Merge pull request #61 from tom-tan/add-tests

Add tests for the examples

Author: mr-c

.travis.yml

@@ -1,3 +1,7 @@
+sudo: required
+services:
+  - docker
+
 language: python
 python:
   - 2.7

_includes/cwl/17-metadata/file-formats.bam

@@ -0,0 +1,7 @@
+aligned_sequences:
+    class: File
+    format: http://edamontology.org/format_2572
+    path: file-formats.bam
+bamstats_report:
+    class: File
+    path: /tmp/bamstats_report.zip

_includes/cwl/17-metadata/sample.yml

@@ -1,3 +1,18 @@
+# Section 2
+- doc: Test for section 2
+  job: 02-1st-example/echo-job.yml
+  tool: 02-1st-example/1st-tool.cwl
+  should_fail: false
+  output: {}
+
+# Section 3
+- doc: Test for section 3
+  job: 03-input/inp-job.yml
+  tool: 03-input/inp.cwl
+  should_fail: false
+  output: {}
+
+# Section 4
 - doc: Test for section 4
   job: 04-output/tar-job.yml
   tool: 04-output/tar.cwl
@@ -8,3 +23,161 @@
       basename: hello.txt
       location: Any
       size: 0
+
+# Section 5
+- doc: Test for section 5
+  job: 05-stdout/echo-job.yml
+  tool: 05-stdout/stdout.cwl
+  output:
+    output:
+      class: File
+      checksum: sha1$47a013e660d408619d894b20806b1d5086aab03b
+      basename: output.txt
+      location: Any
+      size: 13
+
+# Section 6
+- doc: Test for section 6
+  job: 06-params/tar-param-job.yml
+  tool: 06-params/tar-param.cwl
+  output:
+    example_out:
+      class: File
+      checksum: sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709
+      basename: goodbye.txt
+      location: Any
+      size: 0
+
+# Section 7 depends on side-effects
+
+# Section 8
+- doc: Test for section 8
+  job: 08-arguments/arguments-job.yml
+  tool: 08-arguments/arguments.cwl
+  output:
+    classfile:
+      class: File
+      checksum: sha1$fdb876b40ad9ebc7fee873212e02d5940588642e
+      basename: Hello.class
+      location: Any
+      size: 184
+
+# Section 9 depends on side-effects
+
+# Section 10
+- doc: Test for section 10
+  job: 10-array-outputs/array-outputs-job.yml
+  tool: 10-array-outputs/array-outputs.cwl
+  output:
+    output:
+      - class: File
+        basename: baz.txt
+        checksum: sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709
+        location: Any
+        size: 0
+      - class: File
+        basename: foo.txt
+        checksum: sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709
+        location: Any
+        size: 0
+
+# Section 11 depends on side-effects
+# Rest two examples in Section 11 depend on side-effects
+- doc: Test for section 11 (1st example)
+  job: 11-records/record-job1.yml
+  tool: 11-records/record.cwl
+  should_fail: true
+
+# Section 12 depends on side-effects
+# Section 13 depends on side-effects
+# Section 14 depends on side-effects
+
+# Section 15
+- doc: Test for section 15
+  job: 15-staging/arguments-job.yml
+  tool: 15-staging/linkfile.cwl
+  output:
+    classfile:
+      class: File
+      checksum: sha1$fdb876b40ad9ebc7fee873212e02d5940588642e
+      basename: Hello.class
+      location: Any
+      size: 184
+
+# Section 16
+# Note: The checksum and size is always changed for every executions
+- doc: Test for section 16
+  job: 16-file-formats/sample.yml
+  tool: 16-file-formats/metadata_example.cwl
+  output:
+    report:
+      class: File
+      basename: output.txt
+      location: Any
+
+# Section 17
+# Note: The checksum and size is always changed for every executions
+- doc: Test for section 17 (1st example)
+  job: 17-metadata/sample.yml
+  tool: 17-metadata/metadata_example2.cwl
+  output:
+    report:
+      class: File
+      basename: output.txt
+      location: Any
+
+- doc: Test for section 17 (extended example)
+  job: 17-metadata/sample.yml
+  tool: 17-metadata/metadata_example3.cwl
+  output:
+    report:
+      class: File
+      basename: output.txt
+      location: Any
+
+# Section 19
+# See: Issue #48
+# - doc: Test for section 19
+#   job: 19-custom-types/custom-types.yml
+#   tool: 19-custom-types/costom-types.cwl
+#   output:
+#     i5Annotations:
+#       class: File
+#       basename: test_proteins.i5_annotations
+#       location: Any
+#       size: Any # To be fixed
+
+# Section 20
+# See: Issue #48
+# - doc: Test for section 20
+#   job: 20-software-requirements/custom-types.yml
+#   tool: 20-software-requirements/costom-types.cwl
+#   output:
+#     i5Annotations:
+#       class: File
+#       basename: test_proteins.i5_annotations
+#       location: Any
+#       size: Any # To be fixed
+
+# Section 21
+- doc: Test for section 21
+  job: 21-1st-workflow/1st-workflow-job.yml
+  tool: 21-1st-workflow/1st-workflow.cwl
+  output:
+    classout:
+      class: File
+      checksum: sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd
+      basename: Hello.class
+      location: Any
+      size: 419
+
+# Section 22
+- doc: Test for section 22
+  tool: 22-nested-workflows/nestedworkflows.cwl
+  output:
+    classout:
+      class: File
+      checksum: sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd
+      basename: Hello.class
+      location: Any
+      size: 419