API-2832 questionnaire read (#5)

make-configs.sh

@@ -38,4 +38,5 @@ makeConfig patient-generated-data $PROFILE
 configValue patient-generated-data $PROFILE spring.datasource.password '<YourStrong!Passw0rd>'
 configValue patient-generated-data $PROFILE spring.datasource.url 'jdbc:sqlserver://localhost:1633;database=pgd;sendStringParametersAsUnicode=false'
 configValue patient-generated-data $PROFILE spring.datasource.username 'SA'
+configValue patient-generated-data $PROFILE web-exception-key '-sharktopus-v-pteracuda-'
 checkForUnsetValues patient-generated-data $PROFILE

patient-generated-data-local-db/README.md → patient-generated-data-synthetic/README.md

@@ -1,9 +1,8 @@
-# patient-generated-data-local-db
+# patient-generated-data-synthetic
 
-This project builds a SQL Server Docker image
-for local development. This is the operational database for
-Patient Generated Data.
-An H2 database instance is also built for use by integration tests.
+Synthetic data for local and development environments.
+This project also builds a SQL Server Docker image
+for local development, and an H2 database for use by integration tests.
 
 ## Local Development
 

patient-generated-data-local-db/local-db.sh → patient-generated-data-synthetic/local-db.sh

@@ -17,4 +17,4 @@ docker run \
   -p 1633:1433 \
   -d mcr.microsoft.com/mssql/server:2017-latest
 
-mvn clean install -Ppopulaterator -P'!standard'
+mvn clean install -Ppopulaterator -P'!standard' -Dexec.cleanupDaemonThreads=false

patient-generated-data-local-db/pom.xml → patient-generated-data-synthetic/pom.xml

@@ -7,10 +7,12 @@
     <version>7.0.15</version>
     <relativePath/>
   </parent>
-  <artifactId>patient-generated-data-local-db</artifactId>
+  <artifactId>patient-generated-data-synthetic</artifactId>
   <version>0.0.7-SNAPSHOT</version>
   <packaging>jar</packaging>
   <properties>
+    <fhir-resources.version>5.0.11</fhir-resources.version>
+    <javax.el.version>3.0.1-b12</javax.el.version>
     <populaterator.sqlserver>false</populaterator.sqlserver>
   </properties>
   <dependencies>
@@ -22,10 +24,24 @@
       <groupId>com.h2database</groupId>
       <artifactId>h2</artifactId>
     </dependency>
+    <dependency>
+      <groupId>gov.va.api.health</groupId>
+      <artifactId>us-core-r4</artifactId>
+      <version>${fhir-resources.version}</version>
+    </dependency>
     <dependency>
       <groupId>com.microsoft.sqlserver</groupId>
       <artifactId>mssql-jdbc</artifactId>
     </dependency>
+    <dependency>
+      <groupId>org.glassfish</groupId>
+      <artifactId>javax.el</artifactId>
+      <version>${javax.el.version}</version>
+    </dependency>
+    <dependency>
+      <groupId>org.hibernate.validator</groupId>
+      <artifactId>hibernate-validator</artifactId>
+    </dependency>
     <dependency>
       <groupId>org.liquibase</groupId>
       <artifactId>liquibase-core</artifactId>

patient-generated-data-local-db/src/test/java/gov/va/api/health/patientgenerateddata/Populaterator.java → patient-generated-data-synthetic/src/test/java/gov/va/api/health/patientgenerateddata/Populaterator.java

@@ -1,12 +1,23 @@
 package gov.va.api.health.patientgenerateddata;
 
+import static com.google.common.base.Preconditions.checkState;
+import static java.util.stream.Collectors.joining;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import gov.va.api.health.r4.api.resources.Questionnaire;
 import java.io.File;
 import java.sql.Connection;
 import java.sql.DriverManager;
+import java.sql.PreparedStatement;
 import java.util.Collections;
+import java.util.HashSet;
 import java.util.List;
 import java.util.Optional;
+import java.util.Set;
 import java.util.concurrent.TimeUnit;
+import java.util.stream.IntStream;
+import javax.validation.ConstraintViolation;
+import javax.validation.Validation;
 import liquibase.Contexts;
 import liquibase.LabelExpression;
 import liquibase.Liquibase;
@@ -20,6 +31,12 @@
 import lombok.Value;
 
 public final class Populaterator {
+  private static final ObjectMapper MAPPER = new ObjectMapper();
+
+  private static String baseDir() {
+    return System.getProperty("basedir", ".");
+  }
+
   @SneakyThrows
   private static void bootstrap(@NonNull Db db) {
     log("Bootstrapping " + db.name());
@@ -30,7 +47,6 @@ private static void bootstrap(@NonNull Db db) {
     var conn = maybeConn.get();
     for (var n : db.bootstrapDatabases()) {
       log("Creating database " + n);
-      conn.prepareStatement("DROP DATABASE IF EXISTS " + n).execute();
       conn.prepareStatement("CREATE DATABASE " + n).execute();
     }
     conn.commit();
@@ -43,10 +59,9 @@ private static void liquibase(@NonNull Db db) {
     Database database =
         DatabaseFactory.getInstance()
             .findCorrectDatabaseImplementation(new JdbcConnection(connection));
-    String baseDir = System.getProperty("basedir", ".");
     try (Liquibase liquibase =
         new Liquibase(
-            baseDir
+            baseDir()
                 + "/../patient-generated-data/src/main/resources/db/changelog/db.changelog-master.yaml",
             new FileSystemResourceAccessor(),
             database)) {
@@ -61,8 +76,10 @@ private static void log(@NonNull String msg) {
   @SneakyThrows
   public static void main(String[] args) {
     if (Boolean.parseBoolean(System.getProperty("populaterator.h2", "true"))) {
-      String baseDir = System.getProperty("basedir", ".");
-      populate(H2.builder().dbFile(baseDir + "/target/pgd-db").build());
+      String dbFile = baseDir() + "/target/pgd-db";
+      new File(dbFile + ".mv.db").delete();
+      new File(dbFile + ".trace.db").delete();
+      populate(H2.builder().dbFile(dbFile).build());
     }
     if (Boolean.parseBoolean(System.getProperty("populaterator.sqlserver", "false"))) {
       populate(
@@ -73,7 +90,6 @@ public static void main(String[] args) {
               .password("<YourStrong!Passw0rd>")
               .database("pgd")
               .build());
-      System.exit(0);
     }
   }
 
@@ -84,12 +100,43 @@ private static void populate(@NonNull Db db) {
     bootstrap(db);
     liquibase(db);
     var connection = db.connection();
-    // populate individual resources
+    questionnaire(connection);
     connection.commit();
     connection.close();
     log("Finished " + db.name());
   }
 
+  @SneakyThrows
+  private static void questionnaire(@NonNull Connection connection) {
+    Set<String> ids = new HashSet<>();
+    for (File f : new File(baseDir() + "/src/test/resources/questionnaire").listFiles()) {
+      Questionnaire questionnaire = MAPPER.readValue(f, Questionnaire.class);
+      Set<ConstraintViolation<Questionnaire>> violations =
+          Validation.buildDefaultValidatorFactory().getValidator().validate(questionnaire);
+      checkState(violations.isEmpty(), "Invalid payload: " + violations);
+
+      String id = questionnaire.id();
+      checkState(id != null);
+      checkState(!ids.contains(id), "Duplicate ID " + id);
+      ids.add(id);
+
+      try (PreparedStatement statement =
+          connection.prepareStatement(
+              "insert into app.questionnaire ("
+                  + "id,"
+                  + "payload,"
+                  + "version"
+                  + ") values ("
+                  + IntStream.range(0, 3).mapToObj(v -> "?").collect(joining(","))
+                  + ")")) {
+        statement.setObject(1, id);
+        statement.setObject(2, new ObjectMapper().writeValueAsString(questionnaire));
+        statement.setObject(3, 0);
+        statement.execute();
+      }
+    }
+  }
+
   @SneakyThrows
   private static void waitForStartup(@NonNull Db db) {
     for (int i = 1; i <= 30; i++) {
@@ -131,8 +178,6 @@ public Optional<Connection> bootstrapConnection() {
     @Override
     @SneakyThrows
     public Connection connection() {
-      new File(dbFile + ".mv.db").delete();
-      new File(dbFile + ".trace.db").delete();
       return DriverManager.getConnection("jdbc:h2:" + dbFile, "sa", "sa");
     }
   }

