1#!/usr/bin/env cwl-runner
2### Resource Loader
3# Copyright (c) 2021. Harvard University
4#
5# Developed by Research Software Engineering,
6# Faculty of Arts and Sciences, Research Computing (FAS RC)
7# Author: Michael A Bouzinier
8#
9# Licensed under the Apache License, Version 2.0 (the "License");
10# you may not use this file except in compliance with the License.
11# You may obtain a copy of the License at
12#
13# http://www.apache.org/licenses/LICENSE-2.0
14#
15# Unless required by applicable law or agreed to in writing, software
16# distributed under the License is distributed on an "AS IS" BASIS,
17# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
18# See the License for the specific language governing permissions and
19# limitations under the License.
20#
21
22cwlVersion: v1.2
23class: CommandLineTool
24baseCommand: [python, -m, dorieh.platform.util.pg_json_dump]
25
26doc: |
27 This tool ensures that resources required by
28 the processing steps are loaded into the database
29
30
31inputs:
32 database:
33 type: File
34 doc: Path to database connection file, usually database.ini
35 inputBinding:
36 prefix: --db
37 connection_name:
38 type: string
39 doc: The name of the section in the database.ini file
40 inputBinding:
41 prefix: --connection
42 table:
43 type: string
44 doc: the name of the table containing required resource
45 inputBinding:
46 prefix: --table
47
48arguments:
49 - valueFrom: "ensure"
50 prefix: --action
51
52
53outputs:
54 log:
55 type: File
56 outputBinding:
57 glob: "*.log"
58
59 errors:
60 type: stderr
61
62stderr: resource.err