[Gmod-tripal-devel] Slight problem with deleting features.

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[Gmod-tripal-devel] Slight problem with deleting features.

Michael Dondrup-3
Hi again,
I have made a new GFF file of blast results and therefore I am trying to delete all features of
type 'match' and 'match_part' via the Feature->Delete page for a fresh start. I get an error saying
"The Sequence Ontology (SO) term selected for the sequence type is not available in the database. Please check spelling or select another. "
for both types, but I can see the features of this type in the feature view. The delete feature option works for a list of Feature Names entered into the
text area of the same page.

Regards
Michael
 
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Re: [Gmod-tripal-devel] Slight problem with deleting features.

Stephen Ficklin-2
Hi Michael,

I tested deleting features of type 'match' and then 'match_part' on my
end without any troubles.   Can you run these SQL statements and tell me
what you get:


SELECT CVT.cvterm_id
   FROM cvterm CVT
   INNER JOIN cv CV ON CVT.cv_id = CV.cv_id
   LEFT JOIN cvtermsynonym CVTS ON CVTS.cvterm_id = CVT.cvterm_id
WHERE cv.name = 'sequence' AND (CVT.name = 'match' or CVTS.synonym =
'match')

SELECT CVT.cvterm_id
   FROM cvterm CVT
   INNER JOIN cv CV ON CVT.cv_id = CV.cv_id
   LEFT JOIN cvtermsynonym CVTS ON CVTS.cvterm_id = CVT.cvterm_id
WHERE cv.name = 'sequence' AND (CVT.name = 'match_part' or CVTS.synonym
= 'match_part')

Thanks,
Stephen

On 8/24/2013 6:27 AM, Michael Dondrup wrote:

> Hi again,
> I have made a new GFF file of blast results and therefore I am trying to delete all features of
> type 'match' and 'match_part' via the Feature->Delete page for a fresh start. I get an error saying
> "The Sequence Ontology (SO) term selected for the sequence type is not available in the database. Please check spelling or select another."
> for both types, but I can see the features of this type in the feature view. The delete feature option works for a list of Feature Names entered into the
> text area of the same page.
>
> Regards
> Michael
>  
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Re: [Gmod-tripal-devel] Slight problem with deleting features.

Michael Dondrup-3
Hi,
the output is
283 and 285. So they seem to be there. Also, SELECT count(*) FROM cvterm
gives 4544.

also:

licebase=> SELECT CVT.*        
  FROM cvterm CVT
  INNER JOIN cv CV ON CVT.cv_id = CV.cv_id
  LEFT JOIN cvtermsynonym CVTS ON CVTS.cvterm_id = CVT.cvterm_id
WHERE cv.name = 'sequence' AND (CVT.name = 'match' or CVTS.synonym =
'match')

 cvterm_id | cv_id | name  |                                                               definition                                                                | dbxref_id | is_obsolete | is_relationshiptype
-----------+-------+-------+-----------------------------------------------------------------------------------------------------------------------------------------+-----------+-------------+---------------------
       285 |    16 | match | A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4. [SO:ke] |       321 |           0 |                   0
(1 row)



On Aug 26, 2013, at 2:53 PM, Stephen Ficklin wrote:

> Hi Michael,
>
> I tested deleting features of type 'match' and then 'match_part' on my
> end without any troubles.   Can you run these SQL statements and tell me
> what you get:
>
>
> SELECT CVT.cvterm_id
>   FROM cvterm CVT
>   INNER JOIN cv CV ON CVT.cv_id = CV.cv_id
>   LEFT JOIN cvtermsynonym CVTS ON CVTS.cvterm_id = CVT.cvterm_id
> WHERE cv.name = 'sequence' AND (CVT.name = 'match' or CVTS.synonym =
> 'match')
>
> SELECT CVT.cvterm_id
>   FROM cvterm CVT
>   INNER JOIN cv CV ON CVT.cv_id = CV.cv_id
>   LEFT JOIN cvtermsynonym CVTS ON CVTS.cvterm_id = CVT.cvterm_id
> WHERE cv.name = 'sequence' AND (CVT.name = 'match_part' or CVTS.synonym
> = 'match_part')
>
> Thanks,
> Stephen
>
> On 8/24/2013 6:27 AM, Michael Dondrup wrote:
>> Hi again,
>> I have made a new GFF file of blast results and therefore I am trying to delete all features of
>> type 'match' and 'match_part' via the Feature->Delete page for a fresh start. I get an error saying
>> "The Sequence Ontology (SO) term selected for the sequence type is not available in the database. Please check spelling or select another."
>> for both types, but I can see the features of this type in the feature view. The delete feature option works for a list of Feature Names entered into the
>> text area of the same page.
>>
>> Regards
>> Michael
>>
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Re: [Gmod-tripal-devel] Slight problem with deleting features.

Stephen Ficklin-2
Hi Michael,

That is the SQL statement that gets executed in the form validate
function checking to see if the sequence type exists.  So, if that SQL
fails then it gives the error message that you saw (if interested, see
line 72 of the tripal/tripal_feature/includes/tripal_feature-delete.inc
file). You were able to execute the SQL just fine through psql, so I'm
not sure why it would have failed inside of Tripal. It's the same SQL
statement.  The only thing I can think of is that the term may have been
misspelled?

Are there any error messages in your Drupal 'recent logs'?

Stephen

On 8/26/2013 9:19 AM, Michael Dondrup wrote:

> Hi,
> the output is
> 283 and 285. So they seem to be there. Also, SELECT count(*) FROM cvterm
> gives 4544.
>
> also:
>
> licebase=> SELECT CVT.*
>    FROM cvterm CVT
>    INNER JOIN cv CV ON CVT.cv_id = CV.cv_id
>    LEFT JOIN cvtermsynonym CVTS ON CVTS.cvterm_id = CVT.cvterm_id
> WHERE cv.name = 'sequence' AND (CVT.name = 'match' or CVTS.synonym =
> 'match')
>
>   cvterm_id | cv_id | name  |                                                               definition                                                                | dbxref_id | is_obsolete | is_relationshiptype
> -----------+-------+-------+-----------------------------------------------------------------------------------------------------------------------------------------+-----------+-------------+---------------------
>         285 |    16 | match | A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4. [SO:ke] |       321 |           0 |                   0
> (1 row)
>
>
>
> On Aug 26, 2013, at 2:53 PM, Stephen Ficklin wrote:
>
>> Hi Michael,
>>
>> I tested deleting features of type 'match' and then 'match_part' on my
>> end without any troubles.   Can you run these SQL statements and tell me
>> what you get:
>>
>>
>> SELECT CVT.cvterm_id
>>    FROM cvterm CVT
>>    INNER JOIN cv CV ON CVT.cv_id = CV.cv_id
>>    LEFT JOIN cvtermsynonym CVTS ON CVTS.cvterm_id = CVT.cvterm_id
>> WHERE cv.name = 'sequence' AND (CVT.name = 'match' or CVTS.synonym =
>> 'match')
>>
>> SELECT CVT.cvterm_id
>>    FROM cvterm CVT
>>    INNER JOIN cv CV ON CVT.cv_id = CV.cv_id
>>    LEFT JOIN cvtermsynonym CVTS ON CVTS.cvterm_id = CVT.cvterm_id
>> WHERE cv.name = 'sequence' AND (CVT.name = 'match_part' or CVTS.synonym
>> = 'match_part')
>>
>> Thanks,
>> Stephen
>>
>> On 8/24/2013 6:27 AM, Michael Dondrup wrote:
>>> Hi again,
>>> I have made a new GFF file of blast results and therefore I am trying to delete all features of
>>> type 'match' and 'match_part' via the Feature->Delete page for a fresh start. I get an error saying
>>> "The Sequence Ontology (SO) term selected for the sequence type is not available in the database. Please check spelling or select another."
>>> for both types, but I can see the features of this type in the feature view. The delete feature option works for a list of Feature Names entered into the
>>> text area of the same page.
>>>
>>> Regards
>>> Michael
>>>
>>> ------------------------------------------------------------------------------
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>>> AppDynamics. Performance Central is your source for news, insights,
>>> analysis and resources for efficient Application Performance Management.
>>> Visit us today!
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>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>>
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Re: [Gmod-tripal-devel] Slight problem with deleting features.

Michael Dondrup-3
Hi Stephen,

I have now tried to follow this up a bit more, but things seem really weird. I really have no clue what could be going here,
so I am about to give up, which means I will leave the form validation disabled.

I am trying to use the feature delete form. The error seems is raised in function tripal_feature_delete_form_validate.

The processed SQL sent to db_query is the following:

SELECT CVT.cvterm_id FROM cvterm CVT INNER JOIN cv CV on CVT.cv_id = CV.cv_id LEFT JOIN cvtermsynonym CVTS on CVTS.cvterm_id = CVT.cvterm_id WHERE cv.name = 'sequence' and (CVT.name = 'CDS' or CVTS.synonym = 'CDS')

The result of this query is the following as given by var_dump:
resource(264) of type (pgsql result)
or "Resource id #264" via print_r

When I enter the exact SQL via psql using the same user account as the server user, I get a valid result as expected:

licebase=> SELECT CVT.cvterm_id FROM cvterm CVT INNER JOIN cv CV on CVT.cv_id = CV.cv_id LEFT JOIN cvtermsynonym CVTS on CVTS.cvterm_id = CVT.cvterm_id WHERE cv.name = 'sequence' and (CVT.name = 'CDS' or CVTS.synonym = 'CDS')
licebase-> ;
 cvterm_id
-----------
       387
(1 row)

Also the CV term listing is able to find terms containing CDS, so am really sure it is there.
I have also checked pg_last_error() and pg_result_status() but there is no error message all together.  By disabling the form validation, I was able to get a delete job submitted, which is running just fine:
alling: tripal_feature_delete_features(, , CDS, 0, , 159)
Deleting 56954 features
Removing orphaned feature pages
Getting nodes
Getting chado_feature
Verifying all chado_feature Entries
...





