Merge commit '9473c6accefc5e855fc23c0e34ee6ed9f5c35767'

Author: Peter Amstutz

cwltool/schemas/draft-3/Process.yml

@@ -96,8 +96,11 @@ $graph:
         If no ontology is available, file formats may be tested by exact match.
 
         Reasoning about format compatability must be done by checking that an
-        input file format is the same or `rdfs:subClassOf` the format required
-        by the input parameter.
+        input file format is the same, `owl:equivalentClass` or
+        `rdfs:subClassOf` the format required by the input parameter.
+        `owl:equivalentClass` is transitive with `rdfs:subClassOf`, e.g. if
+        `<B> owl:equivalentClass <C>` and `<B> owl:subclassOf <A>` then infer
+        `<C> owl:subclassOf <A>`.
 
         File format ontologies may be provided in the "$schema" metadata at the
         root of the document.  If no ontologies are specified in `$schema`, the
@@ -150,9 +153,7 @@ $graph:
         For input parameters, this must be one or more URIs of a concept nodes
         that represents file formats which are allowed as input to this
         parameter, preferrably defined within an ontology.  If no ontology is
-        available, file formats may be tested by exact match.  See
-        (FormatOntologyRequirement)[#formatontologyrequirement] for more
-        information.
+        available, file formats may be tested by exact match.
 
         For output parameters, this is the file format that will be assigned to
         the output parameter.

cwltool/schemas/draft-3/conformance_test_draft-3.yaml

@@ -496,7 +496,19 @@
         "checksum": "sha1$971d88faeda85a796752ecf752b7e2e34f1337ce"
   tool: draft-3/formattest2.cwl
   doc: |
-    Test format checking against ontology.
+    Test format checking against ontology using subclassOf.
+
+- job: draft-3/formattest2-job.json
+  output:
+    output:
+        "path": "output.txt"
+        "format": "http://edamontology.org/format_1929"
+        "size": 12010
+        "class": "File"
+        "checksum": "sha1$971d88faeda85a796752ecf752b7e2e34f1337ce"
+  tool: draft-3/formattest3.cwl
+  doc: |
+    Test format checking against ontology using equivalentClass.
 
 - tool: draft-3/optional-output.cwl
   job: draft-3/cat-job.json

cwltool/schemas/draft-3/draft-3/formattest3.cwl

@@ -0,0 +1,25 @@
+$namespaces:
+  edam: http://edamontology.org/
+  gx: http://galaxyproject.org/formats/
+$schemas:
+  - EDAM.owl
+  - gx_edam.ttl
+class: CommandLineTool
+cwlVersion: cwl:draft-3.dev3
+description: "Reverse each line using the `rev` command"
+
+inputs:
+  - id: input
+    type: File
+    inputBinding: {}
+    format: gx:fasta
+
+outputs:
+  - id: output
+    type: File
+    outputBinding:
+      glob: output.txt
+    format: $(inputs.input.format)
+
+baseCommand: rev
+stdout: output.txt

cwltool/schemas/draft-3/draft-3/gx_edam.ttl

@@ -0,0 +1,7 @@
+@prefix gx: <http://galaxyproject.org/formats/> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix edam: <http://edamontology.org/> .
+
+gx:fasta a owl:Class .
+gx:fasta owl:equivalentClass edam:format_1929 .

cwltool/schemas/draft-3/invocation.md

@@ -58,13 +58,23 @@ Output files produced by tool execution must be written to the **designated
 output directory**.  The initial current working directory when executing
 the tool must be the designated output directory.
 
-Files may also be written to the **designated temporary directory**.  Any
-files written to the designated temporary directory may be deleted by the
-workflow platform immediately after the tool terminates.
+Files may also be written to the **designated temporary directory**.  This
+directory must be isolated and not shared with other processes.  Any files
+written to the designated temporary directory may be automatically deleted by
+the workflow platform immediately after the tool terminates.
+
+For compatibility, files may be written to the **system temporary directory**
+which must be located at `/tmp`.  Because the system temporary directory may be
+shared with other processes on the system, files placed in the system temporary
+directory are not guaranteed to be deleted automatically.  Correct tools must
+clean up temporary files written to the system temporary directory.  A tool
+must not use the system temporary directory as a backchannel communication with
+other tools.  It is valid for the system temporary directory to be the same as
+the designated temporary directory.
 
 When executing the tool, the tool must execute in a new, empty environment
 with only the environment variables described below; the child process must
-not inherit environment variables from the parent process except where
+not inherit environment variables from the parent process except as
 specified or at user option.
 
   * `HOME` must be set to the designated output directory.
@@ -77,10 +87,10 @@ specified or at user option.
     [DockerRequirement](#DockerRequirement)
 
 An implementation may forbid the tool from writing to any location in the
-runtime environment file system other than the designated temporary
-directory and designated output directory.  An implementation may provide
-read-only input files, and disallow in-place update of input files.  The
-designated temporary directory and designated output directory may reside
+runtime environment file system other than the designated temporary directory,
+system temporary directory, and designated output directory.  An implementation
+may provide read-only input files, and disallow in-place update of input files.
+The designated temporary directory and designated output directory may reside
 on different mount points on different file systems.
 
 The `runtime` section available in [parameter references](#Parameter_references)

cwltool/schemas/site/cwlsite-job.json

@@ -75,7 +75,8 @@
         {
             "source": {
                 "class": "File",
-                "path": "../draft-3/salad/schema_salad/metaschema/metaschema.yml"
+                "path": "../draft-3/salad/schema_salad/metaschema/metaschema.yml",
+                "secondaryFiles": {"$import": "deps.json"}
             },
             "target": "draft-3/SchemaSalad.html",
             "renderlist": [

cwltool/schemas/site/deps.json

@@ -30,10 +30,10 @@
     "path": "../draft-3/salad/schema_salad/metaschema/field_name_schema.yml"
 }, {
     "class": "File",
-    "path": "../draft-3/salad/schema_salad/metaschema/gield_name_src.yml"
+    "path": "../draft-3/salad/schema_salad/metaschema/field_name_src.yml"
 }, {
     "class": "File",
-    "path": "../draft-3/salad/schema_salad/metaschema/gield_name.yml"
+    "path": "../draft-3/salad/schema_salad/metaschema/field_name.yml"
 }, {
     "class": "File",
     "path": "../draft-3/salad/schema_salad/metaschema/ident_res_proc.yml"
@@ -63,7 +63,7 @@
     "path": "../draft-3/salad/schema_salad/metaschema/link_res.yml"
 }, {
     "class": "File",
-    "path": "../draft-3/salad/schema_salad/metaschema/etaschema.yml"
+    "path": "../draft-3/salad/schema_salad/metaschema/metaschema.yml"
 }, {
     "class": "File",
     "path": "../draft-3/salad/schema_salad/metaschema/salad.md"