Minor refactoring. Introducing hip as variable.

ProjectEKA · Jul 29, 2020 · b979a63 · b979a63
1 parent c5d5b5b
commit b979a63
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Showing 16 changed files with 123 additions and 82 deletions.
diff --git a/README.md b/README.md
@@ -7,11 +7,12 @@
 
 ### Random Data Generator For Patients.
 takes the following parameters
-- out - the location directory where the file would be placed. Default in /tmp
-- type - PR (Prescription), DR (DiagnosticReport). Must be provided.
-- name - should be given and if given, will throw error if not found in *patients.properties* file. Will default to 'navjot' if no name is given. You may add more entries in the patients.properties file. Right now can generate for - hina, navjot, janki, nitesh
-- fromDate - provide in format yyyy-MM-dd (e.g 2020-03-21). If not given will default to current date. 
-- number - how many documents to generate. If not given, only 1 is generated. Documents are generated in 2 days interval.     
+- **out** - the location directory where the file would be placed. Default in /tmp
+- **type** - PR (Prescription), DR (DiagnosticReport). Must be provided.
+- **name** - should be given and if given, will throw error if not found in *patients.properties* file. Will default to 'navjot' if no name is given. You may add more entries in the patients.properties file. Right now can generate for - hina, navjot, janki, nitesh
+- **fromDate** - provide in format yyyy-MM-dd (e.g 2020-03-21). If not given will default to current date. 
+- **number** - how many documents to generate. If not given, only 1 is generated. Documents are generated in 2 days interval.
+- **hip** - for which HIP to generate data. If not given, max is the default. Possible values are - max, tmh, wbc. You may change by adding another json in the resources/orgs/ directory.      
 
 ## Build from source
 

diff --git a/build.gradle b/build.gradle
@@ -9,7 +9,7 @@ sourceCompatibility = '11'
 
 jar {
     manifest {
-        attributes('Main-Class': 'in.projecteka.data.Application')
+        attributes('Main-Class': 'in.projecteka.utils.Application')
     }
     from {
         configurations.runtimeClasspath.collect { it.isDirectory() ? it : zipTree(it) }

diff --git a/.../java/in/projecteka/data/Application.java → ...java/in/projecteka/utils/Application.java b/.../java/in/projecteka/data/Application.java → ...java/in/projecteka/utils/Application.java
@@ -1,4 +1,9 @@
-package in.projecteka.data;
+package in.projecteka.utils;
+
+import in.projecteka.utils.data.DiagnosticReportGenerator;
+import in.projecteka.utils.data.DocumentGenerator;
+import in.projecteka.utils.data.PrescriptionGenerator;
+import in.projecteka.utils.data.Utils;
 
 import java.nio.file.Path;
 import java.nio.file.Paths;
@@ -27,15 +32,24 @@ public static void main(String[] args) throws Exception {
         String patientName = getPatientName(checkRequired("name"));
         Date fromDate = getFromDate(checkRequired("fromDate"));
         int number = getNumerOfInstances(checkRequired("number"));
+        String hip = getHip(checkRequired("hip"));
         DocumentGenerator documentGenerator = generators.get(type);
         documentGenerator.init();
         try {
-            documentGenerator.execute(patientName, fromDate, number, location);
+            documentGenerator.execute(patientName, fromDate, number, location, hip);
         } catch (Exception e) {
             e.printStackTrace();
         }
     }
 
+    private static String getHip(String hip) {
+        if (Utils.isBlank(hip)) {
+            System.out.println("hip not provided. Defaulting to max");
+            return "max";
+        }
+        return hip;
+    }
+
     private static String getPatientName(String name) {
         if (Utils.isBlank(name)) {
             System.out.println("name not provided. Defaulting to navjot");

diff --git a/...in/java/in/projecteka/data/Constants.java → ...a/in/projecteka/utils/data/Constants.java b/...in/java/in/projecteka/data/Constants.java → ...a/in/projecteka/utils/data/Constants.java
@@ -1,4 +1,4 @@
-package in.projecteka.data;
+package in.projecteka.utils.data;
 
 public class Constants {
     private static final String EKA_SYSTEM = "https://projecteka.in/%s";

diff --git a/...cteka/data/DiagnosticReportGenerator.java → ...utils/data/DiagnosticReportGenerator.java b/...cteka/data/DiagnosticReportGenerator.java → ...utils/data/DiagnosticReportGenerator.java
@@ -1,10 +1,10 @@
-package in.projecteka.data;
+package in.projecteka.utils.data;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.parser.IParser;
-import in.projecteka.data.model.DiagnosticTest;
-import in.projecteka.data.model.Doctor;
-import in.projecteka.data.model.Obs;
+import in.projecteka.utils.data.model.DiagnosticTest;
+import in.projecteka.utils.data.model.Doctor;
+import in.projecteka.utils.data.model.Obs;
 import org.hl7.fhir.r4.model.Attachment;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.CodeableConcept;
@@ -33,19 +33,8 @@
 import java.util.UUID;
 import java.util.stream.Collectors;
 
