Examples with VersionableTypeVersion org.vcell.util.document.VersionableTypeVersion used on opensource projects

Example 1 with VersionableTypeVersion

use of org.vcell.util.document.VersionableTypeVersion in project vcell by virtualcell.

the class DbDriver method findAllReferences.

/**
 * This method was created in VisualAge.
 * @return java.util.Hashtable
 */
private static void findAllReferences(java.sql.Connection con, VersionableTypeVersion vtv, VersionableFamily refs) throws DataAccessException, SQLException {
    // Get VersionableTypes(tables) which possibly have references to argument vType
    Vector<VersionRef> possibleRefs = VersionTable.getReferencingVersionableTypes(vtv.getVType());
    Enumeration<VersionRef> enum1 = possibleRefs.elements();
    UserTable userTable = UserTable.table;
    while (enum1.hasMoreElements()) {
        VersionRef vr = enum1.nextElement();
        // BEGIN check VersionableType for references to versionKey
        String sql = null;
        VersionTable table = VersionTable.getVersionTable(vr.getVType());
        if (vr.getLinkField() == null) {
            // 
            // direct link between versionable types
            // 
            sql = "SELECT " + table.id.getQualifiedColName() + "," + table.name.getQualifiedColName() + "," + table.ownerRef.getQualifiedColName() + "," + table.privacy.getQualifiedColName() + "," + table.versionBranchPointRef.getQualifiedColName() + "," + table.versionDate.getQualifiedColName() + "," + table.versionFlag.getQualifiedColName() + "," + table.versionAnnot.getQualifiedColName() + "," + table.versionBranchID.getQualifiedColName() + "," + userTable.userid.getQualifiedColName() + " FROM " + table.getTableName() + "," + userTable.getTableName() + " WHERE " + vr.getRefField().getQualifiedColName() + " = " + vtv.getVersion().getVersionKey() + " AND " + table.ownerRef.getQualifiedColName() + " = " + userTable.getTableName() + "." + userTable.id;
        } else {
            // 
            // indirect link between versionable types (Link Table ... e.g. BioModelSimulationLinkTable)
            // 
            sql = "SELECT " + table.id.getQualifiedColName() + "," + table.name.getQualifiedColName() + "," + table.ownerRef.getQualifiedColName() + "," + table.privacy.getQualifiedColName() + "," + table.versionBranchPointRef.getQualifiedColName() + "," + table.versionDate.getQualifiedColName() + "," + table.versionFlag.getQualifiedColName() + "," + table.versionAnnot.getQualifiedColName() + "," + table.versionBranchID.getQualifiedColName() + "," + userTable.userid.getQualifiedColName() + " FROM " + table.getTableName() + "," + userTable.getTableName() + "," + vr.getLinkField().getTableName() + " WHERE " + vr.getRefField().getQualifiedColName() + " = " + vtv.getVersion().getVersionKey() + " AND " + vr.getLinkField().getQualifiedColName() + " = " + table.id.getQualifiedColName() + " AND " + table.ownerRef.getQualifiedColName() + " = " + userTable.id.getQualifiedColName();
        }
        java.sql.Statement stmt = con.createStatement();
        Vector<VersionableTypeVersion> allReferencingVTV = new Vector<VersionableTypeVersion>();
        try {
            // Get KeyValues from statement and put into Vector, so we can close statement(good idea because we are recursive)
            java.sql.ResultSet rset = stmt.executeQuery(sql);
            while (rset.next()) {
                try {
                    BigDecimal groupid = rset.getBigDecimal(VersionTable.privacy_ColumnName);
                    Version version = VersionTable.getVersion(rset, getGroupAccessFromGroupID(con, groupid));
                    VersionableTypeVersion referencingVTV = new VersionableTypeVersion(vr.getVType(), version);
                    allReferencingVTV.addElement(referencingVTV);
                } catch (Throwable e) {
                    throw new DataAccessException(e.getMessage());
                }
            }
        } finally {
            stmt.close();
        }
        // 
        for (int c = 0; c < allReferencingVTV.size(); c += 1) {
            VersionableTypeVersion referencingVTV = allReferencingVTV.elementAt(c);
            // 
            // Add VersionableRelationship to dependants of refs
            // 
            refs.addDependantRelationship(new VersionableRelationship(referencingVTV, vtv));
            // 
            // Check referencingVTV for references to it(Recursion)
            // 
            findAllReferences(con, referencingVTV, refs);
        }
    }
}

Example 2 with VersionableTypeVersion

use of org.vcell.util.document.VersionableTypeVersion in project vcell by virtualcell.

the class DependencyTest method main.

