modified synthea in order to automatically link patients to gluu user…

README.md

@@ -63,20 +63,21 @@ For example:
  - `run_synthea Massachusetts`
  - `run_synthea Alaska Juneau`
  - `run_synthea -s 12345`
- - `run_synthea -p 1000`
  - `run_synthea -s 987 Washington Seattle`
  - `run_synthea -s 21 -p 100 Utah "Salt Lake City"`
  - `run_synthea -m metabolic*`
+ - `run_synthea -m *covid19* -p 1000` COVID 19 test data
 
 Some settings can be changed in `./src/main/resources/synthea.properties`.
 
 Synthea<sup>TM</sup> will output patient records in C-CDA and FHIR formats in `./output`.
 
 ### TCP functionality
-This project has functionality added specifically for TCT which includes:
+This project has functionality added specifically for TCP which includes:
 - Saving data to local files (now using an argument)
 - Sending patients directly to a FHIR server
 - Sending files to AWS S3
+- creating data linked to gluu inum
 
 ### Saving files locally
 In order to save files locally (json format) you have to add the following argument on the command line
@@ -116,16 +117,16 @@ need to follow the steps to configure your programmatic access to AWS.
 For the Role to assume you'll need to user the entire ARN and that role has to be able to see the configured
 bucket.
 
-### Adding Person generated percentage
-If we want to link more than one patient to a single person (empi) we can include
+### Adding patients linked to gluu inum
+In order to create patients linked to a gluu inum the following flag should be added, this flag is mandatory because
+it is handling the population to be created
 ```
--per <percentage>
+-gluu <user's first name>,<patients to be created>,<user's first name>,<patients to be created>
 ```
-this parameter tells synthea to generate a percentage of persons based on the total population parameter (-p), for example
-if we are sending 100 patients, and we want to generate 50% of persona, this will link 2 patients per person, the usage 
-would be as follows
+this parameter tells synthea to generate a certain amount of ALIVE patients based on the configuration, the first name
+must match with a user name being returned from the Person API
 ```
-run_synthea -p 100 -fhir -per 50 
+run_synthea  -fhir -gluu Test,1,greenday,1 
 ```
 ### Synthea<sup>TM</sup> GraphViz
 Generate graphical visualizations of Synthea<sup>TM</sup> rules and modules.

src/main/java/App.java

@@ -1,12 +1,13 @@
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.IOException;
-import java.util.Arrays;
-import java.util.LinkedList;
-import java.util.Queue;
+import java.util.*;
 
+import org.mitre.synthea.client.IPersonService;
 import org.mitre.synthea.engine.Generator;
 import org.mitre.synthea.export.FhirR4;
+import org.mitre.synthea.export.cp.IPersonFetcher;
+import org.mitre.synthea.export.cp.PersonFetcher;
 import org.mitre.synthea.helpers.Config;
 
 /*
@@ -72,16 +73,28 @@ public static void main(String[] args) throws Exception {
             options.saveLocally = true;
           }else if (currArg.equalsIgnoreCase("-s3")) {
               options.saveIntoS3 = true;
-          }else if (currArg.equalsIgnoreCase("-per")) {
-            FhirR4.percentage = Integer.parseInt(argsQ.poll());
+          }else if (currArg.equalsIgnoreCase("-gluu")) {
+            String gluuData = argsQ.poll();
+            String[] data = gluuData.split(",");
+            if((data.length%2)!=0){
+              throw new Exception("Invalid gluu data.");
+            }
+            int population = 0;
+            Map<String,Integer> config = new HashMap<>();
+            for(int x=0;x<data.length-1;x+=2){
+              String username = data[x];
+              int patients = Integer.parseInt(data[x+1]);
+              population+=patients;
+              config.put(username,patients);
+            }
+              options.population = population;
+              FhirR4.population = config;
+            IPersonFetcher personService = new PersonFetcher();
+            FhirR4.persons = personService.getTcpPersons();
           }else if (currArg.equalsIgnoreCase("-cs")) {
             String value = argsQ.poll();
             options.clinicianSeed = Long.parseLong(value);
-          } else if (currArg.equalsIgnoreCase("-p")) {
-            String value = argsQ.poll();
-            options.population = Integer.parseInt(value);
-            FhirR4.total = options.population;
-          } else if (currArg.equalsIgnoreCase("-o")) {
+          }  else if (currArg.equalsIgnoreCase("-o")) {
             String value = argsQ.poll();
             options.overflow = Boolean.parseBoolean(value);
           } else if (currArg.equalsIgnoreCase("-g")) {

