URL encoded template links not working

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URL encoded template links not working

Vallejos, Andrew

RatMine’s URL encoded template links are no longer working.  The error on the page is “internal server error”, and all I get in the logs is a Java servlet exception.  I receive no other error messages.

 

Here is an example of one that I’ve been trying to get working:

http://ratmine.mcw.edu/ratmine/loadQuery.do?skipBuilder=true&query=%3Cquery%20name%3D%22qtl_symbol_to_genes_in_region%22%20model%3D%22genomic%22%20view%3D%22QTL.overlappingFeatures.primaryIdentifier%20QTL.overlappingFeatures.symbol%20QTL.overlappingFeatures.name%20QTL.overlappingFeatures.chromosome.primaryIdentifier%20QTL.overlappingFeatures.chromosomeLocation.start%20QTL.overlappingFeatures.chromosomeLocation.end%22%20longDescription%3D%22Returns%20the%20genes%20located%20with%20a%20particular%20QTL%20region%22%20sortOrder%3D%22QTL.overlappingFeatures.primaryIdentifier%20asc%22%3E%0A%20%20%20%20%3CpathDescription%20pathString%3D%22QTL.overlappingFeatures.chromosome%22%20description%3D%22Chromosome%22%2F%3E%0A%20%20%20%20%3CpathDescription%20pathString%3D%22QTL.overlappingFeatures.chromosomeLocation%22%20description%3D%22Gene%22%2F%3E%0A%20%20%20%20%3CpathDescription%20pathString%3D%22QTL.overlappingFeatures%22%20description%3D%22Gene%22%2F%3E%0A%20%20%20%20%3Cconstraint%20path%3D%22QTL.overlappingFeatures%22%20editable%3D%22false%22%20type%3D%22Gene%22%2F%3E%0A%20%20%20%20%3Cconstraint%20path%3D%22QTL%22%20editable%3D%22true%22%20op%3D%22LOOKUP%22%20value%3D%22Mcs1%22%20extraValue%3D%22%22%2F%3E%0A%20%20%3C%2Fquery%3E

 

Also the bulk download links from the Genomics page also don’t work.  Those are internally URL encoded but here is the snippet from the JSP file:

<im:querylink text="All <i>Rattus norvegicus</i> genes (browse)" skipBuilder="true">

              <query name="" model="genomic" view="Gene.secondaryIdentifier Gene.name Gene.primaryIdentifier Gene.symbol Gene.chromosome.primaryIdentifier Gene.chromosomeLocation.start Gene.chromosomeLocation.end">

                <node path="Gene" type="Gene">

                </node>

                <node path="Gene.organism" type="Organism">

                </node>

                <node path="Gene.organism.name" type="String">

                  <constraint op="=" value="Rattus norvegicus" description="" identifier="" code="A">

                  </constraint>

                </node>

              </query>

            </im:querylink>

 

-Andrew

 

======================

Andrew Vallejos

Web Developer II

Biotechnology and Bioengineering Center

Medical College of Wisconsin

414-955-4104

[hidden email]


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Re: URL encoded template links not working

Julie Sullivan
Hi Andrew,

We did change our Query API but everything should be backwards compatible.  I
went to this page:

http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=2044&species=3

And clicked on the two templates there.

"Gene --> SNPs" worked fine.

"Gene --> QTLs" did not.  I found this error:

Query does not verify: [Subclass Qtl (for path Gene.overlappingFeatures) is not
in the model, Path Gene.overlappingFeatures.trait in view list is not in the
model, Path Gene.overlappingFeatures.lod in view list is not in the model, Path
Gene.overlappingFeatures.pValue in view list is not in the model]
        at org.intermine.pathquery.PathQuery.getRootClass(PathQuery.java:1768)

It looks like you may have to update that query?

(The stacktrace will be in intermine.log, or on the webpage itself if you are
logged in as the administrator.  If not, just "view source".)

I have just written some code that will make this a lot easier, letting you link
in with a template instead of query XML.

Let me know if that fixes your problem (or not).

