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

Example 51 with Version

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

the class DbDriver method groupRemoveUser.

/**
 * This method was created in VisualAge.
 * @return cbit.sql.Versionable
 * @param user cbit.vcell.server.User
 * @param versionable cbit.sql.Versionable
 */
public static void groupRemoveUser(Connection con, KeyFactory keyFactory, User owner, VersionableType vType, KeyValue vKey, String userRemoveFromGroupString, boolean isHiddenFromOwner, DatabaseSyntax dbSyntax) throws SQLException, ObjectNotFoundException, DataAccessException {
    User userRemoveFromGroup = getUserFromUserid(con, userRemoveFromGroupString);
    if (userRemoveFromGroup == null) {
        throw new IllegalArgumentException("User name " + userRemoveFromGroupString + " not found");
    }
    // 
    if ((con == null) || (vType == null) || (owner == null) || (vKey == null) || (userRemoveFromGroup == null)) {
        throw new IllegalArgumentException("Improper parameters for groupRemoveUser userRemoveFromGroupString=" + (userRemoveFromGroupString == null ? "NULL" : userRemoveFromGroupString));
    }
    // 
    Version currentVersion = permissionInit(con, vType, vKey, owner);
    // If userRemoveFromGroup is not in group it is an error, or if not a "real" group
    boolean bExists = false;
    if (currentVersion.getGroupAccess() instanceof GroupAccessSome) {
        bExists = (((GroupAccessSome) currentVersion.getGroupAccess()).isNormalMember(userRemoveFromGroup) && !isHiddenFromOwner) || (((GroupAccessSome) currentVersion.getGroupAccess()).isHiddenMember(userRemoveFromGroup) && isHiddenFromOwner);
    }
    if (!bExists) {
        throw new DataAccessException(userRemoveFromGroup + " not a member of group");
    }
    if (lg.isTraceEnabled())
        lg.trace("DbDriver.groupAccessRemoveUser(user=" + owner + ", type =" + vType + ", key=" + vKey + ")");
    GroupAccessSome currentGroup = (GroupAccessSome) currentVersion.getGroupAccess();
    VersionTable vTable = VersionTable.getVersionTable(vType);
    // 
    // calculate hash after removing user (null if last user in group)
    // 
    BigDecimal newHash = null;
    int count = (currentGroup.getNormalGroupMembers() != null ? currentGroup.getNormalGroupMembers().length : 0) + (currentGroup.getHiddenGroupMembers() != null ? currentGroup.getHiddenGroupMembers().length : 0);
    if (count > 1) {
        // See if group already exists without member and get it's ID
        newHash = currentGroup.calculateHashWithoutMember(userRemoveFromGroup, isHiddenFromOwner);
    }
    // 
    BigDecimal updatedGroupID = null;
    String sql = null;
    // 
    if (newHash != null) {
        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()) {
                // Group already exists,Re-Use
                updatedGroupID = rset.getBigDecimal(GroupTable.table.groupid.toString());
            }
        } finally {
            stmt.close();
        }
    } else {
        // 
        // user was last user in group, new group is the Private Group (AccessNone), groupID is predefined.
        // 
        updatedGroupID = GroupAccess.GROUPACCESS_NONE;
    }
    // 
    if (updatedGroupID == null) {
        updatedGroupID = getNewGroupID(con, keyFactory);
        // 
        // Re-Add Normal users not removed
        // 
        User[] normalUsers = currentGroup.getNormalGroupMembers();
        for (int i = 0; normalUsers != null && i < normalUsers.length; i += 1) {
            if (!(normalUsers[i].compareEqual(userRemoveFromGroup)) || isHiddenFromOwner) {
                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);
            }
        }
        // 
        // Re-Add Hidden users not removed
        // 
        User[] hiddenUsers = currentGroup.getHiddenGroupMembers();
        for (int i = 0; hiddenUsers != null && i < hiddenUsers.length; i += 1) {
            if (!(hiddenUsers[i].compareEqual(userRemoveFromGroup)) || !isHiddenFromOwner) {
                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);
            }
        }
    }
    // 
    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, or just already updated
        // 
        Vector<VersionInfo> versionInfoList = getVersionableInfos(con, owner, vType, false, vKey, true, dbSyntax);
        if (versionInfoList.size() == 0) {
            throw new DataAccessException("Remove User " + userRemoveFromGroup + " Permission to access failed, " + vType.getTypeName() + "(" + vKey + ") record not found");
        } else {
            throw new DataAccessException("Remove User " + userRemoveFromGroup + " Permission to access failed " + vType.getTypeName() + "(" + vKey + ")");
        }
    }
}

Example 52 with Version

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

the class DbDriver method getVersionFromKeyValue.

