diff --git a/MetadataCleanup/.settings/org.eclipse.jdt.core.prefs b/MetadataCleanup/.settings/org.eclipse.jdt.core.prefs index 8000cd6..a698e59 100644 --- a/MetadataCleanup/.settings/org.eclipse.jdt.core.prefs +++ b/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 diff --git a/MetadataCleanup/deployment-artifacts/bin/metadata.jar b/MetadataCleanup/deployment-artifacts/bin/metadata.jar new file mode 100644 index 0000000..852308d Binary files /dev/null and b/MetadataCleanup/deployment-artifacts/bin/metadata.jar differ diff --git a/MetadataCleanup/deployment-artifacts/metadatacleanup.jar b/MetadataCleanup/deployment-artifacts/metadatacleanup.jar new file mode 100644 index 0000000..ed31280 Binary files /dev/null and b/MetadataCleanup/deployment-artifacts/metadatacleanup.jar differ diff --git a/MetadataCleanup/dev.properties b/MetadataCleanup/dev.properties index 38e9d7e..848137e 100644 --- a/MetadataCleanup/dev.properties +++ b/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 diff --git a/MetadataCleanup/lib/cadsrsentinel.xml b/MetadataCleanup/lib/cadsrsentinel.xml index 782295b..6ee8b67 100644 --- a/MetadataCleanup/lib/cadsrsentinel.xml +++ b/MetadataCleanup/lib/cadsrsentinel.xml @@ -15,9 +15,9 @@ L--> - ncidb-dsr-d.nci.nih.gov:1551:dsrdev.NCI.NIH.GOV - sentinel - sentinel0412 + @@-dburl-@@ + @@-credentials-@@ + @@-credentials-@@ Table Row Counts gov.nih.nci.cadsr.sentinel.audits.AuditSummary diff --git a/MetadataCleanup/lib/commons-codec-1.10.jar b/MetadataCleanup/lib/commons-codec-1.10.jar new file mode 100644 index 0000000..1d7417c Binary files /dev/null and b/MetadataCleanup/lib/commons-codec-1.10.jar differ diff --git a/MetadataCleanup/lib/commons-codec-1.3.jar b/MetadataCleanup/lib/commons-codec-1.3.jar deleted file mode 100644 index 957b675..0000000 Binary files a/MetadataCleanup/lib/commons-codec-1.3.jar and /dev/null differ diff --git a/MetadataCleanup/lib/commons-dbcp-1.3.jar b/MetadataCleanup/lib/commons-dbcp-1.3.jar deleted file mode 100644 index d293397..0000000 Binary files a/MetadataCleanup/lib/commons-dbcp-1.3.jar and /dev/null differ diff --git a/MetadataCleanup/lib/commons-dbcp-1.4.jar b/MetadataCleanup/lib/commons-dbcp-1.4.jar new file mode 100644 index 0000000..c4c1c4f Binary files /dev/null and b/MetadataCleanup/lib/commons-dbcp-1.4.jar differ diff --git a/MetadataCleanup/lib/kryo-2.21.jar b/MetadataCleanup/lib/kryo-2.21.jar new file mode 100644 index 0000000..44eae97 Binary files /dev/null and b/MetadataCleanup/lib/kryo-2.21.jar differ diff --git a/MetadataCleanup/lib/kryo-serializers-0.37.jar b/MetadataCleanup/lib/kryo-serializers-0.37.jar new file mode 100644 index 0000000..d999a8f Binary files /dev/null and b/MetadataCleanup/lib/kryo-serializers-0.37.jar differ diff --git a/MetadataCleanup/lib/lexbig.jar b/MetadataCleanup/lib/lexbig.jar index 7d29d7a..9c489dc 100644 Binary files a/MetadataCleanup/lib/lexbig.jar and b/MetadataCleanup/lib/lexbig.jar differ diff --git a/MetadataCleanup/lib/lexevsapi60-beans.jar b/MetadataCleanup/lib/lexevsapi60-beans.jar deleted file mode 100644 index 035d650..0000000 Binary files a/MetadataCleanup/lib/lexevsapi60-beans.jar and /dev/null differ diff --git a/MetadataCleanup/lib/lexevsapi60-orm.jar b/MetadataCleanup/lib/lexevsapi60-orm.jar deleted file mode 100644 index 616f688..0000000 Binary files a/MetadataCleanup/lib/lexevsapi60-orm.jar and /dev/null differ diff --git a/MetadataCleanup/lib/lexevsapi64-beans.jar b/MetadataCleanup/lib/lexevsapi64-beans.jar new file mode 100644 index 0000000..cc77e6d Binary files /dev/null and b/MetadataCleanup/lib/lexevsapi64-beans.jar differ diff --git a/MetadataCleanup/lib/lexevsapi64-framework.jar b/MetadataCleanup/lib/lexevsapi64-framework.jar new file mode 100644 index 0000000..10bfc35 Binary files /dev/null and b/MetadataCleanup/lib/lexevsapi64-framework.jar differ diff --git a/MetadataCleanup/lib/lucene-analyzers-2.4.1.jar b/MetadataCleanup/lib/lucene-analyzers-2.4.1.jar 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b/MetadataCleanup/lib/lucene-queries-5.3.1.jar differ diff --git a/MetadataCleanup/lib/lucene-queryparser-5.3.1.jar b/MetadataCleanup/lib/lucene-queryparser-5.3.1.jar new file mode 100644 index 0000000..12a5e63 Binary files /dev/null and b/MetadataCleanup/lib/lucene-queryparser-5.3.1.jar differ diff --git a/MetadataCleanup/lib/lucene-regex-2.4.0.jar b/MetadataCleanup/lib/lucene-regex-2.4.0.jar deleted file mode 100644 index 474d745..0000000 Binary files a/MetadataCleanup/lib/lucene-regex-2.4.0.jar and /dev/null differ diff --git a/MetadataCleanup/lib/lucene-sandbox-5.3.1.jar b/MetadataCleanup/lib/lucene-sandbox-5.3.1.jar new file mode 100644 index 0000000..3e0712f Binary files /dev/null and b/MetadataCleanup/lib/lucene-sandbox-5.3.1.jar differ diff --git a/MetadataCleanup/lib/lucene-snowball-2.4.0.jar b/MetadataCleanup/lib/lucene-snowball-2.4.0.jar deleted file mode 100644 index 30aead2..0000000 Binary files a/MetadataCleanup/lib/lucene-snowball-2.4.0.jar and /dev/null differ diff --git a/MetadataCleanup/lib/lucene-test-framework-5.3.1.jar b/MetadataCleanup/lib/lucene-test-framework-5.3.1.jar new file mode 100644 index 0000000..1e6ea82 Binary files /dev/null and b/MetadataCleanup/lib/lucene-test-framework-5.3.1.jar differ diff --git a/MetadataCleanup/lib/minlog-1.2.jar b/MetadataCleanup/lib/minlog-1.2.jar new file mode 100644 index 0000000..3d174a6 Binary files /dev/null and b/MetadataCleanup/lib/minlog-1.2.jar differ diff --git a/MetadataCleanup/metadata.properties b/MetadataCleanup/metadata.properties index 5b7fc9a..befc047 100644 --- a/MetadataCleanup/metadata.properties +++ b/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 \ No newline at end of file +OUTPUT.DIR=/local/content/cadsrsentinel/Reports \ No newline at end of file diff --git a/MetadataCleanup/project.properties b/MetadataCleanup/project.properties index 16e6a6b..d9bdcf0 100644 --- a/MetadataCleanup/project.properties +++ b/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 diff --git a/MetadataCleanup/src/java/gov/nih/nci/cadsr/sentinel/database/CaDsrUserCredentials.java b/MetadataCleanup/src/java/gov/nih/nci/cadsr/sentinel/database/CaDsrUserCredentials.java index da01acc..36fbf61 100644 --- a/MetadataCleanup/src/java/gov/nih/nci/cadsr/sentinel/database/CaDsrUserCredentials.java +++ b/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')"; diff --git a/MetadataCleanup/src/java/gov/nih/nci/cadsr/sentinel/database/DBAlertOracle.java b/MetadataCleanup/src/java/gov/nih/nci/cadsr/sentinel/database/DBAlertOracle.java index 6ab5ac1..36dec0c 100644 --- a/MetadataCleanup/src/java/gov/nih/nci/cadsr/sentinel/database/DBAlertOracle.java +++ b/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 list_) + private String[] pasteString(Vector list_) { String temp[] = new String[list_.size()]; for (int ndx = 0; ndx < temp.length; ++ndx) @@ -5204,7 +5204,7 @@ private String[] paste(Vector list_) * @param list_ The vector. * @return The Timestamp array. */ - private Timestamp[] paste(Vector list_) + private Timestamp[] pasteTimestamp(Vector 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); } diff --git a/MetadataCleanup/src/java/gov/nih/nci/cadsr/sentinel/tool/AutoProcessAlerts.java b/MetadataCleanup/src/java/gov/nih/nci/cadsr/sentinel/tool/AutoProcessAlerts.java index 27b578c..fc1a55f 100644 --- a/MetadataCleanup/src/java/gov/nih/nci/cadsr/sentinel/tool/AutoProcessAlerts.java +++ b/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); diff --git a/MetadataCleanup/src/resources/conf/template.web.xml b/MetadataCleanup/src/resources/conf/template.web.xml index a46dc2f..15d61d4 100644 --- a/MetadataCleanup/src/resources/conf/template.web.xml +++ b/MetadataCleanup/src/resources/conf/template.web.xml @@ -27,11 +27,11 @@ L--> jbossDataSource - jdbc/sentinel + jboss/datasources/SentinelDS jbossAuthenticate - jdbc/caDSR + jboss/datasources/caDSRDS DSusername diff --git a/MetadataCleanup/src/resources/sdkapi/application-config-client.xml b/MetadataCleanup/src/resources/sdkapi/application-config-client.xml index 2c3b8dd..d2f1a9f 100644 --- a/MetadataCleanup/src/resources/sdkapi/application-config-client.xml +++ b/MetadataCleanup/src/resources/sdkapi/application-config-client.xml @@ -14,7 +14,7 @@ L--> - + @@ -46,7 +46,7 @@ L--> - + @@ -58,7 +58,7 @@ L--> - + diff --git a/MetadataCleanup/src/resources/sdkapi/log4j.properties