Cheers,
Julie

On 01/20/2011 03:38 PM, Vallejos, Andrew wrote:

> RatMine's URL encoded template links are no longer working.  The error
> on the page is "internal server error", and all I get in the logs is a
> Java servlet exception.  I receive no other error messages.
>
>
>
> Here is an example of one that I've been trying to get working:
>
> http://ratmine.mcw.edu/ratmine/loadQuery.do?skipBuilder=true&query=%3Cqu
> ery%20name%3D%22qtl_symbol_to_genes_in_region%22%20model%3D%22genomic%22
> %20view%3D%22QTL.overlappingFeatures.primaryIdentifier%20QTL.overlapping
> Features.symbol%20QTL.overlappingFeatures.name%20QTL.overlappingFeatures
> .chromosome.primaryIdentifier%20QTL.overlappingFeatures.chromosomeLocati
> on.start%20QTL.overlappingFeatures.chromosomeLocation.end%22%20longDescr
> iption%3D%22Returns%20the%20genes%20located%20with%20a%20particular%20QT
> L%20region%22%20sortOrder%3D%22QTL.overlappingFeatures.primaryIdentifier
> %20asc%22%3E%0A%20%20%20%20%3CpathDescription%20pathString%3D%22QTL.over
> lappingFeatures.chromosome%22%20description%3D%22Chromosome%22%2F%3E%0A%
> 20%20%20%20%3CpathDescription%20pathString%3D%22QTL.overlappingFeatures.
> chromosomeLocation%22%20description%3D%22Gene%22%2F%3E%0A%20%20%20%20%3C
> pathDescription%20pathString%3D%22QTL.overlappingFeatures%22%20descripti
> on%3D%22Gene%22%2F%3E%0A%20%20%20%20%3Cconstraint%20path%3D%22QTL.overla
> ppingFeatures%22%20editable%3D%22false%22%20type%3D%22Gene%22%2F%3E%0A%2
> 0%20%20%20%3Cconstraint%20path%3D%22QTL%22%20editable%3D%22true%22%20op%
> 3D%22LOOKUP%22%20value%3D%22Mcs1%22%20extraValue%3D%22%22%2F%3E%0A%20%20
> %3C%2Fquery%3E
>
>
>
> Also the bulk download links from the Genomics page also don't work.
> Those are internally URL encoded but here is the snippet from the JSP
> file:
>
> <im:querylink text="All<i>Rattus norvegicus</i>  genes (browse)"
> skipBuilder="true">
>
>                <query name="" model="genomic"
> view="Gene.secondaryIdentifier Gene.name Gene.primaryIdentifier
> Gene.symbol Gene.chromosome.primaryIdentifier
> Gene.chromosomeLocation.start Gene.chromosomeLocation.end">
>
>                  <node path="Gene" type="Gene">
>
>                  </node>
>
>                  <node path="Gene.organism" type="Organism">
>
>                  </node>
>
>                  <node path="Gene.organism.name" type="String">
>
>                    <constraint op="=" value="Rattus norvegicus"
> description="" identifier="" code="A">
>
>                    </constraint>
>
>                  </node>
>
>                </query>
>
>              </im:querylink>
>
>
>
> -Andrew
>
>
>
> ======================
>
> 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: URL encoded template links not working

Vallejos, Andrew
I did manually change the query, but it still didn't work.  My first
guess was that I simply needed to find-replace: "Qtl"-"QTL", but I
didn't work for me.

-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On
Behalf Of Julie Sullivan
Sent: Monday, January 24, 2011 9:26 AM
To: [hidden email]
Subject: Re: [InterMine Dev] URL encoded template links not working

Hi Andrew,

We did change our Query API but everything should be backwards
compatible.  I
went to this page:

http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=2044&species=3

And clicked on the two templates there.

"Gene --> SNPs" worked fine.

"Gene --> QTLs" did not.  I found this error:

Query does not verify: [Subclass Qtl (for path Gene.overlappingFeatures)
is not
in the model, Path Gene.overlappingFeatures.trait in view list is not in
the
model, Path Gene.overlappingFeatures.lod in view list is not in the
model, Path
Gene.overlappingFeatures.pValue in view list is not in the model]
        at
org.intermine.pathquery.PathQuery.getRootClass(PathQuery.java:1768)

It looks like you may have to update that query?

(The stacktrace will be in intermine.log, or on the webpage itself if
you are
logged in as the administrator.  If not, just "view source".)

I have just written some code that will make this a lot easier, letting
you link
in with a template instead of query XML.

Let me know if that fixes your problem (or not).