patient-generated-data-synthetic/src/test/resources/questionnaire/3141.json

@@ -0,0 +1,157 @@
+{
+  "resourceType" : "Questionnaire",
+  "id" : "3141",
+  "text" : {
+    "status" : "generated",
+    "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"> <pre> 1.Comorbidity? 1.1 Cardial Comorbidity 1.1.1 Angina? 1.1.2 MI? 1.2 Vascular Comorbidity? ... Histopathology Abdominal pT category? ... </pre> </div>"
+  },
+  "url" : "http://hl7.org/fhir/Questionnaire/3141",
+  "title" : "Cancer Quality Forum Questionnaire 2012",
+  "status" : "draft",
+  "subjectType" : [
+    "Patient"
+  ],
+  "date" : "2012-01",
+  "item" : [
+    {
+      "linkId" : "1",
+      "code" : [
+        {
+          "system" : "http://example.org/system/code/sections",
+          "code" : "COMORBIDITY"
+        }
+      ],
+      "type" : "group",
+      "item" : [
+        {
+          "linkId" : "1.1",
+          "code" : [
+            {
+              "system" : "http://example.org/system/code/questions",
+              "code" : "COMORB"
+            }
+          ],
+          "prefix" : "1",
+          "type" : "choice",
+          "answerValueSet" : "http://hl7.org/fhir/ValueSet/yesnodontknow",
+          "item" : [
+            {
+              "linkId" : "1.1.1",
+              "code" : [
+                {
+                  "system" : "http://example.org/system/code/sections",
+                  "code" : "CARDIAL"
+                }
+              ],
+              "type" : "group",
+              "enableWhen" : [
+                {
+                  "question" : "1.1",
+                  "operator" : "=",
+                  "answerCoding" : {
+                    "system" : "http://terminology.hl7.org/CodeSystem/v2-0136",
+                    "code" : "Y"
+                  }
+                }
+              ],
+              "item" : [
+                {
+                  "linkId" : "1.1.1.1",
+                  "code" : [
+                    {
+                      "system" : "http://example.org/system/code/questions",
+                      "code" : "COMORBCAR"
+                    }
+                  ],
+                  "prefix" : "1.1",
+                  "type" : "choice",
+                  "answerValueSet" : "http://hl7.org/fhir/ValueSet/yesnodontknow",
+                  "item" : [
+                    {
+                      "linkId" : "1.1.1.1.1",
+                      "code" : [
+                        {
+                          "system" : "http://example.org/system/code/questions",
+                          "code" : "COMCAR00",
+                          "display" : "Angina Pectoris"
+                        },
+                        {
+                          "system" : "http://snomed.info/sct",
+                          "code" : "194828000",
+                          "display" : "Angina (disorder)"
+                        }
+                      ],
+                      "prefix" : "1.1.1",
+                      "type" : "choice",
+                      "answerValueSet" : "http://hl7.org/fhir/ValueSet/yesnodontknow"
+                    },
+                    {
+                      "linkId" : "1.1.1.1.2",
+                      "code" : [
+                        {
+                          "system" : "http://snomed.info/sct",
+                          "code" : "22298006",
+                          "display" : "Myocardial infarction (disorder)"
+                        }
+                      ],
+                      "prefix" : "1.1.2",
+                      "type" : "choice",
+                      "answerValueSet" : "http://hl7.org/fhir/ValueSet/yesnodontknow"
+                    }
+                  ]
+                },
+                {
+                  "linkId" : "1.1.1.2",
+                  "code" : [
+                    {
+                      "system" : "http://example.org/system/code/questions",
+                      "code" : "COMORBVAS"
+                    }
+                  ],
+                  "prefix" : "1.2",
+                  "type" : "choice",
+                  "answerValueSet" : "http://hl7.org/fhir/ValueSet/yesnodontknow"
+                }
+              ]
+            }
+          ]
+        }
+      ]
+    },
+    {
+      "linkId" : "2",
+      "code" : [
+        {
+          "system" : "http://example.org/system/code/sections",
+          "code" : "HISTOPATHOLOGY"
+        }
+      ],
+      "type" : "group",
+      "item" : [
+        {
+          "linkId" : "2.1",
+          "code" : [
+            {
+              "system" : "http://example.org/system/code/sections",
+              "code" : "ABDOMINAL"
+            }
+          ],
+          "type" : "group",
+          "item" : [
+            {
+              "linkId" : "2.1.2",
+              "code" : [
+                {
+                  "system" : "http://example.org/system/code/questions",
+                  "code" : "STADPT",
+                  "display" : "pT category"
+                }
+              ],
+              "type" : "choice"
+            }
+          ]
+        }
+      ]
+    }
+  ]
+}