#!/usr/bin/env cwl-runner
### Materialized View Creator
# Copyright (c) 2021. 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: {}
doc: |
This tool is a shortcut to create a materialized view and build
all indices associated with the view
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
table:
type: string
doc: the name of the table to be created
domain:
type: string
doc: the name of the domain
default: medicaid
incremental:
type: boolean
default: false
depends_on:
type: File?
doc: a special field used to enforce dependencies and execution order
steps:
create:
run: create.cwl
doc: Execute DDL
in:
table: table
domain: domain
database: database
connection_name: connection_name
sloppy: incremental
out: [ log, errors ]
index:
run: index.cwl
doc: Build indices
in:
depends_on: create/log
domain: domain
table: table
incremental: incremental
database: database
connection_name: connection_name
out: [ log, errors ]
vacuum:
run: vacuum.cwl
doc: Vacuum the view
in:
depends_on: index/log
domain: domain
table: table
database: database
connection_name: connection_name
out: [ log, errors ]
outputs:
create_log:
type: File
outputSource: create/log
index_log:
type: File
outputSource: index/log
vacuum_log:
type: File
outputSource: vacuum/log
create_err:
type: File
outputSource: create/errors
index_err:
type: File
outputSource: index/errors
vacuum_err:
type: File
outputSource: vacuum/errors