Cheers,
Julie

On 01/20/2011 03:38 PM, Vallejos, Andrew wrote:
> RatMine's URL encoded template links are no longer working.  The error
> on the page is "internal server error", and all I get in the logs is a
> Java servlet exception.  I receive no other error messages.
>
>
>
> Here is an example of one that I've been trying to get working:
>
>
http://ratmine.mcw.edu/ratmine/loadQuery.do?skipBuilder=true&query=%3Cqu
>
ery%20name%3D%22qtl_symbol_to_genes_in_region%22%20model%3D%22genomic%22
>
%20view%3D%22QTL.overlappingFeatures.primaryIdentifier%20QTL.overlapping
>
Features.symbol%20QTL.overlappingFeatures.name%20QTL.overlappingFeatures
>
.chromosome.primaryIdentifier%20QTL.overlappingFeatures.chromosomeLocati
>
on.start%20QTL.overlappingFeatures.chromosomeLocation.end%22%20longDescr
>
iption%3D%22Returns%20the%20genes%20located%20with%20a%20particular%20QT
>
L%20region%22%20sortOrder%3D%22QTL.overlappingFeatures.primaryIdentifier
>
%20asc%22%3E%0A%20%20%20%20%3CpathDescription%20pathString%3D%22QTL.over
>
lappingFeatures.chromosome%22%20description%3D%22Chromosome%22%2F%3E%0A%
>
20%20%20%20%3CpathDescription%20pathString%3D%22QTL.overlappingFeatures.
>
chromosomeLocation%22%20description%3D%22Gene%22%2F%3E%0A%20%20%20%20%3C
>
pathDescription%20pathString%3D%22QTL.overlappingFeatures%22%20descripti
>
on%3D%22Gene%22%2F%3E%0A%20%20%20%20%3Cconstraint%20path%3D%22QTL.overla
>
ppingFeatures%22%20editable%3D%22false%22%20type%3D%22Gene%22%2F%3E%0A%2
>
0%20%20%20%3Cconstraint%20path%3D%22QTL%22%20editable%3D%22true%22%20op%
>
3D%22LOOKUP%22%20value%3D%22Mcs1%22%20extraValue%3D%22%22%2F%3E%0A%20%20

> %3C%2Fquery%3E
>
>
>
> Also the bulk download links from the Genomics page also don't work.
> Those are internally URL encoded but here is the snippet from the JSP
> file:
>
> <im:querylink text="All<i>Rattus norvegicus</i>  genes (browse)"
> skipBuilder="true">
>
>                <query name="" model="genomic"
> view="Gene.secondaryIdentifier Gene.name Gene.primaryIdentifier
> Gene.symbol Gene.chromosome.primaryIdentifier
> Gene.chromosomeLocation.start Gene.chromosomeLocation.end">
>
>                  <node path="Gene" type="Gene">
>
>                  </node>
>
>                  <node path="Gene.organism" type="Organism">
>
>                  </node>
>
>                  <node path="Gene.organism.name" type="String">
>
>                    <constraint op="=" value="Rattus norvegicus"
> description="" identifier="" code="A">
>
>                    </constraint>
>
>                  </node>
>
>                </query>
>
>              </im:querylink>
>
>
>
> -Andrew
>
>
>
> ======================
>
> 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

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
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Re: URL encoded template links not working

Julie Sullivan
What is the error message you get with the updated QTL query?

Here is the error I get for the query on the bulk download on your genomics page:

[Path Gene.chromosome.identifier in view list is not in the model]


On 01/24/2011 03:36 PM, Vallejos, Andrew wrote:

> I did manually change the query, but it still didn't work.  My first
> guess was that I simply needed to find-replace: "Qtl"-"QTL", but I
> didn't work for me.
>
> -----Original Message-----
> From: [hidden email] [mailto:[hidden email]] On
> Behalf Of Julie Sullivan
> Sent: Monday, January 24, 2011 9:26 AM
> To: [hidden email]
> Subject: Re: [InterMine Dev] URL encoded template links not working
>
> Hi Andrew,
>
> We did change our Query API but everything should be backwards
> compatible.  I
> went to this page:
>
> http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=2044&species=3
>
> And clicked on the two templates there.
>
> "Gene -->  SNPs" worked fine.
>
> "Gene -->  QTLs" did not.  I found this error:
>
> Query does not verify: [Subclass Qtl (for path Gene.overlappingFeatures)
> is not
> in the model, Path Gene.overlappingFeatures.trait in view list is not in
> the
> model, Path Gene.overlappingFeatures.lod in view list is not in the
> model, Path
> Gene.overlappingFeatures.pValue in view list is not in the model]
> at
> org.intermine.pathquery.PathQuery.getRootClass(PathQuery.java:1768)
>
> It looks like you may have to update that query?
>
> (The stacktrace will be in intermine.log, or on the webpage itself if
> you are
> logged in as the administrator.  If not, just "view source".)
>
> I have just written some code that will make this a lot easier, letting
> you link
> in with a template instead of query XML.
>
> Let me know if that fixes your problem (or not).
>
> Cheers,
> Julie
>
> On 01/20/2011 03:38 PM, Vallejos, Andrew wrote:
>> RatMine's URL encoded template links are no longer working.  The error
>> on the page is "internal server error", and all I get in the logs is a
>> Java servlet exception.  I receive no other error messages.
>>
>>
>>
>> Here is an example of one that I've been trying to get working:
>>
>>
> http://ratmine.mcw.edu/ratmine/loadQuery.do?skipBuilder=true&query=%3Cqu
>>
> ery%20name%3D%22qtl_symbol_to_genes_in_region%22%20model%3D%22genomic%22
>>
> %20view%3D%22QTL.overlappingFeatures.primaryIdentifier%20QTL.overlapping
>>
> Features.symbol%20QTL.overlappingFeatures.name%20QTL.overlappingFeatures
>>
> .chromosome.primaryIdentifier%20QTL.overlappingFeatures.chromosomeLocati
>>
> on.start%20QTL.overlappingFeatures.chromosomeLocation.end%22%20longDescr
>>
> iption%3D%22Returns%20the%20genes%20located%20with%20a%20particular%20QT
>>
> L%20region%22%20sortOrder%3D%22QTL.overlappingFeatures.primaryIdentifier
>>
> %20asc%22%3E%0A%20%20%20%20%3CpathDescription%20pathString%3D%22QTL.over
>>
> lappingFeatures.chromosome%22%20description%3D%22Chromosome%22%2F%3E%0A%
>>
> 20%20%20%20%3CpathDescription%20pathString%3D%22QTL.overlappingFeatures.
>>
> chromosomeLocation%22%20description%3D%22Gene%22%2F%3E%0A%20%20%20%20%3C
>>
> pathDescription%20pathString%3D%22QTL.overlappingFeatures%22%20descripti
>>
> on%3D%22Gene%22%2F%3E%0A%20%20%20%20%3Cconstraint%20path%3D%22QTL.overla
>>
> ppingFeatures%22%20editable%3D%22false%22%20type%3D%22Gene%22%2F%3E%0A%2
>>
> 0%20%20%20%3Cconstraint%20path%3D%22QTL%22%20editable%3D%22true%22%20op%
>>
> 3D%22LOOKUP%22%20value%3D%22Mcs1%22%20extraValue%3D%22%22%2F%3E%0A%20%20
>> %3C%2Fquery%3E
>>
>>
>>
>> Also the bulk download links from the Genomics page also don't work.
>> Those are internally URL encoded but here is the snippet from the JSP
>> file:
>>
>> <im:querylink text="All<i>Rattus norvegicus</i>   genes (browse)"
>> skipBuilder="true">
>>
>>                 <query name="" model="genomic"
>> view="Gene.secondaryIdentifier Gene.name Gene.primaryIdentifier
>> Gene.symbol Gene.chromosome.primaryIdentifier
>> Gene.chromosomeLocation.start Gene.chromosomeLocation.end">
>>
>>                   <node path="Gene" type="Gene">
>>
>>                   </node>
>>
>>                   <node path="Gene.organism" type="Organism">
>>
>>                   </node>
>>
>>                   <node path="Gene.organism.name" type="String">
>>
>>                     <constraint op="=" value="Rattus norvegicus"
>> description="" identifier="" code="A">
>>
>>                     </constraint>
>>
>>                   </node>
>>
>>                 </query>
>>
>>               </im:querylink>
>>
>>
>>
>> -Andrew
>>
>>
>>
>> ======================
>>
>> 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
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev