[ARVADOS] updated: 1.3.0-1485-g934975a33

Git user git at public.curoverse.com
Thu Sep 5 18:34:50 UTC 2019


Summary of changes:
 .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

       via  934975a33a16ee8bf2ca854d263b98452856373f (commit)
      from  a3c2d73b2a3e87eab35853429f06195e15f1c972 (commit)

Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
revisions in full, below.


commit 934975a33a16ee8bf2ca854d263b98452856373f
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Thu Sep 5 14:32:27 2019 -0400

    15361: Add missing test files
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>

diff --git a/.licenseignore b/.licenseignore
index 28ddf9c29..ad80dc3f4 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 000000000..077f65b74
--- /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 000000000..af0be2f05
--- /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 000000000..780271749
--- /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 000000000..95f50cceb
--- /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

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