Merge d6c6588 into 75933d5

AUTHORS.rst

@@ -8,6 +8,7 @@ The list of contributors in alphabetical order:
 - `Dinos Kousidis <https://orcid.org/0000-0002-4914-4289>`_
 - `Harri Hirvonsalo <https://orcid.org/0000-0002-5503-510X>`_
 - `Jan Okraska <https://orcid.org/0000-0002-1416-3244>`_
+- `Leticia Wanderley <https://orcid.org/0000-0003-4649-6630>`_
 - `Lukas Heinrich <https://orcid.org/0000-0002-4048-7584>`_
 - `Rokas Maciulaitis <https://orcid.org/0000-0003-1064-6967>`_
 - `Sinclert Perez <https://www.linkedin.com/in/sinclert>`_

Dockerfile

@@ -12,6 +12,10 @@ RUN apt-get update && \
       vim-tiny && \
     pip install --upgrade pip
 
+RUN apt-get update && \
+    apt-get upgrade -y && \
+    apt-get install -y git
+
 COPY CHANGES.rst README.rst setup.py /code/
 COPY reana_workflow_controller/version.py /code/reana_workflow_controller/
 

docs/openapi.json

@@ -143,6 +143,10 @@
             "required": true,
             "schema": {
               "properties": {
+                "git_data": {
+                  "description": "GitLab data.",
+                  "type": "object"
+                },
                 "operational_options": {
                   "description": "Operational options.",
                   "type": "object"

reana_workflow_controller/config.py

@@ -114,3 +114,12 @@
 
 WORKFLOW_ENGINE_NAME = 'workflow-engine'
 """Default workflow engine container name."""
+
+REANA_GITLAB_HOST = os.getenv('REANA_GITLAB_HOST', 'CHANGE_ME')
+"""GitLab API HOST"""
+
+REANA_GITLAB_URL = 'https://{}'.format(REANA_GITLAB_HOST)
+"""GitLab API URL"""
+
+REANA_URL = os.getenv('REANA_URL', 'CHANGE_ME')
+"""REANA URL"""

reana_workflow_controller/consumer.py

@@ -13,17 +13,20 @@
 import json
 import uuid
 
+import requests
 from kubernetes.client.rest import ApiException
 from reana_commons.consumer import BaseConsumer
 from reana_commons.k8s.api_client import current_k8s_batchv1_api_client
+from reana_commons.k8s.secrets import REANAUserSecretsStore
 from reana_commons.utils import (calculate_file_access_time,
                                  calculate_hash_of_dir,
                                  calculate_job_input_hash)
 from reana_db.database import Session
 from reana_db.models import Job, JobCache, Workflow, WorkflowStatus
 from sqlalchemy.orm.attributes import flag_modified
 
-from reana_workflow_controller.config import PROGRESS_STATUSES
+from reana_workflow_controller.config import (PROGRESS_STATUSES,
+                                              REANA_GITLAB_URL, REANA_URL)
 from reana_workflow_controller.errors import REANAWorkflowControllerError
 
 
@@ -67,12 +70,37 @@ def _update_workflow_status(workflow_uuid, status, logs):
     """Update workflow status in DB."""
     Workflow.update_workflow_status(Session, workflow_uuid,
                                     status, logs, None)
+    workflow = Session.query(Workflow).filter_by(id_=workflow_uuid)\
+        .one_or_none()
+    if workflow.git_ref:
+        _update_commit_status(workflow, status)
     alive_statuses = \
         [WorkflowStatus.created, WorkflowStatus.running, WorkflowStatus.queued]
     if status not in alive_statuses:
         _delete_workflow_engine_pod(workflow_uuid)
 
 
+def _update_commit_status(workflow, status):
+    if status == WorkflowStatus.finished:
+        state = "success"
+    elif status == WorkflowStatus.failed:
+        state = "failed"
+    elif status == WorkflowStatus.stopped or status == WorkflowStatus.deleted:
+        state = "canceled"
+    else:
+        state = "running"
+    secret_store = REANAUserSecretsStore(workflow.owner_id)
+    gitlab_access_token = secret_store.get_secret_value('gitlab_access_token')
+    target_url = REANA_URL + "/api/workflows/{0}/logs".format(workflow.id_)
+    commit_status_url = REANA_GITLAB_URL + "/api/v4/projects/{0}/" + \
+        "statuses/{1}?access_token={2}&state={3}&target_url={4}"
+    requests.post(commit_status_url.format(workflow.name,
+                                           workflow.git_ref,
+                                           gitlab_access_token,
+                                           state,
+                                           target_url))
+
+
 def _update_run_progress(workflow_uuid, msg):
     """Register succeeded Jobs to DB."""
     workflow = Session.query(Workflow).filter_by(id_=workflow_uuid).\

reana_workflow_controller/rest.py

@@ -249,6 +249,10 @@ def create_workflow():  # noqa
               workflow_name:
                 type: string
                 description: Workflow name. If empty name will be generated.
+              git_data:
+                type: object
+                description: >-
+                  GitLab data.
             required: [reana_specification,
                        workflow_name,
                        operational_options]
@@ -306,6 +310,10 @@ def create_workflow():  # noqa
                 # `workflow_name` contains something else than just ASCII.
                 raise REANAWorkflowNameError('Workflow name {} is not valid.'.
                                              format(workflow_name))
+        git_ref = ''
+        if 'git_data' in request.json:
+            git_data = request.json['git_data']
+            git_ref = git_data['git_commit_sha']
         # add spec and params to DB as JSON
         workflow = Workflow(id_=workflow_uuid,
                             name=workflow_name,
@@ -317,9 +325,17 @@ def create_workflow():  # noqa
                             type_=request.json[
                                 'reana_specification']['workflow']['type'],
                             logs='')
+        workflow.git_ref = git_ref
         Session.add(workflow)
         Session.object_session(workflow).commit()
-        create_workflow_workspace(workflow.get_workspace())
+        if git_ref:
+            create_workflow_workspace(workflow.get_workspace(),
+                                      user_id=user.id_,
+                                      git_url=git_data['git_url'],
+                                      git_branch=git_data['git_branch'],
+                                      git_ref=git_ref)
+        else:
+            create_workflow_workspace(workflow.get_workspace())
         return jsonify({'message': 'Workflow workspace created',
                         'workflow_id': workflow.id_,
                         'workflow_name': _get_workflow_name(workflow)}), 201

reana_workflow_controller/utils.py

@@ -12,14 +12,18 @@
 
 import fs
 from flask import current_app as app
+from git import Repo
 from reana_commons.config import REANA_WORKFLOW_UMASK
+from reana_commons.k8s.secrets import REANAUserSecretsStore
 from reana_db.database import Session
 from reana_db.models import Job, JobCache
 
-from reana_workflow_controller.config import WORKFLOW_TIME_FORMAT
+from reana_workflow_controller.config import (REANA_GITLAB_HOST,
+                                              WORKFLOW_TIME_FORMAT)
 
 
-def create_workflow_workspace(path):
+def create_workflow_workspace(path, user_id=None,
+                              git_url=None, git_branch=None, git_ref=None):
     """Create workflow workspace.
 
     :param path: Relative path to workspace directory.
@@ -28,6 +32,17 @@ def create_workflow_workspace(path):
     os.umask(REANA_WORKFLOW_UMASK)
     reana_fs = fs.open_fs(app.config['SHARED_VOLUME_PATH'])
     reana_fs.makedirs(path, recreate=True)
+    if git_url and git_ref:
+        secret_store = REANAUserSecretsStore(user_id)
+        gitlab_access_token = secret_store\
+            .get_secret_value('gitlab_access_token')
+        url = "https://oauth2:{0}@{1}/{2}.git"\
+            .format(gitlab_access_token, REANA_GITLAB_HOST, git_url)
+        repo = Repo.clone_from(url=url,
+                               to_path=os.path.abspath(
+                                   reana_fs.root_path + '/' + path),
+                               branch=git_branch)
+        repo.head.reset(commit=git_ref)
 
 
 def list_directory_files(directory):

setup.py

@@ -47,6 +47,7 @@
     'Flask-SQLAlchemy>=2.2',
     'Flask>=0.12',
     'fs>=2.0',
+    'gitpython>=2.1',
     'jsonpickle>=0.9.6',
     'marshmallow>=2.13',
     'packaging>=18.0',