Allow $schemas in codegen (#346)

Author: leipzig

schema_salad/python_codegen.py

@@ -246,9 +246,12 @@ def end_class(self, classname, field_names):
 
         self.serializer.write(
             """
-        if top and self.loadingOptions.namespaces:
-            r["$namespaces"] = self.loadingOptions.namespaces
-
+        # top refers to the directory level
+        if top:
+            if self.loadingOptions.namespaces:
+                r["$namespaces"] = self.loadingOptions.namespaces
+            if self.loadingOptions.schemas:
+                r["$schemas"] = self.loadingOptions.schemas
 """
         )
 

schema_salad/python_codegen_support.py

@@ -44,13 +44,15 @@ def __init__(
         self,
         fetcher=None,  # type: Optional[Fetcher]
         namespaces=None,  # type: Optional[Dict[str, str]]
+        schemas=None,  # type: Optional[Dict[str, str]]
         fileuri=None,  # type: Optional[str]
         copyfrom=None,  # type: Optional[LoadingOptions]
         original_doc=None,  # type: Optional[Any]
     ):  # type: (...) -> None
         self.idx = {}  # type: Dict[str, Dict[str, Any]]
         self.fileuri = fileuri  # type: Optional[str]
         self.namespaces = namespaces
+        self.schemas = schemas
         self.original_doc = original_doc
         if copyfrom is not None:
             self.idx = copyfrom.idx
@@ -60,6 +62,8 @@ def __init__(
                 self.fileuri = copyfrom.fileuri
             if namespaces is None:
                 self.namespaces = copyfrom.namespaces
+            if schemas is None:
+                self.schemas = copyfrom.schemas
 
         if fetcher is None:
             import requests
@@ -466,11 +470,13 @@ def _document_load(loader, doc, baseuri, loadingOptions):
         )
 
     if isinstance(doc, MutableMapping):
-        if "$namespaces" in doc:
+        if "$namespaces" in doc or "$schemas" in doc:
             loadingOptions = LoadingOptions(
-                copyfrom=loadingOptions, namespaces=doc["$namespaces"]
+                copyfrom=loadingOptions,
+                namespaces=doc.get("$namespaces", None),
+                schemas=doc.get("$schemas", None),
             )
-            doc = {k: v for k, v in doc.items() if k != "$namespaces"}
+            doc = {k: v for k, v in doc.items() if k not in ["$namespaces", "$schemas"]}
 
         if "$base" in doc:
             baseuri = doc["$base"]

schema_salad/tests/formattest2.cwl

@@ -0,0 +1,28 @@
+$namespaces:
+  edam: http://edamontology.org/
+$schemas:
+  - EDAM.owl
+class: CommandLineTool
+cwlVersion: v1.0
+doc: "Reverse each line using the `rev` command"
+hints:
+  ResourceRequirement:
+    ramMin: 8
+  DockerRequirement:
+    dockerPull: "debian:stretch-slim"
+
+inputs:
+  input:
+    type: File
+    inputBinding: {}
+    format: edam:format_2330
+
+outputs:
+  output:
+    type: File
+    outputBinding:
+      glob: output.txt
+    format: $(inputs.input.format)
+
+baseCommand: rev
+stdout: output.txt

schema_salad/tests/test_schemas_directive.py

@@ -0,0 +1,49 @@
+"""
+Checks for accepting $schemas directive
+
+run individually as py.test -k tests/test_schemas_directive.py
+"""
+
+from typing import Any, Dict, Union, Tuple
+from schema_salad.avro.schema import Names, SchemaParseException
+from schema_salad.schema import load_and_validate, load_schema
+from schema_salad.ref_resolver import Loader
+import os
+
+from .util import get_data
+
+test_dir_name = "tests/"
+
+
+class TestSchemasDirective:
+    """Ensure codegen-produced parsers accept $schemas directives"""
+
+    document_loader = None  # type: Loader
+    avsc_names = None  # type: Union[Names, SchemaParseException]
+    schema_metadata = None  # type: Dict[str, Any]
+    metaschema_loader = None  # type: Loader
+
+    @classmethod
+    def setup_class(cls) -> None:
+        path = get_data("tests/test_schema/CommonWorkflowLanguage.yml")
+        assert path
+        (
+            cls.document_loader,
+            cls.avsc_names,
+            schema_metadata,
+            metaschema_loader,
+        ) = load_schema(path)
+
+    def load_cwl(self, src: str) -> Tuple[Any, Dict[str, Any]]:
+        path = get_data(test_dir_name + src)
+        assert path
+        assert isinstance(self.avsc_names, Names)
+        res = load_and_validate(self.document_loader, self.avsc_names, path, True)
+        return res
+
+    def test_dollarsign_schema(self) -> None:
+        """EDAM.owl as a schema"""
+        res = self.load_cwl(src="formattest2.cwl")
+
+        # EDAM.owl resides in this directory
+        assert os.path.split(str(res[0]["$schemas"][0]))[1] == "EDAM.owl"