Restricting species in the list search

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Restricting species in the list search

Paulo Nuin
Hi everyone

I am trying to make the list search (regular and advanced) only do on one species and not all the species loaded in the system. Now, when we run the search we have some errors on getting results if all the species are selected. But going into advance options and selecting only C. elegans produce results. I tried searching the docs, but honestly I haven’t been able to find any way to do it.

Any help is appreciated.

Thanks

Paulo


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Re: Restricting species in the list search

Joel Richardson-2

Hi Pedro,

Not sure if I can help but I¹ll try. Can you describe in more detail what
you¹re trying to do? I couldn¹t really follow from your email. Thanks.

Cheers,
Joel

--
Joel E. Richardson, Ph.D.
Sr. Research Scientist
Mouse Genome Informatics
The Jackson Laboratory
600 Main Street
Bar Harbor, Maine 04609
207-288-6435
[hidden email]





On 10/10/16, 2:57 PM, "dev on behalf of Paulo Nuin"
<[hidden email] on behalf of [hidden email]> wrote:

>Hi everyone
>
>I am trying to make the list search (regular and advanced) only do on one
>species and not all the species loaded in the system. Now, when we run
>the search we have some errors on getting results if all the species are
>selected. But going into advance options and selecting only C. elegans
>produce results. I tried searching the docs, but honestly I haven¹t been
>able to find any way to do it.
>
>Any help is appreciated.
>
>Thanks
>
>Paulo
>
>
>_______________________________________________
>dev mailing list
>[hidden email]
>https://lists.intermine.org/mailman/listinfo/dev

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Re: Restricting species in the list search

Paulo Nuin
Hi

I want the list in the attached image to have only one species, instead of all the species loaded in the database. When we restrict the search to C. elegans only it works fine, when all (or Any) are selected it gives us an error.

Cheers
Paulo


On Oct 11, 2016, at 6:17 AM, Joel Richardson <[hidden email]> wrote:


Hi Pedro,

Not sure if I can help but Iąll try. Can you describe in more detail what
youąre trying to do? I couldnąt really follow from your email. Thanks.

Cheers,
Joel

--
Joel E. Richardson, Ph.D.
Sr. Research Scientist
Mouse Genome Informatics
The Jackson Laboratory
600 Main Street
Bar Harbor, Maine 04609
207-288-6435
[hidden email]





On 10/10/16, 2:57 PM, "dev on behalf of Paulo Nuin"
<[hidden email] on behalf of [hidden email]> wrote:

Hi everyone

I am trying to make the list search (regular and advanced) only do on one
species and not all the species loaded in the system. Now, when we run
the search we have some errors on getting results if all the species are
selected. But going into advance options and selecting only C. elegans
produce results. I tried searching the docs, but honestly I havenąt been
able to find any way to do it.

Any help is appreciated.

Thanks

Paulo


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Re: Restricting species in the list search

Joel Richardson-2
Interesting. I just tried this at MouseMine and it worked fine. What’s the error? 

-- 
Joel E. Richardson, Ph.D.
Sr. Research Scientist
Mouse Genome Informatics
The Jackson Laboratory
600 Main Street
Bar Harbor, Maine 04609
207-288-6435

From: Paulo Nuin <[hidden email]>
Date: Tuesday, October 11, 2016 at 8:19 AM
To: Joel Richardson <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
Subject: Re: [InterMine Dev] Restricting species in the list search

Hi

I want the list in the attached image to have only one species, instead of all the species loaded in the database. When we restrict the search to C. elegans only it works fine, when all (or Any) are selected it gives us an error.

Cheers
Paulo


On Oct 11, 2016, at 6:17 AM, Joel Richardson <[hidden email]> wrote:


Hi Pedro,

Not sure if I can help but Iąll try. Can you describe in more detail what
youąre trying to do? I couldnąt really follow from your email. Thanks.

Cheers,
Joel

--
Joel E. Richardson, Ph.D.
Sr. Research Scientist
Mouse Genome Informatics
The Jackson Laboratory
600 Main Street
Bar Harbor, Maine 04609
207-288-6435
[hidden email]





On 10/10/16, 2:57 PM, "dev on behalf of Paulo Nuin"
<[hidden email] on behalf of [hidden email]> wrote:

Hi everyone

I am trying to make the list search (regular and advanced) only do on one
species and not all the species loaded in the system. Now, when we run
the search we have some errors on getting results if all the species are
selected. But going into advance options and selecting only C. elegans
produce results. I tried searching the docs, but honestly I havenąt been
able to find any way to do it.

Any help is appreciated.

Thanks

Paulo


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

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The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.


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Re: Restricting species in the list search

Paulo Nuin
the search with many species stall and stays on “Verifying identifiers”.

Cheers
Paulo


On Oct 11, 2016, at 6:24 AM, Joel Richardson <[hidden email]> wrote:

Interesting. I just tried this at MouseMine and it worked fine. What’s the error? 

-- 
Joel E. Richardson, Ph.D.
Sr. Research Scientist
Mouse Genome Informatics
The Jackson Laboratory
600 Main Street
Bar Harbor, Maine 04609
207-288-6435

From: Paulo Nuin <[hidden email]>
Date: Tuesday, October 11, 2016 at 8:19 AM
To: Joel Richardson <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
Subject: Re: [InterMine Dev] Restricting species in the list search

Hi

I want the list in the attached image to have only one species, instead of all the species loaded in the database. When we restrict the search to C. elegans only it works fine, when all (or Any) are selected it gives us an error.

Cheers
Paulo

<Screen Shot 2016-10-11 at 6.17.57 AM.png>
On Oct 11, 2016, at 6:17 AM, Joel Richardson <[hidden email]> wrote:


Hi Pedro,

Not sure if I can help but Iąll try. Can you describe in more detail what
youąre trying to do? I couldnąt really follow from your email. Thanks.

Cheers,
Joel

--
Joel E. Richardson, Ph.D.
Sr. Research Scientist
Mouse Genome Informatics
The Jackson Laboratory
600 Main Street
Bar Harbor, Maine 04609
207-288-6435
[hidden email]





On 10/10/16, 2:57 PM, "dev on behalf of Paulo Nuin"
<[hidden email] on behalf of [hidden email]> wrote:

Hi everyone

I am trying to make the list search (regular and advanced) only do on one
species and not all the species loaded in the system. Now, when we run
the search we have some errors on getting results if all the species are
selected. But going into advance options and selecting only C. elegans
produce results. I tried searching the docs, but honestly I havenąt been
able to find any way to do it.

Any help is appreciated.

Thanks

Paulo


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

---

The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.


---

The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
<Screen Shot 2016-10-11 at 6.17.57 AM.png>


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Re: Restricting species in the list search

Justin Clark-Casey-2
This should be fine and was on my production mine.  I will say that when I tried on my beta mine it was failing just as you describe, but from catalina.out that
was due to SQL connection pool issues (not in itself good but unrelated I should think).  On a Tomcat restart it was fine.  Unfortunately, I didn't think to try
with a single species but I expect this isn't your issue.

Nonetheless, as Joel said, do you see anything on catalina.out when you experience this failure?

On 11/10/16 13:25, Paulo Nuin wrote:

> the search with many species stall and stays on “Verifying identifiers”.
>
> Cheers
> Paulo
>
>
>> On Oct 11, 2016, at 6:24 AM, Joel Richardson <[hidden email] <mailto:[hidden email]>> wrote:
>>
>> Interesting. I just tried this at MouseMine and it worked fine. What’s the error?
>>
>> --
>> Joel E. Richardson, Ph.D.
>> Sr. Research Scientist
>> Mouse Genome Informatics
>> The Jackson Laboratory
>> 600 Main Street
>> Bar Harbor, Maine 04609
>> 207-288-6435
>> [hidden email] <mailto:[hidden email]>
>>
>> From: Paulo Nuin <[hidden email] <mailto:[hidden email]>>
>> Date: Tuesday, October 11, 2016 at 8:19 AM
>> To: Joel Richardson <[hidden email] <mailto:[hidden email]>>
>> Cc: "[hidden email] <mailto:[hidden email]>" <[hidden email] <mailto:[hidden email]>>
>> Subject: Re: [InterMine Dev] Restricting species in the list search
>>
>>> Hi
>>>
>>> I want the list in the attached image to have only one species, instead of all the species loaded in the database. When we restrict the search to C. elegans
>>> only it works fine, when all (or Any) are selected it gives us an error.
>>>
>>> Cheers
>>> Paulo
>>>
>>> <Screen Shot 2016-10-11 at 6.17.57 AM.png>
>>>> On Oct 11, 2016, at 6:17 AM, Joel Richardson <[hidden email] <mailto:[hidden email]>> wrote:
>>>>
>>>>
>>>> Hi Pedro,
>>>>
>>>> Not sure if I can help but Iąll try. Can you describe in more detail what
>>>> youąre trying to do? I couldnąt really follow from your email. Thanks.
>>>>
>>>> Cheers,
>>>> Joel
>>>>
>>>> --
>>>> Joel E. Richardson, Ph.D.
>>>> Sr. Research Scientist
>>>> Mouse Genome Informatics
>>>> The Jackson Laboratory
>>>> 600 Main Street
>>>> Bar Harbor, Maine 04609
>>>> 207-288-6435
>>>> [hidden email] <mailto:[hidden email]>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On 10/10/16, 2:57 PM, "dev on behalf of Paulo Nuin"
>>>> <[hidden email] <mailto:[hidden email]> on behalf of [hidden email] <mailto:[hidden email]>> wrote:
>>>>
>>>>> Hi everyone
>>>>>
>>>>> I am trying to make the list search (regular and advanced) only do on one
>>>>> species and not all the species loaded in the system. Now, when we run
>>>>> the search we have some errors on getting results if all the species are
>>>>> selected. But going into advance options and selecting only C. elegans
>>>>> produce results. I tried searching the docs, but honestly I havenąt been
>>>>> able to find any way to do it.
>>>>>
>>>>> Any help is appreciated.
>>>>>
>>>>> Thanks
>>>>>
>>>>> Paulo
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> dev mailing list
>>>>> [hidden email] <mailto:[hidden email]>
>>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>>
>>>> ---
>>>>
>>>> The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this
>>>> email by mistake, please notify the sender by return email as soon as possible.
>>>>
>>>
>> ---
>>
>> The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email
>> by mistake, please notify the sender by return email as soon as possible.
>> <Screen Shot 2016-10-11 at 6.17.57 AM.png>
>
>
>
> _______________________________________________
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> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev
>
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Re: Restricting species in the list search

Justin Clark-Casey-2
In reply to this post by Paulo Nuin
Unfortunately, I don't think there is any way to restrict the list via configuration at the moment.  The list is being generated by the Java code in
BagBuildController.execute() (via getFieldValues()) and there's no config trapdoor to make it anything other than all organisms in the database.

If you only want to allow users to build lists from identifiers for one species then it doesn't make much sense to have the dropdown anyway.

In the very short term, one possibility would be to replace the dropdown by overriding bagBuild.jsp in your mine (specifically the bit beginning

         <c:if test="${!empty extraBagQueryClass}">

to make it always return extraFieldValue=<your-organism-name> and perhaps let the user know that lists will only be built for this one organism.

Otherwise, it would be great to see a feature request issue for this on github though I don't know when it would get addressed.

Best Regards,

--
Justin Clark-Casey, Synbiomine/InterMine Developer
http://synbiomine.org
http://twitter.com/justincc

On 11/10/16 13:19, Paulo Nuin wrote:

> Hi
>
> I want the list in the attached image to have only one species, instead of all the species loaded in the database. When we restrict the search to C. elegans
> only it works fine, when all (or Any) are selected it gives us an error.
>
> Cheers
> Paulo
>
>
>> On Oct 11, 2016, at 6:17 AM, Joel Richardson <[hidden email] <mailto:[hidden email]>> wrote:
>>
>>
>> Hi Pedro,
>>
>> Not sure if I can help but Iąll try. Can you describe in more detail what
>> youąre trying to do? I couldnąt really follow from your email. Thanks.
>>
>> Cheers,
>> Joel
>>
>> --
>> Joel E. Richardson, Ph.D.
>> Sr. Research Scientist
>> Mouse Genome Informatics
>> The Jackson Laboratory
>> 600 Main Street
>> Bar Harbor, Maine 04609
>> 207-288-6435
>> [hidden email] <mailto:[hidden email]>
>>
>>
>>
>>
>>
>> On 10/10/16, 2:57 PM, "dev on behalf of Paulo Nuin"
>> <[hidden email] on behalf of [hidden email]> wrote:
>>
>>> Hi everyone
>>>
>>> I am trying to make the list search (regular and advanced) only do on one
>>> species and not all the species loaded in the system. Now, when we run
>>> the search we have some errors on getting results if all the species are
>>> selected. But going into advance options and selecting only C. elegans
>>> produce results. I tried searching the docs, but honestly I havenąt been
>>> able to find any way to do it.
>>>
>>> Any help is appreciated.
>>>
>>> Thanks
>>>
>>> Paulo
>>>
>>>
>>> _______________________________________________
>>> dev mailing list
>>> [hidden email]
>>> https://lists.intermine.org/mailman/listinfo/dev
>>
>> ---
>>
>> The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email
>> by mistake, please notify the sender by return email as soon as possible.
>>
>
>
>
> _______________________________________________
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> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev
>
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Re: Restricting species in the list search

Paulo Nuin
Hi Justin

I will try that and report, thanks a lot.

And thanks to everyone that provided help with this.

Cheers
Paulo


On Oct 12, 2016, at 7:13 AM, Justin Clark-Casey <[hidden email]> wrote:

Unfortunately, I don't think there is any way to restrict the list via configuration at the moment.  The list is being generated by the Java code in BagBuildController.execute() (via getFieldValues()) and there's no config trapdoor to make it anything other than all organisms in the database.

If you only want to allow users to build lists from identifiers for one species then it doesn't make much sense to have the dropdown anyway.

In the very short term, one possibility would be to replace the dropdown by overriding bagBuild.jsp in your mine (specifically the bit beginning

       <c:if test="${!empty extraBagQueryClass}">

to make it always return extraFieldValue=<your-organism-name> and perhaps let the user know that lists will only be built for this one organism.

Otherwise, it would be great to see a feature request issue for this on github though I don't know when it would get addressed.

Best Regards,

--
Justin Clark-Casey, Synbiomine/InterMine Developer
http://synbiomine.org
http://twitter.com/justincc

On 11/10/16 13:19, Paulo Nuin wrote:
Hi

I want the list in the attached image to have only one species, instead of all the species loaded in the database. When we restrict the search to C. elegans
only it works fine, when all (or Any) are selected it gives us an error.

Cheers
Paulo


On Oct 11, 2016, at 6:17 AM, Joel Richardson <[hidden email] <[hidden email]>> wrote:


Hi Pedro,

Not sure if I can help but Iąll try. Can you describe in more detail what
youąre trying to do? I couldnąt really follow from your email. Thanks.

Cheers,
Joel

--
Joel E. Richardson, Ph.D.
Sr. Research Scientist
Mouse Genome Informatics
The Jackson Laboratory
600 Main Street
Bar Harbor, Maine 04609
207-288-6435
[hidden email] <[hidden email]>





On 10/10/16, 2:57 PM, "dev on behalf of Paulo Nuin"
<[hidden email] on behalf of [hidden email]> wrote:

Hi everyone

I am trying to make the list search (regular and advanced) only do on one
species and not all the species loaded in the system. Now, when we run
the search we have some errors on getting results if all the species are
selected. But going into advance options and selecting only C. elegans
produce results. I tried searching the docs, but honestly I havenąt been
able to find any way to do it.

Any help is appreciated.

Thanks

Paulo


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The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email
by mistake, please notify the sender by return email as soon as possible.




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