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

Example 11 with VersionInfo

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

the class DbDriver method groupAddUser.

/**
 * This method was created in VisualAge.
 * @return cbit.sql.Versionable
 * @param user cbit.vcell.server.User
 * @param versionable cbit.sql.Versionable
 */
public static void groupAddUser(Connection con, KeyFactory keyFactory, User owner, VersionableType vType, KeyValue vKey, String userAddToGroupString, boolean isHiddenFromOwner, DatabaseSyntax dbSyntax) throws SQLException, ObjectNotFoundException, DataAccessException {
    User userAddToGroup = getUserFromUserid(con, userAddToGroupString);
    if (userAddToGroup == null) {
        throw new IllegalArgumentException("User name " + userAddToGroupString + " not found");
    }
    // 
    if ((con == null) || (vType == null) || (owner == null) || (vKey == null) || (userAddToGroup == null)) {
        throw new IllegalArgumentException("Improper parameters for groupAddUser userAddToGroupString=" + (userAddToGroupString == null ? "NULL" : userAddToGroupString));
    }
    // 
    Version currentVersion = permissionInit(con, vType, vKey, owner);
    // If userAddToGroup is already in group it is an error
    // ----- Also can't add members to GroupAccessAll(Public) (CHANGED!!!) -----
    boolean bExists = false;
    if (currentVersion.getGroupAccess() instanceof GroupAccessSome) {
        bExists = (((GroupAccessSome) currentVersion.getGroupAccess()).isNormalMember(userAddToGroup) && !isHiddenFromOwner) || (((GroupAccessSome) currentVersion.getGroupAccess()).isHiddenMember(userAddToGroup) && isHiddenFromOwner);
    }
    // }
    if (currentVersion.getOwner().compareEqual(userAddToGroup) || bExists) {
        throw new DataAccessException(userAddToGroup + " Already a member of group");
    }
    if (lg.isTraceEnabled())
        lg.trace("DbDriver.groupAddUser(user=" + owner + ", type =" + vType + ", key=" + vKey + ")");
    VersionTable vTable = VersionTable.getVersionTable(vType);
    // 
    // 
    BigDecimal newHash = null;
    // 
    if (currentVersion.getGroupAccess() instanceof GroupAccessSome) {
        // Calculate the hash of the currentVersion's group plus a new user
        GroupAccessSome currentGroup = (GroupAccessSome) currentVersion.getGroupAccess();
        newHash = currentGroup.calculateHashWithNewMember(userAddToGroup, isHiddenFromOwner);
    } else if (currentVersion.getGroupAccess() instanceof GroupAccessNone || currentVersion.getGroupAccess() instanceof GroupAccessAll) {
        // Calculate hash for a new group with only userAddToGroup in it
        KeyValue[] kvArr = new KeyValue[1];
        boolean[] hiddenArr = new boolean[1];
        kvArr[0] = userAddToGroup.getID();
        hiddenArr[0] = isHiddenFromOwner;
        newHash = GroupAccess.calculateHash(kvArr, hiddenArr);
    }
    // 
    BigDecimal updatedGroupID = null;
    // 
    // See if the newly calculated hash is present in the database GroupTable
    // indicating a group we can reuse by reference
    // 
    String sql = "SELECT groupid FROM " + GroupTable.table.getTableName() + " WHERE groupMemberHash = " + newHash.toString();
    java.sql.Statement stmt = con.createStatement();
    try {
        java.sql.ResultSet rset = stmt.executeQuery(sql);
