Merge pull request #104 from common-workflow-language/use-schema-salad

Use schema salad

MANIFEST.in

@@ -1,6 +1,7 @@
 include Makefile gittaggers.py
+include cwltest/cwltest-schema.yml
 include cwltest/tests/*
 include cwltest/tests/test-data/*
+include cwltest/tests/test-data/v1.0/*
 global-exclude *~
 global-exclude *.pyc
-

cwltest/__init__.py

@@ -16,6 +16,8 @@
 import ruamel.yaml as yaml
 import ruamel.yaml.scanner as yamlscanner
 import schema_salad.ref_resolver
+import schema_salad.schema
+import schema_salad.avro.schema
 import pkg_resources  # part of setuptools
 
 import junit_xml
@@ -49,6 +51,7 @@ def prepare_test_command(
     args,  # type: List[str]
     testargs,  # type: Optional[List[str]]
     test,  # type: Dict[str, str]
+    cwd,  # type: str
     verbose=False,  # type: bool
 ):  # type: (...) -> List[str]
     """ Turn the test into a command line. """
@@ -77,9 +80,18 @@ def prepare_test_command(
     test_command.extend(["--outdir={}".format(outdir)])
     if not verbose:
         test_command.extend(["--quiet"])
-    test_command.extend([os.path.normcase(test["tool"])])
-    if test.get("job"):
-        test_command.append(os.path.normcase(test["job"]))
+
+    cwd = schema_salad.ref_resolver.file_uri(cwd)
+    toolpath = test["tool"]
+    if toolpath.startswith(cwd):
+        toolpath = toolpath[len(cwd)+1:]
+    test_command.extend([os.path.normcase(toolpath)])
+
+    jobpath = test.get("job")
+    if jobpath:
+        if jobpath.startswith(cwd):
+            jobpath = jobpath[len(cwd)+1:]
+        test_command.append(os.path.normcase(jobpath))
     return test_command
 
 
@@ -106,8 +118,9 @@ def run_test(
         suffix = "\n"
     try:
         process = None  # type: Optional[subprocess.Popen[str]]
+        cwd = os.getcwd()
         test_command = prepare_test_command(
-            args.tool, args.args, args.testargs, test, verbose
+            args.tool, args.args, args.testargs, test, cwd, verbose
         )
 
         if test.get("short_name"):
@@ -131,7 +144,7 @@ def run_test(
 
         start_time = time.time()
         stderr = subprocess.PIPE if not args.verbose else None
-        process = subprocess.Popen(test_command, stdout=subprocess.PIPE, stderr=stderr, universal_newlines=True)
+        process = subprocess.Popen(test_command, stdout=subprocess.PIPE, stderr=stderr, universal_newlines=True, cwd=cwd)
         outstr, outerr = process.communicate(timeout=timeout)
         return_code = process.poll()
         duration = time.time() - start_time
@@ -342,8 +355,18 @@ def main():  # type: () -> int
         arg_parser().print_help()
         return 1
 
-    with open(args.test) as f:
-        tests = yaml.load(f, Loader=yaml.SafeLoader)
+    schema_resource = pkg_resources.resource_stream(__name__, "cwltest-schema.yml")
+    cache = {"https://w3id.org/cwl/cwltest/cwltest-schema.yml": schema_resource.read().decode("utf-8")}
+    (document_loader,
+     avsc_names,
+     schema_metadata,
+     metaschema_loader) = schema_salad.schema.load_schema("https://w3id.org/cwl/cwltest/cwltest-schema.yml", cache=cache)
+
+    if not isinstance(avsc_names, schema_salad.avro.schema.Names):
+        print(avsc_names)
+        return 1
+
+    tests, metadata = schema_salad.schema.load_and_validate(document_loader, avsc_names, args.test, True)
 
     failures = 0
     unsupported = 0
@@ -378,6 +401,10 @@ def main():  # type: () -> int
             if any((tag in ts for tag in tags)):
                 tests.append(t)
 
+    for t in tests:
+        if t.get("label"):
+            t["short_name"] = t["label"]
+
     if args.l:
         for i, t in enumerate(tests):
             if t.get("short_name"):

cwltest/cwltest-schema.yml

@@ -0,0 +1,26 @@
+$base: "https://w3id.org/cwl/cwltest#"
+$graph:
+  - name: TestCase
+    type: record
+    documentRoot: true
+    fields:
+      id:
+        type: ["null", int, string]
+        jsonldPredicate:
+          _type: "@id"
+          identity: true
+      label: string?
+      short_name: string?
+      doc: string?
+      tags: string[]?
+      tool:
+        type: string
+        jsonldPredicate:
+          _type: "@id"
+      job:
+        type: string?
+        jsonldPredicate:
+          _type: "@id"
+      should_fail: boolean?
+      output:
+        type: Any?

