From 8c8a7c6a9c126728d81b651bfdd20a43a0599ca1 Mon Sep 17 00:00:00 2001
From: mancini <mancini@astron.nl>
Date: Mon, 6 Apr 2020 14:54:59 +0200
Subject: [PATCH] Add log collecting utils
Former-commit-id: 628a183200e3e8292dba97c8cb7e042197b12f76
Former-commit-id: a7c32fe99290735c5a106324a206c39cac6d7008
---
steps/bulk_rename.cwl | 39 +++++++++++++++++++++++++++++++++++
steps/collectlog.cwl | 47 +++++++++++++++++++++++++++++++++++++++++++
2 files changed, 86 insertions(+)
create mode 100644 steps/bulk_rename.cwl
create mode 100644 steps/collectlog.cwl
diff --git a/steps/bulk_rename.cwl b/steps/bulk_rename.cwl
new file mode 100644
index 00000000..d75af405
--- /dev/null
+++ b/steps/bulk_rename.cwl
@@ -0,0 +1,39 @@
+class: CommandLineTool
+cwlVersion: v1.0
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+id: bulk_rename
+baseCommand:
+ - bash
+ - bulk_rename.sh
+inputs:
+ - id: file_list
+ type: 'File[]'
+ inputBinding:
+ position: 0
+ - id: file_prefix
+ type: string
+ - id: file_suffix
+ type: string?
+outputs:
+ - id: output
+ type: 'File[]'
+ outputBinding:
+ glob: "tmp/$(inputs.file_prefix)*"
+label: bulk_rename
+requirements:
+ - class: InitialWorkDirRequirement
+ listing:
+ - entryname: bulk_rename.sh
+ entry: |
+ #!/bin/bash
+ set -e
+ FILE_LIST=("\${@}")
+ FILE_PREFIX=$(inputs.file_prefix)
+ FILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)
+ mkdir tmp
+ for i in "\${!FILE_LIST[@]}"; do
+ cp "\${FILE_LIST[\$i]}" "tmp/\${FILE_PREFIX}_\${i}\${FILE_SUFFIX}"
+ done
+ writable: false
+ - class: InlineJavascriptRequirement
diff --git a/steps/collectlog.cwl b/steps/collectlog.cwl
new file mode 100644
index 00000000..57ee22fd
--- /dev/null
+++ b/steps/collectlog.cwl
@@ -0,0 +1,47 @@
+class: CommandLineTool
+cwlVersion: v1.0
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+id: collectlog
+baseCommand:
+ - bash
+ - collect_logs.sh
+inputs:
+ - id: start_directory
+ type: Directory?
+ - id: log_files
+ type:
+ - File
+ - type: array
+ items: File
+ inputBinding:
+ position: 0
+ - id: sub_directory_name
+ type: string
+outputs:
+ - id: log_dir
+ type: Directory
+ outputBinding:
+ glob: |
+ $(inputs.start_directory === null ? inputs.sub_directory_name: inputs.start_directory.basename)
+label: CollectLog
+requirements:
+ - class: InitialWorkDirRequirement
+ listing:
+ - entryname: collect_logs.sh
+ entry: |
+ #!/bin/bash
+ set -e
+ BASE_DIR="$(inputs.start_directory === null ? "" : inputs.start_directory.basename)"
+ SUB_DIR="$(inputs.sub_directory_name)"
+ if [ -z "$BASE_DIR" ]
+ then
+ OUTPUT_PATH=$SUB_DIR
+ else
+ OUTPUT_PATH=$BASE_DIR/$SUB_DIR
+ fi
+ echo $OUTPUT_PATH
+ mkdir -p $OUTPUT_PATH
+ cp -L $* $OUTPUT_PATH
+ writable: false
+ - class: InlineJavascriptRequirement
--
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