On Aug 26, 2013, at 5:26 PM, Michael Dondrup wrote:

> Hi Stephen,
>
> I tried again, but the error persists. No output in the dblog, nor server logs. Maybe I have fallen victim
> to some lagacy code, I will check that first.
>
> thank you
> Michael
>
> On Aug 26, 2013, at 3:25 PM, Stephen Ficklin wrote:
>
>> Hi Michael,
>>
>> That is the SQL statement that gets executed in the form validate
>> function checking to see if the sequence type exists.  So, if that SQL
>> fails then it gives the error message that you saw (if interested, see
>> line 72 of the tripal/tripal_feature/includes/tripal_feature-delete.inc
>> file). You were able to execute the SQL just fine through psql, so I'm
>> not sure why it would have failed inside of Tripal. It's the same SQL
>> statement.  The only thing I can think of is that the term may have been
>> misspelled?
>>
>> Are there any error messages in your Drupal 'recent logs'?
>>
>> Stephen
>>
>> On 8/26/2013 9:19 AM, Michael Dondrup wrote:
>>> Hi,
>>> the output is
>>> 283 and 285. So they seem to be there. Also, SELECT count(*) FROM cvterm
>>> gives 4544.
>>>
>>> also:
>>>
>>> licebase=> SELECT CVT.*
>>>  FROM cvterm CVT
>>>  INNER JOIN cv CV ON CVT.cv_id = CV.cv_id
>>>  LEFT JOIN cvtermsynonym CVTS ON CVTS.cvterm_id = CVT.cvterm_id
>>> WHERE cv.name = 'sequence' AND (CVT.name = 'match' or CVTS.synonym =
>>> 'match')
>>>
>>> cvterm_id | cv_id | name  |                                                               definition                                                                | dbxref_id | is_obsolete | is_relationshiptype
>>> -----------+-------+-------+-----------------------------------------------------------------------------------------------------------------------------------------+-----------+-------------+---------------------
>>>       285 |    16 | match | A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4. [SO:ke] |       321 |           0 |                   0
>>> (1 row)
>>>
>>>
>>>
>>> On Aug 26, 2013, at 2:53 PM, Stephen Ficklin wrote:
>>>
>>>> Hi Michael,
>>>>
>>>> I tested deleting features of type 'match' and then 'match_part' on my
>>>> end without any troubles.   Can you run these SQL statements and tell me
>>>> what you get:
>>>>
>>>>
>>>> SELECT CVT.cvterm_id
>>>>  FROM cvterm CVT
>>>>  INNER JOIN cv CV ON CVT.cv_id = CV.cv_id
>>>>  LEFT JOIN cvtermsynonym CVTS ON CVTS.cvterm_id = CVT.cvterm_id
>>>> WHERE cv.name = 'sequence' AND (CVT.name = 'match' or CVTS.synonym =
>>>> 'match')
>>>>
>>>> SELECT CVT.cvterm_id
>>>>  FROM cvterm CVT
>>>>  INNER JOIN cv CV ON CVT.cv_id = CV.cv_id
>>>>  LEFT JOIN cvtermsynonym CVTS ON CVTS.cvterm_id = CVT.cvterm_id
>>>> WHERE cv.name = 'sequence' AND (CVT.name = 'match_part' or CVTS.synonym
>>>> = 'match_part')
>>>>
>>>> Thanks,
>>>> Stephen
>>>>
>>>> On 8/24/2013 6:27 AM, Michael Dondrup wrote:
>>>>> Hi again,
>>>>> I have made a new GFF file of blast results and therefore I am trying to delete all features of
>>>>> type 'match' and 'match_part' via the Feature->Delete page for a fresh start. I get an error saying
>>>>> "The Sequence Ontology (SO) term selected for the sequence type is not available in the database. Please check spelling or select another."
>>>>> for both types, but I can see the features of this type in the feature view. The delete feature option works for a list of Feature Names entered into the
>>>>> text area of the same page.
>>>>>
>>>>> Regards
>>>>> Michael
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Introducing Performance Central, a new site from SourceForge and
>>>>> AppDynamics. Performance Central is your source for news, insights,
>>>>> analysis and resources for efficient Application Performance Management.
>>>>> Visit us today!
>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk
>>>>> _______________________________________________
>>>>> Gmod-tripal-devel mailing list
>>>>> [hidden email]
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>>>>
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>>>> AppDynamics. Performance Central is your source for news, insights,
>>>> analysis and resources for efficient Application Performance Management.
>>>> Visit us today!
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>>
>>
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Re: [Gmod-tripal-devel] Slight problem with deleting features.

Stephen Ficklin-2
Hi Michael,

Would you mind adding this code to line 91 of the
tripal_feature-delete.inc and running it again and tell me what the
output is that you see when you try to delete  a feature of a given type:

print_r(array($cvtermsql, $seq_type, $cvterm));

So, the code should look like this:

   // check to make sure the types exists
   if ($seq_type) {
     $cvtermsql = "SELECT CVT.cvterm_id
                   FROM {cvterm} CVT
                      INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
                      LEFT JOIN {cvtermsynonym} CVTS on CVTS.cvterm_id =
CVT.cvterm_id
                   WHERE cv.name = '%s' and (CVT.name = '%s' or
CVTS.synonym = '%s')";
     $cvterm = db_fetch_object(db_query($cvtermsql, 'sequence',
$seq_type, $seq_type));
     print_r(array($cvtermsql, $seq_type, $cvterm));
     if (!$cvterm) {
       form_set_error('seq_type', t("The Sequence Ontology (SO) term
selected for the sequence type is not available in the database. Please
check spelling or select another."));
     }
   }

Thanks,
Stephen

On 9/24/2013 6:05 AM, Michael Dondrup wrote:

> Hi Stephen,
>
> I have now tried to follow this up a bit more, but things seem really weird. I really have no clue what could be going here,
> so I am about to give up, which means I will leave the form validation disabled.
>
> I am trying to use the feature delete form. The error seems is raised in function tripal_feature_delete_form_validate.
>
> The processed SQL sent to db_query is the following:
>
> SELECT CVT.cvterm_id FROM cvterm CVT INNER JOIN cv CV on CVT.cv_id = CV.cv_id LEFT JOIN cvtermsynonym CVTS on CVTS.cvterm_id = CVT.cvterm_id WHERE cv.name = 'sequence' and (CVT.name = 'CDS' or CVTS.synonym = 'CDS')
>
> The result of this query is the following as given by var_dump:
> resource(264) of type (pgsql result)
> or "Resource id #264" via print_r
>
> When I enter the exact SQL via psql using the same user account as the server user, I get a valid result as expected:
>
> licebase=> SELECT CVT.cvterm_id FROM cvterm CVT INNER JOIN cv CV on CVT.cv_id = CV.cv_id LEFT JOIN cvtermsynonym CVTS on CVTS.cvterm_id = CVT.cvterm_id WHERE cv.name = 'sequence' and (CVT.name = 'CDS' or CVTS.synonym = 'CDS')
> licebase-> ;
>   cvterm_id
> -----------
>         387
> (1 row)
>
> Also the CV term listing is able to find terms containing CDS, so am really sure it is there.
> I have also checked pg_last_error() and pg_result_status() but there is no error message all together.  By disabling the form validation, I was able to get a delete job submitted, which is running just fine:
> alling: tripal_feature_delete_features(, , CDS, 0, , 159)
> Deleting 56954 features
> Removing orphaned feature pages
> Getting nodes
> Getting chado_feature
> Verifying all chado_feature Entries
> ...
>
>
>
>
>
> On Aug 26, 2013, at 5:26 PM, Michael Dondrup wrote:
>
>> Hi Stephen,
>>
>> I tried again, but the error persists. No output in the dblog, nor server logs. Maybe I have fallen victim
>> to some lagacy code, I will check that first.
>>
>> thank you
>> Michael
>>
>> On Aug 26, 2013, at 3:25 PM, Stephen Ficklin wrote:
>>
>>> Hi Michael,
>>>
>>> That is the SQL statement that gets executed in the form validate
>>> function checking to see if the sequence type exists.  So, if that SQL
>>> fails then it gives the error message that you saw (if interested, see
>>> line 72 of the tripal/tripal_feature/includes/tripal_feature-delete.inc
>>> file). You were able to execute the SQL just fine through psql, so I'm
>>> not sure why it would have failed inside of Tripal. It's the same SQL
>>> statement.  The only thing I can think of is that the term may have been
>>> misspelled?
>>>
>>> Are there any error messages in your Drupal 'recent logs'?
>>>
>>> Stephen
>>>
>>> On 8/26/2013 9:19 AM, Michael Dondrup wrote:
>>>> Hi,
>>>> the output is
>>>> 283 and 285. So they seem to be there. Also, SELECT count(*) FROM cvterm
>>>> gives 4544.
>>>>
>>>> also:
>>>>
>>>> licebase=> SELECT CVT.*
>>>>   FROM cvterm CVT
>>>>   INNER JOIN cv CV ON CVT.cv_id = CV.cv_id
>>>>   LEFT JOIN cvtermsynonym CVTS ON CVTS.cvterm_id = CVT.cvterm_id
>>>> WHERE cv.name = 'sequence' AND (CVT.name = 'match' or CVTS.synonym =
>>>> 'match')
>>>>
>>>> cvterm_id | cv_id | name  |                                                               definition                                                                | dbxref_id | is_obsolete | is_relationshiptype
>>>> -----------+-------+-------+-----------------------------------------------------------------------------------------------------------------------------------------+-----------+-------------+---------------------
>>>>        285 |    16 | match | A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4. [SO:ke] |       321 |           0 |                   0
>>>> (1 row)
>>>>
>>>>
>>>>
>>>> On Aug 26, 2013, at 2:53 PM, Stephen Ficklin wrote:
>>>>
>>>>> Hi Michael,
>>>>>
>>>>> I tested deleting features of type 'match' and then 'match_part' on my
>>>>> end without any troubles.   Can you run these SQL statements and tell me
>>>>> what you get:
>>>>>
>>>>>
>>>>> SELECT CVT.cvterm_id
>>>>>   FROM cvterm CVT
>>>>>   INNER JOIN cv CV ON CVT.cv_id = CV.cv_id
>>>>>   LEFT JOIN cvtermsynonym CVTS ON CVTS.cvterm_id = CVT.cvterm_id
>>>>> WHERE cv.name = 'sequence' AND (CVT.name = 'match' or CVTS.synonym =
>>>>> 'match')
>>>>>
>>>>> SELECT CVT.cvterm_id
>>>>>   FROM cvterm CVT
>>>>>   INNER JOIN cv CV ON CVT.cv_id = CV.cv_id
>>>>>   LEFT JOIN cvtermsynonym CVTS ON CVTS.cvterm_id = CVT.cvterm_id
>>>>> WHERE cv.name = 'sequence' AND (CVT.name = 'match_part' or CVTS.synonym
>>>>> = 'match_part')
>>>>>
>>>>> Thanks,
>>>>> Stephen
>>>>>
>>>>> On 8/24/2013 6:27 AM, Michael Dondrup wrote:
>>>>>> Hi again,
>>>>>> I have made a new GFF file of blast results and therefore I am trying to delete all features of
>>>>>> type 'match' and 'match_part' via the Feature->Delete page for a fresh start. I get an error saying
>>>>>> "The Sequence Ontology (SO) term selected for the sequence type is not available in the database. Please check spelling or select another."
>>>>>> for both types, but I can see the features of this type in the feature view. The delete feature option works for a list of Feature Names entered into the
>>>>>> text area of the same page.
>>>>>>
>>>>>> Regards
>>>>>> Michael
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>> Introducing Performance Central, a new site from SourceForge and
>>>>>> AppDynamics. Performance Central is your source for news, insights,
>>>>>> analysis and resources for efficient Application Performance Management.
>>>>>> Visit us today!
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>>>>>> _______________________________________________
>>>>>> Gmod-tripal-devel mailing list
>>>>>> [hidden email]
>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>>>>> ------------------------------------------------------------------------------
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>>>>> AppDynamics. Performance Central is your source for news, insights,
>>>>> analysis and resources for efficient Application Performance Management.
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>>>>> _______________________________________________
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>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>>>
>>> ------------------------------------------------------------------------------
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>>> analysis and resources for efficient Application Performance Management.
>>> Visit us today!
>>> http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk
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Re: [Gmod-tripal-devel] Slight problem with deleting features.

