skip $import: with a #local-ref; better handle $import and "run" references to parent directories

MANIFEST.in

@@ -1,3 +1,4 @@
 include MANIFEST.in Makefile
 include cwlupgrader/py.typed
 recursive-include testdata *.cwl
+recursive-include testdata *.yml

setup.py

@@ -24,7 +24,9 @@
     packages=["cwlupgrader", "cwlupgrader.tests"],
     include_package_data=True,
     package_dir={"cwlupgrader.tests": "tests"},
-    package_data={"cwlupgrader.tests": ["../testdata/**/*.cwl"]},
+    package_data={
+        "cwlupgrader.tests": ["../testdata/**/*.cwl", "../testdata/**/*.yml"]
+    },
     install_requires=[
         "setuptools",
         "ruamel.yaml >= 0.16.0, < 0.18",

testdata/v1.0/params_inc.yml

@@ -0,0 +1,120 @@
+  - id: t1
+    type: Any
+    outputBinding:
+      outputEval: $(inputs)
+  - id: t2
+    type: Any
+    outputBinding:
+      outputEval: $(inputs.bar)
+  - id: t3
+    type: Any
+    outputBinding:
+      outputEval: $(inputs['bar'])
+  - id: t4
+    type: Any
+    outputBinding:
+      outputEval: $(inputs["bar"])
+
+  - id: t5
+    type: Any
+    outputBinding:
+      outputEval: $(inputs.bar.baz)
+  - id: t6
+    type: Any
+    outputBinding:
+      outputEval: $(inputs['bar'].baz)
+  - id: t7
+    type: Any
+    outputBinding:
+      outputEval: $(inputs['bar']["baz"])
+  - id: t8
+    type: Any
+    outputBinding:
+      outputEval: $(inputs.bar['baz'])
+
+  - id: t9
+    type: Any
+    outputBinding:
+      outputEval: $(inputs.bar['b az'])
+  - id: t10
+    type: Any
+    outputBinding:
+      outputEval: $(inputs.bar['b\'az'])
+  - id: t11
+    type: Any
+    outputBinding:
+      outputEval: $(inputs.bar["b'az"])
+  - id: t12
+    type: "null"
+    outputBinding:
+      outputEval: $(inputs.bar['b"az'])
+
+  - id: t13
+    type: Any
+    outputBinding:
+      outputEval: -$(inputs.bar.baz)
+  - id: t14
+    type: Any
+    outputBinding:
+      outputEval: -$(inputs['bar'].baz)
+  - id: t15
+    type: Any
+    outputBinding:
+      outputEval: -$(inputs['bar']["baz"])
+  - id: t16
+    type: Any
+    outputBinding:
+      outputEval: -$(inputs.bar['baz'])
+
+  - id: t17
+    type: Any
+    outputBinding:
+      outputEval: $(inputs.bar.baz) $(inputs.bar.baz)
+  - id: t18
+    type: Any
+    outputBinding:
+      outputEval: $(inputs['bar'].baz) $(inputs['bar'].baz)
+  - id: t19
+    type: Any
+    outputBinding:
+      outputEval: $(inputs['bar']["baz"]) $(inputs['bar']["baz"])
+  - id: t20
+    type: Any
+    outputBinding:
+      outputEval: $(inputs.bar['baz']) $(inputs.bar['baz'])
+
+  - id: t21
+    type: Any
+    outputBinding:
+      outputEval: $(inputs.bar['b az']) $(inputs.bar['b az'])
+  - id: t22
+    type: Any
+    outputBinding:
+      outputEval: $(inputs.bar['b\'az']) $(inputs.bar['b\'az'])
+  - id: t23
+    type: Any
+    outputBinding:
+      outputEval: $(inputs.bar["b'az"]) $(inputs.bar["b'az"])
+  - id: t24
+    type: Any
+    outputBinding:
+      outputEval: $(inputs.bar['b"az']) $(inputs.bar['b"az'])
+
+  - id: t25
+    type: Any
+    outputBinding:
+      outputEval: $(inputs.bar.buz[1])
+  - id: t26
+    type: Any
+    outputBinding:
+      outputEval: $(inputs.bar.buz[1]) $(inputs.bar.buz[1])
+
+  - id: t27
+    type: "null"
+    outputBinding:
+      outputEval: $(null)
+
+  - id: t28
+    type: int
+    outputBinding:
+      outputEval: $(inputs.bar.buz.length)

