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workflows.py
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workflows.py
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# -*- coding: utf-8 -*-
#
# This file is part of REANA.
# Copyright (C) 2018, 2019, 2020, 2021, 2022 CERN.
#
# REANA is free software; you can redistribute it and/or modify it
# under the terms of the MIT License; see LICENSE file for more details.
"""Reana-Server workflow-functionality Flask-Blueprint."""
import os
import json
import logging
import traceback
import requests
from bravado.exception import HTTPError
from flask import Blueprint, Response
from flask import jsonify, request, stream_with_context
from jsonschema.exceptions import ValidationError
from reana_commons import workspace
from reana_commons.config import REANA_WORKFLOW_ENGINES
from reana_commons.errors import REANAQuotaExceededError, REANAValidationError
from reana_commons.validation.operational_options import validate_operational_options
from reana_commons.validation.utils import validate_workflow_name
from reana_commons.specification import load_reana_spec
from reana_db.database import Session
from reana_db.models import InteractiveSessionType, RunStatus
from reana_db.utils import _get_workflow_with_uuid_or_name
from webargs import fields, validate
from webargs.flaskparser import use_kwargs
from reana_server.api_client import current_rwc_api_client
from reana_server.config import REANA_HOSTNAME
from reana_server.decorators import check_quota, signin_required
from reana_server.deleter import Deleter, InOrOut
from reana_server.validation import (
validate_inputs,
validate_workspace_path,
validate_workflow,
)
from reana_server.utils import (
_fail_gitlab_commit_build_status,
RequestStreamWithLen,
_load_and_save_yadage_spec,
_get_reana_yaml_from_gitlab,
prevent_disk_quota_excess,
publish_workflow_submission,
clone_workflow,
get_quota_excess_message,
get_workspace_retention_rules,
is_uuid_v4,
)
try:
from urllib import parse as urlparse
except ImportError:
from urlparse import urlparse
blueprint = Blueprint("workflows", __name__)
@blueprint.route("/workflows", methods=["GET"])
@use_kwargs(
{
"page": fields.Int(validate=validate.Range(min=1)),
"size": fields.Int(validate=validate.Range(min=1)),
"include_progress": fields.Bool(location="query"),
"include_workspace_size": fields.Bool(location="query"),
"workflow_id_or_name": fields.Str(),
}
)
@signin_required(token_required=False)
def get_workflows(user, **kwargs): # noqa
r"""Get all current workflows in REANA.
---
get:
summary: Returns list of all current workflows in REANA.
description: >-
This resource return all current workflows in JSON format.
operationId: get_workflows
produces:
- application/json
parameters:
- name: access_token
in: query
description: The API access_token of workflow owner.
required: false
type: string
- name: type
in: query
description: Required. Type of workflows.
required: true
type: string
- name: verbose
in: query
description: Optional flag to show more information.
required: false
type: boolean
- name: search
in: query
description: Filter workflows by name.
required: false
type: string
- name: sort
in: query
description: Sort workflows by creation date (asc, desc).
required: false
type: string
- name: status
in: query
description: Filter workflows by list of statuses.
required: false
type: array
items:
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: include_progress
in: query
description: Include progress information of the workflows.
type: boolean
- name: include_workspace_size
in: query
description: Include size information of the workspace.
type: boolean
- name: workflow_id_or_name
in: query
description: Optional analysis UUID or name to filter.
required: false
type: string
responses:
200:
description: >-
Request succeeded. The response contains the list of all workflows.