Michael Dondrup-3
Here is the output:

Array ( [0] => SELECT CVT.cvterm_id FROM {cvterm} CVT INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id LEFT JOIN {cvtermsynonym} CVTS on CVTS.cvterm_id = CVT.cvterm_id WHERE cv.name = '%s' and (CVT.name = '%s' or CVTS.synonym = '%s') [1] => CDS [2] => )

The problem seems to be that db_query doesn't return something sensible, at least db_fetch_object  doesn't seem to know how to make an object out of it.

On Sep 24, 2013, at 2:29 PM, Stephen Ficklin wrote:

> Hi Michael,
>
> Would you mind adding this code to line 91 of the
> tripal_feature-delete.inc and running it again and tell me what the
> output is that you see when you try to delete  a feature of a given type:
>
> print_r(array($cvtermsql, $seq_type, $cvterm));
>
> So, the code should look like this:
>
>   // check to make sure the types exists
>   if ($seq_type) {
>     $cvtermsql = "SELECT CVT.cvterm_id
>                   FROM {cvterm} CVT
>                      INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
>                      LEFT JOIN {cvtermsynonym} CVTS on CVTS.cvterm_id =
> CVT.cvterm_id
>                   WHERE cv.name = '%s' and (CVT.name = '%s' or
> CVTS.synonym = '%s')";
>     $cvterm = db_fetch_object(db_query($cvtermsql, 'sequence',
> $seq_type, $seq_type));
>     print_r(array($cvtermsql, $seq_type, $cvterm));
>     if (!$cvterm) {
>       form_set_error('seq_type', t("The Sequence Ontology (SO) term
> selected for the sequence type is not available in the database. Please
> check spelling or select another."));
>     }
>   }
>
> Thanks,
> Stephen
>
> On 9/24/2013 6:05 AM, Michael Dondrup wrote:
>> Hi Stephen,
>>
>> I have now tried to follow this up a bit more, but things seem really weird. I really have no clue what could be going here,
>> so I am about to give up, which means I will leave the form validation disabled.
>>
>> I am trying to use the feature delete form. The error seems is raised in function tripal_feature_delete_form_validate.
>>
>> The processed SQL sent to db_query is the following:
>>
>> SELECT CVT.cvterm_id FROM cvterm CVT INNER JOIN cv CV on CVT.cv_id = CV.cv_id LEFT JOIN cvtermsynonym CVTS on CVTS.cvterm_id = CVT.cvterm_id WHERE cv.name = 'sequence' and (CVT.name = 'CDS' or CVTS.synonym = 'CDS')
>>
>> The result of this query is the following as given by var_dump:
>> resource(264) of type (pgsql result)
>> or "Resource id #264" via print_r
>>
>> When I enter the exact SQL via psql using the same user account as the server user, I get a valid result as expected:
>>
>> licebase=> SELECT CVT.cvterm_id FROM cvterm CVT INNER JOIN cv CV on CVT.cv_id = CV.cv_id LEFT JOIN cvtermsynonym CVTS on CVTS.cvterm_id = CVT.cvterm_id WHERE cv.name = 'sequence' and (CVT.name = 'CDS' or CVTS.synonym = 'CDS')
>> licebase-> ;
>>  cvterm_id
>> -----------
>>        387
>> (1 row)
>>
>> Also the CV term listing is able to find terms containing CDS, so am really sure it is there.
>> I have also checked pg_last_error() and pg_result_status() but there is no error message all together.  By disabling the form validation, I was able to get a delete job submitted, which is running just fine:
>> alling: tripal_feature_delete_features(, , CDS, 0, , 159)
>> Deleting 56954 features
>> Removing orphaned feature pages
>> Getting nodes
>> Getting chado_feature
>> Verifying all chado_feature Entries
>> ...
>>
>>
>>
>>
>>
>> On Aug 26, 2013, at 5:26 PM, Michael Dondrup wrote:
>>
>>> Hi Stephen,
>>>
>>> I tried again, but the error persists. No output in the dblog, nor server logs. Maybe I have fallen victim
>>> to some lagacy code, I will check that first.
>>>
>>> thank you
>>> Michael
>>>
>>> On Aug 26, 2013, at 3:25 PM, Stephen Ficklin wrote:
>>>
>>>> Hi Michael,
>>>>
>>>> That is the SQL statement that gets executed in the form validate
>>>> function checking to see if the sequence type exists.  So, if that SQL
>>>> fails then it gives the error message that you saw (if interested, see
>>>> line 72 of the tripal/tripal_feature/includes/tripal_feature-delete.inc
>>>> file). You were able to execute the SQL just fine through psql, so I'm
>>>> not sure why it would have failed inside of Tripal. It's the same SQL
>>>> statement.  The only thing I can think of is that the term may have been
>>>> misspelled?
>>>>
>>>> Are there any error messages in your Drupal 'recent logs'?
>>>>
>>>> Stephen
>>>>
>>>> On 8/26/2013 9:19 AM, Michael Dondrup wrote:
>>>>> Hi,
>>>>> the output is
>>>>> 283 and 285. So they seem to be there. Also, SELECT count(*) FROM cvterm
>>>>> gives 4544.
>>>>>
>>>>> also:
>>>>>
>>>>> licebase=> SELECT CVT.*
>>>>>  FROM cvterm CVT
>>>>>  INNER JOIN cv CV ON CVT.cv_id = CV.cv_id
>>>>>  LEFT JOIN cvtermsynonym CVTS ON CVTS.cvterm_id = CVT.cvterm_id
>>>>> WHERE cv.name = 'sequence' AND (CVT.name = 'match' or CVTS.synonym =
>>>>> 'match')
>>>>>
>>>>> cvterm_id | cv_id | name  |                                                               definition                                                                | dbxref_id | is_obsolete | is_relationshiptype
>>>>> -----------+-------+-------+-----------------------------------------------------------------------------------------------------------------------------------------+-----------+-------------+---------------------
>>>>>       285 |    16 | match | A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4. [SO:ke] |       321 |           0 |                   0
>>>>> (1 row)
>>>>>
>>>>>
>>>>>
>>>>> On Aug 26, 2013, at 2:53 PM, Stephen Ficklin wrote:
>>>>>
>>>>>> Hi Michael,
>>>>>>
>>>>>> I tested deleting features of type 'match' and then 'match_part' on my
>>>>>> end without any troubles.   Can you run these SQL statements and tell me
>>>>>> what you get:
>>>>>>
>>>>>>
>>>>>> SELECT CVT.cvterm_id
>>>>>>  FROM cvterm CVT
>>>>>>  INNER JOIN cv CV ON CVT.cv_id = CV.cv_id
>>>>>>  LEFT JOIN cvtermsynonym CVTS ON CVTS.cvterm_id = CVT.cvterm_id
>>>>>> WHERE cv.name = 'sequence' AND (CVT.name = 'match' or CVTS.synonym =
>>>>>> 'match')
>>>>>>
>>>>>> SELECT CVT.cvterm_id
>>>>>>  FROM cvterm CVT
>>>>>>  INNER JOIN cv CV ON CVT.cv_id = CV.cv_id
>>>>>>  LEFT JOIN cvtermsynonym CVTS ON CVTS.cvterm_id = CVT.cvterm_id
>>>>>> WHERE cv.name = 'sequence' AND (CVT.name = 'match_part' or CVTS.synonym
>>>>>> = 'match_part')
>>>>>>
>>>>>> Thanks,
>>>>>> Stephen
>>>>>>
>>>>>> On 8/24/2013 6:27 AM, Michael Dondrup wrote:
>>>>>>> Hi again,
>>>>>>> I have made a new GFF file of blast results and therefore I am trying to delete all features of
>>>>>>> type 'match' and 'match_part' via the Feature->Delete page for a fresh start. I get an error saying
>>>>>>> "The Sequence Ontology (SO) term selected for the sequence type is not available in the database. Please check spelling or select another."
>>>>>>> for both types, but I can see the features of this type in the feature view. The delete feature option works for a list of Feature Names entered into the
>>>>>>> text area of the same page.
>>>>>>>
>>>>>>> Regards
>>>>>>> Michael
>>>>>>>
>>>>>>> ------------------------------------------------------------------------------
>>>>>>> Introducing Performance Central, a new site from SourceForge and
>>>>>>> AppDynamics. Performance Central is your source for news, insights,
>>>>>>> analysis and resources for efficient Application Performance Management.
>>>>>>> Visit us today!
>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk
>>>>>>> _______________________________________________
>>>>>>> Gmod-tripal-devel mailing list
>>>>>>> [hidden email]
>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>>>>>> ------------------------------------------------------------------------------
>>>>>> Introducing Performance Central, a new site from SourceForge and
>>>>>> AppDynamics. Performance Central is your source for news, insights,
>>>>>> analysis and resources for efficient Application Performance Management.
>>>>>> Visit us today!
>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk
>>>>>> _______________________________________________
>>>>>> Gmod-tripal-devel mailing list
>>>>>> [hidden email]
>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Introducing Performance Central, a new site from SourceForge and
>>>> AppDynamics. Performance Central is your source for news, insights,
>>>> analysis and resources for efficient Application Performance Management.
>>>> Visit us today!
>>>> http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk
>>>> _______________________________________________
>>>> Gmod-tripal-devel mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>
>
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Re: [Gmod-tripal-devel] Slight problem with deleting features.

