[Gmod-tripal-devel] Problem with running Tutorial for V1.0

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[Gmod-tripal-devel] Problem with running Tutorial for V1.0

Daniel Sobral
Hi all,

I've tried to run the tutorial for Tripal V1.0:

I've got some problems when Adding Ontologies, as well as populating the materialized views.

E.g.
>drush pm-enable tripal_feature
The following extensions will be enabled: tripal_feature
Do you really want to continue? (y/n): y
tripal_feature was enabled successfully.                                                                                [ok]
The directory sites/default/files/tripal/tripal_feature has been created.                                               [status]
View 'organism_feature_count' created                                                                                   [status]
Job 'Populate materialized view 'organism_feature_count'' submitted.  Check the jobs page for status          [status]


- When I then run the job, I get an error:
> drush trpjob-run drupal
Calling: tripal_update_mview(2, 6)
pg_query(): Query failed: ERROR:  relation "organism_feature_count" does not exist                                      [warning]
LINE 1: SELECT count(*) as cnt FROM organism_feature_count
                                    ^ database.pgsql.inc:138
ERROR:  relation "organism_feature_count" does not exist                                                      [warning]
LINE 1: SELECT count(*) as cnt FROM organism_feature_count
                                    ^
query: SELECT count(*) as cnt FROM organism_feature_count database.pgsql.inc:159
Calling: tripal_update_mview(2, 7)
pg_query(): Query failed: ERROR:  relation "organism_feature_count" does not exist                                      [warning]
LINE 1: SELECT count(*) as cnt FROM organism_feature_count
                                    ^ database.pgsql.inc:138
ERROR:  relation "organism_feature_count" does not exist                                                      [warning]
LINE 1: SELECT count(*) as cnt FROM organism_feature_count
                                    ^
query: SELECT count(*) as cnt FROM organism_feature_count database.pgsql.inc:159

- Also, Loading the Features CV Ontology throws an error:
Calling: tripal_cv_load_obo_v1_2_id(1, 5)
Opening File sites/all/modules/tripal/tripal_cv/feature_property.obo
Loading terms...
Invalid argument supplied for foreach() obo_loader.inc:204                                                              [warning]
Division by zero obo_loader.inc:230                                                                                     [warning]
0 of 0 records. (0.00%) memory: 34879216
Updating cvtermpath table.  This may take a while...

I'm currently blocked at this step. The database is there, the tables are there...
Any ideas why this may be happening?

Thank you very much,
Daniel


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Re: [Gmod-tripal-devel] Problem with running Tutorial for V1.0

Stephen Ficklin-2
Hi Daniel,

Can you try updating your code to the most recent version?  Just rung
'git pull' in your 'tripal' directory.   I just pushed out some changes
that may help you.  We've been actively developing and rewriting some
code to make it faster and less memory intensive and unfortunately
caused some issues in the process.

If you haven't loaded any data then I would completely uninstall all the
tripal modules except the core and then reinstall.  If this doesn't fix
the problem let me know and we can dig a bit deeper.

Stephen

On 11/16/2012 2:53 PM, Daniel Sobral wrote:

> Hi all,
>
> I've tried to run the tutorial for Tripal V1.0:
>
> I've got some problems when Adding Ontologies, as well as populating the materialized views.
>
> E.g.
>> drush pm-enable tripal_feature
> The following extensions will be enabled: tripal_feature
> Do you really want to continue? (y/n): y
> tripal_feature was enabled successfully.                                                                                [ok]
> The directory sites/default/files/tripal/tripal_feature has been created.                                               [status]
> View 'organism_feature_count' created                                                                                   [status]
> Job 'Populate materialized view 'organism_feature_count'' submitted.  Check the jobs page for status          [status]
>
>
> - When I then run the job, I get an error:
>> drush trpjob-run drupal
> Calling: tripal_update_mview(2, 6)
> pg_query(): Query failed: ERROR:  relation "organism_feature_count" does not exist                                      [warning]
> LINE 1: SELECT count(*) as cnt FROM organism_feature_count
>                                      ^ database.pgsql.inc:138
> ERROR:  relation "organism_feature_count" does not exist                                                      [warning]
> LINE 1: SELECT count(*) as cnt FROM organism_feature_count
>                                      ^
> query: SELECT count(*) as cnt FROM organism_feature_count database.pgsql.inc:159
> Calling: tripal_update_mview(2, 7)
> pg_query(): Query failed: ERROR:  relation "organism_feature_count" does not exist                                      [warning]
> LINE 1: SELECT count(*) as cnt FROM organism_feature_count
>                                      ^ database.pgsql.inc:138
> ERROR:  relation "organism_feature_count" does not exist                                                      [warning]
> LINE 1: SELECT count(*) as cnt FROM organism_feature_count
>                                      ^
> query: SELECT count(*) as cnt FROM organism_feature_count database.pgsql.inc:159
>
> - Also, Loading the Features CV Ontology throws an error:
> Calling: tripal_cv_load_obo_v1_2_id(1, 5)
> Opening File sites/all/modules/tripal/tripal_cv/feature_property.obo
> Loading terms...
> Invalid argument supplied for foreach() obo_loader.inc:204                                                              [warning]
> Division by zero obo_loader.inc:230                                                                                     [warning]
> 0 of 0 records. (0.00%) memory: 34879216
> Updating cvtermpath table.  This may take a while...
>
> I'm currently blocked at this step. The database is there, the tables are there...
> Any ideas why this may be happening?
>
> Thank you very much,
> Daniel
>
>
> ------------------------------------------------------------------------------
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> web console. Get in-depth insight into apps, servers, databases, vmware,
> SAP, cloud infrastructure, etc. Download 30-day Free Trial.
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Re: [Gmod-tripal-devel] Problem with running Tutorial for V1.0

