> 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>
Locked