        if (rset.next()) {
            // There may be more than one, just get the first, all have the same groupid and hash
            // Group already exists,Re-Use the groupid, we don't have to make a new group
            updatedGroupID = rset.getBigDecimal(GroupTable.table.groupid.toString());
        }
    } finally {
        stmt.close();
    }
    // 
    if (updatedGroupID == null) {
        // Create new Group id
        updatedGroupID = getNewGroupID(con, keyFactory);
        int groupMemberCount = 1;
        // Get all the members of the currentVersion Group or skip if currentVersion group is GroupAccessNone
        // Don't worry about GroupAccessAll, we couldn't have gotten this far
        // 
        // Add new User
        // 
        sql = "INSERT INTO " + GroupTable.table.getTableName() + " VALUES ( " + keyFactory.getNewKey(con).toString() + "," + updatedGroupID + "," + userAddToGroup.getID().toString() + "," + (isHiddenFromOwner ? "1" : "0") + "," + newHash + " )";
        updateCleanSQL(con, sql);
        if (currentVersion.getGroupAccess() instanceof GroupAccessSome) {
            // Add all the old Normal Users
            User[] normalUsers = ((GroupAccessSome) currentVersion.getGroupAccess()).getNormalGroupMembers();
            for (int i = 0; normalUsers != null && i < normalUsers.length; i += 1) {
                String userRef = normalUsers[i].getID().toString();
                sql = "INSERT INTO " + GroupTable.table.getTableName() + " VALUES ( " + keyFactory.getNewKey(con).toString() + "," + updatedGroupID + "," + userRef + "," + (false ? "1" : "0") + "," + newHash + " )";
                updateCleanSQL(con, sql);
            }
            // Add all the old Hidden Users
            User[] hiddenUsers = ((GroupAccessSome) currentVersion.getGroupAccess()).getHiddenGroupMembers();
            for (int i = 0; hiddenUsers != null && i < hiddenUsers.length; i += 1) {
                String userRef = hiddenUsers[i].getID().toString();
                sql = "INSERT INTO " + GroupTable.table.getTableName() + " VALUES ( " + keyFactory.getNewKey(con).toString() + "," + updatedGroupID + "," + userRef + "," + (true ? "1" : "0") + "," + newHash + " )";
                updateCleanSQL(con, sql);
            }
        }
    }
    // Update the vTable to point to the new Group
    String set = vTable.privacy.getQualifiedColName() + " = " + updatedGroupID;
    String cond = vTable.id.getQualifiedColName() + " = " + vKey;
    // " AND " + vTable.ownerRef.getQualifiedColName() + " = " + owner.getID();
    sql = DatabasePolicySQL.enforceOwnershipUpdate(owner, vTable, set, cond);
    // System.out.println(sql);
    int numRowsProcessed = updateCleanSQL(con, sql);
    if (numRowsProcessed != 1) {
        // 
        // check if update failed
        // 
        Vector<VersionInfo> versionInfoList = getVersionableInfos(con, owner, vType, false, vKey, true, dbSyntax);
        if (versionInfoList.size() == 0) {
            throw new DataAccessException("Add User " + userAddToGroup + " Permission to access failed, " + vType.getTypeName() + "(" + vKey + ") record not found");
        } else {
            throw new DataAccessException("Add User " + userAddToGroup + " Permission to access failed " + vType.getTypeName() + "(" + vKey + ")");
        }
    }
}