Daniel Sobral
Thanks, it seems to have solved this problem.
I'll continue and check if I see some other issues.

Do you have any expected date for the official release of V1.0?
Do you think the current version is good enough to start any serious
project with it?

Daniel

On 16-11-2012 20:01, Stephen Ficklin wrote:

> Hi Daniel,
>
> Can you try updating your code to the most recent version?  Just rung
> 'git pull' in your 'tripal' directory.   I just pushed out some changes
> that may help you.  We've been actively developing and rewriting some
> code to make it faster and less memory intensive and unfortunately
> caused some issues in the process.
>
> If you haven't loaded any data then I would completely uninstall all the
> tripal modules except the core and then reinstall.  If this doesn't fix
> the problem let me know and we can dig a bit deeper.
>
> Stephen
>
> On 11/16/2012 2:53 PM, Daniel Sobral wrote:
>> Hi all,
>>
>> I've tried to run the tutorial for Tripal V1.0:
>>
>> I've got some problems when Adding Ontologies, as well as populating the materialized views.
>>
>> E.g.
>>> drush pm-enable tripal_feature
>> The following extensions will be enabled: tripal_feature
>> Do you really want to continue? (y/n): y
>> tripal_feature was enabled successfully.                                                                                [ok]
>> The directory sites/default/files/tripal/tripal_feature has been created.                                               [status]
>> View 'organism_feature_count' created                                                                                   [status]
>> Job 'Populate materialized view 'organism_feature_count'' submitted.  Check the jobs page for status          [status]
>>
>>
>> - When I then run the job, I get an error:
>>> drush trpjob-run drupal
>> Calling: tripal_update_mview(2, 6)
>> pg_query(): Query failed: ERROR:  relation "organism_feature_count" does not exist                                      [warning]
>> LINE 1: SELECT count(*) as cnt FROM organism_feature_count
>>                                       ^ database.pgsql.inc:138
>> ERROR:  relation "organism_feature_count" does not exist                                                      [warning]
>> LINE 1: SELECT count(*) as cnt FROM organism_feature_count
>>                                       ^
>> query: SELECT count(*) as cnt FROM organism_feature_count database.pgsql.inc:159
>> Calling: tripal_update_mview(2, 7)
>> pg_query(): Query failed: ERROR:  relation "organism_feature_count" does not exist                                      [warning]
>> LINE 1: SELECT count(*) as cnt FROM organism_feature_count
>>                                       ^ database.pgsql.inc:138
>> ERROR:  relation "organism_feature_count" does not exist                                                      [warning]
>> LINE 1: SELECT count(*) as cnt FROM organism_feature_count
>>                                       ^
>> query: SELECT count(*) as cnt FROM organism_feature_count database.pgsql.inc:159
>>
>> - Also, Loading the Features CV Ontology throws an error:
>> Calling: tripal_cv_load_obo_v1_2_id(1, 5)
>> Opening File sites/all/modules/tripal/tripal_cv/feature_property.obo
>> Loading terms...
>> Invalid argument supplied for foreach() obo_loader.inc:204                                                              [warning]
>> Division by zero obo_loader.inc:230                                                                                     [warning]
>> 0 of 0 records. (0.00%) memory: 34879216
>> Updating cvtermpath table.  This may take a while...
>>
>> I'm currently blocked at this step. The database is there, the tables are there...
>> Any ideas why this may be happening?
>>
>> Thank you very much,
>> Daniel
>>
>>
>> ------------------------------------------------------------------------------
>> Monitor your physical, virtual and cloud infrastructure from a single
>> web console. Get in-depth insight into apps, servers, databases, vmware,
>> SAP, cloud infrastructure, etc. Download 30-day Free Trial.
>> Pricing starts from $795 for 25 servers or applications!
>> http://p.sf.net/sfu/zoho_dev2dev_nov
>> _______________________________________________
>> Gmod-tripal-devel mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>
> ------------------------------------------------------------------------------
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Re: [Gmod-tripal-devel] Problem with running Tutorial for V1.0

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

Great. I'm glad that fixed it.   We are hoping to release v1.0 by the
end of the year.  Although our original goal was August of 2012.  We
didn't make that goal because of other project deadlines that have kept
us from fixing some outstanding issues.  But, in the process we've also
taken the time to fix some of the slowness with loaders and memory
leaks.  So, it's a better package now than if we had released it in August.

