More RatMine Errors

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More RatMine Errors

Vallejos, Andrew

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(DisplayObject.java:377)

        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)

        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.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.java:39)

        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.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]

 


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Re: More RatMine Errors

Richard Smith
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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Re: More RatMine Errors

Vallejos, Andrew
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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http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
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Re: More RatMine Errors

Richard Smith
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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