Merge branch 'loop_prototype' of github.com:common-workflow-language/cwltool into loop_prototype

Author: mr-c

cwltool/checker.py

@@ -386,6 +386,8 @@ def check_all_types(
                                 message="Source is from conditional step, but pickValue is not used",
                             )
                         )
+                    if is_all_output_method_loop_step(param_to_step, parm_id):
+                        src_dict[parm_id]['type'] = {'type': 'array', 'items': src_dict[parm_id]['type']}
             else:
                 parm_id = cast(str, sink[sourceField])
                 if parm_id not in src_dict:
@@ -427,6 +429,9 @@ def check_all_types(
 
                     srcs_of_sink[0]["type"] = src_typ
 
+                if is_all_output_method_loop_step(param_to_step, parm_id):
+                    src_dict[parm_id]['type'] = {'type': 'array', 'items': src_dict[parm_id]['type']}
+
             for src in srcs_of_sink:
                 check_result = check_types(src, sink, linkMerge, valueFrom)
                 if check_result == "warning":
@@ -514,3 +519,16 @@ def is_conditional_step(param_to_step: Dict[str, CWLObjectType], parm_id: str) -
         if source_step.get("when") is not None:
             return True
     return False
+
+
+def is_all_output_method_loop_step(param_to_step: Dict[str, CWLObjectType], parm_id: str) -> bool:
+    source_step = param_to_step.get(parm_id)
+    if source_step is not None:
+        requirements = {
+            **{h['class']: h for h in source_step.get('hints', [])},
+            **{r['class']: r for r in source_step.get('requirements', [])}}
+        if 'http://commonwl.org/cwltool#Loop' in requirements:
+            output_method = requirements['http://commonwl.org/cwltool#Loop'].get('outputMethod', 'last')
+            if output_method == 'all':
+                return True
+    return False

cwltool/extensions-v1.2.yml

@@ -135,6 +135,9 @@ $graph:
       type:
         - string?
         - string[]?
+      jsonldPredicate:
+        "_type": "@id"
+        refScope: 1
     linkMerge:
       type: cwl:LinkMergeMethod?
       jsonldPredicate: "cwl:linkMerge"

mypy-requirements.txt

@@ -1,4 +1,4 @@
-mypy==0.950
+mypy==0.961
 types-requests
 types-setuptools
 types-psutil

requirements.txt

@@ -1,6 +1,7 @@
 requests>=2.4.3
 ruamel.yaml>=0.15,<0.17.22
 rdflib>=4.2.2,<6.2
+rdflib>= 4.2.2, < 6.0.0;python_version<='3.6'
 shellescape>=3.4.1,<3.9
 schema-salad>=8.2.20211104054942,<9
 prov==1.5.1

setup.py

@@ -110,6 +110,7 @@
         # https://github.com/ionrock/cachecontrol/issues/137
         "ruamel.yaml >= 0.15, < 0.17.22",
         "rdflib >= 4.2.2, < 6.2.0",
+        "rdflib >= 4.2.2, < 6.0.0;python_version<='3.6'",
         "shellescape >= 3.4.1, < 3.9",
         "schema-salad >= 8.2.20211104054942, < 9",
         "mypy-extensions",
@@ -134,7 +135,7 @@
         "mock >= 2.0.0",
         "pytest-mock >= 1.10.0",
         "arcp >= 0.2.0",
-        "rdflib-jsonld >= 0.4.0",
+        "rdflib-jsonld>=0.4.0, <= 0.6.1;python_version<='3.6'",
     ],
     entry_points={"console_scripts": ["cwltool=cwltool.main:run"]},
     zip_safe=True,

test-requirements.txt

@@ -4,5 +4,5 @@ mock >= 2.0.0
 pytest-mock >= 1.10.0
 pytest-cov
 arcp >= 0.2.0
-rdflib-jsonld >= 0.4.0
+rdflib-jsonld>=0.4.0, <= 0.6.1;python_version<='3.6'
 -rrequirements.txt