b/MetadataCleanup/src/resources/sdkapi/log4j.properties deleted file mode 100644 index 7e23856..0000000 --- a/MetadataCleanup/src/resources/sdkapi/log4j.properties +++ /dev/null @@ -1,53 +0,0 @@ -#L -# Copyright ScenPro Inc, SAIC-F -# -# Distributed under the OSI-approved BSD 3-Clause License. -# See http://ncip.github.com/cadsr-sentinal/LICENSE.txt for details. -#L - -log4j.rootLogger=ERROR,stdout - - -### direct messages to file hibernate.log ### - -log4j.appender.clientLog=org.apache.log4j.FileAppender -log4j.appender.clientLog.File=./log/client.log -log4j.appender.clientLog.layout=org.apache.log4j.PatternLayout -log4j.appender.clientLog.layout.ConversionPattern=%d{ABSOLUTE} %5p %c{1}:%L - %m%n - - -log4j.appender.stdout=org.apache.log4j.ConsoleAppender -log4j.appender.stdout.layout=org.apache.log4j.PatternLayout -log4j.appender.stdout.layout.ConversionPattern=%d{ABSOLUTE} %5p %c{1}:%L - %m%n - - - -### set log levels - for more verbose logging change 'info' to 'debug' ### - -#log4j.rootLogger=warn, stdout -#log4j.rootLogger=warn, file -#log4j.logger.org.hibernate=info - -### log just the SQL -#log4j.logger.org.hibernate.SQL=debug - -### log JDBC bind parameters ### -#log4j.logger.org.hibernate.type=info - -### log schema export/update ### -#log4j.logger.org.hibernate.tool.hbm2ddl=debug - -### log cache activity ### -#log4j.logger.org.hibernate.cache=debug - -### log JDBC resource acquisition -#log4j.logger.org.hibernate.jdbc=debug - -### enable the following line if you want to track down connection ### -### leakages when using DriverManagerConnectionProvider ### -#log4j.logger.org.hibernate.connection.DriverManagerConnectionProvider=trace - -log4j.logger.gov.nih.nci=error -log4j.logger.org.springframework=error - - diff --git a/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/application-config-client.xml b/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/application-config-client.xml index 2c3b8dd..d2f1a9f 100644 --- a/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/application-config-client.xml +++ b/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/application-config-client.xml @@ -14,7 +14,7 @@ L--> - + @@ -46,7 +46,7 @@ L--> - + @@ -58,7 +58,7 @@ L--> - + diff --git a/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/common/Constants.class b/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/common/Constants.class index df5a461..534a2a1 100644 Binary files a/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/common/Constants.class and b/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/common/Constants.class differ diff --git a/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/audits/AuditReport.class b/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/audits/AuditReport.class index 8aaa102..e944887 100644 Binary files a/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/audits/AuditReport.class and b/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/audits/AuditReport.class differ diff --git a/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/audits/caDSRConceptCleanupEVS$1.class b/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/audits/caDSRConceptCleanupEVS$1.class index 0841655..e475339 100644 Binary files a/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/audits/caDSRConceptCleanupEVS$1.class and b/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/audits/caDSRConceptCleanupEVS$1.class differ diff --git a/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/audits/caDSRConceptCleanupEVS$EVSConcept.class b/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/audits/caDSRConceptCleanupEVS$EVSConcept.class index d2e3b8f..f653a4e 100644 Binary files a/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/audits/caDSRConceptCleanupEVS$EVSConcept.class and 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a/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/audits/caDSRConceptCleanupEVS$EVSVocab.class and b/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/audits/caDSRConceptCleanupEVS$EVSVocab.class differ diff --git a/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/audits/caDSRConceptCleanupEVS$MetaTh.class b/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/audits/caDSRConceptCleanupEVS$MetaTh.class index cbf4faa..5b45162 100644 Binary files a/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/audits/caDSRConceptCleanupEVS$MetaTh.class and b/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/audits/caDSRConceptCleanupEVS$MetaTh.class differ diff --git a/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/audits/caDSRConceptCleanupEVS$NonMetaTh.class b/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/audits/caDSRConceptCleanupEVS$NonMetaTh.class index 9eae542..1d57221 100644 Binary files a/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/audits/caDSRConceptCleanupEVS$NonMetaTh.class and b/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/audits/caDSRConceptCleanupEVS$NonMetaTh.class differ diff --git a/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/audits/caDSRConceptCleanupEVS.class b/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/audits/caDSRConceptCleanupEVS.class index 04d50e1..f668b22 100644 Binary files a/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/audits/caDSRConceptCleanupEVS.class and b/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/audits/caDSRConceptCleanupEVS.class differ diff --git a/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/database/CaDsrUserCredentials$DBAction.class b/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/database/CaDsrUserCredentials$DBAction.class index 5a292c7..69eae31 100644 Binary files a/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/database/CaDsrUserCredentials$DBAction.class and b/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/database/CaDsrUserCredentials$DBAction.class differ diff --git a/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/database/CaDsrUserCredentials$DBActionLockCheck.class b/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/database/CaDsrUserCredentials$DBActionLockCheck.class index 2d51b55..05cbb0d 100644 Binary files a/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/database/CaDsrUserCredentials$DBActionLockCheck.class and 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--git a/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/database/DBProperty.class b/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/database/DBProperty.class index 560b724..9b8b595 100644 Binary files a/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/database/DBProperty.class and b/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/database/DBProperty.class differ diff --git a/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/test/DSRAlertTestCase.class b/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/test/DSRAlertTestCase.class index 1460a24..eab706a 100644 Binary files a/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/test/DSRAlertTestCase.class and b/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/test/DSRAlertTestCase.class differ diff --git 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b/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/util/DSRAlertV1.class differ diff --git a/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/util/SentinelToolProperties.class b/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/util/SentinelToolProperties.class index 20e3190..8efd90a 100644 Binary files a/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/util/SentinelToolProperties.class and b/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/gov/nih/nci/cadsr/sentinel/util/SentinelToolProperties.class differ diff --git a/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/log4j.properties b/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/log4j.properties deleted file mode 100644 index 7e23856..0000000 --- a/MetadataCleanup/src/web/WebRoot/WEB-INF/classes/log4j.properties +++ /dev/null @@ -1,53 +0,0 @@ -#L -# Copyright ScenPro Inc, SAIC-F -# -# Distributed under the OSI-approved BSD 3-Clause License. -# See http://ncip.github.com/cadsr-sentinal/LICENSE.txt for details. -#L - -log4j.rootLogger=ERROR,stdout - - -### direct messages to file hibernate.log ### - -log4j.appender.clientLog=org.apache.log4j.FileAppender -log4j.appender.clientLog.File=./log/client.log -log4j.appender.clientLog.layout=org.apache.log4j.PatternLayout -log4j.appender.clientLog.layout.ConversionPattern=%d{ABSOLUTE} %5p %c{1}:%L - %m%n - - -log4j.appender.stdout=org.apache.log4j.ConsoleAppender -log4j.appender.stdout.layout=org.apache.log4j.PatternLayout -log4j.appender.stdout.layout.ConversionPattern=%d{ABSOLUTE} %5p %c{1}:%L - %m%n - - - -### set log levels - for more verbose logging change 'info' to 'debug' ### - -#log4j.rootLogger=warn, stdout -#log4j.rootLogger=warn, file -#log4j.logger.org.hibernate=info - -### log just the SQL -#log4j.logger.org.hibernate.SQL=debug - -### log JDBC bind parameters ### -#log4j.logger.org.hibernate.type=info - -### log schema export/update ### -#log4j.logger.org.hibernate.tool.hbm2ddl=debug - -### log cache activity ### -#log4j.logger.org.hibernate.cache=debug - -### log JDBC resource acquisition -#log4j.logger.org.hibernate.jdbc=debug - -### enable the following line if you want to track down connection ### -### leakages when using DriverManagerConnectionProvider ### -#log4j.logger.org.hibernate.connection.DriverManagerConnectionProvider=trace - -log4j.logger.gov.nih.nci=error -log4j.logger.org.springframework=error - - diff --git a/docker11/.env b/docker11/.env new file mode 100644 index 0000000..bc92af3 --- /dev/null +++ b/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 + diff --git a/docker11/Dockerfile b/docker11/Dockerfile new file mode 100644 index 0000000..1144b11 --- /dev/null +++ b/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 diff --git a/docker11/README.md b/docker11/README.md new file mode 100644 index 0000000..331e413 --- /dev/null +++ b/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 diff --git a/docker11/docker-compose.yml b/docker11/docker-compose.yml new file mode 100644 index 0000000..9c36b49 --- /dev/null +++ b/docker11/docker-compose.yml @@ -0,0 +1,23 @@ +version: '2' +services: + server: + container_name: cadsr-sentinel11 + image: cadsr-sentinel11 + build: ./ + ports: + - "8086:8080" + environment: + CADSR_DS_TNS_HOST: $CADSR_DS_HOST + CADSR_DS_TNS_PORT: $CADSR_DS_PORT + CADSR_DS_USER: $CADSR_DS_USER + CADSR_DS_PSWD: $CADSR_DS_PSWD + CADSR_DS_TNS_SID: $CADSR_DS_TNS_SID + BRANCH_OR_TAG: $BRANCH_OR_TAG + tag: $tag + tier: $tiername + tiername: $tiername + JBOSS_MODULES_SYSTEM_PKGS: $JBOSS_MODULES_SYSTEM_PKGS + JAVA_OPTS: $JAVA_OPTS + TOOL_BASE_DIR: $TOOL_BASE_DIR + JDEBUG: $JDEBUG + diff --git a/docker11/run.sh b/docker11/run.sh new file mode 100644 index 0000000..e532001 --- /dev/null +++ b/docker11/run.sh @@ -0,0 +1,48 @@ +#~/bin/sh +echo "we are in the /usr/src/sentinel/cadsr-sentinel directory" +echo "tag: " $tag +git pull +if [ $tag != 'origin/master' ] && [ $tag != 'master' ]; then +# git checkout tags/$tag +#this is for branch checkout for now + git checkout $tag +fi +git pull + +# Function to check if wildfly is up # +function wait_for_server() { + until `/opt/wildfly/bin/jboss-cli.sh -c --controller=localhost:19990 ":read-attribute(name=server-state)" 2> /dev/null | grep -q running`; do + sleep 1 + done +} + +cd software +echo "we are in the /usr/src/sentinel/cadsr-sentinel/software directory" +echo "=> build application and copy artifacts to /local/content/sentinel" + +echo ant -file build.xml -Ddebug=false -DBRANCH_OR_TAG=${BRANCH_OR_TAG} -Dtiername=${tiername} -DCADSR.DS.USER=${CADSR_DS_USER} -DCADSR.DS.PSWD=******** -DCADSR.DS.TNS.HOST=${CADSR_DS_TNS_HOST} -DTOOL.BASE.DIR=${TOOL_BASE_DIR} -DTEST=false -DCADSR.DS.TNS.SID=${CADSR_DS_TNS_SID} -DJDEBUG=off -DCADSR.DS.TNS.PORT=${CADSR_DS_TNS_PORT} build-product +ant -file build.xml -Ddebug=false -DBRANCH_OR_TAG=${BRANCH_OR_TAG} -Dtiername=${tiername} -DCADSR.DS.USER=${CADSR_DS_USER} -DCADSR.DS.PSWD=${CADSR_DS_PSWD} -DCADSR.DS.TNS.HOST=${CADSR_DS_TNS_HOST} -DTOOL.BASE.DIR=${TOOL_BASE_DIR} -DTEST=false -DCADSR.DS.TNS.SID=${CADSR_DS_TNS_SID} -DJDEBUG=off -DCADSR.DS.TNS.PORT=${CADSR_DS_TNS_PORT} build-product + +cp deployment-artifacts/cadsrsentinel.war /local/content/cadsrsentinel/bin +cp lib/ojdbc7-12.1.0.2.0.jar /local/content/cadsrsentinel/bin + +echo "=> starting wildfly in background" +/opt/wildfly/bin/standalone.sh -b 0.0.0.0 -bmanagement 0.0.0.0 & + +echo "=> Waiting for the server to boot" +wait_for_server + +echo "=> deploying modules" +/opt/wildfly/bin/jboss-cli.sh --file=deployment-artifacts/jboss/cadsrsentinel_modules.cli + +echo "=> reloading wildfly" +/opt/wildfly/bin/jboss-cli.sh --connect controller=localhost:19990 command=:reload + +echo "=> Waiting for the server to reload" +wait_for_server + +echo "=> shutting wildfly down" +/opt/wildfly/bin/jboss-cli.sh --connect controller=localhost:19990 command=:shutdown + +echo "=> starting wildfly in foreground" +/opt/wildfly/bin/standalone.sh -b 0.0.0.0 -bmanagement 0.0.0.0 diff --git a/software/.classpath b/software/.classpath index b83061a..e83f6e1 100644 --- a/software/.classpath +++ b/software/.classpath @@ -17,7 +17,7 @@ - + @@ -34,24 +34,18 @@ - + - - - - - - - + @@ -64,12 +58,8 @@ - - - - @@ -87,5 +77,22 @@ + + + + + + + + + + + + + + + + + diff --git a/software/.gitignore b/software/.gitignore new file mode 100644 index 0000000..d977570 --- /dev/null +++ b/software/.gitignore @@ -0,0 +1,4 @@ +/bin/ +/deployment-artifacts/ +.DS_Store +*.DS_Store \ No newline at end of file diff --git a/software/.settings/org.eclipse.jdt.core.prefs b/software/.settings/org.eclipse.jdt.core.prefs new file mode 100644 index 0000000..a698e59 --- /dev/null +++ b/software/.settings/org.eclipse.jdt.core.prefs @@ -0,0 +1,12 @@ +eclipse.preferences.version=1 +org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled +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=1.8 +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=1.8 diff --git a/software/build.xml b/software/build.xml index 9a2839c..54b2067 100644 --- a/software/build.xml +++ b/software/build.xml @@ -207,6 +207,22 @@ L--> + + + + + + connectionUrl = ${connectionUrl} + + systemAccountName = ${systemAccountName} + + systemAccountPassword not echoed + + logLevel = ${logLevel} + + host = ${host} + + @@ -219,32 +235,26 @@ L--> - - - - - - - - + + - - + + - - - - + + + + @@ -264,7 +274,7 @@ L--> - + @@ -274,6 +284,7 @@ L--> + @@ -296,7 +307,7 @@ L--> Building distributable JAR files ... - + @@ -306,6 +317,9 @@ L--> + + + @@ -396,6 +410,10 @@ L--> + + + + @@ -492,8 +510,15 @@ L--> + + + + + - + + + @@ -516,7 +541,9 @@ L--> - + + + Deploying war files to web server ... diff --git a/software/cadsrsentinel_modules.cli b/software/cadsrsentinel_modules.cli new file mode 100644 index 0000000..be77d70 --- /dev/null +++ b/software/cadsrsentinel_modules.cli @@ -0,0 +1,73 @@ +connect localhost:19990 + +#1 add the jdbc module it doesn't matter if it's already there +module add --name=com.oracle.jdbc7 --resources=/local/content/cadsrsentinel/bin/ojdbc7-12.1.0.2.0.jar --dependencies=javax.api,javax.transaction.api + +# configure datasource +# is the driver in standalone.xml? +# if not, add +if (outcome != success) of /subsystem=datasources/jdbc-driver=oracle:read-resource + /subsystem=datasources/jdbc-driver=oracle:add( \ + driver-name=oracle, \ + driver-module-name=com.oracle.jdbc7, \ + driver-class-name=oracle.jdbc.driver.OracleDriver, \ + driver-xa-datasource-class-name=oracle.jdbc.xa.client.OracleXADataSource \ + ) {allow-resource-service-restart=true} +end-if + +# is the db connection in standalone.xml? +# if yes remove + if (outcome == success) of /subsystem=datasources/data-source=SentinelDS:read-resource +data-source remove --name=SentinelDS +end-if + +# if yes remove + if (outcome == success) of /subsystem=datasources/data-source=caDSRDS:read-resource +data-source remove --name=caDSRDS +end-if + +# is the db connection in standalone.xml? +# if not, add +if (outcome != success) of /subsystem=datasources/data-source=SentinelDS:read-resource +data-source add \ + --name=SentinelDS \ + --driver-name=oracle \ + --connection-url=jdbc:oracle:thin:@@connectionUrl@ \ + --jndi-name=java:jboss/datasources/SentinelDS \ + --user-name=@systemAccountName@ \ + --password=@systemAccountPassword@ \ + --use-ccm=true \ + --max-pool-size=100 \ + --blocking-timeout-wait-millis=5000 +end-if + +# is the db connection in standalone.xml? +# if not, add +if (outcome != success) of /subsystem=datasources/data-source=caDSRDS:read-resource +data-source add \ + --name=caDSRDS \ + --driver-name=oracle \ + --connection-url=jdbc:oracle:thin:@@connectionUrl@ \ + --jndi-name=java:jboss/datasources/caDSRDS \ + --user-name=@systemAccountName@ \ + --password=@systemAccountPassword@ \ + --use-ccm=true \ + --max-pool-size=100 \ + --blocking-timeout-wait-millis=5000 +end-if + +if (outcome != success) of /subsystem=logging/size-rotating-file-handler=SENTINEL:read-resource +/subsystem=logging:write-attribute(name=use-deployment-logging-config, value=false) +/subsystem=logging:write-attribute(name=add-logging-api-dependencies,value=true) +/subsystem=logging/size-rotating-file-handler=SENTINEL:add(level=@logLevel@, file={"relative-to"=>"jboss.server.log.dir", "path"=>"cadsrsentinel.log"}, append=false, autoflush=true) +/subsystem=logging/size-rotating-file-handler=SENTINEL:write-attribute(name="formatter", value="%d [%t] %-5p [%c : %L] %m%n") +/subsystem=logging/size-rotating-file-handler=SENTINEL:write-attribute(name="rotate-size", value="1m") +/subsystem=logging/size-rotating-file-handler=SENTINEL:write-attribute(name="max-backup-index", value="10") +end-if + + +if (outcome!= success) of /subsystem=logging/logger=gov.nih.nci.cadsr.sentinel:read-resource +/subsystem=logging/logger=gov.nih.nci.cadsr.sentinel:add(use-parent-handlers=false,handlers=["SENTINEL"]) +end-if + +deploy --force /local/content/cadsrsentinel/bin/cadsrsentinel.war \ No newline at end of file diff --git a/software/cadsrsentinel_setup_deploy.cli b/software/cadsrsentinel_setup_deploy.cli new file mode 100644 index 0000000..f6aa6b9 --- /dev/null +++ b/software/cadsrsentinel_setup_deploy.cli @@ -0,0 +1,3 @@ +connect + +deploy --force /local/content/cadsrsentinel/bin/cadsrsentinel.war \ No newline at end of file diff --git a/software/cron/autorun.sh b/software/cron/autorun.sh old mode 100644 new mode 100755 diff --git a/software/dev.properties b/software/dev.properties index 1693eb0..d0c38d9 100644 --- a/software/dev.properties +++ b/software/dev.properties @@ -12,18 +12,18 @@ ## 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=4.0.7 JDEBUG=on TEST=false ######################## ### DB Setting ##### ######################## -CADSR.DS.USER=SENTINEL -CADSR.DS.PSWD=sentinel0412 -CADSR.DS.TNS.HOST=NCIDB-DSR-D.NCI.NIH.GOV -CADSR.DS.TNS.PORT=1551 -CADSR.DS.TNS.SID=DSRDEV +CADSR.DS.USER= +CADSR.DS.PSWD= +CADSR.DS.TNS.HOST= +CADSR.DS.TNS.PORT= +CADSR.DS.TNS.SID= ######################################## ### CronJob File Location SETTINGS ##### diff --git a/software/lib/LexEVSSecurity.jar b/software/lib/LexEVSSecurity.jar index 0c80acb..efb1116 100644 Binary files a/software/lib/LexEVSSecurity.jar and b/software/lib/LexEVSSecurity.jar differ diff --git a/software/lib/cadsrsentinel.xml b/software/lib/cadsrsentinel.xml index 782295b..6ee8b67 100644 --- a/software/lib/cadsrsentinel.xml +++ b/software/lib/cadsrsentinel.xml @@ -15,9 +15,9 @@ L--> - ncidb-dsr-d.nci.nih.gov:1551:dsrdev.NCI.NIH.GOV - sentinel - sentinel0412 + @@-dburl-@@ + @@-credentials-@@ + @@-credentials-@@ Table Row Counts gov.nih.nci.cadsr.sentinel.audits.AuditSummary diff --git a/software/lib/commons-codec-1.10.jar b/software/lib/commons-codec-1.10.jar new file mode 100644 index 0000000..1d7417c Binary files /dev/null and b/software/lib/commons-codec-1.10.jar differ diff --git a/software/lib/commons-codec-1.3.jar b/software/lib/commons-codec-1.3.jar deleted file mode 100644 index 957b675..0000000 Binary files a/software/lib/commons-codec-1.3.jar and /dev/null differ diff --git a/software/lib/commons-dbcp-1.3.jar b/software/lib/commons-dbcp-1.3.jar deleted file mode 100644 index d293397..0000000 Binary files a/software/lib/commons-dbcp-1.3.jar and /dev/null differ diff --git a/software/lib/commons-dbcp-1.4.jar b/software/lib/commons-dbcp-1.4.jar new file mode 100644 index 0000000..c4c1c4f Binary files /dev/null and b/software/lib/commons-dbcp-1.4.jar differ diff --git a/software/lib/commons-httpclient-3.1.jar b/software/lib/commons-httpclient-3.1.jar new file mode 100644 index 0000000..7c59774 Binary files /dev/null and b/software/lib/commons-httpclient-3.1.jar differ diff --git a/software/lib/kryo-2.21.jar b/software/lib/kryo-2.21.jar new file mode 100644 index 0000000..44eae97 Binary files /dev/null and b/software/lib/kryo-2.21.jar differ diff --git a/software/lib/kryo-serializers-0.37.jar b/software/lib/kryo-serializers-0.37.jar new file mode 100644 index 0000000..d999a8f Binary files /dev/null and b/software/lib/kryo-serializers-0.37.jar differ diff --git a/software/lib/lexbig.jar b/software/lib/lexbig.jar index 7d29d7a..dacdc76 100644 Binary files a/software/lib/lexbig.jar and b/software/lib/lexbig.jar differ diff --git a/software/lib/lexevs-client-framework.jar b/software/lib/lexevs-client-framework.jar deleted file mode 100644 index 00a878f..0000000 Binary files a/software/lib/lexevs-client-framework.jar and /dev/null differ diff --git a/software/lib/lexevsapi60-beans.jar b/software/lib/lexevsapi60-beans.jar deleted file mode 100644 index 035d650..0000000 Binary files a/software/lib/lexevsapi60-beans.jar and /dev/null differ diff --git a/software/lib/lexevsapi60-orm.jar b/software/lib/lexevsapi60-orm.jar deleted file mode 100755 index 616f688..0000000 Binary files a/software/lib/lexevsapi60-orm.jar and /dev/null differ diff --git a/software/lib/lexevsapi65-beans.jar b/software/lib/lexevsapi65-beans.jar new file mode 100644 index 0000000..6525a62 Binary files /dev/null and b/software/lib/lexevsapi65-beans.jar differ diff --git a/software/lib/lexevsapi65-framework.jar b/software/lib/lexevsapi65-framework.jar new file mode 100644 index 0000000..bfc724a Binary files /dev/null and b/software/lib/lexevsapi65-framework.jar differ diff --git a/software/lib/log4j.properties b/software/lib/log4j.properties deleted file mode 100644 index 6dfa532..0000000 --- a/software/lib/log4j.properties +++ /dev/null @@ -1,53 +0,0 @@ -#L -# Copyright ScenPro Inc, SAIC-F -# -# Distributed under the OSI-approved BSD 3-Clause License. -# See http://ncip.github.com/cadsr-sentinal/LICENSE.txt for details. -#L - -log4j.rootLogger=DEBUG,stdout - - -### direct messages to file hibernate.log ### - -log4j.appender.clientLog=org.apache.log4j.FileAppender -log4j.appender.clientLog.File=./log/client.log -log4j.appender.clientLog.layout=org.apache.log4j.PatternLayout -log4j.appender.clientLog.layout.ConversionPattern=%d{ABSOLUTE} %5p %c{1}:%L - %m%n - - -log4j.appender.stdout=org.apache.log4j.ConsoleAppender -log4j.appender.stdout.layout=org.apache.log4j.PatternLayout -log4j.appender.stdout.layout.ConversionPattern=%d{ABSOLUTE} %5p %c{1}:%L - %m%n - - - -### set log levels - for more verbose logging change 'info' to 'debug' ### - -#log4j.rootLogger=warn, stdout -#log4j.rootLogger=warn, file -#log4j.logger.org.hibernate=info - -### log just the SQL -#log4j.logger.org.hibernate.SQL=debug - -### log JDBC bind parameters ### -#log4j.logger.org.hibernate.type=info - -### log schema export/update ### -#log4j.logger.org.hibernate.tool.hbm2ddl=debug - -### log cache activity ### -#log4j.logger.org.hibernate.cache=debug - -### log JDBC resource acquisition -#log4j.logger.org.hibernate.jdbc=debug - -### enable the following line if you want to track down connection ### -### leakages when using DriverManagerConnectionProvider ### -#log4j.logger.org.hibernate.connection.DriverManagerConnectionProvider=trace - -log4j.logger.gov.nih.nci=debug -log4j.logger.org.springframework=error - - diff --git a/software/lib/lucene-analyzers-2.4.1.jar b/software/lib/lucene-analyzers-2.4.1.jar deleted file mode 100755 index 6a15904..0000000 Binary files a/software/lib/lucene-analyzers-2.4.1.jar and /dev/null differ diff --git a/software/lib/lucene-analyzers-common-5.3.1.jar b/software/lib/lucene-analyzers-common-5.3.1.jar new file mode 100644 index 0000000..a871384 Binary files /dev/null and b/software/lib/lucene-analyzers-common-5.3.1.jar differ diff --git a/software/lib/lucene-analyzers-phonetic-5.3.1.jar b/software/lib/lucene-analyzers-phonetic-5.3.1.jar new file mode 100644 index 0000000..5493461 Binary files /dev/null and b/software/lib/lucene-analyzers-phonetic-5.3.1.jar differ diff --git a/software/lib/lucene-codecs-5.3.1.jar 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b/software/local.build.properties @@ -9,7 +9,7 @@ JDEBUG=on TEST=false CADSR.DS.USER=SENTINEL CADSR.DS.PSWD=sentinel0412 -CADSR.DS.TNS.HOST=NCIDB-DSR-D.NCI.NIH.GOV +CADSR.DS.TNS.HOST=ncidb-d110-d.NCI.NIH.GOV