Added format unit tests

Author: GlassOfWhiskey

cwl_utils/format.py renamed to cwl_utils/file_formats.py

@@ -2,4 +2,5 @@ cwl-upgrader >= 1.2.3
 packaging
 rdflib
 requests
+CacheControl
 schema-salad >= 8.2, < 9

requirements.txt

@@ -0,0 +1,72 @@
+import xml.sax
+from typing import Optional
+
+import requests
+from pytest import raises
+from rdflib import Graph
+from rdflib.plugins.parsers.notation3 import BadSyntax
+from schema_salad.exceptions import ValidationException
+from schema_salad.fetcher import DefaultFetcher
+
+from cwl_utils.format import check_format
+
+
+def _create_file(format_: Optional[str] = None):
+    obj = {
+        "class": "File",
+        "basename": "example.txt",
+        "size": 23,
+        "contents": "hoopla",
+        "nameroot": "example",
+        "nameext": "txt",
+    }
+    if format_:
+        obj["format"] = format_
+    return obj
+
+
+def _load_format(fetchurl: str):
+    fetcher = DefaultFetcher({}, requests.Session())
+    content = fetcher.fetch_text(fetchurl)
+    graph = Graph()
+    for fmt in ["xml", "turtle", "rdfa"]:
+        try:
+            graph.parse(data=content, format=fmt, publicID=str(fetchurl))
+            break
+        except (xml.sax.SAXParseException, TypeError, BadSyntax):
+            pass
+    return graph
+
+
+def test_check_format():
+    check_format(
+        actual_file=_create_file(format_="http://edamontology.org/format_2330"),
+        input_formats="http://edamontology.org/format_2330",
+        ontology=_load_format("http://edamontology.org/EDAM.owl"),
+    )
+
+
+def test_check_format_no_format():
+    with raises(ValidationException, match=r"File has no 'format' defined: .*"):
+        check_format(
+            actual_file=_create_file(),
+            input_formats="http://edamontology.org/format_2330",
+            ontology=_load_format("http://edamontology.org/EDAM.owl"),
+        )
+
+
+def test_check_format_no_input_formats():
+    with raises(ValidationException, match=r"File has an incompatible format: .*"):
+        check_format(
+            actual_file=_create_file(format_="http://edamontology.org/format_2330"),
+            input_formats=[],
+            ontology=Graph(),
+        )
+
+
+def test_check_format_no_ontology():
+    check_format(
+        actual_file=_create_file(format_="http://edamontology.org/format_2330"),
+        input_formats="http://edamontology.org/format_2330",
+        ontology=Graph(),
+    )