[ARVADOS] created: 1.1.4-175-g6cee296

[Git user]

        at  6cee296e78820c5e4c41a50479c7e7dcf8a50cbb (commit)


commit 6cee296e78820c5e4c41a50479c7e7dcf8a50cbb
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Fri Apr 27 11:16:38 2018 -0400

    13330: Test workflow that generates intermediates.
    
    Also fixes file literal bug.
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>

diff --git a/sdk/cwl/arvados_cwl/pathmapper.py b/sdk/cwl/arvados_cwl/pathmapper.py
index 998890a..6fedb12 100644
--- a/sdk/cwl/arvados_cwl/pathmapper.py
+++ b/sdk/cwl/arvados_cwl/pathmapper.py
@@ -107,6 +107,7 @@ class ArvPathMapper(PathMapper):
         elif obj["location"].startswith("_:") and "contents" in obj:
             with c.open(path + "/" + obj["basename"], "w") as f:
                 f.write(obj["contents"].encode("utf-8"))
+            remap.append((obj["location"], path + "/" + obj["basename"]))
         else:
             raise SourceLine(obj, "location", WorkflowException).makeError("Don't know what to do with '%s'" % obj["location"])
 
diff --git a/sdk/cwl/tests/makes_intermediates/echo.cwl b/sdk/cwl/tests/makes_intermediates/echo.cwl
new file mode 100644
index 0000000..ee09eb7
--- /dev/null
+++ b/sdk/cwl/tests/makes_intermediates/echo.cwl
@@ -0,0 +1,13 @@
+class: CommandLineTool
+cwlVersion: v1.0
+requirements:
+  InitialWorkDirRequirement:
+    listing:
+      - $(inputs.inp1)
+      - $(inputs.inp2)
+      - $(inputs.inp3)
+inputs:
+  inp1: File
+  inp2: [File, Directory]
+outputs: []
+arguments: [echo, $(inputs.inp1), $(inputs.inp2), $(inputs.inp3)]
diff --git a/sdk/cwl/tests/makes_intermediates/hello1.txt b/sdk/cwl/tests/makes_intermediates/hello1.txt
new file mode 100644
index 0000000..e69de29
diff --git a/sdk/cwl/tests/makes_intermediates/run_in_single.cwl b/sdk/cwl/tests/makes_intermediates/run_in_single.cwl
new file mode 100644
index 0000000..bb596b2
--- /dev/null
+++ b/sdk/cwl/tests/makes_intermediates/run_in_single.cwl
@@ -0,0 +1,38 @@
+cwlVersion: v1.0
+class: Workflow
+$namespaces:
+  arv: "http://arvados.org/cwl#"
+requirements:
+  SubworkflowFeatureRequirement: {}
+inputs:
+  inp1:
+    type: File
+    default:
+      class: File
+      location: hello1.txt
+  inp2:
+    type: [File, Directory]
+    default:
+      class: File
+      basename: "hello2.txt"
+      contents: "Hello world"
+  inp3:
+    type: [File, Directory]
+    default:
+      class: Directory
+      basename: inp3
+      listing:
+        - class: File
+          basename: "hello3.txt"
+          contents: "hello world"
+outputs: []
+steps:
+  step1:
+    requirements:
+      arv:RunInSingleContainer: {}
+    in:
+      inp1: inp1
+      inp2: inp2
+      inp3: inp3
+    out: []
+    run: subwf.cwl
diff --git a/sdk/cwl/tests/makes_intermediates/subwf.cwl b/sdk/cwl/tests/makes_intermediates/subwf.cwl
new file mode 100644
index 0000000..1852ab4
--- /dev/null
+++ b/sdk/cwl/tests/makes_intermediates/subwf.cwl
@@ -0,0 +1,15 @@
+cwlVersion: v1.0
+class: Workflow
+inputs:
+  inp1: File
+  inp2: File
+  inp3: Directory
+outputs: []
+steps:
+  step1:
+    in:
+      inp1: inp1
+      inp2: inp2
+      inp3: inp3
+    out: []
+    run: echo.cwl

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