schema:
type: object
properties:
total:
type: integer
items:
type: array
items:
type: object
properties:
id:
type: string
name:
type: string
status:
type: string
size:
type: object
properties:
raw:
type: integer
human_readable:
type: string
user:
type: string
launcher_url:
type: string
x-nullable: true
created:
type: string
session_status:
type: string
session_type:
type: string
session_uri:
type: string
progress:
type: object
properties:
current_command:
type: string
x-nullable: true
current_step_name:
type: string
x-nullable: true
failed:
properties:
job_ids:
items:
type: string
type: array
total:
type: integer
type: object
finished:
properties:
job_ids:
items:
type: string
type: array
total:
type: integer
type: object
run_finished_at:
type: string
x-nullable: true
run_started_at:
type: string
x-nullable: true
run_stopped_at:
type: string
x-nullable: true
running:
properties:
job_ids:
items:
type: string
type: array
total:
type: integer
type: object
total:
properties:
job_ids:
items:
type: string
type: array
total:
type: integer
type: object
examples:
application/json:
[
{
"id": "256b25f4-4cfb-4684-b7a8-73872ef455a1",
"name": "mytest.1",
"status": "running",
"size":{
"raw": 10490000,
"human_readable": "10 MB"
},
"user": "00000000-0000-0000-0000-000000000000",
"created": "2018-06-13T09:47:35.66097",
},
{
"id": "3c9b117c-d40a-49e3-a6de-5f89fcada5a3",
"name": "mytest.2",
"status": "finished",
"size":{
"raw": 12580000,
"human_readable": "12 MB"
},
"user": "00000000-0000-0000-0000-000000000000",
"created": "2018-06-13T09:47:35.66097",
},
{
"id": "72e3ee4f-9cd3-4dc7-906c-24511d9f5ee3",
"name": "mytest.3",
"status": "created",
"size":{
"raw": 184320,
"human_readable": "180 KB"
},
"user": "00000000-0000-0000-0000-000000000000",
"created": "2018-06-13T09:47:35.66097",
},
{
"id": "c4c0a1a6-beef-46c7-be04-bf4b3beca5a1",
"name": "mytest.4",
"status": "created",
"size": {
"raw": 1074000000,
"human_readable": "1 GB"
},
"user": "00000000-0000-0000-0000-000000000000",
"created": "2018-06-13T09:47:35.66097",
}
]
400:
description: >-
Request failed. The incoming payload seems malformed.
schema:
type: object
properties:
message:
type: string
examples:
application/json:
{
"message": "Your request contains not valid JSON."
}
403:
description: >-
Request failed. User is not allowed to access workflow.
schema:
type: object
properties:
message:
type: string
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. User does not exist.
schema:
type: object
properties:
message:
type: string
examples:
application/json:
{
"message": "User 00000000-0000-0000-0000-000000000000 does not
exist."
}
500:
description: >-
Request failed. Internal controller error.
schema:
type: object
properties:
message:
type: string
examples:
application/json:
{
"message": "Something went wrong."
}
"""
try:
type_ = request.args.get("type", "batch")
search = request.args.get("search")
sort = request.args.get("sort", "desc")
status = request.args.getlist("status")
verbose = json.loads(request.args.get("verbose", "false").lower())
response, http_response = current_rwc_api_client.api.get_workflows(
user=str(user.id_),
type=type_,
search=search,
sort=sort,
status=status or None,
verbose=bool(verbose),
**kwargs,
).result()
return jsonify(response), http_response.status_code
except HTTPError as e:
logging.error(traceback.format_exc())
return jsonify(e.response.json()), e.response.status_code
except json.JSONDecodeError:
logging.error(traceback.format_exc())
return jsonify({"message": "Your request contains not valid JSON."}), 400
except ValueError as e:
logging.error(traceback.format_exc())
return jsonify({"message": str(e)}), 403
except Exception as e:
logging.error(traceback.format_exc())
return jsonify({"message": str(e)}), 500
@blueprint.route("/workflows", methods=["POST"])
@signin_required(include_gitlab_login=True)
def create_workflow(user): # noqa
r"""Create a workflow.
---
post:
summary: Creates a new workflow based on a REANA specification file.
description: >-
This resource is expecting a REANA specification in JSON format with
all the necessary information to instantiate a workflow.
operationId: create_workflow
consumes:
- application/json
produces:
- application/json
parameters:
- name: workflow_name
in: query
description: Name of the workflow to be created. If not provided
name will be generated.
required: true
type: string
# probably need to rename this to something more specific
- name: spec
in: query
description: Remote repository which contains a valid REANA
specification.
required: false
type: string
- name: reana_specification
in: body
description: REANA specification with necessary data to instantiate
a workflow.
required: false
schema:
type: object
- name: access_token
in: query
description: The API access_token of workflow owner.
required: false
type: string
responses:
201:
description: >-
Request succeeded. The workflow has been created.
schema:
type: object
properties:
message:
type: string
workflow_id:
type: string
workflow_name:
type: string
examples:
application/json:
{
"message": "The workflow has been successfully created.",
"workflow_id": "cdcf48b1-c2f3-4693-8230-b066e088c6ac",
"workflow_name": "mytest.1"
}
400:
description: >-
Request failed. The incoming payload seems malformed
schema:
type: object
properties:
message:
type: string
examples:
application/json:
{
"message": "Workflow name cannot be a valid UUIDv4."
}
403:
description: >-
Request failed. User is not allowed to access workflow.
schema:
type: object
properties:
message:
type: string
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. User does not exist.
schema:
type: object
properties:
message:
type: string
examples:
application/json:
{
"message": "User 00000000-0000-0000-0000-000000000000 does not
exist."
}
500:
description: >-
Request failed. Internal controller error.
schema:
type: object
properties:
message:
type: string
examples:
application/json:
{
"message": "Internal controller error."
