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Generate list of pub models with sim results 4
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‎README_orphan.md

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@@ -122,12 +122,17 @@ NOTE: enter following after 'java' for debug (-agentlib:jdwp=transport=dt_socket
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4b. Run to save vcml of published modesl with sims that have no data or exceptions removed from vcml
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java -cp ./dbbackupclean/ojdbc6-11.2.0.4.jar:./dbbackupclean/ucp-11.2.0.4.jar:./dbbackupclean/vcell-oracle-0.0.1-SNAPSHOT.jar:./cbit_vcell_tools_IonItems.jar:./maven- jars/jhdf5_2.10-2.9.jar
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-Djava.library.path="./natlibs" cbit.vcell.tools.IonItems "jdbc:oracle:thin:@vcell-db.cam.uchc.edu:1521:vcelldborcl" "/share/apps/vcell3/users" publishedmodelvcml /tmp/ionvcml 0 0
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-Djava.library.path="./natlibs" cbit.vcell.tools.IonItems "jdbc:oracle:thin:@vcell-db.cam.uchc.edu:1521:vcelldborcl" "/share/apps/vcell3/users" publishedmodelvcml /share/apps/vcell3/users/ionvcml 0 0
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4c. Run to read vcml saved from 4b and compare to vcml from db and print the sims that had to be removed
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java -cp ./dbbackupclean/ojdbc6-11.2.0.4.jar:./dbbackupclean/ucp-11.2.0.4.jar:./dbbackupclean/vcell-oracle-0.0.1-SNAPSHOT.jar:./cbit_vcell_tools_IonItems.jar:./maven-jars/jhdf5_2.10-2.9.jar
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-Djava.library.path="./natlibs" cbit.vcell.tools.IonItems "jdbc:oracle:thin:@vcell-db.cam.uchc.edu:1521:vcelldborcl" /tmp/ionvcml publishedmodelvcmldiff
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-Djava.library.path="./natlibs" cbit.vcell.tools.IonItems "jdbc:oracle:thin:@vcell-db.cam.uchc.edu:1521:vcelldborcl" /share/apps/vcell3/users/ionvcml publishedmodelvcmldiff
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4d. Run to save vcml from TestSuit
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java -cp ./dbbackupclean/ojdbc6-11.2.0.4.jar:./dbbackupclean/ucp-11.2.0.4.jar:./dbbackupclean/vcell-oracle-0.0.1-SNAPSHOT.jar:./cbit_vcell_tools_IonItems.jar:./maven-jars/jhdf5_2.10-2.9.jar
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-Djava.library.path="./natlibs" cbit.vcell.tools.IonItems "jdbc:oracle:thin:@vcell-db.cam.uchc.edu:1521:vcelldborcl" /share/apps/vcell3/users/ionts testsuitemodelvcml
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***----------------------------------------------------------------------------------------------------------***
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‎vcell-server/src/main/java/cbit/vcell/tools/IonItems.java

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@@ -35,6 +35,7 @@
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import cbit.vcell.geometry.GeometryThumbnailImageFactoryAWT;
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import cbit.vcell.mathmodel.MathModel;
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import cbit.vcell.messaging.db.SimulationJobTable;
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import cbit.vcell.modeldb.BioModelSimContextLinkTable;
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import cbit.vcell.modeldb.BioModelSimulationLinkTable;
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import cbit.vcell.modeldb.BioModelTable;
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import cbit.vcell.modeldb.DBTopLevel;
@@ -44,6 +45,8 @@
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import cbit.vcell.modeldb.MathModelTable;
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import cbit.vcell.modeldb.PublicationModelLinkTable;
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import cbit.vcell.modeldb.ServerDocumentManager;
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import cbit.vcell.modeldb.TFTestCaseTable;
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import cbit.vcell.modeldb.TFTestSuiteTable;
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import cbit.vcell.modeldb.UserTable;
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import cbit.vcell.modeldb.VersionTable;
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import cbit.vcell.simdata.Cachetable;
@@ -64,6 +67,7 @@
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public class IonItems {
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//See vcell-node1:/opt/build/frm/cbit_vcell_tools_IonItems.info
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private static final String PUBLISHEDMODELVCML = "publishedmodelvcml";
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private static final String TESTSUITEMODELVCML = "testsuitemodelvcml";
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private static final String PUBLICMODELWITHSIMS = "publicmodelwithsims";
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private static final String PUBLISHEDMODELVCMLDIFF = "publishedmodelvcmldiff";
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@@ -119,6 +123,9 @@ public static void main(String[] args) {
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}else if(command.toLowerCase().equals(PUBLISHEDMODELVCMLDIFF)) {
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File dirWithSavedVCML = new File(args[1]);
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readVCMLWithSimsRemoved(con, dirWithSavedVCML);
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}else if (command.toLowerCase().equals(TESTSUITEMODELVCML)) {
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File dirToSaveVCML = new File(args[1]);
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saveVCMLTestSuite(dirToSaveVCML,0,0);
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}
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} catch (Exception e) {
@@ -140,10 +147,120 @@ public static void main(String[] args) {