cwltest/tests/mock_cwl_runner.py

@@ -16,9 +16,9 @@ def main():  # type: ()->int
 
     args = parser.parse_args()
 
-    if args.processfile == UNSUPPORTED_FEATURE_TOOL:
+    if args.processfile.endswith(UNSUPPORTED_FEATURE_TOOL):
         exit(UNSUPPORTED_FEATURE)
-    elif args.processfile == ERROR_TOOL:
+    elif args.processfile.endswith(ERROR_TOOL):
         exit(1)
 
     exit(0)

cwltest/tests/test-data/short-names.yml

@@ -2,6 +2,5 @@
   output: {}
   tool: return-0.cwl
   doc: Test with a short name
-  short_name: opt-error
+  label: opt-error
   tags: [ js, init_work_dir ]
-

cwltest/tests/test_categories.py

@@ -6,12 +6,20 @@
 
 from .util import run_with_mock_cwl_runner, get_data
 import xml.etree.ElementTree as ET
-
+import schema_salad.ref_resolver
 
 class TestCategories(unittest.TestCase):
+    maxDiff = None
+
     def test_unsupported_with_required_tests(self):
-        args = ["--test", get_data("tests/test-data/required-unsupported.yml")]
-        error_code, stdout, stderr = run_with_mock_cwl_runner(args)
+        args = ["--test", schema_salad.ref_resolver.file_uri(get_data("tests/test-data/required-unsupported.yml"))]
+        try:
+            cwd = os.getcwd()
+            os.chdir(get_data("tests/test-data/"))
+            error_code, stdout, stderr = run_with_mock_cwl_runner(args)
+        finally:
+            os.chdir(cwd)
+
         self.assertEqual(error_code, 1)
         print(stderr)
         stderr = re.sub(r" '?--outdir=[^ ]*", "", stderr)
@@ -39,7 +47,7 @@ def test_unsupported_with_required_tests(self):
         )
 
     def test_unsupported_with_optional_tests(self):
-        args = ["--test", get_data("tests/test-data/optional-unsupported.yml")]
+        args = ["--test", schema_salad.ref_resolver.file_uri(get_data("tests/test-data/optional-unsupported.yml"))]
         error_code, stdout, stderr = run_with_mock_cwl_runner(args)
         self.assertEqual(error_code, 0)
         self.assertEqual(
@@ -50,7 +58,7 @@ def test_unsupported_with_optional_tests(self):
         )
 
     def test_error_with_optional_tests(self):
-        args = ["--test", get_data("tests/test-data/optional-error.yml")]
+        args = ["--test", schema_salad.ref_resolver.file_uri(get_data("tests/test-data/optional-error.yml"))]
         error_code, stdout, stderr = run_with_mock_cwl_runner(args)
         self.assertEqual(error_code, 1)
         self.assertIn("1 failures", stderr)
@@ -59,7 +67,7 @@ def test_category_in_junit_xml(self):
         junit_xml_report = get_data("tests/test-data/junit-report.xml")
         args = [
             "--test",
-            get_data("tests/test-data/optional-error.yml"),
+            schema_salad.ref_resolver.file_uri(get_data("tests/test-data/optional-error.yml")),
             "--junit-xml",
             junit_xml_report,
         ]

cwltest/tests/test_prepare.py

@@ -19,6 +19,7 @@ def test_unix_relative_path(self):
                 "job": "v1.0/bwa-mem-job.json",
                 "tags": ["required"],
             },
+            cwd=os.getcwd()
         )
         if os.name == "nt":
             self.assertEqual(command[3], "v1.0\\bwa-mem-tool.cwl")

setup.py

@@ -15,7 +15,7 @@
 except ImportError:
     tagger = egg_info_cmd.egg_info
 
-install_requires = ["schema-salad >= 2", "junit-xml >= 1.8"]
+install_requires = ["schema-salad >= 5.0.20200220195218", "junit-xml >= 1.8"]
 
 needs_pytest = {"pytest", "test", "ptr"}.intersection(sys.argv)
 pytest_runner = ["pytest < 6", "pytest-runner < 5"] if needs_pytest else []