/**
 * This method was created in VisualAge.
 * @return cbit.sql.Version
 * @param keyValue cbit.sql.KeyValue
 * @param vType cbit.sql.VersionableType
 */
private static Version getVersionFromKeyValue(Connection con, VersionableType vType, KeyValue keyValue) throws SQLException, DataAccessException {
    Version version = null;
    // 
    // Get a version from this keyValue
    // 
    String sql = null;
    VersionTable versionTable = VersionTable.getVersionTable(vType);
    UserTable userTable = UserTable.table;
    sql = "SELECT " + versionTable.getTableName() + "." + versionTable.id + "," + versionTable.getTableName() + "." + versionTable.name + "," + versionTable.getTableName() + "." + versionTable.ownerRef + "," + versionTable.getTableName() + "." + versionTable.privacy + "," + versionTable.getTableName() + "." + versionTable.versionBranchPointRef + "," + versionTable.getTableName() + "." + versionTable.versionDate + "," + versionTable.getTableName() + "." + versionTable.versionFlag + "," + versionTable.getTableName() + "." + versionTable.versionAnnot + "," + versionTable.getTableName() + "." + versionTable.versionBranchID + "," + userTable.getTableName() + "." + userTable.userid + " FROM " + versionTable.getTableName() + "," + userTable.getTableName() + " WHERE " + versionTable.getTableName() + "." + versionTable.id + " = " + keyValue + " AND " + versionTable.getTableName() + "." + versionTable.ownerRef + " = " + userTable.getTableName() + "." + userTable.id;
    java.sql.Statement stmt = con.createStatement();
    try {
        java.sql.ResultSet rset = stmt.executeQuery(sql);
        if (rset.next()) {
            BigDecimal groupid = rset.getBigDecimal(VersionTable.privacy_ColumnName);
            version = VersionTable.getVersion(rset, getGroupAccessFromGroupID(con, groupid));
        } else {
            throw new ObjectNotFoundException("Failed to find " + vType.getTypeName() + " (Key=" + keyValue + ")");
        }
    } catch (ObjectNotFoundException e) {
        lg.error("objectNotFound: " + e.getMessage(), e);
        throw e;
    } catch (Exception e) {
        lg.error("failed to get version: " + e.getMessage(), e);
        throw new DataAccessException("Failed to find " + vType.getTypeName() + " (Key=" + keyValue + "). \nError: " + e.getMessage());
    } finally {
        stmt.close();
    }
    return version;
}

Example 53 with Version

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

the class DbDriver method findAllChildren.

/**
 * This method was created in VisualAge.
 * @return java.util.Hashtable
 */
private static void findAllChildren(java.sql.Connection con, VersionableTypeVersion vtv, VersionableFamily refs) throws DataAccessException, SQLException {
    // Get VersionableTypes(tables) which possibly are children of argument vType
    Vector<VersionRef> possibleRefs = VersionTable.getChildVersionableTypes(vtv.getVType());
    Enumeration<VersionRef> enum1 = possibleRefs.elements();
    UserTable userTable = UserTable.table;
    while (enum1.hasMoreElements()) {
        VersionRef vr = enum1.nextElement();
        // BEGIN check VersionableType for children of versionKey
        String sql = null;
        VersionTable table = VersionTable.getVersionTable(vr.getVType());
        VersionTable vtvTable = VersionTable.getVersionTable(vtv.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() + "," + vtvTable.getTableName() + " WHERE " + vr.getRefField().getQualifiedColName() + " = " + table.id.getQualifiedColName() + " AND " + vtvTable.id.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() + " = " + table.id.getQualifiedColName() + " AND " + vr.getLinkField().getQualifiedColName() + " = " + vtv.getVersion().getVersionKey() + " AND " + table.ownerRef.getQualifiedColName() + " = " + userTable.id.getQualifiedColName();
        }
        java.sql.Statement stmt = con.createStatement();
        Vector<VersionableTypeVersion> allChildrenVTV = 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 childVTV = new VersionableTypeVersion(vr.getVType(), version);
                    allChildrenVTV.addElement(childVTV);
                } catch (Throwable e) {
                    throw new DataAccessException(e.getMessage());
                }
            }
        } finally {
            stmt.close();
        }
        // 
        for (int c = 0; c < allChildrenVTV.size(); c += 1) {
            VersionableTypeVersion childVTV = allChildrenVTV.elementAt(c);
            // 
            // Add VersionableRelationship to children of refs
            // 
            refs.addChildRelationship(new VersionableRelationship(vtv, childVTV));
            // 
            // Check referencingVTV for children to it(Recursion)
            // 
            findAllChildren(con, childVTV, refs);
        }
    }
}

Example 54 with Version

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

the class DictionaryDbDriver method getDatabaseSpecies.

