Workflow UUID or name
required: true
type: string
- name: file_name
in: path
description: Required. Name (or path) of the file to be deleted.
required: true
type: string
responses:
200:
description: >-
Requests succeeded. The file has been downloaded.
schema:
type: file
404:
description: >-
Request failed. `file_name` does not exist.
examples:
application/json:
{
"message": "input.csv does not exist"
}
500:
description: >-
Request failed. Internal controller error.
examples:
application/json:
{
"message": "Internal workflow controller error."
}
"""
try:
user_uuid = request.args["user"]
user = User.query.filter(User.id_ == user_uuid).first()
if not user:
return jsonify({"message": "User {} does not exist".format(user)}), 404
workflow = _get_workflow_with_uuid_or_name(workflow_id_or_name, user_uuid)
deleted = remove_files_recursive_wildcard(workflow.workspace_path, file_name)
# update user and workflow resource disk quota
freed_up_bytes = sum(
size.get("size", 0) for size in deleted["deleted"].values()
)
store_workflow_disk_quota(workflow, bytes_to_sum=-freed_up_bytes)
update_users_disk_quota(user, bytes_to_sum=-freed_up_bytes)
return jsonify(deleted), 200
except ValueError:
return (
jsonify(
{
"message": "REANA_WORKON is set to {0}, but "
"that workflow does not exist. "
"Please set your REANA_WORKON environment "
"variable appropriately.".format(workflow_id_or_name)
}
),
404,
)
except KeyError:
return jsonify({"message": "Malformed request."}), 400
except NotFound:
return jsonify({"message": "{0} does not exist.".format(file_name)}), 404
except OSError:
return jsonify({"message": "Error while deleting {}.".format(file_name)}), 500
except Exception as e:
return jsonify({"message": str(e)}), 500
def open_interactive_session(workflow_id_or_name,
interactive_session_type): # noqa
r"""Start an interactive session inside the workflow workspace.
---
post:
summary: Start an interactive session inside the workflow workspace.
description: >-
This resource is expecting a workflow to start an interactive session
within its workspace.
operationId: open_interactive_session
consumes:
- application/json
produces:
- application/json
parameters:
- name: user
in: query
description: Required. UUID of workflow owner.
required: true
type: string
- name: workflow_id_or_name
in: path
description: Required. Workflow UUID or name.
required: true
type: string
- name: interactive_session_type
in: path
description: >-
Optional. Type of interactive session to use, by default Jupyter
Notebook.
required: false
type: string
- name: interactive_session_configuration
in: body
description: >-
Interactive session configuration.
required: false
schema:
type: object
properties:
image:
type: string
description: >-
Replaces the default Docker image of an interactive session.
responses:
200:
description: >-
Request succeeded. The interactive session has been opened.
schema:
type: object
properties:
path:
type: string
examples:
application/json:
{
"path": "/dd4e93cf-e6d0-4714-a601-301ed97eec60",
}
400:
description: >-
Request failed. The incoming data specification seems malformed.
examples:
application/json:
{
"message": "Malformed request."
}
404:
description: >-
Request failed. Either User or Workflow does not exist.
examples:
application/json:
{
"message": "Interactive session type terminl not found, try
with one of: [jupyter]"
}
application/json:
{
"message": "Workflow 256b25f4-4cfb-4684-b7a8-73872ef455a1
does not exist"
}
500:
description: >-
Request failed. Internal controller error.
"""
try:
if interactive_session_type not in INTERACTIVE_SESSION_TYPES:
return jsonify({
"message":
"Interactive session type {0} not found, try "
"with one of: {1}".format(interactive_session_type,
INTERACTIVE_SESSION_TYPES)
}), 404
interactive_session_configuration = request.json or {}
user_uuid = request.args["user"]
workflow = None
workflow = _get_workflow_with_uuid_or_name(workflow_id_or_name,
user_uuid)
kwrm = KubernetesWorkflowRunManager(workflow)
access_path = kwrm.start_interactive_session(
interactive_session_type,
image=interactive_session_configuration.get("image", None))
return jsonify({"path": "{}".format(access_path)}), 200
except (KeyError, ValueError) as e:
status_code = 400 if workflow else 404
return jsonify({"message": str(e)}), status_code
except Exception as e:
return jsonify({"message": str(e)}), 500
def close_interactive_session(workflow_id_or_name): # noqa
r"""Close an interactive workflow session.