}
501:
description: >-
Request failed. Not implemented.
"""
try:
if request.args.get("spec"):
return jsonify("Not implemented"), 501
if not request.is_json:
raise Exception(
"Either remote repository or REANA specification needs to be provided"
)
request_from_gitlab = "object_kind" in request.json
if request_from_gitlab:
(
reana_spec_file,
git_url,
workflow_name,
git_branch,
git_commit_sha,
) = _get_reana_yaml_from_gitlab(request.json, user.id_)
git_data = {
"git_url": git_url,
"git_branch": git_branch,
"git_commit_sha": git_commit_sha,
}
else:
git_data = {}
reana_spec_file = request.json
workflow_name = request.args.get("workflow_name", "")
if user.has_exceeded_quota() and request_from_gitlab:
message = f"User quota exceeded. Please check {REANA_HOSTNAME}"
_fail_gitlab_commit_build_status(user, git_url, git_commit_sha, message)
return jsonify({"message": "Gitlab webhook was processed"}), 200
elif user.has_exceeded_quota():
message = get_quota_excess_message(user)
raise REANAQuotaExceededError(message)
validate_workflow_name(workflow_name)
if is_uuid_v4(workflow_name):
return jsonify({"message": "Workflow name cannot be a valid UUIDv4."}), 400
workflow_engine = reana_spec_file["workflow"]["type"]
if workflow_engine not in REANA_WORKFLOW_ENGINES:
raise Exception("Unknown workflow type.")
operational_options = validate_operational_options(
workflow_engine, reana_spec_file.get("inputs", {}).get("options", {})
)
workspace_root_path = reana_spec_file.get("workspace", {}).get("root_path")
validate_workspace_path(reana_spec_file)
validate_inputs(reana_spec_file)
retention_days = reana_spec_file.get("workspace", {}).get("retention_days")
retention_rules = get_workspace_retention_rules(retention_days)
workflow_dict = {
"reana_specification": reana_spec_file,
"workflow_name": workflow_name,
"operational_options": operational_options,
"retention_rules": retention_rules,
}
if git_data:
workflow_dict["git_data"] = git_data
response, http_response = current_rwc_api_client.api.create_workflow(
workflow=workflow_dict,
user=str(user.id_),
workspace_root_path=workspace_root_path,
).result()
if git_data:
workflow = _get_workflow_with_uuid_or_name(
response["workflow_id"], str(user.id_)
)
# This is necessary for GitLab integration
if workflow.type_ == "yadage":
_load_and_save_yadage_spec(
workflow, workflow_dict["operational_options"]
)
elif workflow.type_ in ["cwl", "snakemake"]:
reana_yaml_path = os.path.join(workflow.workspace_path, "reana.yaml")
workflow.reana_specification = load_reana_spec(
reana_yaml_path, workflow.workspace_path
)
Session.commit()
parameters = request.json
publish_workflow_submission(workflow, user.id_, parameters)
return jsonify(response), http_response.status_code
except HTTPError as e:
logging.error(traceback.format_exc())
return jsonify(e.response.json()), e.response.status_code
except REANAQuotaExceededError as e:
return jsonify({"message": e.message}), 403
except (KeyError, REANAValidationError) as e:
logging.error(traceback.format_exc())
return jsonify({"message": str(e)}), 400
except ValueError as e:
logging.error(traceback.format_exc())
return jsonify({"message": str(e)}), 403
except Exception as e:
logging.error(traceback.format_exc())
return jsonify({"message": str(e)}), 500
@blueprint.route("/workflows/<workflow_id_or_name>/specification", methods=["GET"])
@signin_required()
def get_workflow_specification(workflow_id_or_name, user): # noqa
r"""Get workflow specification.
---
get:
summary: Get the specification used for this workflow run.
description: >-
This resource returns the REANA workflow specification used to start
the workflow run. Resource is expecting a workflow UUID.
operationId: get_workflow_specification
produces:
- application/json
parameters:
- name: access_token
in: query
description: API access_token of workflow owner.
required: false
type: string
- name: workflow_id_or_name
in: path
description: Required. Analysis UUID or name.
required: true
type: string
responses:
200:
description: >-
Request succeeded. Workflow specification is returned.
