Packaging/publication services and analysis execution results data providers for Shiny applications

pom.xml

@@ -302,6 +302,9 @@
     <audit.trail.enabled>false</audit.trail.enabled>
     <audit.trail.log.file>/tmp/atlas/audit/audit.log</audit.trail.log.file>
     <audit.trail.log.extraFile>/tmp/atlas/audit/audit-extra.log</audit.trail.log.extraFile>
+
+    <!-- Shiny -->
+    <shiny.enabled>false</shiny.enabled>
   </properties>
 
   <build>
@@ -1256,6 +1259,15 @@
       <version>2.0.1</version>
       <scope>test</scope>
     </dependency>
+    <dependency>
+      <groupId>com.squareup.okhttp3</groupId>
+      <artifactId>okhttp</artifactId>
+      <version>4.12.0</version>
+    </dependency>
+    <dependency>
+      <groupId>com.fasterxml.jackson.datatype</groupId>
+      <artifactId>jackson-datatype-jsr310</artifactId>
+    </dependency>
   </dependencies>
 
   <profiles>
@@ -1909,5 +1921,107 @@
         </dependency>
       </dependencies>
     </profile>
+    <profile>
+      <id>webapi-shiny</id>
+      <properties>
+        <shiny.enabled>true</shiny.enabled>
+        <shiny.atlas.url>http://localhost/Atlas</shiny.atlas.url>
+        <shiny.output.directory>src/main/resources/shiny</shiny.output.directory>
+        <shiny.app.directory></shiny.app.directory>
+        <spring.profiles.active>default,shiny</spring.profiles.active>
+      </properties>
+      <build>
+        <plugins>
+          <plugin>
+            <groupId>org.apache.maven.plugins</groupId>
+            <artifactId>maven-clean-plugin</artifactId>
+            <version>3.3.2</version>
+            <configuration>
+              <filesets>
+                <fileset>
+                  <directory>${shiny.output.directory}</directory>
+                  <includes>
+                    <include>shiny-cohortCounts.zip</include>
+                    <include>shiny-incidenceRates.zip</include>
+                    <include>shiny-cohortCharacterizations.zip</include>
+                  </includes>
+                </fileset>
+              </filesets>
+            </configuration>
+          </plugin>
+          <plugin>
+            <groupId>org.apache.maven.plugins</groupId>
+            <artifactId>maven-assembly-plugin</artifactId>
+            <version>3.6.0</version>
+            <executions>
+              <execution>
+                <id>build-cohortCounts-archive</id>
+                <goals>
+                  <goal>single</goal>
+                </goals>
+                <phase>generate-resources</phase>
+                <configuration>
+                  <appendAssemblyId>false</appendAssemblyId>
+                  <archiveBaseDirectory>${shiny.app.directory}</archiveBaseDirectory>
+                  <outputDirectory>${shiny.output.directory}</outputDirectory>
+                  <descriptors>
+                    <descriptor>src/main/assembly/shiny-cohortCounts.xml</descriptor>
+                  </descriptors>
+                  <finalName>shiny-cohortCounts</finalName>
+                </configuration>
+              </execution>
+              <execution>
+                <id>build-incidenceRates-archive</id>
+                <goals>
+                  <goal>single</goal>
+                </goals>
+                <phase>generate-resources</phase>
+                <configuration>
+                  <appendAssemblyId>false</appendAssemblyId>
+                  <archiveBaseDirectory>${shiny.app.directory}</archiveBaseDirectory>
+                  <outputDirectory>${shiny.output.directory}</outputDirectory>
+                  <descriptors>
+                    <descriptor>src/main/assembly/shiny-incidenceRates.xml</descriptor>
+                  </descriptors>
+                  <finalName>shiny-incidenceRates</finalName>
+                </configuration>
+              </execution>
+              <execution>
+                <id>build-cohortCharacterizations-archive</id>
+                <goals>
+                  <goal>single</goal>
+                </goals>
+                <phase>generate-resources</phase>
+                <configuration>
+                  <appendAssemblyId>false</appendAssemblyId>
+                  <archiveBaseDirectory>${shiny.app.directory}</archiveBaseDirectory>
+                  <outputDirectory>${shiny.output.directory}</outputDirectory>
+                  <descriptors>
+                    <descriptor>src/main/assembly/shiny-cohortCharacterizations.xml</descriptor>
+                  </descriptors>
+                  <finalName>shiny-cohortCharacterizations</finalName>
+                </configuration>
+              </execution>
+              <execution>
+                <id>build-cohortPathways-archive</id>
+                <goals>
+                  <goal>single</goal>
+                </goals>
+                <phase>generate-resources</phase>
+                <configuration>
+                  <appendAssemblyId>false</appendAssemblyId>
+                  <archiveBaseDirectory>${shiny.app.directory}</archiveBaseDirectory>
+                  <outputDirectory>${shiny.output.directory}</outputDirectory>
+                  <descriptors>
+                    <descriptor>src/main/assembly/shiny-cohortPathways.xml</descriptor>
+                  </descriptors>
+                  <finalName>shiny-cohortPathways</finalName>
+                </configuration>
+              </execution>
+            </executions>
+          </plugin>
+        </plugins>
+      </build>
+    </profile>
   </profiles>
 </project>

