Constant error after 2.x build

[Paulo Nuin]

Hi

I was able to successfully build with 2.x and after the build, deploying the web app (still old version) I am getting the same error on queries and templates:

602340 [http-bio-8080-exec-277] ERROR org.intermine.webservice.server.WebService  - Service failed by internal error. Request parameters:
start: 0
size: 250
query: <query model="genomic" view="Gene.primaryIdentifier Gene.secondaryIdentifier Gene.symbol Gene.alleles.primaryIdentifier Gene.alleles.symbol Gene.alleles.phenotype.identifier Gene.alleles.phenotype.name" sortOrder="Gene.primaryIdentifier ASC" name="gene_to_phenotypes" ><constraint path="Gene.symbol" op="=" value="unc-26" code="A" /></query>
format: json
java.lang.NoSuchMethodError: org.intermine.model.bio.Organism.getTaxonId()Ljava/lang/Integer;

  at org.intermine.bio.web.BioLinkRedirectManager.generateLink(BioLinkRedirectManager.java:72)
  at org.intermine.webservice.server.output.TableCellFormatter.toMap(TableCellFormatter.java:65)
  at org.intermine.webservice.server.query.result.TableRowService$Processor.visitLeft(TableRowService.java:137)
  at org.intermine.webservice.server.query.result.TableRowService$Processor.visitLeft(TableRowService.java:122)
  at org.intermine.webservice.server.core.Either$Left.accept(Either.java:138)
  at org.intermine.webservice.server.query.result.TableRowService.runPathQuery(TableRowService.java:111)
  at org.intermine.webservice.server.query.result.QueryResultService.execute(QueryResultService.java:106)
  at org.intermine.webservice.server.WebService.service(WebService.java:350)
  at org.intermine.webservice.server.query.result.QueryResultServlet.runService(QueryResultServlet.java:61)
  at org.intermine.webservice.server.query.result.QueryResultServlet.doPost(QueryResultServlet.java:43)
  at javax.servlet.http.HttpServlet.service(HttpServlet.java:650)
  at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)

As you can see by the query, organism is not used in it. I still had the entrez error at the end of the build, but I filled the missing taxon IDs and species names on the table.

Any help appreciated

Paulo



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dev mailing list
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[sergio contrino-2]

hi paulo,
in the new release of intermine the taxonid is now a string.
you should use the new code for deploying your webapp.

from your wormmine directory run
./gradlew clean
and then
./gradlew cargoRedeployRemote

with the understanding that you have your tomcat running as specified in
your properties file in ~/.intermine

please let us know if this work
thanks!
sergio



On 17/01/2019 19:25, Paulo Nuin wrote:

> Hi
>
> I was able to successfully build with 2.x and after the build, deploying the web app (still old version) I am getting the same error on queries and templates:
>
> 602340 [http-bio-8080-exec-277] ERROR org.intermine.webservice.server.WebService  - Service failed by internal error. Request parameters:
> start: 0
> size: 250
> query: <query model="genomic" view="Gene.primaryIdentifier Gene.secondaryIdentifier Gene.symbol Gene.alleles.primaryIdentifier Gene.alleles.symbol Gene.alleles.phenotype.identifier Gene.alleles.phenotype.name" sortOrder="Gene.primaryIdentifier ASC" name="gene_to_phenotypes" ><constraint path="Gene.symbol" op="=" value="unc-26" code="A" /></query>
> format: json
> java.lang.NoSuchMethodError: org.intermine.model.bio.Organism.getTaxonId()Ljava/lang/Integer;
>
>    at org.intermine.bio.web.BioLinkRedirectManager.generateLink(BioLinkRedirectManager.java:72)
>    at org.intermine.webservice.server.output.TableCellFormatter.toMap(TableCellFormatter.java:65)
>    at org.intermine.webservice.server.query.result.TableRowService$Processor.visitLeft(TableRowService.java:137)
>    at org.intermine.webservice.server.query.result.TableRowService$Processor.visitLeft(TableRowService.java:122)
>    at org.intermine.webservice.server.core.Either$Left.accept(Either.java:138)
>    at org.intermine.webservice.server.query.result.TableRowService.runPathQuery(TableRowService.java:111)
>    at org.intermine.webservice.server.query.result.QueryResultService.execute(QueryResultService.java:106)
>    at org.intermine.webservice.server.WebService.service(WebService.java:350)
>    at org.intermine.webservice.server.query.result.QueryResultServlet.runService(QueryResultServlet.java:61)
>    at org.intermine.webservice.server.query.result.QueryResultServlet.doPost(QueryResultServlet.java:43)
>    at javax.servlet.http.HttpServlet.service(HttpServlet.java:650)
>    at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
>
> As you can see by the query, organism is not used in it. I still had the entrez error at the end of the build, but I filled the missing taxon IDs and species names on the table.
>
> Any help appreciated
>
> Paulo
>
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev
>

