Fix bug in Q/C pipeline

src/ppktstore/__main__.py

@@ -92,15 +92,16 @@ def qc_phenopackets(
     )
     logger.info('Checking phenopackets')
     checker = ppktstore.qc.configure_qc_checker()
-    outcome = checker.check(phenopacket_store=phenopacket_store)
-    if len(outcome) == 0:
+    results = checker.check(phenopacket_store=phenopacket_store)
+    if results.is_ok():
         logger.info('Found no issues')
         return 0
     else:
         logger.info('Phenopacket store Q/C failed')
-        for checker_name, errors in outcome.items():
-            logger.info('\'%s\' found %d error(s):', checker_name, len(errors))
-            for error in errors:
+
+        for checker_name, issues in results.iter_results():
+            logger.info('\'%s\' found %d error(s):', checker_name, len(issues))
+            for error in issues:
                 logger.info(' - %s', error)
         return 1
 

src/ppktstore/qc/__init__.py

@@ -1,7 +1,7 @@
-from ._api import QcChecker
+from ._api import QcChecker, QcResults
 from ._config import configure_qc_checker
 
 __all__ = [
-    'QcChecker', 
+    'QcChecker', 'QcResults',
     'configure_qc_checker',
 ]

src/ppktstore/qc/_api.py

@@ -4,16 +4,6 @@
 from ppktstore.model import PhenopacketStore
 
 
-class QcChecker(metaclass=abc.ABCMeta):
-
-    @abc.abstractmethod
-    def check(
-        self,
-        phenopacket_store: PhenopacketStore,
-    ) -> typing.Mapping[str, typing.Sequence[str]]:
-        pass
-
-
 class QcCheck(metaclass=abc.ABCMeta):
 
     @abc.abstractmethod
@@ -32,3 +22,33 @@ def apply(
         Check `phenopacket_store` and return a sequence of `str`s with errors.
         """
         pass
+
+
+class QcResults:
+    """
+    Results of the Q/C check suite.
+    """
+
+    def __init__(
+        self,
+        results: typing.Mapping[str, typing.Sequence[str]],
+    ):
+        self._results = results
+
+    def iter_results(
+        self,
+    ) -> typing.Iterator[typing.Tuple[str, typing.Sequence[str]]]:
+        return self._results.items()
+
+    def is_ok(self) -> bool:
+        return all(len(issues) == 0 for issues in self._results.values())
+
+
+class QcChecker(metaclass=abc.ABCMeta):
+
+    @abc.abstractmethod
+    def check(
+        self,
+        phenopacket_store: PhenopacketStore,
+    ) -> QcResults:
+        pass

src/ppktstore/qc/_impl.py

@@ -4,7 +4,7 @@
 
 from ppktstore.model import PhenopacketStore
 
-from ._api import QcCheck, QcChecker
+from ._api import QcCheck, QcChecker, QcResults
 
 
 class UniqueIdsCheck(QcCheck):
@@ -48,11 +48,11 @@ def __init__(
     def check(
         self,
         phenopacket_store: PhenopacketStore,
-    ) -> typing.Mapping[str, typing.Sequence[str]]:
+    ) -> QcResults:
         results = {}
 
         for check in self._checks:
             check_id = check.make_id()
             results[check_id] = check.apply(phenopacket_store)
 
-        return results
+        return QcResults(results=results)