schema:
type: object
properties:
parameters:
type: object
specification:
type: object
properties:
inputs:
type: object
properties:
files:
type: array
items:
type: string
directories:
type: array
items:
type: string
parameters:
type: object
options:
type: object
outputs:
type: object
properties:
files:
type: array
items:
type: string
directories:
type: array
items:
type: string
version:
type: string
workflow:
type: object
properties:
specification:
type: object
x-nullable: true
properties:
steps:
type: array
items:
type: object
type:
type: string
file:
type: string
examples:
application/json:
{
"parameters": {},
"specification": {
"inputs": {
"files": [
"code/helloworld.py",
"data/names.txt"
],
"parameters": {
"helloworld": "code/helloworld.py",
"inputfile": "data/names.txt",
"outputfile": "results/greetings.txt",
"sleeptime": 0
}
},
"outputs": {
"files": [
"results/greetings.txt"
]
},
"version": "0.3.0",
"workflow": {
"specification": {
"steps": [
{
"commands": [
"python \"${helloworld}\" --inputfile \"${inputfile}\" --outputfile \"${outputfile}\" --sleeptime ${sleeptime}"
],
"environment": "python:2.7-slim"
}
]
},
"type": "serial"
}
}
}
403:
description: >-
Request failed. User is not allowed to access workflow.
schema:
type: object
properties:
message:
type: string
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. User 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.
schema:
type: object
properties:
message:
type: string
examples:
application/json:
{
"message": "Internal controller error."
}
"""
try:
if not workflow_id_or_name:
raise ValueError("workflow_id_or_name is not supplied")
workflow = _get_workflow_with_uuid_or_name(workflow_id_or_name, str(user.id_))
return (
jsonify(
{
"specification": workflow.reana_specification,
"parameters": workflow.input_parameters,
}
),
200,
)
except HTTPError as e:
logging.error(traceback.format_exc())
return jsonify(e.response.json()), e.response.status_code
except ValueError as e:
logging.error(traceback.format_exc())
return jsonify({"message": str(e)}), 403
except Exception as e:
logging.error(traceback.format_exc())
return jsonify({"message": str(e)}), 500
@blueprint.route("/workflows/<workflow_id_or_name>/logs", methods=["GET"])
@use_kwargs(
{
"page": fields.Int(validate=validate.Range(min=1)),
"size": fields.Int(validate=validate.Range(min=1)),
}
)
@signin_required()
def get_workflow_logs(workflow_id_or_name, user, **kwargs): # noqa
r"""Get workflow logs.
---
get:
summary: Get workflow logs of a workflow.
description: >-
This resource reports the status of a workflow.
Resource is expecting a workflow UUID.
operationId: get_workflow_logs
produces:
- application/json
parameters:
- name: access_token
in: query
description: API access_token of workflow owner.
required: false
type: string
- name: workflow_id_or_name
in: path
description: Required. Analysis 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.
- 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
responses:
200:
description: >-
Request succeeded. Info about a 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 engine log output>",
"user": "00000000-0000-0000-0000-000000000000"
}
400:
description: >-
Request failed. The incoming data specification seems malformed.
schema:
type: object
properties:
message:
type: string
examples:
application/json:
{
"message": "Malformed request."
}
403:
description: >-
Request failed. User is not allowed to access workflow.
schema:
type: object
properties:
message:
type: string
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. User 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.
schema:
type: object
properties:
message:
type: string
examples:
application/json:
{
"message": "Internal controller error."
}
"""
try:
steps = request.json if request.is_json else None
if not workflow_id_or_name:
raise ValueError("workflow_id_or_name is not supplied")
response, http_response = current_rwc_api_client.api.get_workflow_logs(
user=str(user.id_),
steps=steps or None,
workflow_id_or_name=workflow_id_or_name,
**kwargs,
).result()
return jsonify(response), http_response.status_code
except HTTPError as e:
logging.error(traceback.format_exc())
return jsonify(e.response.json()), e.response.status_code
except ValueError as e:
logging.error(traceback.format_exc())
return jsonify({"message": str(e)}), 403
except Exception as e:
logging.error(traceback.format_exc())
return jsonify({"message": str(e)}), 500
@blueprint.route("/workflows/<workflow_id_or_name>/status", methods=["GET"])
@signin_required()
def get_workflow_status(workflow_id_or_name, user): # noqa
r"""Get workflow status.
---
get:
summary: Get status of a workflow.
description: >-
This resource reports the status of a workflow.
Resource is expecting a workflow UUID.
operationId: get_workflow_status
produces:
- application/json
parameters:
- name: workflow_id_or_name
in: path
description: Required. Analysis UUID or name.
required: true
type: string
- name: access_token
in: query
description: The API access_token of workflow owner.
required: false
type: string
responses:
200:
description: >-
Request succeeded. Info about a 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
progress:
type: object
properties:
run_started_at:
type: string
x-nullable: true
run_finished_at:
type: string
x-nullable: true
run_stopped_at:
type: string
x-nullable: true
total:
type: object
properties:
total:
type: integer
job_ids:
type: array