We are currently using this same development version on a few of our
production sites already so I think you are safe to use it. If you
encounter a problem just email the list and we can help you through
anything.  The only major outstanding problem is the blast extension
module which is currently undergoing a rewrite to make it faster and use
less memory.   But that should be fixed soon.

Stephen

On 11/16/2012 5:12 PM, Daniel Sobral wrote:

> Hi Stephen,
>
> Thanks! It seems to have solved this problem.
> I'm going to explore it a bit more and report if I see any more issues.
>
> Do you have any expected date for the official release of V1.0?
> Do you think it's safe to start a serious project with the current
> version?
>
> Thanks again,
> Daniel
>
> On 16-11-2012 20:01, Stephen Ficklin wrote:
>> Hi Daniel,
>>
>> Can you try updating your code to the most recent version?  Just rung
>> 'git pull' in your 'tripal' directory.   I just pushed out some changes
>> that may help you.  We've been actively developing and rewriting some
>> code to make it faster and less memory intensive and unfortunately
>> caused some issues in the process.
>>
>> If you haven't loaded any data then I would completely uninstall all the
>> tripal modules except the core and then reinstall.  If this doesn't fix
>> the problem let me know and we can dig a bit deeper.
>>
>> Stephen
>>
>> On 11/16/2012 2:53 PM, Daniel Sobral wrote:
>>> Hi all,
>>>
>>> I've tried to run the tutorial for Tripal V1.0:
>>>
>>> I've got some problems when Adding Ontologies, as well as populating
>>> the materialized views.
>>>
>>> E.g.
>>>> drush pm-enable tripal_feature
>>> The following extensions will be enabled: tripal_feature
>>> Do you really want to continue? (y/n): y
>>> tripal_feature was enabled successfully. [ok]
>>> The directory sites/default/files/tripal/tripal_feature has been
>>> created. [status]
>>> View 'organism_feature_count' created [status]
>>> Job 'Populate materialized view 'organism_feature_count''
>>> submitted.  Check the jobs page for status          [status]
>>>
>>>
>>> - When I then run the job, I get an error:
>>>> drush trpjob-run drupal
>>> Calling: tripal_update_mview(2, 6)
>>> pg_query(): Query failed: ERROR:  relation "organism_feature_count"
>>> does not exist                                      [warning]
>>> LINE 1: SELECT count(*) as cnt FROM organism_feature_count
>>>                                       ^ database.pgsql.inc:138
>>> ERROR:  relation "organism_feature_count" does not exist
>>> [warning]
>>> LINE 1: SELECT count(*) as cnt FROM organism_feature_count
>>>                                       ^
>>> query: SELECT count(*) as cnt FROM organism_feature_count
>>> database.pgsql.inc:159
>>> Calling: tripal_update_mview(2, 7)
>>> pg_query(): Query failed: ERROR:  relation "organism_feature_count"
>>> does not exist                                      [warning]
>>> LINE 1: SELECT count(*) as cnt FROM organism_feature_count
>>>                                       ^ database.pgsql.inc:138
>>> ERROR:  relation "organism_feature_count" does not exist
>>> [warning]
>>> LINE 1: SELECT count(*) as cnt FROM organism_feature_count
>>>                                       ^
>>> query: SELECT count(*) as cnt FROM organism_feature_count
>>> database.pgsql.inc:159
>>>
>>> - Also, Loading the Features CV Ontology throws an error:
>>> Calling: tripal_cv_load_obo_v1_2_id(1, 5)
>>> Opening File sites/all/modules/tripal/tripal_cv/feature_property.obo
>>> Loading terms...
>>> Invalid argument supplied for foreach() obo_loader.inc:204 [warning]
>>> Division by zero obo_loader.inc:230 [warning]
>>> 0 of 0 records. (0.00%) memory: 34879216
>>> Updating cvtermpath table.  This may take a while...
>>>
>>> I'm currently blocked at this step. The database is there, the
>>> tables are there...
>>> Any ideas why this may be happening?
>>>
>>> Thank you very much,
>>> Daniel
>>>
>>>
>>> ------------------------------------------------------------------------------
>>>
>>> Monitor your physical, virtual and cloud infrastructure from a single
>>> web console. Get in-depth insight into apps, servers, databases,
>>> vmware,
>>> SAP, cloud infrastructure, etc. Download 30-day Free Trial.
>>> Pricing starts from $795 for 25 servers or applications!
>>> http://p.sf.net/sfu/zoho_dev2dev_nov
>>> _______________________________________________
>>> Gmod-tripal-devel mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>>
>> ------------------------------------------------------------------------------
>>
>> Monitor your physical, virtual and cloud infrastructure from a single
>> web console. Get in-depth insight into apps, servers, databases, vmware,
>> SAP, cloud infrastructure, etc. Download 30-day Free Trial.
>> Pricing starts from $795 for 25 servers or applications!
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>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>


