Hi All,
Thanks for the quick reply.
It seems like indeed my index is not what I think it is so maybe
I'm using the wrong analyzer. Here is the code I use to index the multiple
values of alt_id:
indexWriter = new IndexWriter(FSDirectory.open(new
File(path)),newStandardAnalyzer(Version.
LUCENE_30), true, IndexWriter.MaxFieldLength.UNLIMITED);
for(String geneId : genes.keySet()){
//Update Gene
Document gene = new Document();
gene.add(new Field("type", "gene", Field.Store.YES, Field.Index.ANALYZED
));
gene.add(new Field("id", geneId, Field.Store.YES, Field.Index.ANALYZED));
for(String altId : genes.get(geneId)){
gene.add(new Field("alt_id", altId, Field.Store.YES, Field.Index.ANALYZED
));
}
indexWriter.updateDocument(new Term("id", geneId), gene);
}
I understand that the best approach is to have the values for alt_id as
single tokens, isn't that what the current analyzer does? wich one should
I use instead?
Cheers,
José M. Villaveces
On 25 June 2012 15:58, Erick Erickson <erickerick...@gmail.com> wrote:
> TermQuerys are assumed to be parsed already. So you're
> looking for a _single_ term "ncbi-geneid:379474 or XI.24622".
>
>
> You'd construct something like
> Query query1 = new TermQuery(new Term("type", "gene"));
> Query query2 = new TermQuery(new Term("alt_Id", "ncbi-geneid:379474"));
> Query query3 = new TermQuery(new Term("alt_Id", "unigene:XI.24622"));
>
> BooleanQuery query = new BooleanQuery();
> query.add(query1, BooleanClause.Occur.MUST);
>
> BooleanQuery queryB = new BooleanQuery();
> queryB.add(query2, ...SHOULD);
> queryB.add(query3, ...SHOULD);
>
> query.add(queryB, BooleanClause.Occur.MUST);
>
>
> But this _assumes_ that you have _single tokens_ of the
> form ncbi-geneid:379474 but given that you say that just the
> bare 379474 works, I'm guessing as Ian says that you don't
> have what you think you do in your index, you probably have
> individual tokens like "ncbi-geneid" (or "ncbi" and "geneid" even),
> BC054227, xia, etc. You need to look into your index with Luke
> and see what's actually in there.
>
> You might think about installing Solr, _not_ to power your app, but just
> to play with the admin/analysis page to understand how
> Analysis works with various combinations of tokenizers and filters....
>
> Best
> Erick
>
> On Mon, Jun 25, 2012 at 8:50 AM, <seceval...@gmail.com> wrote:
> > I'm quite new to Lucene and recently, I ran into a problem. I have a
> lucene
> > document that looks like this:
> >
> > --- type ---
> > gene
> >
> > --- id ---
> > xla:379474
> >
> > --- alt_id ---
> > emb:BC054227
> > gb:BC054227
> > ncbi-geneid:379474
> > ncbi-gi:148230166
> > rs:NM_001086315
> > rs:NP_001079784
> > unigene:Xl.24622
> > xla:379474
> >
> >
> > I created the query bellow in order to retrieve that document. It works
> > fine for altId = 379474 but not for altId = ncbi-geneid:379474 or
> Xl.24622.
> > I guessed altId must be escaped and tried String altId =
> > QueryParser.escape(altId) with no luck. What I'm I missing?
> >
> > Query query1 = new TermQuery(new Term("type", "gene"));
> > Query query2 = new TermQuery(new Term("alt_Id", altId));
> >
> > BooleanQuery query = new BooleanQuery();
> > query.add(query1, BooleanClause.Occur.MUST);
> > query.add(query2, BooleanClause.Occur.MUST);
> >
> > By the way I'm running lucene v3.0.
> >
> > Cheers,
> > José M. Villaveces
>
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