allow default files with bad path

cwltool/schemas/README.md

@@ -3,18 +3,20 @@ Common Workflow Language
 
 [![GitHub stars](https://img.shields.io/github/stars/common-workflow-language/common-workflow-language.svg)](https://github.com/common-workflow-language/common-workflow-language/stargazers) [![Gitter](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/common-workflow-language/common-workflow-language?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) [**Support**](#Support)
 
+<a href="https://www.youtube.com/watch?v=86eY8xs-Vo8"><img align="right" src="https://github.com/common-workflow-language/logo/raw/master/intro_video_screenshot_413x193.png" alt="[Video] Common Workflow Language explained in 64 seconds"></a>
 The Common Workflow Language (CWL) is a specification for describing analysis
 workflows and tools in a way that makes them portable and scalable across a
 variety of software and hardware environments, from workstations to cluster,
 cloud, and high performance computing (HPC) environments.  CWL is designed to
 meet the needs of data-intensive science, such as Bioinformatics, Medical
 Imaging, Astronomy, Physics, and Chemistry.
 
+<a href="https://open-stand.org/about-us/principles"><img align="left" src="http://standards.ieee.org/images/openstand/128x128-blue2.png" alt="Open Stand badge"></a>
 CWL is developed by an informal, multi-vendor working group consisting of
 organizations and individuals aiming to enable scientists to share data
 analysis workflows.  [The CWL project is on Github](https://github.com/common-workflow-language/common-workflow-language) and we follow the [Open-Stand.org principles for collaborative open standards development](https://open-stand.org/about-us/principles/)
 
-[![Open Stand badge](http://standards.ieee.org/images/openstand/128x128-blue2.png)](https://open-stand.org/about-us/principles/).
+
 
 CWL builds on technologies such as [JSON-LD](http://json-ld.org)
 for data modeling and [Docker](http://docker.com) for portable runtime
@@ -30,12 +32,7 @@ descriptions.
 
 For developers and advanced users, the current
 [CWL specification (v1.0)](http://www.commonwl.org/v1.0/) provides
-authoritative documentation of the execution of CWL documents.  Links older
-drafts:
-[draft-1](https://github.com/common-workflow-language/common-workflow-language/tree/master/draft-1),
-[draft-2](http://www.commonwl.org/draft-2/),
-[draft-3](http://www.commonwl.org/draft-3/)
-
+authoritative documentation of the execution of CWL documents.
 ### Citation
 
 Please cite https://dx.doi.org/10.6084/m9.figshare.3115156.v2
@@ -137,6 +134,7 @@ Conduct](https://github.com/common-workflow-language/common-workflow-language/bl
 * [Institute for Systems Biology](https://www.systemsbiology.org/)
 * [ELIXIR Europe](https://www.elixir-europe.org/)
 * [BioExcel CoE](http://bioexcel.eu/)
+* [BD2K](https://commonfund.nih.gov/bd2k)
 