src/main/java/org/mitre/synthea/client/IPersonService.java

@@ -0,0 +1,15 @@
+package org.mitre.synthea.client;
+
+import com.google.gson.JsonObject;
+import retrofit2.Call;
+import retrofit2.http.Body;
+import retrofit2.http.GET;
+import retrofit2.http.Headers;
+
+import java.util.List;
+
+public interface IPersonService {
+    @Headers("Content-Type: application/json")
+    @GET("/Prod/person")
+    Call<List<TCPPerson>> getPersons();
+}

src/main/java/org/mitre/synthea/client/TCPPerson.java

@@ -0,0 +1,36 @@
+package org.mitre.synthea.client;
+
+import com.google.gson.annotations.SerializedName;
+
+public class TCPPerson {
+    @SerializedName("last_name")
+    private String lastName;
+    @SerializedName("gluu_id")
+    private String gluuId;
+    @SerializedName("first_name")
+    private String firstNae;
+
+    public String getLastName() {
+        return lastName;
+    }
+
+    public void setLastName(String lastName) {
+        this.lastName = lastName;
+    }
+
+    public String getGluuId() {
+        return gluuId;
+    }
+
+    public void setGluuId(String gluuId) {
+        this.gluuId = gluuId;
+    }
+
+    public String getFirstNae() {
+        return firstNae;
+    }
+
+    public void setFirstNae(String firstNae) {
+        this.firstNae = firstNae;
+    }
+}

src/main/java/org/mitre/synthea/export/FhirR4.java

@@ -9,14 +9,7 @@
 
 import java.awt.geom.Point2D;
 import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Calendar;
-import java.util.Date;
-import java.util.HashMap;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.UUID;
+import java.util.*;
 import java.util.stream.Collectors;
 
 import org.hl7.fhir.r4.model.Address;
@@ -126,6 +119,7 @@
 import org.hl7.fhir.r4.model.codesystems.DoseRateType;
 import org.hl7.fhir.utilities.xhtml.NodeType;
 import org.hl7.fhir.utilities.xhtml.XhtmlNode;
+import org.mitre.synthea.client.TCPPerson;
 import org.mitre.synthea.engine.Components;
 import org.mitre.synthea.engine.Components.Attachment;
 import org.mitre.synthea.helpers.Config;
@@ -164,9 +158,9 @@ public class FhirR4 {
     private static final String UNITSOFMEASURE_URI = "http://unitsofmeasure.org";
     private static final String DICOM_DCM_URI = "http://dicom.nema.org/resources/ontology/DCM";
     private static final String MEDIA_TYPE_URI = "http://terminology.hl7.org/CodeSystem/media-type";
-    public static int counter = 0;
-    public static int total = 0;
-    public static int percentage = 0;
+
+    public static Map<String, Integer> population;
+    public static List<TCPPerson> persons;
 
     @SuppressWarnings("rawtypes")
     private static final Map raceEthnicityCodes = loadRaceEthnicityCodes();
@@ -361,14 +355,20 @@ public static String convertToFHIRJson(Person person, long stopTime) {
     @SuppressWarnings("rawtypes")
     private static BundleEntryComponent basicInfo(Person person, Bundle bundle, long stopTime) {
         String uniqueID = null;
-        if (FhirR4.percentage == 0) {
-            uniqueID = UUID.randomUUID().toString();
-        } else {
-            int picker = ((FhirR4.total * FhirR4.percentage) / 100);
-            if (FhirR4.counter == picker) {
-                FhirR4.counter = 0;
-            }
-            uniqueID = UUID.nameUUIDFromBytes(String.valueOf(FhirR4.counter++).getBytes()).toString();
+        Optional<Map.Entry<String, Integer>> toProcess =
+                FhirR4.population.entrySet().stream().filter(e -> !e.getValue().equals(0)).findFirst();
+        if (!toProcess.isPresent()) {
+            throw new RuntimeException("Bad configuration");
+        }
+
+        Optional<TCPPerson> personConfig = FhirR4.persons.stream().filter(p->p.getFirstNae().equals(toProcess.get().getKey()))
+                .findFirst();
+        if(!personConfig.isPresent()){
+            throw new RuntimeException("Person " + toProcess.get().getKey() + " not found");
+        }
+        uniqueID = UUID.fromString(personConfig.get().getGluuId()).toString();
+        if (person.alive(stopTime)) {
+            toProcess.get().setValue(toProcess.get().getValue() - 1);
         }
         Patient patientResource = new Patient();
 

src/main/java/org/mitre/synthea/export/cp/IPersonFetcher.java

@@ -0,0 +1,10 @@
+package org.mitre.synthea.export.cp;
+
+import org.mitre.synthea.client.TCPPerson;
+
+import java.io.IOException;
+import java.util.List;
+
+public interface IPersonFetcher {
+    List<TCPPerson> getTcpPersons() throws IOException;
+}

src/main/java/org/mitre/synthea/export/cp/PersonFetcher.java

@@ -0,0 +1,44 @@
+package org.mitre.synthea.export.cp;
+
+import com.google.gson.JsonObject;
+import okhttp3.OkHttpClient;
+import org.mitre.synthea.client.IHapiFhirService;
+import org.mitre.synthea.client.IPersonService;
+import org.mitre.synthea.client.TCPPerson;
+import org.mitre.synthea.helpers.Config;
+import retrofit2.Call;
+import retrofit2.Response;
+import retrofit2.Retrofit;
+import retrofit2.converter.gson.GsonConverterFactory;
+
+import java.io.IOException;
+import java.util.List;
+import java.util.concurrent.TimeUnit;
+
+public class PersonFetcher implements IPersonFetcher {
+    private IPersonService personService;
+
+    public PersonFetcher() {
+        OkHttpClient.Builder httpClient = new OkHttpClient.Builder()
+                .callTimeout(2, TimeUnit.MINUTES)
+                .connectTimeout(20, TimeUnit.SECONDS)
+                .readTimeout(2, TimeUnit.MINUTES)
+                .writeTimeout(30, TimeUnit.SECONDS);
+        Retrofit retrofit = new Retrofit.Builder()
+                .baseUrl(Config.get("exporter.person.api"))
+                .addConverterFactory(GsonConverterFactory.create())
+                .client(httpClient.build())
+                .build();
+        this.personService = retrofit.create(IPersonService.class);
+    }
+
+    public List<TCPPerson> getTcpPersons() throws IOException {
+        Call<List<TCPPerson>> res = personService.getPersons();
+        Response<List<TCPPerson>> response = res.execute();
+        if (!response.isSuccessful()) {
+            throw new RuntimeException("Error getting persons");
+        }
+        return response.body();
+
+    }
+}

src/main/resources/synthea.properties

@@ -1,6 +1,7 @@
 # Starting with a properties file because it requires no additional dependencies
 
 exporter.fhir.fhirServer = http://localhost:8080/
+exporter.person.api = https://o5d4mbjac1.execute-api.us-east-1.amazonaws.com/
 exporter.aws.role = arn:aws:iam::789379687343:role/DevDevops
 exporter.aws.bucket = commonhealth-synthea
 exporter.baseDirectory = ./output/