-import static in.projecteka.data.Constants.EKA_LOINC_SYSTEM;
-import static in.projecteka.data.FHIRUtils.addToBundleEntry;
-import static in.projecteka.data.FHIRUtils.createAuthor;
-import static in.projecteka.data.FHIRUtils.createBundle;
-import static in.projecteka.data.FHIRUtils.createEncounter;
-import static in.projecteka.data.FHIRUtils.getDateTimeType;
-import static in.projecteka.data.FHIRUtils.getDiagnosticReportType;
-import static in.projecteka.data.FHIRUtils.getIdentifier;
-import static in.projecteka.data.FHIRUtils.getPatientResource;
-import static in.projecteka.data.FHIRUtils.getReferenceToPatient;
-import static in.projecteka.data.FHIRUtils.getReferenceToResource;
-import static in.projecteka.data.FHIRUtils.loadOrganization;
-import static in.projecteka.data.Utils.randomBool;
+import static in.projecteka.utils.data.Constants.EKA_LOINC_SYSTEM;
+import static in.projecteka.utils.data.Utils.randomBool;
 
 public class DiagnosticReportGenerator implements DocumentGenerator {
     private Properties doctors;
@@ -58,20 +47,22 @@ public void init() throws Exception {
     }
 
     @Override
-    public void execute(String patientName, Date fromDate, int number, Path location) throws Exception {
+    public void execute(String patientName, Date fromDate, int number, Path location, String hipPrefix) throws Exception {
         FhirContext fhirContext = FhirContext.forR4();
         LocalDateTime dateTime = fromDate.toInstant().atZone(ZoneId.systemDefault()).toLocalDateTime();
         for (int i = 0; i < number; i++) {
             Date date = Utils.getNextDate(dateTime, i);
-            Bundle bundle = createDiagnosticReportBundle(date, patientName, "max", fhirContext.newJsonParser());
+            Bundle bundle = createDiagnosticReportBundle(date, patientName, hipPrefix, fhirContext.newJsonParser());
             String encodedString = fhirContext.newJsonParser().encodeResourceToString(bundle);
             List<Bundle.BundleEntryComponent> patientEntries =
                     bundle.getEntry().stream()
                             .filter(e -> e.getResource().getResourceType().equals(ResourceType.Patient))
                             .collect(Collectors.toList());
             Bundle.BundleEntryComponent patientEntry = patientEntries.get(0);
-            String fileName = String.format("%sDiagnosticReportDoc%s.json",
-                    patientEntry.getResource().getId(), Utils.formatDate(date, "yyyyMMdd"));
+            String fileName = String.format("%s%sDiagnosticReportDoc%s.json",
+                    hipPrefix.toUpperCase(),
+                    patientEntry.getResource().getId(),
+                    Utils.formatDate(date, "yyyyMMdd"));
             Path path = Paths.get(location.toString(), fileName);
             System.out.println("Saving DiagnosticReport to file:" + path.toString());
             Utils.saveToFile(path, encodedString);
@@ -80,61 +71,61 @@ public void execute(String patientName, Date fromDate, int number, Path location
     }
 