--
sergio contrino                  InterMine, University of Cambridge
https://sergiocontrino.github.io           http://www.intermine.org
_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev

[Paulo Nuin]

Hi Sergio

Redeploying did the trick, but I still find errors (Tomcat 7 doesn’t work at all, blank page) and with Tomcat 8 I am getting this error

^[2019-01-21 20:41:16,186 [http-nio-8080-exec-15] ERROR (InsertTag$InsertHandler,901) - Can't insert page 'hints.tile' : The requested resource [/tools/wormmine/hints.tile] is not available
]java.io.FileNotFoundException: The requested resource [/tools/wormmine/hints.tile] is not available

over and over when accessing the web app. Pages are blank.

Cheers
Paulo

> On Jan 21, 2019, at 10:30 AM, sergio contrino <[hidden email]> wrote:
>
> hi paulo,
> in the new release of intermine the taxonid is now a string.
> you should use the new code for deploying your webapp.
>
> from your wormmine directory run
> ./gradlew clean
> and then
> ./gradlew cargoRedeployRemote
>
> with the understanding that you have your tomcat running as specified in your properties file in ~/.intermine
>
> please let us know if this work
> thanks!
> sergio
>
>
>
> On 17/01/2019 19:25, Paulo Nuin wrote:
>> Hi
>> I was able to successfully build with 2.x and after the build, deploying the web app (still old version) I am getting the same error on queries and templates:
>> 602340 [http-bio-8080-exec-277] ERROR org.intermine.webservice.server.WebService  - Service failed by internal error. Request parameters:
>> start: 0
>> size: 250
>> query: <query model="genomic" view="Gene.primaryIdentifier Gene.secondaryIdentifier Gene.symbol Gene.alleles.primaryIdentifier Gene.alleles.symbol Gene.alleles.phenotype.identifier Gene.alleles.phenotype.name" sortOrder="Gene.primaryIdentifier ASC" name="gene_to_phenotypes" ><constraint path="Gene.symbol" op="=" value="unc-26" code="A" /></query>
>> format: json
>> java.lang.NoSuchMethodError: org.intermine.model.bio.Organism.getTaxonId()Ljava/lang/Integer;
>>   at org.intermine.bio.web.BioLinkRedirectManager.generateLink(BioLinkRedirectManager.java:72)
>>   at org.intermine.webservice.server.output.TableCellFormatter.toMap(TableCellFormatter.java:65)
>>   at org.intermine.webservice.server.query.result.TableRowService$Processor.visitLeft(TableRowService.java:137)
>>   at org.intermine.webservice.server.query.result.TableRowService$Processor.visitLeft(TableRowService.java:122)
>>   at org.intermine.webservice.server.core.Either$Left.accept(Either.java:138)
>>   at org.intermine.webservice.server.query.result.TableRowService.runPathQuery(TableRowService.java:111)
>>   at org.intermine.webservice.server.query.result.QueryResultService.execute(QueryResultService.java:106)
>>   at org.intermine.webservice.server.WebService.service(WebService.java:350)
>>   at org.intermine.webservice.server.query.result.QueryResultServlet.runService(QueryResultServlet.java:61)
>>   at org.intermine.webservice.server.query.result.QueryResultServlet.doPost(QueryResultServlet.java:43)
>>   at javax.servlet.http.HttpServlet.service(HttpServlet.java:650)
>>   at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
>> As you can see by the query, organism is not used in it. I still had the entrez error at the end of the build, but I filled the missing taxon IDs and species names on the table.
>> Any help appreciated
>> Paulo
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev
>
> --
> sergio contrino                  InterMine, University of Cambridge
> https://sergiocontrino.github.io           http://www.intermine.org

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev

[sergio contrino-2]

hi paulo,
not sure about the error you mention (could you send me a link to the
code you use?).

if in your log file there is also an error of the type

java.lang.ClassNotFoundException:
org.apache.logging.log4j.util.ReflectionUtil

then you should also try the fix (see below) we had to use in same case,
for which at the moment you need to install intermine locally.
thanks!
sergio