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Re: [Gmod-tripal-devel] Problem with running Tutorial for V1.0

Daniel Sobral
Hi Stephen,

The update solved the previous issue but unfortunately I didn't go very far.
When I tried to sync an organism, it throws me an error:

Calling: tripal_organism_sync_organisms(2, 14)
array_fill(): Number of elements must be positive database.inc:253                                                      [warning]
implode(): Invalid arguments passed database.inc:253                                                                    [warning]
array_keys() expects parameter 1 to be array, null given user.module:528                                                [warning]
pg_query(): Query failed: ERROR:  syntax error at or near ")"                                                           [warning]
LINE 1: ...r INNER JOIN permission p ON p.rid = r.rid WHERE r.rid IN ()
                                                                      ^ database.pgsql.inc:138
ERROR:  syntax error at or near ")"                                                                           [warning]
LINE 1: ...r INNER JOIN permission p ON p.rid = r.rid WHERE r.rid IN ()
                                                                      ^
query: SELECT p.perm FROM role r INNER JOIN permission p ON p.rid = r.rid WHERE r.rid IN () database.pgsql.inc:159
Added fruitfly


I've also noticed another issue: whenever I try to upload an image, it always throws an error e.g.:
  • The selected file Citrus_sinensis.jpg could not be uploaded. Only JPEG, PNG and GIF images are allowed.
  • warning: Attempt to modify property of non-object in /var/www/sites/all/modules/tripal/tripal_organism/tripal_organism.module on line 861.
  • The selected file could not be copied, because no file by that name exists. Please check that you supplied the correct filename.
Also, when I click Search Biological Data > Analyses  I've got the following warnings;
  • warning: mb_strlen() expects parameter 1 to be string, array given in /var/www/includes/unicode.inc on line 409.
  • warning: htmlspecialchars() expects parameter 1 to be string, array given in /var/www/includes/bootstrap.inc on line 860.
Not sure whether this is coming from tripal or drupal.
I've used the versions as they are described in the tutorial.


When uploading gff file, I've got the following error from running the job:

WD tripal_core: chado_prepare: 'sel_featureprop_featureid_typeid' statement already prepared with different arguments!  [error]
You want to prepare PREPARE sel_featureprop_featureid_typeid (int, int) AS SELECT * FROM featureprop WHERE feature_id =
$1 AND type_id = $2  ORDER BY rank ASC with Array
(
    [0] => int
    [1] => int
)
 and the existing statement is PREPARE sel_featureprop_featureid_typeid (int) AS SELECT * FROM featureprop WHERE
feature_id = $1 AND type_id IS NULL  ORDER BY rank ASC with Array
(
    [0] => int
)

Invalid argument supplied for foreach() gff_loader.inc:1531                                                             [warning]
WD tripal_core: chado_prepare: 'uqsel_featureprop_featureprop_c1' statement already prepared with different arguments!  [error]
You want to prepare PREPARE uqsel_featureprop_featureprop_c1 (int, int, int) AS SELECT feature_id, type_id, rank FROM
featureprop WHERE feature_id = $1 AND type_id = $2 AND rank = $3  with Array
(
    [0] => int
    [1] => int
    [2] => int
)
 and the existing statement is PREPARE uqsel_featureprop_featureprop_c1 (int, int) AS SELECT feature_id, type_id, rank
FROM featureprop WHERE feature_id = $1 AND type_id IS NULL AND rank = $2  with Array
(
    [0] => int
    [1] => int
)


Same thing when running the fasta:
Calling: tripal_feature_load_fasta(/var/www/sites/default/files/Citrus_sinensis-scaffold00001.fasta, 13, scaffold, , , , , , , , , Update only, 1, 10, Unique name, 16)

NOTE: Loading of this FASTA file is performed using a database transaction.
If the load fails or is terminated prematurely then the entire set of
insertions/updates is rolled back and will not be found in the database

Opening FASTA file /var/www/sites/default/files/Citrus_sinensis-scaffold00001.fasta
WD T_fasta_loader: Failed to find feature '' ('') while matching on unique name                                         [error]
Done

Hope this helps,
Daniel


On 11/17/2012 02:43 AM, Stephen Ficklin wrote:
Hi Daniel,

Great. I'm glad that fixed it.   We are hoping to release v1.0 by the end of the year.  Although our original goal was August of 2012.  We didn't make that goal because of other project deadlines that have kept us from fixing some outstanding issues.  But, in the process we've also taken the time to fix some of the slowness with loaders and memory leaks.  So, it's a better package now than if we had released it in August.

We are currently using this same development version on a few of our production sites already so I think you are safe to use it. If you encounter a problem just email the list and we can help you through anything.  The only major outstanding problem is the blast extension module which is currently undergoing a rewrite to make it faster and use less memory.   But that should be fixed soon.

