Validate study assay sample overlap (#75)

altamisa/apps/isatab_validate.py

@@ -64,7 +64,9 @@ def run_warnings_caught(args):
             StudyValidator(investigation, study_info, studies[s]).validate()
         for a, assay_info in enumerate(study_info.assays):
             if assay_info.path:
-                AssayValidator(investigation, study_info, assay_info, assays[s][a]).validate()
+                AssayValidator(
+                    investigation, study_info, assay_info, assays[s][a], studies[s]
+                ).validate()
 
 
 def main(argv=None):

altamisa/isatab/validate_assay_study.py

@@ -476,7 +476,6 @@ def __init__(
         study_info: models.StudyInfo,
         study: models.Study,
     ):
-
         self._study_info = study_info
         self._assay_info = None
         self._model = study
@@ -495,6 +494,8 @@ class AssayValidator(_AssayAndStudyValidator):
     :param assay_info: The corresponding assay information
     :type assay: models.Assay
     :param assay: The Assay model to validate
+    :type parent_study: models.Study
+    :param parent_study: Optional: The parent Study of the current Assay (for extended validation)
     """
 
     _model_type = MODEL_TYPE_ASSAY
@@ -505,8 +506,42 @@ def __init__(
         study_info: models.StudyInfo,
         assay_info: models.AssayInfo,
         assay: models.Assay,
+        parent_study: models.Study = None,
     ):
         self._study_info = study_info
         self._assay_info = assay_info
         self._model = assay
+        self._parent_study = parent_study
         super().__init__(investigation)
+
+    def validate(self):
+        """Validate the assay"""
+        # Independent validations
+        super().validate()
+        # Study-dependent validations
+        if self._parent_study:
+            self._validate_dependency()
+
+    def _validate_dependency(self):
+        """Validate if assay complies with parent study"""
+
+        # Check if all samples in the assays are declared in the parent study
+        # Collect materials of type "Sample Name"
+        study_samples = [
+            m.name
+            for m in self._parent_study.materials.values()
+            if m.type == table_headers.SAMPLE_NAME
+        ]
+        assay_samples = [
+            m.name for m in self._model.materials.values() if m.type == table_headers.SAMPLE_NAME
+        ]
+        # Collect and list assay samples missing in study
+        samples_not_in_study = [s for s in assay_samples if s not in study_samples]
+        if samples_not_in_study:
+            tpl = "Found samples in assay '{}' but not in parent study '{}':\\n{}"
+            msg = tpl.format(
+                self._assay_info.path.name,
+                self._study_info.info.path.name,
+                ", ".join(samples_not_in_study),
+            )
+            warnings.warn(msg, ModerateIsaValidationWarning)

tests/data/i_warnings/a_warnings.txt

@@ -1,2 +1,3 @@
 Sample Name	Protocol REF	Extract Name	Protocol REF	Labeled Extract Name	Label	Protocol REF	Assay Name	Raw Data File	Raw Data File
 0815-N1	extraction	0815-N1-DNA1	labeling			nucleic acid sequencing	0815-N1-DNA1-WES1	0815-N1-DNA1-WES1_L???_???_R1.fastq.gz	0815-N1-DNA1-WES1_L???_???_R2.fastq.gz
+0815-N2	extraction	0815-N1-DNA1	labeling			nucleic acid sequencing	0815-N1-DNA1-WES1	0815-N1-DNA1-WES1_L???_???_R1.fastq.gz	0815-N1-DNA1-WES1_L???_???_R2.fastq.gz

tests/test_apps.py

@@ -16,7 +16,7 @@ def test_isatab_validate():
     with pytest.warns(IsaWarning) as record:
         assert not isatab_validate.main(argv)
 
-    assert 15 == len(record)
+    assert 17 == len(record)
 
 
 def test_isatab2isatab(tmpdir):