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AvocadoMoonAvocadoMoon
committedJan 23, 2025·
Relocate API Types to Separate Module
·
7.7.0.247.7.0.14
1 parent 48ffe47 commit 4df69f1

40 files changed

+176
-83
lines changed
 

‎pom.xml

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<modules>
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<module>vcell-admin</module>
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<module>vcell-api-types</module>
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<module>vcell-api</module>
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<module>vcell-apiclient</module>
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<module>vcell-client</module>

‎vcell-api-types/pom.xml

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<?xml version="1.0" encoding="UTF-8"?>
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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
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<modelVersion>4.0.0</modelVersion>
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<parent>
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<groupId>org.vcell</groupId>
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<artifactId>vcell-pom</artifactId>
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<version>0.0.1-SNAPSHOT</version>
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</parent>
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<artifactId>vcell-api-types</artifactId>
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<name>vcell-api-types</name>
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<description>Types used for communication.</description>
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<version>1.0.0</version>
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<url>https://maven.apache.org</url>
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<inceptionYear>2025</inceptionYear>
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<organization>
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<name>VCell</name>
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<url>https://vcell.org</url>
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</organization>
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<licenses>
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<license>
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<name>MIT</name>
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<url>https://opensource.org/licenses/MIT</url>
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</license>
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</licenses>
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<developers>
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<developer>
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<id>avocadomoon</id>
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<name>Ezequiel Valencia</name>
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<roles>
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<role>founder</role>
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<role>lead</role>
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<role>developer</role>
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<role>debugger</role>
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<role>reviewer</role>
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<role>support</role>
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<role>maintainer</role>
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</roles>
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</developer>
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</developers>
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<mailingLists>
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<mailingList>
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<name>VCell Open Discussion Forum</name>
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<subscribe>https://groups.google.com/group/vcell-discuss</subscribe>
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<unsubscribe>https://groups.google.com/group/vcell-discuss</unsubscribe>
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<post>vcell-discuss@googlegroups.com</post>
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<archive>https://groups.google.com/group/vcell-discuss</archive>
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</mailingList>
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</mailingLists>
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<scm>
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<connection>scm:git:git://github.com/virtualcell/vcell</connection>
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<developerConnection>scm:git:git@github.com:virtualcell/vcell</developerConnection>
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<tag>HEAD</tag>
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<url>https://github.com/virtualcell/vcell</url>
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</scm>
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<issueManagement>
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<system>Bugzilla</system>
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<url>https://github.com/virtualcell/vcell/issues</url>
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</issueManagement>
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<properties>
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<license.licenseName>MIT</license.licenseName>
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<license.copyrightOwners>UConn Health</license.copyrightOwners>
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</properties>
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<repositories>
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<repository>
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<id>maven-restlet</id>
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<name>Restlet repository</name>
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<url>https://maven.restlet.talend.com</url>
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</repository>
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</repositories>
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<dependencies>
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<dependency>
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<groupId>org.vcell</groupId>
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<artifactId>vcell-core</artifactId>
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<version>0.0.1-SNAPSHOT</version>
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</dependency>
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</dependencies>
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</project>

‎vcell-core/src/main/java/cbit/rmi/event/client/common/AccessTokenRepresentation.java ‎vcell-api-types/src/main/java/org/vcell/api/types/common/AccessTokenRepresentation.java

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package cbit.rmi.event.client.common;
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package org.vcell.api.types.common;
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‎vcell-core/src/main/java/cbit/rmi/event/client/common/ApplicationRepresentation.java ‎vcell-api-types/src/main/java/org/vcell/api/types/common/ApplicationRepresentation.java

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package cbit.rmi.event.client.common;
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package org.vcell.api.types.common;
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public class ApplicationRepresentation {

‎vcell-core/src/main/java/cbit/rmi/event/client/common/BioModelLink.java ‎vcell-api-types/src/main/java/org/vcell/api/types/common/BioModelLink.java