/**
 * Starts the application.
 * @param args an array of command-line arguments
 */
public static void main(java.lang.String[] args) {
    if (args.length != 2) {
        throw new RuntimeException("Usage: DependencyTest VersionableType.toString() keyValue.toString()");
    }
    java.sql.Connection con = null;
    try {
        String versionableTypeS = args[0];
        String keyValueS = args[1];
        // new cbit.sql.KeyValue("1368");
        org.vcell.util.document.KeyValue rootKey = new org.vcell.util.document.KeyValue(keyValueS);
        // cbit.sql.VersionableType.VCImage;
        org.vcell.util.document.VersionableType rootType = null;
        if (VersionableType.VCImage.toString().equals(versionableTypeS)) {
            rootType = VersionableType.VCImage;
        } else if (VersionableType.Geometry.toString().equals(versionableTypeS)) {
            rootType = VersionableType.Geometry;
        } else if (VersionableType.Model.toString().equals(versionableTypeS)) {
            rootType = VersionableType.Model;
        } else if (VersionableType.MathDescription.toString().equals(versionableTypeS)) {
            rootType = VersionableType.MathDescription;
        } else if (VersionableType.SimulationContext.toString().equals(versionableTypeS)) {
            rootType = VersionableType.SimulationContext;
        } else {
            throw new RuntimeException("Improper argument for VersionableType " + versionableTypeS);
        }
        Class.forName("oracle.jdbc.driver.OracleDriver");
        String url = "jdbc:oracle:thin:@nrcamdb.uchc.edu:1521:orc0";
        con = java.sql.DriverManager.getConnection(url, "nrcamdbdev", "bogus");
        System.out.println("Search for References to " + rootType.toString() + " id=" + rootKey.toString());
        VersionableFamily vf = cbit.vcell.modeldb.DbDriver.getAllReferences(con, rootType, rootKey);
        VersionableRelationship[] dependants = vf.getDependantRelationships();
        for (int c = 0; c < dependants.length; c += 1) {
            VersionableRelationship verrel = dependants[c];
            VersionableTypeVersion from = verrel.from();
            VersionableTypeVersion to = verrel.to();
            System.out.println(from.getVType() + " " + from.getVersion().getVersionKey() + "   ==>   " + to.getVType() + " " + to.getVersion().getVersionKey());
        }
        System.out.println("------------------Top Down List-------------------");
        VersionableTypeVersion[] topDown = vf.getDependantsTopDown();
        byte[] spaces = { 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32 };
        for (int c = 0; c < topDown.length; c += 1) {
            System.out.print(topDown[c].getVType());
            System.out.write(spaces, 0, 30 - topDown[c].getVType().toString().length());
            System.out.print(topDown[c].getVersion().getName());
            System.out.write(spaces, 0, 40 - topDown[c].getVersion().getName().length());
            System.out.println(topDown[c].getVersion().getVersionKey());
        }
    } catch (Throwable e) {
        e.printStackTrace(System.out);
    } finally {
        try {
            if (con != null) {
                con.close();
            }
        } catch (java.sql.SQLException e) {
        }
    }
}

Example 3 with VersionableTypeVersion

use of org.vcell.util.document.VersionableTypeVersion in project vcell by virtualcell.

the class ClientRequestManager method createMathModelFromApplication.