testdata/v1.0/subdir/params.cwl

@@ -0,0 +1,19 @@
+class: CommandLineTool
+cwlVersion: v1.0
+hints:
+  ResourceRequirement:
+    ramMin: 8
+inputs:
+  bar:
+    type: Any
+    default: {
+          "baz": "zab1",
+          "b az": 2,
+          "b'az": true,
+          'b"az': null,
+          "buz": ['a', 'b', 'c']
+        }
+
+outputs: {"$import": ../params_inc.yml}
+
+baseCommand: "true"

testdata/v1.1/params_inc.yml

@@ -0,0 +1,120 @@
+- id: t1
+  type: Any
+  outputBinding:
+    outputEval: $(inputs)
+- id: t2
+  type: Any
+  outputBinding:
+    outputEval: $(inputs.bar)
+- id: t3
+  type: Any
+  outputBinding:
+    outputEval: $(inputs['bar'])
+- id: t4
+  type: Any
+  outputBinding:
+    outputEval: $(inputs["bar"])
+
+- id: t5
+  type: Any
+  outputBinding:
+    outputEval: $(inputs.bar.baz)
+- id: t6
+  type: Any
+  outputBinding:
+    outputEval: $(inputs['bar'].baz)
+- id: t7
+  type: Any
+  outputBinding:
+    outputEval: $(inputs['bar']["baz"])
+- id: t8
+  type: Any
+  outputBinding:
+    outputEval: $(inputs.bar['baz'])
+
+- id: t9
+  type: Any
+  outputBinding:
+    outputEval: $(inputs.bar['b az'])
+- id: t10
+  type: Any
+  outputBinding:
+    outputEval: $(inputs.bar['b\'az'])
+- id: t11
+  type: Any
+  outputBinding:
+    outputEval: $(inputs.bar["b'az"])
+- id: t12
+  type: "null"
+  outputBinding:
+    outputEval: $(inputs.bar['b"az'])
+
+- id: t13
+  type: Any
+  outputBinding:
+    outputEval: -$(inputs.bar.baz)
+- id: t14
+  type: Any
+  outputBinding:
+    outputEval: -$(inputs['bar'].baz)
+- id: t15
+  type: Any
+  outputBinding:
+    outputEval: -$(inputs['bar']["baz"])
+- id: t16
+  type: Any
+  outputBinding:
+    outputEval: -$(inputs.bar['baz'])
+
+- id: t17
+  type: Any
+  outputBinding:
+    outputEval: $(inputs.bar.baz) $(inputs.bar.baz)
+- id: t18
+  type: Any
+  outputBinding:
+    outputEval: $(inputs['bar'].baz) $(inputs['bar'].baz)
+- id: t19
+  type: Any
+  outputBinding:
+    outputEval: $(inputs['bar']["baz"]) $(inputs['bar']["baz"])
+- id: t20
+  type: Any
+  outputBinding:
+    outputEval: $(inputs.bar['baz']) $(inputs.bar['baz'])
+
+- id: t21
+  type: Any
+  outputBinding:
+    outputEval: $(inputs.bar['b az']) $(inputs.bar['b az'])
+- id: t22
+  type: Any
+  outputBinding:
+    outputEval: $(inputs.bar['b\'az']) $(inputs.bar['b\'az'])
+- id: t23
+  type: Any
+  outputBinding:
+    outputEval: $(inputs.bar["b'az"]) $(inputs.bar["b'az"])
+- id: t24
+  type: Any
+  outputBinding:
+    outputEval: $(inputs.bar['b"az']) $(inputs.bar['b"az'])
+
+- id: t25
+  type: Any
+  outputBinding:
+    outputEval: $(inputs.bar.buz[1])
+- id: t26
+  type: Any
+  outputBinding:
+    outputEval: $(inputs.bar.buz[1]) $(inputs.bar.buz[1])
+
+- id: t27
+  type: "null"
+  outputBinding:
+    outputEval: $(null)
+
+- id: t28
+  type: int
+  outputBinding:
+    outputEval: $(inputs.bar.buz.length)

