Met requirements

server/src/main/java/org/hl7/davinci/endpoint/controllers/DataController.java

@@ -44,8 +44,8 @@ public class DataController {
   @Autowired
   private ClientRepository clientRepository;
 
-  @Autowired
-  private RemsRepository remsRepository;
+  // @Autowired
+  // private RemsRepository remsRepository;
 
   @Autowired
   private YamlConfig myConfig;
@@ -165,44 +165,4 @@ public RedirectView reload(@RequestParam String vsac_api_key) {
     return new RedirectView(newUrl);
   }
 
-  public void updateComplianceBundleStatus(String uid) {
-    try {
-      TimeUnit.SECONDS.sleep(30);
-    }
-    catch(Exception e)
-    {
-        System.out.println(e);
-      }
-    Rems rems = remsRepository.findById(uid).orElseThrow(() -> new ResponseStatusException(HttpStatus.NOT_FOUND, uid + " not found"));
-    rems.setStatus("Approved");
-    remsRepository.save(rems);
-  }
-
-  public void updateComplianceBundleStatusInBackground (final String uid) {
-    Thread t = new Thread(() -> updateComplianceBundleStatus(uid));
-    t.start();
-  }
-
-  @PostMapping(value = "/api/rems")
-  @CrossOrigin
-  public ResponseEntity<Object> postRems(@RequestBody String jsonData) {
-    JsonNode remsObject = JacksonUtil.toJsonNode(jsonData);
-    String id = UUID.randomUUID().toString().replace("-", "");
-
-    Rems complianceBundle = new Rems();
-    complianceBundle.setCase_number(id);
-    complianceBundle.setComplianceBundle(remsObject);
-    complianceBundle.setStatus("Pending");
-    remsRepository.save(complianceBundle);
-    updateComplianceBundleStatusInBackground(id);
-    return ResponseEntity.ok().body(complianceBundle);
-
-  }
-
-  @CrossOrigin
-  @GetMapping("/api/rems/{id}")
-  public ResponseEntity<Object> getRems(@PathVariable String id) {
-    Rems rems = remsRepository.findById(id).orElseThrow(() -> new ResponseStatusException(HttpStatus.NOT_FOUND, id + " not found"));
-    return ResponseEntity.ok().body(rems);
-  }
 }

server/src/main/java/org/hl7/davinci/endpoint/rems/DatabaseInit.java

@@ -46,22 +46,54 @@ CommandLineRunner initDatabase(DrugsRepository repository, RemsFhirRepository re
         return args -> {
             log.info("Preloading turalio");
             Drug turalio = new Drug();
-
-            String questionnaire = readFile("src/main/java/org/hl7/davinci/endpoint/rems/resources/Turalio/fhir/Questionnaire-R4-DrugHasREMS.json", Charset.defaultCharset());
-            Requirement requirement = new Requirement();
-            RemsFhir remsFhir = new RemsFhir();
-            remsFhir.setResourceType(ResourceType.Questionnaire.toString());
-            JsonNode questionnaireResource = JacksonUtil.toJsonNode(questionnaire);
-            remsFhir.setResource(questionnaireResource);
-            remsFhir.setId("q1");
-            remsFhirRepository.save(remsFhir);
-            requirement.setRequirement(remsFhir);
-            requirement.setDescription("complete questionnaire");
-            turalio.addRequirement(requirement);
             turalio.setId("turalio");
-            repository.save(turalio);
-            requirement.setDrug(turalio);
-            requirementRepository.save(requirement);
+            turalio.setCodeSystem("http://www.nlm.nih.gov/research/umls/rxnorm");
+            turalio.setCode("2183126");
+            repository.save(turalio);;
+
+
+            // patient enrollment form requirement
+            String patientQuestionnaire = readFile("src/main/java/org/hl7/davinci/endpoint/rems/resources/Turalio/fhir/Questionnaire-R4-DrugHasREMS.json", Charset.defaultCharset());
+            Requirement patientEnrollmentRequirement = new Requirement();
+            RemsFhir patientEnrollmentResource = new RemsFhir();
+            patientEnrollmentResource.setResourceType(ResourceType.Questionnaire.toString());
+            JsonNode patientQuestionnaireResource = JacksonUtil.toJsonNode(patientQuestionnaire);
+            patientEnrollmentResource.setResource(patientQuestionnaireResource);
+            patientEnrollmentResource.setId("turalio-patient-enrollment");
+            remsFhirRepository.save(patientEnrollmentResource);
+            patientEnrollmentRequirement.setResource(patientEnrollmentResource);
+            patientEnrollmentRequirement.setDescription("complete patient enrollment questionnaire");
+            patientEnrollmentRequirement.setDrug(turalio);
+            requirementRepository.save(patientEnrollmentRequirement);
+
+             // prescriber enrollment form requirement
+             String prescriberQuestionnaire = readFile("src/main/java/org/hl7/davinci/endpoint/rems/resources/Turalio/Questionnaire-R4-Prescriber-Enrollment.json", Charset.defaultCharset());
+             Requirement prescriberEnrollmentRequirement = new Requirement();
+             RemsFhir prescriberEnrollmentResource = new RemsFhir();
+             prescriberEnrollmentResource.setResourceType(ResourceType.Questionnaire.toString());
+             JsonNode prescriberQuestionnaireResource = JacksonUtil.toJsonNode(prescriberQuestionnaire);
+             prescriberEnrollmentResource.setResource(prescriberQuestionnaireResource);
+             prescriberEnrollmentResource.setId("turalio-prescriber-enrollment");
+             remsFhirRepository.save(prescriberEnrollmentResource);
+             prescriberEnrollmentRequirement.setResource(prescriberEnrollmentResource);
+             prescriberEnrollmentRequirement.setDescription("complete prescriber enrollment questionnaire");
+             prescriberEnrollmentRequirement.setDrug(turalio);
+             requirementRepository.save(prescriberEnrollmentRequirement);
+
+            // prescriber knowledge assessment / certification sub-requirement
+            String prescriberKnowledgeQuestionnaire = readFile("src/main/java/org/hl7/davinci/endpoint/rems/resources/Turalio/Questionnaire-R4-Prescriber-Knowledge-Assessment.json", Charset.defaultCharset());
+            Requirement prescriberCertificationRequirement = new Requirement();
+            RemsFhir prescriberKnowledgeResource = new RemsFhir();
+            prescriberKnowledgeResource.setResourceType(ResourceType.Questionnaire.toString());
+            JsonNode prescriberKnowledgeQuestionnaireResource = JacksonUtil.toJsonNode(prescriberKnowledgeQuestionnaire);
+            prescriberKnowledgeResource.setResource(prescriberKnowledgeQuestionnaireResource);
+            prescriberKnowledgeResource.setId("turalio-prescriber-knowledge-check");
+            remsFhirRepository.save(prescriberKnowledgeResource);
+            prescriberCertificationRequirement.setResource(prescriberKnowledgeResource);
+            prescriberCertificationRequirement.setDescription("complete prescriber knowledge check");
+            prescriberCertificationRequirement.setParent(prescriberEnrollmentRequirement);
+            requirementRepository.save(prescriberCertificationRequirement);
+
         };
     }
 }

