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alex-odysseuswiverngitfedor_glushchenkooleg-odysseus
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Packaging/publication services and analysis execution results data providers for Shiny applications (#2399)
--------- Co-authored-by: wivern <[email protected]> Co-authored-by: git <[email protected]> Co-authored-by: fedor_glushchenko <[email protected]> Co-authored-by: oleg-odysseus <[email protected]>
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‎pom.xml

+114
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@@ -303,6 +303,9 @@
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<audit.trail.log.file>/tmp/atlas/audit/audit.log</audit.trail.log.file>
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<audit.trail.log.file.pattern>/tmp/atlas/audit/audit-%d{yyyy-MM-dd}-%i.log</audit.trail.log.file.pattern>
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<audit.trail.log.extraFile>/tmp/atlas/audit/audit-extra.log</audit.trail.log.extraFile>
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<!-- Shiny -->
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<shiny.enabled>false</shiny.enabled>
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</properties>
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<build>
@@ -1257,6 +1260,15 @@
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<version>2.0.1</version>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>com.squareup.okhttp3</groupId>
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<artifactId>okhttp</artifactId>
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<version>4.12.0</version>
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</dependency>
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<dependency>
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<groupId>com.fasterxml.jackson.datatype</groupId>
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<artifactId>jackson-datatype-jsr310</artifactId>
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</dependency>
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</dependencies>
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<profiles>
@@ -1910,5 +1922,107 @@
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</dependency>
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</dependencies>
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</profile>
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<profile>
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<id>webapi-shiny</id>
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<properties>
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<shiny.enabled>true</shiny.enabled>
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<shiny.atlas.url>http://localhost/Atlas</shiny.atlas.url>
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<shiny.output.directory>src/main/resources/shiny</shiny.output.directory>
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<shiny.app.directory></shiny.app.directory>
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<spring.profiles.active>default,shiny</spring.profiles.active>
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</properties>
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<build>
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<plugins>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-clean-plugin</artifactId>
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<version>3.3.2</version>
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<configuration>
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<filesets>
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<fileset>
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<directory>${shiny.output.directory}</directory>
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<includes>
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<include>shiny-cohortCounts.zip</include>
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<include>shiny-incidenceRates.zip</include>
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<include>shiny-cohortCharacterizations.zip</include>
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</includes>
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</fileset>
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</filesets>
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</configuration>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-assembly-plugin</artifactId>
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<version>3.6.0</version>
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<executions>
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<execution>
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<id>build-cohortCounts-archive</id>
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<goals>
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<goal>single</goal>
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</goals>
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<phase>generate-resources</phase>
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<configuration>
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<appendAssemblyId>false</appendAssemblyId>
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<archiveBaseDirectory>${shiny.app.directory}</archiveBaseDirectory>
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<outputDirectory>${shiny.output.directory}</outputDirectory>
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<descriptors>
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<descriptor>src/main/assembly/shiny-cohortCounts.xml</descriptor>
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</descriptors>
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<finalName>shiny-cohortCounts</finalName>
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</configuration>
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</execution>
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<execution>
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<id>build-incidenceRates-archive</id>
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<goals>
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<goal>single</goal>
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</goals>
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<phase>generate-resources</phase>
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<configuration>
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<appendAssemblyId>false</appendAssemblyId>
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<archiveBaseDirectory>${shiny.app.directory}</archiveBaseDirectory>
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<outputDirectory>${shiny.output.directory}</outputDirectory>
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<descriptors>
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<descriptor>src/main/assembly/shiny-incidenceRates.xml</descriptor>
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</descriptors>
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<finalName>shiny-incidenceRates</finalName>
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</configuration>
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</execution>
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<execution>
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<id>build-cohortCharacterizations-archive</id>
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<goals>
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<goal>single</goal>
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</goals>
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<phase>generate-resources</phase>
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<configuration>
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<appendAssemblyId>false</appendAssemblyId>
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<archiveBaseDirectory>${shiny.app.directory}</archiveBaseDirectory>
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<outputDirectory>${shiny.output.directory}</outputDirectory>
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<descriptors>
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<descriptor>src/main/assembly/shiny-cohortCharacterizations.xml</descriptor>
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</descriptors>
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<finalName>shiny-cohortCharacterizations</finalName>
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</configuration>
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</execution>
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<execution>
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<id>build-cohortPathways-archive</id>
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<goals>
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<goal>single</goal>
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</goals>
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<phase>generate-resources</phase>
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<configuration>
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<appendAssemblyId>false</appendAssemblyId>
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<archiveBaseDirectory>${shiny.app.directory}</archiveBaseDirectory>
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<outputDirectory>${shiny.output.directory}</outputDirectory>
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<descriptors>
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<descriptor>src/main/assembly/shiny-cohortPathways.xml</descriptor>
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</descriptors>
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<finalName>shiny-cohortPathways</finalName>
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</configuration>
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</execution>
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</executions>
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</plugin>
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</plugins>
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</build>
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</profile>
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</profiles>
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</project>