Michael Dondrup-3
I thought must have smth to do with the query SQL. I have tried several more simple queries to see if they work.

So, I thought it might have something to do with the string literal, but it doesn't.
Now it's getting really weird ('works' means the query returns  non-empty result):

    $cvtermsql = "SELECT CVT.cvterm_id FROM cvterm AS CVT WHERE CVT.name = 'glass'"; works! (cv_id = 2, local)
    $cvtermsql = "SELECT CVT.cvterm_id FROM cvterm AS CVT WHERE CVT.name = 'version'"; works! (cv_id = 6, chado_properties)
none of the following terms work:
   project_description (cv_id = 7, tripal),  analysis_type (cv_id = 27, tripal_analysis), accession (12, feature_property),   blastoutput, fraction_identical ,  variant_of (cv_id = 16, sequence) …, exon, CDS, etc.
   
I didn't find any term with cvterm_id > 30 that worked (all queries work in psql). So it looked like something is really broken within that table.

Finally I find that:
$cvtermsql = "SELECT CVT.cvterm_id FROM cvterm AS CVT WHERE CVT.cvterm_id = 29"; works
and
$cvtermsql = "SELECT CVT.cvterm_id FROM cvterm AS CVT WHERE CVT.cvterm_id = 30"; doesn't
   
So it looks like these are the two entries, where 'in between' something breaks:

licebase=> SELECT * from cvterm where cvterm_id >= 29 order by cvterm_id limit 2 ;
 cvterm_id | cv_id |     name      |                                                                                         definition                                                                                          | dbxref_id | is_obsolete | is_relationshiptype
-----------+-------+---------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-----------+-------------+---------------------
        29 |     6 | version       | Chado schema version                                                                                                                                                                        |        29 |           0 |                   0
        30 |    27 | analysis_type | The type of analysis was performed. This value is automatically set by each Tripal Analysis module and should be equal to the module name (e.g. tripal_analysis_blast, tripal_analysis_go). |        30 |           0 |                   0
(2 rows)

That means we have somehow established the fact that all entries in cvterm with id >=30 are invisible to db_query/pg_query. This is the oddest thing I have ever seen.


 





On Sep 25, 2013, at 9:12 AM, Michael Dondrup wrote:

> Here is the output:
>
> Array ( [0] => SELECT CVT.cvterm_id FROM {cvterm} CVT INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id LEFT JOIN {cvtermsynonym} CVTS on CVTS.cvterm_id = CVT.cvterm_id WHERE cv.name = '%s' and (CVT.name = '%s' or CVTS.synonym = '%s') [1] => CDS [2] => )
>
> The problem seems to be that db_query doesn't return something sensible, at least db_fetch_object  doesn't seem to know how to make an object out of it.
>
> On Sep 24, 2013, at 2:29 PM, Stephen Ficklin wrote:
>
>> Hi Michael,
>>
>> Would you mind adding this code to line 91 of the
>> tripal_feature-delete.inc and running it again and tell me what the
>> output is that you see when you try to delete  a feature of a given type:
>>
>> print_r(array($cvtermsql, $seq_type, $cvterm));
>>
>> So, the code should look like this:
>>
>>  // check to make sure the types exists
>>  if ($seq_type) {
>>    $cvtermsql = "SELECT CVT.cvterm_id
>>                  FROM {cvterm} CVT
>>                     INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
>>                     LEFT JOIN {cvtermsynonym} CVTS on CVTS.cvterm_id =
>> CVT.cvterm_id
>>                  WHERE cv.name = '%s' and (CVT.name = '%s' or
>> CVTS.synonym = '%s')";
>>    $cvterm = db_fetch_object(db_query($cvtermsql, 'sequence',
>> $seq_type, $seq_type));
>>    print_r(array($cvtermsql, $seq_type, $cvterm));
>>    if (!$cvterm) {
>>      form_set_error('seq_type', t("The Sequence Ontology (SO) term
>> selected for the sequence type is not available in the database. Please
>> check spelling or select another."));
>>    }
>>  }
>>
>> Thanks,
>> Stephen
>>
>> On 9/24/2013 6:05 AM, Michael Dondrup wrote:
>>> Hi Stephen,
>>>
>>> I have now tried to follow this up a bit more, but things seem really weird. I really have no clue what could be going here,
>>> so I am about to give up, which means I will leave the form validation disabled.
>>>
>>> I am trying to use the feature delete form. The error seems is raised in function tripal_feature_delete_form_validate.
>>>
>>> The processed SQL sent to db_query is the following:
>>>
>>> SELECT CVT.cvterm_id FROM cvterm CVT INNER JOIN cv CV on CVT.cv_id = CV.cv_id LEFT JOIN cvtermsynonym CVTS on CVTS.cvterm_id = CVT.cvterm_id WHERE cv.name = 'sequence' and (CVT.name = 'CDS' or CVTS.synonym = 'CDS')
>>>
>>> The result of this query is the following as given by var_dump:
>>> resource(264) of type (pgsql result)
>>> or "Resource id #264" via print_r
>>>
>>> When I enter the exact SQL via psql using the same user account as the server user, I get a valid result as expected:
>>>
>>> licebase=> SELECT CVT.cvterm_id FROM cvterm CVT INNER JOIN cv CV on CVT.cv_id = CV.cv_id LEFT JOIN cvtermsynonym CVTS on CVTS.cvterm_id = CVT.cvterm_id WHERE cv.name = 'sequence' and (CVT.name = 'CDS' or CVTS.synonym = 'CDS')
>>> licebase-> ;
>>> cvterm_id
>>> -----------
>>>       387
>>> (1 row)
>>>
>>> Also the CV term listing is able to find terms containing CDS, so am really sure it is there.
>>> I have also checked pg_last_error() and pg_result_status() but there is no error message all together.  By disabling the form validation, I was able to get a delete job submitted, which is running just fine:
>>> alling: tripal_feature_delete_features(, , CDS, 0, , 159)
>>> Deleting 56954 features
>>> Removing orphaned feature pages
>>> Getting nodes
>>> Getting chado_feature
>>> Verifying all chado_feature Entries
>>> ...
>>>
>>>
>>>
>>>
>>>
>>> On Aug 26, 2013, at 5:26 PM, Michael Dondrup wrote:
>>>
>>>> Hi Stephen,
>>>>
>>>> I tried again, but the error persists. No output in the dblog, nor server logs. Maybe I have fallen victim
>>>> to some lagacy code, I will check that first.
>>>>
>>>> thank you
>>>> Michael
>>>>
>>>> On Aug 26, 2013, at 3:25 PM, Stephen Ficklin wrote:
>>>>
>>>>> Hi Michael,
>>>>>
>>>>> That is the SQL statement that gets executed in the form validate
>>>>> function checking to see if the sequence type exists.  So, if that SQL
>>>>> fails then it gives the error message that you saw (if interested, see
>>>>> line 72 of the tripal/tripal_feature/includes/tripal_feature-delete.inc
>>>>> file). You were able to execute the SQL just fine through psql, so I'm
>>>>> not sure why it would have failed inside of Tripal. It's the same SQL
>>>>> statement.  The only thing I can think of is that the term may have been
>>>>> misspelled?
>>>>>
>>>>> Are there any error messages in your Drupal 'recent logs'?
>>>>>
>>>>> Stephen
>>>>>
>>>>> On 8/26/2013 9:19 AM, Michael Dondrup wrote:
>>>>>> Hi,
>>>>>> the output is
>>>>>> 283 and 285. So they seem to be there. Also, SELECT count(*) FROM cvterm
>>>>>> gives 4544.
>>>>>>
>>>>>> also:
>>>>>>
>>>>>> licebase=> SELECT CVT.*
>>>>>> FROM cvterm CVT
>>>>>> INNER JOIN cv CV ON CVT.cv_id = CV.cv_id
>>>>>> LEFT JOIN cvtermsynonym CVTS ON CVTS.cvterm_id = CVT.cvterm_id
>>>>>> WHERE cv.name = 'sequence' AND (CVT.name = 'match' or CVTS.synonym =
>>>>>> 'match')
>>>>>>
>>>>>> cvterm_id | cv_id | name  |                                                               definition                                                                | dbxref_id | is_obsolete | is_relationshiptype
>>>>>> -----------+-------+-------+-----------------------------------------------------------------------------------------------------------------------------------------+-----------+-------------+---------------------
>>>>>>      285 |    16 | match | A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4. [SO:ke] |       321 |           0 |                   0
>>>>>> (1 row)
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Aug 26, 2013, at 2:53 PM, Stephen Ficklin wrote:
>>>>>>
>>>>>>> Hi Michael,
>>>>>>>
>>>>>>> I tested deleting features of type 'match' and then 'match_part' on my
>>>>>>> end without any troubles.   Can you run these SQL statements and tell me
>>>>>>> what you get:
>>>>>>>
>>>>>>>
>>>>>>> SELECT CVT.cvterm_id
>>>>>>> FROM cvterm CVT
>>>>>>> INNER JOIN cv CV ON CVT.cv_id = CV.cv_id
>>>>>>> LEFT JOIN cvtermsynonym CVTS ON CVTS.cvterm_id = CVT.cvterm_id
>>>>>>> WHERE cv.name = 'sequence' AND (CVT.name = 'match' or CVTS.synonym =
>>>>>>> 'match')
>>>>>>>
>>>>>>> SELECT CVT.cvterm_id
>>>>>>> FROM cvterm CVT
>>>>>>> INNER JOIN cv CV ON CVT.cv_id = CV.cv_id
>>>>>>> LEFT JOIN cvtermsynonym CVTS ON CVTS.cvterm_id = CVT.cvterm_id
>>>>>>> WHERE cv.name = 'sequence' AND (CVT.name = 'match_part' or CVTS.synonym
>>>>>>> = 'match_part')
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Stephen
>>>>>>>
>>>>>>> On 8/24/2013 6:27 AM, Michael Dondrup wrote:
>>>>>>>> Hi again,
>>>>>>>> I have made a new GFF file of blast results and therefore I am trying to delete all features of
>>>>>>>> type 'match' and 'match_part' via the Feature->Delete page for a fresh start. I get an error saying
>>>>>>>> "The Sequence Ontology (SO) term selected for the sequence type is not available in the database. Please check spelling or select another."
>>>>>>>> for both types, but I can see the features of this type in the feature view. The delete feature option works for a list of Feature Names entered into the
>>>>>>>> text area of the same page.
>>>>>>>>
>>>>>>>> Regards
>>>>>>>> Michael
>>>>>>>>
>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>> Introducing Performance Central, a new site from SourceForge and
>>>>>>>> AppDynamics. Performance Central is your source for news, insights,
>>>>>>>> analysis and resources for efficient Application Performance Management.
>>>>>>>> Visit us today!
>>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk
>>>>>>>> _______________________________________________
>>>>>>>> Gmod-tripal-devel mailing list
>>>>>>>> [hidden email]
>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>>>>>>> ------------------------------------------------------------------------------
>>>>>>> Introducing Performance Central, a new site from SourceForge and
>>>>>>> AppDynamics. Performance Central is your source for news, insights,
>>>>>>> analysis and resources for efficient Application Performance Management.
>>>>>>> Visit us today!
>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk
>>>>>>> _______________________________________________
>>>>>>> Gmod-tripal-devel mailing list
>>>>>>> [hidden email]
>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Introducing Performance Central, a new site from SourceForge and
>>>>> AppDynamics. Performance Central is your source for news, insights,
>>>>> analysis and resources for efficient Application Performance Management.
>>>>> Visit us today!
>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk
>>>>> _______________________________________________
>>>>> Gmod-tripal-devel mailing list
>>>>> [hidden email]
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>>
>>
>> ------------------------------------------------------------------------------
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Re: [Gmod-tripal-devel] Slight problem with deleting features.

