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Online Annotations Search Window #752

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Online Annotations Search Window #752

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7664de9
New window to add annotations
abdulmoiz-m Aug 19, 2022
76d4a2f
Merge branch 'virtualcell:master' into annotations
abdulmoiz-m Aug 31, 2022
b9935b9
Updated ontology nicknames and commented out ontologies not supported…
abdulmoiz-m Sep 9, 2022
d3df859
Merge branch 'virtualcell:master' into annotations
abdulmoiz-m Dec 14, 2022
5348e55
Online Search Links working
abdulmoiz-m Jan 10, 2023
88fcdd3
Online Search Links working
abdulmoiz-m Jan 10, 2023
6a38f1d
Merge branch 'master' into annotations
abdulmoiz-m Jan 10, 2023
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16 changes: 14 additions & 2 deletions vcell-client/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,8 +2,20 @@
<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">
<modelVersion>4.0.0</modelVersion>

<parent>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<source>11</source>
<target>11</target>
</configuration>
</plugin>
</plugins>
</build>

<parent>
<groupId>org.vcell</groupId>
<artifactId>vcell-pom</artifactId>
<version>0.0.1-SNAPSHOT</version>
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258 changes: 129 additions & 129 deletions ...ll/server/manage/ServerConfiguration.java → ...image/gui/manage/ServerConfiguration.java
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Original file line number Diff line number Diff line change
@@ -1,129 +1,129 @@
/*
* Copyright (C) 1999-2011 University of Connecticut Health Center
*
* Licensed under the MIT License (the "License").
* You may not use this file except in compliance with the License.
* You may obtain a copy of the License at:
*
* http://www.opensource.org/licenses/mit-license.php
*/
package cbit.vcell.server.manage;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.io.LineNumberReader;
import java.util.Vector;/**
* Insert the type's description here.
* Creation date: (10/24/2001 2:25:13 PM)
* @author: Ion Moraru
*/
public class ServerConfiguration {
private VCellHost[] allHosts = new VCellHost[0];
/**
* Insert the method's description here.
* Creation date: (10/24/2001 3:29:24 PM)
* @param configurationFile java.io.File
* @exception java.io.IOException The exception description.
* @exception java.io.FileNotFoundException The exception description.
*/
public ServerConfiguration(File configurationFile) throws IOException, FileNotFoundException {
LineNumberReader reader = new LineNumberReader(new FileReader(configurationFile));
Vector hosts = new Vector();
VCellHost host = null;
String line = reader.readLine();
while (line != null) {
if (!line.startsWith("#")) {
if(line.startsWith("hosttype=")) {
if (host != null) hosts.add(host);
String type = line.substring(line.indexOf("=") + 1);
if (type.equals("vcell")) {
host = new VCellHost(VCellHost.VCELL_SERVER);
} else if (type.equals("data")) {
host = new VCellHost(VCellHost.DATA_SERVER);
} else if (type.equals("database")) {
host = new VCellHost(VCellHost.DATABASE_SERVER);
} else if (type.equals("compute")) {
host = new VCellHost(VCellHost.COMPUTE_SERVER);
} else {
host = null;
}
} else if (line.startsWith("name=")) {
if (host != null) host.setName(line.substring(line.indexOf("=") + 1));
} else if (line.startsWith("port=")) {
if (host != null) host.setPort(Integer.parseInt(line.substring(line.indexOf("=") + 1)));
} else if (line.startsWith("startcmd=")) {
if (host != null) host.setStartCommand(line.substring(line.indexOf("=") + 1));
} else if (line.startsWith("stopcmd=")) {
if (host != null) host.setStopCommand(line.substring(line.indexOf("=") + 1));
} else if (line.startsWith("logfile=")) {
if (host != null) host.setLogFile(new File(line.substring(line.indexOf("=") + 1)));
} else if (line.startsWith("restart=")) {
if (host != null) host.setRestartIfDead(Boolean.valueOf(line.substring(line.indexOf("=") + 1)).booleanValue());
}
}
line = reader.readLine();
}
if (host != null) hosts.add(host);
allHosts = ((VCellHost[])org.vcell.util.BeanUtils.getArray(hosts, VCellHost.class));
}
/**
* Insert the method's description here.
* Creation date: (10/24/2001 7:04:58 PM)
* @return cbit.vcell.server.manage.VCellHost[]
*/
public VCellHost[] getComputeServerHosts() {
return getHosts(VCellHost.COMPUTE_SERVER);
}
/**
* Insert the method's description here.
* Creation date: (10/24/2001 7:04:58 PM)
* @return cbit.vcell.server.manage.VCellHost[]
*/
public VCellHost[] getDatabaseServerHosts() {
return getHosts(VCellHost.DATABASE_SERVER);
}
/**
* Insert the method's description here.
* Creation date: (10/24/2001 7:04:58 PM)
* @return cbit.vcell.server.manage.VCellHost[]
*/
public VCellHost[] getDataServerHosts() {
return getHosts(VCellHost.DATA_SERVER);
}
/**
* Insert the method's description here.
* Creation date: (10/24/2001 7:13:10 PM)
* @return cbit.vcell.server.manage.VCellHost[]
* @param hostType int
*/
public VCellHost[] getHosts(int hostType) {
synchronized (allHosts) {
int n = 0;
for (int i=0;i<allHosts.length;i++) {
if (allHosts[i].getType() == hostType) {
n++;
}
}
VCellHost[] hosts = new VCellHost[n];
n = 0;
for (int i=0;i<allHosts.length;i++) {
if (allHosts[i].getType() == hostType) {
hosts[n] = allHosts[i];
n++;
}
}
return hosts;
}
}
/**
* Insert the method's description here.
* Creation date: (10/24/2001 7:04:58 PM)
* @return cbit.vcell.server.manage.VCellHost[]
*/
public VCellHost[] getVCellServerHosts() {
return getHosts(VCellHost.VCELL_SERVER);
}
}
/*
* Copyright (C) 1999-2011 University of Connecticut Health Center
*
* Licensed under the MIT License (the "License").
* You may not use this file except in compliance with the License.
* You may obtain a copy of the License at:
*
* http://www.opensource.org/licenses/mit-license.php
*/