/**
 * Insert the method's description here.
 * Creation date: (2/15/2003 10:12:24 PM)
 * @return cbit.vcell.dictionary.DBSpecies[]
 * @param con java.sql.Connection
 * @param user cbit.vcell.server.User
 * @param bOnlyUser boolean
 */
public DBFormalSpecies[] getDatabaseSpecies(Connection con, User user, String likeString, boolean isBound, FormalSpeciesType speciesType, int restrictSearch, int rowLimit, boolean bOnlyUser) throws SQLException {
    if (speciesType != null && speciesType.equals(FormalSpeciesType.speciesMatchSearch)) {
        FormalSpeciesType.MatchSearchFormalSpeciesType matchSearchFormalSpeciesType = (FormalSpeciesType.MatchSearchFormalSpeciesType) speciesType;
        if (matchSearchFormalSpeciesType.getMatchCriterias() == null || matchSearchFormalSpeciesType.getMatchCriterias().length == 0) {
            return null;
        }
        ArrayList<VCDocumentInfo> matchedVCDocumentInfos = new ArrayList<VCDocumentInfo>();
        Statement stmt = null;
        // OR condition
        // String sql =
        // "SELECT UNIQUE "  +BioModelTable.table.id.getQualifiedColName() +
        // " FROM "  + BioModelTable.table.getTableName() + "," + SpeciesContextModelTable.table.getTableName() +
        // " WHERE " + BioModelTable.table.modelRef.getQualifiedColName() + " = "+ SpeciesContextModelTable.table.modelRef.getQualifiedColName() +
        // " AND (";
        // for (int i = 0; i < matchSearchFormalSpeciesType.getMatchCriterias().length; i++) {
        // sql+=
        // (i>0?" OR ":"") +
        // " LOWER("+SpeciesContextModelTable.table.name.getQualifiedColName()+") LIKE " + "'" + matchSearchFormalSpeciesType.getMatchCriterias()[i] + "'" + " ESCAPE '"+BeanUtils.SQL_ESCAPE_CHARACTER+"'";
        // }
        // sql+=")";
        // AND condition
        String sql = "";
        for (int i = 0; i < matchSearchFormalSpeciesType.getMatchCriterias().length; i++) {
            sql += (i > 0 ? " INTERSECT " : "") + "SELECT UNIQUE " + BioModelTable.table.id.getQualifiedColName() + " FROM " + BioModelTable.table.getTableName() + "," + SpeciesContextModelTable.table.getTableName() + " WHERE " + BioModelTable.table.modelRef.getQualifiedColName() + " = " + SpeciesContextModelTable.table.modelRef.getQualifiedColName() + " AND " + " LOWER(" + SpeciesContextModelTable.table.name.getQualifiedColName() + ") LIKE " + "'" + matchSearchFormalSpeciesType.getMatchCriterias()[i] + "'" + " ESCAPE '" + BeanUtils.SQL_ESCAPE_CHARACTER + "'";
        }
        try {
            stmt = con.createStatement();
            ResultSet rset = stmt.executeQuery(sql);
            while (rset.next()) {
                BigDecimal versionKey = rset.getBigDecimal(1);
                Version version = new Version(new KeyValue(versionKey), null, null, null, null, null, null, null, null);
                matchedVCDocumentInfos.add(new BioModelInfo(version, null, (BioModelChildSummary) null, null));
            }
        } finally {
            if (stmt != null) {
                stmt.close();
            }
        }
        if (matchedVCDocumentInfos.size() == 0) {
            return null;
        }
        return new DBFormalSpecies[] { new MatchedVCDocumentsFromSearch(matchedVCDocumentInfos) };
    }
    if (!speciesType.bValidProperties(restrictSearch)) {
        throw new IllegalArgumentException("Improper properties in restrictSearch");
    }
    if (bOnlyUser && isBound == false) {
        throw new IllegalArgumentException("user not null expects isBound = true");
    }
    if (!((rowLimit == -1) || (rowLimit > 0))) {
        throw new IllegalArgumentException("rowLimit must be -1(Unlimited) or greater than 0");
    }
