[Gmod-tripal-devel] BUG: Branch 7.x-2.x (a68b9af2f768d244ddbc7607dd94d31de55673b2)

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[Gmod-tripal-devel] BUG: Branch 7.x-2.x (a68b9af2f768d244ddbc7607dd94d31de55673b2)

Mara Kim-2
Hello,

I believe there is a bug on the 7.x-2.x branch, commit
a68b9af2f768d244ddbc7607dd94d31de55673b2.

The organism user search does not display the organisms due to the
following error:

SQLSTATE[42P01]: Undefined table: 7 ERROR: relation "organism" does
not exist LINE 5: organism organism ^

A quick scan of the SQL query seems to indicate that the problem is
that either the chado schema is not in the search_path, or the
organism table needs to be qualified with chado.*.

The relevant SQL is below:

SELECT node.nid AS node_nid, organism.common_name AS
organism_common_name, organism.genus AS organism_genus,
organism.species AS organism_species, organism.abbreviation AS
organism_abbreviation
FROM
{organism} organism
LEFT JOIN {chado_organism} chado_organism ON organism.organism_id =
chado_organism.organism_id
LEFT JOIN {node} node_chado_organism ON chado_organism.nid =
node_chado_organism.nid
LEFT JOIN {node} node ON chado_organism.nid = node.nid
WHERE (( (node.nid > '0') ))
ORDER BY organism_common_name ASC, organism_genus ASC, organism_species ASC
LIMIT 25 OFFSET 0



--
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN


------------------------------------------------------------------------------
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Find What Matters Most in Your Big Data with HPCC Systems
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Leverages Graph Analysis for Fast Processing & Easy Data Exploration
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Re: [Gmod-tripal-devel] BUG: Branch 7.x-2.x (a68b9af2f768d244ddbc7607dd94d31de55673b2)

Mara Kim-2
On Mon, Jun 9, 2014 at 11:58 AM, Mara Kim <[hidden email]> wrote:

> Hello,
>
> I believe there is a bug on the 7.x-2.x branch, commit
> a68b9af2f768d244ddbc7607dd94d31de55673b2.
>
> The organism user search does not display the organisms due to the
> following error:
>
> SQLSTATE[42P01]: Undefined table: 7 ERROR: relation "organism" does
> not exist LINE 5: organism organism ^
>
> A quick scan of the SQL query seems to indicate that the problem is
> that either the chado schema is not in the search_path, or the
> organism table needs to be qualified with chado.*.
>
> The relevant SQL is below:
>
> SELECT node.nid AS node_nid, organism.common_name AS
> organism_common_name, organism.genus AS organism_genus,
> organism.species AS organism_species, organism.abbreviation AS
> organism_abbreviation
> FROM
> {organism} organism
> LEFT JOIN {chado_organism} chado_organism ON organism.organism_id =
> chado_organism.organism_id
> LEFT JOIN {node} node_chado_organism ON chado_organism.nid =
> node_chado_organism.nid
> LEFT JOIN {node} node ON chado_organism.nid = node.nid
> WHERE (( (node.nid > '0') ))
> ORDER BY organism_common_name ASC, organism_genus ASC, organism_species ASC
> LIMIT 25 OFFSET 0
>
>
>
> --
> Mara Kim
>
> Ph.D. Candidate
> Computational Biology
> Vanderbilt University
> Nashville, TN



--
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN


------------------------------------------------------------------------------
HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions
Find What Matters Most in Your Big Data with HPCC Systems
Open Source. Fast. Scalable. Simple. Ideal for Dirty Data.
Leverages Graph Analysis for Fast Processing & Easy Data Exploration
http://p.sf.net/sfu/hpccsystems
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Re: [Gmod-tripal-devel] BUG: Branch 7.x-2.x (a68b9af2f768d244ddbc7607dd94d31de55673b2)

Kucheran, Lacey Sanderson
In reply to this post by Mara Kim-2
Hi Mara,

Thanks for the report! I’m home with a baby with pink eye at the moment but hope to look into this for you sometime this week. 

Just a few questions to help with debugging:
- Do you have the patch applied to views which allows the chado namespace to be recognized? (this is the one distributed with tripal_views. It needs to be applied to drupal views)
- Also, is the organism user search view the only one not working for you or are you having this problem with other views to?
- Have you modified the organism tripal views integration through Tripal > Views Integration?

