Examples with DBFormalSpecies cbit.vcell.model.DBFormalSpecies used on opensource projects

Example 11 with DBFormalSpecies

use of cbit.vcell.model.DBFormalSpecies in project vcell by virtualcell.

the class DictionaryDbDriver method getCompoundFromCasID.

/**
 * Returns the compound referenced by the casID
 * @return Compound
 * @param con Connection
 * @param casID String
 */
public FormalCompound getCompoundFromCasID(Connection con, String casID) throws SQLException {
    FormalCompound result = null;
    DBFormalSpecies[] dbfsArr = getDatabaseSpecies(con, null, casID, false, FormalSpeciesType.compound, FormalSpeciesType.COMPOUND_CASID, -1, false);
    if (dbfsArr != null && dbfsArr.length == 1) {
        result = (FormalCompound) dbfsArr[0];
    } else {
        throw new RuntimeException("Expecting only 1 result");
    }
    return result;
}

Example 12 with DBFormalSpecies

use of cbit.vcell.model.DBFormalSpecies in project vcell by virtualcell.

the class DictionaryDbDriver method getEnzymeFromECNumber.

/**
 * Returns the enzyme referenced by the given ECNumber
 * @return Enzyme
 * @param con Connection
 * @param ecNumber String
 */
public FormalEnzyme getEnzymeFromECNumber(Connection con, String ecNumber) throws SQLException {
    FormalEnzyme result = null;
    DBFormalSpecies[] dbfsArr = getDatabaseSpecies(con, null, ecNumber, false, FormalSpeciesType.enzyme, FormalSpeciesType.ENZYME_ECNUMBER, -1, false);
    if (dbfsArr != null && dbfsArr.length > 0) {
        result = (FormalEnzyme) dbfsArr[0];
    } else {
        throw new RuntimeException("Expecting only 1 result");
    }
    return result;
}

Example 13 with DBFormalSpecies

use of cbit.vcell.model.DBFormalSpecies in project vcell by virtualcell.

the class DictionaryDbDriver method getProteinFromSwissProtID.

/**
 * Returns the protein referenced by the given SwissProt Accession Number
 * @return Protein
 * @param con Connection
 * @param swissProtID String
 */
public FormalProtein getProteinFromSwissProtID(Connection con, String swissProtID) throws SQLException {
    FormalProtein result = null;
    DBFormalSpecies[] dbfsArr = getDatabaseSpecies(con, null, swissProtID, false, FormalSpeciesType.protein, FormalSpeciesType.PROTEIN_SWISSPROTID, -1, false);
    if (dbfsArr != null && dbfsArr.length > 0) {
        result = (FormalProtein) dbfsArr[0];
    } else {
        throw new RuntimeException("Expecting only 1 result");
    }
    return result;
}

Example 14 with DBFormalSpecies

use of cbit.vcell.model.DBFormalSpecies in project vcell by virtualcell.

the class ReactStepTable method getSQLUserReactionListQuery.

