1#!/usr/bin/env cwl-runner
2### Table tuner tool (running VACUUM)
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.loader.vacuum]
25requirements:
26 InlineJavascriptRequirement: {}
27 NetworkAccess:
28 networkAccess: True
29
30doc: |
31 This tool runs VACUUM Aanalyze to make subsequent queries
32 more efficient
33
34inputs:
35 #$import: db.yaml
36 registry:
37 type:
38 - File?
39 - string?
40 inputBinding:
41 prefix: --registry
42 doc: |
43 A path to the data model file
44 domain:
45 type: string
46 doc: the name of the domain
47 inputBinding:
48 prefix: --domain
49 table:
50 type: string
51 doc: the name of the table
52 inputBinding:
53 prefix: --table
54 database:
55 type: File
56 doc: Path to database connection file, usually database.ini
57 inputBinding:
58 prefix: --db
59 connection_name:
60 type: string
61 doc: The name of the section in the database.ini file
62 inputBinding:
63 prefix: --connection
64 depends_on:
65 type:
66 - File?
67 - File[]
68 doc: a special field used to enforce dependencies and execution order
69
70
71outputs:
72 log:
73 type: File
74 outputBinding:
75 glob: "*.log"
76 errors:
77 type: stderr
78
79stderr: $("vacuum-" + inputs.table + ".err")