Merge pull request #67 from ResearchObject/upgrade_cwl_utils

upgrade to cwl-utils 0.30

requirements.txt

@@ -1,7 +1,7 @@
 bdbag>=1.4.1
 click~=8.1
-cwl-utils==0.31
+cwl-utils==0.32
 cwlprov==0.1.1
 networkx==3.1
 prov>=1.5.1
-rocrate~=0.9
+rocrate>=0.9,<1

setup.cfg

@@ -32,11 +32,11 @@ python_requires=>=3.8, <4
 install_requires=
     bdbag>=1.4.1
     click~=8.1
-    cwl-utils==0.31
+    cwl-utils==0.32
     cwlprov==0.1.1
     networkx==3.1
     prov>=1.5.1
-    rocrate~=0.9
+    rocrate>=0.9,<1
 
 [options.entry_points]
 console_scripts=

src/runcrate/convert.py

@@ -72,18 +72,18 @@ def convert_cwl_type(cwl_type):
         return s.pop() if len(s) == 1 else sorted(s)
     if isinstance(cwl_type, str):
         return CWL_TYPE_MAP[cwl_type]
-    if cwl_type.type == "enum":
+    if cwl_type.type_ == "enum":
         return "Text"  # use actionOption to represent choices?
-    if cwl_type.type == "array":
+    if cwl_type.type_ == "array":
         return convert_cwl_type(cwl_type.items)
-    if cwl_type.type == "record":
+    if cwl_type.type_ == "record":
         return "PropertyValue"
 
 
 def properties_from_cwl_param(cwl_p):
     def is_structured(cwl_type):
-        return getattr(cwl_type, "type", None) in ("array", "record")
-    additional_type = "Collection" if cwl_p.secondaryFiles else convert_cwl_type(cwl_p.type)
+        return getattr(cwl_type, "type_", None) in ("array", "record")
+    additional_type = "Collection" if cwl_p.secondaryFiles else convert_cwl_type(cwl_p.type_)
     properties = {
         "@type": "FormalParameter",
         "additionalType": additional_type
@@ -95,20 +95,21 @@ def is_structured(cwl_type):
         properties["description"] = cwl_p.label
     if cwl_p.format:
         properties["encodingFormat"] = cwl_p.format
-    if isinstance(cwl_p.type, list) and "null" in cwl_p.type:
+    if isinstance(cwl_p.type_, list) and "null" in cwl_p.type_:
         properties["valueRequired"] = "False"
-    if is_structured(cwl_p.type):
+    if is_structured(cwl_p.type_):
         properties["multipleValues"] = "True"
     if hasattr(cwl_p, "default"):
-        if hasattr(cwl_p.default, "class_") and cwl_p.default.class_ in ("File", "Directory"):
-            default = cwl_p.default.location or cwl_p.default.path
+        if isinstance(cwl_p.default, dict):
+            if cwl_p.default.get("class") in ("File", "Directory"):
+                default = cwl_p.default.get("location", cwl_p.default.get("path"))
             if default:
                 properties["defaultValue"] = default
-        elif not is_structured(cwl_p.type) and cwl_p.default is not None:
+        elif not is_structured(cwl_p.type_) and cwl_p.default is not None:
             properties["defaultValue"] = str(cwl_p.default)
         # TODO: support more cases
-    if getattr(cwl_p.type, "type", None) == "enum":
-        properties["valuePattern"] = "|".join(_.rsplit("/", 1)[-1] for _ in cwl_p.type.symbols)
+    if getattr(cwl_p.type_, "type_", None) == "enum":
+        properties["valuePattern"] = "|".join(_.rsplit("/", 1)[-1] for _ in cwl_p.type_.symbols)
     return properties
 
 

tests/test_cli.py

@@ -26,7 +26,8 @@ def test_cli_convert(data_dir, tmpdir, monkeypatch):
     root = data_dir / "revsort-run-1"
     runner = CliRunner()
     args = ["convert", str(root)]
-    assert runner.invoke(cli, args).exit_code == 0
+    result = runner.invoke(cli, args)
+    assert result.exit_code == 0, result.exception
     crate_zip = tmpdir / f"{root.name}.crate.zip"
     assert crate_zip.is_file()
     crate = ROCrate(crate_zip)
@@ -41,7 +42,8 @@ def test_cli_convert_output(data_dir, tmpdir):
     crate_zip = tmpdir / "crate.zip"
     runner = CliRunner()
     args = ["convert", str(root), "-o", str(crate_zip)]
-    assert runner.invoke(cli, args).exit_code == 0
+    result = runner.invoke(cli, args)
+    assert result.exit_code == 0, result.exception
     assert crate_zip.is_file()
     crate = ROCrate(crate_zip)
     assert not crate.root_dataset.get("license")
@@ -52,7 +54,8 @@ def test_cli_convert_output(data_dir, tmpdir):
     crate_dir = tmpdir / "revsort-run-1-crate"
     runner = CliRunner()
     args = ["convert", str(root), "-o", str(crate_dir)]
-    assert runner.invoke(cli, args).exit_code == 0
+    result = runner.invoke(cli, args)
+    assert result.exit_code == 0, result.exception
     assert crate_dir.is_dir()
     crate = ROCrate(crate_dir)
     assert not crate.root_dataset.get("license")
@@ -66,7 +69,8 @@ def test_cli_convert_license(data_dir, tmpdir):
     license = "MIT"
     runner = CliRunner()
     args = ["convert", str(root), "-o", str(crate_dir), "-l", license]
-    assert runner.invoke(cli, args).exit_code == 0
+    result = runner.invoke(cli, args)
+    assert result.exit_code == 0, result.exception
     crate = ROCrate(crate_dir)
     assert crate.root_dataset["license"] == license
 
@@ -77,7 +81,8 @@ def test_cli_convert_workflow_name(data_dir, tmpdir):
     workflow_name = "RevSort"
     runner = CliRunner()
     args = ["convert", str(root), "-o", str(crate_dir), "-w", workflow_name]
-    assert runner.invoke(cli, args).exit_code == 0
+    result = runner.invoke(cli, args)
+    assert result.exit_code == 0, result.exception
     crate = ROCrate(crate_dir)
     workflow = crate.mainEntity
     assert workflow["name"] == workflow_name
@@ -89,7 +94,8 @@ def test_cli_convert_readme(data_dir, tmpdir):
     readme = data_dir / "README.md"
     runner = CliRunner()
     args = ["convert", str(root), "-o", str(crate_dir), "--readme", readme]
-    assert runner.invoke(cli, args).exit_code == 0
+    result = runner.invoke(cli, args)
+    assert result.exit_code == 0, result.exception
     crate = ROCrate(crate_dir)
     assert crate.get(readme.name)
 
@@ -108,7 +114,7 @@ def test_cli_report_provenance_minimal(data_dir, caplog):
 def test_cli_version():
     runner = CliRunner()
     result = runner.invoke(cli, ["version"])
-    assert result.exit_code == 0
+    assert result.exit_code == 0, result.exception
     assert result.stdout.strip() == __version__
 
 
@@ -118,7 +124,7 @@ def test_cli_run(data_dir, tmpdir, monkeypatch):
     args = ["run", str(crate_dir)]
     monkeypatch.chdir(str(tmpdir))
     result = runner.invoke(cli, args)
-    assert result.exit_code == 0
+    assert result.exit_code == 0, result.exception
     out_path = Path("output.txt")
     assert out_path.is_file()
     crate_out_path = crate_dir / "4bd8e7e358488e833bf32cf5028695292cecb05b"
@@ -131,7 +137,7 @@ def test_cli_run_dir_array(data_dir, tmpdir, monkeypatch):
     args = ["run", str(crate_dir)]
     monkeypatch.chdir(str(tmpdir))
     result = runner.invoke(cli, args)
-    assert result.exit_code == 0
+    assert result.exit_code == 0, result.exception
 
 
 def test_cli_run_file_array(data_dir, tmpdir, monkeypatch):
@@ -140,4 +146,4 @@ def test_cli_run_file_array(data_dir, tmpdir, monkeypatch):
     args = ["run", str(crate_dir)]
     monkeypatch.chdir(str(tmpdir))
     result = runner.invoke(cli, args)
-    assert result.exit_code == 0
+    assert result.exit_code == 0, result.exception