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Error when searching

Scott Cain
Hi Stephen and all,

I'm working on a new Tripal install and while things mostly seem to be
working, there are a few problems:

* GO term stuff doesn't appear on feature or organism pages even
though I've turned them on (would this be a good place to plug how
good the tutorial Stephen wrote for the summer schools is
outstanding?).  I'm using the sample fly data from the course.

* When I try to search for a feature, I get this rather ugly error:

    * warning: pg_query() [function.pg-query]: Query failed: ERROR:
operator does not exist: integer || integer LINE 1: ...d),
MAX(n.changed), MAX(c.last_comment_timestamp) || 1) - 12... ^ HINT: No
operator matches the given name and argument type(s). You might need
to add explicit type casts. in /var/www/includes/database.pgsql.inc on
line 139.
    * user warning: query: SELECT COUNT(*) FROM (SELECT i.type, i.sid,
5 * (2.54144460794 * SUM(i.score * t.count)) + 5 * POW(2,
(GREATEST(MAX(n.created), MAX(n.changed),
MAX(c.last_comment_timestamp) || 1) - 1283883587) * 6.43e-8) + 5 *
(2.0 - 2.0 / (1.0 + MAX(c.comment_count) * 1)) AS score FROM
search_index i INNER JOIN search_total t ON i.word = t.word INNER JOIN
node n ON n.nid = i.sid LEFT JOIN node_comment_statistics c ON c.nid =
i.sid WHERE n.status = 1 AND (i.word = 'fbgn0040037') AND i.type =
'node' GROUP BY i.type, i.sid HAVING COUNT(*) >= 1) n1 in
/var/www/modules/search/search.module on line 958.
    * warning: pg_query() [function.pg-query]: Query failed: ERROR:
operator does not exist: integer || integer LINE 1: ...d),
MAX(n.changed), MAX(c.last_comment_timestamp) || 1) - 12... ^ HINT: No
operator matches the given name and argument type(s). You might need
to add explicit type casts. in /var/www/includes/database.pgsql.inc on
line 139.
    * user warning: query: SELECT i.type, i.sid, 5 * (2.54144460794 *
SUM(i.score * t.count)) + 5 * POW(2, (GREATEST(MAX(n.created),
MAX(n.changed), MAX(c.last_comment_timestamp) || 1) - 1283883587) *
6.43e-8) + 5 * (2.0 - 2.0 / (1.0 + MAX(c.comment_count) * 1)) AS score
FROM search_index i INNER JOIN search_total t ON i.word = t.word INNER
JOIN node n ON n.nid = i.sid LEFT JOIN node_comment_statistics c ON
c.nid = i.sid WHERE n.status = 1 AND (i.word = 'fbgn0040037') AND
i.type = 'node' GROUP BY i.type, i.sid HAVING COUNT(*) >= 1 ORDER BY
score DESC LIMIT 10 OFFSET 0 in /var/www/modules/search/search.module
on line 958.

Could this be because I am using PostgreSQL 8.4?  I hope not (or I
hope there is an easy fix :-) because I need 8.4 for new functionality
in GBrowse.

Scott


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: Error when searching

Stephen Ficklin-2
Hi Scott,

Are you seeing any content for the GO report?

We did find out that the browseable trees that appear above the charts weren't working.   The new PHP version changed the way it handled pass by reference parameters which broke some of the function calls in Tripal.  We just recently put out an incremental release with some of these fixed,   but, we missed one that is causing this particular problem.  If you download the tripal_cv/trees.php 

If you're not seeing any content, can you check to make sure the materialized views are updated using the Tripal interface?

As far as the searching errors, I vaguely remember seeing similar errors.  But I've not encountered that recently and I think I've been using Postgres 8.4 as well.  If you can export and compress your databases and share them out I can try and take a look.

Stephen

On Tue, Sep 7, 2010 at 3:45 PM, Scott Cain <[hidden email]> wrote:
Hi Stephen and all,

I'm working on a new Tripal install and while things mostly seem to be
working, there are a few problems:

* GO term stuff doesn't appear on feature or organism pages even
though I've turned them on (would this be a good place to plug how
good the tutorial Stephen wrote for the summer schools is
outstanding?).  I'm using the sample fly data from the course.

