public static void main(String[] args) throws IOException, SQLException {
ResourceLoader loader = Hsqldb.keggReactionLoader();
loader.addLocation("kegg.reaction", new SystemLocation("/databases/kegg/ligand/reaction"));
if (loader.canBackup()) loader.backup();
long t0 = System.nanoTime();
loader.update();
long t1 = System.nanoTime();
System.out.println(TimeUnit.NANOSECONDS.toMillis(t1 - t0) + " ms");
Connection connection = Hsqldb.keggReactionConnection().getConnection();
DSLContext context = DSL.using(connection, HSQLDB);
System.out.println(context.select().from(REACTION).fetch());
System.out.println(context.select().from(COMPOUND).fetch());
System.out.println(context.select().from(REACTANT).fetch());
System.out.println(context.select().from(PRODUCT).fetch());
connection.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) {
}
}
}
}
