/**
* Creates a map from the ChEBI Compounds resources of secondary to primary parentMap.
*
* @throws IOException problem reading file
* @throws MissingLocationException if ChEBI Compounds resource location is missing
*/
public void createMap() throws IOException, MissingLocationException {
ResourceFileLocation location = getLocation("ChEBI Compounds");
CSVReader csv = new CSVReader(new InputStreamReader(location.open()), '\t');
List<String> header = Arrays.asList(csv.readNext());
int accessionIndex = header.indexOf("CHEBI_ACCESSION");
int parentIndex = header.indexOf("PARENT_ID");
int statusIndex = header.indexOf("STATUS");
Pattern NULL_PATTERN = Pattern.compile("null");
Pattern ACCESSION_PATTERN = Pattern.compile("(?:C[hH]EBI:)?(\\d+)");
String[] row = null;
while ((row = csv.readNext()) != null) {
String accession = row[accessionIndex];
String parent = row[parentIndex];
Character status = row[statusIndex].charAt(0);
Matcher accessionMatcher = ACCESSION_PATTERN.matcher(accession);
Matcher parentMatcher = ACCESSION_PATTERN.matcher(parent);
if (accessionMatcher.find()) {
String childAcc = accessionMatcher.group(1);
String parentAcc = parentMatcher.find() ? parentMatcher.group(1) : childAcc;
childMap.put(parentAcc, "CHEBI:" + childAcc);
childMap.put("CHEBI:" + parentAcc, "CHEBI:" + childAcc);
parentMap.put(childAcc, "CHEBI:" + parentAcc);
parentMap.put("CHEBI:" + childAcc, "CHEBI:" + parentAcc);
statusMap.put(childAcc, status);
statusMap.put("CHEBI:" + childAcc, status);
}
}
location.close();
csv.close();
}
@Override
public void update() throws IOException {
ResourceFileLocation location = getLocation("KEGG Reaction");
HSQLDBLocation connection = connection();
try {
Hsqldb.createReactionSchema(connection.getConnection());
DSLContext create = DSL.using(connection.getConnection(), HSQLDB);
Set<String> compoundIds = Sets.newHashSetWithExpectedSize(10000);
InsertValuesStep2<?, String, String> reactionInsert =
create.insertInto(REACTION, REACTION.ACCESSION, REACTION.EC);
InsertValuesStep1<?, String> compoundInsert = create.insertInto(COMPOUND, COMPOUND.ACCESSION);
List<String[]> reactants = new ArrayList<String[]>(10000);
List<String[]> products = new ArrayList<String[]>(10000);
KEGGReactionParser parser =
new KEGGReactionParser(
location.open(), KEGGField.ENTRY, KEGGField.EQUATION, KEGGField.ENZYME);
Map<KEGGField, StringBuilder> entry;
while ((entry = parser.readNext()) != null) {
if (isCancelled()) break;
String equation = entry.get(KEGGField.EQUATION).toString();
String ec =
entry.containsKey(KEGGField.ENZYME)
? entry.get(KEGGField.ENZYME).toString().trim()
: "";
String[] sides = equation.split("<=>");
String[][] left = getParticipants(sides[0]);
String[][] right = getParticipants(sides[1]);
Matcher matcher = ACCESSION.matcher(entry.get(KEGGField.ENTRY).toString());
if (!ec.isEmpty()) ec = ec.split("\\s+")[0].trim();
if (matcher.find()) {
String accession = matcher.group(1);
reactionInsert.values(accession, ec);
for (String[] participant : left) {
String cid = participant[1];
if (compoundIds.add(cid)) compoundInsert.values(cid);
participant = Arrays.copyOf(participant, 3);
participant[2] = accession;
reactants.add(participant);
}
for (String[] participant : right) {
String cid = participant[1];
if (compoundIds.add(cid)) compoundInsert.values(cid);
participant = Arrays.copyOf(participant, 3);
participant[2] = accession;
products.add(participant);
}
}
}
// do the inserts
fireProgressUpdate("inserting reactions and compounds");
reactionInsert.execute();
compoundInsert.execute();
fireProgressUpdate("inserting reaction relations");
for (int i = 0, end = reactants.size() - 1; i <= end; i++) {
String[] participant = reactants.get(i);
double coef = Double.parseDouble(participant[0]);
String cid = participant[1];
String acc = participant[2];
create
.insertInto(REACTANT)
.set(REACTANT.COEFFICIENT, coef)
.set(
REACTANT.COMPOUND_ID,
create.select(COMPOUND.ID).from(COMPOUND).where(COMPOUND.ACCESSION.eq(cid)))
.set(
REACTANT.REACTION_ID,
create.select(REACTION.ID).from(REACTION).where(REACTION.ACCESSION.eq(acc)))
.execute();
}
for (int i = 0, end = products.size() - 1; i <= end; i++) {
String[] participant = products.get(i);
double coef = Double.parseDouble(participant[0]);
String cid = participant[1];
String acc = participant[2];
create
.insertInto(PRODUCT)
.set(PRODUCT.COEFFICIENT, coef)
.set(
PRODUCT.COMPOUND_ID,
create.select(COMPOUND.ID).from(COMPOUND).where(COMPOUND.ACCESSION.eq(cid)))
.set(
PRODUCT.REACTION_ID,
create.select(REACTION.ID).from(REACTION).where(REACTION.ACCESSION.eq(acc)))
.execute();
}
} catch (SQLException e) {
throw new IOException(e);
} finally {
location.close();
try {
connection.commit();
} catch (SQLException e) {
System.err.println(e.getMessage());
} finally {
try {
connection.close();
} catch (SQLException e) {
}
}
}
}