Merge pull request #1322 from virtualcell/health-sim-status

sim health is now OK:UP, Warning:UP, Critical:DOWN, Uknown:DOWN
virtualcell · Jul 18, 2024 · 762a998 · 762a998
2 parents adc6511 + 081e199
commit 762a998
Show file tree

Hide file tree

Showing 19 changed files with 121 additions and 3,648 deletions.
diff --git a/docker/build/installers/VCell.install4j b/docker/build/installers/VCell.install4j
@@ -109,7 +109,7 @@
     <launcher name="VCell-${compiler:Site}-MacOSX" id="102" icnsFile="${compiler:vcellIcnsFile}">
       <executable name="VCell-${compiler:Site}" iconSet="true" failOnStderrOutput="false" executableMode="gui" checkConsoleParameter="true" dpiAware="false" />
       <splashScreen show="true" bitmapFile="${compiler:vcell5SplashScreenPngFilePath}" textOverlay="true" />
-      <java mainClass="cbit.vcell.client.VCellClientMain" vmParameters="&quot;--add-exports java.desktop/sun.awt.image=ALL-UNNAMED -Dvcell.installDir=${launcher:sys.launcherDirectory}&quot;">
+      <java mainClass="cbit.vcell.client.VCellClientMain" vmParameters="&quot;-Dvcell.installDir=${launcher:sys.launcherDirectory}&quot;">
         <classPath>
           <variable name="vcellClasspathColonSep" separator=":" useRelativePrefix="true" relativePrefix="lib" />
         </classPath>
@@ -118,7 +118,8 @@
         </nativeLibraryDirectories>
       </java>
       <vmOptionsFile mode="content" overwriteMode="1">
-        <content>-Dvcell.autoflushlog=true
+        <content>--add-exports java.desktop/sun.awt.image=ALL-UNNAMED
+-Dvcell.autoflushlog=true
 -Dvcell.thirdPartyLicense=thirdpartylicenses.txt
 -Dvcell.softwareVersion=${compiler:SoftwareVersionString}
 -Dvcell.serverHost=${compiler:rmiHosts}
@@ -147,7 +148,7 @@
     <launcher name="VCell-${compiler:Site}-Windows64" id="345" icnsFile="${compiler:vcellIcnsFile}">
       <executable name="VCell-${compiler:Site}" iconSet="true" failOnStderrOutput="false" executableMode="gui" checkConsoleParameter="true" dpiAware="false" />
       <splashScreen show="true" bitmapFile="${compiler:vcell5SplashScreenPngFilePath}" textOverlay="true" />
-      <java mainClass="cbit.vcell.client.VCellClientMain" vmParameters="&quot;--add-exports java.desktop/sun.awt.image=ALL-UNNAMED -Dvcell.installDir=${launcher:sys.launcherDirectory}&quot;">
+      <java mainClass="cbit.vcell.client.VCellClientMain" vmParameters="&quot;-Dvcell.installDir=${launcher:sys.launcherDirectory}&quot;">
         <classPath>
           <variable name="vcellClasspathColonSep" separator=":" useRelativePrefix="true" relativePrefix="lib" />
         </classPath>
@@ -156,7 +157,8 @@
         </nativeLibraryDirectories>
       </java>
       <vmOptionsFile mode="content" overwriteMode="1">
-        <content>-Dvcell.autoflushlog=true
+        <content>--add-exports java.desktop/sun.awt.image=ALL-UNNAMED
+-Dvcell.autoflushlog=true
 -Dvcell.thirdPartyLicense=thirdpartylicenses.txt
 -Dvcell.softwareVersion=${compiler:SoftwareVersionString}
 -Dvcell.serverHost=${compiler:rmiHosts}
@@ -179,7 +181,7 @@
     <launcher name="VCell-${compiler:Site}-Windows32" id="447" icnsFile="${compiler:vcellIcnsFile}">
       <executable name="VCell-${compiler:Site}" iconSet="true" failOnStderrOutput="false" executableMode="gui" checkConsoleParameter="true" dpiAware="false" />
       <splashScreen show="true" bitmapFile="${compiler:vcell5SplashScreenPngFilePath}" textOverlay="true" />
-      <java mainClass="cbit.vcell.client.VCellClientMain" vmParameters="&quot;--add-exports java.desktop/sun.awt.image=ALL-UNNAMED -Dvcell.installDir=${launcher:sys.launcherDirectory}&quot;">
+      <java mainClass="cbit.vcell.client.VCellClientMain" vmParameters="&quot;-Dvcell.installDir=${launcher:sys.launcherDirectory}&quot;">
         <classPath>
           <variable name="vcellClasspathColonSep" separator=":" useRelativePrefix="true" relativePrefix="lib" />
         </classPath>
@@ -188,7 +190,8 @@
         </nativeLibraryDirectories>
       </java>
       <vmOptionsFile mode="content" overwriteMode="1">
-        <content>-Dvcell.autoflushlog=true
