Added support for mrn to cmo/dmp patient id mapping

mskcc · Aug 16, 2023 · 42460e1 · 42460e1
1 parent e082832
commit 42460e1
Show file tree

Hide file tree

Showing 5 changed files with 179 additions and 0 deletions.
diff --git a/model/src/main/java/org/mskcc/smile/model/web/CrdbCrosswalkTriplet.java b/model/src/main/java/org/mskcc/smile/model/web/CrdbCrosswalkTriplet.java
@@ -0,0 +1,79 @@
+package org.mskcc.smile.model.web;
+
+import com.fasterxml.jackson.core.JsonProcessingException;
+import java.io.Serializable;
+import java.util.ArrayList;
+import javax.persistence.Entity;
+import javax.persistence.Id;
+import org.apache.commons.lang.builder.ToStringBuilder;
+
+@Entity
+public class CrdbCrosswalkTriplet implements Serializable {
+    static String CMO_PATIENT_ID_PREFIX = "C-";
+
+    @Id
+    private String dmpId;
+    private String cmoId;
+    private String ptMrn;
+
+    public CrdbCrosswalkTriplet() {}
+
+    /**
+     * CrdbCrosswalkTriplet constructor
+     * @param crdbValues
+     * @throws JsonProcessingException
+     */
+    public CrdbCrosswalkTriplet(ArrayList<Object> crdbValues) throws Exception {
+        // the crosswalk table may contain records that are missing fields (at least dmp)
+        // we need to handle cases where null is passed into this constructor
+        // Jackson null values to empty string "" does not work, so lets
+        // set null values to "" here in constructor
+        if (crdbValues.get(1) == null) {
+            this.dmpId = "";
+        } else {
+            this.dmpId = crdbValues.get(1).toString();
+        }
+        if (crdbValues.get(0) == null) {
+            this.cmoId = "";
+        } else {
+            this.cmoId = crdbValues.get(0).toString();
+            if (!this.cmoId.startsWith(CMO_PATIENT_ID_PREFIX)) {
+                this.cmoId = CMO_PATIENT_ID_PREFIX + this.cmoId;
+            }
+        }
+        if (crdbValues.get(2) == null) {
+            this.ptMrn = "";
+        } else {
+            this.ptMrn = crdbValues.get(2).toString();
+        }
+    }
+
+    public String getDmpId() {
+        return dmpId;
+    }
+
+    public void setDmpId(String dmpId) {
+        this.dmpId = dmpId;
+    }
+
+    public String getCmoId() {
+        return cmoId;
+    }
+
+    public void setCmoId(String cmoId) {
+        this.cmoId = cmoId;
+    }
+
+    public String getPtMrn() {
+        return ptMrn;
+    }
+
+    public void setPtMrn(String ptMrn) {
+        this.ptMrn = ptMrn;
+    }
+
+    @Override
+    public String toString() {
+        return ToStringBuilder.reflectionToString(this);
+    }
+}
diff --git a/persistence/src/main/java/org/mskcc/smile/persistence/jpa/CrdbRepository.java b/persistence/src/main/java/org/mskcc/smile/persistence/jpa/CrdbRepository.java
@@ -1,6 +1,7 @@
 package org.mskcc.smile.persistence.jpa;
 
 import org.mskcc.smile.model.internal.CrdbMappingModel;
+import org.mskcc.smile.model.web.CrdbCrosswalkTriplet;
 import org.springframework.data.jpa.repository.Query;
 import org.springframework.data.repository.CrudRepository;
 import org.springframework.data.repository.query.Param;
@@ -16,4 +17,8 @@ public interface CrdbRepository extends CrudRepository<CrdbMappingModel, Long> {
             nativeQuery = true)
     Object getCmoPatientIdByInputId(@Param("inputId") String inputId);
     // another query option
+    @Query(value = "SELECT CMO_ID, DMP_ID, PT_MRN "
+           + "FROM CRDB_CMO_LOJ_DMP_MAP WHERE :inputId IN (DMP_ID, PT_MRN, CMO_ID)",
+           nativeQuery = true)
+    Object getCrdbCrosswalkTripletByInputId(@Param("inputId") String inputId);
 }
diff --git a/service/src/main/java/org/mskcc/smile/service/CrdbMappingService.java b/service/src/main/java/org/mskcc/smile/service/CrdbMappingService.java
@@ -1,9 +1,11 @@
 package org.mskcc.smile.service;
 
 import org.mskcc.smile.model.internal.CrdbMappingModel;
+import org.mskcc.smile.model.web.CrdbCrosswalkTriplet;
 