 ## Individual Contributors
 

cwltool/schemas/doc/cli-description-languages-comparison.md

@@ -0,0 +1,53 @@
+# Comparison of Command Line Interface description languages
+
+## Compared languages
+
+* Galaxy v17.05: https://github.com/galaxyproject/galaxy/blob/release_17.05/lib/galaxy/tools/xsd/galaxy.xsd
+* CTD v1.7.0 : https://github.com/WorkflowConversion/CTDSchema/blob/Version_1_7_0/CTD.xsd
+* CWL v1.0: http://www.commonwl.org/v1.0/CommandLineTool.html / https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/CommandLineTool.yml
+
+## Summary
+
+### Tool description
+CTD reflects the perspective of a tool author targetting the KNIME processing unit approach ("nodes"), whereas 
+Galaxy reflects the perspective of a platform centered around non-developer users interacting with a graphical interface.
+
+### Parameters description
+
+### Data/parameter types
+The typing system for parameters in CTD itself is simpler than the other two, providing mainly support for simple types and input/output files, but excluding arrays/lists and complex types. Galaxy adds GUI specific features (`select`, `drill_down`), domain specific features (`color`, `genome_build`, `data_column`), configuration of web services (`base_url`), and tighter integration with workbench internal data management (`library_data`).
+
+### Command line generation
+All of the specifications include a flexible set of possibilities for the generation of command lines, reflecting the effective heterogeneity of the bioinformatics tools ecosystem ;)
+
+## Comparison table
+
+### Tool level
+
+|Galaxy information   |Optional   |CTD information   |Optional  |CWL information   |Optional   |
+|---|---|---|---|---|---|
+|*description*   |X   |description   |X   |label   |X   |
+|*help*   |X   |*manual*   |X   |*doc*   |X   |
+|*citation*   |X   |*citation* (for the underlying tool, DOI or doc URL)   |X   |*SoftwareRequirement.name.specs* (URI)   |X  |
+|   |   |*ExecutableName* (overrides the name attribute)   |X   |*SoftwareRequirement.name.baseCommand[0]* |X  | 
+|   |   |*ExecutablePath* (specific path to the executable)  |X   | | |
+|*command*+*argument* under parameter |  |*CLItype* list of input commands with elements mapping   |X | *arguments* and/or *inputBindings*  |X   |
+| | |*logs* (retrospective on execution information - if so probably out of scope)|X | | |
+|*tool/outputs/data/@from_work_dir* (name of file to consume)  |X |*relocators* (list of parameters, path pairs)|X |*outputBinding* |X |
+|*@version* (version of wrapper)  |X |*@version* (apprarently version of the tool itself)| |*SoftwareRequirements.name.version* (list of known compatible versions of the underlying tool |X |
+|*@name* (just an identifier, not used to build the command itself)||*@name* (also used to build the command itself, unlesss *ExecutableName* is provided)| |baseCommand[0]|X|
+|often part of the *help* text|X|*docURL* (URL to documentation)||||
+|*edam_topics* and *edam_operations* - categories are external to tool definition, in per-server config (toolconf.xml)|X|*category* (any string)|X|can use EDAM or other 3rd party annotation or derive via identifier from external registry or datatype|
+|(often part of help text)|X|*tags*|X|||
+
+### Parameter level 
+
+**Important remark** The structure of the CTD file is slightly different, because it explicitely allows the definition of "sub-tools" through a nested structure of NODE/ITEM elements. A node is a subgroup of parameters, and ITEM is a parameter.
+Therefore, to focus on Parameter-level information, we consider only the ITEM element here for parameter description in CTD.
+
+|Galaxy information   |Optional   |CTD information   |Optional  |CWL information   |Optional   |
+|---|---|---|---|---|---|
+| *param* or *data* |  | *ITEM* |  | *inputs[n]* or *outputs[n]*  |  |
+|*@name*||*@name*||key of *inp|uts* or *outputs* entry||
+|*@type*||*@type* (Defines the possible types available in the type attribute of ITEM and ITEMLIST.)||type||
+

cwltool/schemas/v1.0/CommandLineTool.yml

@@ -36,10 +36,11 @@ $graph:
     - {$include: intro.md}
 
     - |
-      ## Introduction to v1.0
+      ## Introduction to CWL Command Line Tool standard v1.0
 
       This specification represents the first full release from the CWL group.
-      Since draft-3, version 1.0 introduces the following changes and additions:
+      Since draft-3, version 1.0 introduces the following changes and additions
+      to the CWL Command Line Tool standard:
 
         * The [Directory](#Directory) type.
         * Syntax simplifcations: denoted by the `map<>` syntax. Example: inputs

cwltool/schemas/v1.0/Process.yml

@@ -563,7 +563,9 @@ $graph:
 
     - name: default
       type: Any?
-      jsonldPredicate: "cwl:default"
+      jsonldPredicate:
+        _id: cwl:default
+        noLinkCheck: true
       doc: |
         The default value for this parameter if not provided in the input
         object.

cwltool/schemas/v1.0/Workflow.yml

@@ -34,10 +34,11 @@ $graph:
 
     - |
 
-      ## Introduction to v1.0
+      ## Introduction to CWL Workflow standard v1.0
 