package cbit.image.gui.manage;

import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.io.LineNumberReader;
import java.util.Vector;/**
* Insert the type's description here.
* Creation date: (10/24/2001 2:25:13 PM)
* @author: Ion Moraru
*/
public class ServerConfiguration {
private VCellHost[] allHosts = new VCellHost[0];
/**
* Insert the method's description here.
* Creation date: (10/24/2001 3:29:24 PM)
* @param configurationFile java.io.File
* @exception java.io.IOException The exception description.
* @exception java.io.FileNotFoundException The exception description.
*/
public ServerConfiguration(File configurationFile) throws IOException, FileNotFoundException {
LineNumberReader reader = new LineNumberReader(new FileReader(configurationFile));
Vector hosts = new Vector();
VCellHost host = null;
String line = reader.readLine();
while (line != null) {
if (!line.startsWith("#")) {
if(line.startsWith("hosttype=")) {
if (host != null) hosts.add(host);
String type = line.substring(line.indexOf("=") + 1);
if (type.equals("vcell")) {
host = new VCellHost(VCellHost.VCELL_SERVER);
} else if (type.equals("data")) {
host = new VCellHost(VCellHost.DATA_SERVER);
} else if (type.equals("database")) {
host = new VCellHost(VCellHost.DATABASE_SERVER);
} else if (type.equals("compute")) {
host = new VCellHost(VCellHost.COMPUTE_SERVER);
} else {
host = null;
}
} else if (line.startsWith("name=")) {
if (host != null) host.setName(line.substring(line.indexOf("=") + 1));
} else if (line.startsWith("port=")) {
if (host != null) host.setPort(Integer.parseInt(line.substring(line.indexOf("=") + 1)));
} else if (line.startsWith("startcmd=")) {
if (host != null) host.setStartCommand(line.substring(line.indexOf("=") + 1));
} else if (line.startsWith("stopcmd=")) {
if (host != null) host.setStopCommand(line.substring(line.indexOf("=") + 1));
} else if (line.startsWith("logfile=")) {
if (host != null) host.setLogFile(new File(line.substring(line.indexOf("=") + 1)));
} else if (line.startsWith("restart=")) {
if (host != null) host.setRestartIfDead(Boolean.valueOf(line.substring(line.indexOf("=") + 1)).booleanValue());
}
}
line = reader.readLine();
}
if (host != null) hosts.add(host);
allHosts = ((VCellHost[])org.vcell.util.BeanUtils.getArray(hosts, VCellHost.class));
}
/**
* Insert the method's description here.
* Creation date: (10/24/2001 7:04:58 PM)
* @return cbit.vcell.server.manage.VCellHost[]
*/
public VCellHost[] getComputeServerHosts() {
return getHosts(VCellHost.COMPUTE_SERVER);
}
/**
* Insert the method's description here.
* Creation date: (10/24/2001 7:04:58 PM)
* @return cbit.vcell.server.manage.VCellHost[]
*/
public VCellHost[] getDatabaseServerHosts() {
return getHosts(VCellHost.DATABASE_SERVER);
}
/**
* Insert the method's description here.
* Creation date: (10/24/2001 7:04:58 PM)
* @return cbit.vcell.server.manage.VCellHost[]
*/
public VCellHost[] getDataServerHosts() {
return getHosts(VCellHost.DATA_SERVER);
}
/**
* Insert the method's description here.
* Creation date: (10/24/2001 7:13:10 PM)
* @return cbit.vcell.server.manage.VCellHost[]
* @param hostType int
*/
public VCellHost[] getHosts(int hostType) {
synchronized (allHosts) {
int n = 0;
for (int i=0;i<allHosts.length;i++) {
if (allHosts[i].getType() == hostType) {
n++;
}
}
VCellHost[] hosts = new VCellHost[n];
n = 0;
for (int i=0;i<allHosts.length;i++) {
if (allHosts[i].getType() == hostType) {
hosts[n] = allHosts[i];
n++;
}
}
return hosts;
}
}
/**
* Insert the method's description here.
* Creation date: (10/24/2001 7:04:58 PM)
* @return cbit.vcell.server.manage.VCellHost[]
*/
public VCellHost[] getVCellServerHosts() {
return getHosts(VCellHost.VCELL_SERVER);
}
}
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