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

Example 1 with VersionableType

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

the class DbDriver method curate.

/**
 * Insert the method's description here.
 * Creation date: (5/23/2006 10:44:52 AM)
 */
public static VCDocumentInfo curate(CurateSpec curateSpec, Connection con, User user, DatabaseSyntax dbSyntax) throws DataAccessException, SQLException {
    VersionableType vType = null;
    if (curateSpec.getVCDocumentInfo() instanceof BioModelInfo) {
        vType = VersionableType.BioModelMetaData;
    } else if (curateSpec.getVCDocumentInfo() instanceof MathModelInfo) {
        vType = VersionableType.MathModelMetaData;
    } else {
        throw new DataAccessException("Expecting BioModelInfo or MathModelInfo but got type=" + curateSpec.getVCDocumentInfo().getClass().getName());
    }
    KeyValue vKey = curateSpec.getVCDocumentInfo().getVersion().getVersionKey();
    Version dbVersion = getVersionFromKeyValue(con, vType, vKey);
    // Must be owner to curate
    if (!dbVersion.getOwner().compareEqual(user)) {
        throw new PermissionException("Cannot curate " + vType.getTypeName() + " \"" + dbVersion.getName() + "\" (" + vKey + "), not owned by " + user.getName());
    }
    VersionFlag updatedVersionFlag = null;
    if (curateSpec.getCurateType() == CurateSpec.ARCHIVE) {
        if (!dbVersion.getFlag().compareEqual(VersionFlag.Current)) {
            throw new IllegalArgumentException("Only non-archived, non-published documents can be ARCHIVED");
        }
        updatedVersionFlag = VersionFlag.Archived;
    } else if (curateSpec.getCurateType() == CurateSpec.PUBLISH) {
        // Must have PUBLISH rights
        if (!dbVersion.getOwner().isPublisher()) {
            throw new PermissionException("Cannot curate " + vType.getTypeName() + " \"" + dbVersion.getName() + "\" (" + vKey + "), user " + user.getName() + " not granted PUBLISHING rights");
        }
        // Must be ARCHIVED and Public before PUBLISH is allowed
        if (!dbVersion.getFlag().compareEqual(VersionFlag.Archived) || !(dbVersion.getGroupAccess() instanceof GroupAccessAll)) {
            throw new IllegalArgumentException("Only ARCHIVED documents with PUBLIC permission can be PUBLISHED");
        }
        updatedVersionFlag = VersionFlag.Published;
    } else {
        throw new DataAccessException("Expecting CurateType " + CurateSpec.ARCHIVE + "(ARCHIVE) or " + CurateSpec.PUBLISH + "(PUBLISH) but got type=" + curateSpec.getCurateType());
    }
    VersionTable vTable = VersionTable.getVersionTable(vType);
    String set = vTable.versionFlag.getQualifiedColName() + " = " + updatedVersionFlag.getIntValue();
    String cond = vTable.id.getQualifiedColName() + " = " + vKey;
    String sql = DatabasePolicySQL.enforceOwnershipUpdate(user, vTable, set, cond);
    int numRowsProcessed = updateCleanSQL(con, sql);
    // Clear XML
    if (vType.equals(VersionableType.BioModelMetaData)) {
        updateCleanSQL(con, "DELETE FROM " + BioModelXMLTable.table.getTableName() + " WHERE " + BioModelXMLTable.table.bioModelRef.getQualifiedColName() + " = " + vKey.toString());
    } else if (vType.equals(VersionableType.MathModelMetaData)) {
        updateCleanSQL(con, "DELETE FROM " + MathModelXMLTable.table.getTableName() + " WHERE " + MathModelXMLTable.table.mathModelRef.getQualifiedColName() + " = " + vKey.toString());
    }
    VCDocumentInfo dbVCDocumentInfo = (VCDocumentInfo) getVersionableInfos(con, user, vType, false, vKey, false, dbSyntax).elementAt(0);
    return dbVCDocumentInfo;
}

Example 2 with VersionableType

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

the class DbDriver method insertVersionableInit.

/**
 * This method was created in VisualAge.
 * @return cbit.sql.KeyValue
 * @param versionable cbit.sql.Versionable
 * @param pRef cbit.sql.KeyValue
 * @param bCommit boolean
 */
protected Version insertVersionableInit(InsertHashtable hash, Connection con, User user, Versionable versionable, String name, String annot, boolean bVersion) throws SQLException, DataAccessException {
    if (hash.getDatabaseKey(versionable) != null) {
        throw new DataAccessException(versionable + " already inserted in this transaction");
    }
    VersionableType vType = VersionTable.versionableTypeFromVersionable(versionable);
    if (vType.getIsTopLevel() && isNameUsed(con, vType, user, name)) {
        throw new DataAccessException("'" + user.getName() + "' already has a " + vType.getTypeName() + " with name '" + name + "'");
    }
    User owner = user;
    // AccessInfo accessInfo = new AccessInfo(AccessInfo.PRIVATE_CODE);
    GroupAccess accessInfo = new GroupAccessNone();
    KeyValue versionKey = keyFactory.getNewKey(con);
    java.util.Date date = getNewDate(con);
    // if(versionable.getVersion().getVersionKey() != null){
    // throw new DataAccessException("GeomDbDriver:insertVersionable, VersionKey must be null to insert");
    // }
    String versionName = name;
    // Check for Archive and Publish not needed in insert because versionflag is always forced to Current
    VersionFlag versionFlag = null;
    // if(bVersion){
    // versionFlag = VersionFlag.Archived;
    // }else{
    versionFlag = VersionFlag.Current;
    // }
    KeyValue PRefKey = null;
    java.math.BigDecimal branchID = getNewBranchID(con);
    // 
    // Insert Software Version
    // 
    insertSoftwareVersion(con, versionKey);
    // 
    return new Version(versionKey, versionName, owner, accessInfo, PRefKey, branchID, date, versionFlag, annot);
}

Example 3 with VersionableType

use of org.vcell.util.document.VersionableType 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 4 with VersionableType

use of org.vcell.util.document.VersionableType 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;
}

Example 5 with VersionableType

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

the class DBTopLevel method getMathModelXML.

/**
 * This method was created in VisualAge.
 * @return cbit.sql.Versionable
 * @param object cbit.sql.Versionable
 * @param name java.lang.String
 * @param bVersion boolean
 * @exception org.vcell.util.DataAccessException The exception description.
 * @exception java.sql.SQLException The exception description.
 * @exception cbit.sql.RecordChangedException The exception description.
 */
String getMathModelXML(User user, KeyValue key, boolean bEnableRetry) throws DataAccessException, java.sql.SQLException, ObjectNotFoundException {
    Object lock = new Object();
    VersionableType versionableType = VersionableType.MathModelMetaData;
    Connection con = conFactory.getConnection(lock);
    DbDriver driver = getDbDriver(versionableType);
    try {
        // 
        // Getting the corresponding VersionInfo will fail if you don't have permission to the object.
        // This is needed because the DbDriver-level services can return objects directly from the
        // cache without checking for permissions first.
        // 
        // This check is placed in DbTopLevel because this is the client API entry point.
        // Child objects (of the requested object) are given permission by reachablity anyway,
        // so if the user is allowed permission to the parent, no further checks are necessary.
        // 
        Vector<VersionInfo> vInfos = getVersionableInfos(user, key, versionableType, true, true, false);
        if (vInfos.size() == 0) {
            throw new ObjectNotFoundException(versionableType.getTypeName() + " not found");
        }
        return driver.getVersionableXML(con, versionableType, key);
    } catch (Throwable e) {
        lg.error(e.getMessage(), e);
        if (bEnableRetry && isBadConnection(con)) {
            conFactory.failed(con, lock);
            return getMathModelXML(user, key, false);
        } else {
            handle_DataAccessException_SQLException(e);
            // never gets here;
            return null;
        }
    } finally {
        conFactory.release(con, lock);
    }
}