Example 12 with VersionInfo

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

the class DbDriver method getVersionableInfos.

/**
 * This method was created in VisualAge.
 * @return java.lang.Object
 * @param user cbit.vcell.server.User
 * @param vType int
 */
public static Vector<VersionInfo> getVersionableInfos(Connection con, User user, VersionableType vType, boolean bAll, KeyValue versionKey, boolean bCheckPermission, DatabaseSyntax dbSyntax) throws ObjectNotFoundException, SQLException, DataAccessException {
    if (user == null) {
        throw new IllegalArgumentException("Improper parameters for getVersionables");
    }
    // gvilog.print("DbDriver.getVersionableInfo(all=" + bAll + ",user=" + user + ", type="+vType+")");
    String sql;
    StringBuffer conditions = new StringBuffer();
    String special = null;
    VersionTable vTable = VersionTable.getVersionTable(vType);
    boolean bFirstClause = true;
    if (!bAll) {
        conditions.append(vTable.ownerRef.getQualifiedColName() + " = " + user.getID());
        bFirstClause = false;
    }
    if (versionKey != null) {
        if (!bFirstClause) {
            conditions.append(" AND ");
        }
        conditions.append(vTable.id.getQualifiedColName() + " = " + versionKey);
    }
    special = " ORDER BY " + vTable.name.getQualifiedColName() + "," + vTable.versionBranchID.getQualifiedColName() + "," + vTable.versionDate.getQualifiedColName();
    if (vType.equals(VersionableType.BioModelMetaData)) {
        sql = ((BioModelTable) vTable).getInfoSQL(user, conditions.toString(), special, dbSyntax);
    } else if (vType.equals(VersionableType.MathModelMetaData)) {
        sql = ((MathModelTable) vTable).getInfoSQL(user, conditions.toString(), special, dbSyntax);
    } else if (vType.equals(VersionableType.Simulation)) {
        sql = ((SimulationTable) vTable).getInfoSQL(user, conditions.toString(), special, dbSyntax);
    } else if (vType.equals(VersionableType.Geometry)) {
        sql = ((GeometryTable) vTable).getInfoSQL(user, conditions.toString(), special, bCheckPermission, dbSyntax);
    } else if (vType.equals(VersionableType.VCImage)) {
        sql = ((ImageTable) vTable).getInfoSQL(user, conditions.toString(), special, bCheckPermission, dbSyntax);
    } else if (vType.equals(VersionableType.Model)) {
        sql = ((ModelTable) vTable).getInfoSQL(user, conditions.toString(), special, dbSyntax);
    } else if (vType.equals(VersionableType.SimulationContext)) {
        sql = ((SimContextTable) vTable).getInfoSQL(user, conditions.toString(), special, dbSyntax);
    } else if (vType.equals(VersionableType.MathDescription)) {
        sql = ((MathDescTable) vTable).getInfoSQL(user, conditions.toString(), special, dbSyntax);
    } else {
        throw new RuntimeException("VersionInfo not availlable for type '" + vType.getTypeName() + "'");
    }
    // 
    StringBuffer optimizedSQL = new StringBuffer(sql);
    optimizedSQL.insert(7, Table.SQL_GLOBAL_HINT);
    sql = optimizedSQL.toString();
    // 
    // System.out.println("getVersionableInfo--->"+sql);
    VersionInfo vInfo;
    Vector<VersionInfo> vInfoList = new Vector<VersionInfo>();
    // Connection con = conFact.getConnection();
    Statement stmt = con.createStatement();
    try {
        ResultSet rset = stmt.executeQuery(sql);
        while (rset.next()) {
            if (vType.equals(VersionableType.BioModelMetaData)) {
                vInfo = ((BioModelTable) vTable).getInfo(rset, con, dbSyntax);
            } else if (vType.equals(VersionableType.MathModelMetaData)) {
                vInfo = ((MathModelTable) vTable).getInfo(rset, con, dbSyntax);
            } else if (vType.equals(VersionableType.Simulation)) {
                vInfo = ((SimulationTable) vTable).getInfo(rset, con);
            } else if (vType.equals(VersionableType.Geometry)) {
                vInfo = ((GeometryTable) vTable).getInfo(rset, con);
            } else if (vType.equals(VersionableType.VCImage)) {
                vInfo = ((ImageTable) vTable).getInfo(rset, con, dbSyntax);
            } else if (vType.equals(VersionableType.Model)) {
                vInfo = ((ModelTable) vTable).getInfo(rset, con);
            } else if (vType.equals(VersionableType.SimulationContext)) {
                vInfo = ((SimContextTable) vTable).getInfo(rset, con);
            } else if (vType.equals(VersionableType.MathDescription)) {
                vInfo = ((MathDescTable) vTable).getInfo(rset, con);
            } else {
                throw new RuntimeException("VersionInfo not availlable for type '" + vType.getTypeName() + "'");
            }
            // 
            // only add version info record to list if not a duplicate,
            // this occurs because the DatabasePolicySQL.enforceOwnershipSelect() can get the same record several ways.
            // 
            VersionInfo previousVInfo = (vInfoList.size() > 0) ? vInfoList.lastElement() : null;
            if (previousVInfo == null || !previousVInfo.getVersion().getVersionKey().compareEqual(vInfo.getVersion().getVersionKey())) {
                vInfoList.addElement(vInfo);
            }
        }
    } finally {
        stmt.close();
    }
    // return oInfoArray;
    return vInfoList;
}

Example 13 with VersionInfo

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

the class DbDriver method groupSetPublic.