Michael Dondrup-3
And another follow up. I  googled for "pg_query weird" and this turned up as second hit:

http://stackoverflow.com/questions/4340775/pg-query-seems-to-not-execute-queries-in-a-loop
So, without knowing exactly why, I changed drupal/includes/database.pgsql.inc, line 78

 $connection = @pg_connect($conn_string);
to: $connection = @pg_pconnect($conn_string);

So this seems to be more of a PHP Postgres connection bug, but I have no idea why this change fixes things, and
what else might be broken now.

Best
Michael


On Sep 25, 2013, at 11:58 AM, Michael Dondrup wrote:

> I thought must have smth to do with the query SQL. I have tried several more simple queries to see if they work.
>
> So, I thought it might have something to do with the string literal, but it doesn't.
> Now it's getting really weird ('works' means the query returns  non-empty result):
>
>    $cvtermsql = "SELECT CVT.cvterm_id FROM cvterm AS CVT WHERE CVT.name = 'glass'"; works! (cv_id = 2, local)
>    $cvtermsql = "SELECT CVT.cvterm_id FROM cvterm AS CVT WHERE CVT.name = 'version'"; works! (cv_id = 6, chado_properties)
> none of the following terms work:
>   project_description (cv_id = 7, tripal),  analysis_type (cv_id = 27, tripal_analysis), accession (12, feature_property),   blastoutput, fraction_identical ,  variant_of (cv_id = 16, sequence) …, exon, CDS, etc.
>
> I didn't find any term with cvterm_id > 30 that worked (all queries work in psql). So it looked like something is really broken within that table.
>
> Finally I find that:
> $cvtermsql = "SELECT CVT.cvterm_id FROM cvterm AS CVT WHERE CVT.cvterm_id = 29"; works
> and
> $cvtermsql = "SELECT CVT.cvterm_id FROM cvterm AS CVT WHERE CVT.cvterm_id = 30"; doesn't
>
> So it looks like these are the two entries, where 'in between' something breaks:
>
> licebase=> SELECT * from cvterm where cvterm_id >= 29 order by cvterm_id limit 2 ;
> cvterm_id | cv_id |     name      |                                                                                         definition                                                                                          | dbxref_id | is_obsolete | is_relationshiptype
> -----------+-------+---------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-----------+-------------+---------------------
>        29 |     6 | version       | Chado schema version                                                                                                                                                                        |        29 |           0 |                   0
>        30 |    27 | analysis_type | The type of analysis was performed. This value is automatically set by each Tripal Analysis module and should be equal to the module name (e.g. tripal_analysis_blast, tripal_analysis_go). |        30 |           0 |                   0
> (2 rows)
>
> That means we have somehow established the fact that all entries in cvterm with id >=30 are invisible to db_query/pg_query. This is the oddest thing I have ever seen.
>
>
>
>
>
>
>
>
> On Sep 25, 2013, at 9:12 AM, Michael Dondrup wrote:
>
>> Here is the output:
>>
>> Array ( [0] => SELECT CVT.cvterm_id FROM {cvterm} CVT INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id LEFT JOIN {cvtermsynonym} CVTS on CVTS.cvterm_id = CVT.cvterm_id WHERE cv.name = '%s' and (CVT.name = '%s' or CVTS.synonym = '%s') [1] => CDS [2] => )
>>
>> The problem seems to be that db_query doesn't return something sensible, at least db_fetch_object  doesn't seem to know how to make an object out of it.
>>
>> On Sep 24, 2013, at 2:29 PM, Stephen Ficklin wrote:
>>
>>> Hi Michael,
>>>
>>> Would you mind adding this code to line 91 of the
>>> tripal_feature-delete.inc and running it again and tell me what the
>>> output is that you see when you try to delete  a feature of a given type:
>>>
>>> print_r(array($cvtermsql, $seq_type, $cvterm));
>>>
>>> So, the code should look like this:
>>>
>>> // check to make sure the types exists
>>> if ($seq_type) {
>>>   $cvtermsql = "SELECT CVT.cvterm_id
>>>                 FROM {cvterm} CVT
>>>                    INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
>>>                    LEFT JOIN {cvtermsynonym} CVTS on CVTS.cvterm_id =
>>> CVT.cvterm_id
>>>                 WHERE cv.name = '%s' and (CVT.name = '%s' or
>>> CVTS.synonym = '%s')";
>>>   $cvterm = db_fetch_object(db_query($cvtermsql, 'sequence',
>>> $seq_type, $seq_type));
>>>   print_r(array($cvtermsql, $seq_type, $cvterm));
>>>   if (!$cvterm) {
>>>     form_set_error('seq_type', t("The Sequence Ontology (SO) term
>>> selected for the sequence type is not available in the database. Please
>>> check spelling or select another."));
>>>   }
>>> }
>>>
>>> Thanks,
>>> Stephen
>>>
>>> On 9/24/2013 6:05 AM, Michael Dondrup wrote:
>>>> Hi Stephen,
>>>>
>>>> I have now tried to follow this up a bit more, but things seem really weird. I really have no clue what could be going here,
>>>> so I am about to give up, which means I will leave the form validation disabled.
>>>>
>>>> I am trying to use the feature delete form. The error seems is raised in function tripal_feature_delete_form_validate.
>>>>
>>>> The processed SQL sent to db_query is the following:
>>>>
>>>> SELECT CVT.cvterm_id FROM cvterm CVT INNER JOIN cv CV on CVT.cv_id = CV.cv_id LEFT JOIN cvtermsynonym CVTS on CVTS.cvterm_id = CVT.cvterm_id WHERE cv.name = 'sequence' and (CVT.name = 'CDS' or CVTS.synonym = 'CDS')
>>>>
>>>> The result of this query is the following as given by var_dump:
>>>> resource(264) of type (pgsql result)
>>>> or "Resource id #264" via print_r
>>>>
>>>> When I enter the exact SQL via psql using the same user account as the server user, I get a valid result as expected:
>>>>
>>>> licebase=> SELECT CVT.cvterm_id FROM cvterm CVT INNER JOIN cv CV on CVT.cv_id = CV.cv_id LEFT JOIN cvtermsynonym CVTS on CVTS.cvterm_id = CVT.cvterm_id WHERE cv.name = 'sequence' and (CVT.name = 'CDS' or CVTS.synonym = 'CDS')
>>>> licebase-> ;
>>>> cvterm_id
>>>> -----------
>>>>      387
>>>> (1 row)
>>>>
>>>> Also the CV term listing is able to find terms containing CDS, so am really sure it is there.
>>>> I have also checked pg_last_error() and pg_result_status() but there is no error message all together.  By disabling the form validation, I was able to get a delete job submitted, which is running just fine:
>>>> alling: tripal_feature_delete_features(, , CDS, 0, , 159)
>>>> Deleting 56954 features
>>>> Removing orphaned feature pages
>>>> Getting nodes
>>>> Getting chado_feature
>>>> Verifying all chado_feature Entries
>>>> ...
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On Aug 26, 2013, at 5:26 PM, Michael Dondrup wrote:
>>>>
>>>>> Hi Stephen,
>>>>>
>>>>> I tried again, but the error persists. No output in the dblog, nor server logs. Maybe I have fallen victim
>>>>> to some lagacy code, I will check that first.
>>>>>
>>>>> thank you
>>>>> Michael
>>>>>
>>>>> On Aug 26, 2013, at 3:25 PM, Stephen Ficklin wrote:
>>>>>
>>>>>> Hi Michael,
>>>>>>
>>>>>> That is the SQL statement that gets executed in the form validate
>>>>>> function checking to see if the sequence type exists.  So, if that SQL
>>>>>> fails then it gives the error message that you saw (if interested, see
>>>>>> line 72 of the tripal/tripal_feature/includes/tripal_feature-delete.inc
>>>>>> file). You were able to execute the SQL just fine through psql, so I'm
>>>>>> not sure why it would have failed inside of Tripal. It's the same SQL
>>>>>> statement.  The only thing I can think of is that the term may have been
>>>>>> misspelled?
>>>>>>
>>>>>> Are there any error messages in your Drupal 'recent logs'?
>>>>>>
>>>>>> Stephen
>>>>>>
>>>>>> On 8/26/2013 9:19 AM, Michael Dondrup wrote:
>>>>>>> Hi,
>>>>>>> the output is
>>>>>>> 283 and 285. So they seem to be there. Also, SELECT count(*) FROM cvterm
>>>>>>> gives 4544.
>>>>>>>
>>>>>>> also:
>>>>>>>
>>>>>>> licebase=> SELECT CVT.*
>>>>>>> FROM cvterm CVT
>>>>>>> INNER JOIN cv CV ON CVT.cv_id = CV.cv_id
>>>>>>> LEFT JOIN cvtermsynonym CVTS ON CVTS.cvterm_id = CVT.cvterm_id
>>>>>>> WHERE cv.name = 'sequence' AND (CVT.name = 'match' or CVTS.synonym =
>>>>>>> 'match')
>>>>>>>
>>>>>>> cvterm_id | cv_id | name  |                                                               definition                                                                | dbxref_id | is_obsolete | is_relationshiptype
>>>>>>> -----------+-------+-------+-----------------------------------------------------------------------------------------------------------------------------------------+-----------+-------------+---------------------
>>>>>>>     285 |    16 | match | A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4. [SO:ke] |       321 |           0 |                   0
>>>>>>> (1 row)
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Aug 26, 2013, at 2:53 PM, Stephen Ficklin wrote:
>>>>>>>
>>>>>>>> Hi Michael,
>>>>>>>>
>>>>>>>> I tested deleting features of type 'match' and then 'match_part' on my
>>>>>>>> end without any troubles.   Can you run these SQL statements and tell me
>>>>>>>> what you get:
>>>>>>>>
>>>>>>>>
>>>>>>>> SELECT CVT.cvterm_id
>>>>>>>> FROM cvterm CVT
>>>>>>>> INNER JOIN cv CV ON CVT.cv_id = CV.cv_id
>>>>>>>> LEFT JOIN cvtermsynonym CVTS ON CVTS.cvterm_id = CVT.cvterm_id
>>>>>>>> WHERE cv.name = 'sequence' AND (CVT.name = 'match' or CVTS.synonym =
>>>>>>>> 'match')
>>>>>>>>
>>>>>>>> SELECT CVT.cvterm_id
>>>>>>>> FROM cvterm CVT
>>>>>>>> INNER JOIN cv CV ON CVT.cv_id = CV.cv_id
>>>>>>>> LEFT JOIN cvtermsynonym CVTS ON CVTS.cvterm_id = CVT.cvterm_id
>>>>>>>> WHERE cv.name = 'sequence' AND (CVT.name = 'match_part' or CVTS.synonym
>>>>>>>> = 'match_part')
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Stephen
>>>>>>>>
>>>>>>>> On 8/24/2013 6:27 AM, Michael Dondrup wrote:
>>>>>>>>> Hi again,
>>>>>>>>> I have made a new GFF file of blast results and therefore I am trying to delete all features of
>>>>>>>>> type 'match' and 'match_part' via the Feature->Delete page for a fresh start. I get an error saying
>>>>>>>>> "The Sequence Ontology (SO) term selected for the sequence type is not available in the database. Please check spelling or select another."
>>>>>>>>> for both types, but I can see the features of this type in the feature view. The delete feature option works for a list of Feature Names entered into the
>>>>>>>>> text area of the same page.
>>>>>>>>>
>>>>>>>>> Regards
>>>>>>>>> Michael
>>>>>>>>>
>>>>>>>>> ------------------------------------------------------------------------------
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Re: [Gmod-tripal-devel] Slight problem with deleting features.

Stephen Ficklin-2
Hi Michael,

I think I see what is wrong.  Can you do the following:

1) Switch your change of pg_pconnect back to pg_connect in the Drupal code
2) Edit line 90 of the tripal_feature-delete.inc, and change the
function call of 'db_query' to 'chado_query'.

Can you let me know if that fixes your problem?

Thanks,
Stephen


On 9/25/2013 7:37 AM, Michael Dondrup wrote:

> And another follow up. I  googled for "pg_query weird" and this turned up as second hit:
>
> http://stackoverflow.com/questions/4340775/pg-query-seems-to-not-execute-queries-in-a-loop
> So, without knowing exactly why, I changed drupal/includes/database.pgsql.inc, line 78
>
>   $connection = @pg_connect($conn_string);
> to: $connection = @pg_pconnect($conn_string);
>
> So this seems to be more of a PHP Postgres connection bug, but I have no idea why this change fixes things, and
> what else might be broken now.
>
> Best
> Michael
>
>
> On Sep 25, 2013, at 11:58 AM, Michael Dondrup wrote:
>
>> I thought must have smth to do with the query SQL. I have tried several more simple queries to see if they work.
>>
>> So, I thought it might have something to do with the string literal, but it doesn't.
>> Now it's getting really weird ('works' means the query returns  non-empty result):
>>
>>     $cvtermsql = "SELECT CVT.cvterm_id FROM cvterm AS CVT WHERE CVT.name = 'glass'"; works! (cv_id = 2, local)
>>     $cvtermsql = "SELECT CVT.cvterm_id FROM cvterm AS CVT WHERE CVT.name = 'version'"; works! (cv_id = 6, chado_properties)
>> none of the following terms work:
>>    project_description (cv_id = 7, tripal),  analysis_type (cv_id = 27, tripal_analysis), accession (12, feature_property),   blastoutput, fraction_identical ,  variant_of (cv_id = 16, sequence) …, exon, CDS, etc.
>>
>> I didn't find any term with cvterm_id > 30 that worked (all queries work in psql). So it looked like something is really broken within that table.
>>
>> Finally I find that:
>> $cvtermsql = "SELECT CVT.cvterm_id FROM cvterm AS CVT WHERE CVT.cvterm_id = 29"; works
>> and
>> $cvtermsql = "SELECT CVT.cvterm_id FROM cvterm AS CVT WHERE CVT.cvterm_id = 30"; doesn't
>>
>> So it looks like these are the two entries, where 'in between' something breaks:
>>
>> licebase=> SELECT * from cvterm where cvterm_id >= 29 order by cvterm_id limit 2 ;
>> cvterm_id | cv_id |     name      |                                                                                         definition                                                                                          | dbxref_id | is_obsolete | is_relationshiptype
>> -----------+-------+---------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-----------+-------------+---------------------
>>         29 |     6 | version       | Chado schema version                                                                                                                                                                        |        29 |           0 |                   0
>>         30 |    27 | analysis_type | The type of analysis was performed. This value is automatically set by each Tripal Analysis module and should be equal to the module name (e.g. tripal_analysis_blast, tripal_analysis_go). |        30 |           0 |                   0
>> (2 rows)
>>
>> That means we have somehow established the fact that all entries in cvterm with id >=30 are invisible to db_query/pg_query. This is the oddest thing I have ever seen.
>>
>>
>>
>>
>>
>>
>>
>>
>> On Sep 25, 2013, at 9:12 AM, Michael Dondrup wrote:
>>
>>> Here is the output:
>>>
>>> Array ( [0] => SELECT CVT.cvterm_id FROM {cvterm} CVT INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id LEFT JOIN {cvtermsynonym} CVTS on CVTS.cvterm_id = CVT.cvterm_id WHERE cv.name = '%s' and (CVT.name = '%s' or CVTS.synonym = '%s') [1] => CDS [2] => )
>>>
>>> The problem seems to be that db_query doesn't return something sensible, at least db_fetch_object  doesn't seem to know how to make an object out of it.
>>>
>>> On Sep 24, 2013, at 2:29 PM, Stephen Ficklin wrote:
>>>
>>>> Hi Michael,
>>>>
>>>> Would you mind adding this code to line 91 of the
>>>> tripal_feature-delete.inc and running it again and tell me what the
>>>> output is that you see when you try to delete  a feature of a given type:
>>>>
>>>> print_r(array($cvtermsql, $seq_type, $cvterm));
>>>>
>>>> So, the code should look like this:
>>>>
>>>> // check to make sure the types exists
>>>> if ($seq_type) {
>>>>    $cvtermsql = "SELECT CVT.cvterm_id
>>>>                  FROM {cvterm} CVT
>>>>                     INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
>>>>                     LEFT JOIN {cvtermsynonym} CVTS on CVTS.cvterm_id =
>>>> CVT.cvterm_id
>>>>                  WHERE cv.name = '%s' and (CVT.name = '%s' or
>>>> CVTS.synonym = '%s')";
>>>>    $cvterm = db_fetch_object(db_query($cvtermsql, 'sequence',
>>>> $seq_type, $seq_type));
>>>>    print_r(array($cvtermsql, $seq_type, $cvterm));
>>>>    if (!$cvterm) {
>>>>      form_set_error('seq_type', t("The Sequence Ontology (SO) term
>>>> selected for the sequence type is not available in the database. Please
>>>> check spelling or select another."));
>>>>    }
>>>> }
>>>>
>>>> Thanks,
>>>> Stephen
>>>>
>>>> On 9/24/2013 6:05 AM, Michael Dondrup wrote:
>>>>> Hi Stephen,
>>>>>
>>>>> I have now tried to follow this up a bit more, but things seem really weird. I really have no clue what could be going here,
>>>>> so I am about to give up, which means I will leave the form validation disabled.
>>>>>
>>>>> I am trying to use the feature delete form. The error seems is raised in function tripal_feature_delete_form_validate.
>>>>>
>>>>> The processed SQL sent to db_query is the following:
>>>>>
>>>>> SELECT CVT.cvterm_id FROM cvterm CVT INNER JOIN cv CV on CVT.cv_id = CV.cv_id LEFT JOIN cvtermsynonym CVTS on CVTS.cvterm_id = CVT.cvterm_id WHERE cv.name = 'sequence' and (CVT.name = 'CDS' or CVTS.synonym = 'CDS')
>>>>>
>>>>> The result of this query is the following as given by var_dump:
>>>>> resource(264) of type (pgsql result)
>>>>> or "Resource id #264" via print_r
>>>>>
>>>>> When I enter the exact SQL via psql using the same user account as the server user, I get a valid result as expected:
>>>>>
>>>>> licebase=> SELECT CVT.cvterm_id FROM cvterm CVT INNER JOIN cv CV on CVT.cv_id = CV.cv_id LEFT JOIN cvtermsynonym CVTS on CVTS.cvterm_id = CVT.cvterm_id WHERE cv.name = 'sequence' and (CVT.name = 'CDS' or CVTS.synonym = 'CDS')
>>>>> licebase-> ;
>>>>> cvterm_id
>>>>> -----------
>>>>>       387
>>>>> (1 row)
>>>>>
>>>>> Also the CV term listing is able to find terms containing CDS, so am really sure it is there.
>>>>> I have also checked pg_last_error() and pg_result_status() but there is no error message all together.  By disabling the form validation, I was able to get a delete job submitted, which is running just fine:
>>>>> alling: tripal_feature_delete_features(, , CDS, 0, , 159)
>>>>> Deleting 56954 features
>>>>> Removing orphaned feature pages
>>>>> Getting nodes
>>>>> Getting chado_feature
>>>>> Verifying all chado_feature Entries
>>>>> ...
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Aug 26, 2013, at 5:26 PM, Michael Dondrup wrote:
>>>>>
>>>>>> Hi Stephen,
>>>>>>
>>>>>> I tried again, but the error persists. No output in the dblog, nor server logs. Maybe I have fallen victim
>>>>>> to some lagacy code, I will check that first.
>>>>>>
>>>>>> thank you
>>>>>> Michael
>>>>>>
>>>>>> On Aug 26, 2013, at 3:25 PM, Stephen Ficklin wrote:
>>>>>>
>>>>>>> Hi Michael,
>>>>>>>
>>>>>>> That is the SQL statement that gets executed in the form validate
>>>>>>> function checking to see if the sequence type exists.  So, if that SQL
>>>>>>> fails then it gives the error message that you saw (if interested, see
>>>>>>> line 72 of the tripal/tripal_feature/includes/tripal_feature-delete.inc
>>>>>>> file). You were able to execute the SQL just fine through psql, so I'm
>>>>>>> not sure why it would have failed inside of Tripal. It's the same SQL
>>>>>>> statement.  The only thing I can think of is that the term may have been
>>>>>>> misspelled?
>>>>>>>
>>>>>>> Are there any error messages in your Drupal 'recent logs'?
>>>>>>>
>>>>>>> Stephen
>>>>>>>
>>>>>>> On 8/26/2013 9:19 AM, Michael Dondrup wrote:
>>>>>>>> Hi,
>>>>>>>> the output is
>>>>>>>> 283 and 285. So they seem to be there. Also, SELECT count(*) FROM cvterm
>>>>>>>> gives 4544.
>>>>>>>>
>>>>>>>> also:
>>>>>>>>
>>>>>>>> licebase=> SELECT CVT.*
>>>>>>>> FROM cvterm CVT
>>>>>>>> INNER JOIN cv CV ON CVT.cv_id = CV.cv_id
>>>>>>>> LEFT JOIN cvtermsynonym CVTS ON CVTS.cvterm_id = CVT.cvterm_id
>>>>>>>> WHERE cv.name = 'sequence' AND (CVT.name = 'match' or CVTS.synonym =
>>>>>>>> 'match')
>>>>>>>>
>>>>>>>> cvterm_id | cv_id | name  |                                                               definition                                                                | dbxref_id | is_obsolete | is_relationshiptype
>>>>>>>> -----------+-------+-------+-----------------------------------------------------------------------------------------------------------------------------------------+-----------+-------------+---------------------
>>>>>>>>      285 |    16 | match | A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4. [SO:ke] |       321 |           0 |                   0
>>>>>>>> (1 row)
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On Aug 26, 2013, at 2:53 PM, Stephen Ficklin wrote:
>>>>>>>>
>>>>>>>>> Hi Michael,
>>>>>>>>>
>>>>>>>>> I tested deleting features of type 'match' and then 'match_part' on my
>>>>>>>>> end without any troubles.   Can you run these SQL statements and tell me
>>>>>>>>> what you get:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> SELECT CVT.cvterm_id
>>>>>>>>> FROM cvterm CVT
>>>>>>>>> INNER JOIN cv CV ON CVT.cv_id = CV.cv_id
>>>>>>>>> LEFT JOIN cvtermsynonym CVTS ON CVTS.cvterm_id = CVT.cvterm_id
>>>>>>>>> WHERE cv.name = 'sequence' AND (CVT.name = 'match' or CVTS.synonym =
>>>>>>>>> 'match')
>>>>>>>>>
>>>>>>>>> SELECT CVT.cvterm_id
>>>>>>>>> FROM cvterm CVT
>>>>>>>>> INNER JOIN cv CV ON CVT.cv_id = CV.cv_id
>>>>>>>>> LEFT JOIN cvtermsynonym CVTS ON CVTS.cvterm_id = CVT.cvterm_id
>>>>>>>>> WHERE cv.name = 'sequence' AND (CVT.name = 'match_part' or CVTS.synonym
>>>>>>>>> = 'match_part')
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>> Stephen
>>>>>>>>>
>>>>>>>>> On 8/24/2013 6:27 AM, Michael Dondrup wrote:
>>>>>>>>>> Hi again,
>>>>>>>>>> I have made a new GFF file of blast results and therefore I am trying to delete all features of
>>>>>>>>>> type 'match' and 'match_part' via the Feature->Delete page for a fresh start. I get an error saying
>>>>>>>>>> "The Sequence Ontology (SO) term selected for the sequence type is not available in the database. Please check spelling or select another."
>>>>>>>>>> for both types, but I can see the features of this type in the feature view. The delete feature option works for a list of Feature Names entered into the
>>>>>>>>>> text area of the same page.
>>>>>>>>>>
>>>>>>>>>> Regards
>>>>>>>>>> Michael
>>>>>>>>>>
>>>>>>>>>> ------------------------------------------------------------------------------
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Re: [Gmod-tripal-devel] Slight problem with deleting features.

Michael Dondrup-3
Hi Stephen,

thank you so much, yes I can confirm that this works.
I edited 1), restarted the web-server, edited 2) and now it works,
I changed line 90 back to "db_query" for verification, and it doesn't work.
(It seemed just strange that  db_query would still see the first 29 rows of the table and that it works for you, but maybe this
depends on what the last used connection was?)

Michael


On Sep 25, 2013, at 2:59 PM, Stephen Ficklin wrote:

> Hi Michael,
>
> I think I see what is wrong.  Can you do the following:
>
> 1) Switch your change of pg_pconnect back to pg_connect in the Drupal code
> 2) Edit line 90 of the tripal_feature-delete.inc, and change the
> function call of 'db_query' to 'chado_query'.
>
> Can you let me know if that fixes your problem?
>
> Thanks,
> Stephen
>
>
> On 9/25/2013 7:37 AM, Michael Dondrup wrote:
>> And another follow up. I  googled for "pg_query weird" and this turned up as second hit:
>>
>> http://stackoverflow.com/questions/4340775/pg-query-seems-to-not-execute-queries-in-a-loop
>> So, without knowing exactly why, I changed drupal/includes/database.pgsql.inc, line 78
>>
>>  $connection = @pg_connect($conn_string);
>> to: $connection = @pg_pconnect($conn_string);
>>
>> So this seems to be more of a PHP Postgres connection bug, but I have no idea why this change fixes things, and
>> what else might be broken now.
>>
>> Best
>> Michael
>>
>>
>> On Sep 25, 2013, at 11:58 AM, Michael Dondrup wrote:
>>
>>> I thought must have smth to do with the query SQL. I have tried several more simple queries to see if they work.
>>>
>>> So, I thought it might have something to do with the string literal, but it doesn't.
>>> Now it's getting really weird ('works' means the query returns  non-empty result):
>>>
>>>    $cvtermsql = "SELECT CVT.cvterm_id FROM cvterm AS CVT WHERE CVT.name = 'glass'"; works! (cv_id = 2, local)
>>>    $cvtermsql = "SELECT CVT.cvterm_id FROM cvterm AS CVT WHERE CVT.name = 'version'"; works! (cv_id = 6, chado_properties)
>>> none of the following terms work:
>>>   project_description (cv_id = 7, tripal),  analysis_type (cv_id = 27, tripal_analysis), accession (12, feature_property),   blastoutput, fraction_identical ,  variant_of (cv_id = 16, sequence) …, exon, CDS, etc.
>>>
>>> I didn't find any term with cvterm_id > 30 that worked (all queries work in psql). So it looked like something is really broken within that table.
>>>
>>> Finally I find that:
>>> $cvtermsql = "SELECT CVT.cvterm_id FROM cvterm AS CVT WHERE CVT.cvterm_id = 29"; works
>>> and
>>> $cvtermsql = "SELECT CVT.cvterm_id FROM cvterm AS CVT WHERE CVT.cvterm_id = 30"; doesn't
>>>
>>> So it looks like these are the two entries, where 'in between' something breaks:
>>>
>>> licebase=> SELECT * from cvterm where cvterm_id >= 29 order by cvterm_id limit 2 ;
>>> cvterm_id | cv_id |     name      |                                                                                         definition                                                                                          | dbxref_id | is_obsolete | is_relationshiptype
>>> -----------+-------+---------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-----------+-------------+---------------------
>>>        29 |     6 | version       | Chado schema version                                                                                                                                                                        |        29 |           0 |                   0
>>>        30 |    27 | analysis_type | The type of analysis was performed. This value is automatically set by each Tripal Analysis module and should be equal to the module name (e.g. tripal_analysis_blast, tripal_analysis_go). |        30 |           0 |                   0
>>> (2 rows)
>>>
>>> That means we have somehow established the fact that all entries in cvterm with id >=30 are invisible to db_query/pg_query. This is the oddest thing I have ever seen.
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> On Sep 25, 2013, at 9:12 AM, Michael Dondrup wrote:
>>>
>>>> Here is the output:
>>>>
>>>> Array ( [0] => SELECT CVT.cvterm_id FROM {cvterm} CVT INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id LEFT JOIN {cvtermsynonym} CVTS on CVTS.cvterm_id = CVT.cvterm_id WHERE cv.name = '%s' and (CVT.name = '%s' or CVTS.synonym = '%s') [1] => CDS [2] => )
>>>>
>>>> The problem seems to be that db_query doesn't return something sensible, at least db_fetch_object  doesn't seem to know how to make an object out of it.
>>>>
>>>> On Sep 24, 2013, at 2:29 PM, Stephen Ficklin wrote:
>>>>
>>>>> Hi Michael,
>>>>>
>>>>> Would you mind adding this code to line 91 of the
>>>>> tripal_feature-delete.inc and running it again and tell me what the
>>>>> output is that you see when you try to delete  a feature of a given type:
>>>>>
>>>>> print_r(array($cvtermsql, $seq_type, $cvterm));
>>>>>
>>>>> So, the code should look like this:
>>>>>
>>>>> // check to make sure the types exists
>>>>> if ($seq_type) {
>>>>>   $cvtermsql = "SELECT CVT.cvterm_id
>>>>>                 FROM {cvterm} CVT
>>>>>                    INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
>>>>>                    LEFT JOIN {cvtermsynonym} CVTS on CVTS.cvterm_id =
>>>>> CVT.cvterm_id
>>>>>                 WHERE cv.name = '%s' and (CVT.name = '%s' or
>>>>> CVTS.synonym = '%s')";
>>>>>   $cvterm = db_fetch_object(db_query($cvtermsql, 'sequence',
>>>>> $seq_type, $seq_type));
>>>>>   print_r(array($cvtermsql, $seq_type, $cvterm));
>>>>>   if (!$cvterm) {
>>>>>     form_set_error('seq_type', t("The Sequence Ontology (SO) term
>>>>> selected for the sequence type is not available in the database. Please
>>>>> check spelling or select another."));
>>>>>   }
>>>>> }
>>>>>
>>>>> Thanks,
>>>>> Stephen
>>>>>
>>>>> On 9/24/2013 6:05 AM, Michael Dondrup wrote:
>>>>>> Hi Stephen,
>>>>>>
>>>>>> I have now tried to follow this up a bit more, but things seem really weird. I really have no clue what could be going here,
>>>>>> so I am about to give up, which means I will leave the form validation disabled.
>>>>>>
>>>>>> I am trying to use the feature delete form. The error seems is raised in function tripal_feature_delete_form_validate.
>>>>>>
>>>>>> The processed SQL sent to db_query is the following:
>>>>>>
>>>>>> SELECT CVT.cvterm_id FROM cvterm CVT INNER JOIN cv CV on CVT.cv_id = CV.cv_id LEFT JOIN cvtermsynonym CVTS on CVTS.cvterm_id = CVT.cvterm_id WHERE cv.name = 'sequence' and (CVT.name = 'CDS' or CVTS.synonym = 'CDS')
>>>>>>
>>>>>> The result of this query is the following as given by var_dump:
>>>>>> resource(264) of type (pgsql result)
>>>>>> or "Resource id #264" via print_r
>>>>>>
>>>>>> When I enter the exact SQL via psql using the same user account as the server user, I get a valid result as expected:
>>>>>>
>>>>>> licebase=> SELECT CVT.cvterm_id FROM cvterm CVT INNER JOIN cv CV on CVT.cv_id = CV.cv_id LEFT JOIN cvtermsynonym CVTS on CVTS.cvterm_id = CVT.cvterm_id WHERE cv.name = 'sequence' and (CVT.name = 'CDS' or CVTS.synonym = 'CDS')
>>>>>> licebase-> ;
>>>>>> cvterm_id
>>>>>> -----------
>>>>>>      387
