From 934975a33a16ee8bf2ca854d263b98452856373f Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Thu, 5 Sep 2019 14:32:27 -0400 Subject: [PATCH] 15361: Add missing test files Arvados-DCO-1.1-Signed-off-by: Peter Amstutz --- .licenseignore | 1 + sdk/cwl/tests/wf/feddemo | 1 + sdk/cwl/tests/wf/revsort/revsort.cwl | 62 +++++++++++++++++++++++++++ sdk/cwl/tests/wf/revsort/revtool.cwl | 45 +++++++++++++++++++ sdk/cwl/tests/wf/revsort/sorttool.cwl | 42 ++++++++++++++++++ 5 files changed, 151 insertions(+) create mode 120000 sdk/cwl/tests/wf/feddemo create mode 100644 sdk/cwl/tests/wf/revsort/revsort.cwl create mode 100644 sdk/cwl/tests/wf/revsort/revtool.cwl create mode 100644 sdk/cwl/tests/wf/revsort/sorttool.cwl diff --git a/.licenseignore b/.licenseignore index 28ddf9c290..ad80dc3f4b 100644 --- a/.licenseignore +++ b/.licenseignore @@ -79,3 +79,4 @@ lib/dispatchcloud/test/sshkey_* *.asc sdk/java-v2/build.gradle sdk/java-v2/settings.gradle +sdk/cwl/tests/wf/feddemo \ No newline at end of file diff --git a/sdk/cwl/tests/wf/feddemo b/sdk/cwl/tests/wf/feddemo new file mode 120000 index 0000000000..077f65b741 --- /dev/null +++ b/sdk/cwl/tests/wf/feddemo @@ -0,0 +1 @@ +../../../../doc/user/cwl/federated \ No newline at end of file diff --git a/sdk/cwl/tests/wf/revsort/revsort.cwl b/sdk/cwl/tests/wf/revsort/revsort.cwl new file mode 100644 index 0000000000..af0be2f05d --- /dev/null +++ b/sdk/cwl/tests/wf/revsort/revsort.cwl @@ -0,0 +1,62 @@ +# Copyright (C) The Arvados Authors. All rights reserved. +# +# SPDX-License-Identifier: Apache-2.0 + +# +# This is a two-step workflow which uses "revtool" and "sorttool" defined above. +# +class: Workflow +doc: "Reverse the lines in a document, then sort those lines." +cwlVersion: v1.0 + + +# The inputs array defines the structure of the input object that describes +# the inputs to the workflow. +# +# The "reverse_sort" input parameter demonstrates the "default" field. If the +# field "reverse_sort" is not provided in the input object, the default value will +# be used. +inputs: + input: + type: File + doc: "The input file to be processed." + reverse_sort: + type: boolean + default: true + doc: "If true, reverse (decending) sort" + +# The "outputs" array defines the structure of the output object that describes +# the outputs of the workflow. +# +# Each output field must be connected to the output of one of the workflow +# steps using the "connect" field. Here, the parameter "#output" of the +# workflow comes from the "#sorted" output of the "sort" step. +outputs: + output: + type: File + outputSource: sorted/output + doc: "The output with the lines reversed and sorted." + +# The "steps" array lists the executable steps that make up the workflow. +# The tool to execute each step is listed in the "run" field. +# +# In the first step, the "inputs" field of the step connects the upstream +# parameter "#input" of the workflow to the input parameter of the tool +# "revtool.cwl#input" +# +# In the second step, the "inputs" field of the step connects the output +# parameter "#reversed" from the first step to the input parameter of the +# tool "sorttool.cwl#input". +steps: + rev: + in: + input: input + out: [output] + run: revtool.cwl + + sorted: + in: + input: rev/output + reverse: reverse_sort + out: [output] + run: sorttool.cwl diff --git a/sdk/cwl/tests/wf/revsort/revtool.cwl b/sdk/cwl/tests/wf/revsort/revtool.cwl new file mode 100644 index 0000000000..780271749a --- /dev/null +++ b/sdk/cwl/tests/wf/revsort/revtool.cwl @@ -0,0 +1,45 @@ +# Copyright (C) The Arvados Authors. All rights reserved. +# +# SPDX-License-Identifier: Apache-2.0 + +# +# Simplest example command line program wrapper for the Unix tool "rev". +# +class: CommandLineTool +cwlVersion: v1.0 +doc: "Reverse each line using the `rev` command" + +hints: + ResourceRequirement: + ramMin: 8 + +# The "inputs" array defines the structure of the input object that describes +# the inputs to the underlying program. Here, there is one input field +# defined that will be called "input" and will contain a "File" object. +# +# The input binding indicates that the input value should be turned into a +# command line argument. In this example inputBinding is an empty object, +# which indicates that the file name should be added to the command line at +# a default location. +inputs: + input: + type: File + inputBinding: {} + +# The "outputs" array defines the structure of the output object that +# describes the outputs of the underlying program. Here, there is one +# output field defined that will be called "output", must be a "File" type, +# and after the program executes, the output value will be the file +# output.txt in the designated output directory. +outputs: + output: + type: File + outputBinding: + glob: output.txt + +# The actual program to execute. +baseCommand: rev + +# Specify that the standard output stream must be redirected to a file called +# output.txt in the designated output directory. +stdout: output.txt diff --git a/sdk/cwl/tests/wf/revsort/sorttool.cwl b/sdk/cwl/tests/wf/revsort/sorttool.cwl new file mode 100644 index 0000000000..95f50cceb4 --- /dev/null +++ b/sdk/cwl/tests/wf/revsort/sorttool.cwl @@ -0,0 +1,42 @@ +# Copyright (C) The Arvados Authors. All rights reserved. +# +# SPDX-License-Identifier: Apache-2.0 + +# Example command line program wrapper for the Unix tool "sort" +# demonstrating command line flags. +class: CommandLineTool +doc: "Sort lines using the `sort` command" +cwlVersion: v1.0 +hints: + ResourceRequirement: + ramMin: 8 + +# This example is similar to the previous one, with an additional input +# parameter called "reverse". It is a boolean parameter, which is +# intepreted as a command line flag. The value of "prefix" is used for +# flag to put on the command line if "reverse" is true, if "reverse" is +# false, no flag is added. +# +# This example also introduced the "position" field. This indicates the +# sorting order of items on the command line. Lower numbers are placed +# before higher numbers. Here, the "-r" (same as "--reverse") flag (if +# present) will be added to the command line before the input file path. +inputs: + - id: reverse + type: boolean + inputBinding: + position: 1 + prefix: "-r" + - id: input + type: File + inputBinding: + position: 2 + +outputs: + - id: output + type: File + outputBinding: + glob: output.txt + +baseCommand: sort +stdout: output.txt -- 2.30.2