* When I try to search for a feature, I get this rather ugly error:

   * warning: pg_query() [function.pg-query]: Query failed: ERROR:
operator does not exist: integer || integer LINE 1: ...d),
MAX(n.changed), MAX(c.last_comment_timestamp) || 1) - 12... ^ HINT: No
operator matches the given name and argument type(s). You might need
to add explicit type casts. in /var/www/includes/database.pgsql.inc on
line 139.
   * user warning: query: SELECT COUNT(*) FROM (SELECT i.type, i.sid,
5 * (2.54144460794 * SUM(i.score * t.count)) + 5 * POW(2,
(GREATEST(MAX(n.created), MAX(n.changed),
MAX(c.last_comment_timestamp) || 1) - 1283883587) * 6.43e-8) + 5 *
(2.0 - 2.0 / (1.0 + MAX(c.comment_count) * 1)) AS score FROM
search_index i INNER JOIN search_total t ON i.word = t.word INNER JOIN
node n ON n.nid = i.sid LEFT JOIN node_comment_statistics c ON c.nid =
i.sid WHERE n.status = 1 AND (i.word = 'fbgn0040037') AND i.type =
'node' GROUP BY i.type, i.sid HAVING COUNT(*) >= 1) n1 in
/var/www/modules/search/search.module on line 958.
   * warning: pg_query() [function.pg-query]: Query failed: ERROR:
operator does not exist: integer || integer LINE 1: ...d),
MAX(n.changed), MAX(c.last_comment_timestamp) || 1) - 12... ^ HINT: No
operator matches the given name and argument type(s). You might need
to add explicit type casts. in /var/www/includes/database.pgsql.inc on
line 139.
   * user warning: query: SELECT i.type, i.sid, 5 * (2.54144460794 *
SUM(i.score * t.count)) + 5 * POW(2, (GREATEST(MAX(n.created),
MAX(n.changed), MAX(c.last_comment_timestamp) || 1) - 1283883587) *
6.43e-8) + 5 * (2.0 - 2.0 / (1.0 + MAX(c.comment_count) * 1)) AS score
FROM search_index i INNER JOIN search_total t ON i.word = t.word INNER
JOIN node n ON n.nid = i.sid LEFT JOIN node_comment_statistics c ON
c.nid = i.sid WHERE n.status = 1 AND (i.word = 'fbgn0040037') AND
i.type = 'node' GROUP BY i.type, i.sid HAVING COUNT(*) >= 1 ORDER BY
score DESC LIMIT 10 OFFSET 0 in /var/www/modules/search/search.module
on line 958.

Could this be because I am using PostgreSQL 8.4?  I hope not (or I
hope there is an easy fix :-) because I need 8.4 for new functionality
in GBrowse.

Scott


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


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Enter the Intel(R) Threading Challenge 2010.
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Re: Error when searching

Scott Cain
Hi Stephen,

I put a dump at

  http://scottcain.net/chado_dump.bz2

it's got fly data as well as P. ultimum data from Carson in it.

I've never seen anything for the GO report.  I'm using php 5.2, if
that matters (I avoided 5.3 at Mike Caudy's suggestion).  I'll try the
new trees.php tomorrow to see if that makes a difference.

Thanks,
Scott


On Tue, Sep 7, 2010 at 5:46 PM, Stephen Ficklin <[hidden email]> wrote:

> Hi Scott,
> Are you seeing any content for the GO report?
> We did find out that the browseable trees that appear above the charts
> weren't working.   The new PHP version changed the way it handled pass by
> reference parameters which broke some of the function calls in Tripal.  We
> just recently put out an incremental release with some of these fixed,
> but, we missed one that is causing this particular problem.  If you download
> the tripal_cv/trees.php
> If you're not seeing any content, can you check to make sure the
> materialized views are updated using the Tripal interface?
> As far as the searching errors, I vaguely remember seeing similar errors.
>  But I've not encountered that recently and I think I've been using Postgres
> 8.4 as well.  If you can export and compress your databases and share them
> out I can try and take a look.
> Stephen
>
> On Tue, Sep 7, 2010 at 3:45 PM, Scott Cain <[hidden email]> wrote:
>>
>> Hi Stephen and all,
>>
>> I'm working on a new Tripal install and while things mostly seem to be
>> working, there are a few problems:
>>
>> * GO term stuff doesn't appear on feature or organism pages even
>> though I've turned them on (would this be a good place to plug how
>> good the tutorial Stephen wrote for the summer schools is
>> outstanding?).  I'm using the sample fly data from the course.
>>
>> * When I try to search for a feature, I get this rather ugly error:
>>
>>    * warning: pg_query() [function.pg-query]: Query failed: ERROR:
>> operator does not exist: integer || integer LINE 1: ...d),
>> MAX(n.changed), MAX(c.last_comment_timestamp) || 1) - 12... ^ HINT: No
>> operator matches the given name and argument type(s). You might need
>> to add explicit type casts. in /var/www/includes/database.pgsql.inc on
>> line 139.
>>    * user warning: query: SELECT COUNT(*) FROM (SELECT i.type, i.sid,
>> 5 * (2.54144460794 * SUM(i.score * t.count)) + 5 * POW(2,
>> (GREATEST(MAX(n.created), MAX(n.changed),
>> MAX(c.last_comment_timestamp) || 1) - 1283883587) * 6.43e-8) + 5 *
>> (2.0 - 2.0 / (1.0 + MAX(c.comment_count) * 1)) AS score FROM
>> search_index i INNER JOIN search_total t ON i.word = t.word INNER JOIN
>> node n ON n.nid = i.sid LEFT JOIN node_comment_statistics c ON c.nid =
>> i.sid WHERE n.status = 1 AND (i.word = 'fbgn0040037') AND i.type =
>> 'node' GROUP BY i.type, i.sid HAVING COUNT(*) >= 1) n1 in
>> /var/www/modules/search/search.module on line 958.
>>    * warning: pg_query() [function.pg-query]: Query failed: ERROR:
>> operator does not exist: integer || integer LINE 1: ...d),
>> MAX(n.changed), MAX(c.last_comment_timestamp) || 1) - 12... ^ HINT: No
>> operator matches the given name and argument type(s). You might need
>> to add explicit type casts. in /var/www/includes/database.pgsql.inc on
>> line 139.
>>    * user warning: query: SELECT i.type, i.sid, 5 * (2.54144460794 *
>> SUM(i.score * t.count)) + 5 * POW(2, (GREATEST(MAX(n.created),
>> MAX(n.changed), MAX(c.last_comment_timestamp) || 1) - 1283883587) *
>> 6.43e-8) + 5 * (2.0 - 2.0 / (1.0 + MAX(c.comment_count) * 1)) AS score
>> FROM search_index i INNER JOIN search_total t ON i.word = t.word INNER
>> JOIN node n ON n.nid = i.sid LEFT JOIN node_comment_statistics c ON
>> c.nid = i.sid WHERE n.status = 1 AND (i.word = 'fbgn0040037') AND
>> i.type = 'node' GROUP BY i.type, i.sid HAVING COUNT(*) >= 1 ORDER BY
>> score DESC LIMIT 10 OFFSET 0 in /var/www/modules/search/search.module
>> on line 958.
>>
>> Could this be because I am using PostgreSQL 8.4?  I hope not (or I
>> hope there is an easy fix :-) because I need 8.4 for new functionality
>> in GBrowse.
>>
>> Scott
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Show off your parallel programming skills.
Enter the Intel(R) Threading Challenge 2010.
http://p.sf.net/sfu/intel-thread-sfd
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Re: Error when searching

Scott Cain
Hi Stephen,

I put in the newer trees.php and that didn't make a difference.  In
the organism page, I see

  There are currently no Gene Ontology (GO) reports for this organism

I know you are really busy, but I'd really like to see this on my
poster for the Genome Informatics meeting next week.

Thanks,
Scott


On Tue, Sep 7, 2010 at 10:54 PM, Scott Cain <[hidden email]> wrote:

> Hi Stephen,
>
> I put a dump at
>
>  http://scottcain.net/chado_dump.bz2
>
> it's got fly data as well as P. ultimum data from Carson in it.
>
> I've never seen anything for the GO report.  I'm using php 5.2, if
> that matters (I avoided 5.3 at Mike Caudy's suggestion).  I'll try the
> new trees.php tomorrow to see if that makes a difference.
>
> Thanks,
> Scott
>
>
> On Tue, Sep 7, 2010 at 5:46 PM, Stephen Ficklin <[hidden email]> wrote:
>> Hi Scott,
>> Are you seeing any content for the GO report?
>> We did find out that the browseable trees that appear above the charts
>> weren't working.   The new PHP version changed the way it handled pass by
>> reference parameters which broke some of the function calls in Tripal.  We
>> just recently put out an incremental release with some of these fixed,
>> but, we missed one that is causing this particular problem.  If you download
>> the tripal_cv/trees.php
>> If you're not seeing any content, can you check to make sure the
>> materialized views are updated using the Tripal interface?
>> As far as the searching errors, I vaguely remember seeing similar errors.
>>  But I've not encountered that recently and I think I've been using Postgres
>> 8.4 as well.  If you can export and compress your databases and share them
>> out I can try and take a look.
>> Stephen
>>
>> On Tue, Sep 7, 2010 at 3:45 PM, Scott Cain <[hidden email]> wrote:
>>>
>>> Hi Stephen and all,
>>>
>>> I'm working on a new Tripal install and while things mostly seem to be
>>> working, there are a few problems:
>>>
>>> * GO term stuff doesn't appear on feature or organism pages even
>>> though I've turned them on (would this be a good place to plug how
>>> good the tutorial Stephen wrote for the summer schools is
>>> outstanding?).  I'm using the sample fly data from the course.
>>>
>>> * When I try to search for a feature, I get this rather ugly error:
>>>
>>>    * warning: pg_query() [function.pg-query]: Query failed: ERROR:
>>> operator does not exist: integer || integer LINE 1: ...d),
>>> MAX(n.changed), MAX(c.last_comment_timestamp) || 1) - 12... ^ HINT: No
>>> operator matches the given name and argument type(s). You might need
>>> to add explicit type casts. in /var/www/includes/database.pgsql.inc on
>>> line 139.
>>>    * user warning: query: SELECT COUNT(*) FROM (SELECT i.type, i.sid,
>>> 5 * (2.54144460794 * SUM(i.score * t.count)) + 5 * POW(2,
>>> (GREATEST(MAX(n.created), MAX(n.changed),
>>> MAX(c.last_comment_timestamp) || 1) - 1283883587) * 6.43e-8) + 5 *
>>> (2.0 - 2.0 / (1.0 + MAX(c.comment_count) * 1)) AS score FROM
>>> search_index i INNER JOIN search_total t ON i.word = t.word INNER JOIN
>>> node n ON n.nid = i.sid LEFT JOIN node_comment_statistics c ON c.nid =
>>> i.sid WHERE n.status = 1 AND (i.word = 'fbgn0040037') AND i.type =
>>> 'node' GROUP BY i.type, i.sid HAVING COUNT(*) >= 1) n1 in
>>> /var/www/modules/search/search.module on line 958.
>>>    * warning: pg_query() [function.pg-query]: Query failed: ERROR:
>>> operator does not exist: integer || integer LINE 1: ...d),
>>> MAX(n.changed), MAX(c.last_comment_timestamp) || 1) - 12... ^ HINT: No
>>> operator matches the given name and argument type(s). You might need
>>> to add explicit type casts. in /var/www/includes/database.pgsql.inc on
>>> line 139.
>>>    * user warning: query: SELECT i.type, i.sid, 5 * (2.54144460794 *
>>> SUM(i.score * t.count)) + 5 * POW(2, (GREATEST(MAX(n.created),
>>> MAX(n.changed), MAX(c.last_comment_timestamp) || 1) - 1283883587) *
>>> 6.43e-8) + 5 * (2.0 - 2.0 / (1.0 + MAX(c.comment_count) * 1)) AS score
>>> FROM search_index i INNER JOIN search_total t ON i.word = t.word INNER
>>> JOIN node n ON n.nid = i.sid LEFT JOIN node_comment_statistics c ON
>>> c.nid = i.sid WHERE n.status = 1 AND (i.word = 'fbgn0040037') AND
>>> i.type = 'node' GROUP BY i.type, i.sid HAVING COUNT(*) >= 1 ORDER BY
>>> score DESC LIMIT 10 OFFSET 0 in /var/www/modules/search/search.module
>>> on line 958.
>>>
>>> Could this be because I am using PostgreSQL 8.4?  I hope not (or I
>>> hope there is an easy fix :-) because I need 8.4 for new functionality
>>> in GBrowse.
>>>
>>> Scott
>>>
>>>
>>> --
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain
>>> dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: Error when searching

Stephen Ficklin-2
In reply to this post by Scott Cain
Hi Scott,

My apologies for my very late reply to your email below.  I'm getting
settled at my new job and have now been able to look at this.  

The error message you received when searching for a feature is a bug in
Drupal.  You can read about here:  http://drupal.org/node/488166

There is a patch that can be applied to Drupal that works.  It can be
downloaded from post #19 on that same page.  To apply the patch I downloaded
and placed it into my Drupal directory and then issued this command:

patch -p0 < 488166-fix-reroll.patch

Hope that helps if you haven't already figured it out.

Stephen

-----Original Message-----
From: Scott Cain [mailto:[hidden email]]
Sent: Tuesday, September 07, 2010 3:46 PM
To: Stephen Ficklin
Cc: [hidden email]
Subject: Error when searching

Hi Stephen and all,

I'm working on a new Tripal install and while things mostly seem to be
working, there are a few problems:

* GO term stuff doesn't appear on feature or organism pages even
though I've turned them on (would this be a good place to plug how
good the tutorial Stephen wrote for the summer schools is
outstanding?).  I'm using the sample fly data from the course.

* When I try to search for a feature, I get this rather ugly error:

    * warning: pg_query() [function.pg-query]: Query failed: ERROR:
operator does not exist: integer || integer LINE 1: ...d),
MAX(n.changed), MAX(c.last_comment_timestamp) || 1) - 12... ^ HINT: No
operator matches the given name and argument type(s). You might need
to add explicit type casts. in /var/www/includes/database.pgsql.inc on
line 139.
    * user warning: query: SELECT COUNT(*) FROM (SELECT i.type, i.sid,
5 * (2.54144460794 * SUM(i.score * t.count)) + 5 * POW(2,
(GREATEST(MAX(n.created), MAX(n.changed),
MAX(c.last_comment_timestamp) || 1) - 1283883587) * 6.43e-8) + 5 *
(2.0 - 2.0 / (1.0 + MAX(c.comment_count) * 1)) AS score FROM
search_index i INNER JOIN search_total t ON i.word = t.word INNER JOIN
node n ON n.nid = i.sid LEFT JOIN node_comment_statistics c ON c.nid =
i.sid WHERE n.status = 1 AND (i.word = 'fbgn0040037') AND i.type =
'node' GROUP BY i.type, i.sid HAVING COUNT(*) >= 1) n1 in
/var/www/modules/search/search.module on line 958.
    * warning: pg_query() [function.pg-query]: Query failed: ERROR:
operator does not exist: integer || integer LINE 1: ...d),
MAX(n.changed), MAX(c.last_comment_timestamp) || 1) - 12... ^ HINT: No
operator matches the given name and argument type(s). You might need
to add explicit type casts. in /var/www/includes/database.pgsql.inc on
line 139.
    * user warning: query: SELECT i.type, i.sid, 5 * (2.54144460794 *
SUM(i.score * t.count)) + 5 * POW(2, (GREATEST(MAX(n.created),
MAX(n.changed), MAX(c.last_comment_timestamp) || 1) - 1283883587) *
6.43e-8) + 5 * (2.0 - 2.0 / (1.0 + MAX(c.comment_count) * 1)) AS score
FROM search_index i INNER JOIN search_total t ON i.word = t.word INNER
JOIN node n ON n.nid = i.sid LEFT JOIN node_comment_statistics c ON
c.nid = i.sid WHERE n.status = 1 AND (i.word = 'fbgn0040037') AND
i.type = 'node' GROUP BY i.type, i.sid HAVING COUNT(*) >= 1 ORDER BY
score DESC LIMIT 10 OFFSET 0 in /var/www/modules/search/search.module
on line 958.

Could this be because I am using PostgreSQL 8.4?  I hope not (or I
hope there is an easy fix :-) because I need 8.4 for new functionality
in GBrowse.

Scott


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


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