Finally got blipkit started from java via jpl
Fri, 2009-10-16 11:17 | by Samuel Lampa
Furthermore, CLASSPATH has to be:
Finally got blipkit started from java via jpl :)
- (Thanks to Andrew Koster on the SWIPL mailing list, who made me continue researching the LD_PRELOAD trick!)
In order to get the jpl java examples to work, LD_LIBRARY_PATH has to contain:
/usr/lib/jvm/java-1.5.0-sun-1.5.0.19/jre/lib/i386/client/:/usr/lib/jvm/java-1.5.0-sun-1.5.0.19/jre/lib/i386/
Furthermore, CLASSPATH has to be:
/usr/local/lib/pl-5.7.15/lib/jpl.jar:/home/samuel/install/swi-prolog/pl57/packages/jpl/examples/java/Test
Now firing up blipkit works, when calling Java from commandline!!! :).
Running the command:
LD_PRELOAD=/usr/local/lib/pl-5.7.15/lib/i686-linux/libjpl.so java -Djava.library.path=/usr/local/lib/pl-5.7.15/lib/i686-linux/ Test
... I get:
-G0 -A0 -T0 -g main -t halt -s /home/samuel/blipstart.pl % library(swi_hooks) compiled into pce_swi_hooks 0.00 sec, 2,060 bytes % /home/samuel/.plrc compiled 0.00 sec, 704 bytes % bio(bioprolog_util) compiled into bioprolog_util 0.01 sec, 42,180 bytes % bio(mode) compiled into mode 0.00 sec, 7,788 bytes % bio(dbmeta) compiled into dbmeta 0.04 sec, 244,516 bytes % library(option) compiled into swi_option 0.00 sec, 8,640 bytes % library(sgml) compiled into sgml 0.01 sec, 41,308 bytes % library(quintus) compiled into quintus 0.01 sec, 11,552 bytes % rewrite compiled into rewrite 0.01 sec, 17,668 bytes % library(uri) compiled into uri 0.00 sec, 5,940 bytes % library(record) compiled into record 0.01 sec, 15,332 bytes % rdf_parser compiled into rdf_parser 0.03 sec, 74,800 bytes % library(gensym) compiled into gensym 0.00 sec, 2,436 bytes % rdf_triple compiled into rdf_triple 0.00 sec, 19,132 bytes % library(rdf) compiled into rdf 0.04 sec, 153,032 bytes % library(assoc) compiled into assoc 0.00 sec, 12,104 bytes % library(sgml_write) compiled into sgml_write 0.01 sec, 51,600 bytes % library(nb_set) compiled into nb_set 0.00 sec, 3,216 bytes % rdf_cache compiled into rdf_cache 0.00 sec, 8,592 bytes % library(semweb/rdf_db) compiled into rdf_db 0.09 sec, 309,936 bytes % library(utf8) compiled into utf8 0.01 sec, 7,200 bytes % library(url) compiled into url 0.02 sec, 61,000 bytes % library(readutil) compiled into read_util 0.01 sec, 8,800 bytes % library(socket) compiled into socket 0.00 sec, 5,608 bytes % library(base64) compiled into base64 0.00 sec, 9,156 bytes % library(http/http_open) compiled into http_open 0.04 sec, 108,672 bytes % library(date) compiled into date 0.00 sec, 9,508 bytes % library(semweb/rdf_http_plugin) compiled into rdf_http_plugin 0.04 sec, 124,608 bytes % bio(io) compiled into io 0.19 sec, 737,684 bytes % bio(metadata_db) compiled into metadata_db 0.01 sec, 16,688 bytes % bio(blipkit_shell_dcg) compiled into blipkit_shell_dcg 0.00 sec, 4,600 bytes % bio(tabling) compiled into tabling 0.00 sec, 9,488 bytes % bio(blipkit) compiled into blipkit 0.23 sec, 862,060 bytes % bio(graph) compiled into graph 0.01 sec, 18,220 bytes % bio(macros_transitive) compiled into macros_transitive 0.00 sec, 3,516 bytes % bio(ontol_db) compiled into ontol_db 0.04 sec, 113,000 bytes % bio(stats_distributions) compiled into stats_distributions 0.01 sec, 25,396 bytes % bio(curation_db) compiled into curation_db 0.02 sec, 58,088 bytes % bio(textmatch) compiled into textmatch 0.00 sec, 5,296 bytes % bio(macros_lookup) compiled into macros_lookup 0.00 sec, 9,152 bytes % bio(ontol_lookup) compiled into ontol_lookup 0.00 sec, 16,924 bytes % bio(ontol_writer) compiled into ontol_writer 0.01 sec, 1,016 bytes % bio(ontol_writer_text) compiled into ontol_writer_text 0.00 sec, 20,660 bytes % library(rbtrees) compiled into rbtrees 0.01 sec, 45,648 bytes % library(thread_pool) compiled into thread_pool 0.02 sec, 66,712 bytes % library(memfile) compiled into memory_file 0.00 sec, 3,900 bytes % library(broadcast) compiled into broadcast 0.00 sec, 3,988 bytes % library(settings) compiled into settings 0.00 sec, 24,568 bytes % dcg_basics compiled into dcg_basics 0.00 sec, 11,964 bytes % library(pairs) compiled into pairs 0.00 sec, 4,380 bytes % html_write compiled into html_write 0.02 sec, 61,332 bytes % http_exception compiled into http_exception 0.00 sec, 3,716 bytes % mimetype compiled into mimetype 0.00 sec, 6,512 bytes % mimepack compiled into mime_pack 0.00 sec, 5,572 bytes % http_header compiled into http_header 0.06 sec, 193,528 bytes % http_stream compiled into http_stream 0.00 sec, 3,988 bytes % http_wrapper compiled into httpd_wrapper 0.07 sec, 211,776 bytes % library(http/thread_httpd) compiled into thread_httpd 0.10 sec, 301,516 bytes % library(http/http_session) compiled into http_session 0.00 sec, 14,852 bytes % bio(xml_writer) compiled into xml_writer 0.01 sec, 8,124 bytes % bio(serval) compiled into serval 0.12 sec, 377,788 bytes % bio(ontol_writer_obo) compiled into ontol_writer_obo 0.13 sec, 426,512 bytes % bio(blipkit_ontol) compiled into blipkit_ontol 0.23 sec, 747,860 bytes % library(oset) compiled into oset 0.00 sec, 8,264 bytes % library(ordsets) compiled into ordsets 0.01 sec, 17,120 bytes % bio(phylo_db) compiled into phylo_db 0.03 sec, 106,012 bytes % bio(blipkit_phylo) compiled into blipkit_phylo 0.03 sec, 118,896 bytes % bio(fasta_db) compiled into fasta_db 0.00 sec, 1,812 bytes % bio(gencode) compiled into gencode 0.03 sec, 87,032 bytes % bio(suffixtree) compiled into suffixtree 0.00 sec, 19,216 bytes % bio(iupac) compiled into iupac 0.01 sec, 2,764 bytes % bio(bioseq) compiled into bioseq 0.04 sec, 126,644 bytes % bio(blipkit_fasta) compiled into blipkit_fasta 0.05 sec, 137,536 bytes % bio(sb_db) compiled into sb_db 0.00 sec, 12,268 bytes % bio(blipkit_sb) compiled into blipkit_sb 0.01 sec, 29,616 bytes % library(http/http_client) compiled into http_client 0.01 sec, 17,264 bytes % bio(web_fetch) compiled into web_fetch 0.02 sec, 21,792 bytes % bio(xml_transform) compiled into xml_transform 0.01 sec, 18,572 bytes % bio(web_fetch_google) compiled into web_fetch_google 0.01 sec, 36,604 bytes % bio(web_fetch_yahoo) compiled into web_fetch_yahoo 0.00 sec, 3,140 bytes % bio(web_fetch_ncbi) compiled into web_fetch_ncbi 0.01 sec, 8,464 bytes % bio(web_search_expander) compiled into web_search_expander 0.00 sec, 11,608 bytes % bio(blipkit_web) compiled into blipkit_web 0.05 sec, 136,152 bytes % /home/samuel/blipstart.pl compiled 0.63 sec, 2,072,576 bytes test 0...% test.pl compiled 0.00 sec, 2,220 bytes passed. test 1...passed. test 2...passed. test 3...passed. test 4...passed. test 5...passed. test 6...passed. test 7...passed. test 8...passed. test 9...passed. test 10...passed. test 11...passed. test 101...00000000000000000000111111111111111111112222222222222222222233333333333333333333444444444444444444445555555555555555555566666666666666666666777777777777777777778888888888888888888899999999999999999999passed.
The content of the Test.java is (I modified it to enforce loading blipkit):
//tabstop=4
//*****************************************************************************/
// Project: jpl
//
// File: $Id$
// Date: $Date$
// Author: Fred Dushin <fadushin@syr.edu>
//
//
// Description:
//
//
// -------------------------------------------------------------------------
// Copyright (c) 1998 Fred Dushin
// All rights reserved.
//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Library Public License
// as published by the Free Software Foundation; either version 2
// of the License, or (at your option) any later version.
//
// This library is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU Library Public License for more details.
//*****************************************************************************/
import java.io.BufferedInputStream;
import java.io.DataInputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.Hashtable;
import jpl.Query; // empirically, we need this, but I don't know why...
import jpl.PrologException;
import jpl.*;
public class Test
{
public static void
main( java.lang.String argv[] )
{
String[] blipInitFile;
blipInitFile = readFileToStringArray("/home/samuel/blipstart");
for (int i=1; i<blipInitFile.length; i++) {
if (blipInitFile[i] != null) {
System.out.println(blipInitFile[i]);
}
}
JPL.setDefaultInitArgs(blipInitFile);
JPL.init(); // we don't need this with the current JPL (lazy init-on-demand)
run_tests();
}
public static String[] readFileToStringArray(String filePath) {
File file = new File(filePath);
FileInputStream fis = null;
BufferedInputStream bis = null;
DataInputStream dis = null;
List<String> stringBuffer = new ArrayList<String>();
try {
fis = new FileInputStream(file);
// Here BufferedInputStream is added for fast reading.
bis = new BufferedInputStream(fis);
dis = new DataInputStream(bis);
// dis.available() returns 0 if the file does not have more lines.
int i = 0;
while (dis.available() != 0) {
stringBuffer.add(dis.readLine());
}
// dispose all the resources after using them.
fis.close();
bis.close();
dis.close();
} catch (FileNotFoundException e) {
e.printStackTrace();
} catch (IOException e) {
e.printStackTrace();
}
String[] result = stringBuffer.toArray(new String[]{});
return result;
}
static void
run_tests()
{
test_0();
test_1();
test_2();
test_3();
test_4();
test_5();
test_6();
test_7();
test_8();
test_9();
test_10();
test_11();
test_101();
}
static void
test_0()
{
System.out.print( "test 0..." );
Query query =
new Query("consult('test.pl')");
if ( !query.hasSolution() ){
System.out.println( "consult('test.pl') failed" );
System.exit( 1 );
}
System.out.println( "passed." );
}
static Term a =
new Atom( "a" );
static Term b =
new Atom( "b" );
static Term f_a =
new Compound(
"f",
new Term[] {a}
);
static Term pair_a_b =
new Compound(
"-",
new Term[] {a,b}
);
static void
test_1()
{
System.out.print( "test 1..." );
Query query =
new Query("p(a)");
if ( !query.hasSolution() ){
System.out.println( "p(a) failed" );
System.exit( 1 );
}
System.out.println( "passed." );
}
static void
test_2()
{
System.out.print( "test 2..." );
Query query =
new Query(
"p",
new Term[] {f_a}
);
if ( !query.hasSolution() ){
System.out.println( "p(f(a)) failed" );
System.exit( 1 );
}
System.out.println( "passed." );
}
static void
test_3()
{
System.out.print( "test 3..." );
Query query =
new Query(
"p",
new Term[] {pair_a_b}
);
if ( !query.hasSolution() ){
System.out.println( "p( a-b ) failed" );
System.exit( 1 );
}
System.out.println( "passed." );
}
static void
test_4()
{
System.out.print( "test 4..." );
Variable X = new Variable("X");
Query query =
new Query(
"p",
new Term[] {X}
);
Term[] target = new Term[] {a,f_a,pair_a_b,new Variable("_")};
Hashtable[] solutions = query.allSolutions();
if ( solutions.length != 4 ){
System.out.println( "p(X) failed:" );
System.out.println( "\tExpected: 4 solutions" );
System.out.println( "\tGot: " + solutions.length );
System.exit( 1 );
}
for ( int i = 0; i < solutions.length-1; ++i ){
Term binding = (Term)solutions[i].get( "X" );
if ( ! binding.equals( target[i] ) ){
System.out.println( "p(X) failed" );
System.out.println( "\tExpected: " + target[i]);
System.out.println( "\tGot: " + binding);
System.exit( 1 );
}
}
System.out.println( "passed." );
}
static void
test_5()
{
System.out.print( "test 5..." );
Variable X = new Variable("X");
Variable Y = new Variable("Y");
Query query =
new Query(
"p",
new Term[] {X,Y}
);
Term[] x_target = new Term[] {a,a};
Term[] y_target = new Term[] {a,b};
Hashtable[] solutions = query.allSolutions();
if ( solutions.length != 2 ){
System.out.println( "p(X, Y) failed:" );
System.out.println( "\tExpected: 2 solutions" );
System.out.println( "\tGot: " + solutions.length );
System.exit( 1 );
}
for ( int i = 0; i < solutions.length; ++i ){
Object x_binding = solutions[i].get("X");
if ( ! x_binding.equals( x_target[i] ) ){
System.out.println( "p(X, Y) failed:" );
System.out.println( "\tExpected: " + x_target[i] );
System.out.println( "\tGot: " + x_binding );
System.exit( 1 );
}
Object y_binding = solutions[i].get("Y");
if ( ! y_binding.equals( y_target[i] ) ){
System.out.println( "p( X, Y ) failed:" );
System.out.println( "\tExpected: " + y_target[i] );
System.out.println( "\tGot: " + y_binding );
System.exit( 1 );
}
}
System.out.println( "passed." );
}
static void
test_6()
{
System.out.print( "test 6..." );
Variable X = new Variable("X");
Query query =
new Query(
"p",
new Term[] {X,X}
);
Term[] x_target = new Term[] {a};
Hashtable[] solutions = query.allSolutions();
if ( solutions.length != 1 ){
System.out.println( "p(X, X) failed:" );
System.out.println( "\tExpected: 1 solution" );
System.out.println( "\tGot: " + solutions.length );
System.exit( 1 );
}
for ( int i = 0; i < solutions.length; ++i ){
Object x_binding = solutions[i].get("X");
if ( ! x_binding.equals( x_target[i] ) ){
System.out.println( "p(X, X) failed:" );
System.out.println( "\tExpected: " + x_target[i] );
System.out.println( "\tGot: " + x_binding );
System.exit( 1 );
}
}
System.out.println( "passed." );
}
static void
test_7()
{
System.out.print( "test 7..." );
Variable X = new Variable("X");
Variable Y = new Variable("Y");
Query query =
new Query(
"r",
new Term[] {
new Compound(
"f",
new Term[] {X,X}
),
Y
}
);
Hashtable[] solutions = query.allSolutions();
if ( solutions.length != 2 ){
System.out.println( "r(f(X,X), Y) failed:" );
System.out.println( "\tExpected: 2 solutions" );
System.out.println( "\tGot: " + solutions.length );
System.exit( 1 );
}
Object x_binding, y_binding;
x_binding = solutions[0].get("X");
y_binding = solutions[0].get("Y");
if ( x_binding != y_binding ){
System.out.println( "r(f(X,X), Y) failed:" );
System.out.println( Util.toString( solutions[0] ) );
System.out.println( "\tThe variables to which X and Y are bound in the first solution should be identical." );
System.exit( 1 );
}
x_binding = solutions[1].get("X");
y_binding = solutions[1].get("Y");
if ( x_binding == y_binding ){
System.out.println( "r(f(X,X), Y) failed:" );
System.out.println( Util.toString( solutions[1] ) );
System.out.println( "\tThe variables to which X and Y are bound in the second solution should be distinct." );
System.exit( 1 );
}
if ( x_binding.equals( y_binding ) ){
System.out.println( "r(f(X,X), Y) failed:" );
System.out.println( Util.toString( solutions[1] ) );
System.out.println( "\tThe variables to which X and Y are bound in the second solution should not be \"equal\"." );
System.exit( 1 );
}
/*
if ( ! solutions[0].get("X").equals( solutions[1].get("X") ) ){
System.out.println( "r(f(X,X), Y) failed:" );
System.out.println( Util.toString( solutions[0] ) );
System.out.println(
"\tThe variable to which X is bound in the first solution (" + solutions[0].get("X") + ")\n" +
"\tshould be equal to the variable to which X is bound in the second (" + solutions[1].get("X") + ")");
System.exit( 1 );
}
*/
System.out.println( "passed." );
}
static void
test_8()
{
System.out.print( "test 8..." );
Variable X = new Variable("X");
Query query =
new Query(
"r",
new Term[] {
new Compound(
"f",
new Term[] {X,X}
),
X
}
);
Hashtable[] solutions = query.allSolutions();
if ( solutions.length != 2 ){
System.out.println( "r( f( X, X ), X ) failed:" );
System.out.println( "\tExpected: 2 solutions" );
System.out.println( "\tGot: " + solutions.length );
System.exit( 1 );
}
/*
if ( ! solutions[0].get("X").equals( solutions[1].get("X") ) ){
System.out.println( "r( f( X, X ), X ) failed:" );
System.out.println( Util.toString( solutions[0] ) );
System.out.println(
"\tThe variable to which X is bound in the first solution\n" +
"\tshould be equal to the variable to which X is bound in the second." );
System.exit( 1 );
}
*/
System.out.println( "passed." );
}
// corresponds with Prolog List: [a-a,a-b]
static Term test_9_solution =
Util.termArrayToList(
new Term[] {
new Compound( "-", new Term[] {a,a}),
new Compound( "-", new Term[] {a,b})
}
);
static void
test_9()
{
System.out.print( "test 9..." );
Variable X = new Variable("X");
Variable Y = new Variable("Y");
Variable XYs = new Variable("XYs");
Query query =
new Query(
"bagof",
new Term[] {
new Compound(
"-",
new Term[] {X,Y}
),
new Compound(
"p",
new Term[] {X,Y}
),
XYs
}
);
Hashtable[] solutions = query.allSolutions();
if ( solutions.length != 1 ){
System.out.println( "bagof(X-Y, p(X,Y), XYs) failed:" );
System.out.println( "\tExpected: 1 solution" );
System.out.println( "\tGot: " + solutions.length );
System.exit( 1 );
}
Term term = (Term) solutions[0].get("XYs");
// if ( ! (term instanceof List) ){
if ( ! (term instanceof Compound && ".".equals(((Compound)term).name()) && ((Compound)term).arity()==2) ){
System.out.println( "bagof(X-Y, p(X,Y), XYs) failed:" );
System.out.println( "\tExpected: XYs to be a List" );
System.out.println( "\tGot: " + term );
System.exit( 1 );
}
if ( ! term.equals( test_9_solution ) ){
System.out.println( "bagof(X-Y, p(X,Y), XYs) failed:" );
System.out.println( "\tExpected: " + test_9_solution );
System.out.println( "\tGot: " + term );
System.exit( 1 );
}
System.out.println( "passed." );
}
static void
test_10()
{
System.out.print( "test 10..." );
Query query =
new Query( "t" );
try {
boolean b = query.hasSolution();
System.out.println( "t failed:" );
System.out.println( "\tExpected: JPLException" );
System.out.println( "\tGot: " + b );
System.exit( 1 );
} catch ( PrologException e ){
}
System.out.println( "passed." );
}
static void
test_11()
{
System.out.print( "test 11..." );
Term tuple =
new Compound(
"t",
new Term[]{
new Atom( "a" ),
new Atom( "b" ),
new Atom( "c" ),
new Atom( "d" ),
new Atom( "e" )
}
);
try {
Variable X = new Variable("X");
Query query = new Query( "tuple", new Term[] {X} );
java.util.Hashtable solution = query.oneSolution();
Term result = (Term) solution.get("X");
if ( result == null || ! result.equals( tuple ) ){
System.out.println( "failed:" );
System.out.println( "\tresult: " + result );
System.out.println( "\ttuple: " + tuple );
System.exit( 1 );
}
Term term;
term = new Atom( "a" );
if ( ((Compound)result).arg( 1 ) == null || !((Compound)result).arg( 1 ).equals( term ) ){
System.out.println( "failed:" );
System.out.println( "\t((Compound)result).arg( 1 ): " + ((Compound)result).arg( 1 ) );
System.out.println( "\tterm : " + term );
System.exit( 1 );
}
term = new Atom( "b" );
if ( ((Compound)result).arg( 2 ) == null || !((Compound)result).arg( 2 ).equals( term ) ){
System.out.println( "failed:" );
System.out.println( "\t((Compound)result).arg( 2 ): " + ((Compound)result).arg( 2 ) );
System.out.println( "\tterm : " + term );
System.exit( 1 );
}
term = new Atom( "e" );
if ( ((Compound)result).arg( 5 ) == null || !((Compound)result).arg( 5 ).equals( term ) ){
System.out.println( "failed:" );
System.out.println( "\t((Compound)result).arg( 5 ): " + ((Compound)result).arg( 5 ) );
System.out.println( "\tterm : " + term );
System.exit( 1 );
}
// arg0(6) throws an exception, as I'd expect it to...
// if ( ((Compound)result).arg( 7 ) != null ){
// System.out.println( "failed:" );
// System.out.println( "\t((Compound)result).arg( 7 ): " + ((Compound)result).arg( 7 ) );
// System.out.println( "\tshould be null" );
// System.exit( 1 );
// }
} catch ( PrologException e ){
System.out.println( "failed" );
e.printStackTrace();
System.exit( 1 );
}
System.out.println( "passed." );
}
static void
test_101()
{
System.out.print( "test 101..." );
Thread[] threads = new Thread[10];
for ( int i = 0; i < threads.length; ++i ){
threads[i] = new QueryThread( i );
}
for ( int i = 0; i < threads.length; ++i ){
threads[i].start();
}
for ( int i = 0; i < threads.length; ++i ){
try {
threads[i].join();
} catch ( InterruptedException ie ){
ie.printStackTrace();
System.exit( 1 );
}
}
System.out.println( "passed." );
}
private static class
QueryThread extends Thread
{
private int id_ = -1;
public
QueryThread( int id )
{
this.id_ = id;
}
public java.lang.String
toString()
{
return "(QueryThread id=" + id_ + ")";
}
public void
run()
{
Query query =
new Query(
"p",
new Term[] {
new Atom("a"),
new Atom("a")
}
);
for ( int i = 0; i < 10; ++i ){
try {
query.hasSolution();
} catch ( jpl.JPLException e ){
System.out.println( "Threaded p( a, a ) threw exception: " + e);
System.exit( 1 );
}
System.out.print( id_ );
Thread.yield();
}
for ( int i = 0; i < 10; ++i ){
// synchronized ( Query.lock() ){
try {
while ( query.hasMoreSolutions() ){
Thread.yield();
query.nextSolution();
}
} catch ( jpl.JPLException e ){
System.out.println( "Threaded p( a, a ) threw exception: " + e);
System.exit( 1 );
}
System.out.print( id_ );
// }
}
}
}
// more to come??
}Furthermore, for startup, the two files
- ~/blipstart
- ~/blipstart.pl are used. Here are the contents of them:
Contents of ~/blipstart
-L0 -G0 -A0 -T0 -g main -t halt -s /home/samuel/blipstart.pl
Contents of ~/blipstart.pl
user:file_search_path(bio, blipkit(attic)).
user:file_search_path(bio, blipkit(biblio)).
user:file_search_path(bio, blipkit(bionlp)).
user:file_search_path(bio, blipkit(blipcore)).
user:file_search_path(bio, blipkit(curation)).
user:file_search_path(bio, blipkit(genomic)).
user:file_search_path(bio, blipkit(homol)).
user:file_search_path(bio, blipkit(metadata)).
user:file_search_path(bio, blipkit(obolog)).
user:file_search_path(bio, blipkit(omim)).
user:file_search_path(bio, blipkit(ontograph)).
user:file_search_path(bio, blipkit(ontol)).
user:file_search_path(bio, blipkit('ontol/thea')).
user:file_search_path(bio, blipkit(pheno)).
user:file_search_path(bio, blipkit(phylo)).
user:file_search_path(bio, blipkit(rdft)).
user:file_search_path(bio, blipkit(sb)).
user:file_search_path(bio, blipkit(serval)).
user:file_search_path(bio, blipkit(sql)).
user:file_search_path(bio, blipkit(stats)).
user:file_search_path(bio, blipkit(structure)).
user:file_search_path(bio, blipkit(variation)).
user:file_search_path(bio, blipkit(web)).
user:file_search_path(bio, blipkit(xml)).
:- use_module(bio(blipkit)).
:- use_module(bio(blipkit_ontol)).
:- use_module(bio(blipkit_phylo)).
:- use_module(bio(blipkit_fasta)).
:- use_module(bio(blipkit_sb)).
:- use_module(bio(blipkit_web)).Recent blog posts
- I created a Udemy course on my favourite linux commandline productivity techniques
- My top-languages-per-use-case list
- The smallest pipeable python script
- Vote for ProcessWire to be packaged as a BitNami image
- Calling Java from Python without the JVM startup latency: NailGun and JPype
- New Google+ communities: Bioclipse, Cheminformatics, Semantic MediaWiki
- Don't use Swedish keyboard with vim/screen/bash
- Easier debugging of Go programs on the command line with CGDB
- Profiling and creating call graphs for Go programs with "go tool pprof"
- Python-like generator functions in Go
Comments
Just a sidenote, that I
Just a sidenote, that I needed to store somewhere, about the dependencies for blipkit:
I also had to: ...change the
I now found a not on my disktop that I also had to change the file
/usr/bin/go2prologlike so:-->
You saved my day
I've been searching for clues why I'm getting null when I do get on Hashtable.
I was following this official tutorial about JPL.
http://www.swi-prolog.org/packages/jpl/java_api/getting_started.html
After checking your code, I found it.
You have to declare a Variable with a string.
And, do get with the initial string.
Thank you very much.
Hidenari