‎src/main/assembly/shiny-cohortCharacterizations.xml

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

‎src/main/assembly/shiny-cohortCounts.xml

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

‎src/main/assembly/shiny-cohortPathways.xml

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

‎src/main/assembly/shiny-incidenceRates.xml

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

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

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

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

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import org.ohdsi.webapi.service.TherapyPathResultsService;
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import org.ohdsi.webapi.service.UserService;
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import org.ohdsi.webapi.service.VocabularyService;
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import org.ohdsi.webapi.shiny.ShinyController;
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import org.ohdsi.webapi.source.SourceController;
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import org.springframework.beans.factory.InitializingBean;
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import org.springframework.beans.factory.annotation.Value;
@@ -47,6 +48,8 @@ public class JerseyConfig extends ResourceConfig implements InitializingBean {
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@Value("${jersey.resources.root.package}")
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private String rootPackage;
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@Value("${shiny.enabled:false}")
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private Boolean shinyEnabled;
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5154
public JerseyConfig() {
5255
RuntimeDelegate.setInstance(new org.glassfish.jersey.internal.RuntimeDelegateImpl());
@@ -94,5 +97,8 @@ protected void configure() {
9497
.in(Singleton.class);
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}
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});
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if (shinyEnabled) {
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register(ShinyController.class);
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}
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}
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}

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

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public PathwayPopulationResultsDTO getGenerationResults(
432432
@PathParam("generationId") final Long generationId
433433
) {
434-
435-
PathwayAnalysisResult resultingPathways = pathwayService.getResultingPathways(generationId);
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List<PathwayCodeDTO> eventCodeDtos = resultingPathways.getCodes()
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.stream()
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.map(entry -> {
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PathwayCodeDTO dto = new PathwayCodeDTO();
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dto.setCode(entry.getCode());
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dto.setName(entry.getName());
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dto.setIsCombo(entry.isCombo());
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return dto;
445-
})
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.collect(Collectors.toList());
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448-
List<TargetCohortPathwaysDTO> pathwayDtos = resultingPathways.getCohortPathwaysList()
449-
.stream()
450-
.map(cohortResults -> {
451-
if (cohortResults.getPathwaysCounts() == null) {
452-
return null;
453-
}
454-
455-
List<PathwayPopulationEventDTO> eventDTOs = cohortResults.getPathwaysCounts()
456-
.entrySet()
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.stream()
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.map(entry -> new PathwayPopulationEventDTO(entry.getKey(), entry.getValue()))
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.collect(Collectors.toList());
460-
return new TargetCohortPathwaysDTO(cohortResults.getCohortId(), cohortResults.getTargetCohortCount(), cohortResults.getTotalPathwaysCount(), eventDTOs);
461-
})
462-
.filter(Objects::nonNull)
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.collect(Collectors.toList());
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465-
return new PathwayPopulationResultsDTO(eventCodeDtos, pathwayDtos);
434+
return pathwayService.getGenerationResults(generationId);
466435
}
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private PathwayAnalysisDTO reloadAndConvert(Integer id) {

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

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44
import org.ohdsi.webapi.pathway.domain.PathwayAnalysisEntity;
55
import org.ohdsi.webapi.pathway.domain.PathwayAnalysisGenerationEntity;
66
import org.ohdsi.webapi.pathway.dto.PathwayAnalysisDTO;
7+
import org.ohdsi.webapi.pathway.dto.PathwayPopulationResultsDTO;
78
import org.ohdsi.webapi.pathway.dto.PathwayVersionFullDTO;
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import org.ohdsi.webapi.pathway.dto.internal.PathwayAnalysisResult;
910
import org.ohdsi.webapi.shiro.annotations.PathwayAnalysisGenerationId;
@@ -69,4 +70,8 @@ public interface PathwayService extends HasTags<Integer> {
6970
PathwayVersion saveVersion(int id);
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7172
List<PathwayAnalysisDTO> listByTags(TagNameListRequestDTO requestDTO);
73+
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PathwayAnalysisDTO getByGenerationId(Integer id);
75+
76+
PathwayPopulationResultsDTO getGenerationResults(Long generationId);
7277
}

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