testdata/v1.1/subdir/params.cwl

@@ -0,0 +1,18 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.1
+class: CommandLineTool
+requirements:
+  NetworkAccess:
+    networkAccess: true
+  LoadListingRequirement:
+    loadListing: deep_listing
+hints:
+  ResourceRequirement:
+    ramMin: 8
+inputs:
+  bar:
+    type: Any
+    default: {"baz": "zab1", "b az": 2, "b'az": true, 'b"az': null, "buz": ['a', 'b',
+        'c']}
+baseCommand: "true"
+outputs: {"$import": ../params_inc.yml}

tests/test_complete.py

@@ -37,54 +37,54 @@ def test_draft3_tool_long_form_arrays(tmp_path: Path) -> None:
 def test_invalid_target(tmp_path: Path) -> None:
     """Test for invalid target version"""
     doc = load_cwl_document(get_data("testdata/v1.0/listing_deep1.cwl"))
-    result = upgrade_document(doc, str(tmp_path), "invalid-version")
+    result = upgrade_document(doc, tmp_path, tmp_path, "invalid-version")
     assert result is None
 
 
 def test_v1_0_to_v1_1_load_listing(tmp_path: Path) -> None:
     """Basic CWL v1.0 to CWL v1.1 test with LoadListingRequirement (map notation)."""
     doc = load_cwl_document(get_data("testdata/v1.0/listing_deep1.cwl"))
-    upgraded = upgrade_document(doc, str(tmp_path), "v1.1")
+    upgraded = upgrade_document(doc, tmp_path, tmp_path, "v1.1")
     expected = load_cwl_document(get_data("testdata/v1.1/listing_deep1.cwl"))
     assert upgraded == expected
 
 
 def test_v1_0_to_v1_1_load_listing_arr(tmp_path: Path) -> None:
     """Basic CWL v1.0 to CWL v1.1 test with LoadListingRequirement (array notation)."""
     doc = load_cwl_document(get_data("testdata/v1.0/listing_deep1-arr.cwl"))
-    upgraded = upgrade_document(doc, str(tmp_path), "v1.1")
+    upgraded = upgrade_document(doc, tmp_path, tmp_path, "v1.1")
     expected = load_cwl_document(get_data("testdata/v1.1/listing_deep1-arr.cwl"))
     assert upgraded == expected
 
 
 def test_v1_0_to_v1_1_network_access(tmp_path: Path) -> None:
     """Basic CWL v1.0 to CWL v1.1 test with NetworkAccess."""
     doc = load_cwl_document(get_data("testdata/v1.0/networkaccess.cwl"))
-    upgraded = upgrade_document(doc, str(tmp_path), "v1.1")
+    upgraded = upgrade_document(doc, tmp_path, tmp_path, "v1.1")
     expected = load_cwl_document(get_data("testdata/v1.1/networkaccess.cwl"))
     assert upgraded == expected
 
 
 def test_v1_1_to_v1_2(tmp_path: Path) -> None:
     """Basic CWL v1.1 to CWL v1.2 test."""
     doc = load_cwl_document(get_data("testdata/v1.1/listing_deep1.cwl"))
-    upgraded = upgrade_document(doc, str(tmp_path), "v1.2")
+    upgraded = upgrade_document(doc, tmp_path, tmp_path, "v1.2")
     expected = load_cwl_document(get_data("testdata/v1.2/listing_deep1.cwl"))
     assert upgraded == expected
 
 
 def test_v1_2_to_v1_2(tmp_path: Path) -> None:
     """CWL v1.2 to CWL v1.2 no change test."""
     doc = load_cwl_document(get_data("testdata/v1.2/networkaccess.cwl"))
-    upgraded = upgrade_document(doc, str(tmp_path), "v1.2")
+    upgraded = upgrade_document(doc, tmp_path, tmp_path, "v1.2")
     expected = load_cwl_document(get_data("testdata/v1.2/networkaccess.cwl"))
     assert upgraded == expected
 
 
 def test_v1_2_to_latest(tmp_path: Path) -> None:
     """CWL v1.2 to latest no change test."""
     doc = load_cwl_document(get_data("testdata/v1.2/networkaccess.cwl"))
-    upgraded = upgrade_document(doc, str(tmp_path), "latest")
+    upgraded = upgrade_document(doc, tmp_path, tmp_path, "latest")
     expected = load_cwl_document(get_data("testdata/v1.2/networkaccess.cwl"))
     assert upgraded == expected