src/main/assembly/shiny-cohortCharacterizations.xml

@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8" ?>
+<assembly xmlns="http://maven.apache.org/ASSEMBLY/2.2.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+          xsi:schemaLocation="http://maven.apache.org/ASSEMBLY/2.2.0 https://maven.apache.org/xsd/assembly-2.2.0.xsd">
+    <id>shiny-cohortCharacterizations</id>
+    <formats>
+        <format>zip</format>
+    </formats>
+    <includeBaseDirectory>false</includeBaseDirectory>
+    <fileSets>
+        <fileSet>
+            <directory>./apps/cohortCharacterization</directory>
+            <excludes>
+                <exclude>data/**</exclude>
+            </excludes>
+            <outputDirectory>/</outputDirectory>
+        </fileSet>
+    </fileSets>
+</assembly>

src/main/assembly/shiny-cohortCounts.xml

@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8" ?>
+<assembly xmlns="http://maven.apache.org/ASSEMBLY/2.2.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+          xsi:schemaLocation="http://maven.apache.org/ASSEMBLY/2.2.0 https://maven.apache.org/xsd/assembly-2.2.0.xsd">
+    <id>shiny-cohortCounts</id>
+    <formats>
+        <format>zip</format>
+    </formats>
+    <includeBaseDirectory>false</includeBaseDirectory>
+    <fileSets>
+        <fileSet>
+            <directory>./apps/cohortCounts</directory>
+            <excludes>
+                <exclude>data/**</exclude>
+            </excludes>
+            <outputDirectory>/</outputDirectory>
+        </fileSet>
+    </fileSets>
+</assembly>

src/main/assembly/shiny-cohortPathways.xml

@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8" ?>
+<assembly xmlns="http://maven.apache.org/ASSEMBLY/2.2.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+          xsi:schemaLocation="http://maven.apache.org/ASSEMBLY/2.2.0 https://maven.apache.org/xsd/assembly-2.2.0.xsd">
+    <id>shiny-incidenceRates</id>
+    <formats>
+        <format>zip</format>
+    </formats>
+    <includeBaseDirectory>false</includeBaseDirectory>
+    <fileSets>
+        <fileSet>
+            <directory>./apps/cohortPathways</directory>
+            <excludes>
+                <exclude>data/**</exclude>
+            </excludes>
+            <outputDirectory>/</outputDirectory>
+        </fileSet>
+    </fileSets>
+</assembly>

src/main/assembly/shiny-incidenceRates.xml

@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8" ?>
+<assembly xmlns="http://maven.apache.org/ASSEMBLY/2.2.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+          xsi:schemaLocation="http://maven.apache.org/ASSEMBLY/2.2.0 https://maven.apache.org/xsd/assembly-2.2.0.xsd">
+    <id>shiny-incidenceRates</id>
+    <formats>
+        <format>zip</format>
+    </formats>
+    <includeBaseDirectory>false</includeBaseDirectory>
+    <fileSets>
+        <fileSet>
+            <directory>./apps/IncidenceRate</directory>
+            <excludes>
+                <exclude>data/**</exclude>
+            </excludes>
+            <outputDirectory>/</outputDirectory>
+        </fileSet>
+    </fileSets>
+</assembly>

src/main/java/org/ohdsi/webapi/Constants.java

@@ -90,9 +90,13 @@ interface Variables {
   }
 
   interface Headers {
+    String ACCESS_CONTROL_EXPOSE_HEADERS = "Access-Control-Expose-Headers";
     String AUTH_PROVIDER = "x-auth-provider";
     String USER_LANGAUGE = "User-Language";
     String ACTION_LOCATION = "action-location";
+    String BEARER = "Bearer";
+    String X_AUTH_ERROR = "x-auth-error";
+    String CONTENT_DISPOSITION = "Content-Disposition";
   }
 
   interface SecurityProviders {

src/main/java/org/ohdsi/webapi/JerseyConfig.java

@@ -30,6 +30,7 @@
 import org.ohdsi.webapi.service.TherapyPathResultsService;
 import org.ohdsi.webapi.service.UserService;
 import org.ohdsi.webapi.service.VocabularyService;
+import org.ohdsi.webapi.shiny.ShinyController;
 import org.ohdsi.webapi.source.SourceController;
 import org.springframework.beans.factory.InitializingBean;
 import org.springframework.beans.factory.annotation.Value;
@@ -47,6 +48,8 @@ public class JerseyConfig extends ResourceConfig implements InitializingBean {
 
     @Value("${jersey.resources.root.package}")
     private String rootPackage;
+    @Value("${shiny.enabled:false}")
+    private Boolean shinyEnabled;
 
     public JerseyConfig() {
        RuntimeDelegate.setInstance(new org.glassfish.jersey.internal.RuntimeDelegateImpl());
@@ -94,5 +97,8 @@ protected void configure() {
                         .in(Singleton.class);
             }
         });
+        if (shinyEnabled) {
+            register(ShinyController.class);
+        }
     }
 }

src/main/java/org/ohdsi/webapi/pathway/PathwayController.java

@@ -431,38 +431,7 @@ public String getGenerationDesign(
 	public PathwayPopulationResultsDTO getGenerationResults(
 					@PathParam("generationId") final Long generationId
 	) {
-
-		PathwayAnalysisResult resultingPathways = pathwayService.getResultingPathways(generationId);
-
-		List<PathwayCodeDTO> eventCodeDtos = resultingPathways.getCodes()
-						.stream()
-						.map(entry -> {
-							PathwayCodeDTO dto = new PathwayCodeDTO();
-							dto.setCode(entry.getCode());
-							dto.setName(entry.getName());
-							dto.setIsCombo(entry.isCombo());
-							return dto;
-						})
-						.collect(Collectors.toList());
-
-		List<TargetCohortPathwaysDTO> pathwayDtos = resultingPathways.getCohortPathwaysList()
-						.stream()
-						.map(cohortResults -> {
-							if (cohortResults.getPathwaysCounts() == null) {
-								return null;
-							}
-
-							List<PathwayPopulationEventDTO> eventDTOs = cohortResults.getPathwaysCounts()
-											.entrySet()
-											.stream()
-											.map(entry -> new PathwayPopulationEventDTO(entry.getKey(), entry.getValue()))
-											.collect(Collectors.toList());
-							return new TargetCohortPathwaysDTO(cohortResults.getCohortId(), cohortResults.getTargetCohortCount(), cohortResults.getTotalPathwaysCount(), eventDTOs);
-						})
-						.filter(Objects::nonNull)
-						.collect(Collectors.toList());
-
-		return new PathwayPopulationResultsDTO(eventCodeDtos, pathwayDtos);
+		return pathwayService.getGenerationResults(generationId);
 	}
 
 	private PathwayAnalysisDTO reloadAndConvert(Integer id) {

src/main/java/org/ohdsi/webapi/pathway/PathwayService.java

@@ -4,6 +4,7 @@
 import org.ohdsi.webapi.pathway.domain.PathwayAnalysisEntity;
 import org.ohdsi.webapi.pathway.domain.PathwayAnalysisGenerationEntity;
 import org.ohdsi.webapi.pathway.dto.PathwayAnalysisDTO;
+import org.ohdsi.webapi.pathway.dto.PathwayPopulationResultsDTO;
 import org.ohdsi.webapi.pathway.dto.PathwayVersionFullDTO;
 import org.ohdsi.webapi.pathway.dto.internal.PathwayAnalysisResult;
 import org.ohdsi.webapi.shiro.annotations.PathwayAnalysisGenerationId;
@@ -69,4 +70,8 @@ public interface PathwayService extends HasTags<Integer> {
     PathwayVersion saveVersion(int id);
 
     List<PathwayAnalysisDTO> listByTags(TagNameListRequestDTO requestDTO);
+
+    PathwayAnalysisDTO getByGenerationId(Integer id);
+
+    PathwayPopulationResultsDTO getGenerationResults(Long generationId);
 }