API-2835 QuestionnaireResponse synthetic data (#7)

department-of-veterans-affairs · Nov 16, 2020 · db86088 · db86088
1 parent 4ec4672
commit db86088
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Showing 6 changed files with 243 additions and 11 deletions.
diff --git a/patient-generated-data-synthetic/pom.xml b/patient-generated-data-synthetic/pom.xml
@@ -11,7 +11,7 @@
   <version>0.0.9-SNAPSHOT</version>
   <packaging>jar</packaging>
   <properties>
-    <fhir-resources.version>5.0.11</fhir-resources.version>
+    <fhir-resources.version>5.0.13</fhir-resources.version>
     <javax.el.version>3.0.1-b12</javax.el.version>
     <populaterator.sqlserver>false</populaterator.sqlserver>
   </properties>

diff --git a/...ed-data-synthetic/src/test/java/gov/va/api/health/patientgenerateddata/Populaterator.java b/...ed-data-synthetic/src/test/java/gov/va/api/health/patientgenerateddata/Populaterator.java
@@ -5,10 +5,12 @@
 
 import com.fasterxml.jackson.databind.ObjectMapper;
 import gov.va.api.health.r4.api.resources.Questionnaire;
+import gov.va.api.health.r4.api.resources.QuestionnaireResponse;
 import java.io.File;
 import java.sql.Connection;
 import java.sql.DriverManager;
 import java.sql.PreparedStatement;
+import java.util.Collection;
 import java.util.Collections;
 import java.util.HashSet;
 import java.util.List;
@@ -101,6 +103,7 @@ private static void populate(@NonNull Db db) {
     liquibase(db);
     var connection = db.connection();
     questionnaire(connection);
+    questionnaireResponse(connection);
     connection.commit();
     connection.close();
     log("Finished " + db.name());
@@ -120,15 +123,8 @@ private static void questionnaire(@NonNull Connection connection) {
       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(","))
-                  + ")")) {
+      String sqlInsert = sqlInsert("app.Questionnaire", List.of("id", "payload", "version"));
+      try (PreparedStatement statement = connection.prepareStatement(sqlInsert)) {
         statement.setObject(1, id);
         statement.setObject(2, new ObjectMapper().writeValueAsString(questionnaire));
         statement.setObject(3, 0);
@@ -137,6 +133,42 @@ private static void questionnaire(@NonNull Connection connection) {
     }
   }
 
+  @SneakyThrows
+  private static void questionnaireResponse(@NonNull Connection connection) {
+    Set<String> ids = new HashSet<>();
+
+    for (File f : new File(baseDir() + "/src/test/resources/questionnaireResponse").listFiles()) {
+      QuestionnaireResponse response = MAPPER.readValue(f, QuestionnaireResponse.class);
+      Set<ConstraintViolation<QuestionnaireResponse>> violations =
+          Validation.buildDefaultValidatorFactory().getValidator().validate(response);
+      checkState(violations.isEmpty(), "Invalid payload: " + violations);
+
+      String id = response.id();
+      checkState(id != null);
+      checkState(!ids.contains(id), "Duplicate ID " + id);
+      ids.add(id);
+
+      String sqlInsert =
+          sqlInsert("app.QuestionnaireResponse", List.of("id", "payload", "version"));
+      try (PreparedStatement statement = connection.prepareStatement(sqlInsert)) {
+        statement.setObject(1, id);
+        statement.setObject(2, new ObjectMapper().writeValueAsString(response));
+        statement.setObject(3, 0);
+        statement.execute();
+      }
+    }
+  }
+
+  private static String sqlInsert(@NonNull String table, @NonNull Collection<String> columns) {
+    return "insert into "
+        + table
+        + " ("
+        + columns.stream().collect(joining(","))
+        + ") values ("
+        + IntStream.range(0, columns.size()).mapToObj(v -> "?").collect(joining(","))
+        + ")";
+  }
+
   @SneakyThrows
   private static void waitForStartup(@NonNull Db db) {
     for (int i = 1; i <= 30; i++) {

