Merge pull request #46 from hubmapconsortium/phillips/multi_assay_ref…

…actor

Update to accommodate multi-assay

src/ingest_validation_tests/codex_common_errors_validator.py

@@ -45,13 +45,14 @@ class CodexCommonErrorsValidator(Validator):
 
     description = "Test for common problems found in CODEX"
     cost = 1.0
+    required = "codex"
 
     def collect_errors(self, **kwargs) -> List[str]:
         """
         Return the errors found by this validator
         """
         del kwargs
-        if self.assay_type != "CODEX":
+        if self.required not in self.contains and self.assay_type.lower() != self.required:
             return []  # We only test CODEX data
         rslts = []
         for path in self.paths:

src/ingest_validation_tests/codex_json_validator.py

@@ -9,11 +9,12 @@
 class CodexJsonValidator(Validator):
     description = "Check CODEX JSON against schema"
     cost = 1.0
+    required = "codex"
 
     def collect_errors(self, **kwargs) -> List[str]:
         del kwargs
-        if "codex" not in self.assay_type.lower():
-            return []
+        if self.required not in self.contains and self.assay_type.lower() != self.required:
+            return []  # We only test CODEX data
 
         schema_path = Path(__file__).parent / "codex_schema.json"
         schema = json.loads(schema_path.read_text())

src/ingest_validation_tests/publication_validator.py

@@ -21,13 +21,14 @@ class PublicationValidator(Validator):
     cost = 1.0
     base_url_re = r"(\s*\{\{\s*base_url\s*\}\})/(.*)"
     url_re = r"[Uu][Rr][Ll]"
+    required = "publication"
 
     def collect_errors(self, **kwargs) -> List[str]:
         """
         Return the errors found by this validator
         """
         del kwargs
-        if self.assay_type != "Publication":
+        if self.required not in self.contains and self.assay_type.lower() != self.required:
             return []  # We only test Publication data
         rslt = []
         for path in self.paths: