BaseTask¶
The base class for most ClarityNLP tasks. Provides most of the wiring needed to run individual algorithms.
Arguments¶
| Name | Type | Required | Notes |
|---|---|---|---|
| termset | termset | See implementation | |
| excluded_termset | termset | No | If terms are present, feature should be excluded from results (depends on task implementation) |
| documentset | documentset | No | |
| cohort | cohort | No |
Results¶
| Name | Type | Notes |
|---|---|---|
| pipeline_type | str | Pipeline type internal to ClarityNLP. |
| pipeline_id | int | Pipeline ID internal to ClarityNLP. |
| job_id | int | Job ID |
| batch | int | Batch number of documents |
| owner | str | Job owner |
| nlpql_feature | str | Feature used in NLPQL define |
| inserted_date | date | Date result written to data store |
| concept_code | int | Code specified by user to assign to OMOP concept id. |
| phenotype_final | bool | final flag designated in NLPQL; displays in final results |
| report_id | str | Document report ID, if document level result |
| subject | str | Document subject/patient, if document level result |
| report_date | str | Document report date, if document level result |
| report_type | str | Document report type, if document level result |
| source | str | Document source, if document level result |
| solr_id | str | Document Solr id field, if document level result |
Functions¶
run()¶
Main function that sets up documents and runs the task execution.
output()¶
Gets Luigi file, used for job communication or temp output.
set_name(name)¶
Sets name of task.
write_result_data(temp_file: File, mongo_client: MongoClient, doc: dict, data: dict, prefix: str=’’, phenotype_final: bool=False)¶
Writes results to MongoDB.
write_multiple_result_data(temp_file: File, mongo_client: MongoClient, doc: dict, data: list, prefix: str=’’)¶
Writes results to MongoDB as a list.
write_log_data(job_status: str, status_message: str)¶
Writes log message to the job_status table.
run_custom_task(temp_file: File, mongo_client: MongoClient)¶
The primary function for tasks to implement to run tasks.
get_document_text(doc: dict, clean=True)¶
Returns a string containing the text of a given Solr document.
get_boolean(key: str, default=False)¶
Looks up custom argument with matching key of type bool.
get_integer(key: str, default=-1)¶
Looks up custom argument with matching key of type int.
get_string(key: str, default=’’)¶
Looks up custom argument with matching key of type str.