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Re: [TM4J-users] Tolog query problems
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From: Richard G. <ric...@ya...> - 2005-03-07 19:52:02
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Hi Kal,
Thanks for the prompt reply, as ever.
I have a small 2.5MB TM (compared with my other TM's which are 50MB and over) which I can send you
tomorrow, and which was produced for the same project these queries were generated for. If that is
still too large, let me know what size you are after and I'll generate one for you tomorrow.
Cheers,
Richard.
--- Kal Ahmed <ka...@te...> wrote:
> Hi Richard,
>
> Some of these NPEs probably are bugs in the tolog code. I don't think
> that the parser currently supports the = operator, but it should
> support /=. That said, the changes that were introduced to tolog 1.2
> may have caused the implementation of /= to break. Biggest problem in
> implementing this query language is that Ontopia hadn't produced a
> formal language specification when I wrote the code, so a lot was my
> guess work based on what documentation was available. I don't know if
> that is changed now or not.
>
> Anyway, thanks for your detailed report. Its going to take me some time
> to get through all of these, but if you have time to make a minimum
> test set (small TM and a set of queries which work on Omnigator and
> fail in TM4J), then it would really help me out in sorting out "bugs"
> from *ahem* "features" :-). If you don't have time, don't worry - I'll
> get on to it and let you know how things go.
>
> Cheers,
>
> Kal
>
> On 7 Mar 2005, at 15:46, Richard Gregory wrote:
>
> > Hi All,
> >
> > I'm trying to execute a tolog query in a TM4J program, and I've
> > encountered a number of problems.
> > Apologies for the length of this mail, but it seemed that whichever
> > way I tried to solve the
> > problem I hit another one which confused me.
> >
> > The query I want to execute, which works fine in the Omnigator, is:
> >
> > TologResultsSet results = queryEval.execute("select $PROTEIN from " +
> > "at-has-go(t-protein-ydl101c : tt-protein, $RESULT : tt-go), " +
> > "$RESULT /= t-go-0000004, " +
> > "$RESULT /= t-go-0000006, " +
> > "at-has-go($PROTEIN : tt-protein, $RESULT : tt-go), " +
> > "$PROTEIN /= t-protein-ydl101c " +
> > "order by $PROTEIN?");
> >
> > This give an NullPointerException
> >
> > Exception caught: java.lang.NullPointerException
> > java.lang.NullPointerException
> > at org.tm4j.tologx.parser.Variable.equals(Variable.java:31)
> > at java.util.ArrayList.indexOf(ArrayList.java:220)
> > at java.util.ArrayList.contains(ArrayList.java:201)
> > at
> > org.tm4j.tologx.parser.ClauseList.addVariable(ClauseList.java:156)
> > at
> > org.tm4j.tologx.parser.ClauseList.addClause(ClauseList.java:165)
> > at
> > org.tm4j.tologx.parser.TologParser.opclause(TologParser.java:1134)
> > at
> > org.tm4j.tologx.parser.TologParser.clause(TologParser.java:789)
> > at
> > org.tm4j.tologx.parser.TologParser.clauselist(TologParser.java:443)
> > at
> > org.tm4j.tologx.parser.TologParser.query(TologParser.java:498)
> > at
> > org.tm4j.tologx.memory.QueryEvaluatorImpl.prepareQuery(QueryEvaluatorIm
> > pl.java:151)
> > at
> > org.tm4j.tologx.memory.QueryEvaluatorImpl.execute(QueryEvaluatorImpl.ja
> > va:165)
> > at
> > mips.genre.topicmaps.TologBugTests.main(TologBugTests.java:150)
> >
> > I think the source of the problem is the lines:
> >
> > "$RESULT /= t-go-0000004, " +
> > "$RESULT /= t-go-0000006, " +
> >
> > If I comment these out, as below, it works fine, even with the similar
> > "$PROTEIN /=
> > t-protein-ydl101c " still in the query. Both these topics exist in the
> > topic map. so I know that
> > isn't the problem. From the testing I've done with various quries, I
> > get the same excpetion if I
> > use a statement like this in a query, except when it's the last
> > statement (apart from an "order
> > by"), so could there be a problem with the comma after a topic id,
> > used in this way is parsed?
> >
> > TologResultsSet results = queryEval.execute("select $PROTEIN from " +
> > "at-has-go(t-protein-ydl101c : tt-protein, $RESULT : tt-go), " +
> > //"$RESULT /= t-go-0000004, " +
> > //"$RESULT /= t-go-0000006, " +
> > "at-has-go($PROTEIN : tt-protein, $RESULT : tt-go), " +
> > "$PROTEIN /= t-protein-ydl101c " +
> > "order by $PROTEIN?");
> >
> > Having encountered this problem, I looked for other ways to formulate
> > the query. First I tried
> > using "not" statements with an "=", instead of using the "/=".
> >
> > TologResultsSet results = queryEval.execute("select $PROTEIN from " +
> > "at-has-go(t-protein-ydl101c : tt-protein, $RESULT : tt-go), " +
> > "not($RESULT = t-go-0000004), " +
> > "not($RESULT = t-go-0000006), " +
> > "at-has-go($PROTEIN : tt-protein, $RESULT : tt-go), " +
> > "$PROTEIN /= t-protein-ydl101c " +
> > "order by $PROTEIN?");
> >
> > Again, this query works fine in the omnigator, but I get an excpetion
> > with TM4J.
> >
> > Exception caught: org.tm4j.tologx.TologParserException: Error parsing
> > query string.
> > org.tm4j.tologx.TologParserException: Error parsing query string.
> > at
> > org.tm4j.tologx.memory.QueryEvaluatorImpl.prepareQuery(QueryEvaluatorIm
> > pl.java:155)
> > at
> > org.tm4j.tologx.memory.QueryEvaluatorImpl.execute(QueryEvaluatorImpl.ja
> > va:165)
> > at
> > mips.genre.topicmaps.TologBugTests.main(TologBugTests.java:150)
> > Caused by: line 1:103: unexpected char: '='
> > at
> > org.tm4j.tologx.parser.TologLexer.nextToken(TologLexer.java:212)
> > at antlr.TokenBuffer.fill(TokenBuffer.java:69)
> > at antlr.TokenBuffer.LA(TokenBuffer.java:80)
> > at antlr.LLkParser.LA(LLkParser.java:52)
> > at antlr.Parser.match(Parser.java:212)
> > at
> > org.tm4j.tologx.parser.TologParser.clause(TologParser.java:776)
> > at
> > org.tm4j.tologx.parser.TologParser.clauselist(TologParser.java:437)
> > at
> > org.tm4j.tologx.parser.TologParser.notclause(TologParser.java:851)
> > at
> > org.tm4j.tologx.parser.TologParser.clause(TologParser.java:734)
> > at
> > org.tm4j.tologx.parser.TologParser.clauselist(TologParser.java:443)
> > at
> > org.tm4j.tologx.parser.TologParser.query(TologParser.java:498)
> > at
> > org.tm4j.tologx.memory.QueryEvaluatorImpl.prepareQuery(QueryEvaluatorIm
> > pl.java:151)
> > ... 2 more
> >
> > It seems the query parser is taking exception (excuse the pun) to the
> > "=". I did some more testing
> > with other query variations using the "=" comparator, such as
> >
> > TologResultsSet results = queryEval.execute("select $PROTEIN from " +
> > "at-has-go(t-protein-ydl101c : tt-protein, $RESULT : tt-go), " +
> > "$RESULT = t-go-0006468, " +
> > "at-has-go($PROTEIN : tt-protein, $RESULT : tt-go), " +
> > "$PROTEIN /= t-protein-ydl101c " +
> > "order by $PROTEIN?");
> >
> > String[] replacements = {"GO:0006468"};
> > TologResultsSet results = queryEval.execute(
> > "select $PROTEIN from " +
> > "at-has-go(t-protein-ydl101c : tt-protein, $RESULT : tt-go), " +
> > "topic-name($GO1, $GO1_NAME), " +
> > "value($GO1_NAME, %1), " +
> > "$RESULT = $GO1, " +
> > "at-has-go($PROTEIN : tt-protein, $RESULT : tt-go), " +
> > "$PROTEIN /= t-protein-ydl101c" +
> > "order by $PROTEIN?", replacements);
> >
> > These give the same excpetion.
> >
> > I next looked at getting topics by name, and going back to using the
> > "/=" comparator.
> >
> > TologResultsSet results = queryEval.execute(
> > "select $PROTEIN from " +
> > "at-has-go(t-protein-ydl101c : tt-protein, $RESULT : tt-go), " +
> > "topic-name($GO1, $GO1_NAME), " +
> > "value($GO1_NAME, \"GO:0000004\"), " +
> > "topic-name($GO2, $GO2_NAME), " +
> > "value($GO2_NAME, \"GO:0000006\"), " +
> > "$RESULT /= $GO1, " +
> > "$RESULT /= $GO2, " +
> > "at-has-go($PROTEIN : tt-protein, $RESULT : tt-go), " +
> > "$PROTEIN /= t-protein-ydl101c " +
> > "order by $PROTEIN?");
> >
> > Again, this query worked fine in the omnigator, but I got an exception
> > with TM4J.
> >
> > Exception caught: org.tm4j.tologx.TologParserException: Error parsing
> > query string.
> > org.tm4j.tologx.TologParserException: Error parsing query string.
> > at
> > org.tm4j.tologx.memory.QueryEvaluatorImpl.prepareQuery(QueryEvaluatorIm
> > pl.java:155)
> > at
> > org.tm4j.tologx.memory.QueryEvaluatorImpl.execute(QueryEvaluatorImpl.ja
> > va:165)
> > at
> > mips.genre.topicmaps.TologBugTests.main(TologBugTests.java:120)
> > Caused by: line 1:128: unexpected token: "GO:0000004"
> > at
> > org.tm4j.tologx.parser.TologParser.expr(TologParser.java:1244)
> > at
> > org.tm4j.tologx.parser.TologParser.pair(TologParser.java:1151)
> > at
> > org.tm4j.tologx.parser.TologParser.predclause(TologParser.java:1085)
> > at
> > org.tm4j.tologx.parser.TologParser.clause(TologParser.java:786)
> > at
> > org.tm4j.tologx.parser.TologParser.clauselist(TologParser.java:443)
> > at
> > org.tm4j.tologx.parser.TologParser.query(TologParser.java:498)
> > at
> > org.tm4j.tologx.memory.QueryEvaluatorImpl.prepareQuery(QueryEvaluatorIm
> > pl.java:151)
> > ... 2 more
> >
> > I next tried to pass the topic names in from an array. Because I
> > ultimately want to repeat the
> > query with other protein topic ID's, I tried to pass this in from the
> > array as well.
> >
> > String[] replacements = {"t-protein-ydl101c", "GO:0000004",
> > "GO:0000006"};
> > TologResultsSet results = queryEval.execute(
> > "select $PROTEIN from " +
> > "at-has-go(%1 : tt-protein, $RESULT : tt-go), " +
> > "topic-name($GO1, $GO1_NAME), " +
> > "value($GO1_NAME, %2), " +
> > "topic-name($GO2, $GO2_NAME), " +
> > "value($GO2_NAME, %3), " +
> > "$RESULT /= $GO1, " +
> > "$RESULT /= $GO2, " +
> > "at-has-go($PROTEIN : tt-protein, $RESULT : tt-go), " +
> > "$PROTEIN /= %1 " +
> > "order by $PROTEIN?", replacements);
> >
> > This gives yet another excpetion.
> >
> > Exception caught: org.tm4j.tologx.TologProcessingException: Type
> > mismatch in replacement %1. A
> > Topic was expected.
> > org.tm4j.tologx.TologProcessingException: Type mismatch in replacement
> > %1. A Topic was expected.
> > at
> > org.tm4j.tologx.parser.ClauseList.doReplacement(ClauseList.java:216)
> > at
> > org.tm4j.tologx.parser.TologQuery.execute(TologQuery.java:154)
> > at
> > org.tm4j.tologx.memory.PreparedQueryImpl.execute(PreparedQueryImpl.java
> > :56)
> > at
> > org.tm4j.tologx.memory.QueryEvaluatorImpl.execute(QueryEvaluatorImpl.ja
> > va:174)
> > at
> > mips.genre.topicmaps.TologBugTests.main(TologBugTests.java:119)
> >
> > I did find away around it, creating a string variable to hold the
> > topic ID, and concatenating this
> > into the query string.
> >
> > String[] replacements = {"GO:0000004", "GO:0000006"};
> > String proteinID = "t-protein-ydl101c";
> > TologResultsSet results = queryEval.execute(
> > "select $PROTEIN from " +
> > "at-has-go(" + proteinID + " : tt-protein, $RESULT : tt-go), " +
> > "topic-name($GO1, $GO1_NAME), " +
> > "value($GO1_NAME, %2), " +
> > "topic-name($GO2, $GO2_NAME), " +
> > "value($GO2_NAME, %3), " +
> > "$RESULT /= $GO1, " +
> > "$RESULT /= $GO2, " +
> > "at-has-go($PROTEIN : tt-protein, $RESULT : tt-go), " +
> > "$PROTEIN /= " + proteinID + " " +
> > "order by $PROTEIN?", replacements);
> >
> > This now works, and gives me the functionality I want, but I've no
> > idea why the earleir queries
> > gave the exceptions they did.
> >
> > Has anyone else experienced anything like these problems, or can
> > anyone explain them? I'm really
> > confused by these, especially when the queries worked in the
> > omnigator, so if anyone can offer an
> > explanation, even "tm4j bug" (sorry, Kal) I'd be grateful.
> >
> > Cheers,
> >
> > Richard.
> >
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> >
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>
>
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