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}
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private static void saveVCMLTestSuite(File dirToSaveVCML,long startSimKey,long endSimKey) throws Exception{
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// select distinct vc_biomodelsimcontext.biomodelref modelkey
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// from vc_tftestsuite,vc_tftestcase,vc_biomodelsimcontext
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// where vc_tftestsuite.tsversion='88_alpha_from_87_alpha'
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// and vc_tftestcase.testsuiteref=vc_tftestsuite.id
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// and vc_tftestcase.bmappref is not null
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// and vc_tftestcase.bmappref=vc_biomodelsimcontext.id
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// union
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// select distinct vc_mathmodel.id modelkey
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// from vc_tftestsuite,vc_tftestcase,vc_mathmodel
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// where vc_tftestsuite.tsversion='88_alpha_from_87_alpha'
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// and vc_tftestcase.testsuiteref=vc_tftestsuite.id
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// and vc_tftestcase.mathmodelref is not null
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// and vc_tftestcase.mathmodelref=vc_mathmodel.id;
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String modelKeyStr = "modelkey";
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String userKeyStr = "userkey";
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String useridStr = "userid";
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String modelUserKeyStr = modelKeyStr+","+UserTable.table.id.getQualifiedColName()+" "+userKeyStr+","+UserTable.table.userid.getQualifiedColName()+" "+useridStr;
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String testSuitTestCaseLink =
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TFTestSuiteTable.table.tsVersion.getQualifiedColName()+"="+"'88_alpha_from_87_alpha'"+
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" AND "+TFTestCaseTable.table.testSuiteRef.getQualifiedColName()+"="+TFTestSuiteTable.table.id.getQualifiedColName();
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String testSuitAndUserStr = TFTestSuiteTable.table.getTableName()+","+TFTestCaseTable.table.getTableName()+","+UserTable.table.getTableName();
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String bioModelTypeStr = "biomodel";
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String mathModelTypeStr = "mathmodel";
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String modelTypeKeyStr = "modeltype";
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String sql =
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"SELECT distinct "+"'"+bioModelTypeStr+"' "+modelTypeKeyStr+","+BioModelTable.table.id.getQualifiedColName()+" "+modelUserKeyStr+
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" FROM "+testSuitAndUserStr+","+BioModelSimContextLinkTable.table.getTableName()+","+BioModelTable.table.getTableName()+
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" WHERE "+testSuitTestCaseLink+" AND "+TFTestCaseTable.table.bmAppRef.getQualifiedColName()+" IS NOT NULL"+
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" AND "+TFTestCaseTable.table.bmAppRef.getQualifiedColName()+"="+BioModelSimContextLinkTable.table.id.getQualifiedColName()+
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" AND "+BioModelSimContextLinkTable.table.bioModelRef.getQualifiedColName()+"="+BioModelTable.table.id.getQualifiedColName()+
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" AND "+BioModelTable.table.ownerRef.getQualifiedColName()+"="+UserTable.table.id.getQualifiedColName()+
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" UNION "+
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"SELECT distinct "+"'"+mathModelTypeStr+"' "+modelTypeKeyStr+","+MathModelTable.table.id.getQualifiedColName()+" "+modelUserKeyStr+
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" FROM "+testSuitAndUserStr+","+MathModelTable.table.getTableName()+
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" WHERE "+testSuitTestCaseLink+" AND "+TFTestCaseTable.table.mathModelRef.getQualifiedColName()+" IS NOT NULL"+
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" AND "+TFTestCaseTable.table.mathModelRef.getQualifiedColName()+"="+MathModelTable.table.id.getQualifiedColName()+
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" AND "+MathModelTable.table.ownerRef.getQualifiedColName()+"="+UserTable.table.id.getQualifiedColName();
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Statement stmt = null;
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try {
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stmt = con.createStatement();
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//ArrayList<VCDocument> successDocs = new ArrayList<VCDocument>();
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DatabaseServerImpl databaseServerImpl = new DatabaseServerImpl(connFac,null);
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ArrayList<Object[]> modeKeyAndUser = new ArrayList<Object[]>();
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ResultSet rset = stmt.executeQuery(sql);
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while(rset.next()) {
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BigDecimal modelKeyBigDecimal = rset.getBigDecimal(modelKeyStr);
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KeyValue modelKey = new KeyValue(modelKeyBigDecimal);
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String modelType = rset.getString(modelTypeKeyStr);
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if(startSimKey == 0 || (modelKeyBigDecimal.longValue() >= startSimKey && modelKeyBigDecimal.longValue() <= endSimKey)) {
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User user = new User(rset.getString(useridStr), new KeyValue(rset.getBigDecimal(userKeyStr)));
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modeKeyAndUser.add(new Object[] {(modelType.equals(bioModelTypeStr)?VCDocumentType.BIOMODEL_DOC:VCDocumentType.MATHMODEL_DOC),modelKey,user});
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}
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}
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rset.close();
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stmt.close();
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VCDocument vcDoc = null;
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for(int ii=0;ii<modeKeyAndUser.size();ii++) {
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try {
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VCDocumentType vcDocType = (VCDocumentType)modeKeyAndUser.get(ii)[0];
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KeyValue modelKey = (KeyValue)modeKeyAndUser.get(ii)[1];
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User user = (User)modeKeyAndUser.get(ii)[2];
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//-----NOTE: (privacy, versionflag) may not match between xml and database (because privacy and versionflag can be set without saving model)
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//some models regenerated from xml will not have same privacy and versionflag matched in query from database (the database values are correct, ignore the xml values)
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BigString modelXML = (vcDocType == VCDocumentType.BIOMODEL_DOC?databaseServerImpl.getBioModelXML(user, modelKey):databaseServerImpl.getMathModelXML(user, modelKey));
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vcDoc = null;
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if(vcDocType == VCDocumentType.BIOMODEL_DOC) {
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BioModel bm = cbit.vcell.xml.XmlHelper.XMLToBioModel(new XMLSource(modelXML.toString()));
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bm.refreshDependencies();
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vcDoc = bm;
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}else {
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MathModel mm = cbit.vcell.xml.XmlHelper.XMLToMathModel(new XMLSource(modelXML.toString()));
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mm.refreshDependencies();
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vcDoc = mm;
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}
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//if(true) {
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// System.out.println(modelKey+" "+user+" "+vcDoc);
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// continue;
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//}
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String docXml = null;
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if(vcDoc.getDocumentType() == VCDocument.VCDocumentType.BIOMODEL_DOC) {
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docXml = XmlHelper.bioModelToXML(((BioModel)vcDoc));
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}else {
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docXml = XmlHelper.mathModelToXML(((MathModel)vcDoc));
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}
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PrintWriter pw = new PrintWriter(new File(dirToSaveVCML,vcDoc.getVersion().getVersionKey().toString()+".xml"));
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pw.write(docXml);
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pw.close();
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// }
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} catch (Exception e) {
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System.out.println("----------GENERALERROR "+vcDoc.getVersion().getVersionKey());
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e.printStackTrace();
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if(vcDoc != null) {
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PrintWriter pw = new PrintWriter(new File(dirToSaveVCML,vcDoc.getVersion().getVersionKey().toString()+"_exception.xml"));
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pw.write("");
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pw.close();
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}
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}
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}
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} finally{
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if(stmt != null){try{stmt.close();}catch(Exception e){e.printStackTrace();}}
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}
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}
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public static void usage() {
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System.out.println("cbit.vcell.tools.IonItems jdbc:oracle:thin:@VCELL_DB_HOST:1521:VCEL_DB_NAME vcellUsersRootDir "+PUBLICMODELWITHSIMS+" {true,false print more info}}");
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System.out.println("cbit.vcell.tools.IonItems jdbc:oracle:thin:@VCELL_DB_HOST:1521:VCEL_DB_NAME vcellUsersRootDir "+PUBLISHEDMODELVCML+" dirToSaveVCML, startSimKey endSimKey");
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System.out.println("cbit.vcell.tools.IonItems jdbc:oracle:thin:@VCELL_DB_HOST:1521:VCEL_DB_NAME dirWithSavedVCML "+PUBLISHEDMODELVCMLDIFF);
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System.out.println("cbit.vcell.tools.IonItems jdbc:oracle:thin:@VCELL_DB_HOST:1521:VCEL_DB_NAME dirToSaveVCML "+TESTSUITEMODELVCML);
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System.exit(1);
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}
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