1)
rm -rf
~/.gradle/caches/modules-2/files-2/org.apache.logging.log4j/log4j-1.2-api/2.10.0/
2)
in your intermine checkout:
change your build.gradle (updating the log4j-1.2-api version to an older
version) to match this one

https://github.com/intermine/humanmine/files/2687178/build.gradle.txt

3)
install intermine locally. In your intermine checkout:
https://github.com/intermine/humanmine/files/2687178/build.gradle.txt
cd intermine
./gradlew install

4)
in your mine checkout:
a)
rm this line (if present)
org.intermine.model.bio.MPTerm.autocomplete = name
from the file
dbmodel/resources/objectstoresummary.config.properties
b)

./gradlew clean
./gradlew cargoReDeployRemote -stacktrace --no-daemon

(a longer discussion can be found here
https://github.com/intermine/humanmine/issues/2 )


On 21/01/2019 20:44, Paulo Nuin wrote:

> Hi Sergio
>
> Redeploying did the trick, but I still find errors (Tomcat 7 doesn’t work at all, blank page) and with Tomcat 8 I am getting this error
>
> ^[2019-01-21 20:41:16,186 [http-nio-8080-exec-15] ERROR (InsertTag$InsertHandler,901) - Can't insert page 'hints.tile' : The requested resource [/tools/wormmine/hints.tile] is not available
> ]java.io.FileNotFoundException: The requested resource [/tools/wormmine/hints.tile] is not available
>
> over and over when accessing the web app. Pages are blank.
>
> Cheers
> Paulo
>
>
>
>
>
>
>> On Jan 21, 2019, at 10:30 AM, sergio contrino <[hidden email]> wrote:
>>
>> hi paulo,
>> in the new release of intermine the taxonid is now a string.
>> you should use the new code for deploying your webapp.
>>
>> from your wormmine directory run
>> ./gradlew clean
>> and then
>> ./gradlew cargoRedeployRemote
>>
>> with the understanding that you have your tomcat running as specified in your properties file in ~/.intermine
>>
>> please let us know if this work
>> thanks!
>> sergio
>>
>>
>>
>> On 17/01/2019 19:25, Paulo Nuin wrote:
>>> Hi
>>> I was able to successfully build with 2.x and after the build, deploying the web app (still old version) I am getting the same error on queries and templates:
>>> 602340 [http-bio-8080-exec-277] ERROR org.intermine.webservice.server.WebService  - Service failed by internal error. Request parameters:
>>> start: 0
>>> size: 250
>>> query: <query model="genomic" view="Gene.primaryIdentifier Gene.secondaryIdentifier Gene.symbol Gene.alleles.primaryIdentifier Gene.alleles.symbol Gene.alleles.phenotype.identifier Gene.alleles.phenotype.name" sortOrder="Gene.primaryIdentifier ASC" name="gene_to_phenotypes" ><constraint path="Gene.symbol" op="=" value="unc-26" code="A" /></query>
>>> format: json
>>> java.lang.NoSuchMethodError: org.intermine.model.bio.Organism.getTaxonId()Ljava/lang/Integer;
>>>    at org.intermine.bio.web.BioLinkRedirectManager.generateLink(BioLinkRedirectManager.java:72)
>>>    at org.intermine.webservice.server.output.TableCellFormatter.toMap(TableCellFormatter.java:65)
>>>    at org.intermine.webservice.server.query.result.TableRowService$Processor.visitLeft(TableRowService.java:137)
>>>    at org.intermine.webservice.server.query.result.TableRowService$Processor.visitLeft(TableRowService.java:122)
>>>    at org.intermine.webservice.server.core.Either$Left.accept(Either.java:138)
>>>    at org.intermine.webservice.server.query.result.TableRowService.runPathQuery(TableRowService.java:111)
>>>    at org.intermine.webservice.server.query.result.QueryResultService.execute(QueryResultService.java:106)
>>>    at org.intermine.webservice.server.WebService.service(WebService.java:350)
>>>    at org.intermine.webservice.server.query.result.QueryResultServlet.runService(QueryResultServlet.java:61)
>>>    at org.intermine.webservice.server.query.result.QueryResultServlet.doPost(QueryResultServlet.java:43)
>>>    at javax.servlet.http.HttpServlet.service(HttpServlet.java:650)
>>>    at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
>>> As you can see by the query, organism is not used in it. I still had the entrez error at the end of the build, but I filled the missing taxon IDs and species names on the table.
>>> Any help appreciated
>>> Paulo
>>> _______________________________________________
>>> dev mailing list
>>> [hidden email]
>>> https://lists.intermine.org/mailman/listinfo/dev
>>
>> --
>> sergio contrino                  InterMine, University of Cambridge
>> https://sergiocontrino.github.io           http://www.intermine.org
>