Something that often helps when tripal views integration goes awry is to delete all the integrations (Tripal Views Integrations then “Delete ALL Integrations”) but if you have any custom integrations make sure to export them (and save the export code) first because they will be deleted as well! They will be automatically re-generated when you go to Structure > Views (safest) or any chado view.

BACKGROUND:
The Tripal views adds the chado. prefix to table names once the patch mentioned above is applied. Which tables are in the chado namespace is handled via the views integration.

~Lacey

PS. The commit ID is awesome information to include! Thanks!!

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-4975
Room 3C06 Agriculture
Department of Plant Sciences
University of Saskatchewan

On Jun 9, 2014, at 10:58 AM, Mara Kim <[hidden email]> wrote:

Hello,

I believe there is a bug on the 7.x-2.x branch, commit
a68b9af2f768d244ddbc7607dd94d31de55673b2.

The organism user search does not display the organisms due to the
following error:

SQLSTATE[42P01]: Undefined table: 7 ERROR: relation "organism" does
not exist LINE 5: organism organism ^

A quick scan of the SQL query seems to indicate that the problem is
that either the chado schema is not in the search_path, or the
organism table needs to be qualified with chado.*.

The relevant SQL is below:

SELECT node.nid AS node_nid, organism.common_name AS
organism_common_name, organism.genus AS organism_genus,
organism.species AS organism_species, organism.abbreviation AS
organism_abbreviation
FROM
{organism} organism
LEFT JOIN {chado_organism} chado_organism ON organism.organism_id =
chado_organism.organism_id
LEFT JOIN {node} node_chado_organism ON chado_organism.nid =
node_chado_organism.nid
LEFT JOIN {node} node ON chado_organism.nid = node.nid
WHERE (( (node.nid > '0') ))
ORDER BY organism_common_name ASC, organism_genus ASC, organism_species ASC
LIMIT 25 OFFSET 0



--
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN


------------------------------------------------------------------------------
HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions
Find What Matters Most in Your Big Data with HPCC Systems
Open Source. Fast. Scalable. Simple. Ideal for Dirty Data.
Leverages Graph Analysis for Fast Processing & Easy Data Exploration
http://www.hpccsystems.com
_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel


------------------------------------------------------------------------------
HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions
Find What Matters Most in Your Big Data with HPCC Systems
Open Source. Fast. Scalable. Simple. Ideal for Dirty Data.
Leverages Graph Analysis for Fast Processing & Easy Data Exploration
http://p.sf.net/sfu/hpccsystems
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Re: [Gmod-tripal-devel] BUG: Branch 7.x-2.x (a68b9af2f768d244ddbc7607dd94d31de55673b2)

Mara Kim-2
I assume you are talking about the
`views-sql-compliant-three-tier-naming-1971160-22.patch`?  If so, then
no...

Other views are also having this issue, so I have a feeling that it
must be because I need this patch.

As far as I know, we have not made any changes to the View
Integration, although Brian (CC-ed) might have done some
modifications.

How should I go about applying this patch?

On Tue, Jun 10, 2014 at 3:42 PM, Kucheran, Lacey Sanderson
<[hidden email]> wrote:

> Hi Mara,
>
> Thanks for the report! I’m home with a baby with pink eye at the moment but
> hope to look into this for you sometime this week.
>
> Just a few questions to help with debugging:
> - Do you have the patch applied to views which allows the chado namespace to
> be recognized? (this is the one distributed with tripal_views. It needs to
> be applied to drupal views)
> - Also, is the organism user search view the only one not working for you or
> are you having this problem with other views to?
> - Have you modified the organism tripal views integration through Tripal >
> Views Integration?
>
> Something that often helps when tripal views integration goes awry is to
> delete all the integrations (Tripal Views Integrations then “Delete ALL
> Integrations”) but if you have any custom integrations make sure to export
> them (and save the export code) first because they will be deleted as well!
> They will be automatically re-generated when you go to Structure > Views
> (safest) or any chado view.
>
> BACKGROUND:
> The Tripal views adds the chado. prefix to table names once the patch
> mentioned above is applied. Which tables are in the chado namespace is
> handled via the views integration.
>
> ~Lacey
>
> PS. The commit ID is awesome information to include! Thanks!!
>
> ------------------------------------------------------
> Lacey-Anne Sanderson
> Bioinformaticist
> Pulse Crop Breeding and Genetics
> Phone: (306) 966-4975
> Email: [hidden email]
> Room 3C06 Agriculture
> Department of Plant Sciences
> University of Saskatchewan
>
> On Jun 9, 2014, at 10:58 AM, Mara Kim <[hidden email]> wrote:
>
> Hello,
>
> I believe there is a bug on the 7.x-2.x branch, commit
> a68b9af2f768d244ddbc7607dd94d31de55673b2.
>
> The organism user search does not display the organisms due to the
> following error:
>
> SQLSTATE[42P01]: Undefined table: 7 ERROR: relation "organism" does
> not exist LINE 5: organism organism ^
>
> A quick scan of the SQL query seems to indicate that the problem is
> that either the chado schema is not in the search_path, or the
> organism table needs to be qualified with chado.*.
>
> The relevant SQL is below:
>
> SELECT node.nid AS node_nid, organism.common_name AS
> organism_common_name, organism.genus AS organism_genus,
> organism.species AS organism_species, organism.abbreviation AS
> organism_abbreviation
> FROM
> {organism} organism
> LEFT JOIN {chado_organism} chado_organism ON organism.organism_id =
> chado_organism.organism_id
> LEFT JOIN {node} node_chado_organism ON chado_organism.nid =
> node_chado_organism.nid
> LEFT JOIN {node} node ON chado_organism.nid = node.nid
> WHERE (( (node.nid > '0') ))
> ORDER BY organism_common_name ASC, organism_genus ASC, organism_species ASC
> LIMIT 25 OFFSET 0
>
>
>
> --
> Mara Kim
>
> Ph.D. Candidate
> Computational Biology
> Vanderbilt University
> Nashville, TN
>
>
> ------------------------------------------------------------------------------
> HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions
> Find What Matters Most in Your Big Data with HPCC Systems
> Open Source. Fast. Scalable. Simple. Ideal for Dirty Data.
> Leverages Graph Analysis for Fast Processing & Easy Data Exploration
> http://www.hpccsystems.com
> _______________________________________________
> Gmod-tripal-devel mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>
>



--
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN


------------------------------------------------------------------------------
HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions
Find What Matters Most in Your Big Data with HPCC Systems
Open Source. Fast. Scalable. Simple. Ideal for Dirty Data.
Leverages Graph Analysis for Fast Processing & Easy Data Exploration
http://p.sf.net/sfu/hpccsystems
_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
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Re: [Gmod-tripal-devel] BUG: Branch 7.x-2.x (a68b9af2f768d244ddbc7607dd94d31de55673b2)

Stephen Ficklin-2
Hi Mara,

You can find the steps for applying the patch in the Tripal v2.0
Tutorial at this section:
http://www.gmod.org/wiki/Tripal_Tutorial_v2.0#Applying_Patches

Stephen

On 6/10/2014 5:10 PM, Mara Kim wrote:

> I assume you are talking about the
> `views-sql-compliant-three-tier-naming-1971160-22.patch`?  If so, then
> no...
>
> Other views are also having this issue, so I have a feeling that it
> must be because I need this patch.
>
> As far as I know, we have not made any changes to the View
> Integration, although Brian (CC-ed) might have done some
> modifications.
>
> How should I go about applying this patch?
>
> On Tue, Jun 10, 2014 at 3:42 PM, Kucheran, Lacey Sanderson
> <[hidden email]> wrote:
>> Hi Mara,
>>
>> Thanks for the report! I’m home with a baby with pink eye at the moment but
>> hope to look into this for you sometime this week.
>>
>> Just a few questions to help with debugging:
>> - Do you have the patch applied to views which allows the chado namespace to
>> be recognized? (this is the one distributed with tripal_views. It needs to
>> be applied to drupal views)
>> - Also, is the organism user search view the only one not working for you or
>> are you having this problem with other views to?
>> - Have you modified the organism tripal views integration through Tripal >
>> Views Integration?
>>
>> Something that often helps when tripal views integration goes awry is to
>> delete all the integrations (Tripal Views Integrations then “Delete ALL
>> Integrations”) but if you have any custom integrations make sure to export
>> them (and save the export code) first because they will be deleted as well!
>> They will be automatically re-generated when you go to Structure > Views
>> (safest) or any chado view.
>>
>> BACKGROUND:
>> The Tripal views adds the chado. prefix to table names once the patch
>> mentioned above is applied. Which tables are in the chado namespace is
>> handled via the views integration.
>>
>> ~Lacey
>>
>> PS. The commit ID is awesome information to include! Thanks!!
>>
>> ------------------------------------------------------
>> Lacey-Anne Sanderson
>> Bioinformaticist
>> Pulse Crop Breeding and Genetics
>> Phone: (306) 966-4975
>> Email: [hidden email]
>> Room 3C06 Agriculture
>> Department of Plant Sciences
>> University of Saskatchewan
>>
>> On Jun 9, 2014, at 10:58 AM, Mara Kim <[hidden email]> wrote:
>>
>> Hello,
>>
>> I believe there is a bug on the 7.x-2.x branch, commit
>> a68b9af2f768d244ddbc7607dd94d31de55673b2.
>>
>> The organism user search does not display the organisms due to the
>> following error:
>>
>> SQLSTATE[42P01]: Undefined table: 7 ERROR: relation "organism" does
>> not exist LINE 5: organism organism ^
>>
>> A quick scan of the SQL query seems to indicate that the problem is
>> that either the chado schema is not in the search_path, or the
>> organism table needs to be qualified with chado.*.
>>
>> The relevant SQL is below:
>>
>> SELECT node.nid AS node_nid, organism.common_name AS
>> organism_common_name, organism.genus AS organism_genus,
>> organism.species AS organism_species, organism.abbreviation AS
>> organism_abbreviation
>> FROM
>> {organism} organism
>> LEFT JOIN {chado_organism} chado_organism ON organism.organism_id =
>> chado_organism.organism_id
>> LEFT JOIN {node} node_chado_organism ON chado_organism.nid =
>> node_chado_organism.nid
>> LEFT JOIN {node} node ON chado_organism.nid = node.nid
>> WHERE (( (node.nid > '0') ))
>> ORDER BY organism_common_name ASC, organism_genus ASC, organism_species ASC
>> LIMIT 25 OFFSET 0
>>
>>
>>
>> --
>> Mara Kim
>>
>> Ph.D. Candidate
>> Computational Biology
>> Vanderbilt University
>> Nashville, TN
>>
>>
>> ------------------------------------------------------------------------------
>> HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions
>> Find What Matters Most in Your Big Data with HPCC Systems
>> Open Source. Fast. Scalable. Simple. Ideal for Dirty Data.
>> Leverages Graph Analysis for Fast Processing & Easy Data Exploration
>> http://www.hpccsystems.com
>> _______________________________________________
>> Gmod-tripal-devel mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>>
>>
>
>


------------------------------------------------------------------------------
HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions
Find What Matters Most in Your Big Data with HPCC Systems
Open Source. Fast. Scalable. Simple. Ideal for Dirty Data.
Leverages Graph Analysis for Fast Processing & Easy Data Exploration
http://p.sf.net/sfu/hpccsystems
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Re: [Gmod-tripal-devel] BUG: Branch 7.x-2.x (a68b9af2f768d244ddbc7607dd94d31de55673b2)

Mara Kim-2
That fixed everything.  I can't believe I somehow applied the bytea
patch and not this one. XD

Thank you, guys.

On Tue, Jun 10, 2014 at 4:12 PM, Stephen Ficklin <[hidden email]> wrote:

> Hi Mara,
>
> You can find the steps for applying the patch in the Tripal v2.0 Tutorial at
> this section: http://www.gmod.org/wiki/Tripal_Tutorial_v2.0#Applying_Patches
>
> Stephen
>
>
> On 6/10/2014 5:10 PM, Mara Kim wrote:
>>
>> I assume you are talking about the
>> `views-sql-compliant-three-tier-naming-1971160-22.patch`?  If so, then
>> no...
>>
>> Other views are also having this issue, so I have a feeling that it
>> must be because I need this patch.
>>
>> As far as I know, we have not made any changes to the View
>> Integration, although Brian (CC-ed) might have done some
>> modifications.
>>
>> How should I go about applying this patch?
>>
>> On Tue, Jun 10, 2014 at 3:42 PM, Kucheran, Lacey Sanderson
>> <[hidden email]> wrote:
>>>
>>> Hi Mara,
>>>
>>> Thanks for the report! I’m home with a baby with pink eye at the moment
>>> but
>>> hope to look into this for you sometime this week.
>>>
>>> Just a few questions to help with debugging:
>>> - Do you have the patch applied to views which allows the chado namespace
>>> to
>>> be recognized? (this is the one distributed with tripal_views. It needs
>>> to
>>> be applied to drupal views)
>>> - Also, is the organism user search view the only one not working for you
>>> or
>>> are you having this problem with other views to?
>>> - Have you modified the organism tripal views integration through Tripal
>>> >
>>> Views Integration?
>>>
>>> Something that often helps when tripal views integration goes awry is to
>>> delete all the integrations (Tripal Views Integrations then “Delete ALL
>>> Integrations”) but if you have any custom integrations make sure to
>>> export
>>> them (and save the export code) first because they will be deleted as
>>> well!
>>> They will be automatically re-generated when you go to Structure > Views
>>> (safest) or any chado view.
>>>
>>> BACKGROUND:
>>> The Tripal views adds the chado. prefix to table names once the patch
>>> mentioned above is applied. Which tables are in the chado namespace is
>>> handled via the views integration.
>>>
>>> ~Lacey
>>>
>>> PS. The commit ID is awesome information to include! Thanks!!
>>>
>>> ------------------------------------------------------
>>> Lacey-Anne Sanderson
>>> Bioinformaticist
>>> Pulse Crop Breeding and Genetics
>>> Phone: (306) 966-4975
>>> Email: [hidden email]
>>> Room 3C06 Agriculture
>>> Department of Plant Sciences
>>> University of Saskatchewan
>>>
>>> On Jun 9, 2014, at 10:58 AM, Mara Kim <[hidden email]> wrote:
>>>
>>> Hello,
>>>
>>> I believe there is a bug on the 7.x-2.x branch, commit
>>> a68b9af2f768d244ddbc7607dd94d31de55673b2.
>>>
>>> The organism user search does not display the organisms due to the
>>> following error:
>>>
>>> SQLSTATE[42P01]: Undefined table: 7 ERROR: relation "organism" does
>>> not exist LINE 5: organism organism ^
>>>
>>> A quick scan of the SQL query seems to indicate that the problem is
>>> that either the chado schema is not in the search_path, or the
>>> organism table needs to be qualified with chado.*.
>>>
>>> The relevant SQL is below:
>>>
>>> SELECT node.nid AS node_nid, organism.common_name AS
>>> organism_common_name, organism.genus AS organism_genus,
>>> organism.species AS organism_species, organism.abbreviation AS
>>> organism_abbreviation
>>> FROM
>>> {organism} organism
>>> LEFT JOIN {chado_organism} chado_organism ON organism.organism_id =
>>> chado_organism.organism_id
>>> LEFT JOIN {node} node_chado_organism ON chado_organism.nid =
>>> node_chado_organism.nid
>>> LEFT JOIN {node} node ON chado_organism.nid = node.nid
>>> WHERE (( (node.nid > '0') ))
>>> ORDER BY organism_common_name ASC, organism_genus ASC, organism_species
>>> ASC
>>> LIMIT 25 OFFSET 0
>>>
>>>
>>>
>>> --
>>> Mara Kim
>>>
>>> Ph.D. Candidate
>>> Computational Biology
>>> Vanderbilt University
>>> Nashville, TN
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions
>>> Find What Matters Most in Your Big Data with HPCC Systems
>>> Open Source. Fast. Scalable. Simple. Ideal for Dirty Data.
>>> Leverages Graph Analysis for Fast Processing & Easy Data Exploration
>>> http://www.hpccsystems.com
>>> _______________________________________________
>>> Gmod-tripal-devel mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>>>
>>>
>>
>>
>
>



--
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN


------------------------------------------------------------------------------
HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions
Find What Matters Most in Your Big Data with HPCC Systems
Open Source. Fast. Scalable. Simple. Ideal for Dirty Data.
Leverages Graph Analysis for Fast Processing & Easy Data Exploration
http://p.sf.net/sfu/hpccsystems
_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel