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Re: [TM4J-users] Tolog query problems
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From: Kal A. <ka...@te...> - 2005-03-07 21:11:47
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Hi Richard,
Lets try with the 2.5MB file to start with - if its a real pain, I'll
yell ;-)
Cheers,
Kal
On 7 Mar 2005, at 19:51, Richard Gregory wrote:
> 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 $PROTEIN?");
>>>
>>> This give an NullPointerException
>>>
>>> Exception caught: java.lang.NullPointerException
>>> java.lang.NullPointerException
>>> at org.tm4j.tologx.parser.Variable.equals(Variable.java:31)
>>> at java.util.ArrayList.indexOf(ArrayList.java:220)
>>> at java.util.ArrayList.contains(ArrayList.java:201)
>>> at
>>> org.tm4j.tologx.parser.ClauseList.addVariable(ClauseList.java:156)
>>> at
>>> org.tm4j.tologx.parser.ClauseList.addClause(ClauseList.java:165)
>>> at
>>> org.tm4j.tologx.parser.TologParser.opclause(TologParser.java:1134)
>>> at
>>> org.tm4j.tologx.parser.TologParser.clause(TologParser.java:789)
>>> at
>>> org.tm4j.tologx.parser.TologParser.clauselist(TologParser.java:443)
>>> at
>>> org.tm4j.tologx.parser.TologParser.query(TologParser.java:498)
>>> at
>>> org.tm4j.tologx.memory.QueryEvaluatorImpl.prepareQuery(QueryEvaluator
>>> Im
>>> pl.java:151)
>>> at
>>> org.tm4j.tologx.memory.QueryEvaluatorImpl.execute(QueryEvaluatorImpl.
>>> ja
>>> va:165)
>>> at
>>> mips.genre.topicmaps.TologBugTests.main(TologBugTests.java:150)
>>>
>>> I think the source of the problem is the lines:
>>>
>>> "$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(QueryEvaluator
>>> Im
>>> 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(QueryEvaluator
>>> Im
>>> 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(QueryEvaluator
>>> Im
>>> 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(QueryEvaluator
>>> Im
>>> 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.ja
>>> va
>>> :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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>>>
>>
>>
>
> Send instant messages to your online friends
> http://uk.messenger.yahoo.com
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>
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