Stephen

On 11/16/2012 5:12 PM, Daniel Sobral wrote:
Hi Stephen,

Thanks! It seems to have solved this problem.
I'm going to explore it a bit more and report if I see any more issues.

Do you have any expected date for the official release of V1.0?
Do you think it's safe to start a serious project with the current version?

Thanks again,
Daniel

On 16-11-2012 20:01, Stephen Ficklin wrote:
Hi Daniel,

Can you try updating your code to the most recent version?  Just rung
'git pull' in your 'tripal' directory.   I just pushed out some changes
that may help you.  We've been actively developing and rewriting some
code to make it faster and less memory intensive and unfortunately
caused some issues in the process.

If you haven't loaded any data then I would completely uninstall all the
tripal modules except the core and then reinstall.  If this doesn't fix
the problem let me know and we can dig a bit deeper.

Stephen

On 11/16/2012 2:53 PM, Daniel Sobral wrote:
Hi all,

I've tried to run the tutorial for Tripal V1.0:

I've got some problems when Adding Ontologies, as well as populating the materialized views.

E.g.
drush pm-enable tripal_feature
The following extensions will be enabled: tripal_feature
Do you really want to continue? (y/n): y
tripal_feature was enabled successfully. [ok]
The directory sites/default/files/tripal/tripal_feature has been created. [status]
View 'organism_feature_count' created [status]
Job 'Populate materialized view 'organism_feature_count'' submitted.  Check the jobs page for status          [status]


- When I then run the job, I get an error:
drush trpjob-run drupal
Calling: tripal_update_mview(2, 6)
pg_query(): Query failed: ERROR:  relation "organism_feature_count" does not exist                                      [warning]
LINE 1: SELECT count(*) as cnt FROM organism_feature_count
                                      ^ database.pgsql.inc:138
ERROR:  relation "organism_feature_count" does not exist [warning]
LINE 1: SELECT count(*) as cnt FROM organism_feature_count
                                      ^
query: SELECT count(*) as cnt FROM organism_feature_count database.pgsql.inc:159
Calling: tripal_update_mview(2, 7)
pg_query(): Query failed: ERROR:  relation "organism_feature_count" does not exist                                      [warning]
LINE 1: SELECT count(*) as cnt FROM organism_feature_count
                                      ^ database.pgsql.inc:138
ERROR:  relation "organism_feature_count" does not exist [warning]
LINE 1: SELECT count(*) as cnt FROM organism_feature_count
                                      ^
query: SELECT count(*) as cnt FROM organism_feature_count database.pgsql.inc:159

- Also, Loading the Features CV Ontology throws an error:
Calling: tripal_cv_load_obo_v1_2_id(1, 5)
Opening File sites/all/modules/tripal/tripal_cv/feature_property.obo
Loading terms...
Invalid argument supplied for foreach() obo_loader.inc:204 [warning]
Division by zero obo_loader.inc:230 [warning]
0 of 0 records. (0.00%) memory: 34879216
Updating cvtermpath table.  This may take a while...

I'm currently blocked at this step. The database is there, the tables are there...
Any ideas why this may be happening?

Thank you very much,
Daniel


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Re: [Gmod-tripal-devel] Problem with running Tutorial for V1.0

Stephen Ficklin-2
Hi Daniel,

I'll take a look at these and get back to you.  I'll try and do that before tomorrow.  I have some other items in the queue that I have to tackle.   Have you tried clearing the Drupal cache?

Thanks,
Stephen

On 11/19/2012 6:21 AM, Daniel Sobral wrote:
Hi Stephen,

The update solved the previous issue but unfortunately I didn't go very far.
When I tried to sync an organism, it throws me an error:

Calling: tripal_organism_sync_organisms(2, 14)
array_fill(): Number of elements must be positive database.inc:253                                                      [warning]
implode(): Invalid arguments passed database.inc:253                                                                    [warning]
array_keys() expects parameter 1 to be array, null given user.module:528                                                [warning]
pg_query(): Query failed: ERROR:  syntax error at or near ")"                                                           [warning]
LINE 1: ...r INNER JOIN permission p ON p.rid = r.rid WHERE r.rid IN ()
                                                                      ^ database.pgsql.inc:138
ERROR:  syntax error at or near ")"                                                                           [warning]
LINE 1: ...r INNER JOIN permission p ON p.rid = r.rid WHERE r.rid IN ()
                                                                      ^
query: SELECT p.perm FROM role r INNER JOIN permission p ON p.rid = r.rid WHERE r.rid IN () database.pgsql.inc:159
Added fruitfly


I've also noticed another issue: whenever I try to upload an image, it always throws an error e.g.:
  • The selected file Citrus_sinensis.jpg could not be uploaded. Only JPEG, PNG and GIF images are allowed.
  • warning: Attempt to modify property of non-object in /var/www/sites/all/modules/tripal/tripal_organism/tripal_organism.module on line 861.
  • The selected file could not be copied, because no file by that name exists. Please check that you supplied the correct filename.
Also, when I click Search Biological Data > Analyses  I've got the following warnings;
  • warning: mb_strlen() expects parameter 1 to be string, array given in /var/www/includes/unicode.inc on line 409.
  • warning: htmlspecialchars() expects parameter 1 to be string, array given in /var/www/includes/bootstrap.inc on line 860.
Not sure whether this is coming from tripal or drupal.
I've used the versions as they are described in the tutorial.


