Merge branch 'recursive_directory' of https://github.com/gijzelaerr/c…

…ommon-workflow-language
common-workflow-language · Jul 20, 2017 · 71efb7b · 71efb7b
2 parents c50c150 + d736a0e
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diff --git a/v1.0/conformance_test_v1.0.yaml b/v1.0/conformance_test_v1.0.yaml
@@ -995,4 +995,58 @@
     args: [-A,'2',-B,baz,-C,'10','9','8','7','6','5','4','3','2','1']
   job: v1.0/empty.json
   tool: v1.0/inline-js.cwl
-  doc: Test InlineJavascriptRequirement with multiple expressions in the same tool
+  doc: Test InlineJavascriptRequirement with multiple expressions in the same tool
+
+- job: v1.0/recursive-input-directory.yml
+  output:
+    output_dir: {
+        "basename": "work_dir",
+        "class": "Directory",
+        "listing": [
+            {
+                "basename": "a",
+                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+                "class": "File",
+                "location": "work_dir/a",
+                "size": 0
+            },
+            {
+                "basename": "b",
+                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+                "class": "File",
+                "location": "work_dir/b",
+                "size": 0
+            },
+            {
+                "basename": "c",
+                "class": "Directory",
+                "listing": [
+                    {
+                        "basename": "d",
+                        "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+                        "class": "File",
+                        "location": "work_dir/c/d",
+                        "size": 0
+                    }
+                ],
+                "location": "work_dir/c",
+            },
+            {
+                "basename": "e",
+                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+                "class": "File",
+                "location": "work_dir/e",
+                "size": 0
+            },
+        ],
+        "location": "work_dir",
+      }
+    test_result: {
+        "basename": "output.txt",
+        "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+        "class": "File",
+        "location": "output.txt",
+        "size": 0
+      }
+  tool: v1.0/recursive-input-directory.cwl
+  doc: Test if a writable input directory is recursivly copied and writable
diff --git a/v1.0/v1.0/recursive-input-directory.cwl b/v1.0/v1.0/recursive-input-directory.cwl
@@ -0,0 +1,34 @@
+cwlVersion: v1.0
+class: CommandLineTool
+requirements:
+  - class: InlineJavascriptRequirement
+  - class: InitialWorkDirRequirement
+    listing:
+      - entry: $(inputs.input_dir)
+        entryname: work_dir
+        writable: true
+  - class: ShellCommandRequirement
+stdout: output.txt
+arguments:
+ - shellQuote: false
+   valueFrom: |
+    touch work_dir/e;
+    if [ ! -w work_dir ]; then echo work_dir not writable; fi;
+    if [ -L work_dir ]; then echo work_dir is a symlink; fi;
+    if [ ! -w work_dir/a ]; then echo work_dir/a not writable; fi;
+    if [ -L work_dir/a ]; then echo work_dir/a is a symlink; fi;
+    if [ ! -w work_dir/c ]; then echo work_dir/c not writable; fi;
+    if [ -L work_dir/c ]; then echo work_dir/c is a symlink; fi;
+    if [ ! -w work_dir/c/d ]; then echo work_dir/c/d not writable; fi;
+    if [ -L work_dir/c/d ]; then echo work_dir/c/d is a symlink; fi;
+    if [ ! -w work_dir/e ]; then echo work_dir/e not writable; fi;
+    if [ -L work_dir/e ]; then echo work_dir/e is a symlink ; fi;
+inputs:
+  input_dir: Directory
+outputs:
+  output_dir:
+    type: Directory
+    outputBinding:
+      glob: work_dir
+  test_result:
+    type: stdout
diff --git a/v1.0/v1.0/recursive-input-directory.yml b/v1.0/v1.0/recursive-input-directory.yml
@@ -0,0 +1,3 @@
+input_dir:
+  class: Directory
+  location: testdir
diff --git a/v1.1.0-dev1/conformance_test_v1.1.0-dev1.yaml b/v1.1.0-dev1/conformance_test_v1.1.0-dev1.yaml
@@ -1001,3 +1001,57 @@
   job: v1.1.0-dev1/default_path_job.yml
   tool: v1.1.0-dev1/default_path.cwl
   doc: Test warning instead of error when default path is not found
+
+- job: v1.1.0-dev1/recursive-input-directory.yml
+  output:
+    output_dir: {
+        "basename": "work_dir",
+        "class": "Directory",
+        "listing": [
+            {
+                "basename": "a",
+                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+                "class": "File",
+                "location": "work_dir/a",
+                "size": 0
+            },
+            {
+                "basename": "b",
+                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+                "class": "File",
+                "location": "work_dir/b",
+                "size": 0
+            },
+            {
+                "basename": "c",
+                "class": "Directory",
+                "listing": [
+                    {
+                        "basename": "d",
+                        "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+                        "class": "File",
+                        "location": "work_dir/c/d",
+                        "size": 0
+                    }
+                ],
+                "location": "work_dir/c",
+            },
+            {
+                "basename": "e",
+                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+                "class": "File",
+                "location": "work_dir/e",
+                "size": 0
+            },
+        ],
+        "location": "work_dir",
+      }
+    test_result: {
+        "basename": "output.txt",
+        "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+        "class": "File",
+        "location": "output.txt",
+        "size": 0
+      }
+  tool: v1.1.0-dev1/recursive-input-directory.cwl
+  doc: Test if a writable input directory is recursivly copied and writable
diff --git a/v1.1.0-dev1/v1.1.0-dev1/recursive-input-directory.cwl b/v1.1.0-dev1/v1.1.0-dev1/recursive-input-directory.cwl
@@ -0,0 +1,34 @@
+cwlVersion: v1.1.0-dev1
+class: CommandLineTool
+requirements:
+  - class: InlineJavascriptRequirement
+  - class: InitialWorkDirRequirement
+    listing:
+      - entry: $(inputs.input_dir)
+        entryname: work_dir
+        writable: true
+  - class: ShellCommandRequirement
+stdout: output.txt
+arguments:
+ - shellQuote: false
+   valueFrom: |
+    touch work_dir/e;
+    if [ ! -w work_dir ]; then echo work_dir not writable; fi;
+    if [ -L work_dir ]; then echo work_dir is a symlink; fi;
+    if [ ! -w work_dir/a ]; then echo work_dir/a not writable; fi;
+    if [ -L work_dir/a ]; then echo work_dir/a is a symlink; fi;
+    if [ ! -w work_dir/c ]; then echo work_dir/c not writable; fi;
+    if [ -L work_dir/c ]; then echo work_dir/c is a symlink; fi;
+    if [ ! -w work_dir/c/d ]; then echo work_dir/c/d not writable; fi;
+    if [ -L work_dir/c/d ]; then echo work_dir/c/d is a symlink; fi;
+    if [ ! -w work_dir/e ]; then echo work_dir/e not writable; fi;
+    if [ -L work_dir/e ]; then echo work_dir/e is a symlink ; fi;
+inputs:
+  input_dir: Directory
+outputs:
+  output_dir:
+    type: Directory
+    outputBinding:
+      glob: work_dir
+  test_result:
+    type: stdout
diff --git a/v1.1.0-dev1/v1.1.0-dev1/recursive-input-directory.yml b/v1.1.0-dev1/v1.1.0-dev1/recursive-input-directory.yml
@@ -0,0 +1,3 @@
+input_dir:
+  class: Directory
+  location: testdir