diff --git a/patient-generated-data-synthetic/src/test/resources/questionnaireResponse/3141.json b/patient-generated-data-synthetic/src/test/resources/questionnaireResponse/3141.json
@@ -0,0 +1,69 @@
+{
+  "resourceType" : "QuestionnaireResponse",
+  "id" : "3141",
+  "text" : {
+    "status" : "generated",
+    "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">      <pre>            Comorbidity? YES              Cardial Comorbidity? YES                Angina? YES                MI? NO              Vascular Comorbidity?                (no answers)              ...            Histopathology              Abdominal                pT category: 1a              ...          </pre>    </div>"
+  },
+  "status" : "completed",
+  "authored" : "2013-02-19T14:15:00-05:00",
+  "item" : [
+    {
+      "linkId" : "1",
+      "item" : [
+        {
+          "linkId" : "1.1",
+          "answer" : [
+            {
+              "valueCoding" : {
+                "system" : "http://cancer.questionnaire.org/system/code/yesno",
+                "code" : "1",
+                "display" : "Yes"
+              },
+              "item" : [
+                {
+                  "linkId" : "1.1.1",
+                  "item" : [
+                    {
+                      "linkId" : "1.1.1.1",
+                      "answer" : [
+                        {
+                          "valueCoding" : {
+                            "system" : "http://cancer.questionnaire.org/system/code/yesno",
+                            "code" : "1"
+                          }
+                        }
+                      ]
+                    },
+                    {
+                      "linkId" : "1.1.1.2",
+                      "answer" : [
+                        {
+                          "valueCoding" : {
+                            "system" : "http://cancer.questionnaire.org/system/code/yesno",
+                            "code" : "1"
+                          }
+                        }
+                      ]
+                    },
+                    {
+                      "linkId" : "1.1.1.3",
+                      "answer" : [
+                        {
+                          "valueCoding" : {
+                            "system" : "http://cancer.questionnaire.org/system/code/yesno",
+                            "code" : "0"
+                          }
+                        }
+                      ]
+                    }
+                  ]
+                }
+              ]
+            }
+          ]
+        }
+      ]
+    }
+  ]
+}
diff --git a/patient-generated-data-synthetic/src/test/resources/questionnaireResponse/f201.json b/patient-generated-data-synthetic/src/test/resources/questionnaireResponse/f201.json
@@ -0,0 +1,92 @@
+{
+  "resourceType" : "QuestionnaireResponse",
+  "id" : "f201",
+  "text" : {
+    "status" : "generated",
+    "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: f201</p><p><b>status</b>: completed</p><p><b>subject</b>: <a>Roel</a></p><p><b>authored</b>: 18/06/2013 12:00:00 AM</p><p><b>author</b>: <a>Practitioner/f201</a></p><p><b>source</b>: <a>Practitioner/f201</a></p><blockquote><p><b>item</b></p><p><b>linkId</b>: 1</p><h3>Items</h3><table><tr><td>-</td></tr><tr><td>*</td></tr></table></blockquote><blockquote><p><b>item</b></p><p><b>linkId</b>: 2</p><p><b>text</b>: General questions</p><h3>Items</h3><table><tr><td>-</td></tr><tr><td>*</td></tr><tr><td>*</td></tr><tr><td>*</td></tr><tr><td>*</td></tr></table></blockquote><blockquote><p><b>item</b></p><p><b>linkId</b>: 3</p><p><b>text</b>: Intoxications</p><h3>Items</h3><table><tr><td>-</td></tr><tr><td>*</td></tr><tr><td>*</td></tr></table></blockquote></div>"
+  },
+  "status" : "completed",
+  "authored" : "2013-06-18T00:00:00+01:00",
+  "item" : [
+    {
+      "linkId" : "1",
+      "item" : [
+        {
+          "linkId" : "1.1",
+          "text" : "Do you have allergies?",
+          "answer" : [
+            {
+              "valueString" : "I am allergic to house dust"
+            }
+          ]
+        }
+      ]
+    },
+    {
+      "linkId" : "2",
+      "text" : "General questions",
+      "item" : [
+        {
+          "linkId" : "2.1",
+          "text" : "What is your gender?",
+          "answer" : [
+            {
+              "valueString" : "Male"
+            }
+          ]
+        },
+        {
+          "linkId" : "2.2",
+          "text" : "What is your date of birth?",
+          "answer" : [
+            {
+              "valueDate" : "1960-03-13"
+            }
+          ]
+        },
+        {
+          "linkId" : "2.3",
+          "text" : "What is your country of birth?",
+          "answer" : [
+            {
+              "valueString" : "The Netherlands"
+            }
+          ]
+        },
+        {
+          "linkId" : "2.4",
+          "text" : "What is your marital status?",
+          "answer" : [
+            {
+              "valueString" : "married"
+            }
+          ]
+        }
+      ]
+    },
+    {
+      "linkId" : "3",
+      "text" : "Intoxications",
+      "item" : [
+        {
+          "linkId" : "3.1",
+          "text" : "Do you smoke?",
+          "answer" : [
+            {
+              "valueString" : "No"
+            }
+          ]
+        },
+        {
+          "linkId" : "3.2",
+          "text" : "Do you drink alchohol?",
+          "answer" : [
+            {
+              "valueString" : "No, but I used to drink"
+            }
+          ]
+        }
+      ]
+    }
+  ]
+}
diff --git a/...erated-data/src/main/java/gov/va/api/health/patientgenerateddata/QuestionnaireEntity.java b/...erated-data/src/main/java/gov/va/api/health/patientgenerateddata/QuestionnaireEntity.java
@@ -17,7 +17,7 @@
 @Data
 @Entity
 @Builder
-@Table(name = "questionnaire", schema = "app")
+@Table(name = "Questionnaire", schema = "app")
 @NoArgsConstructor(access = AccessLevel.PRIVATE)
 @AllArgsConstructor(access = AccessLevel.PRIVATE)
 @EqualsAndHashCode(onlyExplicitlyIncluded = true)

diff --git a/patient-generated-data/src/main/resources/db/changelog/db.changelog-master.yaml b/patient-generated-data/src/main/resources/db/changelog/db.changelog-master.yaml
@@ -33,3 +33,42 @@ databaseChangeLog:
                   type: int
                   constraints:
                     nullable: false
+
+  - changeSet:
+      id: 3
+      author: pteracuda
+      changes:
+        # table renames are *not* case sensitive, so rename to a temporary name first
+        - renameTable:
+            schemaName: app
+            oldTableName: questionnaire
+            newTableName: questionnaire_temp
+        - renameTable:
+            schemaName: app
+            oldTableName: questionnaire_temp
+            newTableName: Questionnaire
+
+  - changeSet:
+      id: 4
+      author: pteracuda
+      changes:
+        - createTable:
+            tableName: QuestionnaireResponse
+            schemaName: app
+            columns:
+              - column:
+                  name: id
+                  type: varchar(32)
+                  constraints:
+                    primaryKey: true
+                    nullable: false
+              - column:
+                  name: payload
+                  type: clob
+                  constraints:
+                    nullable: false
+              - column:
+                  name: version
+                  type: int
+                  constraints:
+                    nullable: false