When uploading gff file, I've got the following error from running the job:

WD tripal_core: chado_prepare: 'sel_featureprop_featureid_typeid' statement already prepared with different arguments!  [error]
You want to prepare PREPARE sel_featureprop_featureid_typeid (int, int) AS SELECT * FROM featureprop WHERE feature_id =
$1 AND type_id = $2  ORDER BY rank ASC with Array
(
    [0] => int
    [1] => int
)
 and the existing statement is PREPARE sel_featureprop_featureid_typeid (int) AS SELECT * FROM featureprop WHERE
feature_id = $1 AND type_id IS NULL  ORDER BY rank ASC with Array
(
    [0] => int
)

Invalid argument supplied for foreach() gff_loader.inc:1531                                                             [warning]
WD tripal_core: chado_prepare: 'uqsel_featureprop_featureprop_c1' statement already prepared with different arguments!  [error]
You want to prepare PREPARE uqsel_featureprop_featureprop_c1 (int, int, int) AS SELECT feature_id, type_id, rank FROM
featureprop WHERE feature_id = $1 AND type_id = $2 AND rank = $3  with Array
(
    [0] => int
    [1] => int
    [2] => int
)
 and the existing statement is PREPARE uqsel_featureprop_featureprop_c1 (int, int) AS SELECT feature_id, type_id, rank
FROM featureprop WHERE feature_id = $1 AND type_id IS NULL AND rank = $2  with Array
(
    [0] => int
    [1] => int
)


Same thing when running the fasta:
Calling: tripal_feature_load_fasta(/var/www/sites/default/files/Citrus_sinensis-scaffold00001.fasta, 13, scaffold, , , , , , , , , Update only, 1, 10, Unique name, 16)

NOTE: Loading of this FASTA file is performed using a database transaction.
If the load fails or is terminated prematurely then the entire set of
insertions/updates is rolled back and will not be found in the database

Opening FASTA file /var/www/sites/default/files/Citrus_sinensis-scaffold00001.fasta
WD T_fasta_loader: Failed to find feature '' ('') while matching on unique name                                         [error]
Done

Hope this helps,
Daniel


On 11/17/2012 02:43 AM, Stephen Ficklin wrote:
Hi Daniel,

Great. I'm glad that fixed it.   We are hoping to release v1.0 by the end of the year.  Although our original goal was August of 2012.  We didn't make that goal because of other project deadlines that have kept us from fixing some outstanding issues.  But, in the process we've also taken the time to fix some of the slowness with loaders and memory leaks.  So, it's a better package now than if we had released it in August.

We are currently using this same development version on a few of our production sites already so I think you are safe to use it. If you encounter a problem just email the list and we can help you through anything.  The only major outstanding problem is the blast extension module which is currently undergoing a rewrite to make it faster and use less memory.   But that should be fixed soon.

Stephen

On 11/16/2012 5:12 PM, Daniel Sobral wrote:
Hi Stephen,

Thanks! It seems to have solved this problem.
I'm going to explore it a bit more and report if I see any more issues.

Do you have any expected date for the official release of V1.0?
Do you think it's safe to start a serious project with the current version?

Thanks again,
Daniel

On 16-11-2012 20:01, Stephen Ficklin wrote:
Hi Daniel,

Can you try updating your code to the most recent version?  Just rung
'git pull' in your 'tripal' directory.   I just pushed out some changes
that may help you.  We've been actively developing and rewriting some
code to make it faster and less memory intensive and unfortunately
caused some issues in the process.

If you haven't loaded any data then I would completely uninstall all the
tripal modules except the core and then reinstall.  If this doesn't fix
the problem let me know and we can dig a bit deeper.

Stephen

On 11/16/2012 2:53 PM, Daniel Sobral wrote:
Hi all,

I've tried to run the tutorial for Tripal V1.0:

I've got some problems when Adding Ontologies, as well as populating the materialized views.

