Re: dev Digest, Vol 136, Issue 11

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Re: dev Digest, Vol 136, Issue 11

kkarra@stanford.edu
It was not the same exact error, but, restarting solr ,  re-creating the ‘cores’ and running the post processes should help.

> On Nov 20, 2020, at 4:00 AM, [hidden email] wrote:
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> Today's Topics:
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>   1. Re: Issues with SO terms ([hidden email])
>   2. Re: solr is broken... ([hidden email])
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 19 Nov 2020 16:23:01 +0000
> From: [hidden email]
> To: Paulo Nuin <[hidden email]>
> Cc: [hidden email]
> Subject: Re: [InterMine Dev] Issues with SO terms
> Message-ID: <[hidden email]>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
> forgot to reply all...
> sergio
>
> On 2020-11-19 16:10, [hidden email] wrote:
>> hi paulo,
>> the modification in dev happened after the 4.2.0 release, so just
>> updating won't help.
>> to use a locally updated file please install locally. something like
>> cd bio && ./gradlew clean install
>> should do it in your case, for a complete install see command below.
>> thanks!
>> sergio
>>
>>
>> (cd plugin && ./gradlew clean install)&&
>> (cd intermine && ./gradlew clean install) &&
>> (cd bio && ./gradlew clean install) &&
>> (cd bio/sources && ./gradlew clean install)  &&
>> (cd bio/postprocess/ && ./gradlew clean install)
>>
>>
>> On 2020-11-19 15:54, Paulo Nuin wrote:
>>> Hi Sergio
>>>
>>> Thanks. I am updating to 4.2.0, I guess this one points to the newest
>>> OBO.
>>>
>>> Also, how do I use my own version of InterMine? I don’t get the
>>> bio/core/src/main/resources/so.obo locally.
>>>
>>> Cheers
>>>
>>> Paulo
>>>
>>>> On Nov 19, 2020, at 1:57 AM, [hidden email] wrote:
>>>>
>>>> hi paulo,
>>>> you can merge the dev branch of intermine, or just update the file
>>>> bio/core/src/main/resources/so.obo
>>>> (with an updated so.obo from
>>>> https://raw.githubusercontent.com/The-Sequence-Ontology/SO-Ontologies/master/Ontology_Files/so.obo)
>>>>
>>>> please let me know if you have still have issues.
>>>> thanks
>>>> sergio
>>>>
>>>> On 2020-11-18 23:41, Paulo Nuin wrote:
>>>>> Hi everyone
>>>>> I am having trouble adding new terms included in our new GFF3, even
>>>>> though the term was added to /dbmodel/resources/so_terms. In can it
>>>>> is
>>>>> circular_ncRNA and the output of the builddb process from gradle
>>>>> The following terms specified in so_terms are not valid Sequence
>>>>> Ontology terms according to so.obo: circular_ncRNA
>>>>> I still have some old code from previous version with the so.obo and
>>>>> the circular_ncRNA is not included in the file, but I am guessing
>>>>> this
>>>>> is an older file. I can see the term on the SO website
>>>>> http://www.sequenceontology.org/browser/current_release/term/SO:0002291
>>>>> Is there a way to use another so.obo and make the term accepted?
>>>>> Thanks
>>>>> Paulo
>>>>> _______________________________________________
>>>>> dev mailing list
>>>>> [hidden email]
>>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 20 Nov 2020 10:59:22 +0000
> From: [hidden email]
> To: Joe Carlson <[hidden email]>
> Cc: InterMine Devs <[hidden email]>
> Subject: Re: [InterMine Dev] solr is broken...
> Message-ID: <[hidden email]>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
> Hi Joe,
> not sure if it was a typo but when you hit the schema/fields endpoint
> you need to specify the collection name
> e.g. http://localhost:8983/solr/biotestmine-search/schema/fields 
> otherwise it returns 500
>
> Daniela
>
>
>> Hi Folks,
>>
>> I have to admit I’ve been neglecting our intermine instance for the
>> past couple months. Only today i was told that search was broken and
>> I’m a bit flummoxed as to what is wrong.
>>
>> It’s a standard setup of solr 7.2.1 and used to work. The one
>> nonstandard issue is that we’re running everything in containers now.
>> Hitting the /solr/ endpoint works, but /solr/schema/fields gives a 500
>> response. The error message I see on the console
>>
>>> Nov 18, 2020 10:53:40 PM org.restlet.Restlet handle
>>> WARNING: Unable to start the Restlet
>>> Internal Server Error (500) - No SolrRequestInfo in this Thread!
>>>        at
>>> org.apache.solr.rest.RestManager.getRestManager(RestManager.java:241)
>>>        at
>>> org.apache.solr.rest.SolrSchemaRestApi.createInboundRoot(SolrSchemaRestApi.java:71)
>>>        at
>>> org.restlet.Application.getInboundRoot(Application.java:272)
>> …< long stack trace here>
>>>        at java.lang.Thread.run(Thread.java:748)
>>>
>>> Nov 18, 2020 10:53:40 PM org.restlet.Restlet handle
>>> WARNING: Unable to start the Restlet
>>> Nov 18, 2020 10:53:40 PM org.restlet.routing.Filter doHandle
>>> WARNING: The filter
>>> org.restlet.engine.application.RangeFilter@5045cb9d was executed
>>> without a next Restlet attached to it.
>>
>>
>> Now, first, what is a Restlet and why was it unable to start?
>> solr tries to grab as much memory it can for indexes. For me the start
>> page shows that memory usage is 99.5% (250 out of 251Gb.) is this
>> worrisome? The JVM memory is at 19%, though. Is the memory usage an
>> issue?
>> Has anyone had a problem like this?
>>
>> Thanks,
>>
>> Joe
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> End of dev Digest, Vol 136, Issue 11
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