Sentinel 4.0.7 java11 032819

MetadataCleanup/.settings/org.eclipse.jdt.core.prefs

@@ -1,11 +1,12 @@
 eclipse.preferences.version=1
 org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
-org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
+org.eclipse.jdt.core.compiler.codegen.methodParameters=do not generate
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
 org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
-org.eclipse.jdt.core.compiler.compliance=1.6
+org.eclipse.jdt.core.compiler.compliance=1.8
 org.eclipse.jdt.core.compiler.debug.lineNumber=generate
 org.eclipse.jdt.core.compiler.debug.localVariable=generate
 org.eclipse.jdt.core.compiler.debug.sourceFile=generate
 org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
 org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
-org.eclipse.jdt.core.compiler.source=1.6
+org.eclipse.jdt.core.compiler.source=1.8

MetadataCleanup/dev.properties

@@ -12,7 +12,7 @@
 ## also need to provide tiername=dev in the PTE form in order for this file to be invoked
 
 
-appl.release=4.0.3
+appl.release=4.0.4
 JDEBUG=on
 TEST=false
 

MetadataCleanup/lib/cadsrsentinel.xml

@@ -15,9 +15,9 @@ L-->
 
         <!-- Specify the caDSR database being used by the Sentinel Tool.
         -->
-        <entry key="DSurl">ncidb-dsr-d.nci.nih.gov:1551:dsrdev.NCI.NIH.GOV</entry>
-        <entry key="DSusername">sentinel</entry>
-        <entry key="DSpassword">sentinel0412</entry>
+        <entry key="DSurl">@@-dburl-@@</entry>
+        <entry key="DSusername">@@-credentials-@@</entry>
+        <entry key="DSpassword">@@-credentials-@@</entry>
 
         <entry key="audit.0.title">Table Row Counts</entry>
         <entry key="audit.0.class">gov.nih.nci.cadsr.sentinel.audits.AuditSummary</entry>

MetadataCleanup/metadata.properties

@@ -9,4 +9,4 @@
 
 TOOL.METADATA.MAXMSG=0
 Appl.version=1.0.1
-OUTPUT.DIR=C:/priv-file-repo/lexevsdb/bin/SentinelToolTestScript/Reports
+OUTPUT.DIR=/local/content/cadsrsentinel/Reports

MetadataCleanup/project.properties

@@ -6,7 +6,7 @@
 #L
 
 ### Project specific properties that normally don't need to be updated within a release
-appl.release=4.0.3
+appl.release=4.0.4
 
 help.url=https://wiki.nci.nih.gov/x/z4AFBw
 

MetadataCleanup/src/java/gov/nih/nci/cadsr/sentinel/database/CaDsrUserCredentials.java

@@ -107,7 +107,7 @@ public class CaDsrUserCredentials
 
     private Logger _logger = Logger.getLogger(CaDsrUserCredentials.class);
 
-    private static String _jndiName = "java:/jdbc/caDSR";
+    private static String _jndiName = "java:jboss/datasources/caDSRDS";
 
     private static final String CHECKOPTIONS = "select COUNT(*) from sbrext.tool_options_view_ext "
         + "where tool_name = 'caDSR' and property in ('LOCKOUT.TIMER', 'LOCKOUT.THRESHOLD')";

