Merge pull request #23 from mzmine/library-handler

Library handler

library_spectra_validation/library_handler.py

@@ -1,36 +1,163 @@
 from matchms.importing import load_spectra
 from matchms.filtering.SpectrumProcessor import SpectrumProcessor
 from filters import PRIMARY_FILTERS
+from validation_pipeline import Modification, SpectrumRepairer, SpectrumValidator
 
 class LibraryHandler:
     """Stores the 3 different types of spectra. Correct, repaired, wrong.
     Has internal organization using spectrum ids"""
 
-    def __init__(self, f, pipeline):
-        #todo modify default pipeline 
+    def __init__(self, f):
         metadata_field_harmonization = SpectrumProcessor(predefined_pipeline=None,
                                                          additional_filters=PRIMARY_FILTERS)
         self.spectra = metadata_field_harmonization.process_spectrums(load_spectra(f))
-        self.pipeline = pipeline
-        self.spectra_dictionary = {
-            'valid': None, #[id1, id2,...]
-            'repaired': None, #[id1:[modifications],..]
-            'invalid': None #also a dictionary
-        }
-        self.modifications = {} #todo change to Modifications class
-
-    def clean_and_validate_spectrum(self, spectrum_id):
-        spectrum = self.spectra[spectrum_id]
-        modifications = self.pipeline.run(spectrum)
-        spectrum_id.update_spectra_dictionary(spectrum_id, modifications)
-        self.modifications.append(modifications)
-
-    def update_spectra_dictionary(self, spectrum_id, modifications):
-        self.spectra_dictionary[modifications["spectra_quality"]["updated"]].append(spectrum_id) #valid, repaired,...
-        if ((modifications["spectra_quality"]["updated"] != None) &
-            (modifications["spectra_quality"]["updated"] != modifications["spectra_quality"]["previous"])):
-            self.spectra_dictionary[modifications["spectra_quality"]["previous"]].remove(spectrum_id)
-
-    def run(self):
+        self.spectrum_repairer = SpectrumRepairer()
+        self.spectrum_validator = SpectrumValidator()
+        self.validated_spectra = []
+        self.nonvalidated_spectra = []
+        self.modifications = {} 
+        self.failed_requirements = {}
+
+        self.initial_run()
+
+    def initial_run(self):
         for spectrum_id in range(len(self.spectra)):
-            self.clean_and_validate_spectrum(spectrum_id)
+            spectrum = self.spectra[spectrum_id]
+            modifications, spectrum = self.spectrum_repairer.process_spectrum_store_modifications(spectrum)
+            self.modifications[spectrum_id] = modifications
+
+            self.failed_requirements[spectrum_id] = self.spectrum_validator.process_spectrum_store_failed_filters(
+                spectrum)
+            self.update_spectra_quality_lists(spectrum_id)
+            self.spectra[spectrum_id] = spectrum
+
+        # iterate over all failed requirements
+        # it's almost streamlit
+        # for the dashboard run should use spectrum id
+        # for spectrum_id in range(len(self.spectra)):
+        #     if len(self.failed_requirements[spectrum_id]) != 0:
+        #         self.pass_user_validation_info(spectrum_id)
+        #         #todo should we grab here state variable from streamlit - accept or change
+        #         # self.user_approve_repair(spectrum_id)
+        #         # self.user_metadat_change(spectrum_id)
+
+    def update_spectra_quality_lists(self, spectrum_id):
+        """Will update validated_spectra and nonvalidated_spectra list for this spectrum_id"""
+        valid_spectrum = True
+        if len(self.failed_requirements[spectrum_id]) != 0:
+            valid_spectrum = False
+        for modification in self.modifications[spectrum_id]:
+            if modification.validated_by_user is False:
+                valid_spectrum = False
+
+        if valid_spectrum is True:
+            if spectrum_id not in self.validated_spectra:
+                self.validated_spectra.append(spectrum_id)
+            if spectrum_id in self.nonvalidated_spectra:
+                self.nonvalidated_spectra.remove(spectrum_id)
+        else:
+            if spectrum_id not in self.nonvalidated_spectra:
+                self.nonvalidated_spectra.append(spectrum_id)
+            if spectrum_id in self.validated_spectra:
+                self.validated_spectra.remove(spectrum_id)
+
+    def return_user_validation_info(self, spectrum_id):
+        """
+        Returns all info related to spectrum_id
+        """
+        assert spectrum_id in self.nonvalidated_spectra
+
+        modifications = self.modifications[spectrum_id]
+        failed_requirements = self.failed_requirements[spectrum_id]
+
+        return modifications, failed_requirements, self.spectra[spectrum_id]
+
+    def approve_repair(self, spectrum_id, field_name):