server/src/main/java/org/hl7/davinci/endpoint/rems/controller/RemsController.java

@@ -1,16 +1,41 @@
 package org.hl7.davinci.endpoint.rems.controller;
 
+import com.google.gson.Gson;
+import com.google.gson.GsonBuilder;
+import com.google.gson.JsonObject;
+import com.google.gson.JsonParser;
+import com.fasterxml.jackson.databind.JsonNode;
+import com.vladmihalcea.hibernate.type.json.internal.JacksonUtil;
+import org.hl7.davinci.endpoint.rems.database.requirement.MetRequirement;
+import org.hl7.davinci.endpoint.rems.database.requirement.MetRequirementRepository;
+import org.hl7.davinci.endpoint.rems.database.requirement.Requirement;
+
 import org.hl7.davinci.endpoint.Application;
 import org.hl7.davinci.endpoint.rems.database.drugs.Drug;
 import org.hl7.davinci.endpoint.rems.database.drugs.DrugsRepository;
 import org.springframework.beans.factory.annotation.Autowired;
+import  org.hl7.davinci.endpoint.rems.database.rems.Rems;
+import  org.hl7.davinci.endpoint.rems.database.rems.RemsRepository;
 import org.springframework.http.MediaType;
 import org.springframework.http.ResponseEntity;
 import org.springframework.web.bind.annotation.CrossOrigin;
 import org.springframework.web.bind.annotation.GetMapping;
 import org.springframework.web.bind.annotation.PathVariable;
 import org.springframework.web.bind.annotation.RestController;
 
+import org.springframework.core.io.Resource;
+import org.springframework.http.HttpHeaders;
+import org.springframework.http.MediaType;
+import org.springframework.web.bind.annotation.*;
+import org.springframework.http.ResponseEntity;
+import org.springframework.web.servlet.view.RedirectView;
+import java.util.Optional;
+import java.util.UUID;
+import java.util.concurrent.TimeUnit;
+import org.springframework.web.server.ResponseStatusException;
+import org.springframework.http.HttpStatus;
+import java.util.Arrays;
+
 import javax.servlet.http.HttpServletRequest;
 import java.io.IOException;
 import java.util.logging.Logger;
@@ -25,7 +50,13 @@ public class RemsController {
     @Autowired
     private DrugsRepository drugsRepository;
 