---
post:
summary: Close an interactive workflow session.
description: >-
This resource is expecting a workflow to close an interactive session
within its workspace.
operationId: close_interactive_session
consumes:
- application/json
produces:
- application/json
parameters:
- name: user
in: query
description: Required. UUID of workflow owner.
required: true
type: string
- name: workflow_id_or_name
in: path
description: Required. Workflow UUID or name.
required: true
type: string
responses:
200:
description: >-
Request succeeded. The interactive session has been closed.
schema:
type: object
properties:
message:
type: string
examples:
application/json:
{
"message": "The interactive session has been closed",
}
400:
description: >-
Request failed. The incoming data specification seems malformed.
examples:
application/json:
{
"message": "Malformed request."
}
404:
description: >-
Request failed. Either User or Workflow does not exist.
examples:
application/json:
{
"message": "Workflow 256b25f4-4cfb-4684-b7a8-73872ef455a1
does not exist"
}
500:
description: >-
Request failed. Internal controller error.
"""
try:
user_uuid = request.args["user"]
workflow = None
workflow = _get_workflow_with_uuid_or_name(workflow_id_or_name,
user_uuid)
if workflow.interactive_session_name is None:
return jsonify({
"message":
"Workflow - {} has no open interactive session.".format(
workflow_id_or_name)
}), 404
kwrm = KubernetesWorkflowRunManager(workflow)
kwrm.stop_interactive_session()
return jsonify({"message":
"The interactive session has been closed"}), 200
except (KeyError, ValueError) as e:
status_code = 400 if workflow else 404
return jsonify({"message": str(e)}), status_code
except Exception as e:
return jsonify({"message": str(e)}), 500
def get_files(workflow_id_or_name): # noqa
r"""List all files contained in a workspace.
---
get:
summary: Returns the workspace file list.
description: >-
This resource retrieves the file list of a workspace, given
its workflow UUID.
operationId: get_files
produces:
- multipart/form-data
parameters:
- name: user
in: query
description: Required. UUID of workflow owner.
required: true
type: string
- name: workflow_id_or_name
in: path
description: Required. Workflow UUID or name.
required: true
type: string
responses:
200:
description: >-
Requests succeeded. The list of code|input|output files has been
retrieved.
schema:
type: array
items:
type: object
properties:
name:
type: string
last-modified:
type: string
size:
type: integer
400:
description: >-
Request failed. The incoming data specification seems malformed.
404:
description: >-
Request failed. Workflow does not exist.
examples:
application/json:
{
"message": "Workflow 256b25f4-4cfb-4684-b7a8-73872ef455a1 does
not exist."
}
500:
description: >-
Request failed. Internal controller error.
examples:
application/json:
{
"message": "Internal workflow controller error."
}
"""
try:
user_uuid = request.args["user"]
user = User.query.filter(User.id_ == user_uuid).first()
if not user:
return jsonify({"message": "User {} does not exist".format(user)}), 404
file_type = (
request.args.get("file_type") if request.args.get("file_type") else "input"
)
workflow = _get_workflow_with_uuid_or_name(workflow_id_or_name, user_uuid)
file_list = list_directory_files(
os.path.join(
current_app.config["SHARED_VOLUME_PATH"], workflow.workspace_path
)
)
return jsonify(file_list), 200
except ValueError:
return (
jsonify(
{
"message": "REANA_WORKON is set to {0}, but "
"that workflow does not exist. "
"Please set your REANA_WORKON environment "
"variable appropriately.".format(workflow_id_or_name)
}
),
404,
)
except KeyError:
return jsonify({"message": "Malformed request."}), 400
except CreateFailed:
return jsonify({"message": "Workspace does not exist."}), 404
except Exception as e:
return jsonify({"message": str(e)}), 500
def download_file(workflow_id_or_name, file_name): # noqa
r"""Download a file from the workspace.
