From bd3e0a105044c0b61c3b07649c6c284f5f1a641b Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Thu, 3 May 2018 12:34:05 -0400 Subject: [PATCH] 12256: Add a bunch of test cases. Arvados-DCO-1.1-Signed-off-by: Peter Amstutz --- sdk/cwl/tests/arvados-tests.yml | 43 +++++++++++++++++++++ sdk/cwl/tests/wf-defaults/default-dir1.cwl | 15 +++++++ sdk/cwl/tests/wf-defaults/default-dir2.cwl | 14 +++++++ sdk/cwl/tests/wf-defaults/default-dir3.cwl | 12 ++++++ sdk/cwl/tests/wf-defaults/default-dir4.cwl | 20 ++++++++++ sdk/cwl/tests/wf-defaults/default-dir5.cwl | 21 ++++++++++ sdk/cwl/tests/wf-defaults/default-dir6.cwl | 11 ++++++ sdk/cwl/tests/wf-defaults/default-dir6a.cwl | 10 +++++ sdk/cwl/tests/wf-defaults/default-dir7.cwl | 17 ++++++++ sdk/cwl/tests/wf-defaults/default-dir7a.cwl | 7 ++++ sdk/cwl/tests/wf-defaults/inp1/hello.txt | 0 sdk/cwl/tests/wf-defaults/wf1.cwl | 9 +++++ sdk/cwl/tests/wf-defaults/wf2.cwl | 9 +++++ sdk/cwl/tests/wf-defaults/wf3.cwl | 9 +++++ sdk/cwl/tests/wf-defaults/wf4.cwl | 13 +++++++ sdk/cwl/tests/wf-defaults/wf5.cwl | 13 +++++++ sdk/cwl/tests/wf-defaults/wf6.cwl | 15 +++++++ sdk/cwl/tests/wf-defaults/wf7.cwl | 15 +++++++ 18 files changed, 253 insertions(+) create mode 100644 sdk/cwl/tests/wf-defaults/default-dir1.cwl create mode 100644 sdk/cwl/tests/wf-defaults/default-dir2.cwl create mode 100644 sdk/cwl/tests/wf-defaults/default-dir3.cwl create mode 100644 sdk/cwl/tests/wf-defaults/default-dir4.cwl create mode 100644 sdk/cwl/tests/wf-defaults/default-dir5.cwl create mode 100644 sdk/cwl/tests/wf-defaults/default-dir6.cwl create mode 100644 sdk/cwl/tests/wf-defaults/default-dir6a.cwl create mode 100644 sdk/cwl/tests/wf-defaults/default-dir7.cwl create mode 100644 sdk/cwl/tests/wf-defaults/default-dir7a.cwl create mode 100644 sdk/cwl/tests/wf-defaults/inp1/hello.txt create mode 100644 sdk/cwl/tests/wf-defaults/wf1.cwl create mode 100644 sdk/cwl/tests/wf-defaults/wf2.cwl create mode 100644 sdk/cwl/tests/wf-defaults/wf3.cwl create mode 100644 sdk/cwl/tests/wf-defaults/wf4.cwl create mode 100644 sdk/cwl/tests/wf-defaults/wf5.cwl create mode 100644 sdk/cwl/tests/wf-defaults/wf6.cwl create mode 100644 sdk/cwl/tests/wf-defaults/wf7.cwl diff --git a/sdk/cwl/tests/arvados-tests.yml b/sdk/cwl/tests/arvados-tests.yml index 1950867b74..172e6a97b1 100644 --- a/sdk/cwl/tests/arvados-tests.yml +++ b/sdk/cwl/tests/arvados-tests.yml @@ -182,3 +182,46 @@ output: {} tool: secondaryFiles/example3.cwl doc: Discover secondaryFiles on default values + +- job: null + output: + out: null + tool: wf-defaults/wf1.cwl + doc: "Can have separate default parameters including directory and file inside same directory" + +- job: null + output: + out: null + tool: wf-defaults/wf2.cwl + doc: "Can have a parameter default value that is a directory literal with a file literal" + +- job: null + output: + out: null + tool: wf-defaults/wf3.cwl + doc: "Do not accept a directory literal without a basename + should_fail: true + +- job: null + output: + out: null + tool: wf-defaults/wf4.cwl + doc: default in embedded subworkflow + +- job: null + output: + out: null + tool: wf-defaults/wf5.cwl + doc: default in embedded subworkflow + +- job: null + output: + out: null + tool: wf-defaults/wf6.cwl + doc: default in RunInSingleContainer step + +- job: null + output: + out: null + tool: wf-defaults/wf7.cwl + doc: workflow level default in RunInSingleContainer diff --git a/sdk/cwl/tests/wf-defaults/default-dir1.cwl b/sdk/cwl/tests/wf-defaults/default-dir1.cwl new file mode 100644 index 0000000000..ed09e6e27f --- /dev/null +++ b/sdk/cwl/tests/wf-defaults/default-dir1.cwl @@ -0,0 +1,15 @@ +cwlVersion: v1.0 +class: CommandLineTool +inputs: + inp2: + type: Directory + default: + class: Directory + location: inp1 + inp1: + type: File + default: + class: File + location: inp1/hello.txt +outputs: [] +arguments: [echo, $(inputs.inp1), $(inputs.inp2)] \ No newline at end of file diff --git a/sdk/cwl/tests/wf-defaults/default-dir2.cwl b/sdk/cwl/tests/wf-defaults/default-dir2.cwl new file mode 100644 index 0000000000..c826464716 --- /dev/null +++ b/sdk/cwl/tests/wf-defaults/default-dir2.cwl @@ -0,0 +1,14 @@ +cwlVersion: v1.0 +class: CommandLineTool +inputs: + inp2: + type: Directory + default: + class: Directory + basename: inp2 + listing: + - class: File + basename: "hello.txt" + contents: "hello world" +outputs: [] +arguments: [echo, $(inputs.inp2)] \ No newline at end of file diff --git a/sdk/cwl/tests/wf-defaults/default-dir3.cwl b/sdk/cwl/tests/wf-defaults/default-dir3.cwl new file mode 100644 index 0000000000..ab7b0a4c6f --- /dev/null +++ b/sdk/cwl/tests/wf-defaults/default-dir3.cwl @@ -0,0 +1,12 @@ +cwlVersion: v1.0 +class: CommandLineTool +inputs: + inp2: + type: Directory + default: + class: Directory + listing: + - class: File + location: "inp1/hello.txt" +outputs: [] +arguments: [echo, $(inputs.inp2)] \ No newline at end of file diff --git a/sdk/cwl/tests/wf-defaults/default-dir4.cwl b/sdk/cwl/tests/wf-defaults/default-dir4.cwl new file mode 100644 index 0000000000..cd57ff34cd --- /dev/null +++ b/sdk/cwl/tests/wf-defaults/default-dir4.cwl @@ -0,0 +1,20 @@ +cwlVersion: v1.0 +class: Workflow +inputs: [] +outputs: [] +$namespaces: + arv: "http://arvados.org/cwl#" +steps: + step1: + in: [] + out: [] + run: + class: CommandLineTool + inputs: + inp2: + type: Directory + default: + class: Directory + location: inp1 + outputs: [] + arguments: [echo, $(inputs.inp2)] \ No newline at end of file diff --git a/sdk/cwl/tests/wf-defaults/default-dir5.cwl b/sdk/cwl/tests/wf-defaults/default-dir5.cwl new file mode 100644 index 0000000000..d4f667c034 --- /dev/null +++ b/sdk/cwl/tests/wf-defaults/default-dir5.cwl @@ -0,0 +1,21 @@ +cwlVersion: v1.0 +class: Workflow +inputs: [] +outputs: [] +$namespaces: + arv: "http://arvados.org/cwl#" +steps: + step1: + in: [] + out: [] + run: + id: stepid + class: CommandLineTool + inputs: + inp2: + type: Directory + default: + class: Directory + location: inp1 + outputs: [] + arguments: [echo, $(inputs.inp2)] \ No newline at end of file diff --git a/sdk/cwl/tests/wf-defaults/default-dir6.cwl b/sdk/cwl/tests/wf-defaults/default-dir6.cwl new file mode 100644 index 0000000000..597ea96da3 --- /dev/null +++ b/sdk/cwl/tests/wf-defaults/default-dir6.cwl @@ -0,0 +1,11 @@ +cwlVersion: v1.0 +class: Workflow +inputs: [] +outputs: [] +$namespaces: + arv: "http://arvados.org/cwl#" +steps: + step1: + in: [] + out: [] + run: default-dir6a.cwl \ No newline at end of file diff --git a/sdk/cwl/tests/wf-defaults/default-dir6a.cwl b/sdk/cwl/tests/wf-defaults/default-dir6a.cwl new file mode 100644 index 0000000000..76437a2982 --- /dev/null +++ b/sdk/cwl/tests/wf-defaults/default-dir6a.cwl @@ -0,0 +1,10 @@ +cwlVersion: v1.0 +class: CommandLineTool +inputs: + inp2: + type: Directory + default: + class: Directory + location: inp1 +outputs: [] +arguments: [echo, $(inputs.inp2)] \ No newline at end of file diff --git a/sdk/cwl/tests/wf-defaults/default-dir7.cwl b/sdk/cwl/tests/wf-defaults/default-dir7.cwl new file mode 100644 index 0000000000..4e6372b620 --- /dev/null +++ b/sdk/cwl/tests/wf-defaults/default-dir7.cwl @@ -0,0 +1,17 @@ +cwlVersion: v1.0 +class: Workflow +inputs: + inp2: + type: Directory + default: + class: Directory + location: inp1 +outputs: [] +$namespaces: + arv: "http://arvados.org/cwl#" +steps: + step1: + in: + inp2: inp2 + out: [] + run: default-dir7a.cwl \ No newline at end of file diff --git a/sdk/cwl/tests/wf-defaults/default-dir7a.cwl b/sdk/cwl/tests/wf-defaults/default-dir7a.cwl new file mode 100644 index 0000000000..df9009ada5 --- /dev/null +++ b/sdk/cwl/tests/wf-defaults/default-dir7a.cwl @@ -0,0 +1,7 @@ +cwlVersion: v1.0 +class: CommandLineTool +inputs: + inp2: + type: Directory +outputs: [] +arguments: [echo, $(inputs.inp2)] \ No newline at end of file diff --git a/sdk/cwl/tests/wf-defaults/inp1/hello.txt b/sdk/cwl/tests/wf-defaults/inp1/hello.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/sdk/cwl/tests/wf-defaults/wf1.cwl b/sdk/cwl/tests/wf-defaults/wf1.cwl new file mode 100644 index 0000000000..45faa8937c --- /dev/null +++ b/sdk/cwl/tests/wf-defaults/wf1.cwl @@ -0,0 +1,9 @@ +cwlVersion: v1.0 +class: Workflow +inputs: [] +outputs: [] +steps: + step1: + in: [] + out: [] + run: default-dir1.cwl \ No newline at end of file diff --git a/sdk/cwl/tests/wf-defaults/wf2.cwl b/sdk/cwl/tests/wf-defaults/wf2.cwl new file mode 100644 index 0000000000..7ba96eea4d --- /dev/null +++ b/sdk/cwl/tests/wf-defaults/wf2.cwl @@ -0,0 +1,9 @@ +cwlVersion: v1.0 +class: Workflow +inputs: [] +outputs: [] +steps: + step1: + in: [] + out: [] + run: default-dir2.cwl \ No newline at end of file diff --git a/sdk/cwl/tests/wf-defaults/wf3.cwl b/sdk/cwl/tests/wf-defaults/wf3.cwl new file mode 100644 index 0000000000..911650d61f --- /dev/null +++ b/sdk/cwl/tests/wf-defaults/wf3.cwl @@ -0,0 +1,9 @@ +cwlVersion: v1.0 +class: Workflow +inputs: [] +outputs: [] +steps: + step1: + in: [] + out: [] + run: default-dir3.cwl \ No newline at end of file diff --git a/sdk/cwl/tests/wf-defaults/wf4.cwl b/sdk/cwl/tests/wf-defaults/wf4.cwl new file mode 100644 index 0000000000..d6e65afd6c --- /dev/null +++ b/sdk/cwl/tests/wf-defaults/wf4.cwl @@ -0,0 +1,13 @@ +cwlVersion: v1.0 +class: Workflow +inputs: [] +outputs: [] +$namespaces: + arv: "http://arvados.org/cwl#" +requirements: + SubworkflowFeatureRequirement: {} +steps: + step1: + in: [] + out: [] + run: default-dir4.cwl \ No newline at end of file diff --git a/sdk/cwl/tests/wf-defaults/wf5.cwl b/sdk/cwl/tests/wf-defaults/wf5.cwl new file mode 100644 index 0000000000..631af182b9 --- /dev/null +++ b/sdk/cwl/tests/wf-defaults/wf5.cwl @@ -0,0 +1,13 @@ +cwlVersion: v1.0 +class: Workflow +inputs: [] +outputs: [] +$namespaces: + arv: "http://arvados.org/cwl#" +requirements: + SubworkflowFeatureRequirement: {} +steps: + step1: + in: [] + out: [] + run: default-dir5.cwl \ No newline at end of file diff --git a/sdk/cwl/tests/wf-defaults/wf6.cwl b/sdk/cwl/tests/wf-defaults/wf6.cwl new file mode 100644 index 0000000000..bd26cc1d1b --- /dev/null +++ b/sdk/cwl/tests/wf-defaults/wf6.cwl @@ -0,0 +1,15 @@ +cwlVersion: v1.0 +class: Workflow +inputs: [] +outputs: [] +$namespaces: + arv: "http://arvados.org/cwl#" +requirements: + SubworkflowFeatureRequirement: {} +steps: + step1: + requirements: + arv:RunInSingleContainer: {} + in: [] + out: [] + run: default-dir6.cwl \ No newline at end of file diff --git a/sdk/cwl/tests/wf-defaults/wf7.cwl b/sdk/cwl/tests/wf-defaults/wf7.cwl new file mode 100644 index 0000000000..ac07b9dbb2 --- /dev/null +++ b/sdk/cwl/tests/wf-defaults/wf7.cwl @@ -0,0 +1,15 @@ +cwlVersion: v1.0 +class: Workflow +inputs: [] +outputs: [] +$namespaces: + arv: "http://arvados.org/cwl#" +requirements: + SubworkflowFeatureRequirement: {} +steps: + step1: + requirements: + arv:RunInSingleContainer: {} + in: [] + out: [] + run: default-dir7.cwl \ No newline at end of file -- 2.30.2