-    @GetMapping(value = "/rems/{id}")
+    @Autowired
+    private RemsRepository remsRepository;
+
+    @Autowired
+    private MetRequirementRepository metRequirementsRepository;
+
+    @GetMapping(value = "/drug/{id}")
     @CrossOrigin
     public ResponseEntity<Drug> getRequirements(HttpServletRequest request, @PathVariable String id) throws IOException {
         Drug drug = drugsRepository.findById(id).get();
@@ -41,4 +72,87 @@ private ResponseEntity<Drug> processRequirements(Drug drug) {
                 .contentType(MediaType.parseMediaType(MediaType.APPLICATION_JSON_VALUE))
                 .body(drug);
     }
+
+    public void updateRemsRequestStatus(String uid) {
+        try {
+          TimeUnit.SECONDS.sleep(30);
+        }
+        catch(Exception e)
+        {
+            System.out.println(e);
+          }
+        Rems rems = remsRepository.findById(uid).orElseThrow(() -> new ResponseStatusException(HttpStatus.NOT_FOUND, uid + " not found"));
+        rems.setStatus("Approved");
+        remsRepository.save(rems);
+      }
+
+      public void updateRemsRequestStatusInBackground (final String uid) {
+        Thread t = new Thread(() -> updateRemsRequestStatus(uid));
+        t.start();
+      }
+
+      @PostMapping(value = "/rems")
+      @CrossOrigin
+      public ResponseEntity<Object> postRems(@RequestBody String jsonData) {
+        JsonNode remsObject = JacksonUtil.toJsonNode(jsonData);
+        String id = UUID.randomUUID().toString().replace("-", "");
+
+        JsonNode params = getResource(remsObject, remsObject.get("entry").get(0).get("resource").get("focus").get("parameters").get("reference").textValue());
+
+        String prescriptionReference = "";
+        for (JsonNode param : params.get("parameter")) {
+            if (param.get("name").textValue().equals("prescription")) {
+                prescriptionReference = param.get("reference").textValue();
+            }
+        }
+
+        JsonNode presciption = getResource(remsObject, prescriptionReference);
+        String prescriptionSystem = presciption.get("medicationCodeableConcept").get("coding").get(0).get("system").textValue();
+        String prescriptionCode = presciption.get("medicationCodeableConcept").get("coding").get(0).get("code").textValue();
+        Drug drug = drugsRepository.findDrugByCode(prescriptionSystem, prescriptionCode).get(0);
+
+
+
+        Rems remsRequest = new Rems();
+        remsRequest.setCase_number(id);
+        remsRequest.setStatus("Pending");
+        remsRequest.setResource(remsObject);
+        remsRepository.save(remsRequest);
+
+        // this loop needs to change to handle multiple levels of sub-requirement conditions
+        // this loop needs to also handle parsing out resources for each requirement - may need to be separate endpoints
+        for (Requirement requirement : drug.getRequirements()) {
+            MetRequirement metReq = new MetRequirement();
+            metReq.setRequirement(requirement);
+            metReq.setRemsRequest(remsRequest);
+            remsRequest.addMetRequirement(metReq);
+            metRequirementsRepository.save(metReq);
+        }
+        remsRepository.save(remsRequest);
+        updateRemsRequestStatusInBackground(id);
+        return ResponseEntity.ok().body(remsRequest);
+
+      }
+
+      @CrossOrigin
+      @GetMapping("/rems/{id}")
+      public ResponseEntity<Object> getRems(@PathVariable String id) {
+        Rems rems = remsRepository.findById(id).orElseThrow(() -> new ResponseStatusException(HttpStatus.NOT_FOUND, id + " not found"));
+        return ResponseEntity.ok().body(rems);
+      }
+
+      public JsonNode getResource(JsonNode bundle, String resourceReference) {
+        String[] temp = resourceReference.split("/");
+        String _resourceType = temp[0];
+        String _id = temp[1];
+
+        for (int i = 0; i < bundle.get("entry").size(); i++) {
+          if ((bundle.get("entry").get(i).get("resource").get("resourceType").textValue().equals(_resourceType))
+            && (bundle.get("entry").get(i).get("resource").get("id").textValue().equals(_id))) {
+            return bundle.get("entry").get(i).get("resource");
+          }
+        }
+        return null;
+      }
+
 }

server/src/main/java/org/hl7/davinci/endpoint/rems/database/drugs/Drug.java

@@ -24,7 +24,7 @@ public class Drug {
     @Column(name = "createdAt", nullable = false)
     private String createdAt;
 
-    @OneToMany(mappedBy="drug")
+    @OneToMany(mappedBy="drug", fetch = FetchType.EAGER, cascade = CascadeType.ALL)
     private List<Requirement> requirements = new ArrayList<>();
 
     public Drug() {

server/src/main/java/org/hl7/davinci/endpoint/rems/database/drugs/DrugsRepository.java

