pbcommand Client to SMRT Link Services and Service Data Models¶

Python client to SMRT Link Services and Service Data Models

class pbcommand.services.ServiceAccessLayer(base_url, port, debug=False, sleep_time=2)[source]¶

Bases: object

General Client Access Layer for interfacing with the job types on SMRT Link Analysis Services

Parameters:	base_url – base url of the SL Server (e.g, smrtlink-alpha, or http://smrtlink-alpha) port – port of the SL server debug – set improved debugging output on Services request failures sleep_time – sleep time (in seconds) between polling for job status

JOB_DEFAULT_TIMEOUT = 1800¶

ROOT_DS = '/secondary-analysis/datasets'¶

ROOT_JM = '/secondary-analysis/job-manager'¶

ROOT_JOBS = '/secondary-analysis/job-manager/jobs'¶

ROOT_PT = '/secondary-analysis/resolved-pipeline-templates'¶

create_by_pipeline_template_id(name, pipeline_template_id, epoints, task_options=())[source]¶

Creates and runs a pbsmrtpipe pipeline by pipeline template id

create_logger_resource(idx, name, description)[source]¶

get_alignmentset_by_id(int_or_uuid)[source]¶

get_alignmentsets()[source]¶

get_analysis_job_by_id(job_id)[source]¶

Get an Analysis job by id or UUID or return None

Return type:	ServiceJob

get_analysis_job_datastore(job_id)[source]¶

Get DataStore output from (pbsmrtpipe) analysis job

get_analysis_job_entry_points(job_id)[source]¶

get_analysis_job_report_attrs(job_id)[source]¶

Return a dict of all the Report Attributes

get_analysis_job_report_details(job_id, report_uuid)[source]¶

get_analysis_job_reports(job_id)[source]¶

Get list of DataStore ReportFile types output from (pbsmrtpipe) analysis job

get_analysis_job_tasks(job_id_or_uuid)[source]¶

Get all the Task associated with a Job by UUID or Int Id

get_analysis_jobs()[source]¶

Return type:	list[ServiceJob]

get_barcodeset_by_id(int_or_uuid)[source]¶

get_barcodesets()[source]¶

get_ccsreadset_by_id(int_or_uuid)[source]¶

get_ccsreadsets()[source]¶

get_dataset_by_id(dataset_type, int_or_uuid)[source]¶

Get a Dataset using the DataSetMetaType and (int|uuid) of the dataset

get_dataset_by_uuid(int_or_uuid, ignore_errors=False)[source]¶

The recommend model is to look up DataSet type by explicit MetaType

Returns None if the dataset was not found

get_fasta_convert_jobs()[source]¶

Return type:	list[ServiceJob]

get_hdfsubreadset_by_id(int_or_uuid)[source]¶

get_hdfsubreadsets()[source]¶

get_import_dataset_job_datastore(job_id)[source]¶

Get a List of Service DataStore files from an import DataSet job

get_import_dataset_jobs()[source]¶

Return type:	list[ServiceJob]

get_import_job_by_id(job_id)[source]¶

get_import_job_report_attrs(job_id)[source]¶

Return a dict of all the Report Attributes

get_import_job_report_details(job_id, report_uuid)[source]¶

get_import_job_reports(job_id)[source]¶

get_import_job_tasks(job_id_or_uuid)[source]¶

get_job_by_id(job_id)[source]¶

Get a Job by int id

get_job_by_type_and_id(job_type, job_id)[source]¶

get_merge_dataset_job_datastore(job_id)[source]¶

get_merge_dataset_jobs()[source]¶

Return type:	list[ServiceJob]

get_pipeline_template_by_id(pipeline_template_id)[source]¶

get_referenceset_by_id(int_or_uuid)[source]¶

get_referencesets()[source]¶

get_status()[source]¶

Get status of the server

Return type:	dict

get_subreadset_by_id(int_or_uuid)[source]¶

get_subreadsets()[source]¶

import_dataset_barcode(path)[source]¶

import_dataset_hdfsubread(path)[source]¶

import_dataset_reference(path)[source]¶

import_dataset_subread(path)[source]¶

import_fasta(fasta_path, name, organism, ploidy)[source]¶

Convert fasta file to a ReferenceSet and Import. Returns a Job

log_progress_update(job_type_id, job_id, message, level, source_id)[source]¶

This is the generic job logging mechanism

run_by_pipeline_template_id(name, pipeline_template_id, epoints, task_options=(), time_out=1800)[source]¶

Blocks and runs a job with a timeout

run_import_dataset_barcode(path, time_out=10)[source]¶

run_import_dataset_by_type(dataset_type, path_to_xml)[source]¶

run_import_dataset_hdfsubread(path, time_out=10)[source]¶

run_import_dataset_reference(path, time_out=10)[source]¶

run_import_dataset_subread(path, time_out=10)[source]¶

run_import_fasta(fasta_path, name, organism, ploidy, time_out=1800)[source]¶

Import a Reference into a Block

run_import_local_dataset(path)[source]¶

Import a file from FS that is local to where the services are running

Returns a JobResult instance

Return type:	JobResult

to_summary()[source]¶

Returns a summary of System status, DataSets, and Jobs in the system

Return type:	str

uri¶

class pbcommand.services.ServiceJob(ix, job_uuid, name, state, path, job_type, created_at, settings, is_active=True, smrtlink_version=None, created_by=None, updated_at=None, error_message=None)[source]¶

Bases: object

Parameters:

ix (int) – Job Integer Id job_uuid (str) – Globally unique Job UUID name (str) – Display name of job state (str) – Job State path – Absolute Path to the job directory job_type (str) – Job Type created_at (DateTime) – when the job was created at settings (dict) – dict of job specific settings is_active (bool) – If the Job is active (only active jobs are displayed in the SL UI) smrtlink_version (str | None) – SMRT Link Version (if known) created_by (str | None) – User that created the job updated_at (DateTime | None) – when the last update of the job occurred error_message (str | None) – Error message if the job has failed

static from_d(d)[source]¶

Convert from Service JSON response to ServiceJob instance

was_successful()[source]¶

Return type:	bool

class pbcommand.services.JobTypes[source]¶

Bases: object

SMRT Link Analysis JOb Types

classmethod ALL()[source]¶

ALL allowed SL Analysis Job Types

CONVERT_FASTA = 'convert-fasta-reference'¶

IMPORT_DS = 'import-dataset'¶

IMPORT_DSTORE = 'import-datastore'¶

MERGE_DS = 'merge-datasets'¶

MOCK_PB_PIPE = 'mock-pbsmrtpipe'¶

PB_PIPE = 'pbsmrtpipe'¶

class pbcommand.services.JobStates[source]¶

Bases: object

Allowed SMRT Link Service Job states

ALL = ('RUNNING', 'CREATED', 'FAILED', 'SUCCESSFUL', 'SUBMITTED')¶

ALL_COMPLETED = ('FAILED', 'SUCCESSFUL')¶

CREATED = 'CREATED'¶

FAILED = 'FAILED'¶

RUNNING = 'RUNNING'¶

SUBMITTED = 'SUBMITTED'¶

SUCCESSFUL = 'SUCCESSFUL'¶

class pbcommand.services.ServiceEntryPoint(entry_id, dataset_type, path_or_uri)[source]¶

Bases: object

Entry Points to initialize Pipelines

static from_d(d)[source]¶

Convert from Service JSON response to ServiceEntryPoint instance

resource¶

Backwards compatible with path_or_uri

to_d()[source]¶