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Release/0003 #83

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merged 4 commits into from
Sep 27, 2023
Merged

Release/0003 #83

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3dc96b5
[ALS-4947] Add anyRecordOfMulti field to the query object (#77)
ramari16 Aug 30, 2023
a43a209
[ALS-4980] Update PicSureService to match contract with PIC-SURe API
Gcolon021 Sep 18, 2023
e8c62bc
[ALS-5052] Update to use docker tomcat image (#82)
ramari16 Sep 22, 2023
064f495
Merge branch 'master' into release/0003
ramari16 Sep 25, 2023
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13 changes: 2 additions & 11 deletions docker/pic-sure-hpds/Dockerfile
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Original file line number Diff line number Diff line change
@@ -1,11 +1,2 @@
FROM docker.io/alpine:3.16

RUN apk add --no-cache --purge -uU bash && rm -rf /var/cache/apk/* /tmp/*

RUN apk add --no-cache --purge -uU curl wget unzip

RUN apk add --no-cache --purge openjdk11

ADD hpds-war-1.0-SNAPSHOT-war-exec.jar /hpds.jar

EXPOSE 8080
FROM tomcat:9-jre11-openjdk-slim
ADD hpds-war-1.0-SNAPSHOT.war /usr/local/tomcat/webapps/ROOT.war
12 changes: 6 additions & 6 deletions service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/PicSureService.java
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Expand Up @@ -225,8 +225,8 @@ private QueryStatus convertToQueryStatus(AsyncResult entity) {
@Path("/query/{resourceQueryId}/result")
@Produces(MediaType.TEXT_PLAIN_VALUE)
@Override
public Response queryResult(@PathParam("resourceQueryId") String queryId, QueryRequest resultRequest) {
AsyncResult result = queryService.getResultFor(queryId);
public Response queryResult(@PathParam("resourceQueryId") UUID queryId, QueryRequest resultRequest) {
AsyncResult result = queryService.getResultFor(queryId.toString());
if (result == null) {
// This happens sometimes when users immediately request the status for a query
// before it can be initialized. We wait a bit and try again before throwing an
Expand All @@ -237,7 +237,7 @@ public Response queryResult(@PathParam("resourceQueryId") String queryId, QueryR
return Response.status(500).build();
}

result = queryService.getResultFor(queryId);
result = queryService.getResultFor(queryId.toString());
if (result == null) {
return Response.status(404).build();
}
Expand All @@ -253,8 +253,8 @@ public Response queryResult(@PathParam("resourceQueryId") String queryId, QueryR
@POST
@Path("/query/{resourceQueryId}/status")
@Override
public QueryStatus queryStatus(@PathParam("resourceQueryId") String queryId, QueryRequest request) {
return convertToQueryStatus(queryService.getStatusFor(queryId));
public QueryStatus queryStatus(@PathParam("resourceQueryId") UUID queryId, QueryRequest request) {
return convertToQueryStatus(queryService.getStatusFor(queryId.toString()));
}

@POST
Expand Down Expand Up @@ -328,7 +328,7 @@ private Response _querySync(QueryRequest resultRequest) throws IOException {
QueryStatus status = query(resultRequest);
while (status.getResourceStatus().equalsIgnoreCase("RUNNING")
|| status.getResourceStatus().equalsIgnoreCase("PENDING")) {
status = queryStatus(status.getResourceResultId(), null);
status = queryStatus(UUID.fromString(status.getResourceResultId()), null);
}
log.info(status.toString());

Expand Down
46 changes: 6 additions & 40 deletions war/pom.xml
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Expand Up @@ -20,30 +20,6 @@
<build>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.tomcat.maven</groupId>
<artifactId>tomcat7-maven-plugin</artifactId>
<version>2.0</version>
<executions>
<execution>
<id>default-cli</id>
<goals>
<goal>run</goal>
</goals>
<configuration>
<port>13000</port>
<path>/jaxrs-service</path>
<useSeparateTomcatClassLoader>true</useSeparateTomcatClassLoader>
<jpda>true</jpda>
<systemProperties>
<JAVA_OPTS>-Xms256m -Xmx512m</JAVA_OPTS>
</systemProperties>
</configuration>
</execution>
</executions>
<configuration>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
Expand Down Expand Up @@ -90,22 +66,12 @@
</executions>
</plugin>
<plugin>
<groupId>org.apache.tomcat.maven</groupId>
<artifactId>tomcat7-maven-plugin</artifactId>
<executions>
<execution>
<id>tomcat-run</id>
<goals>
<goal>exec-war-only</goal>
</goals>
<phase>package</phase>
<configuration>
<attachArtifact>true</attachArtifact>
<buildDirectory>../docker/pic-sure-hpds</buildDirectory>
<path>/</path>
</configuration>
</execution>
</executions>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>3.3.1</version>
<configuration>
<outputDirectory>docker/pic-sure-hpds</outputDirectory>
</configuration>
</plugin>
</plugins>
</build>
Expand Down
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