@@ -5,6 +5,8 @@
 import org.springframework.data.rest.core.annotation.RepositoryRestResource;
 import org.springframework.stereotype.Repository;
 import org.springframework.web.bind.annotation.CrossOrigin;
+import org.springframework.data.repository.query.Param;
+
 
 import java.util.List;
 
@@ -18,5 +20,7 @@ public interface DrugsRepository extends CrudRepository<Drug, String> {
             "SELECT r FROM Drug r")
     List<Drug> findLogs();
 
+    @Query("SELECT r FROM Drug r where r.codeSystem = :system and r.code = :code")
+    List<Drug> findDrugByCode(@Param("system") String system, @Param("code") String code);
 }
 

server/src/main/java/org/hl7/davinci/endpoint/rems/database/fhir/RemsFhir.java

@@ -22,7 +22,7 @@ public class RemsFhir {
     private String createdAt;
 
     @Type(type = "json")
-    @Column(columnDefinition = "json", name = "complianceBundle", nullable = false, length = 10000000)
+    @Column(columnDefinition = "json", name = "resource", nullable = false, length = 10000000)
     private JsonNode resource;
 
 

server/src/main/java/org/hl7/davinci/endpoint/database/Rems.java → server/src/main/java/org/hl7/davinci/endpoint/rems/database/rems/Rems.java

@@ -1,4 +1,9 @@
-package org.hl7.davinci.endpoint.database;
+package  org.hl7.davinci.endpoint.rems.database.rems;
+import org.hl7.davinci.endpoint.rems.database.requirement.MetRequirement;
+import java.util.ArrayList;
+import java.util.List;
+import javax.persistence.*;
+
 
 import javax.persistence.Column;
 import javax.persistence.Entity;
@@ -18,13 +23,17 @@ public class Rems {
   @Column(name = "case_number", nullable = false, length = 100)
   private String case_number;
 
-  @Type(type = "json")
-  @Column(columnDefinition = "json", name = "complianceBundle", nullable = false, length = 10000000)
-  private JsonNode complianceBundle;
 
   @Column(name = "status", nullable = false, length = 100)
   private String status;
 
+  @Type(type = "json")
+  @Column(columnDefinition = "json", name = "resource", nullable = false, length = 10000000)
+  private JsonNode resource;
+
+  @OneToMany(mappedBy="remsRequest", fetch = FetchType.EAGER, cascade = CascadeType.ALL)
+  private List<MetRequirement> metRequirements = new ArrayList<>();
+
   public void Rems() {}
 
   public String getCase_number() {
@@ -35,19 +44,31 @@ public void setCase_number(String id) {
     this.case_number = id;
   }
 
-  public JsonNode getComplianceBundle() {
-    return this.complianceBundle;
-  }
-
-  public void setComplianceBundle(JsonNode jsonParam) {
-    this.complianceBundle = jsonParam;
-  }
-
   public String getStatus() {
     return this.status;
   }
 
   public void setStatus(String statusParam) {
     this.status = statusParam;
   }
+
+  public List<MetRequirement> getMetRequirements() {
+    return this.metRequirements;
+}
+
+public void setMetRequirement(List<MetRequirement> metRequirements) {
+    this.metRequirements = metRequirements;
+}
+
+public void addMetRequirement(MetRequirement metRequirement)  {
+    this.metRequirements.add(metRequirement);
+}
+
+public JsonNode getResource() {
+  return this.resource;
+}
+
+public void setResource(JsonNode resource) {
+  this.resource = resource;
+}
 }

server/src/main/java/org/hl7/davinci/endpoint/database/RemsRepository.java → server/src/main/java/org/hl7/davinci/endpoint/rems/database/rems/RemsRepository.java

@@ -1,4 +1,4 @@
-package org.hl7.davinci.endpoint.database;
+package org.hl7.davinci.endpoint.rems.database.rems;
 
 import org.springframework.data.jpa.repository.Query;
 import org.springframework.data.repository.CrudRepository;

server/src/main/java/org/hl7/davinci/endpoint/database/RemsService.java → server/src/main/java/org/hl7/davinci/endpoint/rems/database/rems/RemsService.java

@@ -1,4 +1,4 @@
-package org.hl7.davinci.endpoint.database;
+package org.hl7.davinci.endpoint.rems.database.rems;
 
 public interface RemsService {
   Iterable<Rems> findAll();

server/src/main/java/org/hl7/davinci/endpoint/database/RemsServiceImpl.java → server/src/main/java/org/hl7/davinci/endpoint/rems/database/rems/RemsServiceImpl.java

@@ -1,4 +1,4 @@
-package org.hl7.davinci.endpoint.database;
+package org.hl7.davinci.endpoint.rems.database.rems;
 
 import org.springframework.beans.factory.annotation.Autowired;