Added functionality for user input

library_spectra_validation/library_handler.py

@@ -1,36 +1,107 @@
 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
+        self.spectrum_repairer = SpectrumRepairer()
+        self.spectrum_validator = SpectrumValidator()
+        self.validated_spectra = []
+        self.nonvalidated_spectra = []
+        self.modifications = {} 
+        self.failed_requirements = {}
 
     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)
+        self.modifications[spectrum_id] = self.spectrum_repairer.process_spectrum_store_modifications(spectrum)
+        self.failed_requirements[spectrum_id] = self.spectrum_validator.process_spectrum_store_failed_filters(spectrum)
+        self.update_spectra_lists(spectrum_id)
 
-    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 update_spectra_lists(self, spectrum_id):
+        if len(self.failed_requirements[spectrum_id]) == 0:
+            self.validated_spectra.append(spectrum_id)
+            self.nonvalidated_spectra.pop(spectrum_id) #todo populate with all ids after loading!
+            # todo in case user modifies do the opposite
+
+    def pass_user_validation_info(self, spectrum_id):
+        '''
+        This function is called only for nonvalidated spectra
+        '''
+        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 user_approve_repair(self, field_name, approved_all: bool, rejected_all: bool, spectrum_id):
+        '''
+        This function allows user to accept or decline all or part of modifications
+        '''
+        modifications = self.modifications[spectrum_id]
+        if approved_all:
+            for modification in modifications:
+                if modification.metadata_field == field_name:
+                    # self.modifications[spectrum_id].pop(modification) #todo test this!!
+                    self.modifications[spectrum_id].validated_by_user = True
+        #if user rejects the changes
+        #todo implement the case when user rejects not all changes
+        elif rejected_all:
+            for modification in modifications:
+                #todo should we use before/original/first modification
+                self.spectra[spectrum_id].get(modification.metadata_field).set(modification.before)
+            modifications.pop(spectrum_id)
+            self.failed_requirements[spectrum_id] = self.spectrum_validator.process_spectrum_store_failed_filters(self.spectra[spectrum_id])
+            self.update_spectra_lists(spectrum_id)
+        else: 
+            #todo implement!!!!
+            #only the last one
+            return None
+
+
+    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.
+        '''
+        self.spectra[spectrum_id].set(field_name, user_input) #todo this is correct, fix everywhere
+        #todo add user-defined modification to modifications list
+        self.modifications[spectrum_id].append("User-defined modification in the field " +
+                                               field_name + 
+                                               ". Value changed to " +
+                                               user_input)
+        self.failed_requirements[spectrum_id] = self.spectrum_validator.process_spectrum_store_failed_filters(self.spectra[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])
 
     def run(self):
+        #first check
+        for spectrum_id in range(len(self.spectra)):
+            self.clean_and_validate_spectrum(spectrum_id)
+        # 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)):
-            self.clean_and_validate_spectrum(spectrum_id)
+            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)
+
+
+

library_spectra_validation/tests/test_spectra_loading.py

@@ -1,4 +1,4 @@
+from library_spectra_validation.library_handler import LibraryHandler
+
 def test_load_spectra():
-    """This is a first test that is not functional yet, to test the CI pipeline"""
-    print("test_succesfull")
-    assert True
+    library_handler = LibraryHandler("./examples/test_case_correct.mgf")