Merge pull request #18 from mzmine/validation_pipeline

First implementation of SpectrumValidator and Modification

library_spectra_validation/validation_pipeline.py

@@ -8,11 +8,84 @@
 Add index handling - when a spectrum is processed, its id is added to the corresponding list
 """
 
-class ValidationPipeline:
+import logging
+from typing import Iterable, List, Optional, Union
+from matchms.filtering.SpectrumProcessor import SpectrumProcessor
 
-    def __init__(self, spectrum) -> None:
-        pass
+logger = logging.getLogger("matchms")
 
-    def run(spectrum):
-        #here run all the checks and modifications
-        return modifications #{'quality':, 'metadata adduct': {'previous':..., 'updated':....}}
+class Modification:
+    def __init__(self, metadata_field, before, after, logging_message, validated_by_user):
+        self.metadata_field = metadata_field
+        self.before = before
+        self.after = after
+        # self.original =
+        self.logging_message = logging_message
+        self.validated_by_user = validated_by_user
+
+
+def find_modifications(spectrum_old, spectrum_new, logging_message: str):
+    """Checks which modifications have been made in a filter step"""
+    modifications = []
+    metadata_fields_to_check = ["parent_mass", "precursor_mz", "adduct", "smiles",
+                                "compound_name", "inchi", "inchikey", "charge", "ionmode"]
+    for metadata_field in metadata_fields_to_check:
+        if spectrum_old.get(metadata_field) != spectrum_new.get(metadata_field):
+            modifications.append(
+                Modification(metadata_field=metadata_field,
+                             before=spectrum_old.get(metadata_field),
+                             after=spectrum_new(metadata_field),
+                             logging_message=logging_message,
+                             validated_by_user=False))
+    return modifications
+
+
+class SpectrumRepairer(SpectrumProcessor):
+    def __init__(self, predefined_pipeline: Optional[str] = 'default',
+                 additional_filters: Iterable[Union[str, List[dict]]] = ()):
+        super().__init__(predefined_pipeline,
+                         additional_filters)
+
+    def process_spectrum(self, spectrum,
+                         processing_report=None):
+        raise AttributeError("process spectrum is not a valid method of SpectrumValidator")
+
+    def process_spectrum_store_modifications(self, spectrum) -> List[Modification]:
+        if not self.filters:
+            raise TypeError("No filters to process")
+        modifications = []
+        for filter_func in self.filters:
+            # todo capture logging
+            logging_message = ""
+            spectrum_out = filter_func(spectrum)
+            modifications += find_modifications(spectrum_old=spectrum,
+                                                spectrum_new=spectrum_out,
+                                                logging_message=logging_message)
+            if spectrum_out is None:
+                raise AttributeError("SpectrumRepairer is only expected to repair spectra, not set to None")
+            spectrum = spectrum_out
+        return modifications
+
+
+class SpectrumValidator(SpectrumProcessor):
+    def __init__(self):
+        # todo add the fields each requirement checks.
+        fields_checked_by_filter = {filter_name: [fields_checked]}
+        super().__init__(predefined_pipeline=None,
+                         additional_filters=list(fields_checked_by_filter.keys()))
+
+    def process_spectrum(self, spectrum,
+                         processing_report=None):
+        raise AttributeError("process spectrum is not a valid method of SpectrumValidator")
+
+    def process_spectrum_store_failed_filters(self, spectrum) -> List[Modification]:
+        if not self.filters:
+            raise TypeError("No filters to process")
+        failed_requirements = []
+        for filter_func in self.filters:
+            # todo capture logging
+            logging_message = ""
+            spectrum_out = filter_func(spectrum)
+            if spectrum_out is None:
+                failed_requirements += logging_message
+        return failed_requirements