E.g.
drush pm-enable tripal_feature
The following extensions will be enabled: tripal_feature
Do you really want to continue? (y/n): y
tripal_feature was enabled successfully. [ok]
The directory sites/default/files/tripal/tripal_feature has been created. [status]
View 'organism_feature_count' created [status]
Job 'Populate materialized view 'organism_feature_count'' submitted.  Check the jobs page for status          [status]


- When I then run the job, I get an error:
drush trpjob-run drupal
Calling: tripal_update_mview(2, 6)
pg_query(): Query failed: ERROR:  relation "organism_feature_count" does not exist                                      [warning]
LINE 1: SELECT count(*) as cnt FROM organism_feature_count
                                      ^ database.pgsql.inc:138
ERROR:  relation "organism_feature_count" does not exist [warning]
LINE 1: SELECT count(*) as cnt FROM organism_feature_count
                                      ^
query: SELECT count(*) as cnt FROM organism_feature_count database.pgsql.inc:159
Calling: tripal_update_mview(2, 7)
pg_query(): Query failed: ERROR:  relation "organism_feature_count" does not exist                                      [warning]
LINE 1: SELECT count(*) as cnt FROM organism_feature_count
                                      ^ database.pgsql.inc:138
ERROR:  relation "organism_feature_count" does not exist [warning]
LINE 1: SELECT count(*) as cnt FROM organism_feature_count
                                      ^
query: SELECT count(*) as cnt FROM organism_feature_count database.pgsql.inc:159

- Also, Loading the Features CV Ontology throws an error:
Calling: tripal_cv_load_obo_v1_2_id(1, 5)
Opening File sites/all/modules/tripal/tripal_cv/feature_property.obo
Loading terms...
Invalid argument supplied for foreach() obo_loader.inc:204 [warning]
Division by zero obo_loader.inc:230 [warning]
0 of 0 records. (0.00%) memory: 34879216
Updating cvtermpath table.  This may take a while...

I'm currently blocked at this step. The database is there, the tables are there...
Any ideas why this may be happening?

Thank you very much,
Daniel


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Re: [Gmod-tripal-devel] Problem with running Tutorial for V1.0

Stephen Ficklin-2
In reply to this post by Daniel Sobral
Hi Daniel,

Just an update, I ran a test on the 6.x-1x version that I have and I had no problems syncing organisms, loading images or importing the GFF file.  So, I'm wiping clean my database and starting over to see if I can reproduce the errors you are encountering.   We have made so many changes to the code since that tutorial was put together for the GMOD workshop.  So, unfortunately it may be that your site is suffering from some side-effects of problems before I merged in the most recent code that you just updated.   

Of the problems you are having, I can reproduce one of them.  I do see the error messages on the Analyses search page.  So, that we can address.

Stephen

On 11/19/2012 6:21 AM, Daniel Sobral wrote:
Hi Stephen,

The update solved the previous issue but unfortunately I didn't go very far.
When I tried to sync an organism, it throws me an error:

Calling: tripal_organism_sync_organisms(2, 14)
array_fill(): Number of elements must be positive database.inc:253                                                      [warning]
implode(): Invalid arguments passed database.inc:253                                                                    [warning]
array_keys() expects parameter 1 to be array, null given user.module:528                                                [warning]
pg_query(): Query failed: ERROR:  syntax error at or near ")"                                                           [warning]
LINE 1: ...r INNER JOIN permission p ON p.rid = r.rid WHERE r.rid IN ()
                                                                      ^ database.pgsql.inc:138
ERROR:  syntax error at or near ")"                                                                           [warning]
LINE 1: ...r INNER JOIN permission p ON p.rid = r.rid WHERE r.rid IN ()
                                                                      ^
query: SELECT p.perm FROM role r INNER JOIN permission p ON p.rid = r.rid WHERE r.rid IN () database.pgsql.inc:159
Added fruitfly


I've also noticed another issue: whenever I try to upload an image, it always throws an error e.g.:
  • The selected file Citrus_sinensis.jpg could not be uploaded. Only JPEG, PNG and GIF images are allowed.
  • warning: Attempt to modify property of non-object in /var/www/sites/all/modules/tripal/tripal_organism/tripal_organism.module on line 861.
  • The selected file could not be copied, because no file by that name exists. Please check that you supplied the correct filename.
Also, when I click Search Biological Data > Analyses  I've got the following warnings;
  • warning: mb_strlen() expects parameter 1 to be string, array given in /var/www/includes/unicode.inc on line 409.
  • warning: htmlspecialchars() expects parameter 1 to be string, array given in /var/www/includes/bootstrap.inc on line 860.
Not sure whether this is coming from tripal or drupal.
I've used the versions as they are described in the tutorial.


When uploading gff file, I've got the following error from running the job:

WD tripal_core: chado_prepare: 'sel_featureprop_featureid_typeid' statement already prepared with different arguments!  [error]
You want to prepare PREPARE sel_featureprop_featureid_typeid (int, int) AS SELECT * FROM featureprop WHERE feature_id =
$1 AND type_id = $2  ORDER BY rank ASC with Array
(
    [0] => int
    [1] => int
)
 and the existing statement is PREPARE sel_featureprop_featureid_typeid (int) AS SELECT * FROM featureprop WHERE
feature_id = $1 AND type_id IS NULL  ORDER BY rank ASC with Array
(
    [0] => int
)