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package cbit.rmi.event.client.common;
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package org.vcell.api.types.common;
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public class BioModelLink {
44
public final static String bmid = "bioModelKey";

‎vcell-core/src/main/java/cbit/rmi/event/client/common/BiomodelRepresentation.java ‎vcell-api-types/src/main/java/org/vcell/api/types/common/BiomodelRepresentation.java

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package cbit.rmi.event.client.common;
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package org.vcell.api.types.common;
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public class BiomodelRepresentation {

‎vcell-core/src/main/java/cbit/rmi/event/client/common/MathModelLink.java ‎vcell-api-types/src/main/java/org/vcell/api/types/common/MathModelLink.java

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package cbit.rmi.event.client.common;
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package org.vcell.api.types.common;
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public class MathModelLink {

‎vcell-core/src/main/java/cbit/rmi/event/client/common/SimDataRepresentation.java ‎vcell-api-types/src/main/java/org/vcell/api/types/common/SimDataRepresentation.java

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package cbit.rmi.event.client.common;
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package org.vcell.api.types.common;
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‎vcell-core/src/main/java/cbit/rmi/event/client/common/SimDataValuesRepresentation.java ‎vcell-api-types/src/main/java/org/vcell/api/types/common/SimDataValuesRepresentation.java

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@@ -1,4 +1,4 @@
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package cbit.rmi.event.client.common;
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package org.vcell.api.types.common;
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‎vcell-core/src/main/java/cbit/rmi/event/client/common/SimDataVariableRepresentation.java ‎vcell-api-types/src/main/java/org/vcell/api/types/common/SimDataVariableRepresentation.java

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package cbit.rmi.event.client.common;
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package org.vcell.api.types.common;
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‎vcell-core/src/main/java/cbit/rmi/event/client/common/SimDataVariableValuesRepresentation.java ‎vcell-api-types/src/main/java/org/vcell/api/types/common/SimDataVariableValuesRepresentation.java

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package cbit.rmi.event.client.common;
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package org.vcell.api.types.common;
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‎vcell-core/src/main/java/cbit/rmi/event/client/common/SimpleJobStatusRepresentation.java ‎vcell-api-types/src/main/java/org/vcell/api/types/common/SimpleJobStatusRepresentation.java

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package cbit.rmi.event.client.common;
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package org.vcell.api.types.common;
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import java.util.Date;
44

‎vcell-core/src/main/java/cbit/rmi/event/client/common/SimulationRepresentation.java ‎vcell-api-types/src/main/java/org/vcell/api/types/common/SimulationRepresentation.java

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package cbit.rmi.event.client.common;
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package org.vcell.api.types.common;
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‎vcell-core/src/main/java/cbit/rmi/event/client/common/SimulationTaskRepresentation.java ‎vcell-api-types/src/main/java/org/vcell/api/types/common/SimulationTaskRepresentation.java

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package cbit.rmi.event.client.common;
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package org.vcell.api.types.common;
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public class SimulationTaskRepresentation {

‎vcell-core/src/main/java/cbit/rmi/event/client/common/UserInfo.java ‎vcell-api-types/src/main/java/org/vcell/api/types/common/UserInfo.java

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* http://www.opensource.org/licenses/mit-license.php
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*/
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package cbit.rmi.event.client.common;
11+
package org.vcell.api.types.common;
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1313
import java.util.Date;
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‎vcell-core/src/main/java/cbit/rmi/event/client/events/BroadcastEventRepresentation.java ‎vcell-api-types/src/main/java/org/vcell/api/types/events/BroadcastEventRepresentation.java

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package cbit.rmi.event.client.events;
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package org.vcell.api.types.events;
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public class BroadcastEventRepresentation {
44

‎vcell-core/src/main/java/cbit/rmi/event/client/events/DataJobEventRepresentation.java ‎vcell-api-types/src/main/java/org/vcell/api/types/events/DataJobEventRepresentation.java

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package cbit.rmi.event.client.events;
1+
package org.vcell.api.types.events;
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public class DataJobEventRepresentation {
44