    if ((((restrictSearch & FormalSpeciesType.COMPOUND_ID) != 0) && (restrictSearch != FormalSpeciesType.COMPOUND_ID)) || (((restrictSearch & FormalSpeciesType.ENZYME_ID) != 0) && (restrictSearch != FormalSpeciesType.ENZYME_ID)) || (((restrictSearch & FormalSpeciesType.PROTEIN_ID) != 0) && (restrictSearch != FormalSpeciesType.PROTEIN_ID))) {
        throw new RuntimeException("Incompatible search properties together");
    }
    likeString = likeString.toUpperCase();
    // Columns always needed
    String columns = (speciesType.equals(FormalSpeciesType.compound) ? CompoundTable.table.getTableName() + ".*" + "," + CompoundAliasTable.table.name.getQualifiedColName() + "," + CompoundAliasTable.table.preferred.getQualifiedColName() : "") + (speciesType.equals(FormalSpeciesType.enzyme) ? EnzymeTable.table.getTableName() + ".*" + "," + EnzymeAliasTable.table.name.getQualifiedColName() + "," + EnzymeAliasTable.table.preferred.getQualifiedColName() : "") + (speciesType.equals(FormalSpeciesType.protein) ? ProteinTable.table.getTableName() + ".*" + "," + ProteinAliasTable.table.name.getQualifiedColName() + "," + ProteinAliasTable.table.preferred.getQualifiedColName() : "");
    // Columns if Bound (aliased because id in other tables)
    String dbSpeciesTable_id_alias = "dbspecies_id";
    if (isBound) {
        columns = columns + "," + DBSpeciesTable.table.id.getQualifiedColName() + " " + dbSpeciesTable_id_alias;
    }
    // Tables always needed
    String tables = (speciesType.equals(FormalSpeciesType.compound) ? CompoundTable.table.getTableName() + "," + CompoundAliasTable.table.getTableName() : "") + (speciesType.equals(FormalSpeciesType.enzyme) ? EnzymeTable.table.getTableName() + "," + EnzymeAliasTable.table.getTableName() : "") + (speciesType.equals(FormalSpeciesType.protein) ? ProteinTable.table.getTableName() + "," + ProteinAliasTable.table.getTableName() : "");
    // Tables if Bound
    if (isBound) {
        tables = tables + "," + DBSpeciesTable.table.getTableName();
        if (bOnlyUser) {
            tables = tables + "," + SpeciesContextModelTable.table.getTableName() + "," + SpeciesTable.table.getTableName() + "," + ModelTable.table.getTableName();
        }
    }
    String condition = "";
    // Conditions always needed
    condition = condition + (speciesType.equals(FormalSpeciesType.compound) ? CompoundTable.table.id.getQualifiedColName() + "=" + CompoundAliasTable.table.compoundRef.getQualifiedColName() : "") + (speciesType.equals(FormalSpeciesType.enzyme) ? EnzymeTable.table.id.getQualifiedColName() + "=" + EnzymeAliasTable.table.enzymeRef.getQualifiedColName() : "") + (speciesType.equals(FormalSpeciesType.protein) ? ProteinTable.table.id.getQualifiedColName() + "=" + ProteinAliasTable.table.proteinRef.getQualifiedColName() : "");
    java.util.Vector<String> likeConditions = new java.util.Vector<String>();
    if (speciesType.equals(FormalSpeciesType.compound)) {
        if ((restrictSearch & FormalSpeciesType.COMPOUND_ID) != 0) {
            likeConditions.add(" UPPER(" + CompoundTable.table.id.getQualifiedColName() + ") = " + likeString);
        }
        if ((restrictSearch & FormalSpeciesType.COMPOUND_ALIAS) != 0) {
            likeConditions.add(" UPPER(" + CompoundAliasTable.table.name.getQualifiedColName() + ") LIKE " + "'" + likeString + "'" + " ESCAPE '/'");
        }
        if ((restrictSearch & FormalSpeciesType.COMPOUND_KEGGID) != 0) {
            likeConditions.add(" UPPER(" + CompoundTable.table.keggID.getQualifiedColName() + ") LIKE " + "'" + likeString + "'" + " ESCAPE '/'");
        }
        if ((restrictSearch & FormalSpeciesType.COMPOUND_CASID) != 0) {
            likeConditions.add(" UPPER(" + CompoundTable.table.casID.getQualifiedColName() + ") LIKE " + "'" + likeString + "'" + " ESCAPE '/'");
