Weird exception with Lucene index - Neo4j

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Message from discussion Weird exception with Lucene index
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Date: Sat, 19 May 2012 21:11:23 -0400
Message-ID: <CAOukiEkp520UjdFxAy62ac=mYWcQBUrfe616E3Jx55Mc+dd...@mail.gmail.com>
Subject: Re: [Neo4j] Weird exception with Lucene index
From: Pablo Pareja <ppar...@era7.com>
To: neo4j@googlegroups.com
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Ok, thanks ;)

Pablo

On Sat, May 19, 2012 at 9:03 PM, David Montag <
david.mon...@neotechnology.com> wrote:

> It shouldn't be corrupted. It's just that 1.7 uses a later Lucene version
> that 1.5 can't read.
>
> -David
> On May 19, 2012 6:00 PM, "Pablo Pareja" <ppar...@era7.com> wrote:
>
>> Hi David,
>>
>> Thanks for the quick response. You're right!
>> I was combining two different programs and one of them has a version
>> around 1.5 whilst the other one is built with 1.7, (silly me... :P )
>> I probably corrupted the DB then, because I was adding new content when
>> using the program compiled with 1.5 to a previously created DB with 1.7
>> version ....
>>
>> Cheers,
>>
>> Pablo
>>
>> On Sat, May 19, 2012 at 8:54 PM, David Montag <
>> david.mon...@neotechnology.com> wrote:
>>
>>> Hi Pablo,
>>>
>>> That's most likely caused by a version mismatch. What Neo4j version was
>>> the store created with, and which version are you using to access it? Are
>>> you running embedded?
>>>
>>> Thanks,
>>> David
>>> On May 19, 2012 5:43 PM, "Pablo Pareja" <ppar...@era7.com> wrote:
>>>
>>>> Hi,
>>>>
>>>> I'm getting this exception when using a Lucene index and don't have any
>>>> idea why I might be getting it:
>>>>
>>>> SEVERE: null
>>>> java.lang.RuntimeException:
>>>> org.apache.lucene.index.CorruptIndexException: unrecognized format -3 in
>>>> file "_2q.fnm"
>>>>         at
>>>> org.neo4j.index.impl.lucene.LuceneDataSource.getIndexWriter(LuceneDataSource.java:606)
>>>>         at
>>>> org.neo4j.index.impl.lucene.LuceneDataSource.getIndexSearcher(LuceneDataSource.java:489)
>>>>         at
>>>> org.neo4j.index.impl.lucene.LuceneIndex.query(LuceneIndex.java:248)
>>>>         at
>>>> org.neo4j.index.impl.lucene.LuceneIndex.get(LuceneIndex.java:187)
>>>>         at
>>>> com.era7.bioinfo.bio4jmodel.util.NodeRetriever.getNCBITaxonByTaxId(NodeRetriever.java:278)
>>>>         at
>>>> com.era7.bioinfo.mg7.CountTaxonomyFreqs.main(CountTaxonomyFreqs.java:86)
>>>>         at
>>>> com.era7.bioinfo.mg7.CountTaxonomyFreqs.execute(CountTaxonomyFreqs.java:44)
>>>>         at
>>>> com.era7.lib.bioinfo.bioinfoutil.ExecuteFromFile.main(ExecuteFromFile.java:66)
>>>>         at com.era7.bioinfo.mg7.MG7.main(MG7.java:34)
>>>> Caused by: org.apache.lucene.index.CorruptIndexException: unrecognized
>>>> format -3 in file "_2q.fnm"
>>>>         at org.apache.lucene.index.FieldInfos.read(FieldInfos.java:349)
>>>>         at org.apache.lucene.index.FieldInfos.<init>(FieldInfos.java:71)
>>>>         at
>>>> org.apache.lucene.index.IndexWriter.getFieldInfos(IndexWriter.java:1197)
>>>>         at
>>>> org.apache.lucene.index.IndexWriter.getCurrentFieldInfos(IndexWriter.java:1213)
>>>>         at
>>>> org.apache.lucene.index.IndexWriter.<init>(IndexWriter.java:1149)
>>>>         at
>>>> org.neo4j.index.impl.lucene.LuceneDataSource.getIndexWriter(LuceneDataSource.java:593)
>>>>         ... 8 more
>>>>
>>>> I'm using Neo4j 1.7 on a Linux machine.
>>>> Any clues?
>>>> Thanks!
>>>>
>>>>
>>>> Pablo
>>>> --
>>>> Pablo Pareja Tobes
>>>>
>>>> My site     http://about.me/pablopareja
>>>> LinkedIn    http://www.linkedin.com/in/pabloparejatobes
>>>> Twitter       http://www.twitter.com/pablopareja
>>>>
>>>> Creator of Bio4j --> http://www.bio4j.com
>>>>
>>>> http://www.ohnosequences.com
>>>>
>>>>
>>
>>
>> --
>> Pablo Pareja Tobes
>>
>> My site     http://about.me/pablopareja
>> LinkedIn    http://www.linkedin.com/in/pabloparejatobes
>> Twitter       http://www.twitter.com/pablopareja
>>
>> Creator of Bio4j --> http://www.bio4j.com
>>
>> http://www.ohnosequences.com
>>
>>


-- 
Pablo Pareja Tobes

My site     http://about.me/pablopareja
LinkedIn    http://www.linkedin.com/in/pabloparejatobes
Twitter       http://www.twitter.com/pablopareja

Creator of Bio4j --> http://www.bio4j.com

http://www.ohnosequences.com

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<div>Ok, thanks ;)</div><div><br></div><div>Pablo</div><br><div class=3D"gm=
ail_quote">On Sat, May 19, 2012 at 9:03 PM, David Montag <span dir=3D"ltr">=
&lt;<a href=3D"mailto:david.mon...@neotechnology.com" target=3D"_blank">dav=
id.mon...@neotechnology.com</a>&gt;</span> wrote:<br>
<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
x #ccc solid;padding-left:1ex"><p>It shouldn&#39;t be corrupted. It&#39;s j=
ust that 1.7 uses a later Lucene version that 1.5 can&#39;t read.</p><span =
class=3D"HOEnZb"><font color=3D"#888888">
<p>-David</p></font></span><div class=3D"HOEnZb"><div class=3D"h5">
<div class=3D"gmail_quote">On May 19, 2012 6:00 PM, &quot;Pablo Pareja&quot=
; &lt;<a href=3D"mailto:ppar...@era7.com" target=3D"_blank">ppar...@era7.co=
m</a>&gt; wrote:<br type=3D"attribution"><blockquote class=3D"gmail_quote" =
style=3D"margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">

Hi David,=A0<div><br></div><div>Thanks for the quick response. You&#39;re r=
ight!=A0</div><div>I was combining two different programs and one of them h=
as a version around 1.5 whilst the other one is built with 1.7, (silly me..=
. :P )</div>


<div>I probably corrupted the DB then, because I was adding new content whe=
n using the program compiled with 1.5 to a previously created DB with 1.7 v=
ersion ....=A0</div><div><br></div><div>Cheers,</div><div><br></div><div>


Pablo=A0<br><br><div class=3D"gmail_quote">On Sat, May 19, 2012 at 8:54 PM,=
 David Montag <span dir=3D"ltr">&lt;<a href=3D"mailto:david.montag@neotechn=
ology.com" target=3D"_blank">david.mon...@neotechnology.com</a>&gt;</span> =
wrote:<br>


<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
x #ccc solid;padding-left:1ex"><p>Hi Pablo,</p>
<p>That&#39;s most likely caused by a version mismatch. What Neo4j version =
was the store created with, and which version are you using to access it? A=
re you running embedded? </p>
<p>Thanks,<br>
David </p><div><div>
<div class=3D"gmail_quote">On May 19, 2012 5:43 PM, &quot;Pablo Pareja&quot=
; &lt;<a href=3D"mailto:ppar...@era7.com" target=3D"_blank">ppar...@era7.co=
m</a>&gt; wrote:<br type=3D"attribution"><blockquote class=3D"gmail_quote" =
style=3D"margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">



Hi,<div><br></div><div>I&#39;m getting this exception when using a Lucene i=
ndex and don&#39;t have any idea why I might be getting it:</div><div><br><=
/div><div><div>SEVERE: null</div><div>java.lang.RuntimeException: org.apach=
e.lucene.index.CorruptIndexException: unrecognized format -3 in file &quot;=
_2q.fnm&quot;</div>




<div>=A0 =A0 =A0 =A0 at org.neo4j.index.impl.lucene.LuceneDataSource.getInd=
exWriter(LuceneDataSource.java:606)</div><div>=A0 =A0 =A0 =A0 at org.neo4j.=
index.impl.lucene.LuceneDataSource.getIndexSearcher(LuceneDataSource.java:4=
89)</div><div>




=A0 =A0 =A0 =A0 at org.neo4j.index.impl.lucene.LuceneIndex.query(LuceneInde=
x.java:248)</div><div>=A0 =A0 =A0 =A0 at org.neo4j.index.impl.lucene.Lucene=
Index.get(LuceneIndex.java:187)</div><div>=A0 =A0 =A0 =A0 at com.era7.bioin=
fo.bio4jmodel.util.NodeRetriever.getNCBITaxonByTaxId(NodeRetriever.java:278=
)</div>




<div>=A0 =A0 =A0 =A0 at com.era7.bioinfo.mg7.CountTaxonomyFreqs.main(CountT=
axonomyFreqs.java:86)</div><div>=A0 =A0 =A0 =A0 at com.era7.bioinfo.mg7.Cou=
ntTaxonomyFreqs.execute(CountTaxonomyFreqs.java:44)</div><div>=A0 =A0 =A0 =
=A0 at com.era7.lib.bioinfo.bioinfoutil.ExecuteFromFile.main(ExecuteFromFil=
e.java:66)</div>




