#!/usr/bin/env cwl-runner
### Process Medicare inpatient admissions data inside the database
# 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 processes raw Medicare admissions (aka Medpar or inpatient
admissions - ip) data. The assumed initial state
is that raw data (medpar files) are already in the database. We assume
that the data for each year is in a separate table. The first step
combines these disparate tables into a single view, creating uniform
columns.
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
limit:
type: string?
doc: limit number of records processed (for debugging)
depends_on:
type: File?
doc: a special field used to enforce dependencies and execution order
steps:
create_ip:
run: medicare_combine_tables.cwl
doc: >
Combines patient summaries from disparate summary tables
(one table per year) into a single view: medicare.ip
in:
database: database
connection_name: connection_name
table:
valueFrom: "ip"
out: [ log, errors ]
create_admissions_table:
run: create.cwl
doc: Create empty admissions table based on medicare.ip view
in:
database: database
connection_name: connection_name
domain:
valueFrom: "medicare"
table:
valueFrom: "admissions"
depends_on: create_ip/log
out: [ log, errors ]
populate_admissions_table:
run: create.cwl
doc: Creates `Enrollments` Table from the view
in:
depends_on: create_admissions_table/log
table:
valueFrom: "admissions"
domain:
valueFrom: "medicare"
action:
valueFrom: "insert"
database: database
limit: limit
connection_name: connection_name
out: [ log, errors ]
index_admissions_table:
run: index.cwl
doc: Build indices
in:
depends_on: populate_admissions_table/log
table:
valueFrom: "admissions"
domain:
valueFrom: "medicare"
incremental:
valueFrom: $(false)
database: database
connection_name: connection_name
out: [ log, errors ]
vacuum_admissions_table:
run: vacuum.cwl
doc: Vacuum the view
in:
depends_on: index_admissions_table/log
table:
valueFrom: "admissions"
domain:
valueFrom: "medicare"
database: database
connection_name: connection_name
out: [ log, errors ]
outputs:
ip_create_log:
type: File
outputSource: create_ip/log
ip_create_err:
type: File
outputSource: create_ip/errors
adm_create_log:
type: File
outputSource: create_admissions_table/log
adm_create_err:
type: File
outputSource: create_admissions_table/errors
adm_populate_log:
type: File
outputSource: populate_admissions_table/log
adm_populate_err:
type: File
outputSource: populate_admissions_table/errors
adm_index_log:
type: File
outputSource: index_admissions_table/log
adm_index_err:
type: File
outputSource: index_admissions_table/errors
adm_vacuum_log:
type: File
outputSource: vacuum_admissions_table/log
adm_vacuum_err:
type: File
outputSource: vacuum_admissions_table/errors