13365: Add tests to confirm regressions are fixed.

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

diff --git a/sdk/cwl/tests/arvados-tests.sh b/sdk/cwl/tests/arvados-tests.sh
index d3c1e90637d5419320b0115b386780d6321d9975..4869e3e524153af30feb6a654e65e2cac6c57f3f 100755 (executable)
--- a/sdk/cwl/tests/arvados-tests.sh
+++ b/sdk/cwl/tests/arvados-tests.sh
@@ -9,4 +9,7 @@ fi
 if ! arv-get f225e6259bdd63bc7240599648dde9f1+97 > /dev/null ; then
     arv-put --portable-data-hash hg19/*
 fi
+if ! arv-get 4d8a70b1e63b2aad6984e40e338e2373+69 > /dev/null ; then
+    arv-put --portable-data-hash secondaryFiles/hello.txt*
+fi
 exec cwltest --test arvados-tests.yml --tool arvados-cwl-runner $@ -- --disable-reuse --compute-checksum

diff --git a/sdk/cwl/tests/arvados-tests.yml b/sdk/cwl/tests/arvados-tests.yml
index 934fe47c64b185272e9427e35f61b0d81d197506..1950867b74fd4c14c29ea6aaba6427aedf2b75d8 100644 (file)
--- a/sdk/cwl/tests/arvados-tests.yml
+++ b/sdk/cwl/tests/arvados-tests.yml
@@ -172,3 +172,13 @@
     out: null
   tool: wf/runin-reqs-wf4.cwl
   doc: "RunInSingleContainer discovers static resource request in subworkflow steps"
+
+- job: secondaryFiles/inp3.yml
+  output: {}
+  tool: secondaryFiles/example1.cwl
+  doc: Discover secondaryFiles at runtime if they are in keep
+
+- job: null
+  output: {}
+  tool: secondaryFiles/example3.cwl
+  doc: Discover secondaryFiles on default values

diff --git a/sdk/cwl/tests/secondaryFiles/example1.cwl b/sdk/cwl/tests/secondaryFiles/example1.cwl
new file mode 100644 (file)
index 0000000..540edcf
--- /dev/null
+++ b/sdk/cwl/tests/secondaryFiles/example1.cwl
@@ -0,0 +1,20 @@
+class: Workflow
+cwlVersion: v1.0
+inputs:
+  toplevel_input: File
+outputs: []
+steps:
+  step1:
+    in:
+      step_input: toplevel_input
+    out: []
+    run:
+      id: sub
+      class: CommandLineTool
+      inputs:
+        step_input:
+          type: File
+          secondaryFiles:
+            - .idx
+      outputs: []
+      baseCommand: echo

diff --git a/sdk/cwl/tests/secondaryFiles/example3.cwl b/sdk/cwl/tests/secondaryFiles/example3.cwl
new file mode 100644 (file)
index 0000000..892973b
--- /dev/null
+++ b/sdk/cwl/tests/secondaryFiles/example3.cwl
@@ -0,0 +1,12 @@
+class: CommandLineTool
+cwlVersion: v1.0
+inputs:
+  step_input:
+    type: File
+    secondaryFiles:
+      - .idx
+    default:
+      class: File
+      location: hello.txt
+outputs: []
+baseCommand: echo

diff --git a/sdk/cwl/tests/secondaryFiles/hello.txt b/sdk/cwl/tests/secondaryFiles/hello.txt
new file mode 100644 (file)
index 0000000..e69de29

diff --git a/sdk/cwl/tests/secondaryFiles/hello.txt.idx b/sdk/cwl/tests/secondaryFiles/hello.txt.idx
new file mode 100644 (file)
index 0000000..e69de29

diff --git a/sdk/cwl/tests/secondaryFiles/inp3.yml b/sdk/cwl/tests/secondaryFiles/inp3.yml
new file mode 100644 (file)
index 0000000..1107623
--- /dev/null
+++ b/sdk/cwl/tests/secondaryFiles/inp3.yml
@@ -0,0 +1,3 @@
+toplevel_input:
+  class: File
+  location: keep:4d8a70b1e63b2aad6984e40e338e2373+69/hello.txt
\ No newline at end of file