     private Bundle createDiagnosticReportBundle(Date date, String patientName, String hipPrefix, IParser parser) throws Exception {
-        Bundle bundle = createBundle(date, hipPrefix);
-        Patient patientResource = getPatientResource(patientName, patients);
+        Bundle bundle = FHIRUtils.createBundle(date, hipPrefix);
+        Patient patientResource = FHIRUtils.getPatientResource(patientName, patients);
         Reference patientRef = new Reference();
         patientRef.setResource(patientResource);
         Composition reportDoc = new Composition();
         reportDoc.setId(UUID.randomUUID().toString());
         reportDoc.setDate(bundle.getTimestamp());
-        reportDoc.setIdentifier(getIdentifier(reportDoc.getId(), hipPrefix, "document"));
+        reportDoc.setIdentifier(FHIRUtils.getIdentifier(reportDoc.getId(), hipPrefix, "document"));
         reportDoc.setStatus(Composition.CompositionStatus.FINAL);
-        reportDoc.setType(getDiagnosticReportType());
+        reportDoc.setType(FHIRUtils.getDiagnosticReportType());
         reportDoc.setTitle("Diagnostic Report Document");
-        addToBundleEntry(bundle, reportDoc, false);
-        Practitioner author = createAuthor(hipPrefix, doctors);
-        addToBundleEntry(bundle, author, false);
+        FHIRUtils.addToBundleEntry(bundle, reportDoc, false);
+        Practitioner author = FHIRUtils.createAuthor(hipPrefix, doctors);
+        FHIRUtils.addToBundleEntry(bundle, author, false);
         reportDoc.addAuthor().setResource(author);
         if (randomBool()) {
             reportDoc.getAuthor().get(0).setDisplay(Doctor.getDisplay(author));
         }
-        addToBundleEntry(bundle, patientResource, false);
-        reportDoc.setSubject(getReferenceToPatient(patientResource));
+        FHIRUtils.addToBundleEntry(bundle, patientResource, false);
+        reportDoc.setSubject(FHIRUtils.getReferenceToPatient(patientResource));
         Composition.SectionComponent section = reportDoc.addSection();
         section.setTitle("# Diagnostic Report");
-        section.setCode(getDiagnosticReportType());
+        section.setCode(FHIRUtils.getDiagnosticReportType());
 
-        Encounter encounter = createEncounter("Outpatient visit", "AMB", reportDoc.getDate());
-        encounter.setSubject(getReferenceToPatient(patientResource));
-        addToBundleEntry(bundle, encounter, false);
-        Reference referenceToResource = getReferenceToResource(encounter);
+        Encounter encounter = FHIRUtils.createEncounter("Outpatient visit", "AMB", reportDoc.getDate());
+        encounter.setSubject(FHIRUtils.getReferenceToPatient(patientResource));
+        FHIRUtils.addToBundleEntry(bundle, encounter, false);
+        Reference referenceToResource = FHIRUtils.getReferenceToResource(encounter);
         reportDoc.setEncounter(referenceToResource);
 
         DiagnosticReport report = new DiagnosticReport();
         report.setId(UUID.randomUUID().toString());
         report.setStatus(DiagnosticReport.DiagnosticReportStatus.FINAL);
-        section.getEntry().add(getReferenceToResource(report));
-        addToBundleEntry(bundle, report, false);
-        report.setSubject(getReferenceToPatient(patientResource));
+        section.getEntry().add(FHIRUtils.getReferenceToResource(report));
+        FHIRUtils.addToBundleEntry(bundle, report, false);
+        report.setSubject(FHIRUtils.getReferenceToPatient(patientResource));
         if (randomBool()) {
             report.setEncounter(referenceToResource);
         }
 
         report.setIssued(date);
         if (randomBool()) {
-            report.setEffective(getDateTimeType(date));
+            report.setEffective(FHIRUtils.getDateTimeType(date));
         }
 
-        Organization organization = parser.parseResource(Organization.class, loadOrganization(hipPrefix));
-        addToBundleEntry(bundle, organization, true);
-        report.setPerformer(Collections.singletonList(getReferenceToResource(organization)));
+        Organization organization = parser.parseResource(Organization.class, FHIRUtils.loadOrganization(hipPrefix));
+        FHIRUtils.addToBundleEntry(bundle, organization, true);
+        report.setPerformer(Collections.singletonList(FHIRUtils.getReferenceToResource(organization)));
 
         Practitioner interpreter = author;
         if (randomBool()) {
-            interpreter = createAuthor(hipPrefix, doctors);
-            addToBundleEntry(bundle, interpreter, false);
+            interpreter = FHIRUtils.createAuthor(hipPrefix, doctors);
+            FHIRUtils.addToBundleEntry(bundle, interpreter, false);
         }
-        report.setResultsInterpreter(Collections.singletonList(getReferenceToResource(interpreter)));
+        report.setResultsInterpreter(Collections.singletonList(FHIRUtils.getReferenceToResource(interpreter)));
         report.setCode(getDiagnosticTestCode(DiagnosticTest.getRandomTest()));
 
         if (randomBool()) {
@@ -153,8 +144,8 @@ private Bundle createDiagnosticReportBundle(Date date, String patientName, Strin
 
         if (randomBool()) {
             DocumentReference docReference = getReportAsDocReference(author);
-            addToBundleEntry(bundle, docReference, false);
-            section.getEntry().add(getReferenceToResource(docReference));
+            FHIRUtils.addToBundleEntry(bundle, docReference, false);
+            section.getEntry().add(FHIRUtils.getReferenceToResource(docReference));
         }
 
