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Remove mongodb conflicts #10782

Merged
merged 6 commits into from
May 7, 2024
Merged

Remove mongodb conflicts #10782

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39da80e
Update web_and_data docker image
haynescd May 6, 2024
3d9d343
Update mvn cmd
haynescd May 6, 2024
01f45dc
Add back mongodb springboot
haynescd May 6, 2024
b2c31ca
Update to use only spring boot mongodb and remove QueryOperator class
haynescd May 7, 2024
ef42727
Revert change to dockerfile
haynescd May 7, 2024
cfefb06
Merge branch 'master' into demo-docker-updates
haynescd May 7, 2024
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2 changes: 1 addition & 1 deletion docker/web-and-data/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -74,4 +74,4 @@ COPY --from=build ${DEPENDENCY}/BOOT-INF/classes $PORTAL_WEB_HOME/
# add entrypoint
COPY --from=build /cbioportal/docker/web-and-data/docker-entrypoint.sh /usr/local/bin/
ENTRYPOINT ["docker-entrypoint.sh"]
CMD ["sh", "-c", "java $(echo $JAVA_OPTS) -cp /cbioportal-webapp:/cbioportal-webapp/lib/* org.cbioportal.PortalApplication $(echo $WEBAPP_OPTS)"]
CMD ["sh", "-c", "java $(echo $JAVA_OPTS) -cp /cbioportal-webapp:/cbioportal-webapp/lib/* org.cbioportal.PortalApplication $(echo $WEBAPP_OPTS)"]
15 changes: 4 additions & 11 deletions pom.xml
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Expand Up @@ -190,11 +190,6 @@
<artifactId>jjwt-jackson</artifactId>
<version>${io-jsonwebtoken.version}</version>
</dependency>
<dependency>
<groupId>org.mongodb</groupId>
<artifactId>bson</artifactId>
<version>${mongodb_bson.version}</version>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
Expand Down Expand Up @@ -229,11 +224,6 @@
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-cache</artifactId>
</dependency>
<dependency>
<groupId>org.mongodb</groupId>
<artifactId>mongo-java-driver</artifactId>
<version>${mongo_java_driver.version}</version>
</dependency>
<dependency>
<groupId>com.datumbox</groupId>
<artifactId>datumbox-framework-lib</artifactId>
Expand Down Expand Up @@ -314,7 +304,10 @@
<artifactId>h2</artifactId>
<scope>test</scope>
</dependency>

<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-data-mongodb</artifactId>
</dependency>
<!-- JitPack Publishing -->
<dependency>
<groupId>com.github.jitpack</groupId>
Expand Down
31 changes: 17 additions & 14 deletions src/main/java/org/cbioportal/web/SessionServiceController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,6 @@
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.collect.ImmutableMap;
import com.mongodb.BasicDBObject;
import com.mongodb.QueryOperators;
import io.swagger.v3.oas.annotations.media.ArraySchema;
import io.swagger.v3.oas.annotations.media.Content;
import io.swagger.v3.oas.annotations.media.Schema;
Expand Down Expand Up @@ -64,7 +63,11 @@
public class SessionServiceController {

private static final Logger LOG = LoggerFactory.getLogger(SessionServiceController.class);


private static final String QUERY_OPERATOR_ALL = "$all";
private static final String QUERY_OPERATOR_SIZE = "$size";
private static final String QUERY_OPERATOR_AND = "$and";

@Autowired
SessionServiceRequestHandler sessionServiceRequestHandler;

Expand Down Expand Up @@ -337,11 +340,11 @@ public ResponseEntity<List<VirtualStudy>> fetchUserGroups(
basicDBObjects
.add(new BasicDBObject("data.users", Pattern.compile(userName(), Pattern.CASE_INSENSITIVE)));
basicDBObjects.add(new BasicDBObject("data.origin",
new BasicDBObject(QueryOperators.ALL, studyIds)));
new BasicDBObject(QUERY_OPERATOR_ALL, studyIds)));
basicDBObjects.add(new BasicDBObject("data.origin",
new BasicDBObject(QueryOperators.SIZE, studyIds.size())));
new BasicDBObject(QUERY_OPERATOR_SIZE, studyIds.size())));

