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

Use schema salad

Author: tetron

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/return-0.cwl

@@ -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 ]
-