Invalid argument supplied for foreach() gff_loader.inc:1531                                                             [warning]
WD tripal_core: chado_prepare: 'uqsel_featureprop_featureprop_c1' statement already prepared with different arguments!  [error]
You want to prepare PREPARE uqsel_featureprop_featureprop_c1 (int, int, int) AS SELECT feature_id, type_id, rank FROM
featureprop WHERE feature_id = $1 AND type_id = $2 AND rank = $3  with Array
(
    [0] => int
    [1] => int
    [2] => int
)
 and the existing statement is PREPARE uqsel_featureprop_featureprop_c1 (int, int) AS SELECT feature_id, type_id, rank
FROM featureprop WHERE feature_id = $1 AND type_id IS NULL AND rank = $2  with Array
(
    [0] => int
    [1] => int
)


Same thing when running the fasta:
Calling: tripal_feature_load_fasta(/var/www/sites/default/files/Citrus_sinensis-scaffold00001.fasta, 13, scaffold, , , , , , , , , Update only, 1, 10, Unique name, 16)

NOTE: Loading of this FASTA file is performed using a database transaction.
If the load fails or is terminated prematurely then the entire set of
insertions/updates is rolled back and will not be found in the database

Opening FASTA file /var/www/sites/default/files/Citrus_sinensis-scaffold00001.fasta
WD T_fasta_loader: Failed to find feature '' ('') while matching on unique name                                         [error]
Done

Hope this helps,
Daniel


On 11/17/2012 02:43 AM, Stephen Ficklin wrote:
Hi Daniel,

Great. I'm glad that fixed it.   We are hoping to release v1.0 by the end of the year.  Although our original goal was August of 2012.  We didn't make that goal because of other project deadlines that have kept us from fixing some outstanding issues.  But, in the process we've also taken the time to fix some of the slowness with loaders and memory leaks.  So, it's a better package now than if we had released it in August.

We are currently using this same development version on a few of our production sites already so I think you are safe to use it. If you encounter a problem just email the list and we can help you through anything.  The only major outstanding problem is the blast extension module which is currently undergoing a rewrite to make it faster and use less memory.   But that should be fixed soon.

Stephen

On 11/16/2012 5:12 PM, Daniel Sobral wrote:
Hi Stephen,

Thanks! It seems to have solved this problem.
I'm going to explore it a bit more and report if I see any more issues.

Do you have any expected date for the official release of V1.0?
Do you think it's safe to start a serious project with the current version?

Thanks again,
Daniel

On 16-11-2012 20:01, Stephen Ficklin wrote:
Hi Daniel,

Can you try updating your code to the most recent version?  Just rung
'git pull' in your 'tripal' directory.   I just pushed out some changes
that may help you.  We've been actively developing and rewriting some
code to make it faster and less memory intensive and unfortunately
caused some issues in the process.

If you haven't loaded any data then I would completely uninstall all the
tripal modules except the core and then reinstall.  If this doesn't fix
the problem let me know and we can dig a bit deeper.

Stephen

On 11/16/2012 2:53 PM, Daniel Sobral wrote:
Hi all,

I've tried to run the tutorial for Tripal V1.0:

I've got some problems when Adding Ontologies, as well as populating the materialized views.

E.g.
drush pm-enable tripal_feature
The following extensions will be enabled: tripal_feature
Do you really want to continue? (y/n): y
tripal_feature was enabled successfully. [ok]
The directory sites/default/files/tripal/tripal_feature has been created. [status]
View 'organism_feature_count' created [status]
Job 'Populate materialized view 'organism_feature_count'' submitted.  Check the jobs page for status          [status]


- When I then run the job, I get an error:
drush trpjob-run drupal
Calling: tripal_update_mview(2, 6)
pg_query(): Query failed: ERROR:  relation "organism_feature_count" does not exist                                      [warning]
LINE 1: SELECT count(*) as cnt FROM organism_feature_count
                                      ^ database.pgsql.inc:138
ERROR:  relation "organism_feature_count" does not exist [warning]
LINE 1: SELECT count(*) as cnt FROM organism_feature_count
                                      ^
query: SELECT count(*) as cnt FROM organism_feature_count database.pgsql.inc:159
Calling: tripal_update_mview(2, 7)
pg_query(): Query failed: ERROR:  relation "organism_feature_count" does not exist                                      [warning]
LINE 1: SELECT count(*) as cnt FROM organism_feature_count
                                      ^ database.pgsql.inc:138
ERROR:  relation "organism_feature_count" does not exist [warning]
LINE 1: SELECT count(*) as cnt FROM organism_feature_count
                                      ^
query: SELECT count(*) as cnt FROM organism_feature_count database.pgsql.inc:159

- Also, Loading the Features CV Ontology throws an error:
Calling: tripal_cv_load_obo_v1_2_id(1, 5)
Opening File sites/all/modules/tripal/tripal_cv/feature_property.obo
Loading terms...
Invalid argument supplied for foreach() obo_loader.inc:204 [warning]
Division by zero obo_loader.inc:230 [warning]
0 of 0 records. (0.00%) memory: 34879216
Updating cvtermpath table.  This may take a while...

I'm currently blocked at this step. The database is there, the tables are there...
Any ideas why this may be happening?

Thank you very much,
Daniel


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