MetadataCleanup/src/java/gov/nih/nci/cadsr/sentinel/database/DBAlertOracle.java

@@ -5190,7 +5190,7 @@ public AlertRec[] selectAlerts(Timestamp target_)
      *        The vector.
      * @return The string array.
      */
-    private String[] paste(Vector<String> list_)
+    private String[] pasteString(Vector<String> list_)
     {
         String temp[] = new String[list_.size()];
         for (int ndx = 0; ndx < temp.length; ++ndx)
@@ -5204,7 +5204,7 @@ private String[] paste(Vector<String> list_)
      * @param list_ The vector.
      * @return The Timestamp array.
      */
-    private Timestamp[] paste(Vector<Timestamp> list_)
+    private Timestamp[] pasteTimestamp(Vector<Timestamp> list_)
     {
         Timestamp temp[] = new Timestamp[list_.size()];
         for (int ndx = 0; ndx < temp.length; ++ndx)
@@ -5265,12 +5265,12 @@ private ACData[] copyResults(ResultSet rs_) throws SQLException
             {
                 if (!oldrec.isEquivalent(rec))
                 {
-                    clist = paste(changes);
-                    olist = paste(oval);
-                    nlist = paste(nval);
-                    dlist = paste(dval);
-                    tlist = paste(tabl);
-                    blist = paste(chgby);
+                    clist = pasteString(changes);
+                    olist = pasteString(oval);
+                    nlist = pasteString(nval);
+                    dlist = pasteTimestamp(dval);
+                    tlist = pasteString(tabl);
+                    blist = pasteString(chgby);
                     oldrec.setChanges(clist, olist, nlist, dlist, tlist, blist);
                     data.add(oldrec);
 
@@ -5309,12 +5309,12 @@ private ACData[] copyResults(ResultSet rs_) throws SQLException
         }
         if (oldrec != null)
         {
-            clist = paste(changes);
-            olist = paste(oval);
-            nlist = paste(nval);
-            dlist = paste(dval);
-            tlist = paste(tabl);
-            blist = paste(chgby);
+            clist = pasteString(changes);
+            olist = pasteString(oval);
+            nlist = pasteString(nval);
+            dlist = pasteTimestamp(dval);
+            tlist = pasteString(tabl);
+            blist = pasteString(chgby);
             oldrec.setChanges(clist, olist, nlist, dlist, tlist, blist);
             data.add(oldrec);
         }

MetadataCleanup/src/java/gov/nih/nci/cadsr/sentinel/tool/AutoProcessAlerts.java

@@ -1849,7 +1849,7 @@ private int getResources()
             _style = "";
         }  */
     	try {
-    		FileInputStream propFile = new FileInputStream("/priv-file-repo/lexevsdb/bin/SentinelToolTestScript/metadata.properties");
+    		FileInputStream propFile = new FileInputStream("/local/content/cadsrsentinel/bin/metadata.properties");
 
 	        Properties p = new Properties(System.getProperties());
 	        p.load(propFile);

MetadataCleanup/src/resources/conf/template.web.xml

@@ -27,11 +27,11 @@ L-->
     </init-param>
     <init-param>
       <param-name>jbossDataSource</param-name>
-      <param-value>jdbc/sentinel</param-value>
+      <param-value>jboss/datasources/SentinelDS</param-value>
     </init-param>
     <init-param>
       <param-name>jbossAuthenticate</param-name>
-      <param-value>jdbc/caDSR</param-value>
+      <param-value>jboss/datasources/caDSRDS</param-value>
     </init-param>
     <init-param>
       <param-name>DSusername</param-name>

MetadataCleanup/src/resources/sdkapi/application-config-client.xml

@@ -14,7 +14,7 @@ L-->
                   <map>
                         <entry key="APPLICATION_SERVICE_BEAN" value-ref="LexEVSApplicationService"/>
                         <entry key="AUTHENTICATION_SERVICE_BEAN" value-ref="EvsAuthenticationProvider"/>
-                        <entry key="APPLICATION_SERVICE_URL" value="http://lexevsapi60.nci.nih.gov/lexevsapi60/http/applicationService"/>
+                        <entry key="APPLICATION_SERVICE_URL" value="https://lexevsapi6.nci.nih.gov/lexevsapi64/http/applicationService"/>
                         <entry key="APPLICATION_SERVICE_CONFIG" value-ref="LexEVSApplicationServiceConfig"/>
                   </map>
             </constructor-arg>
@@ -46,7 +46,7 @@ L-->
       </bean>     
 