‎vcell-core/src/main/java/cbit/rmi/event/client/events/EventWrapper.java ‎vcell-api-types/src/main/java/org/vcell/api/types/events/EventWrapper.java

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package cbit.rmi.event.client.events;
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package org.vcell.api.types.events;
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public class EventWrapper {
44

‎vcell-core/src/main/java/cbit/rmi/event/client/events/ExportEventRepresentation.java ‎vcell-api-types/src/main/java/org/vcell/api/types/events/ExportEventRepresentation.java

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package cbit.rmi.event.client.events;
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package org.vcell.api.types.events;
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public class ExportEventRepresentation {
44

‎vcell-core/src/main/java/cbit/rmi/event/client/events/ExportHumanReadableDataSpec.java ‎vcell-api-types/src/main/java/org/vcell/api/types/events/ExportHumanReadableDataSpec.java

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package cbit.rmi.event.client.events;
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package org.vcell.api.types.events;
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import java.util.ArrayList;
44
import java.util.HashMap;

‎vcell-core/src/main/java/cbit/rmi/event/client/events/ExportTimeSpecs.java ‎vcell-api-types/src/main/java/org/vcell/api/types/events/ExportTimeSpecs.java

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package cbit.rmi.event.client.events;
1+
package org.vcell.api.types.events;
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public class ExportTimeSpecs {
44
public final int beginTimeIndex;

‎vcell-core/src/main/java/cbit/rmi/event/client/events/ExportVariableSpecs.java ‎vcell-api-types/src/main/java/org/vcell/api/types/events/ExportVariableSpecs.java

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package cbit.rmi.event.client.events;
1+
package org.vcell.api.types.events;
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public class ExportVariableSpecs {
44
public final String[] variableNames;

‎vcell-core/src/main/java/cbit/rmi/event/client/events/SimulationJobStatusEventRepresentation.java ‎vcell-api-types/src/main/java/org/vcell/api/types/events/SimulationJobStatusEventRepresentation.java

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package cbit.rmi.event.client.events;
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package org.vcell.api.types.events;
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public class SimulationJobStatusEventRepresentation {
44

‎vcell-core/src/main/java/cbit/rmi/event/client/events/SimulationJobStatusRepresentation.java ‎vcell-api-types/src/main/java/org/vcell/api/types/events/SimulationJobStatusRepresentation.java

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package cbit.rmi.event.client.events;
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package org.vcell.api.types.events;
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import java.util.Date;
44

‎vcell-core/src/main/java/cbit/rmi/event/client/DTOOldAPI.java ‎vcell-api-types/src/main/java/org/vcell/api/types/utils/DTOOldAPI.java

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package cbit.rmi.event.client;
1+
package org.vcell.api.types.utils;
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import cbit.rmi.event.DataJobEvent;
44
import cbit.rmi.event.ExportEvent;
55
import cbit.rmi.event.SimulationJobStatusEvent;
6-
import cbit.rmi.event.client.common.SimpleJobStatusRepresentation;
7-
import cbit.rmi.event.client.events.*;
86
import cbit.vcell.export.server.HumanReadableExportData;
97
import cbit.vcell.export.server.TimeSpecs;
108
import cbit.vcell.export.server.VariableSpecs;
@@ -15,6 +13,9 @@
1513
import cbit.vcell.solver.Simulation;
1614
import cbit.vcell.solver.VCSimulationIdentifier;
1715
import cbit.vcell.solver.server.SimulationMessage;
16+
import org.vcell.api.types.common.SimpleJobStatusRepresentation;
17+
import org.vcell.api.types.common.UserInfo;
18+
import org.vcell.api.types.events.*;
1819
import org.vcell.util.document.*;
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2021
import java.io.BufferedInputStream;
@@ -252,17 +253,17 @@ public static SimulationJobStatusEventRepresentation simulationJobStatusEventToJ
252253
return eventRep;
253254
}
254255

255-
public static cbit.rmi.event.client.common.UserInfo getApiUserInfo(UserInfo userInfo){
256-
cbit.rmi.event.client.common.UserInfo apiUserInfo = new cbit.rmi.event.client.common.UserInfo(
256+
public static UserInfo getApiUserInfo(org.vcell.util.document.UserInfo userInfo){
257+
UserInfo apiUserInfo = new UserInfo(
257258
(userInfo.id!=null) ? userInfo.id.toString() : null,
258259
userInfo.userid, userInfo.digestedPassword0.getString(), userInfo.email, userInfo.wholeName,
259260
userInfo.title, userInfo.company, userInfo.country, userInfo.notify, userInfo.insertDate);
260261
return apiUserInfo;
261262
}
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263264

264-
public static UserInfo fromApiUserInfo(cbit.rmi.event.client.common.UserInfo apiUserInfo) {
265-
UserInfo userInfo = new UserInfo();
265+
public static org.vcell.util.document.UserInfo fromApiUserInfo(UserInfo apiUserInfo) {
266+
org.vcell.util.document.UserInfo userInfo = new org.vcell.util.document.UserInfo();
266267
userInfo.id = new KeyValue(apiUserInfo.id);
267268
userInfo.userid = apiUserInfo.userid;
268269
userInfo.digestedPassword0 = UserLoginInfo.DigestedPassword.createAlreadyDigested(apiUserInfo.digestedPassword0);

‎vcell-api/pom.xml

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<artifactId>joda-time</artifactId>
163163
<version>${joda-time.version}</version>
164164
</dependency>
165+
<dependency>
166+
<groupId>org.vcell</groupId>
167+
<artifactId>vcell-api-types</artifactId>
168+
<version>1.0.0</version>
169+
</dependency>
165170
</dependencies>
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</project>

‎vcell-api/src/main/java/org/vcell/rest/VCellApiApplication.java

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118118
public static final String SIMDATA = "simdata";
119119
public static final String SIMDATAID = "simdataid";
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121-
public static final String EVENTS = "events";
121+
public static final String EVENTS = "org/vcell/api/types";
122122
public static final String EVENTS_BEGINTIMESTAMP = "beginTimestamp";
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public static final String N5DATA = "n5data";

‎vcell-api/src/main/java/org/vcell/rest/admin/AdminJobsRestlet.java

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package org.vcell.rest.admin;
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3+
import org.vcell.api.types.common.SimpleJobStatusRepresentation;
34
import org.apache.logging.log4j.LogManager;
45
import org.apache.logging.log4j.Logger;
56
import org.restlet.Context;
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1213
import org.restlet.data.Status;
1314
import org.restlet.engine.adapter.HttpRequest;
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import org.restlet.ext.json.JsonRepresentation;
15-
import cbit.rmi.event.client.common.SimpleJobStatusRepresentation;
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import cbit.rmi.event.client.DTOOldAPI;
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import org.vcell.rest.VCellApiApplication;
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1918
import com.google.gson.Gson;
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import cbit.vcell.server.SimpleJobStatusQuerySpec;
2221
import cbit.vcell.server.SimulationJobStatus;
22+
import org.vcell.api.types.utils.DTOOldAPI;
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2424
public final class AdminJobsRestlet extends Restlet {
2525
private final static Logger lg = LogManager.getLogger(AdminJobsRestlet.class);

‎vcell-api/src/main/java/org/vcell/rest/events/EventsRestlet.java

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package org.vcell.rest.events;
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3+
import org.vcell.api.types.events.EventWrapper;
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import org.apache.logging.log4j.LogManager;
45
import org.apache.logging.log4j.Logger;
56
import org.restlet.Context;
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import org.restlet.data.Status;
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import org.restlet.engine.adapter.HttpRequest;
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import org.restlet.ext.json.JsonRepresentation;
15-
import cbit.rmi.event.client.events.EventWrapper;
1616
import org.vcell.rest.VCellApiApplication;
1717
import org.vcell.rest.VCellApiApplication.AuthenticationPolicy;
1818
import org.vcell.util.document.User;

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