[ARVADOS] updated: 1.1.2-19-g9e74f69

[Git user]

Summary of changes:
 sdk/cwl/tests/arvados-tests.yml                    |  5 +++++
 .../cwl/tests/secondary/dir/hg19.fa                |  0
 .../cwl/tests/secondary/dir/hg19.fa.amb            |  0
 .../cwl/tests/secondary/dir/hg19.fa.ann            |  0
 .../cwl/tests/secondary/dir/hg19.fa.fai            |  0
 sdk/cwl/tests/secondary/ls.cwl                     | 11 +++++++++++
 sdk/cwl/tests/secondary/sub.cwl                    | 17 ++++++++++++++++
 sdk/cwl/tests/secondary/wf-job.yml                 |  3 +++
 sdk/cwl/tests/secondary/wf.cwl                     | 23 ++++++++++++++++++++++
 9 files changed, 59 insertions(+)
 copy tools/crunchstat-summary/tests/__init__.py => sdk/cwl/tests/secondary/dir/hg19.fa (100%)
 copy tools/crunchstat-summary/tests/__init__.py => sdk/cwl/tests/secondary/dir/hg19.fa.amb (100%)
 copy tools/crunchstat-summary/tests/__init__.py => sdk/cwl/tests/secondary/dir/hg19.fa.ann (100%)
 copy tools/crunchstat-summary/tests/__init__.py => sdk/cwl/tests/secondary/dir/hg19.fa.fai (100%)
 create mode 100644 sdk/cwl/tests/secondary/ls.cwl
 create mode 100644 sdk/cwl/tests/secondary/sub.cwl
 create mode 100644 sdk/cwl/tests/secondary/wf-job.yml
 create mode 100644 sdk/cwl/tests/secondary/wf.cwl

       via  9e74f69b3ae6abbbc497c8fd2adeef41c96de251 (commit)
      from  2a3daf14afb93de4d65108019a7a1d35aa1052ad (commit)

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commit 9e74f69b3ae6abbbc497c8fd2adeef41c96de251
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Tue Jan 9 09:31:39 2018 -0500

    12913: Add integration test for fix
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>

diff --git a/sdk/cwl/tests/arvados-tests.yml b/sdk/cwl/tests/arvados-tests.yml
index f6271b8..cfb2fa4 100644
--- a/sdk/cwl/tests/arvados-tests.yml
+++ b/sdk/cwl/tests/arvados-tests.yml
@@ -123,3 +123,8 @@
     out: out
   tool: wf/runin-wf.cwl
   doc: "RunInSingleContainer cwl.input.json needs to be consistent with pathmapper manipulations"
+
+- job: secondary/wf-job.yml
+  output: {}
+  tool: secondary/wf.cwl
+  doc: "RunInSingleContainer applies secondaryFile discovery & manipulation before generating cwl.input.yml"
diff --git a/sdk/cwl/tests/secondary/dir/hg19.fa b/sdk/cwl/tests/secondary/dir/hg19.fa
new file mode 100644
index 0000000..e69de29
diff --git a/sdk/cwl/tests/secondary/dir/hg19.fa.amb b/sdk/cwl/tests/secondary/dir/hg19.fa.amb
new file mode 100644
index 0000000..e69de29
diff --git a/sdk/cwl/tests/secondary/dir/hg19.fa.ann b/sdk/cwl/tests/secondary/dir/hg19.fa.ann
new file mode 100644
index 0000000..e69de29
diff --git a/sdk/cwl/tests/secondary/dir/hg19.fa.fai b/sdk/cwl/tests/secondary/dir/hg19.fa.fai
new file mode 100644
index 0000000..e69de29
diff --git a/sdk/cwl/tests/secondary/ls.cwl b/sdk/cwl/tests/secondary/ls.cwl
new file mode 100644
index 0000000..b37990a
--- /dev/null
+++ b/sdk/cwl/tests/secondary/ls.cwl
@@ -0,0 +1,11 @@
+cwlVersion: v1.0
+class: CommandLineTool
+inputs:
+  i:
+    type: File
+    inputBinding:
+      position: 1
+    secondaryFiles:
+      - .fai
+outputs: []
+arguments: [ls, $(inputs.i), $(inputs.i.path).fai]
diff --git a/sdk/cwl/tests/secondary/sub.cwl b/sdk/cwl/tests/secondary/sub.cwl
new file mode 100644
index 0000000..5d2c699
--- /dev/null
+++ b/sdk/cwl/tests/secondary/sub.cwl
@@ -0,0 +1,17 @@
+cwlVersion: v1.0
+class: Workflow
+$namespaces:
+  arv: "http://arvados.org/cwl#"
+  cwltool: "http://commonwl.org/cwltool#"
+inputs:
+  i:
+    type: File
+    secondaryFiles:
+      - .fai
+outputs: []
+steps:
+  step1:
+    in:
+      i: i
+    out: []
+    run: ls.cwl
diff --git a/sdk/cwl/tests/secondary/wf-job.yml b/sdk/cwl/tests/secondary/wf-job.yml
new file mode 100644
index 0000000..8b9dd83
--- /dev/null
+++ b/sdk/cwl/tests/secondary/wf-job.yml
@@ -0,0 +1,3 @@
+i:
+  class: File
+  location: keep:f225e6259bdd63bc7240599648dde9f1+97/hg19.fa
diff --git a/sdk/cwl/tests/secondary/wf.cwl b/sdk/cwl/tests/secondary/wf.cwl
new file mode 100644
index 0000000..248aefd
--- /dev/null
+++ b/sdk/cwl/tests/secondary/wf.cwl
@@ -0,0 +1,23 @@
+cwlVersion: v1.0
+class: Workflow
+$namespaces:
+  arv: "http://arvados.org/cwl#"
+  cwltool: "http://commonwl.org/cwltool#"
+requirements:
+  SubworkflowFeatureRequirement: {}
+inputs:
+  i:
+    type: File
+    # secondaryFiles:
+    #   - .fai
+    #   - .ann
+    #   - .amb
+outputs: []
+steps:
+  step1:
+    in:
+      i: i
+    out: []
+    run: sub.cwl
+    requirements:
+      arv:RunInSingleContainer: {}

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