Fix #77: Unify v1*_only parameter into target_version (#79)

Author: tom-tan

cwlupgrader/main.py

@@ -76,43 +76,78 @@ def run(args: argparse.Namespace) -> int:
                 if args.v1_1_only:
                     _logger.info("Skipping v1.1 document as requested: %s.", path)
                     continue
+
+            if args.v1_only:
+                target_version = "v1.0"
+            elif args.v1_1_only:
+                target_version = "v1.1"
+            else:
+                target_version = "latest"
             upgraded_document = upgrade_document(
-                document, args.v1_only, args.v1_1_only, args.dir, imports
+                document,
+                args.dir,
+                target_version=target_version,
+                imports=imports,
             )
             write_cwl_document(upgraded_document, Path(path).name, args.dir)
     return 0
 
 
 def upgrade_document(
-    document: Any, v1_only: bool, v1_1_only: bool, output_dir: str, imports: Set[str]
+    document: Any,
+    output_dir: str,
+    target_version: Optional[str] = "latest",
+    imports: Optional[Set[str]] = None,
 ) -> Any:
+    if imports is None:
+        imports = set()
+    supported_versions = ["v1.0", "v1.1", "v1.2", "latest"]
+    if target_version not in supported_versions:
+        _logger.error(f"Unsupported target cwlVersion: {target_version}")
+        return
     version = document["cwlVersion"]
     if version == "cwl:draft-3" or version == "draft-3":
-        if v1_only:
+        if target_version == "v1.0":
             main_updater = draft3_to_v1_0
             inner_updater = _draft3_to_v1_0
-        elif v1_1_only:
+        elif target_version == "v1.1":
             main_updater = draft3_to_v1_1
             inner_updater = _draft3_to_v1_1
-        else:
+        elif target_version == "v1.2":
             main_updater = draft3_to_v1_2
             inner_updater = _draft3_to_v1_2
+        elif target_version == "latest":
+            main_updater = draft3_to_v1_2
+            inner_updater = _draft3_to_v1_2
+        else:
+            pass  # does not happen
     elif version == "v1.0":
-        if v1_only:
+        if target_version == "v1.0":
             _logger.info("Skipping v1.0 document as requested.")
             return
-        elif v1_1_only:
+        elif target_version == "v1.1":
             main_updater = v1_0_to_v1_1
             inner_updater = _v1_0_to_v1_1
-        else:
+        elif target_version == "v1.2":
+            main_updater = v1_0_to_v1_2
+            inner_updater = _v1_0_to_v1_2
+        elif target_version == "latest":
             main_updater = v1_0_to_v1_2
             inner_updater = _v1_0_to_v1_2
+        else:
+            pass  # does not happen
     elif version == "v1.1":
-        if v1_1_only:
+        if target_version == "v1.1":
             _logger.info("Skipping v1.1 document as requested.")
             return
-        main_updater = v1_1_to_v1_2
-        inner_updater = _v1_1_to_v1_2
+        elif target_version == "v1.2":
+            main_updater = v1_1_to_v1_2
+            inner_updater = _v1_1_to_v1_2
+        elif target_version == "latest":
+            main_updater = v1_1_to_v1_2
+            inner_updater = _v1_1_to_v1_2
+        else:
+            pass  # does not happen? How to do the case that base version is v1.0?
     else:
         _logger.error(f"Unsupported cwlVersion: {version}")
     process_imports(document, imports, inner_updater, output_dir)

testdata/v1.0/listing_deep1.cwl

@@ -0,0 +1,13 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: v1.0
+requirements:
+  InlineJavascriptRequirement: {}
+inputs:
+  d: Directory
+outputs:
+  out:
+    type: boolean
+    outputBinding:
+      outputEval: '$(inputs.d.listing.length === 1 && inputs.d.listing[0].listing.length === 1)'
+baseCommand: "true"

testdata/v1.1/listing_deep1.cwl

@@ -0,0 +1,15 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: v1.1
+requirements:
+  LoadListingRequirement:
+    loadListing: deep_listing
+  InlineJavascriptRequirement: {}
+inputs:
+  d: Directory
+outputs:
+  out:
+    type: boolean
+    outputBinding:
+      outputEval: '$(inputs.d.listing.length === 1 && inputs.d.listing[0].listing.length === 1)'
+baseCommand: "true"

testdata/v1.2/listing_deep1.cwl

@@ -0,0 +1,15 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: v1.2
+requirements:
+  LoadListingRequirement:
+    loadListing: deep_listing
+  InlineJavascriptRequirement: {}
+inputs:
+  d: Directory
+outputs:
+  out:
+    type: boolean
+    outputBinding:
+      outputEval: '$(inputs.d.listing.length === 1 && inputs.d.listing[0].listing.length === 1)'
+baseCommand: "true"

tests/test_complete.py

@@ -1,7 +1,7 @@
 import filecmp
 from pathlib import Path
 
-from cwlupgrader.main import main
+from cwlupgrader.main import load_cwl_document, main, upgrade_document
 
 from .util import get_data
 
@@ -15,3 +15,24 @@ def test_draft3_workflow(tmp_path: Path) -> None:
         shallow=False,
     )
     assert result
+
+
+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")
+    assert result is None
+
+
+def test_v1_0_to_v1_1(tmp_path: Path) -> None:
+    """Basic CWL v1.0 to CWL v1.1 test."""
+    doc = load_cwl_document(get_data("testdata/v1.0/listing_deep1.cwl"))
+    upgraded = upgrade_document(doc, str(tmp_path), "v1.1")
+    assert doc == upgraded
+
+
+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")
+    assert doc == upgraded