--
sergio contrino                  InterMine, University of Cambridge
https://sergiocontrino.github.io           http://www.intermine.org
_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev

[Paulo Nuin]

HI Sergio

Did everything you mentioned, with a fresh copy of the repository and got to a point where I could see the header of the page but the browser reported that it couldn’t find 

wormminetheme.css

I don’t know where to put the CSS I commented out on

src/main/webapp/WEB-INF/web.properties

And redeployed the web app, and got back to the same hints.tile error.  I changed 

theme = wormmine

to

theme = humanmine 

And I am still stuck on the same error. Our code is on

https://github.com/WormBase/WormMine

I am trying locally with another install I have and I will see what happens.

Cheers

Paulo

On Jan 22, 2019, at 7:22 AM, sergio contrino <[hidden email]> wrote:

hi paulo,
not sure about the error you mention (could you send me a link to the code you use?).

if in your log file there is also an error of the type

java.lang.ClassNotFoundException: org.apache.logging.log4j.util.ReflectionUtil

then you should also try the fix (see below) we had to use in same case, for which at the moment you need to install intermine locally.
thanks!
sergio


1)
rm -rf ~/.gradle/caches/modules-2/files-2/org.apache.logging.log4j/log4j-1.2-api/2.10.0/
2)
in your intermine checkout:
change your build.gradle (updating the log4j-1.2-api version to an older version) to match this one

https://github.com/intermine/humanmine/files/2687178/build.gradle.txt

3)
install intermine locally. In your intermine checkout:
https://github.com/intermine/humanmine/files/2687178/build.gradle.txt
cd intermine
./gradlew install

4)
in your mine checkout:
a)
rm this line (if present)
org.intermine.model.bio.MPTerm.autocomplete = name
from the file
dbmodel/resources/objectstoresummary.config.properties
b)

./gradlew clean
./gradlew cargoReDeployRemote -stacktrace --no-daemon

(a longer discussion can be found here
https://github.com/intermine/humanmine/issues/2 )


On 21/01/2019 20:44, Paulo Nuin wrote:

Hi Sergio
Redeploying did the trick, but I still find errors (Tomcat 7 doesn’t work at all, blank page) and with Tomcat 8 I am getting this error
^[2019-01-21 20:41:16,186 [http-nio-8080-exec-15] ERROR (InsertTag$InsertHandler,901) - Can't insert page 'hints.tile' : The requested resource [/tools/wormmine/hints.tile] is not available
]java.io.FileNotFoundException: The requested resource [/tools/wormmine/hints.tile] is not available
over and over when accessing the web app. Pages are blank.
Cheers
Paulo

On Jan 21, 2019, at 10:30 AM, sergio contrino <[hidden email]> wrote:

hi paulo,
in the new release of intermine the taxonid is now a string.
you should use the new code for deploying your webapp.

from your wormmine directory run
./gradlew clean
and then
./gradlew cargoRedeployRemote

with the understanding that you have your tomcat running as specified in your properties file in ~/.intermine

please let us know if this work
thanks!
sergio



On 17/01/2019 19:25, Paulo Nuin wrote:

Hi
I was able to successfully build with 2.x and after the build, deploying the web app (still old version) I am getting the same error on queries and templates:
602340 [http-bio-8080-exec-277] ERROR org.intermine.webservice.server.WebService  - Service failed by internal error. Request parameters:
start: 0
size: 250
query: <query model="genomic" view="Gene.primaryIdentifier Gene.secondaryIdentifier Gene.symbol Gene.alleles.primaryIdentifier Gene.alleles.symbol Gene.alleles.phenotype.identifier Gene.alleles.phenotype.name" sortOrder="Gene.primaryIdentifier ASC" name="gene_to_phenotypes" ><constraint path="Gene.symbol" op="=" value="unc-26" code="A" /></query>
format: json
java.lang.NoSuchMethodError: org.intermine.model.bio.Organism.getTaxonId()Ljava/lang/Integer;
  at org.intermine.bio.web.BioLinkRedirectManager.generateLink(BioLinkRedirectManager.java:72)
  at org.intermine.webservice.server.output.TableCellFormatter.toMap(TableCellFormatter.java:65)
  at org.intermine.webservice.server.query.result.TableRowService$Processor.visitLeft(TableRowService.java:137)
  at org.intermine.webservice.server.query.result.TableRowService$Processor.visitLeft(TableRowService.java:122)
  at org.intermine.webservice.server.core.Either$Left.accept(Either.java:138)
  at org.intermine.webservice.server.query.result.TableRowService.runPathQuery(TableRowService.java:111)
  at org.intermine.webservice.server.query.result.QueryResultService.execute(QueryResultService.java:106)
  at org.intermine.webservice.server.WebService.service(WebService.java:350)
  at org.intermine.webservice.server.query.result.QueryResultServlet.runService(QueryResultServlet.java:61)
  at org.intermine.webservice.server.query.result.QueryResultServlet.doPost(QueryResultServlet.java:43)
  at javax.servlet.http.HttpServlet.service(HttpServlet.java:650)
  at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
As you can see by the query, organism is not used in it. I still had the entrez error at the end of the build, but I filled the missing taxon IDs and species names on the table.
Any help appreciated
Paulo
_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev

--
sergio contrino                  InterMine, University of Cambridge
https://sergiocontrino.github.io           http://www.intermine.org

--
sergio contrino                  InterMine, University of Cambridge
https://sergiocontrino.github.io           http://www.intermine.org

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev

[sergio contrino-2]

thank you paulo,
i have cloned your repo.

there was a path in need of upgrade in the docs
https://intermine.readthedocs.io/en/latest/webapp/layout/

regarding the theme location: it should be in
webapp/src/main/webapp/themes
of your wormmine code
you can create the themes directory and put in your css file, or
probably just copy your
intermine/webapp/main/resources/webapp/themes/wormmine/
directory from the intermine v1 repo to your wormmine one.

please let me know if this helps (or not...)
thanks!
sergio


On 23/01/2019 02:37, Paulo Nuin wrote:

> HI Sergio
>
> Did everything you mentioned, with a fresh copy of the repository and
> got to a point where I could see the header of the page but the browser
> reported that it couldn’t find
>
> wormminetheme.css
>
> I don’t know where to put the CSS I commented out on
>
> src/main/webapp/WEB-INF/web.properties
>
> And redeployed the web app, and got back to the same hints.tile error.
>   I changed
>
> theme = wormmine
>
> to
>
> theme = humanmine
>
> And I am still stuck on the same error. Our code is on
>
> https://github.com/WormBase/WormMine
>
>
> I am trying locally with another install I have and I will see what happens.
>
> Cheers
> Paulo
>
>
>
>
>> On Jan 22, 2019, at 7:22 AM, sergio contrino <[hidden email]
>> <mailto:[hidden email]>> wrote:
>>
>> hi paulo,
>> not sure about the error you mention (could you send me a link to the
>> code you use?).
>>
>> if in your log file there is also an error of the type
>>
>> java.lang.ClassNotFoundException:
>> org.apache.logging.log4j.util.ReflectionUtil
>>
>> then you should also try the fix (see below) we had to use in same
>> case, for which at the moment you need to install intermine locally.
>> thanks!
>> sergio
>>
>>
>> 1)
>> rm -rf
>> ~/.gradle/caches/modules-2/files-2/org.apache.logging.log4j/log4j-1.2-api/2.10.0/
>> 2)
>> in your intermine checkout:
>> change your build.gradle (updating the log4j-1.2-api version to an
>> older version) to match this one
>>
>> https://github.com/intermine/humanmine/files/2687178/build.gradle.txt
>>
>> 3)
>> install intermine locally. In your intermine checkout:
>> https://github.com/intermine/humanmine/files/2687178/build.gradle.txt
>> cd intermine
>> ./gradlew install
>>
>> 4)
>> in your mine checkout:
>> a)
>> rm this line (if present)
>> org.intermine.model.bio.MPTerm.autocomplete = name
>> from the file
>> dbmodel/resources/objectstoresummary.config.properties
>> b)
>>
>> ./gradlew clean
>> ./gradlew cargoReDeployRemote -stacktrace --no-daemon
>>
>> (a longer discussion can be found here
>> https://github.com/intermine/humanmine/issues/2 )
>>
>>
>> On 21/01/2019 20:44, Paulo Nuin wrote:
>>> Hi Sergio
>>> Redeploying did the trick, but I still find errors (Tomcat 7 doesn’t
>>> work at all, blank page) and with Tomcat 8 I am getting this error
>>> ^[2019-01-21 20:41:16,186 [http-nio-8080-exec-15] ERROR
>>> (InsertTag$InsertHandler,901) - Can't insert page 'hints.tile' : The
>>> requested resource [/tools/wormmine/hints.tile] is not available
>>> ]java.io.FileNotFoundException: The requested resource
>>> [/tools/wormmine/hints.tile] is not available
>>> over and over when accessing the web app. Pages are blank.
>>> Cheers
>>> Paulo