---
get:
summary: Returns the requested file.
description: >-
This resource is expecting a workflow UUID and a filename existing
inside the workspace to return its content.
operationId: download_file
produces:
- multipart/form-data
parameters:
- name: user
in: query
description: Required. UUID of workflow owner.
required: true
type: string
- name: workflow_id_or_name
in: path
description: Required. Workflow UUID or name
required: true
type: string
- name: file_name
in: path
description: Required. Name (or path) of the file to be downloaded.
required: true
type: string
- name: preview
in: query
description: >-
Optional flag to return a previewable response of the file
(corresponding mime-type).
required: false
type: boolean
responses:
200:
description: >-
Requests succeeded. The file has been downloaded.
schema:
type: file
400:
description: >-
Request failed. The incoming data specification seems malformed.
404:
description: >-
Request failed. `file_name` does not exist.
examples:
application/json:
{
"message": "input.csv does not exist"
}
500:
description: >-
Request failed. Internal controller error.
examples:
application/json:
{
"message": "Internal workflow controller error."
}
"""
try:
user_uuid = request.args["user"]
user = User.query.filter(User.id_ == user_uuid).first()
if not user:
return jsonify({"message": "User {} does not exist".format(user)}), 404
workflow = _get_workflow_with_uuid_or_name(workflow_id_or_name, user_uuid)
absolute_workflow_workspace_path = os.path.join(
current_app.config["SHARED_VOLUME_PATH"], workflow.workspace_path
)
preview = json.loads(request.args.get("preview", "false").lower())
response_mime_type = "multipart/form-data"
file_mime_type = mimetypes.guess_type(file_name)[0]
# Only display image files as preview
if preview and file_mime_type and file_mime_type.startswith("image"):
response_mime_type = file_mime_type
return (
send_from_directory(
absolute_workflow_workspace_path,
file_name,
mimetype=response_mime_type,
as_attachment=True,
),
200,
)
except ValueError:
return (
jsonify(
{
"message": "REANA_WORKON is set to {0}, but "
"that workflow does not exist. "
"Please set your REANA_WORKON environment "
"variable appropriately.".format(workflow_id_or_name)
}
),
404,
)
except KeyError:
return jsonify({"message": "Malformed request."}), 400
except NotFound as e:
return jsonify({"message": "{0} does not exist.".format(file_name)}), 404
except Exception as e:
return jsonify({"message": str(e)}), 500
def delete_file(workflow_id_or_name, file_name): # noqa
r"""Delete a file from the workspace.
---
delete:
summary: Delete the specified file.
description: >-
This resource is expecting a workflow UUID and a filename existing
inside the workspace to be deleted.
operationId: delete_file
produces:
- application/json
parameters:
- name: user
in: query
description: Required. UUID of workflow owner.
required: true
type: string
- name: workflow_id_or_name
in: path
description: Required. Workflow UUID or name
required: true
type: string
- name: file_name
in: path
description: Required. Name (or path) of the file to be deleted.
required: true
type: string
responses:
200:
description: >-
Requests succeeded. The file has been downloaded.
schema:
type: file
404:
description: >-
Request failed. `file_name` does not exist.
examples:
application/json:
{
"message": "input.csv does not exist"
}
500:
description: >-
Request failed. Internal controller error.
examples:
application/json:
{
"message": "Internal workflow controller error."
}
"""
try:
user_uuid = request.args['user']
user = User.query.filter(User.id_ == user_uuid).first()
if not user:
return jsonify(
{'message': 'User {} does not exist'.format(user)}), 404
workflow = _get_workflow_with_uuid_or_name(workflow_id_or_name,
user_uuid)
abs_path_to_workspace = os.path.join(
current_app.config['SHARED_VOLUME_PATH'], workflow.workspace_path)
deleted = remove_files_recursive_wildcard(
abs_path_to_workspace, file_name)
return jsonify(deleted), 200
except ValueError:
return jsonify({'message': 'REANA_WORKON is set to {0}, but '
'that workflow does not exist. '
'Please set your REANA_WORKON environment '
'variable appropriately.'.
format(workflow_id_or_name)}), 404
except KeyError:
return jsonify({"message": "Malformed request."}), 400
except NotFound as e:
return jsonify(
{"message": "{0} does not exist.".format(file_name)}), 404
except OSError as e:
return jsonify(
{"message": "Error while deleting {}.".format(file_name)}), 500
except Exception as e:
return jsonify({"message": str(e)}), 500