        }
        if ((restrictSearch & FormalSpeciesType.COMPOUND_FORMULA) != 0) {
            likeConditions.add(" UPPER(" + CompoundTable.table.formula.getQualifiedColName() + ") LIKE " + "'" + likeString + "'" + " ESCAPE '/'");
        }
    } else if (speciesType.equals(FormalSpeciesType.enzyme)) {
        if ((restrictSearch & FormalSpeciesType.ENZYME_ID) != 0) {
            likeConditions.add(" UPPER(" + EnzymeTable.table.id.getQualifiedColName() + ") = " + likeString);
        }
        if ((restrictSearch & FormalSpeciesType.ENZYME_ALIAS) != 0) {
            likeConditions.add(" UPPER(" + EnzymeAliasTable.table.name.getQualifiedColName() + ") LIKE " + "'" + likeString + "'" + " ESCAPE '/'");
        }
        if ((restrictSearch & FormalSpeciesType.ENZYME_SYSNAME) != 0) {
            likeConditions.add(" UPPER(" + EnzymeTable.table.sysname.getQualifiedColName() + ") LIKE " + "'" + likeString + "'" + " ESCAPE '/'");
        }
        if ((restrictSearch & FormalSpeciesType.ENZYME_ECNUMBER) != 0) {
            likeConditions.add(" UPPER(" + EnzymeTable.table.ecNumber.getQualifiedColName() + ") LIKE " + "'" + likeString + "'" + " ESCAPE '/'");
        }
        // if((restrictSearch & FormalSpeciesType.ENZYME_ECNUMBER) != 0){likeConditions.add(" UPPER("+EnzymeTable.table.ecNumber.getQualifiedColName() + ") LIKE " + "'EC "+likeString+"'");}
        if ((restrictSearch & FormalSpeciesType.ENZYME_REACTION) != 0) {
            likeConditions.add(" UPPER(" + EnzymeTable.table.reaction.getQualifiedColName() + ") LIKE " + "'" + likeString + "'" + " ESCAPE '/'");
        }
        if ((restrictSearch & FormalSpeciesType.ENZYME_CASID) != 0) {
            likeConditions.add(" UPPER(" + EnzymeTable.table.casID.getQualifiedColName() + ") LIKE " + "'" + likeString + "'" + " ESCAPE '/'");
        }
    } else if (speciesType.equals(FormalSpeciesType.protein)) {
        if ((restrictSearch & FormalSpeciesType.PROTEIN_ID) != 0) {
            likeConditions.add(" UPPER(" + ProteinTable.table.id.getQualifiedColName() + ") = " + likeString);
        }
        if ((restrictSearch & FormalSpeciesType.PROTEIN_ALIAS) != 0) {
            likeConditions.add(" UPPER(" + ProteinAliasTable.table.name.getQualifiedColName() + ") LIKE " + "'" + likeString + "'" + " ESCAPE '/'");
        }
        if ((restrictSearch & FormalSpeciesType.PROTEIN_ACCESSION) != 0) {
            likeConditions.add(" UPPER(" + ProteinTable.table.accessionNumber.getQualifiedColName() + ") LIKE " + "'" + likeString + "'" + " ESCAPE '/'");
        }
        if ((restrictSearch & FormalSpeciesType.PROTEIN_SWISSPROTID) != 0) {
            likeConditions.add(" UPPER(" + ProteinTable.table.swissProtEntryName.getQualifiedColName() + ") LIKE " + "'" + likeString + "'" + " ESCAPE '/'");
        }
        if ((restrictSearch & FormalSpeciesType.PROTEIN_ORGANISM) != 0) {
            likeConditions.add(" UPPER(" + ProteinTable.table.organism.getQualifiedColName() + ") LIKE " + "'" + likeString + "'" + " ESCAPE '/'");
        }
        if ((restrictSearch & FormalSpeciesType.PROTEIN_KEYWORD) != 0) {
            likeConditions.add(" UPPER(" + ProteinTable.table.keywords.getQualifiedColName() + ") LIKE " + "'" + likeString + "'" + " ESCAPE '/'");
        }
        if ((restrictSearch & FormalSpeciesType.PROTEIN_DESCR) != 0) {
            likeConditions.add(" UPPER(" + ProteinTable.table.description.getQualifiedColName() + ") LIKE " + "'" + likeString + "'" + " ESCAPE '/'");
        }
    } else {
        throw new RuntimeException(speciesType.getName() + " Unsupported");
    }
    if (likeConditions.size() > 0) {
        condition = condition + " AND ( ";
        for (int i = 0; i < likeConditions.size(); i += 1) {
            String newCondition = (String) likeConditions.get(i);
            if (i != 0) {
                condition = condition + " OR ";
            }
            condition = condition + newCondition;
        }
        condition = condition + ")";
    }
    if (isBound) {
        condition = condition + " AND " + (speciesType.equals(FormalSpeciesType.compound) ? CompoundTable.table.id.getQualifiedColName() + "=" + DBSpeciesTable.table.compoundRef.getQualifiedColName() : "") + (speciesType.equals(FormalSpeciesType.enzyme) ? EnzymeTable.table.id.getQualifiedColName() + "=" + DBSpeciesTable.table.enzymeRef.getQualifiedColName() : "") + (speciesType.equals(FormalSpeciesType.protein) ? ProteinTable.table.id.getQualifiedColName() + "=" + DBSpeciesTable.table.proteinRef.getQualifiedColName() : "");
        if (bOnlyUser) {
            condition = condition + " AND " + SpeciesContextModelTable.table.speciesRef.getQualifiedColName() + " = " + SpeciesTable.table.id.getQualifiedColName() + " AND " + SpeciesTable.table.dbSpeciesRef.getQualifiedColName() + " = " + DBSpeciesTable.table.id.getQualifiedColName() + " AND " + SpeciesContextModelTable.table.modelRef.getQualifiedColName() + " = " + ModelTable.table.id.getQualifiedColName() + " AND " + ModelTable.table.ownerRef.getQualifiedColName() + " = " + user.getID();
        }
    }
    // ORDER BY 'id' must not be changed, used to collect multiple aliasnames into same info object
    String orderBy = (speciesType.equals(FormalSpeciesType.compound) ? CompoundTable.table.id.getQualifiedColName() : "") + (speciesType.equals(FormalSpeciesType.enzyme) ? EnzymeTable.table.id.getQualifiedColName() : "") + (speciesType.equals(FormalSpeciesType.protein) ? ProteinTable.table.id.getQualifiedColName() : "");
    String sql = "SELECT " + columns + " FROM " + tables + " WHERE " + condition + " ORDER BY " + orderBy;
    DBFormalSpecies[] databaseSpecies = null;
    Statement stmt = con.createStatement();
    if (rowLimit > 0) {
        stmt.setMaxRows(rowLimit);
    }
    try {
        ResultSet rset = stmt.executeQuery(sql);
        if (speciesType.equals(FormalSpeciesType.compound)) {
            databaseSpecies = CompoundTable.table.getCompounds(rset, isBound);
        } else if (speciesType.equals(FormalSpeciesType.enzyme)) {
            databaseSpecies = EnzymeTable.table.getEnzymes(rset, isBound);
        } else if (speciesType.equals(FormalSpeciesType.protein)) {
            databaseSpecies = ProteinTable.table.getProteins(rset, isBound);
        } else {
            throw new RuntimeException("FormalSpeciesType=" + speciesType.getName() + " Unsupported");
        }
    } finally {
        // Release resources include resultset
        stmt.close();
    }
    // 
    return databaseSpecies;
}

Example 55 with Version

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

the class GeomDbDriver method updateVersionable.

/**
 * This method was created in VisualAge.
 * @return cbit.image.VCImage
 * @param user cbit.vcell.server.User
 * @param image cbit.image.VCImage
 */
public KeyValue updateVersionable(InsertHashtable hash, QueryHashtable dbc, Connection con, User user, Geometry geometry, KeyValue updatedImageKey, boolean bVersion) throws DataAccessException, SQLException, RecordChangedException {
    Version newVersion = null;
    try {
        newVersion = updateVersionableInit(hash, con, user, geometry, bVersion);
        insertGeometry(hash, dbc, con, user, geometry, updatedImageKey, newVersion, bVersion);
    } catch (ImageException e) {
        lg.error(e.getMessage(), e);
        throw new DataAccessException("ImageException: " + e.getMessage());
    }
    return newVersion.getVersionKey();
}