/**
 * Insert the method's description here. Creation date: (5/24/2004 12:22:11 PM)
 *
 * @param windowID java.lang.String
 */
public void createMathModelFromApplication(final BioModelWindowManager requester, final String name, final SimulationContext simContext) {
    if (simContext == null) {
        PopupGenerator.showErrorDialog(requester, "Selected Application is null, cannot generate corresponding math model");
        return;
    }
    switch(simContext.getApplicationType()) {
        case NETWORK_STOCHASTIC:
            break;
        case RULE_BASED_STOCHASTIC:
        case NETWORK_DETERMINISTIC:
    }
    AsynchClientTask task1 = new AsynchClientTask("Creating MathModel from BioModel Application", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            MathModel newMathModel = new MathModel(null);
            // Get corresponding mathDesc to create new mathModel.
            MathDescription mathDesc = simContext.getMathDescription();
            MathDescription newMathDesc = null;
            newMathDesc = new MathDescription(name + "_" + (new java.util.Random()).nextInt());
            try {
                if (mathDesc.getGeometry().getDimension() > 0 && mathDesc.getGeometry().getGeometrySurfaceDescription().getGeometricRegions() == null) {
                    mathDesc.getGeometry().getGeometrySurfaceDescription().updateAll();
                }
            } catch (ImageException e) {
                e.printStackTrace(System.out);
                throw new RuntimeException("Geometric surface generation error:\n" + e.getMessage());
            } catch (GeometryException e) {
                e.printStackTrace(System.out);
                throw new RuntimeException("Geometric surface generation error:\n" + e.getMessage());
            }
            newMathDesc.setGeometry(mathDesc.getGeometry());
            newMathDesc.read_database(new CommentStringTokenizer(mathDesc.getVCML_database()));
            newMathDesc.isValid();
            newMathModel.setName(name);
            newMathModel.setMathDescription(newMathDesc);
            hashTable.put("newMathModel", newMathModel);
        }
    };
    AsynchClientTask task2 = new AsynchClientTask("Creating MathModel from BioModel Application", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            MathModel newMathModel = (MathModel) hashTable.get("newMathModel");
            DocumentWindowManager windowManager = createDocumentWindowManager(newMathModel);
            if (simContext.getBioModel().getVersion() != null) {
                ((MathModelWindowManager) windowManager).setCopyFromBioModelAppVersionableTypeVersion(new VersionableTypeVersion(VersionableType.BioModelMetaData, simContext.getBioModel().getVersion()));
            }
            DocumentWindow dw = getMdiManager().createNewDocumentWindow(windowManager);
            setFinalWindow(hashTable, dw);
        }
    };
    ClientTaskDispatcher.dispatch(requester.getComponent(), new Hashtable<String, Object>(), new AsynchClientTask[] { task1, task2 }, false);
}

Example 4 with VersionableTypeVersion

use of org.vcell.util.document.VersionableTypeVersion in project vcell by virtualcell.

the class DatabaseWindowManager method findModelsUsingSelectedGeometry.