         return bundle;
@@ -163,22 +154,22 @@ private Bundle createDiagnosticReportBundle(Date date, String patientName, Strin
     private void addObservvationsToBundle(IParser parser, Bundle bundle, DiagnosticReport report) {
         Observation observation = parser.parseResource(Observation.class, Obs.getObservationResString());
         observation.setId(UUID.randomUUID().toString());
-        addToBundleEntry(bundle, observation, true);
-        report.addResult(getReferenceToResource(observation));
+        FHIRUtils.addToBundleEntry(bundle, observation, true);
+        report.addResult(FHIRUtils.getReferenceToResource(observation));
     }
 
     private DocumentReference getReportAsDocReference(Practitioner author) throws IOException {
         DocumentReference documentReference = new DocumentReference();
         documentReference.setStatus(Enumerations.DocumentReferenceStatus.CURRENT);
         documentReference.setId(UUID.randomUUID().toString());
-        documentReference.setType(getDiagnosticReportType());
+        documentReference.setType(FHIRUtils.getDiagnosticReportType());
         CodeableConcept concept = new CodeableConcept();
         Coding coding = concept.addCoding();
         coding.setSystem(EKA_LOINC_SYSTEM);
         coding.setCode("30954-2");
         coding.setDisplay("Surgical Pathology Report");
         documentReference.setType(concept);
-        documentReference.setAuthor(Collections.singletonList(getReferenceToResource(author)));
+        documentReference.setAuthor(Collections.singletonList(FHIRUtils.getReferenceToResource(author)));
         DocumentReference.DocumentReferenceContentComponent content = documentReference.addContent();
         content.setAttachment(getSurgicalReportAsAttachment());
         return  documentReference;

diff --git a/...in/projecteka/data/DocumentGenerator.java → ...jecteka/utils/data/DocumentGenerator.java b/...in/projecteka/data/DocumentGenerator.java → ...jecteka/utils/data/DocumentGenerator.java
@@ -1,9 +1,9 @@
-package in.projecteka.data;
+package in.projecteka.utils.data;
 
 import java.nio.file.Path;
 import java.util.Date;
 
 public interface DocumentGenerator {
     void init() throws Exception;
-    void execute(String patientName, Date fromDate, int number, Path location) throws Exception;
+    void execute(String patientName, Date fromDate, int number, Path location, String hipPrefix) throws Exception;
 }
diff --git a/...in/java/in/projecteka/data/FHIRUtils.java → ...a/in/projecteka/utils/data/FHIRUtils.java b/...in/java/in/projecteka/data/FHIRUtils.java → ...a/in/projecteka/utils/data/FHIRUtils.java
@@ -1,6 +1,6 @@
-package in.projecteka.data;
+package in.projecteka.utils.data;
 
-import in.projecteka.data.model.Doctor;
+import in.projecteka.utils.data.model.Doctor;
 import lombok.SneakyThrows;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.CodeableConcept;
@@ -65,7 +65,7 @@ static Bundle createBundle(Date forDate, String hipDomain) {
     }
 
     static Practitioner createAuthor(String hipPrefix, Properties doctors) {
-        String details = (String) doctors.get(String.valueOf(Utils.randomInt(1, 3)));
+        String details = (String) doctors.get(String.valueOf(Utils.randomInt(1, doctors.size())));
         Doctor doc = Doctor.parse(details);
         Practitioner practitioner = new Practitioner();
         practitioner.setId(hipPrefix.toUpperCase() + doc.getDocId());
@@ -79,7 +79,7 @@ static Patient getPatientResource(String name, Properties patients) throws Excep
         if (patientDetail == null) {
             throw new Exception("Can not identify patient with name: " + name);
         }
-        in.projecteka.data.model.Patient patient = in.projecteka.data.model.Patient.parse((String) patientDetail);
+        in.projecteka.utils.data.model.Patient patient = in.projecteka.utils.data.model.Patient.parse((String) patientDetail);
         Patient patientResource = new Patient();
         patientResource.setId(patient.getHid());
         patientResource.setName(Collections.singletonList(getHumanName(patient.getName(), null, null)));

diff --git a/...rojecteka/data/PrescriptionGenerator.java → ...eka/utils/data/PrescriptionGenerator.java b/...rojecteka/data/PrescriptionGenerator.java → ...eka/utils/data/PrescriptionGenerator.java
@@ -1,8 +1,8 @@
-package in.projecteka.data;
+package in.projecteka.utils.data;
 
 import ca.uhn.fhir.context.FhirContext;
-import in.projecteka.data.model.Doctor;
-import in.projecteka.data.model.Medicine;
+import in.projecteka.utils.data.model.Doctor;
+import in.projecteka.utils.data.model.Medicine;
 import org.hl7.fhir.r4.model.Binary;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.CodeableConcept;
@@ -39,20 +39,22 @@ public void init() throws Exception {
         patients = Utils.loadFromFile("/patients.properties");
     }
 
-    public void execute(String patientName, Date fromDate, int number, Path location) throws Exception {
+    public void execute(String patientName, Date fromDate, int number, Path location, String hipPrefix) throws Exception {
         FhirContext fhirContext = FhirContext.forR4();
         LocalDateTime dateTime = fromDate.toInstant().atZone(ZoneId.systemDefault()).toLocalDateTime();
         for (int i = 0; i < number; i++) {
             Date date = Utils.getNextDate(dateTime, i);
-            Bundle bundle = createPrescriptionBundle(date, patientName, "max");
+            Bundle bundle = createPrescriptionBundle(date, patientName, hipPrefix);
             String encodedString = fhirContext.newJsonParser().encodeResourceToString(bundle);
             List<Bundle.BundleEntryComponent> patientEntries =
                     bundle.getEntry().stream()
                             .filter(e -> e.getResource().getResourceType().equals(ResourceType.Patient))
                             .collect(Collectors.toList());
             Bundle.BundleEntryComponent patientEntry = patientEntries.get(0);
-            String fileName = String.format("%sPrescriptionDoc%s.json",
-                    patientEntry.getResource().getId(), Utils.formatDate(date, "yyyyMMdd"));
+            String fileName = String.format("%s%sPrescriptionDoc%s.json",
+                    hipPrefix.toUpperCase(),
+                    patientEntry.getResource().getId(),
+                    Utils.formatDate(date, "yyyyMMdd"));
             Path path = Paths.get(location.toString(), fileName);
             System.out.println("Saving Prescription to file:" + path.toString());
             Utils.saveToFile(path, encodedString);

diff --git a/src/main/java/in/projecteka/data/Utils.java → .../java/in/projecteka/utils/data/Utils.java b/src/main/java/in/projecteka/data/Utils.java → .../java/in/projecteka/utils/data/Utils.java
@@ -1,4 +1,4 @@
-package in.projecteka.data;
+package in.projecteka.utils.data;
 
 import org.hl7.fhir.r4.model.Meta;
 

diff --git a/...projecteka/data/model/DiagnosticTest.java → ...teka/utils/data/model/DiagnosticTest.java b/...projecteka/data/model/DiagnosticTest.java → ...teka/utils/data/model/DiagnosticTest.java
@@ -1,6 +1,6 @@
-package in.projecteka.data.model;
+package in.projecteka.utils.data.model;
 
-import in.projecteka.data.Utils;
+import in.projecteka.utils.data.Utils;
 import lombok.AllArgsConstructor;
 import lombok.Data;
 

diff --git a/...java/in/projecteka/data/model/Doctor.java → ...n/projecteka/utils/data/model/Doctor.java b/...java/in/projecteka/data/model/Doctor.java → ...n/projecteka/utils/data/model/Doctor.java
@@ -1,4 +1,4 @@
-package in.projecteka.data.model;
+package in.projecteka.utils.data.model;
 
 import lombok.AllArgsConstructor;
 import lombok.Data;

diff --git a/...va/in/projecteka/data/model/Medicine.java → ...projecteka/utils/data/model/Medicine.java b/...va/in/projecteka/data/model/Medicine.java → ...projecteka/utils/data/model/Medicine.java
@@ -1,4 +1,4 @@
-package in.projecteka.data.model;
+package in.projecteka.utils.data.model;
 
 import lombok.AllArgsConstructor;
 import lombok.Data;

diff --git a/...in/java/in/projecteka/data/model/Obs.java → ...a/in/projecteka/utils/data/model/Obs.java b/...in/java/in/projecteka/data/model/Obs.java → ...a/in/projecteka/utils/data/model/Obs.java
@@ -1,7 +1,6 @@
-package in.projecteka.data.model;
+package in.projecteka.utils.data.model;
 
-import ca.uhn.fhir.parser.IParser;
-import in.projecteka.data.Utils;
+import in.projecteka.utils.data.Utils;
 import lombok.AllArgsConstructor;
 import lombok.Data;
 

diff --git a/...ava/in/projecteka/data/model/Patient.java → .../projecteka/utils/data/model/Patient.java b/...ava/in/projecteka/data/model/Patient.java → .../projecteka/utils/data/model/Patient.java
@@ -1,4 +1,4 @@
-package in.projecteka.data.model;
+package in.projecteka.utils.data.model;
 
 import lombok.AllArgsConstructor;
 import lombok.Data;