>>>> On Jan 21, 2019, at 10:30 AM, sergio contrino
>>>> <[hidden email]> wrote:
>>>>
>>>> hi paulo,
>>>> in the new release of intermine the taxonid is now a string.
>>>> you should use the new code for deploying your webapp.
>>>>
>>>> from your wormmine directory run
>>>> ./gradlew clean
>>>> and then
>>>> ./gradlew cargoRedeployRemote
>>>>
>>>> with the understanding that you have your tomcat running as
>>>> specified in your properties file in ~/.intermine
>>>>
>>>> please let us know if this work
>>>> thanks!
>>>> sergio
>>>>
>>>>
>>>>
>>>> On 17/01/2019 19:25, Paulo Nuin wrote:
>>>>> Hi
>>>>> I was able to successfully build with 2.x and after the build,
>>>>> deploying the web app (still old version) I am getting the same
>>>>> error on queries and templates:
>>>>> 602340 [http-bio-8080-exec-277] ERROR
>>>>> org.intermine.webservice.server.WebService  - Service failed by
>>>>> internal error. Request parameters:
>>>>> start: 0
>>>>> size: 250
>>>>> query: <query model="genomic" view="Gene.primaryIdentifier
>>>>> Gene.secondaryIdentifier Gene.symbol Gene.alleles.primaryIdentifier
>>>>> Gene.alleles.symbol Gene.alleles.phenotype.identifier
>>>>> Gene.alleles.phenotype.name" sortOrder="Gene.primaryIdentifier ASC"
>>>>> name="gene_to_phenotypes" ><constraint path="Gene.symbol" op="="
>>>>> value="unc-26" code="A" /></query>
>>>>> format: json
>>>>> java.lang.NoSuchMethodError:
>>>>> org.intermine.model.bio.Organism.getTaxonId()Ljava/lang/Integer;
>>>>>   at
>>>>> org.intermine.bio.web.BioLinkRedirectManager.generateLink(BioLinkRedirectManager.java:72)
>>>>>   at
>>>>> org.intermine.webservice.server.output.TableCellFormatter.toMap(TableCellFormatter.java:65)
>>>>>   at
>>>>> org.intermine.webservice.server.query.result.TableRowService$Processor.visitLeft(TableRowService.java:137)
>>>>>   at
>>>>> org.intermine.webservice.server.query.result.TableRowService$Processor.visitLeft(TableRowService.java:122)
>>>>>   at
>>>>> org.intermine.webservice.server.core.Either$Left.accept(Either.java:138)
>>>>>   at
>>>>> org.intermine.webservice.server.query.result.TableRowService.runPathQuery(TableRowService.java:111)
>>>>>   at
>>>>> org.intermine.webservice.server.query.result.QueryResultService.execute(QueryResultService.java:106)
>>>>>   at
>>>>> org.intermine.webservice.server.WebService.service(WebService.java:350)
>>>>>   at
>>>>> org.intermine.webservice.server.query.result.QueryResultServlet.runService(QueryResultServlet.java:61)
>>>>>   at
>>>>> org.intermine.webservice.server.query.result.QueryResultServlet.doPost(QueryResultServlet.java:43)
>>>>>   at javax.servlet.http.HttpServlet.service(HttpServlet.java:650)
>>>>>   at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
>>>>> As you can see by the query, organism is not used in it. I still
>>>>> had the entrez error at the end of the build, but I filled the
>>>>> missing taxon IDs and species names on the table.
>>>>> Any help appreciated
>>>>> Paulo
>>>>> _______________________________________________
>>>>> dev mailing list
>>>>> [hidden email]
>>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>>
>>>> --
>>>> sergio contrino                  InterMine, University of Cambridge
>>>> https://sergiocontrino.github.io           http://www.intermine.org
>>
>> --
>> sergio contrino                  InterMine, University of Cambridge
>> https://sergiocontrino.github.io           http://www.intermine.org
>

--
sergio contrino                  InterMine, University of Cambridge
https://sergiocontrino.github.io           http://www.intermine.org
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