Draft study data export service

src/main/java/org/cbioportal/service/impl/ExportService.java

@@ -0,0 +1,76 @@
+package org.cbioportal.service.impl;
+
+import org.apache.commons.lang3.tuple.Pair;
+import org.cbioportal.model.*;
+import org.cbioportal.service.*;
+import org.cbioportal.service.exception.MolecularProfileNotFoundException;
+import org.cbioportal.service.exception.PatientNotFoundException;
+import org.cbioportal.service.exception.SampleNotFoundException;
+import org.cbioportal.service.exception.StudyNotFoundException;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+
+import java.util.List;
+import java.util.Map;
+import java.util.stream.Collectors;
+
+@Service
+public class ExportService {
+
+    @Autowired
+    PatientService patientService;
+
+    @Autowired
+    SampleService sampleService;
+
+    @Autowired
+    ClinicalDataService clinicalDataService;
+
+    @Autowired
+    MutationService mutationService;
+
+    @Autowired
+    MolecularProfileService molecularProfileService; 
+
+    public void exportData(Map<String, List<String>> samples) throws SampleNotFoundException, StudyNotFoundException, PatientNotFoundException, MolecularProfileNotFoundException {
+        if (samples.size() > 1) {
+            //virtual study
+        }
+        for (Map.Entry<String, List<String>> studySamples: samples.entrySet()) {
+            String studyId = studySamples.getKey();
+            for (String sampleId: studySamples.getValue()) {
+                Sample sample = sampleService.getSampleInStudy(studyId, sampleId);
+                String patientStableId = sample.getPatientStableId();
+                String sampleStableId = sample.getStableId();
+                List<ClinicalData> sampleClinicalData = clinicalDataService.getAllClinicalDataOfSampleInStudy(studyId, sampleStableId, null, null, null, null, null, null);
+                for (ClinicalData sampleClinicalDatum : sampleClinicalData) {
+                   ClinicalAttribute clinicalAttribute = sampleClinicalDatum.getClinicalAttribute();
+                   sampleClinicalDatum.getAttrId();
+                   sampleClinicalDatum.getAttrValue();
+                }
+                Patient patient = patientService.getPatientInStudy(studyId, patientStableId);
+                List<ClinicalData> patientClinicalData = clinicalDataService.getAllClinicalDataOfPatientInStudy(studyId, patientStableId, null, null, null, null, null, null);
+                for (ClinicalData patientClinicalDataItem : patientClinicalData) {
+                    ClinicalAttribute clinicalAttribute = patientClinicalDataItem.getClinicalAttribute();
+                    patientClinicalDataItem.getAttrId();
+                    patientClinicalDataItem.getAttrValue();
+                }
+            }
+            List<MolecularProfileCaseIdentifier> molecularProfileCaseIdentifiers = molecularProfileService.getMolecularProfileCaseIdentifiers(List.of(studyId), studySamples.getValue());
+            for (MolecularProfileCaseIdentifier molecularProfileCaseIdentifier : molecularProfileCaseIdentifiers) {
+               MolecularProfile molecularProfile = molecularProfileService.getMolecularProfile(molecularProfileCaseIdentifier.getMolecularProfileId());
+               MolecularProfile.MolecularAlterationType molecularAlterationType = molecularProfile.getMolecularAlterationType();
+               molecularProfile.getDatatype();
+               molecularProfile.getName();
+               switch (molecularAlterationType) {
+                   case MUTATION_EXTENDED -> {
+                       List<Mutation> mutationList = mutationService.getMutationsInMultipleMolecularProfilesByGeneQueries(List.of(molecularProfileCaseIdentifier.getMolecularProfileId()), studySamples.getValue(), List.of(), "DETAILED", 10000, 1, null, null);
+                       for (Mutation mutation : mutationList) {
+                           mutation.getChr();
+                       }
+                   }
+               }
+            }
+        }
+    }
+}