<div>=A0 =A0 =A0 =A0 at com.era7.bioinfo.mg7.MG7.main(MG7.java:34)</div><di=
v>Caused by: org.apache.lucene.index.CorruptIndexException: unrecognized fo=
rmat -3 in file &quot;_2q.fnm&quot;</div><div>=A0 =A0 =A0 =A0 at org.apache=
.lucene.index.FieldInfos.read(FieldInfos.java:349)</div>




<div>=A0 =A0 =A0 =A0 at org.apache.lucene.index.FieldInfos.&lt;init&gt;(Fie=
ldInfos.java:71)</div><div>=A0 =A0 =A0 =A0 at org.apache.lucene.index.Index=
Writer.getFieldInfos(IndexWriter.java:1197)</div><div>=A0 =A0 =A0 =A0 at or=
g.apache.lucene.index.IndexWriter.getCurrentFieldInfos(IndexWriter.java:121=
3)</div>




<div>=A0 =A0 =A0 =A0 at org.apache.lucene.index.IndexWriter.&lt;init&gt;(In=
dexWriter.java:1149)</div><div>=A0 =A0 =A0 =A0 at org.neo4j.index.impl.luce=
ne.LuceneDataSource.getIndexWriter(LuceneDataSource.java:593)</div><div>=A0=
 =A0 =A0 =A0 ... 8 more</div>




<div><br></div><div>I&#39;m using Neo4j 1.7 on a Linux machine.</div><div>A=
ny clues?</div><div>Thanks!</div><div><br></div><div><br></div><div>Pablo</=
div>-- <br>Pablo Pareja Tobes=A0<div><br><div>My site =A0 =A0=A0<a href=3D"=
http://about.me/pablopareja" target=3D"_blank">http://about.me/pablopareja<=
/a><div>




<div><div>LinkedIn =A0 =A0<a href=3D"http://www.linkedin.com/in/pablopareja=
tobes" target=3D"_blank">http://www.linkedin.com/in/pabloparejatobes</a></d=
iv><div>Twitter =A0 =A0 =A0=A0<a href=3D"http://www.twitter.com/pablopareja=
" target=3D"_blank">http://www.twitter.com/pablopareja</a></div>




<div><br></div><div>Creator of Bio4j --&gt; <a href=3D"http://www.bio4j.com=
" target=3D"_blank">http://www.bio4j.com</a></div><div><br></div><div><a hr=
ef=3D"http://www.ohnosequences.com" target=3D"_blank">http://www.ohnosequen=
ces.com</a></div>




</div></div></div></div><br>
</div>
</blockquote></div>
</div></div></blockquote></div><br><br clear=3D"all"><div><br></div>-- <br>=
Pablo Pareja Tobes=A0<div><br><div>My site =A0 =A0=A0<a href=3D"http://abou=
t.me/pablopareja" target=3D"_blank">http://about.me/pablopareja</a><div><di=
v><div>LinkedIn =A0 =A0<a href=3D"http://www.linkedin.com/in/pabloparejatob=
es" target=3D"_blank">http://www.linkedin.com/in/pabloparejatobes</a></div>


<div>Twitter =A0 =A0 =A0=A0<a href=3D"http://www.twitter.com/pablopareja" t=
arget=3D"_blank">http://www.twitter.com/pablopareja</a></div><div><br></div=
><div>Creator of Bio4j --&gt; <a href=3D"http://www.bio4j.com" target=3D"_b=
lank">http://www.bio4j.com</a></div>


<div><br></div><div><a href=3D"http://www.ohnosequences.com" target=3D"_bla=
nk">http://www.ohnosequences.com</a></div></div></div></div></div><br>
</div>
</blockquote></div>
</div></div></blockquote></div><br><br clear=3D"all"><div><br></div>-- <br>=
Pablo Pareja Tobes=A0<div><br><div>My site =A0 =A0=A0<a href=3D"http://abou=
t.me/pablopareja" target=3D"_blank">http://about.me/pablopareja</a><div><di=
v><div>LinkedIn =A0 =A0<a href=3D"http://www.linkedin.com/in/pabloparejatob=
es" target=3D"_blank">http://www.linkedin.com/in/pabloparejatobes</a></div>
<div>Twitter =A0 =A0 =A0=A0<a href=3D"http://www.twitter.com/pablopareja" t=
arget=3D"_blank">http://www.twitter.com/pablopareja</a></div><div><br></div=
><div>Creator of Bio4j --&gt; <a href=3D"http://www.bio4j.com" target=3D"_b=
lank">http://www.bio4j.com</a></div>
<div><br></div><div><a href=3D"http://www.ohnosequences.com" target=3D"_bla=
nk">http://www.ohnosequences.com</a></div></div></div></div></div><br>

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