#!/usr/bin/env cwl-runner
### Creates helper tables for Medicare QC
# Copyright (c) 2022. Harvard University
#
# Developed by Research Software Engineering,
# Faculty of Arts and Sciences, Research Computing (FAS RC)
# Author: Michael A Bouzinier
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
cwlVersion: v1.2
class: Workflow
requirements:
SubworkflowFeatureRequirement: {}
StepInputExpressionRequirement: {}
InlineJavascriptRequirement: {}
doc: |
This workflow creates helper tables to be used in Quality Checks (QC)
for Medicare data
inputs:
database:
type: File
doc: Path to database connection file, usually database.ini
connection_name:
type: string
doc: The name of the section in the database.ini file
depends_on:
type: File?
doc: a special field used to enforce dependencies and execution order
steps:
create_enrl_qc_view:
run: create.cwl
doc: >
Creates a joined view with Beneficiaries and Enrollments tables
in:
database: database
connection_name: connection_name
table:
valueFrom: "qc_enrl_bene"
domain:
valueFrom: "medicare"
out: [ log, errors ]
create_adm_qc_view:
run: create.cwl
doc: >
Creates a union of admissions validated records and records
discarded because of validation issues
in:
database: database
connection_name: connection_name
table:
valueFrom: "qc_adm_union"
domain:
valueFrom: "medicare"
out: [ log, errors ]
create_enrollments_qc_table:
run: matview.cwl
doc: Creates a table with aggregate data for beneficiaries and enrollments
in:
depends_on: create_enrl_qc_view/log
table:
valueFrom: "qc_enrollments"
domain:
valueFrom: "medicare"
database: database
connection_name: connection_name
out:
- create_log
- index_log
- vacuum_log
- create_err
- index_err
- vacuum_err
create_admissions_qc_table:
run: matview.cwl
doc: Creates a table with aggregate data for inpatient admissions
in:
depends_on: create_adm_qc_view/log
table:
valueFrom: "qc_admissions"
domain:
valueFrom: "medicare"
database: database
connection_name: connection_name
out:
- create_log
- index_log
- vacuum_log
- create_err
- index_err
- vacuum_err
outputs:
ev_create_log:
type: File
outputSource: create_enrl_qc_view/log
ev_create_err:
type: File
outputSource: create_enrl_qc_view/errors
av_create_log:
type: File
outputSource: create_adm_qc_view/log
av_create_err:
type: File
outputSource: create_adm_qc_view/errors
enrollmen343_create_log:
type: File
outputSource: create_enrollments_qc_table/create_log
enrollmen343_index_log:
type: File
outputSource: create_enrollments_qc_table/index_log
enrollmen343_vacuum_log:
type: File
outputSource: create_enrollments_qc_table/vacuum_log
enrollmen343_create_err:
type: File
outputSource: create_enrollments_qc_table/create_err
enrollmen343_index_err:
type: File
outputSource: create_enrollments_qc_table/index_err
enrollmen343_vacuum_err:
type: File
outputSource: create_enrollments_qc_table/vacuum_err
admission697_create_log:
type: File
outputSource: create_admissions_qc_table/create_log
admission697_index_log:
type: File
outputSource: create_admissions_qc_table/index_log
admission697_vacuum_log:
type: File
outputSource: create_admissions_qc_table/vacuum_log
admission697_create_err:
type: File
outputSource: create_admissions_qc_table/create_err
admission697_index_err:
type: File
outputSource: create_admissions_qc_table/index_err
admission697_vacuum_err:
type: File
outputSource: create_admissions_qc_table/vacuum_err