1#!/usr/bin/env cwl-runner
2### FTS Parser
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.cms.registry]
25
26doc: |
27 This tool examines a directory with raw CMS data, looking
28 for File Transfer Summary (FTS) files. It examnines each
29 FTS file under directory (recursively) and creates a unified
30 data model for input raw CMS data. If any FTS files for
31 different years are incompatible with one another, a
32 warning is reported. However, so far we found that all years
33 are compatible.
34
35
36inputs:
37 input:
38 type: Directory
39 inputBinding:
40 prefix: --input
41 doc: |
42 A path to directory, containing unpacked CMS
43 files. The tool will recursively look in subdirectories
44 for FTS files
45 output:
46 type: string
47 default: "cms.yaml"
48 doc: A path to a file name with resulting data model
49 inputBinding:
50 prefix: --output
51
52outputs:
53 log:
54 type: File?
55 outputBinding:
56 glob: "registry*.log"
57 model:
58 type: File?
59 outputBinding:
60 glob: "*.yaml"
61 errors:
62 type: stderr
63
64stderr: parse_fts.err