 public interface CrdbMappingService {
     String getCmoPatientIdbyDmpId(String dmpId);
     String getCmoPatientIdByInputId(String inputId);
     CrdbMappingModel getCrdbMappingModelByInputId(String inputId) throws Exception;
+    CrdbCrosswalkTriplet getCrdbCrosswalkTripletByInputId(String inputId) throws Exception;
 }
diff --git a/service/src/main/java/org/mskcc/smile/service/impl/CrdbMappingServiceImpl.java b/service/src/main/java/org/mskcc/smile/service/impl/CrdbMappingServiceImpl.java
@@ -8,6 +8,7 @@
 import java.util.concurrent.Future;
 import java.util.concurrent.TimeUnit;
 import org.mskcc.smile.model.internal.CrdbMappingModel;
+import org.mskcc.smile.model.web.CrdbCrosswalkTriplet;
 import org.mskcc.smile.persistence.jpa.CrdbRepository;
 import org.mskcc.smile.service.CrdbMappingService;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -80,6 +81,22 @@ public Object call() {
         return null;
     }
 
+    @Override
+    public CrdbCrosswalkTriplet getCrdbCrosswalkTripletByInputId(String inputId) throws Exception {
+        Callable<Object> task = new Callable<Object>() {
+                @Override
+                public Object call() {
+                    return crdbRepository.getCrdbCrosswalkTripletByInputId(inputId);
+                }
+            };
+        Object result = runQueryWithForcedTimeout(task);
+        if (result != null) {
+            ArrayList<Object> crdbValues = mapper.convertValue(result, ArrayList.class);
+            return new CrdbCrosswalkTriplet(crdbValues);
+        }
+        return null;
+    }
+
     private Object runQueryWithForcedTimeout(Callable<Object> task) {
         Future<Object> future = executor.submit(task);
         try {

diff --git a/web/src/main/java/org/mskcc/smile/web/CrosswalkController.java b/web/src/main/java/org/mskcc/smile/web/CrosswalkController.java
@@ -0,0 +1,76 @@
+package org.mskcc.smile.web;
+
+import io.swagger.annotations.Api;
+import io.swagger.annotations.ApiOperation;
+import io.swagger.annotations.ApiParam;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import org.mskcc.smile.model.web.CrdbCrosswalkTriplet;
+import org.mskcc.smile.service.CrdbMappingService;
+import org.mskcc.smile.service.exception.SmileWebServiceException;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.context.annotation.PropertySource;
+import org.springframework.http.HttpHeaders;
+import org.springframework.http.HttpStatus;
+import org.springframework.http.ResponseEntity;
+import org.springframework.web.bind.annotation.CrossOrigin;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestBody;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RestController;
+
+@RestController
+@CrossOrigin(origins = "*")
+@RequestMapping(value = "/")
+@Api(tags = "crosswalk-controller", description = "Crosswalk Controller")
+@PropertySource("classpath:/maven.properties")
+public class CrosswalkController {
+
+    @Value("${smile.schema_version}")
+    private String smileSchemaVersion;
+
+    @Autowired
+    private CrdbMappingService crdbMappingService;
+
+    @Autowired
+    public CrosswalkController(CrdbMappingService crdbMappingService) {
+        this.crdbMappingService = crdbMappingService;
+    }
+
+    /**
+     * Returns a list of mrn-dmp-cmo patient id triplets given a list of MRNs.
+     * Only triplets that exist in the crdb crosswalk table are returned.
+     * @param mrns
+     * @return ResponseEntity
+     * @throws Exception
+     */
+    @ApiOperation(value = "Returns a list of mrn-dmp-cmo patient id triplets given a list of MRNs.",
+        nickname = "fetchIDTripletListPOST")
+    @RequestMapping(value = "/crosswalk",
+        method = RequestMethod.POST,
+        produces = "application/json")
+    public ResponseEntity<List<CrdbCrosswalkTriplet>> fetchIDTripletListPOST(@ApiParam(value =
+        "List of MRNs", required = true, allowMultiple = true)
+        @RequestBody List<String> mrns) throws Exception {
+        List<CrdbCrosswalkTriplet> tripletList = new ArrayList<>();
+        for (String mrn: mrns) {
+            CrdbCrosswalkTriplet triplet = crdbMappingService.getCrdbCrosswalkTripletByInputId(mrn);
+            if (triplet != null) {
+                tripletList.add(triplet);
+            }
+        }
+        return ResponseEntity.ok()
+                .headers(responseHeaders())
+                .body(tripletList);
+    }
+
+    private HttpHeaders responseHeaders() {
+        HttpHeaders headers  = new HttpHeaders();
+        headers.set("smile-schema-version", smileSchemaVersion);
+        return headers;
+    }
+}