       This specification represents the first full release from the CWL group.
-      Since draft-3, this draft introduces the following changes and additions:
+      Since draft-3, this draft introduces the following changes and additions
+      to the CWL Workflow standard:
 
         * The `inputs` and `outputs` fields have been renamed `in` and `out`.
         * Syntax simplifcations: denoted by the `map<>` syntax. Example: `in`
@@ -260,7 +261,9 @@ $graph:
       doc: |
         The default value for this parameter if there is no `source`
         field.
-      jsonldPredicate: "cwl:default"
+      jsonldPredicate:
+        _id: "cwl:default"
+        noLinkCheck: true
     - name: valueFrom
       type:
         - "null"

cwltool/schemas/v1.0/conformance_test_v1.0.yaml

@@ -981,3 +981,14 @@
       size: 15
   tool: v1.0/imported-hint.cwl
   doc: Test hints with $import
+
+- output: {}
+  job: v1.0/default_path_job.yml
+  tool: v1.0/default_path.cwl
+  doc: Test warning instead of error when default path is not found
+
+- output:
+    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

cwltool/schemas/v1.0/v1.0/default_path.cwl

@@ -0,0 +1,10 @@
+cwlVersion: v1.0
+class: CommandLineTool
+inputs:
+  - id: "file1"
+    type: File
+    default:
+      class: File
+      path: default.txt
+outputs: []
+arguments: [cat,$(inputs.file1.path)]

cwltool/schemas/v1.0/v1.0/default_path_job.yml

@@ -0,0 +1,3 @@
+file1:
+  class: File
+  path: hello.txt

cwltool/schemas/v1.0/v1.0/inline-js.cwl

@@ -0,0 +1,38 @@
+cwlVersion: v1.0
+class: CommandLineTool
+baseCommand: echo
+
+requirements:
+  - class: InlineJavascriptRequirement
+
+inputs:
+  - id: args.py
+    type: File
+    default:
+      class: File
+      location: args.py
+    inputBinding:
+      position: -1
+
+outputs:
+  - id: args
+    type:
+      type: array
+      items: string
+
+baseCommand: python
+
+arguments:
+  - prefix: -A
+    valueFrom: $(1+1)
+  - prefix: -B
+    valueFrom: $("/foo/bar/baz".split('/').slice(-1)[0])
+  - prefix: -C
+    valueFrom: |
+      ${
+        var r = [];
+        for (var i = 10; i >= 1; i--) {
+          r.push(i);
+        }
+        return r;
+      }

cwltool/schemas/v1.1.0-dev1/Process.yml

@@ -564,7 +564,9 @@ $graph:
 
     - name: default
       type: Any?
-      jsonldPredicate: "cwl:default"
+      jsonldPredicate:
+        _id: cwl:default
+        noLinkCheck: true
       doc: |
         The default value for this parameter if not provided in the input
         object.

cwltool/schemas/v1.1.0-dev1/Workflow.yml

@@ -267,7 +267,9 @@ $graph:
       doc: |
         The default value for this parameter if there is no `source`
         field.
-      jsonldPredicate: "cwl:default"
+      jsonldPredicate:
+        _id: "cwl:default"
+        noLinkCheck: true
     - name: valueFrom
       type:
         - "null"

cwltool/schemas/v1.1.0-dev1/conformance_test_v1.1.0-dev1.yaml

@@ -992,3 +992,8 @@
       size: 15
   tool: v1.1.0-dev1/imported-hint.cwl
   doc: Test hints with $import
+
+- output: {}
+  job: v1.0/default_path_job.yml
+  tool: v1.0/default_path.cwl
+  doc: Test warning instead of error when default path is not found

cwltool/schemas/v1.1.0-dev1/v1.1.0-dev1/default_path.cwl

@@ -0,0 +1,10 @@
+cwlVersion: v1.0
+class: CommandLineTool
+inputs:
+  - id: "file1"
+    type: File
+    default:
+      class: File
+      path: default.txt
+outputs: []
+arguments: [cat,$(inputs.file1.path)]

cwltool/schemas/v1.1.0-dev1/v1.1.0-dev1/default_path_job.yml

@@ -0,0 +1,3 @@
+file1:
+  class: File
+  path: hello.txt