package org.tgdb.export;
import org.tgdb.export.GQLScanner;
import java.util.*;
import java.sql.*;
public class GQLTranslator {
private StringBuffer m_from = null;
private StringBuffer m_where1 = null;
private StringBuffer m_where2 = null;
private String m_gqlstring = null;
private GQLScanner m_gqlsc = null;
private Hashtable m_vids = null;
private Hashtable m_vidTables = null;
private Hashtable m_mids = null;
private Hashtable m_midTables = null;
private String m_pid = null;
private String m_suid = null;
private String m_gsid = null;
private Vector m_comments = null; // Contains errors and warnings
private Vector m_code_snippet = null; // Contains the corresponding code
private Connection m_conn = null;
// Returns all warnings and error that has been encounterd during translation
public Vector getComments() {
return (Vector) m_comments.clone();
}
// Returns all the corresponding code snippets to the warnings and errors
public Vector getCode() {
return (Vector) m_code_snippet.clone();
}
public GQLTranslator(String pid, String suid, String gqlstring, Connection conn) {
m_gqlstring = gqlstring.replace('\"','\'');
m_pid = pid;
m_suid = suid;
m_gsid = null;
m_conn = conn;
m_gqlsc = new GQLScanner(m_gqlstring);
m_vidTables = new Hashtable();
m_vids = new Hashtable();
m_midTables = new Hashtable();
m_mids = new Hashtable();
m_from = new StringBuffer(512);
m_where1 = new StringBuffer(512);
m_where2 = new StringBuffer(512);
m_comments = new Vector();
m_code_snippet = new Vector();
}
public GQLTranslator(String pid, String suid, String gsid, String gqlstring, Connection conn) {
m_gqlstring = gqlstring.replace('\"','\'');
m_pid = pid;
m_pid = pid;
m_suid = suid;
m_gsid = gsid;
m_conn = conn;
m_gqlsc = new GQLScanner(m_gqlstring);
m_vidTables = new Hashtable();
m_vids = new Hashtable();
m_midTables = new Hashtable();
m_mids = new Hashtable();
m_from = new StringBuffer(512);
m_where1 = new StringBuffer(512);
m_where2 = new StringBuffer(512);
m_comments = new Vector();
m_code_snippet = new Vector();
}
public String translate() {
m_comments.removeAllElements();
m_code_snippet.removeAllElements();
String token = null;
// First we add the constraint that individuals must be part of this sampling unit
m_from.append("V_INDIVIDUALS_GQL ind ");
m_where1.append("ind.pid = " + m_pid + " AND ind.suid = " + m_suid + " ");
if (m_gsid != null) {
m_from.append(", V_R_IND_GRP_2 grp ");
m_where1.append("AND ind.iid = grp.iid AND grp.gsid = " + m_gsid + " ");
}
while (m_gqlsc.hasMoreTokens()) {
token = m_gqlsc.getNextToken();
dispatchToken(token);
}
return getTranslation();
}
private String getTranslation() {
StringBuffer output = new StringBuffer(2000);
output.append("FROM\n")
.append(m_from.toString())
.append("\nWHERE\n")
.append(m_where1.toString())
.append(" AND\n(\n")
.append(m_where2.toString())
.append(")");
return output.toString();
}
private void dispatchToken(String token) {
// I suppose it is enough if we recognise the standard tokens S., I., P. and G.
if (token.regionMatches(0, "S.", 0, 2)) { // Set command
dispatchSet(token.substring(2));
} else if (token.regionMatches(0, "I.", 0, 2)) { // Individual constraints
dispatchInd(token.substring(2));
} else if (token.regionMatches(0, "P.", 0, 2)) { // Phenotype constraints
dispatchPhe(token.substring(2));
} else if (token.regionMatches(0, "G.", 0, 2)) { // Genotype constraints
dispatchGen(token.substring(2));
} else {
m_where2.append(token + " ");
}
}
private void dispatchSet(String token) {
String grouping = null;
String group = null;
int suid = 0;
int gsid = 0;
int gid = 0;
int index = 0;
index = token.indexOf(".");
if (index > 0) {
grouping = token.substring(0, index);
token = token.substring(index + 1);
if (token.length() > 0) {
group = token.toString();
}
} else { // There are no group specified, that is token only contains tha grouping name
grouping = token;
}
// Now, let's find out the gsid and the gid;
Statement stmt = null;
ResultSet rset = null;
try {
if (grouping != null) {
stmt = m_conn.createStatement();
rset = stmt.executeQuery("SELECT GSID FROM V_GROUPINGS_1 WHERE NAME='" + grouping + "' AND suid=" + m_suid);
if (rset.next()) {
gsid = rset.getInt("GSID");
} else {
m_comments.addElement("Warning: Grouping doesn't exist for this sampling unit.");
m_code_snippet.addElement("S." + grouping);
gsid = -1;
}
rset.close();
stmt.close();
if (group != null) {
stmt = m_conn.createStatement();
rset = stmt.executeQuery("SELECT GID FROM V_GROUPS_1 WHERE NAME='" + group + "' AND gsid=" + gsid);
if (rset.next()) {
gid = rset.getInt("GID");
} else {
m_comments.addElement("Warning: Group doesn't exist");
m_code_snippet.addElement("S." + grouping + "." + group);
gid = -1;
}
}
}
} catch (SQLException e) {
// write something smart
m_comments.addElement("Error: Syntax error.");
m_code_snippet.addElement("S." + token);
} finally {
try {
if (rset != null) rset.close();
if (stmt != null) stmt.close();
} catch (SQLException ignored) {}
}
m_where2.append("\n\t(ind.iid IN (SELECT DISTINCT iid FROM V_SETS_GQL WHERE suid=" + m_suid + " ");
if (grouping != null)
m_where2.append("AND GSID=" + gsid + " ");
if (group != null)
m_where2.append("AND GID=" + gid + " ");
m_where2.append(") )\n");
}
private void dispatchInd(String token) {
String oper = null;
if ("IDENTITY".equalsIgnoreCase(token))
oper = "IDENTITY";
else if ("IID".equalsIgnoreCase(token))
oper = "IID";
else if ("ALIAS".equalsIgnoreCase(token))
oper = "ALIAS";
else if ("BIRTH_DATE".equalsIgnoreCase(token))
oper = "BIRTH_DATE";
else if ("MOTHER".equalsIgnoreCase(token))
oper= "MIDENTITY";
else if ("FATHER".equalsIgnoreCase(token))
oper = "FIDENTITY";
else if ("SEX".equalsIgnoreCase(token))
oper = "SEX";
else if (token.length() == 0)
oper = "ALIAS";
else
oper = "";
m_where2.append("ind." + oper + " ");
}
private void dispatchPhe(String token) {
String vname = null;
String oper = null;
String tableName = null;
int vid = 0;
int index = 0;
index = token.indexOf(".");
if (index > 0) {
vname = token.substring(0, index);
oper = token.substring(index + 1);
if ("VALUE".equalsIgnoreCase(oper))
oper = "VALUE";
else if ("DATE".equalsIgnoreCase(oper))
oper = "DATE_";
else {
m_comments.addElement("Error: Unknown suffix '" + oper + "'.");
m_code_snippet.addElement("P." + token);
oper = "VALUE"; // Why not?
}
} else { //
vname = token.toString();
oper = "VALUE";
}
// Check if this variable already has been used
if (m_vids.containsKey(vname)) {
vid = Integer.parseInt( (String) m_vids.get(vname));
tableName = (String) m_vidTables.get(Integer.toString(vid));
// This table has alredy been added to the from-String-Buffer and the join with
// individuals has also been done.
} else {
// This is the first occurence of this variable.
Statement stmt = null;
ResultSet rset = null;
try {
stmt = m_conn.createStatement();
rset = stmt.executeQuery("SELECT VID FROM V_VARIABLES_1 WHERE SUID=" + m_suid + " AND NAME='" + vname + "'");
if (rset.next()) {
vid = rset.getInt("VID");
} else {
m_comments.addElement("Warning: Variable doesn't exist for this sampling unit.");
m_code_snippet.addElement("P." + vname);
vid = -1;
}
} catch (SQLException e) {
m_comments.addElement("Error: Syntax error.");
m_code_snippet.addElement("P." + token);
} finally {
try {
if (rset != null) rset.close();
if (stmt != null) stmt.close();
} catch (SQLException ignored) {}
}
tableName = "P" + (m_vids.size() + 1);
m_vids.put(vname, Integer.toString(vid));
m_vidTables.put(Integer.toString(vid), tableName);
m_from.append(", V_PHENOTYPES_GQL " + tableName + " ");
m_where1.append("AND\n")
.append(tableName + ".iid=ind.iid AND\n")
.append(tableName + ".vid=" + vid + " ");
}
m_where2.append(tableName + "." + oper + " ");
}
private void dispatchGen(String token) {
String mname = null;
String oper = null;
String tableName = null;
int mid = 0;
int index = 0;
index = token.indexOf(".");
if (index > 0) {
mname = token.substring(0, index);
oper = token.substring(index + 1);
if ("A1".equalsIgnoreCase(oper))
oper = "A1NAME";
else if ("R1".equalsIgnoreCase(oper))
oper = "RAW1";
else if ("A2".equalsIgnoreCase(oper))
oper = "A2NAME";
else if ("R2".equalsIgnoreCase(oper))
oper = "RAW2";
else {
m_comments.addElement("Error: Unknown suffix '" + oper + "'.");
m_code_snippet.addElement("G." + token);
oper = "A1NAME"; // Why not?
}
} else { // Error!!! marker name must be followed by any of the following A1, A2, R1 or R2
// Do something damn it
m_comments.addElement("Error: Marker not specified.");
m_code_snippet.addElement("G." + token);
return;
}
// Check if this marker already has been used
if (m_mids.containsKey(mname)) {
// Alrighty than
mid = Integer.parseInt( (String) m_mids.get(mname));
tableName = (String) m_midTables.get(Integer.toString(mid));
// This table has alredy been added to the from-String-Buffer and the join with
// individuals has also been done.
} else {
// This is the first occurence of this marker.
Statement stmt = null;
ResultSet rset = null;
try {
stmt = m_conn.createStatement();
rset = stmt.executeQuery("SELECT MID FROM V_MARKERS_1 WHERE SUID=" + m_suid + " AND NAME='" + mname + "'");
if (rset.next()) {
mid = rset.getInt("MID");
} else {
m_comments.addElement("Warning: Marker doesn't exist for this sampling unit.");
m_code_snippet.addElement("G." + mname);
mid = -1;
}
} catch (SQLException e) {
m_comments.addElement("Error: Syntax error.");
m_code_snippet.addElement("G." + token);
} finally {
try {
if (rset != null) rset.close();
if (stmt != null) stmt.close();
} catch (SQLException ignored) {}
}
tableName = "G" + (m_mids.size() + 1);
m_mids.put(mname, Integer.toString(mid));
m_midTables.put(Integer.toString(mid), tableName);
m_from.append(", V_GENOTYPES_GQL " + tableName + " ");
m_where1.append("AND\n")
.append(tableName + ".iid=ind.iid AND\n")
.append(tableName + ".mid=" + mid + " ");
}
m_where2.append(tableName + "." + oper + " ");
}
}