3. API¶

3.1. REANA API client¶

REANA REST API base client.

class reana_commons.api_client.BaseAPIClient(service, http_client=None)¶: REANA API client code.

class reana_commons.api_client.JobControllerAPIClient(service, http_client=None)¶

REANA-Job-Controller http client class.

check_if_cached(job_spec, step, workflow_workspace)¶: Check if job result is in cache.

check_status(job_id)¶: Check status of a job.

get_logs(job_id)¶: Get logs of a job.

submit(workflow_uuid='', experiment='', image='', cmd='', prettified_cmd='', workflow_workspace='', job_name='', cvmfs_mounts='false', compute_backend=None, kerberos=False, kubernetes_uid=None, unpacked_img=False, voms_proxy=False)¶

Submit a job to RJC API.

Workflow_workspace:
Parameters:	job_name – Name of the job. experiment – Experiment the job belongs to. image – Identifier of the Docker image which will run the job. cmd – String which represents the command to execute. It can be modified by the workflow engine i.e. prepending `cd /some/dir/`.
Prettified_cmd:	Original command submitted by the user.
	Path to the workspace of the workflow.
Cvmfs_mounts:	String with CVMFS volumes to mount in job pods.
Compute_backend:
	Job compute backend.
Kerberos:	Decides if kerberos should be provided for job container.
Voms_proxy:	Decides if grid proxy should be provided for job container.
Kubernetes_uid:	Overwrites the default user id in the job container.
Unpacked_img:	Decides if unpacked iamges should be used.
Returns:	Returns a dict with the `job_id`.

reana_commons.api_client.get_current_api_client(component)¶: Proxy which returns current API client for a given component.

3.2. REANA Kubernetes API client¶

Kubernetes API Client.

reana_commons.k8s.api_client.create_api_client(api='BatchV1')¶

Create Kubernetes API client using config.

Parameters:	api – String which represents which Kubernetes API to spawn. By default BatchV1.
Returns:	Kubernetes python client object for a specific API i.e. BatchV1.

REANA Kubernetes volumes.

reana_commons.k8s.volumes.get_k8s_cvmfs_volume(repository)¶

Render k8s CVMFS volume template.

Parameters:	repository – CVMFS repository to be mounted.
Returns:	k8s CVMFS volume spec as a dictionary.

reana_commons.k8s.volumes.get_reana_shared_volume()¶

Return REANA shared volume as k8s spec.

Depending on the configured storage backend REANA will use just a local volume in the host VM or a persistent volume claim which provides access to a network file system.

Returns:	k8s shared volume spec as a dictionary.

reana_commons.k8s.volumes.get_shared_volume(workflow_workspace)¶

Get shared CephFS/hostPath volume to a given job spec.

Parameters:	workflow_workspace – Absolute path to the job’s workflow workspace.
Returns:	Tuple consisting of the Kubernetes volumeMount and the volume.

3.3. REANA AMQP Publisher¶

REANA-Commons module to manage AMQP connections on REANA.

class reana_commons.publisher.BasePublisher(queue, routing_key, connection=None, exchange=None, durable=False)¶

Base publisher to MQ.

close()¶: Close connection.

class reana_commons.publisher.WorkflowStatusPublisher(**kwargs)¶

Progress publisher to MQ.

publish_workflow_status(workflow_uuid, status, logs='', message=None)¶

Publish workflow status using the configured.

Parameters:

workflow_uudid – String which represents the workflow UUID.
status – Integer which represents the status of the workflow, this is defined in the reana-db Workflow models.
logs – String which represents the logs which the workflow has produced as output.
message – Dictionary which includes additional information can be attached such as the overall progress of the workflow.

class reana_commons.publisher.WorkflowSubmissionPublisher(**kwargs)¶

Workflow submission publisher.

publish_workflow_submission(user_id, workflow_id_or_name, parameters)¶: Publish workflow submission parameters.

3.4. REANA AMQP Consumer¶

REANA-Commons module to manage AMQP consuming on REANA.

class reana_commons.consumer.BaseConsumer(queue=None, connection=None, message_default_format=None)¶

Base RabbitMQ consumer.

get_consumers(Consumer, channel)¶

Map consumers to specific queues.

Parameters:	Consumer – A `kombu.Consumer` to use for instantiating consumers. channel – A `kombu.transport.virtual.AbstractChannel`.

on_message(body, message)¶

Implement this method to manipulate the data received.

Parameters:	body – The received message already decoded in the specified format. message – A `kombu.transport.virtual.Message`.

3.5. REANA Serial workflow utilities¶

REANA Workflow Engine Serial implementation utils.

reana_commons.serial.serial_load(workflow_file, specification, parameters=None, original=None, **kwargs)¶

Validate and return a expanded REANA Serial workflow specification.

Parameters:	workflow_file – A specification file compliant with REANA Serial workflow specification.
Returns:	A dictionary which represents the valid Serial workflow with all parameters expanded.

3.6. REANA utilities¶

REANA-Commons utils.

reana_commons.utils.build_caching_info_message(job_spec, job_id, workflow_workspace, workflow_json, result_path)¶: Build the caching info message with correct formatting.

reana_commons.utils.build_progress_message(total=None, running=None, finished=None, failed=None, cached=None)¶: Build the progress message with correct formatting.

reana_commons.utils.build_unique_component_name(component_type, id=None)¶

Use REANA component type and id build a human readable component name.

Parameters:	component_type – One of `reana_commons.config.REANA_COMPONENT_TYPES`. id – Unique identifier, if not specified a new UUID4 is created.
Returns:	String representing the component name, i.e. reana-run-job-123456.

reana_commons.utils.calculate_file_access_time(workflow_workspace)¶: Calculate access times of files in workspace.

reana_commons.utils.calculate_hash_of_dir(directory, file_list=None)¶: Calculate hash of directory.

reana_commons.utils.calculate_job_input_hash(job_spec, workflow_json)¶: Calculate md5 hash of job specification and workflow json.

reana_commons.utils.check_connection_to_job_controller(port=5000)¶: Check connection from workflow engine to job controller.

reana_commons.utils.click_table_printer(headers, _filter, data)¶: Generate space separated output for click commands.

reana_commons.utils.copy_openapi_specs(output_path, component)¶: Copy generated and validated openapi specs to reana-commons module.

reana_commons.utils.create_cvmfs_persistent_volume_claim(cvmfs_volume)¶: Create CVMFS persistent volume claim.

reana_commons.utils.create_cvmfs_storage_class(cvmfs_volume)¶: Create CVMFS storage class.

reana_commons.utils.format_cmd(cmd)¶: Return command in a valid format.

reana_commons.utils.get_workflow_status_change_verb(status)¶

Give the correct verb conjugation depending on status tense.

Parameters:	status – String which represents the status the workflow changed to.

reana_commons.utils.get_workspace_disk_usage(workspace, summarize=False, block_size=None)¶: Retrieve disk usage information of a workspace.

reana_commons.utils.render_cvmfs_pvc(cvmfs_volume)¶: Render REANA_CVMFS_PVC_TEMPLATE.

reana_commons.utils.render_cvmfs_sc(cvmfs_volume)¶: Render REANA_CVMFS_SC_TEMPLATE.

3.7. REANA errors¶

REANA Commons errors.

exception reana_commons.errors.MissingAPIClientConfiguration¶: REANA Server URL is not set.

exception reana_commons.errors.REANASecretAlreadyExists¶: The referenced secret already exists.

exception reana_commons.errors.REANASecretDoesNotExist(missing_secrets_list=None)¶: The referenced REANA secret does not exist.

exception reana_commons.errors.REANAValidationError(message)¶: Validation error.