        <bean id="AppService" class="org.springframework.remoting.httpinvoker.HttpInvokerProxyFactoryBean" singleton="false">
-            <property name="serviceUrl" value="http://lexevsapi60.nci.nih.gov/lexevsapi60/http/applicationService"/>
+            <property name="serviceUrl" value="https://lexevsapi6.nci.nih.gov/lexevsapi64/http/applicationService"/>
             <property name="serviceInterface" value="org.LexGrid.LexBIG.caCore.interfaces.LexEVSApplicationService"/>
             <property name="httpInvokerRequestExecutor">
                  <bean class="org.LexGrid.LexBIG.caCore.client.proxy.ProxyUnwrappingHttpInvokerRequestExecutor">
@@ -58,7 +58,7 @@ L-->
       <bean id="EvsAuthenticationProvider" class="org.acegisecurity.providers.rcp.RemoteAuthenticationProvider">
             <property name="remoteAuthenticationManager">
                   <bean class="org.springframework.remoting.httpinvoker.HttpInvokerProxyFactoryBean">
-                      <property name="serviceUrl" value="http://lexevsapi60.nci.nih.gov/lexevsapi60/http/applicationService"/>
+                      <property name="serviceUrl" value="https://lexevsapi6.nci.nih.gov/lexevsapi64/http/applicationService"/>
                       <property name="serviceInterface" value="org.acegisecurity.providers.rcp.RemoteAuthenticationManager"/>
                   </bean>
             </property>

MetadataCleanup/src/web/WebRoot/WEB-INF/classes/application-config-client.xml

@@ -14,7 +14,7 @@ L-->
                   <map>
                         <entry key="APPLICATION_SERVICE_BEAN" value-ref="LexEVSApplicationService"/>
                         <entry key="AUTHENTICATION_SERVICE_BEAN" value-ref="EvsAuthenticationProvider"/>
-                        <entry key="APPLICATION_SERVICE_URL" value="http://lexevsapi60.nci.nih.gov/lexevsapi60/http/applicationService"/>
+                        <entry key="APPLICATION_SERVICE_URL" value="https://lexevsapi6.nci.nih.gov/lexevsapi64/http/applicationService"/>
                         <entry key="APPLICATION_SERVICE_CONFIG" value-ref="LexEVSApplicationServiceConfig"/>
                   </map>
             </constructor-arg>
@@ -46,7 +46,7 @@ L-->
       </bean>     
 
        <bean id="AppService" class="org.springframework.remoting.httpinvoker.HttpInvokerProxyFactoryBean" singleton="false">
-            <property name="serviceUrl" value="http://lexevsapi60.nci.nih.gov/lexevsapi60/http/applicationService"/>
+            <property name="serviceUrl" value="https://lexevsapi6.nci.nih.gov/lexevsapi64/http/applicationService"/>
             <property name="serviceInterface" value="org.LexGrid.LexBIG.caCore.interfaces.LexEVSApplicationService"/>
             <property name="httpInvokerRequestExecutor">
                  <bean class="org.LexGrid.LexBIG.caCore.client.proxy.ProxyUnwrappingHttpInvokerRequestExecutor">
@@ -58,7 +58,7 @@ L-->
       <bean id="EvsAuthenticationProvider" class="org.acegisecurity.providers.rcp.RemoteAuthenticationProvider">
             <property name="remoteAuthenticationManager">
                   <bean class="org.springframework.remoting.httpinvoker.HttpInvokerProxyFactoryBean">
-                      <property name="serviceUrl" value="http://lexevsapi60.nci.nih.gov/lexevsapi60/http/applicationService"/>
+                      <property name="serviceUrl" value="https://lexevsapi6.nci.nih.gov/lexevsapi64/http/applicationService"/>
                       <property name="serviceInterface" value="org.acegisecurity.providers.rcp.RemoteAuthenticationManager"/>
                   </bean>
             </property>

docker11/.env

@@ -0,0 +1,18 @@
+# default environment variables. Use these to set variables of they dont exist in local env #
+CADSR_DS_TNS_HOST=changeme
+CADSR_DS_TNS_PORT=changeme
+CADSR_DS_USER=USER
+CADSR_DS_PSWD=PASSWD
+CADSR_DS_TNS_HOST=changeme
+CADSR_DS_TNS_SID=changeme
+#tag=origin/master
+BRANCH_OR_TAG=sentinel-4.0.7-java11-032819
+tag=sentinel-4.0.7-java11-032819
+debug=false
+TEST=false
+tiername=changetiername
+TOOL_BASE_DIR=/local/content
+JDEBUG=ON
+JBOSS_MODULES_SYSTEM_PKGS=org.jboss.byteman
+JAVA_OPTS=-Xms1024m -Xmx2048m -XX:MetaspaceSize=128M -XX:MaxMetaspaceSize=512m -Djava.net.preferIPv4Stack=true -Djboss.modules.system.pkgs=$JBOSS_MODULES_SYSTEM_PKGS -Djava.awt.headless=true
+

docker11/Dockerfile

@@ -0,0 +1,51 @@
+from cbiit/centos7_base
+# update packages and install packages for application #
+RUN yum -y update && yum -y install git java-11-openjdk-devel sudo util-linux wget epel-release \ 
+    && yum clean all
+
+# set env variables
+ENV PATH=/opt/apache-maven/bin:$PATH \
+    JAVA_HOME=/usr/lib/jvm/java-11-openjdk \
+    WILDFLY_VERSION=16.0.0.Final
+
+# change to /tmp directory for code downloads #
+WORKDIR /tmp
+RUN wget https://archive.apache.org/dist/maven/maven-3/3.5.4/binaries/apache-maven-3.5.4-bin.tar.gz \
+    && tar xvfz apache-maven-3.5.4-bin.tar.gz \
+    && mv apache-maven-3.5.4 /opt \
+    && ln -s /opt/apache-maven-3.5.4 /opt/apache-maven
+RUN sudo groupadd -r wildfly && sudo useradd -r -g wildfly -d /opt/wildfly -s /sbin/nologin wildfly \ 
+    && wget https://download.jboss.org/wildfly/$WILDFLY_VERSION/wildfly-$WILDFLY_VERSION.tar.gz -P /tmp \
+    && tar xf /tmp/wildfly-$WILDFLY_VERSION.tar.gz -C /opt/ \
+    && ln -s /opt/wildfly-$WILDFLY_VERSION /opt/wildfly \ 
+    && chown -RH wildfly: /opt/wildfly
+RUN wget http://archive.apache.org/dist/ant/binaries/apache-ant-1.9.9-bin.tar.gz \
+    && tar xvfz apache-ant-1.9.9-bin.tar.gz \
+    && mv apache-ant-1.9.9 /opt
+
+ENV PATH=/opt/apache-maven/bin:/opt/apache-ant-1.9.9/bin:$PATH
+
+# copy entrypoint to /usr/bin and chown to wildfly #
+COPY run.sh /usr/bin/run.sh
+RUN chown wildfly /usr/bin/run.sh && chmod 700 /usr/bin/run.sh
+
+# create local content directories, change owner to wildfly #
+RUN mkdir -p /local/content/cadsrsentinel/config /local/content/cadsrsentinel/bin /local/content/cadsrsentinel/htdocs/dtd /local/content/cadsrsentinel/reports /local/content/autorun_log \
+    && chown -RH wildfly /local/content/cadsrsentinel
+
+# make directory for pulling code from github and change owner to wildfly #
+RUN mkdir /usr/src/sentinel && chown -RH wildfly: /usr/src/sentinel
+
+# change user to wildfly #
+USER wildfly
+
+# replace jboss port 9990 with 19990 #
+RUN sed -i 's/9990/19990/g' /opt/wildfly/standalone/configuration/standalone.xml    
+
+# change to source code workdir #
+WORKDIR /usr/src/sentinel
+RUN git clone https://github.com/CBIIT/cadsr-sentinel
+WORKDIR /usr/src/sentinel/cadsr-sentinel
+
+EXPOSE 8080
+ENTRYPOINT /usr/bin/run.sh 

docker11/README.md

@@ -0,0 +1,16 @@
+docker-compose configuration for cadsr-sentinel11
+=====
+
+## Requirements ##
+The following environment variables are required:
+BRANCH_OR_TAG=sentinel-4.0.7-sprint01-01
+tiername
+CADSR.DS.USER
+CADSR.DS.TNS.HOST
+CADSR.DS.TNS.PORT
+TOOL.BASE.DIR
+CADSR.DS.TNS.SID
+
+## To build ##
+1. cd docker directory
+2. docker-compose up -d