/**
 * This method was created in VisualAge.
 * @return cbit.sql.Versionable
 * @param owner cbit.vcell.server.User
 * @param versionable cbit.sql.Versionable
 */
public static void groupSetPublic(Connection con, User owner, VersionableType vType, KeyValue vKey, DatabaseSyntax dbSyntax) throws SQLException, ObjectNotFoundException, DataAccessException {
    if ((con == null) || (vType == null) || (owner == null) || (vKey == null)) {
        throw new IllegalArgumentException("Improper parameters for groupAccessSetPublic");
    }
    // 
    Version currentVersion = permissionInit(con, vType, vKey, owner);
    if (lg.isTraceEnabled())
        lg.trace("DbDriver.groupSetPublic(owner=" + owner + ", type =" + vType + ", key=" + vKey + ")");
    BigDecimal updatedGroupID = GroupAccess.GROUPACCESS_ALL;
    VersionTable vTable = VersionTable.getVersionTable(vType);
    String set = vTable.privacy.getQualifiedColName() + " = " + updatedGroupID;
    String cond = vTable.id.getQualifiedColName() + " = " + vKey;
    // " AND " + vTable.ownerRef.getQualifiedColName() + " = " + owner.getID();
    String sql = DatabasePolicySQL.enforceOwnershipUpdate(owner, vTable, set, cond);
    // System.out.println(sql);
    int numRowsProcessed = updateCleanSQL(con, sql);
    if (numRowsProcessed != 1) {
        // 
        // check if update failed, or just already updated
        // 
        Vector<VersionInfo> versionInfoList = getVersionableInfos(con, owner, vType, false, vKey, true, dbSyntax);
        if (versionInfoList.size() == 0) {
            throw new DataAccessException("groupSetPublic failed " + vType.getTypeName() + "(" + vKey + ") record not found");
        } else {
            throw new DataAccessException("groupSetPublic failed " + vType.getTypeName() + "(" + vKey + ")");
        }
    }
}

Example 14 with VersionInfo

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

the class DBTopLevel method getBioModelXML.

/**
 * 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 getBioModelXML(User user, KeyValue key, boolean bEnableRetry) throws DataAccessException, java.sql.SQLException, ObjectNotFoundException {
    Object lock = new Object();
    Connection con = conFactory.getConnection(lock);
    DbDriver driver = getDbDriver(VersionableType.BioModelMetaData);
    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.BioModelMetaData, true, true, false);
        if (vInfos.size() == 0) {
            throw new ObjectNotFoundException(VersionableType.BioModelMetaData.getTypeName() + " not found");
        }
        return driver.getVersionableXML(con, VersionableType.BioModelMetaData, key);
    } catch (Throwable e) {
        lg.error(e.getMessage(), e);
        if (bEnableRetry && isBadConnection(con)) {
            conFactory.failed(con, lock);
            return getBioModelXML(user, key, false);
        } else {
            handle_DataAccessException_SQLException(e);
            // never gets here;
            return null;
        }
    } finally {
        conFactory.release(con, lock);
    }
}

Example 15 with VersionInfo

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

the class ClientRequestManager method createSelectDocTask.

private AsynchClientTask createSelectDocTask(final TopLevelWindowManager requester) {
    AsynchClientTask selectDocumentTypeTask = new AsynchClientTask("Select/Load geometry", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            String[][] docTypeoptions = new String[][] { { "BioModel names" }, { "MathModel names" } };
            VCDocumentType[] sourceDocumentTypes = new VCDocumentType[] { VCDocumentType.BIOMODEL_DOC, VCDocumentType.MATHMODEL_DOC };
            VCAssert.assertTrue(docTypeoptions.length == sourceDocumentTypes.length, "Label and types mismatch");
            int[] geomType = DialogUtils.showComponentOKCancelTableList(JOptionPane.getFrameForComponent(requester.getComponent()), "Select different Geometry", new String[] { "Search by" }, docTypeoptions, ListSelectionModel.SINGLE_SELECTION);
            final int selectedType = geomType[0];
            VCDocumentType sourceDocumentType = sourceDocumentTypes[selectedType];
            VersionInfo vcVersionInfo = null;
            if (geomType[0] == 3) {
                ImageDbTreePanel imageDbTreePanel = new ImageDbTreePanel();
                imageDbTreePanel.setDocumentManager(getDocumentManager());
                imageDbTreePanel.setPreferredSize(new java.awt.Dimension(200, 400));
                vcVersionInfo = DialogUtils.getDBTreePanelSelection(requester.getComponent(), imageDbTreePanel, "OK", "Select Image:");
            } else {
                vcVersionInfo = selectDocumentFromType(sourceDocumentType, requester);
            }
            hashTable.put(VERSIONINFO_KEY, vcVersionInfo);
        }
    };
    return selectDocumentTypeTask;
}