Re: dev Digest, Vol 18, Issue 10

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Re: dev Digest, Vol 18, Issue 10

kkarra@stanford.edu
Hi,

I have a successful build up at
http://dough.stanford.edu:8080/yeastmine-dev/begin.do (Thanks to Julie!!)

I still have quite a bit of work to do.

-Kalpana

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Sent: Wednesday, November 17, 2010 4:00:01 AM
Subject: dev Digest, Vol 18, Issue 10

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Today's Topics:

   1. Re: More RatMine Errors (Richard Smith)


----------------------------------------------------------------------

Message: 1
Date: Tue, 16 Nov 2010 13:28:13 +0000
From: Richard Smith <[hidden email]>
Subject: Re: [InterMine Dev] More RatMine Errors
To: "Vallejos, Andrew" <[hidden email]>
Cc: [hidden email]
Message-ID: <[hidden email]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Right, that does seem to be the case.

I'd do an audit of all the keys and see if one of them is missing the
chromosome key.  Or it could be that the key is correct but one of the
sources isn't setting Chromosome.organism.

Cheers,
Richard.




Vallejos, Andrew wrote:

> Alright,
>
> So from this I am gathering that my gff and genes sources are using
> different keys than the rest of my sources?
>
> -Andrew
>
> secondaryidentifier | symbol | primaryidentifier | length | id | name |
> scoretype | score | chromosomeid | chrom
> osomelocationid | organismid | sequenceid | sequenceontologytermid |
> class
> ---------------------+--------+-------------------+--------+----+------+
> -----------+-------+--------------+------
> ----------------+------------+------------+------------------------+----
> ---
> (0 rows)
>
> production-rat=# select * from tracker where id=321000002;
> ERROR:  column "id" does not exist
> LINE 1: select * from tracker where id=321000002;
>                                     ^
> production-rat=# select * from tracker where objectid=321000002;
>  objectid  |      fieldname       | sourcename | version
> -----------+----------------------+------------+---------
>  321000002 | scoreType            | rat-gff    |       2
>  321000002 | sequenceOntologyTerm | rat-gff    |       2
>  321000002 | secondaryIdentifier  | rat-gff    |       2
>  321000002 | chromosome           | rat-gff    |       2
>  321000002 | score                | rat-gff    |       2
>  321000002 | length               | rat-gff    |       2
>  321000002 | name                 | rat-gff    |       2
>  321000002 | chromosomeLocation   | rat-gff    |       2
>  321000002 | sequence             | rat-gff    |       2
>  321000002 | symbol               | rat-gff    |       2
>  321000002 | primaryIdentifier    | rat-gff    |       2
>  321000002 | length               | rat-genes  |       0
>  321000002 | name                 | rat-genes  |       0
>  321000002 | sequence             | rat-genes  |       0
>  321000002 | primaryIdentifier    | rat-genes  |       0
>  321000002 | id                   | rat-genes  |       0
>  321000002 | scoreType            | rat-genes  |       0
>  321000002 | organism             | rat-genes  |       0
>  321000002 | sequenceOntologyTerm | rat-genes  |       0
>  321000002 | secondaryIdentifier  | rat-genes  |       0
>  321000002 | chromosome           | rat-genes  |       0
>  321000002 | score                | rat-genes  |       0
>  321000002 | chromosomeLocation   | rat-genes  |       0
>  321000002 | symbol               | rat-genes  |       0
> (24 rows)
>
> production-rat=# select * from tracker where objectid=321133575;
>  objectid  |         fieldname          |   sourcename    | version
> -----------+----------------------------+-----------------+---------
>  321133575 | upstreamIntergenicRegion   | rat-affy-probes |     203
>  321133575 | sequence                   | rat-affy-probes |     203
>  321133575 | scoreType                  | rat-affy-probes |     203
>  321133575 | downstreamIntergenicRegion | rat-affy-probes |     203
>  321133575 | score                      | rat-affy-probes |     203
>  321133575 | upstreamIntergenicRegion   | rat-do-annot    |      24
>  321133575 | sequence                   | rat-do-annot    |      24
>  321133575 | scoreType                  | rat-do-annot    |      24
>  321133575 | downstreamIntergenicRegion | rat-do-annot    |      24
>  321133575 | score                      | rat-do-annot    |      24
>  321133575 | upstreamIntergenicRegion   | go-annotation   |      20
>  321133575 | sequence                   | go-annotation   |      20
>  321133575 | scoreType                  | go-annotation   |      20
>  321133575 | sequenceOntologyTerm       | go-annotation   |      20
>  321133575 | downstreamIntergenicRegion | go-annotation   |      20
>  321133575 | score                      | go-annotation   |      20
>  321133575 | upstreamIntergenicRegion   | uniprot-rat     |       9
>  321133575 | sequence                   | uniprot-rat     |       9
>  321133575 | scoreType                  | uniprot-rat     |       9
>  321133575 | sequenceOntologyTerm       | uniprot-rat     |       9
>  321133575 | downstreamIntergenicRegion | uniprot-rat     |       9
>  321133575 | score                      | uniprot-rat     |       9
>  321133575 | upstreamIntergenicRegion   | rat-pharmgkb    |       3
>  321133575 | pharmGKBidentifier         | rat-pharmgkb    |       3
>  321133575 | sequence                   | rat-pharmgkb    |       3
>  321133575 | scoreType                  | rat-pharmgkb    |       3
>  321133575 | downstreamIntergenicRegion | rat-pharmgkb    |       3
>  321133575 | score                      | rat-pharmgkb    |       3
>  321133575 | upstreamIntergenicRegion   | rat-gff         |       2
>  321133575 | pharmGKBidentifier         | rat-gff         |       2
>  321133575 | length                     | rat-gff         |       2
>  321133575 | sequence                   | rat-gff         |       2
>  321133575 | scoreType                  | rat-gff         |       2
>  321133575 | sequenceOntologyTerm       | rat-gff         |       2
>  321133575 | downstreamIntergenicRegion | rat-gff         |       2
>  321133575 | chromosome                 | rat-gff         |       2
>  321133575 | score                      | rat-gff         |       2
>  321133575 | chromosomeLocation         | rat-gff         |       2
>  321133575 | upstreamIntergenicRegion   | rat-genes       |       1
>  321133575 | pharmGKBidentifier         | rat-genes       |       1
>  321133575 | ncbiGeneNumber             | rat-genes       |       1
>  321133575 | length                     | rat-genes       |       1
>  321133575 | name                       | rat-genes       |       1
>  321133575 | sequence                   | rat-genes       |       1
>  321133575 | description                | rat-genes       |       1
>  321133575 | primaryIdentifier          | rat-genes       |       1
>  321133575 | id                         | rat-genes       |       1
>  321133575 | geneType                   | rat-genes       |       1
>  321133575 | scoreType                  | rat-genes       |       1
>  321133575 | downstreamIntergenicRegion | rat-genes       |       1
>  321133575 | sequenceOntologyTerm       | rat-genes       |       1
>  321133575 | organism                   | rat-genes       |       1
>  321133575 | secondaryIdentifier        | rat-genes       |       1
>  321133575 | chromosome                 | rat-genes       |       1
>  321133575 | score                      | rat-genes       |       1
>  321133575 | ensemblIdentifier          | rat-genes       |       1
>  321133575 | chromosomeLocation         | rat-genes       |       1
>  321133575 | nomenclatureStatus         | rat-genes       |       1
>  321133575 | symbol                     | rat-genes       |       1
>  321133575 | fishBand                   | rat-genes       |       1
> (60 rows)
>
> -----Original Message-----
> From: Richard Smith [mailto:[hidden email]]
> Sent: Friday, November 12, 2010 9:46 AM
> To: Vallejos, Andrew
> Cc: [hidden email]
> Subject: Re: [InterMine Dev] More RatMine Errors
>
> Hi Andrew,
> It looks like the problem is that the gene references a chromosome that
> doesn't exist in the database.  This is usually down to merging errors.
>
> Can you verify that with some SQL queries:
>
> select * from chromosome where id = 321000002;
>
> select * from tracker where objectid = 321000002;
>
> select * from tracker where objectid = 321133575;
>
>
> This should give some idea whether the chromosome actually exists,
> and what loaded the gene/chromosome that caused the problem.
>
> If this is the problem then you could take a look at the keys
> for the sources you're using and see if any of them are loading
> chromosomes but are missing the key.
>
> Let me know the results of the queries.
>
> Cheers,
> Richard.
>
>
>
>
> Vallejos, Andrew wrote:
>> Alright...so I found some more errors from the log files.  To recap...
>> RatMine throws an error when navigating to a gene page.  Or when quick
>> searching tries to display a gene.
>>
>>  
>>
>> Caused by: java.lang.RuntimeException: IllegalAccessException while
>> trying to get value of field "chromosome" in object: Gene
>> [chromosome=321000002, chromosomeLocation=322005082,
>> description="component of the small nuclear ribonucleoprotein (snRNP)
>> complex; may be involved in tissue-specific alternative RNA processing
>> events, such as pre-mRNA splicing", downstreamIntergenicRegion=null,
>> ensemblIdentifier="null", fishBand="q22", geneType="protein-coding",
>> id="321133575", length="22055", name="small nuclear ribonucleoprotein
>> polypeptide N", ncbiGeneNumber="81781", nomenclatureStatus="APPROVED",
>> organism=321000000, pharmGKBidentifier="PA36005",
>> primaryIdentifier="621306", score="null", scoreType="null",
>> secondaryIdentifier="RGD:621306", sequence=null,
>> sequenceOntologyTerm=322000004, symbol="Snrpn",
>> upstreamIntergenicRegion=null]
>>
>>         at
> org.intermine.api.util.PathUtil.resolvePath(PathUtil.java:68)
>>         at
>>
> org.intermine.web.logic.results.DisplayObject.getFieldValues(DisplayObje
>> ct.java:377)
>>
>>         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>>
>>         at
>>
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.jav
>> a:39)
>>
>>         at
>>
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
>> Impl.java:25)
>>
>>         at java.lang.reflect.Method.invoke(Method.java:597)
>>
>>         at javax.el.BeanELResolver.getValue(BeanELResolver.java:62)
>>
>>         ... 76 more
>>
>> Caused by: java.lang.IllegalAccessException: Couldn't get field
>> "[interface org.intermine.model.bio.Gene].chromosome" (a
>> org.intermine.model.bio.Chromosome)
>>
>>         at
> org.intermine.util.TypeUtil.getFieldValue(TypeUtil.java:105)
>>         at
> org.intermine.api.util.PathUtil.resolvePath(PathUtil.java:60)
>>         ... 82 more
>>
>> Caused by: java.lang.reflect.InvocationTargetException
>>
>>         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>>
>>         at
>>
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.jav
>> a:39)
>>
>>         at
>>
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
>> Impl.java:25)
>>
>>         at java.lang.reflect.Method.invoke(Method.java:597)
>>
>>         at org.intermine.util.TypeUtil.getFieldValue(TypeUtil.java:96)
>>
>>         ... 83 more
>>
>> Caused by: java.lang.NullPointerException: Error retrieving object
> from
>> proxy with ID 321000002 for class org.intermine.model.bio.Chromosome
>> from ObjectStore os.production
>>
>>         at
>>
> org.intermine.objectstore.proxy.ProxyReference.getObject(ProxyReference.
>> java:60)
>>
>>         at
>> org.intermine.model.bio.GeneShadow.getChromosome(GeneShadow.java:159)
>>
>>         ... 88 more
>>
>>  
>>
>> ======================
>>
>> Andrew Vallejos
>>
>> Web Developer II
>>
>> Biotechnology and Bioengineering Center
>>
>> Medical College of Wisconsin
>>
>> 414-955-4104
>>
>> [hidden email]
>>
>>  
>>
>>
>>
>>
>>
> ------------------------------------------------------------------------
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>
>




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