/**
 * Insert the method's description here.
 * Creation date: (7/12/2003 2:59:27 PM)
 * @return java.lang.String
 * @param likeString java.lang.String
 */
public String getSQLUserReactionListQuery(ReactionQuerySpec rqs, User user, DatabaseSyntax dbSyntax) {
    String reactant_or_flux_likeString = rqs.getReactantLikeString();
    String catalyst_likeString = rqs.getCatalystLikeString();
    String product_likeString = rqs.getProductLikeString();
    DBFormalSpecies reactant_or_flux_dbspecies = rqs.getReactantBoundSpecies();
    DBFormalSpecies catalyst_dbspecies = rqs.getCatalystBoundSpecies();
    DBFormalSpecies product_dbspecies = rqs.getProductBoundSpecies();
    String repWildCard = rqs.getAnyReactionParticipantLikeString();
    DBFormalSpecies typeWildCard = rqs.getAnyReactionParticipantBoundSpecies();
    // Get list of distinct USER reactions that are visible to user
    // 
    // Create comma-separated lists of dbspeciesid
    // 
    StringBuffer reactant_flux_list = new StringBuffer();
    StringBuffer catalyst_list = new StringBuffer();
    StringBuffer product_list = new StringBuffer();
    if (reactant_or_flux_dbspecies != null) {
        reactant_flux_list.append(reactant_or_flux_dbspecies.getDBFormalSpeciesKey().toString());
    }
    if (catalyst_dbspecies != null) {
        catalyst_list.append(catalyst_dbspecies.getDBFormalSpeciesKey().toString());
    }
    if (product_dbspecies != null) {
        product_list.append(product_dbspecies.getDBFormalSpeciesKey().toString());
    }
    // Creat conditions for flux,reaction,catalyst,product
    boolean[] bNeedsDBSpeciesTableArr = new boolean[3];
    StringBuffer[] subConditionsArr = new StringBuffer[3];
    for (int i = 0; i < 3; i += 1) {
        boolean bHasLike = false;
        boolean bHasDBspid = false;
        StringBuffer subConditions = new StringBuffer();
        subConditionsArr[i] = subConditions;
        if (i == 0) {
            bHasLike = (reactant_or_flux_likeString != null && reactant_or_flux_likeString.length() > 0);
            bHasDBspid = (reactant_or_flux_dbspecies != null);
            if (!bHasLike && !bHasDBspid) {
                continue;
            }
            subConditions.append("(");
            subConditions.append("(vc_reactpart_sub.role = 'reactant' OR vc_reactpart_sub.role = 'flux') AND ");
            if (bHasLike) {
                subConditions.append("upper(vc_species_sub.commonname) LIKE upper('" + reactant_or_flux_likeString + "')");
                if (bHasDBspid) {
                    subConditions.append(" OR ");
                }
            }
            if (bHasDBspid) {
                bNeedsDBSpeciesTableArr[i] = true;
                // subConditions.append("vc_species_sub.dbspeciesref IN ("+reactant_flux_list.toString()+")");
                subConditions.append("vc_species_sub.dbspeciesref = vc_dbspecies_sub.id AND (");
                subConditions.append("vc_dbspecies_sub.compoundref IN (" + reactant_flux_list.toString() + ") OR ");
                subConditions.append("vc_dbspecies_sub.enzymeref IN (" + reactant_flux_list.toString() + ") OR ");
                subConditions.append("vc_dbspecies_sub.proteinref IN (" + reactant_flux_list.toString() + ")");
                subConditions.append(")");
            }
            subConditions.append(")");
        } else if (i == 1) {
            bHasLike = (catalyst_likeString != null && catalyst_likeString.length() > 0);
            bHasDBspid = (catalyst_dbspecies != null);
            if (!bHasLike && !bHasDBspid) {
                continue;
            }
            if (subConditions.length() > 0) {
                subConditions.append(" AND ");
            }
            subConditions.append("(");
            subConditions.append("vc_reactpart_sub.role = 'catalyst' AND ");
            if (bHasLike) {
                subConditions.append("upper(vc_species_sub.commonname) LIKE upper('" + catalyst_likeString + "')");
                if (bHasDBspid) {
                    subConditions.append(" OR ");
                }
            }
            if (bHasDBspid) {
                bNeedsDBSpeciesTableArr[i] = true;
                // subConditions.append("vc_species_sub.dbspeciesref IN ("+catalyst_list.toString()+")");
                subConditions.append("vc_species_sub.dbspeciesref = vc_dbspecies_sub.id AND (");
                subConditions.append("vc_dbspecies_sub.compoundref IN (" + catalyst_list.toString() + ") OR ");
                subConditions.append("vc_dbspecies_sub.enzymeref IN (" + catalyst_list.toString() + ") OR ");
                subConditions.append("vc_dbspecies_sub.proteinref IN (" + catalyst_list.toString() + ")");
                subConditions.append(")");
            }
            subConditions.append(")");
        } else if (i == 2) {
            bHasLike = (product_likeString != null && product_likeString.length() > 0);
            bHasDBspid = (product_dbspecies != null);
            if (!bHasLike && !bHasDBspid) {
                continue;
            }
            if (subConditions.length() > 0) {
                subConditions.append(" AND ");
            }
            subConditions.append("(");
            subConditions.append("vc_reactpart_sub.role = 'product' AND ");
            if (bHasLike) {