BasicDBObject queryDBObject = new BasicDBObject(QueryOperators.AND, basicDBObjects);
BasicDBObject queryDBObject = new BasicDBObject(QUERY_OPERATOR_AND, basicDBObjects);

RestTemplate restTemplate = new RestTemplate();

Expand Down Expand Up @@ -372,12 +375,12 @@ public void updateUserPageSettings(@RequestBody PageSettingsData settingsData, H
basicDBObjects
.add(new BasicDBObject("data.owner", Pattern.compile(userName(), Pattern.CASE_INSENSITIVE)));
basicDBObjects.add(new BasicDBObject("data.origin",
new BasicDBObject(QueryOperators.ALL, settingsData.getOrigin())));
new BasicDBObject(QUERY_OPERATOR_ALL, settingsData.getOrigin())));
basicDBObjects.add(new BasicDBObject("data.origin",
new BasicDBObject(QueryOperators.SIZE, settingsData.getOrigin().size())));
new BasicDBObject(QUERY_OPERATOR_SIZE, settingsData.getOrigin().size())));
basicDBObjects.add(new BasicDBObject("data.page", settingsData.getPage().name()));

BasicDBObject queryDBObject = new BasicDBObject(QueryOperators.AND, basicDBObjects);
BasicDBObject queryDBObject = new BasicDBObject(QUERY_OPERATOR_AND, basicDBObjects);

PageSettings pageSettings = getRecentlyUpdatePageSettings(queryDBObject.toString());

Expand Down Expand Up @@ -443,12 +446,12 @@ public ResponseEntity<PageSettingsData> getPageSettings(@RequestBody PageSetting
basicDBObjects
.add(new BasicDBObject("data.owner", Pattern.compile(userName(), Pattern.CASE_INSENSITIVE)));
basicDBObjects.add(new BasicDBObject("data.origin",
new BasicDBObject(QueryOperators.ALL, pageSettingsIdentifier.getOrigin())));
new BasicDBObject(QUERY_OPERATOR_ALL, pageSettingsIdentifier.getOrigin())));
basicDBObjects.add(new BasicDBObject("data.origin",
new BasicDBObject(QueryOperators.SIZE, pageSettingsIdentifier.getOrigin().size())));
new BasicDBObject(QUERY_OPERATOR_SIZE, pageSettingsIdentifier.getOrigin().size())));
basicDBObjects.add(new BasicDBObject("data.page", pageSettingsIdentifier.getPage().name()));

BasicDBObject queryDBObject = new BasicDBObject(QueryOperators.AND, basicDBObjects);
BasicDBObject queryDBObject = new BasicDBObject(QUERY_OPERATOR_AND, basicDBObjects);

PageSettings pageSettings = getRecentlyUpdatePageSettings(queryDBObject.toString());

Expand All @@ -471,10 +474,10 @@ public ResponseEntity<List<CustomDataSession>> fetchCustomProperties(

List<BasicDBObject> basicDBObjects = new ArrayList<>();
basicDBObjects.add(new BasicDBObject("data.users", Pattern.compile(userName(), Pattern.CASE_INSENSITIVE)));
basicDBObjects.add(new BasicDBObject("data.origin", new BasicDBObject(QueryOperators.ALL, studyIds)));
basicDBObjects.add(new BasicDBObject("data.origin", new BasicDBObject(QueryOperators.SIZE, studyIds.size())));
basicDBObjects.add(new BasicDBObject("data.origin", new BasicDBObject(QUERY_OPERATOR_ALL, studyIds)));
basicDBObjects.add(new BasicDBObject("data.origin", new BasicDBObject(QUERY_OPERATOR_SIZE, studyIds.size())));

BasicDBObject queryDBObject = new BasicDBObject(QueryOperators.AND, basicDBObjects);
BasicDBObject queryDBObject = new BasicDBObject(QUERY_OPERATOR_AND, basicDBObjects);

RestTemplate restTemplate = new RestTemplate();

Expand Down
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