/**
 * Insert the method's description here.
 * Creation date: (11/6/2005 9:15:25 AM)
 */
public void findModelsUsingSelectedGeometry() {
    AsynchClientTask findModelsTask = new AsynchClientTask("Finding Models...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            VCDocumentInfo selectedDocument = getPanelSelection();
            if (!(selectedDocument instanceof GeometryInfo)) {
                PopupGenerator.showErrorDialog(DatabaseWindowManager.this, "DatabaseWindowManager.findModelsUsingSelectedGeometry expected a GeometryInfo\nbut got type=" + selectedDocument.getClass().getName() + " instead");
                return;
            }
            ReferenceQuerySpec rqs = new ReferenceQuerySpec(VersionableType.Geometry, selectedDocument.getVersion().getVersionKey());
            // try{
            ReferenceQueryResult rqr = getRequestManager().getDocumentManager().findReferences(rqs);
            // cbit.vcell.modeldb.VersionableTypeVersion[] children = (rqr.getVersionableFamily().bChildren()?rqr.getVersionableFamily().getUniqueChildren():null);
            VersionableTypeVersion[] dependants = (rqr.getVersionableFamily().bDependants() ? rqr.getVersionableFamily().getUniqueDependants() : null);
            // System.out.println("\n");
            // if(children != null){
            // for(int i=0;i<children.length;i+= 1){
            // if( children[i] != rqr.getVersionableFamily().getTarget()){
            // System.out.println("Children "+children[i]+" key="+children[i].getVersion().getVersionKey()+" date="+children[i].getVersion().getDate());
            // }
            // }
            // }else{
            // System.out.println("No Children");
            // }
            // if(dependants != null){
            // for(int i=0;i<dependants.length;i+= 1){
            // if( dependants[i] != rqr.getVersionableFamily().getTarget()){
            // System.out.println("Dependants "+dependants[i]+" key="+dependants[i].getVersion().getVersionKey()+" date="+dependants[i].getVersion().getDate());
            // }
            // }
            // }else{
            // System.out.println("No Dependants");
            // }
            // System.out.println("\nVersionableRelationships");
            // cbit.vcell.modeldb.VersionableRelationship[] vrArr = rqr.getVersionableFamily().getDependantRelationships();
            // for(int i=0;i<vrArr.length;i+= 1){
            // System.out.println(vrArr[i].from() +" -> "+vrArr[i].to());
            // }
            Hashtable<String, Object> choices = new Hashtable<String, Object>();
            if (dependants != null) {
                // System.out.println("\nMajor Relationships");
                for (int i = 0; i < dependants.length; i += 1) {
                    boolean isBioModel = dependants[i].getVType().equals(VersionableType.BioModelMetaData);
                    boolean isTop = isBioModel || dependants[i].getVType().equals(VersionableType.MathModelMetaData);
                    if (isTop) {
                        VersionableRelationship[] vrArr2 = rqr.getVersionableFamily().getDependantRelationships();
                        for (int j = 0; j < vrArr2.length; j += 1) {
                            if ((vrArr2[j].from() == dependants[i]) && vrArr2[j].to().getVType().equals((isBioModel ? VersionableType.SimulationContext : VersionableType.MathDescription))) {
                                for (int k = 0; k < vrArr2.length; k += 1) {
                                    if ((vrArr2[k].from() == vrArr2[j].to()) && vrArr2[k].to().getVType().equals(VersionableType.Geometry)) {
                                        String s = (isBioModel ? "BioModel" : "MathModel") + "  " + "\"" + dependants[i].getVersion().getName() + "\"  (" + dependants[i].getVersion().getDate() + ")" + (isBioModel ? " (App=\"" + vrArr2[k].from().getVersion().getName() + "\")" : /*+" -> "*/
                                        "");
                                        // +" Geometry="+vrArr2[k].to().getVersion().getName()+" "+vrArr2[k].to().getVersion().getDate();
                                        choices.put(s, dependants[i]);
                                    // System.out.println(s);
                                    }
                                }
                            }
                        }
                    }
                }
            }
            if (choices.size() > 0) {
                Object[] listObj = choices.keySet().toArray();
                Object o = DialogUtils.showListDialog(getComponent(), listObj, "Models Referencing Geometry (Select To Open) " + selectedDocument.getVersion().getName() + " " + selectedDocument.getVersion().getDate());
                if (o != null) {
                    VersionableTypeVersion v = (VersionableTypeVersion) choices.get(o);
                    // System.out.println(v);
                    if (v.getVType().equals(VersionableType.BioModelMetaData)) {
                        BioModelInfo bmi = getRequestManager().getDocumentManager().getBioModelInfo(v.getVersion().getVersionKey());
                        getRequestManager().openDocument(bmi, DatabaseWindowManager.this, true);
                    } else if (v.getVType().equals(VersionableType.MathModelMetaData)) {
                        MathModelInfo mmi = getRequestManager().getDocumentManager().getMathModelInfo(v.getVersion().getVersionKey());
                        getRequestManager().openDocument(mmi, DatabaseWindowManager.this, true);
                    }
                }
            } else {
                if (dependants == null) {
                    DialogUtils.showInfoDialog(getComponent(), "No Model references found.\n" + (rqr.getVersionableFamily().getTarget().getVersion().getFlag().isArchived() ? "Info: Not Deletable (key=" + rqr.getVersionableFamily().getTarget().getVersion().getVersionKey() + ") because legacy ARCHIVE set" : ""));
                } else {
                    DialogUtils.showInfoDialog(getComponent(), "No current Model references found.\n" + "Geometry has internal database references from\n" + "previously linked Model(s).\n" + "Not Deletable until database is culled (daily).");
                }
            // return;
            }
        // }catch(DataAccessException e){
        // DialogUtils.showErrorDialog(getComponent(), "Error find Geometry Model references\n"+e.getClass().getName()+"\n"+e.getMessage());
        // }
        }
    };
    ClientTaskDispatcher.dispatch(getComponent(), new Hashtable<String, Object>(), new AsynchClientTask[] { findModelsTask }, false);
}