CADSR.DS.TNS.PORT=1551 CADSR.DS.TNS.SID=DSRDEV #JBOSS.SERVER.DIR=C:/apps/jboss-5.1.0.GA/server/default diff --git a/software/prod.properties b/software/prod.properties new file mode 100644 index 0000000..0df96d3 --- /dev/null +++ b/software/prod.properties @@ -0,0 +1,31 @@ +#L +# Copyright ScenPro Inc, SAIC-F +# +# Distributed under the OSI-approved BSD 3-Clause License. +# See http://ncip.github.com/cadsr-sentinal/LICENSE.txt for details. +#L + +## These properties are specific for the NCICBIIT DEV tier. The values for the properties +## whose values are empty in the file will need to be supplied in the PTE forms and supplied +## through the -D option by the Systems Team + +## also need to provide tiername=dev in the PTE form in order for this file to be invoked + + +JDEBUG=on +TEST=false + +######################## +### DB Setting ##### +######################## +CADSR.DS.USER=SENTINEL +CADSR.DS.PSWD= +CADSR.DS.TNS.HOST= +CADSR.DS.TNS.PORT= +CADSR.DS.TNS.SID= + +######################################## +### CronJob File Location SETTINGS ##### +######################################## +TOOL.BASE.DIR=/local/content + diff --git a/software/project.properties b/software/project.properties index 16e6a6b..68b62c0 100644 --- a/software/project.properties +++ b/software/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=4.0.7 help.url=https://wiki.nci.nih.gov/x/z4AFBw diff --git a/software/qa.properties b/software/qa.properties index b82b366..49fa7c1 100644 --- a/software/qa.properties +++ b/software/qa.properties @@ -12,6 +12,7 @@ ## also need to provide tiername=dev in the PTE form in order for this file to be invoked +appl.release=4.0.7 JDEBUG=on TEST=false diff --git a/software/src/java/gov/nih/nci/cadsr/sentinel/audits/AuditConceptToEVS.java b/software/src/java/gov/nih/nci/cadsr/sentinel/audits/AuditConceptToEVS.java index c2207b0..bfbc338 100644 --- a/software/src/java/gov/nih/nci/cadsr/sentinel/audits/AuditConceptToEVS.java +++ b/software/src/java/gov/nih/nci/cadsr/sentinel/audits/AuditConceptToEVS.java @@ -21,7 +21,9 @@ import java.util.List; import java.util.Vector; +import org.LexGrid.LexBIG.DataModel.Collections.ConceptReferenceList; import org.LexGrid.LexBIG.DataModel.Collections.LocalNameList; +import org.LexGrid.LexBIG.DataModel.Collections.ResolvedConceptReferenceList; import org.LexGrid.LexBIG.DataModel.Collections.SortOptionList; import org.LexGrid.LexBIG.DataModel.Core.CodingSchemeVersionOrTag; import org.LexGrid.LexBIG.DataModel.Core.ResolvedConceptReference; @@ -31,6 +33,7 @@ import org.LexGrid.LexBIG.LexBIGService.CodedNodeSet; import org.LexGrid.LexBIG.LexBIGService.LexBIGService; import org.LexGrid.LexBIG.Utility.Constructors; +import org.LexGrid.LexBIG.Utility.ConvenienceMethods; import org.LexGrid.LexBIG.Utility.Iterators.ResolvedConceptReferencesIterator; import org.LexGrid.LexBIG.Utility.LBConstants.MatchAlgorithms; //import org.LexGrid.LexBIG.caCore.interfaces.LexEVSService; @@ -345,14 +348,16 @@ public CodedNodeSet search(LexBIGService service_) try { CodingSchemeVersionOrTag cvt = new CodingSchemeVersionOrTag(); cvt.setTag("PRODUCTION"); - cns = service_.getNodeSet("NCI Metathesaurus", cvt, null); - cns = cns.restrictToMatchingProperties( + cns = service_.getNodeSet("NCI Metathesaurus", cvt, null); + ConceptReferenceList crefs = ConvenienceMethods.createConceptReferenceList(new String[]{_rec._preferredName},"NCI Metathesaurus"); + cns.restrictToCodes(crefs); + /*cns = cns.restrictToMatchingProperties( Constructors.createLocalNameList("conceptCode"), null, _rec._preferredName, MatchAlgorithms.exactMatch.name(), null - ); + );*/ } catch (Exception e) { e.printStackTrace(); //System.out.println("in search :" + e.getMessage()); @@ -522,13 +527,15 @@ public CodedNodeSet search(LexBIGService service_) CodingSchemeVersionOrTag cvt = new CodingSchemeVersionOrTag(); cvt.setTag("PRODUCTION"); cns = service_.getNodeSet(_rec._origin, cvt, null); - cns = cns.restrictToMatchingProperties( + ConceptReferenceList crefs = ConvenienceMethods.createConceptReferenceList(new String[]{_rec._preferredName},_vocab._vocab); + cns.restrictToCodes(crefs); + /*cns = cns.restrictToMatchingProperties( Constructors.createLocalNameList("conceptCode"), null, _rec._preferredName, MatchAlgorithms.exactMatch.name(), null - ); + );*/ } catch (Exception e) { e.printStackTrace(); } @@ -681,15 +688,12 @@ private Vector validate() EVSVocab[] vocabs = parseProperties(_db.selectEVSVocabs()); // Get the EVS URL and establish the application service. - //String evsURL = _db.selectEvsUrl(); - + String evsURL = _db.selectEvsUrl(); //LexEVSService service; LexBIGService service; try { - service = (LexBIGService)ApplicationServiceProvider.getApplicationService("EvsServiceInfo"); - //service = (LexEVSService) ApplicationServiceProvider - // .getApplicationServiceFromUrl(evsURL, "EvsServiceInfo"); + service = (LexBIGService) ApplicationServiceProvider.getApplicationServiceFromUrl(evsURL, "EvsServiceInfo"); } catch (Exception ex) @@ -764,7 +768,7 @@ private Vector validate() ed.reset(); ed._rec = rec; - //System.out.println(rec._preferredName + " : " + vocab._display + " : " + vocab._source + " : " + vocab._vocab); + _logger.debug(rec._preferredName + " : " + vocab._display + " : " + vocab._source + " : " + vocab._vocab); CodedNodeSet cns = ed.search(service); if (cns == null) { //didn't find corresponding EVS concept, not a valid code @@ -776,6 +780,8 @@ private Vector validate() { // Get the attributes for the concept code. ed._cons = resolveNodeSet(cns, true); + //ResolvedConceptReferenceList cnList = cns.resolveToList(null, null, null, 100); + //_logger.debug("Concepts count : "+cnList.getResolvedConceptReferenceCount()); } catch (ApplicationException ex) { diff --git a/software/src/java/gov/nih/nci/cadsr/sentinel/audits/caDSRConceptCleanupEVS.java b/software/src/java/gov/nih/nci/cadsr/sentinel/audits/caDSRConceptCleanupEVS.java index ee8d55d..0612fd0 100644 --- a/software/src/java/gov/nih/nci/cadsr/sentinel/audits/caDSRConceptCleanupEVS.java +++ b/software/src/java/gov/nih/nci/cadsr/sentinel/audits/caDSRConceptCleanupEVS.java @@ -42,6 +42,7 @@ import org.LexGrid.LexBIG.LexBIGService.CodedNodeSet; import org.LexGrid.LexBIG.LexBIGService.LexBIGService; import org.LexGrid.LexBIG.Utility.Constructors; +import org.LexGrid.LexBIG.Utility.ConvenienceMethods; import org.LexGrid.LexBIG.Utility.Iterators.ResolvedConceptReferencesIterator; import org.LexGrid.LexBIG.Utility.LBConstants.MatchAlgorithms; import org.LexGrid.LexBIG.caCore.interfaces.LexEVSService; @@ -358,13 +359,15 @@ public CodedNodeSet search(LexBIGService service_) CodingSchemeVersionOrTag cvt = new CodingSchemeVersionOrTag(); cvt.setTag("PRODUCTION"); cns = service_.getNodeSet("NCI Metathesaurus", cvt, null); - cns = cns.restrictToMatchingProperties( + /*cns = cns.restrictToMatchingProperties( Constructors.createLocalNameList("conceptCode"), null, _rec._preferredName, MatchAlgorithms.exactMatch.name(), null - ); + );*/ + ConceptReferenceList crefs = ConvenienceMethods.createConceptReferenceList(new String[]{_rec._preferredName},"NCI Metathesaurus"); + cns.restrictToCodes(crefs); } catch (Exception e) { e.printStackTrace(); } @@ -496,13 +499,15 @@ public CodedNodeSet search(LexBIGService service_) CodingSchemeVersionOrTag cvt = new CodingSchemeVersionOrTag(); cvt.setTag("PRODUCTION"); cns = service_.getNodeSet(_rec._origin, cvt, null); - cns = cns.restrictToMatchingProperties( + /*cns = cns.restrictToMatchingProperties( Constructors.createLocalNameList("conceptCode"), null, _rec._preferredName, MatchAlgorithms.exactMatch.name(), null - ); + );*/ + ConceptReferenceList crefs = ConvenienceMethods.createConceptReferenceList(new String[]{_rec._preferredName},_vocab._vocab); + cns.restrictToCodes(crefs); } catch (Exception e) { e.printStackTrace(); } @@ -595,7 +600,8 @@ private Vector validate() //System.out.println("No of Concepts (validate): " + concepts.size()); // Get the EVS URL and establish the application service. - //String evsURL = _db.selectEvsUrl(); + String evsURL = _db.selectEvsUrl(); + _logger.debug("caDSRConceptCleanupEVS API URL " + evsURL); int numConceptsUpdate = meta.getMaxNumMsgs(_maxMsgs, concepts.size()); //check property //System.out.println("Maximum limit on concepts to update through metadata clenup: " + numConceptsUpdate); @@ -604,8 +610,7 @@ private Vector validate() LexBIGService service; try { - service = (LexBIGService)ApplicationServiceProvider.getApplicationService("EvsServiceInfo"); - //service = (LexEVSService) ApplicationServiceProvider.getApplicationServiceFromUrl(evsURL, "EvsServiceInfo"); + service = (LexBIGService) ApplicationServiceProvider.getApplicationServiceFromUrl(evsURL, "EvsServiceInfo"); } catch (Exception ex) @@ -715,6 +720,7 @@ else if (ex.toString().indexOf("Invalid conceptID") > -1) // Failed to retrieve EVS concept if (ed._cons.size() == 0) { + _logger.debug("Failed to retrieve concept"); break; } diff --git a/software/src/java/gov/nih/nci/cadsr/sentinel/daily/CleanStrings.java b/software/src/java/gov/nih/nci/cadsr/sentinel/daily/CleanStrings.java index e6f9907..01bc50f 100644 --- a/software/src/java/gov/nih/nci/cadsr/sentinel/daily/CleanStrings.java +++ b/software/src/java/gov/nih/nci/cadsr/sentinel/daily/CleanStrings.java @@ -142,6 +142,7 @@ public void apply(String[] list_, String prop_) throws Exception String sql = _sqlUpdate.replace("$table$", list_[0]); sql = sql.replace("$sets$", sets.substring(comma.length())); sql = sql.replace("$wheres$", wheres.substring(or.length())); + _logger.info("do update sql : "+sql); _logger.debug(sql); // Execute the UPDATE @@ -183,6 +184,7 @@ public void apply(String[] list_, String prop_) throws Exception unions += union + sql.replace("$col$", list_[cnt]); } sql = unions.substring(union.length()); + _logger.info(" --- do select sql:" + sql); _logger.debug(sql); // Execute the SELECT @@ -282,6 +284,7 @@ public void doClean(String propFile) throws Exception { // For every table/column set do the cleanup. String tabCol = _propList.getProperty(prop); + _logger.info("Processing [" + prop + "] [" + tabCol + "]"); _logger.debug("Processing [" + prop + "] [" + tabCol + "]"); String[] parts = tabCol.split(" "); if (parts.length < 2) diff --git a/software/src/java/gov/nih/nci/cadsr/sentinel/database/CaDsrUserCredentials.java b/software/src/java/gov/nih/nci/cadsr/sentinel/database/CaDsrUserCredentials.java index da01acc..a0bfb00 100644 --- a/software/src/java/gov/nih/nci/cadsr/sentinel/database/CaDsrUserCredentials.java +++ b/software/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";//"java:/jdbc/caDSR"; private static final String CHECKOPTIONS = "select COUNT(*) from sbrext.tool_options_view_ext " + "where tool_name = 'caDSR' and property in ('LOCKOUT.TIMER', 'LOCKOUT.THRESHOLD')"; @@ -174,12 +174,13 @@ public CaDsrUserCredentials() public void validateCredentials(String applUser_, String applPswd_, String localUser_, String localPswd_) throws Exception { initialize(applUser_, applPswd_); - + _logger.debug("Inside validate Credentials - applUser_: "+applUser_+" :: localUser_: "+localUser_); String msg; if (isLocked(localUser_)) { msg = "User is locked " + localUser_; _logger.info(msg); + System.out.println("msg: "+msg); throw new Exception(msg); } else if (!isValidCredentials(localUser_, localPswd_)) @@ -338,6 +339,8 @@ private void doSQL(DBAction obj_) } catch (SQLException ex) { + _logger.debug("SQLException user: " + obj_.getConnectionUser() + " Pswd: " + obj_.getConnectionPswd()); + _logger.info("SQLException user: " + obj_.getConnectionUser() + " Pswd: " + obj_.getConnectionPswd()); exceptionMessage(obj_, ex, null); } catch (NamingException ex) @@ -346,6 +349,8 @@ private void doSQL(DBAction obj_) } catch (Exception ex) { + _logger.debug("Exception user: " + obj_.getConnectionUser() + " Pswd: " + obj_.getConnectionPswd()); + _logger.info("Exception user: " + obj_.getConnectionUser() + " Pswd: " + obj_.getConnectionPswd()); exceptionMessage(obj_, ex, null); } finally diff --git a/software/src/java/gov/nih/nci/cadsr/sentinel/database/DBAlertOracle.java b/software/src/java/gov/nih/nci/cadsr/sentinel/database/DBAlertOracle.java index 6ab5ac1..bb23cbe 100644 --- a/software/src/java/gov/nih/nci/cadsr/sentinel/database/DBAlertOracle.java +++ b/software/src/java/gov/nih/nci/cadsr/sentinel/database/DBAlertOracle.java @@ -230,6 +230,10 @@ public class DBAlertOracle implements DBAlert {">=", "<", "<", ">"}, {">=", "<", ">=", "<"} }; + + private static final String _TOOLNAME = "SENTINEL"; + + private static final String _EVSACCESSURL = "LexEVSAPI-URL"; private static final String _CONTEXT = "CONTEXT"; @@ -5190,7 +5194,7 @@ public AlertRec[] selectAlerts(Timestamp target_) * The vector. * @return The string array. */ - private String[] paste(Vector list_) + private String[] pasteString(Vector list_) { String temp[] = new String[list_.size()]; for (int ndx = 0; ndx < temp.length; ++ndx) @@ -5204,7 +5208,7 @@ private String[] paste(Vector list_) * @param list_ The vector. * @return The Timestamp array. */ - private Timestamp[] paste(Vector list_) + private Timestamp[] pasteTimestamp(Vector list_) { Timestamp temp[] = new Timestamp[list_.size()]; for (int ndx = 0; ndx < temp.length; ++ndx) @@ -5265,12 +5269,12 @@ 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 +5313,12 @@ 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); } @@ -8289,7 +8293,7 @@ public String[] selectStatReportEmails() */ public String selectEvsUrl() { - String select = "select value from sbrext.tool_options_view_ext where tool_name = 'EVS' and property = 'URL'"; + String select = "select value from sbrext.tool_options_view_ext where tool_name = '"+_TOOLNAME+"' and property = '"+_EVSACCESSURL+"'"; String[] list = getBasicData0(select); diff --git a/software/src/java/gov/nih/nci/cadsr/sentinel/tags/FootTag.java b/software/src/java/gov/nih/nci/cadsr/sentinel/tags/FootTag.java index 879fc11..aa6e2e0 100644 --- a/software/src/java/gov/nih/nci/cadsr/sentinel/tags/FootTag.java +++ b/software/src/java/gov/nih/nci/cadsr/sentinel/tags/FootTag.java @@ -18,6 +18,8 @@ import gov.nih.nci.cadsr.sentinel.ui.AlertPlugIn; import java.io.IOException; +import java.io.InputStream; +import java.util.Properties; import javax.servlet.ServletContext; import javax.servlet.http.HttpServletRequest; @@ -68,13 +70,18 @@ public int doEndTag() if (msgnum == 0){ privacyUrl = db.selectPrivacyNoticeUrl(); }else { - privacyUrl = "http://www.nih.gov/about/privacy.htm"; + privacyUrl = "https://www.nih.gov/about/privacy.htm"; } db.close(); api.setPrivacyUrl(privacyUrl); } - String jboss = Version.getInstance().getMajor() + "." + Version.getInstance().getMinor() + "." + Version.getInstance().getRevision(); + String jboss = "8.2.0"; + /*Properties p = new Properties(); + InputStream in = InputStream.class.getResourceAsStream("/org/jboss/version.properties"); + p.load(in); + jboss = p.getProperty("version.major");*/ + //Version.getInstance().getMajor() + "." + Version.getInstance().getMinor() + "." + Version.getInstance().getRevision(); MessageResources msgs = (MessageResources) pageContext .findAttribute(Globals.MESSAGES_KEY); JspWriter out = pageContext.getOut(); @@ -85,11 +92,11 @@ public int doEndTag() + " (" + jboss + "/" + System.getProperty("java.version") + ")" + "\n" + "\n\n" - + "\"Email\n" - + "\"National\n" - + "\"Department\n" - + "\"National\n" - + "\"USA.gov\"\n" + + "\"Email\n" + + "\"National\n" + + "\"Department\n" + + "\"National\n" + + "\"USA.gov\"\n" + "Privacy Notice\n" + "\n\n\n"); } diff --git a/software/src/java/gov/nih/nci/cadsr/sentinel/tags/HeadTag.java b/software/src/java/gov/nih/nci/cadsr/sentinel/tags/HeadTag.java index d08ca0c..854ab62 100644 --- a/software/src/java/gov/nih/nci/cadsr/sentinel/tags/HeadTag.java +++ b/software/src/java/gov/nih/nci/cadsr/sentinel/tags/HeadTag.java @@ -58,16 +58,17 @@ public int doEndTag() JspWriter out = pageContext.getOut(); out.print( - "\n" - + "\n" - + "\n" - + "\n" + "
\n" - + "\"Brand\n" - + "\"Tagline
\n" + + "\n" + + "" + + "\n" + + "\n" + + "
\n" + + "\"Brand\"SentinelU.S. National Institutes of Health
\n" + "
\n" + "\n" - + "\n" - + "\n" + + "\n" + + "\n" + "
\"Sentinel

" + msgs.getMessage(_key) + "

\"caDSR

" + msgs.getMessage(_key) + "

\n" ); diff --git a/software/src/java/gov/nih/nci/cadsr/sentinel/tool/AutoProcessAlerts.java b/software/src/java/gov/nih/nci/cadsr/sentinel/tool/AutoProcessAlerts.java index a6df337..0463d2a 100644 --- a/software/src/java/gov/nih/nci/cadsr/sentinel/tool/AutoProcessAlerts.java +++ b/software/src/java/gov/nih/nci/cadsr/sentinel/tool/AutoProcessAlerts.java @@ -17,7 +17,6 @@ import gov.nih.nci.cadsr.sentinel.audits.AuditReport; import gov.nih.nci.cadsr.sentinel.database.DBAlert; import gov.nih.nci.cadsr.sentinel.database.DBAlertUtil; -import gov.nih.nci.cadsr.sentinel.ui.AlertPlugIn; import java.io.BufferedReader; import java.io.FileInputStream; @@ -838,10 +837,11 @@ public void run() * @param end_ * The end of the date range. */ - public void manualRun(AlertPlugIn api_, AlertRec rec_, Timestamp start_, Timestamp end_) + public void manualRun(DataSource dsManual_, String userNameManual_, AlertRec rec_, Timestamp start_, Timestamp end_) { AlertThread at = new AlertThread(rec_); - _api = api_; + _dsManual = dsManual_; + _userNameManual = userNameManual_; _start = start_; _end = end_; _id = "Manual " + rec_.getCreator(); @@ -1785,16 +1785,21 @@ private Timestamp setToMidnight(Timestamp time_) * @return The list of alerts. */ private AlertRec[] getAlertList() - { + { AlertRec recs[] = null; + try { // Get the eligible Alerts. recs = _db.selectAlerts(_today); - + } catch (Exception ex) { + _logger.error("In AlertList Exception: "+_db+" today: "+_today); + ex.printStackTrace(); + } // Did we get anything? if (recs != null && (recs.length == 0 || recs[0] == null)) recs = null; return recs; + } /** @@ -1857,11 +1862,11 @@ private int getResources() { _db = DBAlertUtil.factory(); int rc = -1; - if (_api != null) + if ((_dsManual != null) && (_userNameManual != null)) { - DataSource ds = _api.getDataSource(); + DataSource ds = _dsManual; _dsurl = ds.getClass().getName() + " " + ds.toString(); - rc = _db.open(ds, _api.getUser()); + rc = _db.open(ds, _userNameManual); } else if (_dsurl != null) rc = _db.open(_dsurl, _user, _pswd); @@ -2443,7 +2448,8 @@ private void writeUrlMsgs() private int _urlRunCalls; - private AlertPlugIn _api; + private DataSource _dsManual; + private String _userNameManual; private String[] _audits; diff --git a/software/src/java/gov/nih/nci/cadsr/sentinel/ui/Run.java b/software/src/java/gov/nih/nci/cadsr/sentinel/ui/Run.java index e231a32..b957939 100644 --- a/software/src/java/gov/nih/nci/cadsr/sentinel/ui/Run.java +++ b/software/src/java/gov/nih/nci/cadsr/sentinel/ui/Run.java @@ -94,7 +94,7 @@ else if (form.getNextScreen().equals(Constants._ACTRUN)) // Run the alert and report. AlertPlugIn var = (AlertPlugIn) request_.getSession().getServletContext().getAttribute(DBAlert._DATASOURCE); - pa.manualRun(var, rec, start, end); + pa.manualRun(var.getDataSource(), var.getUser(), rec, start, end); // Tell the user we have submitted the Alert. request_.setAttribute(Constants._ACTRUN, ub.getWorking().getName()); diff --git a/software/src/resources/conf/template.CleanStrings.xml b/software/src/resources/conf/template.CleanStrings.xml index ede064c..a5d55b7 100644 --- a/software/src/resources/conf/template.CleanStrings.xml +++ b/software/src/resources/conf/template.CleanStrings.xml @@ -22,15 +22,15 @@ L--> update - sbr.admin_components_view long_name preferred_definition + sbr.class_scheme_items_view csi_name description comments sbr.classification_schemes_view long_name preferred_definition change_note sbr.contexts_view description - sbr.data_elements_view long_name preferred_definition change_note question + sbr.data_element_concepts_view long_name preferred_definition change_note sbr.definitions_view definition sbr.designations_view name - sbr.value_domains_view long_name preferred_definition change_note + sbr.value_meanings_view long_name description comments preferred_definition change_note definition_source sbrext.object_classes_view_ext long_name preferred_definition change_note sbrext.properties_view_ext long_name preferred_definition change_note diff --git a/software/src/resources/conf/template.cadsrsentinel.xml b/software/src/resources/conf/template.cadsrsentinel.xml index a34217d..fb65ff4 100644 --- a/software/src/resources/conf/template.cadsrsentinel.xml +++ b/software/src/resources/conf/template.cadsrsentinel.xml @@ -46,8 +46,8 @@ L--> caDSR / EVS Concept inconsistencies gov.nih.nci.cadsr.sentinel.audits.AuditConceptToEVS - NCI Thesaurus Concept cleanup - gov.nih.nci.cadsr.sentinel.audits.caDSRConceptCleanupEVS + + + + + + + + + + @CADSR.DS.FULLURL@ + @CADSR.DS.USER@ + @CADSR.DS.PSWD@ + + Table Row Counts + gov.nih.nci.cadsr.sentinel.audits.AuditSummary + + Object Classes not owned by NCIP + gov.nih.nci.cadsr.sentinel.audits.AuditUsedObjectClasses + + Unused Object Classes + gov.nih.nci.cadsr.sentinel.audits.AuditUnusedObjectClasses + + Unused Properties + gov.nih.nci.cadsr.sentinel.audits.AuditUnusedProperties + + Unused Concepts + gov.nih.nci.cadsr.sentinel.audits.AuditUnusedConcepts + + Unused Data Element Concepts + gov.nih.nci.cadsr.sentinel.audits.AuditUnusedDEC + + Data Elements missing Question Text + gov.nih.nci.cadsr.sentinel.audits.AuditMissingQuestionText + + Administered Components missing a Public ID + gov.nih.nci.cadsr.sentinel.audits.AuditMissingPublicID + + caDSR / EVS Concept inconsistencies + gov.nih.nci.cadsr.sentinel.audits.AuditConceptToEVS + + NCI Thesaurus Concept cleanup + gov.nih.nci.cadsr.sentinel.audits.caDSRConceptCleanupEVS + + + + diff --git a/software/src/resources/conf/template.web.xml b/software/src/resources/conf/template.web.xml index a46dc2f..15d61d4 100644 --- a/software/src/resources/conf/template.web.xml +++ b/software/src/resources/conf/template.web.xml @@ -27,11 +27,11 @@ L--> jbossDataSource - jdbc/sentinel + jboss/datasources/SentinelDS jbossAuthenticate - jdbc/caDSR + jboss/datasources/caDSRDS DSusername diff --git a/software/src/resources/db-sql/insert_evs_url.sql b/software/src/resources/db-sql/insert_evs_url.sql new file mode 100644 index 0000000..c366aa2 --- /dev/null +++ b/software/src/resources/db-sql/insert_evs_url.sql @@ -0,0 +1,9 @@ +/* +Run the below statement for a new environment/DB only. +*/ +INSERT INTO "SBREXT"."TOOL_OPTIONS_EXT" (TOOL_NAME, PROPERTY, VALUE, DATE_CREATED, CREATED_BY, DESCRIPTION, LOCALE) VALUES ('SENTINEL', 'LexEVSAPI-URL', 'https://lexevsapi65.nci.nih.gov/lexevsapi65', sysdate, 'SBREXT', 'The URL for EVS API access used in Sentinel.', 'US') +/ +select tool_name, property, VALUE from sbrext.tool_options_view_ext where Tool_name = 'SENTINEL' and Property = 'LexEVSAPI-URL' +/ +commit +/ diff --git a/software/src/resources/scripts/autorun.sh b/software/src/resources/scripts/autorun.sh index 8061dab..3900c9d 100644 --- a/software/src/resources/scripts/autorun.sh +++ b/software/src/resources/scripts/autorun.sh @@ -5,18 +5,19 @@ echo "\$Header: /share/content/gforge/sentinel/sentinel/scripts/autorun.sh,v 1.1 echo "\$Name: not supported by cvs2svn $" DATE=`date +%Y%m%d` -JAVA_HOME=/usr/jdk1.6.0_45 +JAVA_HOME=/usr/java8 BASE_DIR=/local/content/cadsrsentinel/bin - + export JAVA_HOME BASE_DIR - -ORACLE_HOME=/app/oracle/product/dbhome/9.2.0 -PATH=$ORACLE_HOME/bin:$PATH -LD_LIBRARY_PATH=$ORACLE_HOME/lib:$LD_LIBRARY_PATH -TNS_ADMIN=$ORACLE_HOME/network/admin -JAVA_PARMS='-Xms512m -Xmx512m -XX:PermSize=64m' - -export JAVA_PARMS ORACLE_HOME TNS_ADMIN PATH LD_LIBRARY_PATH + +#ORACLE_HOME=/app/oracle/product/dbhome/9.2.0 +#PATH=$ORACLE_HOME/bin:$PATH +#LD_LIBRARY_PATH=$ORACLE_HOME/lib:$LD_LIBRARY_PATH +#TNS_ADMIN=$ORACLE_HOME/network/admin +JAVA_PARMS='-Xms1024m -Xmx2048m -XX:MaxMetaspaceSize=512m' + +#export JAVA_PARMS ORACLE_HOME TNS_ADMIN PATH LD_LIBRARY_PATH +export JAVA_PARMS echo "Executing new job as `id`" echo "Executing on `date`" @@ -32,6 +33,10 @@ done export CP +echo $JAVA_HOME/bin/java -client $JAVA_PARMS -classpath $BASE_DIR:$CP gov.nih.nci.cadsr.sentinel.tool.AutoProcessAlerts $BASE_DIR/log4j.xml true $BASE_DIR/cadsrsentinel.xml + +$JAVA_HOME/bin/java -client $JAVA_PARMS -classpath $BASE_DIR:$CP gov.nih.nci.cadsr.sentinel.tool.AutoProcessAlerts $BASE_DIR/log4j.xml true $BASE_DIR/cadsrsentinel.xml + echo $JAVA_HOME/bin/java -client $JAVA_PARMS -classpath $BASE_DIR:$CP gov.nih.nci.cadsr.sentinel.daily.SimpleSQL $BASE_DIR/log4j.xml $BASE_DIR/SimpleSQL.xml $JAVA_HOME/bin/java -client $JAVA_PARMS -classpath $BASE_DIR:$CP gov.nih.nci.cadsr.sentinel.daily.SimpleSQL $BASE_DIR/log4j.xml $BASE_DIR/SimpleSQL.xml @@ -42,11 +47,4 @@ $JAVA_HOME/bin/java -client $JAVA_PARMS -classpath $BASE_DIR:$CP gov.nih.nci.cad echo $JAVA_HOME/bin/java -client $JAVA_PARMS -classpath $BASE_DIR:$CP gov.nih.nci.cadsr.sentinel.daily.CleanOCR $BASE_DIR/log4j.xml $BASE_DIR/CleanOCR.xml -$JAVA_HOME/bin/java -client $JAVA_PARMS -classpath $BASE_DIR:$CP gov.nih.nci.cadsr.sentinel.daily.CleanOCR $BASE_DIR/log4j.xml $BASE_DIR/CleanOCR.xml - -echo $JAVA_HOME/bin/java -client $JAVA_PARMS -classpath $BASE_DIR:$CP gov.nih.nci.cadsr.sentinel.tool.AutoProcessAlerts $BASE_DIR/log4j.xml true $BASE_DIR/cadsrsentinel.xml - -$JAVA_HOME/bin/java -client $JAVA_PARMS -classpath $BASE_DIR:$CP gov.nih.nci.cadsr.sentinel.tool.AutoProcessAlerts $BASE_DIR/log4j.xml true $BASE_DIR/cadsrsentinel.xml - - - +$JAVA_HOME/bin/java -client $JAVA_PARMS -classpath $BASE_DIR:$CP gov.nih.nci.cadsr.sentinel.daily.CleanOCR $BASE_DIR/log4j.xml $BASE_DIR/CleanOCR.xml \ No newline at end of file diff --git a/software/src/resources/scripts/metadatacleanupscript.sh b/software/src/resources/scripts/metadatacleanupscript.sh new file mode 100644 index 0000000..08d95e2 --- /dev/null +++ b/software/src/resources/scripts/metadatacleanupscript.sh @@ -0,0 +1,38 @@ +#!/bin/bash + +echo "Executing Auto Run for Sentinel Tool" +echo "\$Header: /share/content/gforge/sentinel/sentinel/scripts/autorun.sh,v 1.10 2009-07-24 15:36:50 davet Exp $" +echo "\$Name: not supported by cvs2svn $" + +DATE=`date +%Y%m%d` +JAVA_HOME=/usr/java8 +BASE_DIR=/local/content/cadsrsentinel/bin + +export JAVA_HOME BASE_DIR + +#ORACLE_HOME=/app/oracle/product/dbhome/9.2.0 +#PATH=$ORACLE_HOME/bin:$PATH +#LD_LIBRARY_PATH=$ORACLE_HOME/lib:$LD_LIBRARY_PATH +#TNS_ADMIN=$ORACLE_HOME/network/admin +JAVA_PARMS='-Xms512m -Xmx512m -XX:MaxMetaspaceSize=64m' + +#export JAVA_PARMS ORACLE_HOME TNS_ADMIN PATH LD_LIBRARY_PATH +export JAVA_PARMS + +echo "Executing new job as `id`" +echo "Executing on `date`" + +find $BASE_DIR/../reports -mtime +20 -exec rm {} \; + +for x in $BASE_DIR/*.jar +do + +CP=$CP:$x + +done + +export CP + +echo $JAVA_HOME/bin/java -client $JAVA_PARMS -classpath $BASE_DIR:$CP gov.nih.nci.cadsr.sentinel.tool.AutoProcessAlerts $BASE_DIR/log4j.xml true $BASE_DIR/metadatacleanup.xml + +$JAVA_HOME/bin/java -client $JAVA_PARMS -classpath $BASE_DIR:$CP gov.nih.nci.cadsr.sentinel.tool.AutoProcessAlerts $BASE_DIR/log4j.xml true $BASE_DIR/metadatacleanup.xml \ No newline at end of file diff --git a/software/src/resources/sdkapi/application-config-client.xml b/software/src/resources/sdkapi/application-config-client.xml index 2c3b8dd..8efbcd5 100644 --- a/software/src/resources/sdkapi/application-config-client.xml +++ b/software/src/resources/sdkapi/application-config-client.xml @@ -1,12 +1,4 @@ - - - @@ -14,7 +6,7 @@ L--> - + @@ -24,13 +16,9 @@ L--> - - - - @@ -46,7 +34,7 @@ L--> - + @@ -58,7 +46,7 @@ L--> - + @@ -78,17 +66,11 @@ L--> <bean id="DistributedProxyHelper" class="org.LexGrid.LexBIG.caCore.client.proxy.LexEVSProxyHelperImpl" singleton="false"> </bean> - - <bean id="DataServiceProxyHelper" class="org.LexGrid.LexBIG.caCore.client.proxy.DataServiceProxyHelperImpl" singleton="false"> - </bean> <bean id="interceptor" class="org.LexGrid.LexBIG.caCore.client.proxy.LexEVSApplicationServiceProxy"> <property name="proxyFactory"> <ref bean="DistributedProxyHelper"/> </property> - <property name="dataServiceProxyHelper"> - <ref bean="DataServiceProxyHelper"/> - </property> </bean> <bean id="applicationService" class="org.springframework.aop.framework.ProxyFactoryBean"> <property name="target"> diff --git a/software/src/resources/sdkapi/log4j.properties b/software/src/resources/sdkapi/log4j.properties deleted file mode 100644 index 7e23856..0000000 --- a/software/src/resources/sdkapi/log4j.properties +++ /dev/null @@ -1,53 +0,0 @@ -#L -# Copyright ScenPro Inc, SAIC-F -# -# Distributed under the OSI-approved BSD 3-Clause License. -# See http://ncip.github.com/cadsr-sentinal/LICENSE.txt for details. -#L - -log4j.rootLogger=ERROR,stdout - - -### direct messages to file hibernate.log ### - -log4j.appender.clientLog=org.apache.log4j.FileAppender -log4j.appender.clientLog.File=./log/client.log -log4j.appender.clientLog.layout=org.apache.log4j.PatternLayout -log4j.appender.clientLog.layout.ConversionPattern=%d{ABSOLUTE} %5p %c{1}:%L - %m%n - - -log4j.appender.stdout=org.apache.log4j.ConsoleAppender -log4j.appender.stdout.layout=org.apache.log4j.PatternLayout -log4j.appender.stdout.layout.ConversionPattern=%d{ABSOLUTE} %5p %c{1}:%L - %m%n - - - -### set log levels - for more verbose logging change 'info' to 'debug' ### - -#log4j.rootLogger=warn, stdout -#log4j.rootLogger=warn, file -#log4j.logger.org.hibernate=info - -### log just the SQL -#log4j.logger.org.hibernate.SQL=debug - -### log JDBC bind parameters ### -#log4j.logger.org.hibernate.type=info - -### log schema export/update ### -#log4j.logger.org.hibernate.tool.hbm2ddl=debug - -### log cache activity ### -#log4j.logger.org.hibernate.cache=debug - -### log JDBC resource acquisition -#log4j.logger.org.hibernate.jdbc=debug - -### enable the following line if you want to track down connection ### -### leakages when using DriverManagerConnectionProvider ### -#log4j.logger.org.hibernate.connection.DriverManagerConnectionProvider=trace - -log4j.logger.gov.nih.nci=error -log4j.logger.org.springframework=error - - diff --git a/software/src/web/WebRoot/.gitignore b/software/src/web/WebRoot/.gitignore new file mode 100644 index 0000000..08922f1 --- /dev/null +++ b/software/src/web/WebRoot/.gitignore @@ -0,0 +1 @@ +/WEB-INF/ diff --git a/software/src/web/WebRoot/WEB-INF/web.xml b/software/src/web/WebRoot/WEB-INF/web.xml new file mode 100644 index 0000000..1221418 --- /dev/null +++ b/software/src/web/WebRoot/WEB-INF/web.xml @@ -0,0 +1,97 @@ + + + + + + + + Empty web.xml file for Web Application + + process + org.apache.struts.action.ActionServlet + + config + /WEB-INF/struts-config.xml + + + debug + 0 + + + jbossDataSource + jboss/datasources/SentinelDS + + + jbossAuthenticate + jboss/datasources/caDSRDS + + + DSusername + SENTINEL + + + DSpassword + sentinel0412 + + 1 + + + process + /do/* + + + 35 + + + html + text/html + + + txt + text/plain + + + + jsp/index.jsp + + + + /tags/struts-bean + /WEB-INF/tld/struts-bean.tld + + + + /tags/struts-html + /WEB-INF/tld/struts-html.tld + + + + /tags/struts-logic + /WEB-INF/tld/struts-logic.tld + + + + /tags/struts-nested + /WEB-INF/tld/struts-nested.tld + + + /tags/dsralert + /WEB-INF/tld/dsralert.tld + + + /WEB-INF/struts-html.tld + /WEB-INF/tld/struts-html.tld + + + /WEB-INF/struts-bean.tld + /WEB-INF/tld/struts-bean.tld + + diff --git a/software/src/web/WebRoot/images/CBIIT-36px-Logo-COLOR_contrast.png b/software/src/web/WebRoot/images/CBIIT-36px-Logo-COLOR_contrast.png new file mode 100644 index 0000000..ad81076 Binary files /dev/null and b/software/src/web/WebRoot/images/CBIIT-36px-Logo-COLOR_contrast.png differ diff --git a/software/src/web/WebRoot/images/caDSR_logo2_contrast.png b/software/src/web/WebRoot/images/caDSR_logo2_contrast.png new file mode 100644 index 0000000..a3e8026 Binary files /dev/null and b/software/src/web/WebRoot/images/caDSR_logo2_contrast.png differ diff --git a/software/src/web/WebRoot/images/sentinel_banner_2.gif b/software/src/web/WebRoot/images/sentinel_banner_2.gif new file mode 100644 index 0000000..d31a222 Binary files /dev/null and b/software/src/web/WebRoot/images/sentinel_banner_2.gif differ diff --git a/software/src/web/WebRoot/images/tagline_nologo_nih.gif b/software/src/web/WebRoot/images/tagline_nologo_nih.gif new file mode 100644 index 0000000..388954f Binary files /dev/null and b/software/src/web/WebRoot/images/tagline_nologo_nih.gif differ diff --git a/software/src/web/WebRoot/jsp/logon.jsp b/software/src/web/WebRoot/jsp/logon.jsp index 2ef2bf0..af4ac58 100644 --- a/software/src/web/WebRoot/jsp/logon.jsp +++ b/software/src/web/WebRoot/jsp/logon.jsp @@ -19,14 +19,7 @@ L--%> - <bean:message key="logon.title" /> - -
- - Skip Navigation - -
- + <bean:message key="logon.title" /> @@ -37,6 +30,12 @@ L--%> +
+ + Skip Navigation + +
+ - -
- - > +
diff --git a/software/template.build.properties b/software/template.build.properties index 28fb1d9..6c45f47 100644 --- a/software/template.build.properties +++ b/software/template.build.properties @@ -11,11 +11,11 @@ # $Name: not supported by cvs2svn $ database.server=server -database.port=1551 -database.name=sid -database.schema=SBREXT -database.user=sentinel -database.password=sentinel0412 +database.port=@@-DB-PORT-@@ +database.name=@@-DB-NAME-@@ +database.schema=@@-DB-SCHEMA-@@ +database.user=@@-DB-USER-@@ +database.password=@@-DB-CREDENTIALS-@@ database.url=jdbc:oracle:thin:${database.user}/${database.password}@${database.server}:${database.port}:${database.name} JDEBUG=on