                subConditions.append("upper(vc_species_sub.commonname) LIKE upper('" + product_likeString + "')");
                if (bHasDBspid) {
                    subConditions.append(" OR ");
                }
            }
            if (bHasDBspid) {
                bNeedsDBSpeciesTableArr[i] = true;
                // subConditions.append("vc_species_sub.dbspeciesref IN ("+product_list.toString()+")");
                subConditions.append("vc_species_sub.dbspeciesref = vc_dbspecies_sub.id AND (");
                subConditions.append("vc_dbspecies_sub.compoundref IN (" + product_list.toString() + ") OR ");
                subConditions.append("vc_dbspecies_sub.enzymeref IN (" + product_list.toString() + ") OR ");
                subConditions.append("vc_dbspecies_sub.proteinref IN (" + product_list.toString() + ")");
                subConditions.append(")");
            }
            subConditions.append(")");
        }
    }
    // 
    String sql = null;
    Field specialBMField = new Field("id bmid", SQLDataType.integer, "");
    specialBMField.setTableName(BioModelTable.table.getTableName());
    Field[] f = { // 1
    ReactStepTable.table.name, // 2
    ReactStepTable.table.id, // 3
    ReactStepTable.table.reactType, // 4
    ReactPartTable.table.role, // 5
    ReactPartTable.table.stoich, // 6
    SpeciesTable.table.commonName, // 7
    specialBMField, // 8
    ReactStepTable.table.structRef };
    Table[] t = { ReactStepTable.table, BioModelTable.table, ReactPartTable.table, SpeciesContextModelTable.table, SpeciesTable.table };
    // 
    // 
    // Non-WildCard subcondition
    boolean hadPreviousCondiiton = false;
    String searchConditions = "";
    for (int i = 0; i < 3; i += 1) {
        if (subConditionsArr[i].length() > 0) {
            // 
            if (hadPreviousCondiiton) {
                searchConditions += " INTERSECT ";
            }
            hadPreviousCondiiton = true;
            // 
            searchConditions += "(" + " SELECT " + Table.SQL_GLOBAL_HINT + " DISTINCT " + " vc_reactstep_sub.id " + " FROM " + ReactStepTable.table.getTableName() + " vc_reactstep_sub" + "," + ReactPartTable.table.getTableName() + " vc_reactpart_sub" + "," + SpeciesContextModelTable.table.getTableName() + " vc_modelsc_sub" + "," + SpeciesTable.table.getTableName() + " vc_species_sub" + (bNeedsDBSpeciesTableArr[i] ? "," + DBSpeciesTable.table.getTableName() + " vc_dbspecies_sub" : "") + " WHERE " + subConditionsArr[i].toString() + " AND " + " vc_species_sub.id=vc_modelsc_sub.speciesref AND " + " vc_modelsc_sub.modelref = " + BioModelTable.table.modelRef.getQualifiedColName() + " AND " + " vc_modelsc_sub.id=vc_reactpart_sub.scref AND " + " vc_reactpart_sub.reactstepref=vc_reactstep_sub.id " + ")";
        }
    }
    // WildCard subcondtion
    if (repWildCard != null || typeWildCard != null) {
        searchConditions = "(" + " SELECT " + Table.SQL_GLOBAL_HINT + " DISTINCT " + " vc_reactstep_sub.id " + " FROM " + ReactStepTable.table.getTableName() + " vc_reactstep_sub" + "," + ReactPartTable.table.getTableName() + " vc_reactpart_sub" + "," + SpeciesContextModelTable.table.getTableName() + " vc_modelsc_sub" + "," + SpeciesTable.table.getTableName() + " vc_species_sub" + (typeWildCard != null ? "," + DBSpeciesTable.table.getTableName() + " vc_dbspecies_sub" : "") + " WHERE " + "(" + (repWildCard != null ? "upper(vc_species_sub.commonname) LIKE upper('" + repWildCard + "')" : "") + (repWildCard != null && typeWildCard != null ? " OR  " : "") + (typeWildCard != null ? "(" + "vc_species_sub.dbspeciesref IS NOT NULL AND " + "vc_species_sub.dbspeciesref = vc_dbspecies_sub.id AND " + "(" + "vc_dbspecies_sub.compoundref=" + typeWildCard.getDBFormalSpeciesKey() + " OR " + "vc_dbspecies_sub.enzymeref=" + typeWildCard.getDBFormalSpeciesKey() + " OR " + "vc_dbspecies_sub.proteinref=" + typeWildCard.getDBFormalSpeciesKey() + ")" + ")" : "") + ")" + " AND " + " vc_species_sub.id=vc_modelsc_sub.speciesref AND " + " vc_modelsc_sub.modelref = " + BioModelTable.table.modelRef.getQualifiedColName() + " AND " + " vc_modelsc_sub.id=vc_reactpart_sub.scref AND " + " vc_reactpart_sub.reactstepref=vc_reactstep_sub.id " + ")";
    }
    // 
    // 
    // 
    String condition = "";
    if (searchConditions.length() > 0) {
        condition += ReactStepTable.table.id.getQualifiedColName() + " IN " + "(" + searchConditions + ")" + " AND ";
    }
    condition += SpeciesTable.table.id.getQualifiedColName() + " = " + SpeciesContextModelTable.table.speciesRef.getQualifiedColName() + " AND " + SpeciesContextModelTable.table.id.getQualifiedColName() + " = " + ReactPartTable.table.scRef.getQualifiedColName() + " AND " + ReactPartTable.table.reactStepRef.getQualifiedColName() + " = " + ReactStepTable.table.id.getQualifiedColName() + " AND " + ReactStepTable.table.modelRef.getQualifiedColName() + " = " + BioModelTable.table.modelRef.getQualifiedColName();
    String special = " ORDER BY " + ReactStepTable.table.id.getQualifiedColName();
    sql = DatabasePolicySQL.enforceOwnershipSelect(user, f, t, (OuterJoin) null, condition, special, dbSyntax, true);
    StringBuffer sb = new StringBuffer(sql);
    // LOBs cannot be accessed if the query uses the DISTINCT or UNIQUE keyword
    sb.insert(7, Table.SQL_GLOBAL_HINT + " DISTINCT ");
    return sb.toString();
}