Example 5 with VersionableTypeVersion

use of org.vcell.util.document.VersionableTypeVersion in project vcell by virtualcell.

the class FieldDataWindowManager method findReferencingModels.

public boolean findReferencingModels(final ExternalDataIdentifier targetExtDataID, boolean bShowReferencingModelsList) throws DataAccessException, UserCancelException {
    ReferenceQuerySpec rqs = new ReferenceQuerySpec(targetExtDataID);
    ReferenceQueryResult rqr = getRequestManager().getDocumentManager().findReferences(rqs);
    VersionableTypeVersion[] dependants = null;
    Hashtable<VersionableTypeVersion, String[]> choices = new Hashtable<VersionableTypeVersion, String[]>();
    boolean bDanglingReferences = false;
    VersionableType bioModelType = VersionableType.BioModelMetaData;
    VersionableType mathModelType = VersionableType.MathModelMetaData;
    if (rqr != null) {
        dependants = (rqr.getVersionableFamily().bDependants() ? rqr.getVersionableFamily().getUniqueDependants() : null);
        if (dependants != null) {
            for (int i = 0; i < dependants.length; i += 1) {
                boolean isBioModel = dependants[i].getVType().equals(bioModelType);
                boolean isTop = isBioModel || dependants[i].getVType().equals(mathModelType);
                if (isTop) {
                    VersionableRelationship[] vrArr2 = rqr.getVersionableFamily().getDependantRelationships();
                    for (int j = 0; j < vrArr2.length; j += 1) {
                        if ((vrArr2[j].from() == dependants[i]) && vrArr2[j].to().getVType().equals((isBioModel ? VersionableType.SimulationContext : VersionableType.MathDescription))) {
                            for (int k = 0; k < vrArr2.length; k += 1) {
                                boolean bAdd = false;
                                if (k == j && vrArr2[k].from().getVType().equals(mathModelType)) {
                                    bAdd = true;
                                }
                                if ((vrArr2[k].from() == vrArr2[j].to()) && vrArr2[k].to().getVType().equals(VersionableType.MathDescription)) {
                                    bAdd = true;
                                }
                                if (bAdd) {
                                    choices.put(dependants[i], new String[] { dependants[i].getVersion().getName(), (isBioModel ? bioModelType.getTypeName() : mathModelType.getTypeName()), (isBioModel ? vrArr2[k].from().getVersion().getName() : ""), dependants[i].getVersion().getVersionKey().toString() });
                                }
                            }
                        }
                    }
                }
            }
            bDanglingReferences = (choices.size() == 0);
        } else {
            bDanglingReferences = true;
        }
    }
    // FieldDataFileOperationResults fdfor = getRequestManager().getDocumentManager().fieldDataFileOperation(
    // FieldDataFileOperationSpec.createDependantFuncsFieldDataFileOperationSpec(targetExtDataID));
    FieldDataFileOperationResults fdfor = null;
    boolean bHasReferences = false;
    if (choices.size() > 0 || fdfor != null) {
        bHasReferences = true;
        if (bShowReferencingModelsList) {
            String[] columnNames = new String[] { "Model", "Type", "Description" };
            Vector<VersionableType> varTypeV = new Vector<VersionableType>();
            Vector<KeyValue> keyValV = new Vector<KeyValue>();
            Vector<String[]> choicesV = new Vector<String[]>();
            String[][] modelListData = choices.values().toArray(new String[0][0]);
            for (int i = 0; i < modelListData.length; i++) {
                choicesV.add(new String[] { modelListData[i][0], modelListData[i][1], "Model Variable - " + (modelListData[i][2].length() == 0 ? "" : "App='" + modelListData[i][2] + "'") + " version[" + modelListData[i][3] + "]" });
                varTypeV.add((modelListData[i][1].equals(bioModelType.getTypeName()) ? bioModelType : mathModelType));
                keyValV.add(new KeyValue(modelListData[i][3]));
            }
            for (int i = 0; fdfor != null && i < fdfor.dependantFunctionInfo.length; i++) {
                String functionNames = "";
                for (int j = 0; j < fdfor.dependantFunctionInfo[i].funcNames.length; j++) {
                    functionNames += (j > 0 ? "," : "") + fdfor.dependantFunctionInfo[i].funcNames[j];
                }
                choicesV.add(new String[] { fdfor.dependantFunctionInfo[i].referenceSourceName, fdfor.dependantFunctionInfo[i].referenceSourceType, "Data Viewer Function(s) '" + functionNames + "' - " + (fdfor.dependantFunctionInfo[i].applicationName == null ? "" : "App='" + fdfor.dependantFunctionInfo[i].applicationName + "' ") + (fdfor.dependantFunctionInfo[i].simulationName == null ? "" : "Sim='" + fdfor.dependantFunctionInfo[i].simulationName + "' ") + "version[" + fdfor.dependantFunctionInfo[i].refSourceVersionDate + "]" });
                if (fdfor.dependantFunctionInfo[i].referenceSourceType.equals(FieldDataFileOperationResults.FieldDataReferenceInfo.FIELDDATATYPENAME)) {
                    varTypeV.add(null);
                } else if (fdfor.dependantFunctionInfo[i].referenceSourceType.equals(bioModelType.getTypeName())) {
                    varTypeV.add(bioModelType);
                } else if (fdfor.dependantFunctionInfo[i].referenceSourceType.equals(mathModelType.getTypeName())) {
                    varTypeV.add(mathModelType);
                } else {
                    throw new IllegalArgumentException("Unknown reference source type " + fdfor.dependantFunctionInfo[i].referenceSourceType);
                }
                keyValV.add(fdfor.dependantFunctionInfo[i].refSourceVersionKey);
            }
            int[] selectionArr = PopupGenerator.showComponentOKCancelTableList(getComponent(), "References to Field Data (Select To Open) " + targetExtDataID.getName(), columnNames, choicesV.toArray(new String[0][0]), ListSelectionModel.SINGLE_SELECTION);
            if (selectionArr != null && selectionArr.length > 0) {
                if (varTypeV.elementAt(selectionArr[0]) != null) {
                    if (varTypeV.elementAt(selectionArr[0]).equals(bioModelType)) {
                        BioModelInfo bmi = getRequestManager().getDocumentManager().getBioModelInfo(keyValV.elementAt(selectionArr[0]));
                        getRequestManager().openDocument(bmi, FieldDataWindowManager.this, true);
                    } else if (varTypeV.elementAt(selectionArr[0]).equals(mathModelType)) {
                        MathModelInfo mmi = getRequestManager().getDocumentManager().getMathModelInfo(keyValV.elementAt(selectionArr[0]));
                        getRequestManager().openDocument(mmi, FieldDataWindowManager.this, true);
                    } else {
                        throw new IllegalArgumentException("Not expecting varType " + varTypeV.elementAt(selectionArr[0]));
                    }
                } else {
                    PopupGenerator.showInfoDialog(this, "use FiledDataManager to view FieldData '" + choicesV.elementAt(selectionArr[0])[0] + "'");
                }
            }
        }
    } else {
        if (!bDanglingReferences) {
            bHasReferences = false;
            if (bShowReferencingModelsList) {
                PopupGenerator.showInfoDialog(this, "No Model references found for Field Data " + targetExtDataID.getName());
            }
        } else {
            bHasReferences = true;
            if (bShowReferencingModelsList) {
                PopupGenerator.showInfoDialog(this, "No current Model references found.\n" + "Field Data has internal database references from\n" + "previously linked Model(s) that have been deleted.\n" + "Note: Field Data '" + targetExtDataID.getName() + "' is not deletable\n" + "until database is culled (daily).");
            }
        }
    }
    return bHasReferences;
}