+        """Accepts every modification done to a field_name"""
+        # Accepts every modification so far.
+        for modification in self.modifications[spectrum_id]:
+            if modification.metadata_field == field_name:
+                modification.validated_by_user = True
+        self.update_spectra_quality_lists(spectrum_id)
+
+    def approve_all_repairs(self, spectrum_id):
+        """Accepts all modifications done for a spectrum"""
+        for modification in self.modifications[spectrum_id]:
+            modification.validated_by_user = True
+        self.update_spectra_quality_lists(spectrum_id)
+
+    def decline_last_repair(self, spectrum_id, field_name):
+        """Undo the last modification made to a field"""
+        for mod_idx, modification in enumerate(self.modifications[spectrum_id]):
+            # Checks if it is the correct metadata field and if it was the last changed made
+            if modification.metadata_field == field_name and modification.after == self.spectra[spectrum_id].get(field_name):
+                # undo change
+                spectrum = self.spectra[spectrum_id]
+                spectrum.set(field_name, modification.before)
+                self.spectra[spectrum_id] = spectrum
+                # remove the modification from the list of modifications
+                del self.modifications[spectrum_id][mod_idx]
+                # todo run validation after.
+
+    def decline_all_repairs_on_a_field(self, spectrum_id, field_name):
+        """Undoes all the repairs for a specific field.
+
+        This is achieved by iteratively removing the last added repair"""
+        nr_of_modifications_to_field = len([modification for modification in self.modifications[spectrum_id]
+                                            if modification.metadata_field == field_name])
+        # Removes all the modifications until the last one was removed.
+        for _ in range(nr_of_modifications_to_field):
+            self.decline_last_repair(spectrum_id, field_name)
+            # todo run validation after.
+
+    def decline_all_repairs_spectrum(self, spectrum_id):
+        """Undoes all modifications made to a spectrum"""
+        while len(self.modifications[spectrum_id]) > 0:
+            for mod_idx, modification in enumerate(self.modifications[spectrum_id]):
+                field_name = modification.metadata_field
+                # Checks if it was the last changed made
+                if modification.after == self.spectra[spectrum_id].get(field_name):
+                    # undo change
+                    spectrum = self.spectra[spectrum_id]
+                    spectrum.set(field_name, modification.before)
+                    self.spectra[spectrum_id] = spectrum
+                    # remove the modification from the list of modifications
+                    del self.modifications[spectrum_id][mod_idx]
+
+    def decline_wrapper(self, spectrum_id, field_name, only_last_repair: bool):
+        if field_name is None:
+            self.decline_all_repairs_spectrum(spectrum_id)
+        elif only_last_repair:
+            self.decline_last_repair(spectrum_id, field_name)
+        else:
+            self.decline_all_repairs_on_a_field(spectrum_id, field_name)
+
+        self.failed_requirements[spectrum_id] = self.spectrum_validator.process_spectrum_store_failed_filters(self.spectra[spectrum_id])
+        self.update_spectra_quality_lists(spectrum_id)
+
+    def user_metadata_change(self, field_name, user_input, spectrum_id):
+        """This function takes user defined metadata and rewrites the required field in spectra
+        The info on user-defined modifications is added to modifications dictionary and mandatory
+        validation is rerun.
+        """
+        # Add a user defined modification
+        self.modifications[spectrum_id].append(
+            Modification(metadata_field=field_name, before=self.spectra[spectrum_id].get(field_name),
+                         after=user_input, logging_message="Manual change", validated_by_user=True))
+        self.spectra[spectrum_id].set(field_name, user_input)
+        self.failed_requirements[spectrum_id] = self.spectrum_validator.process_spectrum_store_failed_filters(self.spectra[spectrum_id])
+        self.update_spectra_quality_lists(spectrum_id)
+
+
+    def user_rerun_repair(self, spectrum_id, rerun: bool):
+        '''
+        The function behind user's choice to rerun the repairment and validation
+        Should be linked to a button in a dashboard
+        '''
+        if rerun: #todo do we even need it??
+            self.modifications[spectrum_id] = self.spectrum_repairer.process_spectrum_store_modifications(self.spectra[spectrum_id])
+            self.failed_requirements[spectrum_id] = self.spectrum_validator.process_spectrum_store_failed_filters(self.spectra[spectrum_id])
+
+
+
+

library_spectra_validation/tests/test_library_handler.py

@@ -0,0 +1,63 @@
+from library_handler import LibraryHandler
+
+
+def test_init_library_handler():
+    LibraryHandler("./examples/test_case_correct.mgf")
+
+
+def test_approve_repairs():
+    library_handler = LibraryHandler("./examples/test_case_correct.mgf")
+    spectrum_id = 0
+    library_handler.approve_repair(spectrum_id=spectrum_id, field_name="inchi")
+    assert library_handler.modifications[spectrum_id][0].validated_by_user is True
+
+
+def test_approve_all_repairs():
+    library_handler = LibraryHandler("./examples/test_case_correct.mgf")
+    spectrum_id = 0
+    library_handler.approve_all_repairs(spectrum_id=spectrum_id)
+    for modification in library_handler.modifications[spectrum_id]:
+        assert modification.validated_by_user is True
+
+
+def test_decline_last_repairs():
+    library_handler = LibraryHandler("./examples/test_case_correct.mgf")
+    spectrum_id = 0
+    library_handler.decline_last_repair(spectrum_id=spectrum_id, field_name="inchi")
+    assert len(library_handler.modifications[0]) == 1
+
+
+def test_decline_all_repairs_on_a_field():
+    library_handler = LibraryHandler("./examples/test_case_correct.mgf")
+    spectrum_id = 0
+    # todo add test that actually has multiple repairs for one field
+    library_handler.decline_all_repairs_on_a_field(spectrum_id=spectrum_id, field_name="inchi")
+    assert len(library_handler.modifications[0]) == 1
+
+
+def test_decline_all_repairs_spectrum():
+    library_handler = LibraryHandler("./examples/test_case_correct.mgf")
+    spectrum_id = 0
+    library_handler.decline_all_repairs_spectrum(spectrum_id=spectrum_id)
+    assert len(library_handler.modifications[0]) == 0
+
+    # todo check that change is undone
+
+
+def test_decline_wrapper():
+    library_handler = LibraryHandler("./examples/test_case_correct.mgf")
+    original_spectrum = library_handler.spectra[0]
+    spectrum_id = 0
+    library_handler.decline_wrapper(spectrum_id=spectrum_id, field_name=None, only_last_repair=False)
+    assert len(library_handler.modifications[0]) == 0
+    # check that changes were undone
+    assert original_spectrum == library_handler.spectra[spectrum_id]
+    assert len(library_handler.failed_requirements[spectrum_id]) == 3
+    assert spectrum_id in library_handler.nonvalidated_spectra
+
+
+def test_user_metadata_change():
+    library_handler = LibraryHandler("./examples/test_case_correct.mgf")
+    spectrum_id = 0
+    library_handler.user_metadata_change(spectrum_id=spectrum_id, field_name="smiles", user_input="CCC")
+    assert library_handler.spectra[spectrum_id].get("smiles") == "CCC"

library_spectra_validation/validation_pipeline.py

@@ -9,21 +9,28 @@
 """
 
 import logging
-from typing import Iterable, List, Optional, Union
+from typing import Iterable, List, Optional, Union, Tuple
 from matchms.filtering.SpectrumProcessor import SpectrumProcessor
+from matchms import Spectrum
 
 logger = logging.getLogger("matchms")
 
+
 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
 
 
+class RequirementFailure:
+    def __init__(self, metadata_field, logging_message):
+        self.metadata_field = metadata_field
+        self.logging_message = logging_message       
+
+
 def find_modifications(spectrum_old, spectrum_new, logging_message: str):
     """Checks which modifications have been made in a filter step"""
     modifications = []
@@ -34,7 +41,7 @@ def find_modifications(spectrum_old, spectrum_new, logging_message: str):
             modifications.append(
                 Modification(metadata_field=metadata_field,
                              before=spectrum_old.get(metadata_field),
-                             after=spectrum_new(metadata_field),
+                             after=spectrum_new.get(metadata_field),
                              logging_message=logging_message,
                              validated_by_user=False))
     return modifications
@@ -50,7 +57,7 @@ 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]:
+    def process_spectrum_store_modifications(self, spectrum) -> Tuple[List[Modification], Spectrum]:
         if not self.filters:
             raise TypeError("No filters to process")
         modifications = []
@@ -64,21 +71,31 @@ def process_spectrum_store_modifications(self, spectrum) -> List[Modification]:
             if spectrum_out is None:
                 raise AttributeError("SpectrumRepairer is only expected to repair spectra, not set to None")
             spectrum = spectrum_out
-        return modifications
+        return modifications, spectrum
 
 
 class SpectrumValidator(SpectrumProcessor):
     def __init__(self):
-        # todo add the fields each requirement checks.
-        fields_checked_by_filter = {filter_name: [fields_checked]}
+        self.fields_checked_by_filter = {
+            "require_precursor_mz": ["precursor_mz"],
+            "require_valid_annotation": ["smiles", "inchi", "inchikey"],
+            "require_correct_ionmode": ["ionmode", "adduct", "charge"],
+            # "require_parent_mass_match_smiles": ["smiles", "parent_mass"]
+        }
+        # todo require adduct, precursor mz and parent mass match.
+        # todo add all the checks for formatting. That everything is filled and of the expected format.
         super().__init__(predefined_pipeline=None,
-                         additional_filters=list(fields_checked_by_filter.keys()))
-
+                         additional_filters=("require_precursor_mz",
+                                             "require_valid_annotation",
+                                             ("require_correct_ionmode", {"ion_mode_to_keep": "both"}),
+                                             # ("require_parent_mass_match_smiles", {'mass_tolerance': 0.1}),
+                                             ))
+        # todo add require parent mass match smiles after matchms release.
     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]:
+    def process_spectrum_store_failed_filters(self, spectrum) -> List[RequirementFailure]:
         if not self.filters:
             raise TypeError("No filters to process")
         failed_requirements = []
@@ -87,5 +104,8 @@ def process_spectrum_store_failed_filters(self, spectrum) -> List[Modification]:
             logging_message = ""
             spectrum_out = filter_func(spectrum)
             if spectrum_out is None:
-                failed_requirements += logging_message
+                fields_changed = self.fields_checked_by_filter[filter_func.__name__]
+                for field_changed in fields_changed:
+                    failed_requirements.append(RequirementFailure(field_changed,
+                                                                  logging_message))
         return failed_requirements