+        <content>--add-exports java.desktop/sun.awt.image=ALL-UNNAMED
+-Dvcell.autoflushlog=true
 -Dvcell.thirdPartyLicense=thirdpartylicenses.txt
 -Dvcell.softwareVersion=${compiler:SoftwareVersionString}
 -Dvcell.serverHost=${compiler:rmiHosts}
@@ -212,7 +215,7 @@
     <launcher name="VCell-${compiler:Site}-Linux32" id="534" icnsFile="${compiler:vcellIcnsFile}">
       <executable name="VCell-${compiler:Site}" failOnStderrOutput="false" executableMode="gui" checkConsoleParameter="true" dpiAware="false" />
       <splashScreen bitmapFile="${compiler:vcell5SplashScreenPngFilePath}" />
-      <java mainClass="cbit.vcell.client.VCellClientMain" vmParameters="&quot;--add-exports java.desktop/sun.awt.image=ALL-UNNAMED -Dvcell.installDir=${launcher:sys.launcherDirectory}&quot;">
+      <java mainClass="cbit.vcell.client.VCellClientMain" vmParameters="&quot;-Dvcell.installDir=${launcher:sys.launcherDirectory}&quot;">
         <classPath>
           <variable name="vcellClasspathColonSep" separator=":" useRelativePrefix="true" relativePrefix="lib" />
         </classPath>
@@ -221,7 +224,8 @@
         </nativeLibraryDirectories>
       </java>
       <vmOptionsFile mode="content" overwriteMode="1">
-        <content>-Dvcell.autoflushlog=true
+        <content>--add-exports java.desktop/sun.awt.image=ALL-UNNAMED
+-Dvcell.autoflushlog=true
 -Dvcell.thirdPartyLicense=thirdpartylicenses.txt
 -Dvcell.softwareVersion=${compiler:SoftwareVersionString}
 -Dvcell.serverHost=${compiler:rmiHosts}
@@ -241,7 +245,7 @@
     <launcher name="VCell-${compiler:Site}-Linux64" id="627" icnsFile="${compiler:vcellIcnsFile}">
       <executable name="VCell-${compiler:Site}" failOnStderrOutput="false" executableMode="gui" checkConsoleParameter="true" dpiAware="false" />
       <splashScreen bitmapFile="${compiler:vcell5SplashScreenPngFilePath}" />
-      <java mainClass="cbit.vcell.client.VCellClientMain" vmParameters="&quot;--add-exports java.desktop/sun.awt.image=ALL-UNNAMED -Dvcell.installDir=${launcher:sys.launcherDirectory}&quot;">
+      <java mainClass="cbit.vcell.client.VCellClientMain" vmParameters="&quot;-Dvcell.installDir=${launcher:sys.launcherDirectory}&quot;">
         <classPath>
           <variable name="vcellClasspathColonSep" separator=":" useRelativePrefix="true" relativePrefix="lib" />
         </classPath>
@@ -250,7 +254,8 @@
         </nativeLibraryDirectories>
       </java>
       <vmOptionsFile mode="content" overwriteMode="1">
-        <content>-Dvcell.autoflushlog=true
+        <content>--add-exports java.desktop/sun.awt.image=ALL-UNNAMED
+-Dvcell.autoflushlog=true
 -Dvcell.thirdPartyLicense=thirdpartylicenses.txt
 -Dvcell.serverHost=${compiler:rmiHosts}
 -Dvcell.serverPrefix.v0=${compiler:serverPrefixV0}
@@ -270,7 +275,7 @@
     <launcher name="VCell-${compiler:Site}-Linux64-sbmltovcml" id="1880" excludeFromMenu="true">
       <executable name="VCell-${compiler:Site}-sbmltovcml" iconSet="true" redirectStderr="false" failOnStderrOutput="false" executableMode="console" checkConsoleParameter="true" dpiAware="false" />
       <splashScreen bitmapFile="${compiler:vcell5SplashScreenPngFilePath}" />
-      <java mainClass="org.vcell.sbml.SbmlVcmlConverter" vmParameters="&quot;--add-exports java.desktop/sun.awt.image=ALL-UNNAMED -Dvcell.installDir=${launcher:sys.launcherDirectory}&quot;">
+      <java mainClass="org.vcell.sbml.SbmlVcmlConverter" vmParameters="&quot;-Dvcell.installDir=${launcher:sys.launcherDirectory}&quot;">
         <classPath>
           <variable name="vcellClasspathColonSep" separator=":" useRelativePrefix="true" relativePrefix="lib" />
         </classPath>
@@ -279,7 +284,8 @@
         </nativeLibraryDirectories>
       </java>
       <vmOptionsFile mode="content" overwriteMode="1">
-        <content>-Dvcell.autoflushlog=true
+        <content>--add-exports java.desktop/sun.awt.image=ALL-UNNAMED
+-Dvcell.autoflushlog=true
 -Dvcell.thirdPartyLicense=thirdpartylicenses.txt
 -Dvcell.serverHost=${compiler:rmiHosts}
 -Dvcell.serverPrefix.v0=${compiler:serverPrefixV0}

