Add CWL v1.2 spec to package.

Add test for CWL 1.2 parsing

Closes #99

Author: kghose

benten/000.package.data/schema-v1.2.0.json

@@ -77,7 +77,7 @@ def _resolve_path(self, path: P):
             return P(self.cfg_path, path)
 
     def _copy_missing_language_files(self):
-        for src_file in default_config_data_dir.glob("schema*.json"):
+        for src_file in default_config_data_dir.glob("schema-*.json"):
             dst_file = P(self.cfg_path, src_file.name)
             if not dst_file.exists():
                 shutil.copy(str(src_file), str(dst_file))

benten/configuration.py

@@ -12,7 +12,7 @@
 logger = logging.getLogger(__name__)
 
 
-latest_published_cwl_version = "v1.2.0-dev3"
+latest_published_cwl_version = "v1.2.0"
 process_types = ["CommandLineTool", "ExpressionTool", "Workflow"]
 
 

benten/cwl/specification.py

@@ -1,3 +1,3 @@
 #  Copyright (c) 2019-2020 Seven Bridges. See LICENSE
 
-__version__ = "2020.06.03"
+__version__ = "2020.09.15"

benten/version.py

@@ -0,0 +1,22 @@
+class: Workflow
+cwlVersion: v1.2
+inputs:
+  val: int
+
+steps:
+
+  step1:
+    in:
+      in1: val
+      a_new_var: val
+    run: foo.cwl
+    when: $(inputs.a_new_var > 2)
+    out: [out1]
+
+outputs:
+  out1: 
+    type: string?
+    outputSource: step1/out1
+
+requirements: 
+  InlineJavascriptRequirement: {}

tests/cwl/cwl-v1.2/cond-wf-001.cwl

@@ -0,0 +1,10 @@
+class: CommandLineTool
+cwlVersion: v1.2
+inputs:
+  in1: int
+baseCommand: [echo]
+outputs:
+  out1:
+    type: string
+    outputBinding:
+      outputEval: foo $(inputs.in1)

tests/cwl/cwl-v1.2/foo.cwl

@@ -21,7 +21,7 @@ def test_ebi_wf_cmsearch_multimodel():
 
 def test_mass_wf_load():
     type_dicts = load_type_dicts()
-    for wf_dir in ["ebi/workflows", "mgi/subworkflows", "mgi/pipelines"]:
+    for wf_dir in ["ebi/workflows", "mgi/subworkflows", "mgi/pipelines", "cwl-v1.2"]:
         path = current_path / "cwl" / wf_dir
         for fname in path.glob("*.cwl"):
             _ = load(doc_path=fname, type_dicts=type_dicts)