diff --git a/pom.xml b/pom.xml
@@ -96,12 +96,8 @@
 		<activemq-broker.version>5.18.3</activemq-broker.version>
 		<activemq-client.version>5.18.3</activemq-client.version>
 		<axis.version>1.4</axis.version>
-		<axis-wsdl4j.version>1.2</axis-wsdl4j.version>
-		<bcprov-jdk15on.version>1.70</bcprov-jdk15on.version>
-		<bcpkix-jdk15on.version>1.70</bcpkix-jdk15on.version>
 		<bio-formats.version>6.1.1</bio-formats.version>
 		<biojava.version>6.0.4</biojava.version>
-		<biomodels-wslib.version>1.21</biomodels-wslib.version>
 		<colt.version>1.2.0</colt.version>
 		<combine-archive.version>1.4.1</combine-archive.version>
 		<commons-beanutils.version>1.9.4</commons-beanutils.version>
@@ -121,8 +117,6 @@
 		<guice.version>7.0.0</guice.version>
 		<httpclient.version>4.5.11</httpclient.version>
 		<httpcore.version>4.4.13</httpcore.version>
-		<imagej2.version>2.3.0</imagej2.version>
-		<imagej.version>${imagej2.version}</imagej.version>
 		<itext.version>2.1.7</itext.version>
 		<quarkus-itext.version>3.0.5</quarkus-itext.version>
 		<quarkus-logging-json.version>3.1.0</quarkus-logging-json.version>
@@ -162,7 +156,6 @@
 		<mongodb-driver-sync.version>5.0.0</mongodb-driver-sync.version>
 		<n5.version>3.0.0</n5.version>
 		<netcdf.version>4.3.22</netcdf.version>
-		<netty.version>3.2.10.Final</netty.version>
 		<nitrite.version>2.1.1</nitrite.version>
 		<ojdbc-bom.version>23.3.0.23.09</ojdbc-bom.version>
 		<opencsv.version>5.7.1</opencsv.version>

diff --git a/vcell-api/pom.xml b/vcell-api/pom.xml
@@ -157,10 +157,10 @@
 				</exclusion>
 			</exclusions>
 		</dependency>
-<!--		<dependency>-->
-<!--			<groupId>joda-time</groupId>-->
-<!--			<artifactId>joda-time</artifactId>-->
-<!--			<version>${joda-time.version}</version>-->
-<!--		</dependency>-->
+		<dependency>
+			<groupId>joda-time</groupId>
+			<artifactId>joda-time</artifactId>
+			<version>${joda-time.version}</version>
+		</dependency>
 	</dependencies>
 </project>
diff --git a/vcell-api/src/main/java/org/vcell/rest/health/HealthService.java b/vcell-api/src/main/java/org/vcell/rest/health/HealthService.java
@@ -70,26 +70,28 @@ public static class NagiosStatus {
 		int nagiosStatusCode;
 		String message;
 		Long elapsedTime_MS;
+		String tags;
 
 		// exit with parsed nagios code (0-OK,1-Warning,2-Critical,3-Unknown)
-		NagiosStatus(String nagiosStatusName, int nagiosStatusCode, String message, Long elapsedTime_MS){
+		NagiosStatus(String nagiosStatusName, int nagiosStatusCode, String message, Long elapsedTime_MS, String tags){
 			this.nagiosStatusName = nagiosStatusName;
 			this.nagiosStatusCode = nagiosStatusCode;
 			this.message = message;
 			this.elapsedTime_MS = elapsedTime_MS;
+			this.tags = tags;
 		}
 
 		static NagiosStatus OK(Long elapsedTime_MS) {
-			return new NagiosStatus("OK",0,null,elapsedTime_MS);
+			return new NagiosStatus("OK",0,null,elapsedTime_MS, "UP");
 		}
 		static NagiosStatus Warning(Long elapsedTime_MS) {
-			return new NagiosStatus("Warning",1,null,elapsedTime_MS);
+			return new NagiosStatus("Warning",1,null,elapsedTime_MS, "UP WARNING");
 		}
 		static NagiosStatus Critical(Long elapsedTime_MS, String message) {
-			return new NagiosStatus("Critical",2,message,elapsedTime_MS);
+			return new NagiosStatus("Critical",2,message,elapsedTime_MS, "DOWN");
 		}
 		static NagiosStatus Unknown() {
-			return new NagiosStatus("Unknown",3,null,null);
+			return new NagiosStatus("Unknown",3,null,null, "WARNING");
 		}
 	}
 

diff --git a/vcell-apiclient/pom.xml b/vcell-apiclient/pom.xml
@@ -109,32 +109,6 @@
 			<artifactId>log4j-1.2-api</artifactId>
 			<version>${log4j-1.2-api.version}</version>
 		</dependency>
-		<dependency>
-			<groupId>org.bitbucket.b_c</groupId>
-			<artifactId>jose4j</artifactId>
-			<version>0.9.3</version>
-			<exclusions>
-				<exclusion>
-					<groupId>org.slf4j</groupId>
-					<artifactId>slf4j-api</artifactId>
-				</exclusion>
-			</exclusions>
-		</dependency>
-<dependency>
-  <groupId>javax.xml.bind</groupId>
-  <artifactId>jaxb-api</artifactId>
-  <version>2.3.0</version>
-</dependency>
-<dependency>
-  <groupId>com.sun.xml.bind</groupId>
-  <artifactId>jaxb-core</artifactId>
-  <version>2.3.0</version>
-</dependency>
-<dependency>
-  <groupId>com.sun.xml.bind</groupId>
-  <artifactId>jaxb-impl</artifactId>
-  <version>2.3.0</version>
-</dependency>
 		<dependency>
 			<groupId>org.vcell</groupId>
 			<artifactId>vcell-restclient</artifactId>

diff --git a/vcell-apiclient/src/main/java/org/vcell/api/client/VCellApiClient.java b/vcell-apiclient/src/main/java/org/vcell/api/client/VCellApiClient.java
@@ -3,9 +3,6 @@
 import com.google.gson.Gson;
 import com.nimbusds.oauth2.sdk.ParseException;
 import org.apache.http.*;
-import org.apache.http.auth.AuthScope;
-import org.apache.http.auth.UsernamePasswordCredentials;
-import org.apache.http.client.AuthCache;
 import org.apache.http.client.ClientProtocolException;
 import org.apache.http.client.HttpResponseException;
 import org.apache.http.client.ResponseHandler;
@@ -18,15 +15,20 @@
 import org.apache.http.entity.ByteArrayEntity;
 import org.apache.http.entity.ContentType;
 import org.apache.http.entity.StringEntity;
-import org.apache.http.impl.auth.BasicScheme;
-import org.apache.http.impl.client.*;
+import org.apache.http.impl.client.CloseableHttpClient;
+import org.apache.http.impl.client.DefaultRedirectStrategy;
+import org.apache.http.impl.client.HttpClientBuilder;
+import org.apache.http.impl.client.HttpClients;
 import org.apache.http.util.EntityUtils;
 import org.apache.http.util.TextUtils;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.vcell.api.client.query.BioModelsQuerySpec;
 import org.vcell.api.client.query.SimTasksQuerySpec;
-import org.vcell.api.common.*;
+import org.vcell.api.common.BiomodelRepresentation;
+import org.vcell.api.common.SimulationRepresentation;
+import org.vcell.api.common.SimulationTaskRepresentation;
+import org.vcell.api.common.UserInfo;
 import org.vcell.api.common.events.EventWrapper;
 import org.vcell.restclient.ApiClient;
 import org.vcell.restclient.ApiException;

diff --git a/vcell-client/pom.xml b/vcell-client/pom.xml
@@ -150,24 +150,6 @@
 			<artifactId>picocli</artifactId>
 			<version>${picocli.version}</version>
 		</dependency>
-
-		<dependency>
-			<groupId>xalan</groupId>
-			<artifactId>xalan</artifactId>
-			<version>${xalan.version}</version>
-		</dependency>
-
-    <dependency>
-      <groupId>org.eclipse.jetty</groupId>
-      <artifactId>jetty-server</artifactId>
-		<version>${jetty.version}</version>
-    </dependency>
-		<dependency>
-			<groupId>org.json</groupId>
-			<artifactId>json</artifactId>
-			<version>20220924</version>
-		</dependency>
-
 	</dependencies>
 	<profiles>
 		<profile>

diff --git a/vcell-client/src/main/java/cbit/vcell/client/desktop/biomodel/annotations/UniProtSearch.java b/vcell-client/src/main/java/cbit/vcell/client/desktop/biomodel/annotations/UniProtSearch.java
@@ -1,5 +1,10 @@
 package cbit.vcell.client.desktop.biomodel.annotations;
 
+import com.google.gson.JsonArray;
+import com.google.gson.JsonElement;
+import com.google.gson.JsonObject;
+import com.google.gson.JsonParser;
+
 import java.io.BufferedReader;
 import java.io.IOException;
 import java.io.InputStreamReader;
@@ -8,7 +13,6 @@
 import java.util.ArrayList;
 import java.util.List;
 
-import org.json.*;
 
 public class UniProtSearch {
 
@@ -44,42 +48,50 @@ public List<SearchElement> search(String searchTerm, int searchSize, String orga
 
         System.out.println(response);
         System.out.println("Parsing JSON\n");
-        JSONObject obj = new JSONObject(response);
-//        String accession = obj.getJSONObject("pageInfo").getString("pageName");
-        JSONArray results = obj.getJSONArray("results"); // notice that `"posts": [...]`
-        for (int i = 0; i < results.length(); i++) {
-            JSONObject result = results.getJSONObject(i);
-            String accession = result.getString("primaryAccession");
+        searchElements.addAll(parseResponse(response));
+
+//        System.out.println("\nSearch Elements:");
+//        for (SearchElement element: searchElements) {
+//            System.out.println(element.toString()+"\n");
+//        }
+
+        //        System.out.println("Status Code: " + response.statusCode());
+//        System.out.println("Response Body:\n" + response.body());
+        return searchElements;
+    }
+
+
+    private static List<SearchElement> parseResponse(String response) {
+        List<SearchElement> searchElements = new ArrayList<>();
+        JsonElement jelement = JsonParser.parseString(response);
+        JsonObject jobject = jelement.getAsJsonObject();
+        JsonArray results = jobject.getAsJsonArray("results");
+
+        for (JsonElement resultElement : results) {
+            JsonObject result = resultElement.getAsJsonObject();
+            String accession = result.get("primaryAccession").getAsString();
 
             System.out.println("Accession: " + accession);
             String name;
             if (result.toString().contains("submissionNames")) {
                 name = result
-                        .getJSONObject("proteinDescription")
-                        .getJSONArray("submissionNames")
-                        .getJSONObject(0)
-                        .getJSONObject("fullName")
-                        .getString("value");
+                        .getAsJsonObject("proteinDescription")
+                        .getAsJsonArray("submissionNames")
+                        .get(0).getAsJsonObject()
+                        .getAsJsonObject("fullName")
+                        .get("value").getAsString();
             } else {
-                name = results.getJSONObject(i)
-                        .getJSONObject("proteinDescription")
-                        .getJSONObject("recommendedName")
-                        .getJSONObject("fullName")
-                        .getString("value");
+                name = result
+                        .getAsJsonObject("proteinDescription")
+                        .getAsJsonObject("recommendedName")
+                        .getAsJsonObject("fullName")
+                        .get("value").getAsString();
             }
-            System.out.println("Name: " + name+"\n");
+            System.out.println("Name: " + name + "\n");
 
-            //Add searchElements to list
+            // Add searchElements to list
             searchElements.add(new SearchElement(name, accession));
         }
-
-//        System.out.println("\nSearch Elements:");
-//        for (SearchElement element: searchElements) {
-//            System.out.println(element.toString()+"\n");
-//        }
-
-        //        System.out.println("Status Code: " + response.statusCode());
-//        System.out.println("Response Body:\n" + response.body());
         return searchElements;
     }