>>>>>> (1 row)
>>>>>>
>>>>>> Also the CV term listing is able to find terms containing CDS, so am really sure it is there.
>>>>>> I have also checked pg_last_error() and pg_result_status() but there is no error message all together.  By disabling the form validation, I was able to get a delete job submitted, which is running just fine:
>>>>>> alling: tripal_feature_delete_features(, , CDS, 0, , 159)
>>>>>> Deleting 56954 features
>>>>>> Removing orphaned feature pages
>>>>>> Getting nodes
>>>>>> Getting chado_feature
>>>>>> Verifying all chado_feature Entries
>>>>>> ...
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Aug 26, 2013, at 5:26 PM, Michael Dondrup wrote:
>>>>>>
>>>>>>> Hi Stephen,
>>>>>>>
>>>>>>> I tried again, but the error persists. No output in the dblog, nor server logs. Maybe I have fallen victim
>>>>>>> to some lagacy code, I will check that first.
>>>>>>>
>>>>>>> thank you
>>>>>>> Michael
>>>>>>>
>>>>>>> On Aug 26, 2013, at 3:25 PM, Stephen Ficklin wrote:
>>>>>>>
>>>>>>>> Hi Michael,
>>>>>>>>
>>>>>>>> That is the SQL statement that gets executed in the form validate
>>>>>>>> function checking to see if the sequence type exists.  So, if that SQL
>>>>>>>> fails then it gives the error message that you saw (if interested, see
>>>>>>>> line 72 of the tripal/tripal_feature/includes/tripal_feature-delete.inc
>>>>>>>> file). You were able to execute the SQL just fine through psql, so I'm
>>>>>>>> not sure why it would have failed inside of Tripal. It's the same SQL
>>>>>>>> statement.  The only thing I can think of is that the term may have been
>>>>>>>> misspelled?
>>>>>>>>
>>>>>>>> Are there any error messages in your Drupal 'recent logs'?
>>>>>>>>
>>>>>>>> Stephen
>>>>>>>>
>>>>>>>> On 8/26/2013 9:19 AM, Michael Dondrup wrote:
>>>>>>>>> Hi,
>>>>>>>>> the output is
>>>>>>>>> 283 and 285. So they seem to be there. Also, SELECT count(*) FROM cvterm
>>>>>>>>> gives 4544.
>>>>>>>>>
>>>>>>>>> also:
>>>>>>>>>
>>>>>>>>> licebase=> SELECT CVT.*
>>>>>>>>> FROM cvterm CVT
>>>>>>>>> INNER JOIN cv CV ON CVT.cv_id = CV.cv_id
>>>>>>>>> LEFT JOIN cvtermsynonym CVTS ON CVTS.cvterm_id = CVT.cvterm_id
>>>>>>>>> WHERE cv.name = 'sequence' AND (CVT.name = 'match' or CVTS.synonym =
>>>>>>>>> 'match')
>>>>>>>>>
>>>>>>>>> cvterm_id | cv_id | name  |                                                               definition                                                                | dbxref_id | is_obsolete | is_relationshiptype
>>>>>>>>> -----------+-------+-------+-----------------------------------------------------------------------------------------------------------------------------------------+-----------+-------------+---------------------
>>>>>>>>>     285 |    16 | match | A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4. [SO:ke] |       321 |           0 |                   0
>>>>>>>>> (1 row)
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Aug 26, 2013, at 2:53 PM, Stephen Ficklin wrote:
>>>>>>>>>
>>>>>>>>>> Hi Michael,
>>>>>>>>>>
>>>>>>>>>> I tested deleting features of type 'match' and then 'match_part' on my
>>>>>>>>>> end without any troubles.   Can you run these SQL statements and tell me
>>>>>>>>>> what you get:
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> SELECT CVT.cvterm_id
>>>>>>>>>> FROM cvterm CVT
>>>>>>>>>> INNER JOIN cv CV ON CVT.cv_id = CV.cv_id
>>>>>>>>>> LEFT JOIN cvtermsynonym CVTS ON CVTS.cvterm_id = CVT.cvterm_id
>>>>>>>>>> WHERE cv.name = 'sequence' AND (CVT.name = 'match' or CVTS.synonym =
>>>>>>>>>> 'match')
>>>>>>>>>>
>>>>>>>>>> SELECT CVT.cvterm_id
>>>>>>>>>> FROM cvterm CVT
>>>>>>>>>> INNER JOIN cv CV ON CVT.cv_id = CV.cv_id
>>>>>>>>>> LEFT JOIN cvtermsynonym CVTS ON CVTS.cvterm_id = CVT.cvterm_id
>>>>>>>>>> WHERE cv.name = 'sequence' AND (CVT.name = 'match_part' or CVTS.synonym
>>>>>>>>>> = 'match_part')
>>>>>>>>>>
>>>>>>>>>> Thanks,
>>>>>>>>>> Stephen
>>>>>>>>>>
>>>>>>>>>> On 8/24/2013 6:27 AM, Michael Dondrup wrote:
>>>>>>>>>>> Hi again,
>>>>>>>>>>> I have made a new GFF file of blast results and therefore I am trying to delete all features of
>>>>>>>>>>> type 'match' and 'match_part' via the Feature->Delete page for a fresh start. I get an error saying
>>>>>>>>>>> "The Sequence Ontology (SO) term selected for the sequence type is not available in the database. Please check spelling or select another."
>>>>>>>>>>> for both types, but I can see the features of this type in the feature view. The delete feature option works for a list of Feature Names entered into the
>>>>>>>>>>> text area of the same page.
>>>>>>>>>>>
>>>>>>>>>>> Regards
>>>>>>>>>>> Michael
>>>>>>>>>>>
>>>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>>>> Introducing Performance Central, a new site from SourceForge and
>>>>>>>>>>> AppDynamics. Performance Central is your source for news, insights,
>>>>>>>>>>> analysis and resources for efficient Application Performance Management.
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>>>>>>>>>>> _______________________________________________
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>>>>>>>> ------------------------------------------------------------------------------
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>>>>>>>> _______________________________________________
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>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>>>>>
>>>>> ------------------------------------------------------------------------------
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>
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Re: [Gmod-tripal-devel] Slight problem with deleting features.

Stephen Ficklin-2
Oh good. I'm glad that fixed it.  I have committed the code fix to the
development branch 6.x-1.x

Thanks,
Stephen

On 9/25/2013 9:14 AM, Michael Dondrup wrote:

> Hi Stephen,
>
> thank you so much, yes I can confirm that this works.
> I edited 1), restarted the web-server, edited 2) and now it works,
> I changed line 90 back to "db_query" for verification, and it doesn't work.
> (It seemed just strange that  db_query would still see the first 29 rows of the table and that it works for you, but maybe this
> depends on what the last used connection was?)
>
> Michael
>
>
> On Sep 25, 2013, at 2:59 PM, Stephen Ficklin wrote:
>
>> Hi Michael,
>>
>> I think I see what is wrong.  Can you do the following:
>>
>> 1) Switch your change of pg_pconnect back to pg_connect in the Drupal code
>> 2) Edit line 90 of the tripal_feature-delete.inc, and change the
>> function call of 'db_query' to 'chado_query'.
>>
>> Can you let me know if that fixes your problem?
>>
>> Thanks,
>> Stephen
>>
>>
>> On 9/25/2013 7:37 AM, Michael Dondrup wrote:
>>> And another follow up. I  googled for "pg_query weird" and this turned up as second hit:
>>>
>>> http://stackoverflow.com/questions/4340775/pg-query-seems-to-not-execute-queries-in-a-loop
>>> So, without knowing exactly why, I changed drupal/includes/database.pgsql.inc, line 78
>>>
>>>   $connection = @pg_connect($conn_string);
>>> to: $connection = @pg_pconnect($conn_string);
>>>
>>> So this seems to be more of a PHP Postgres connection bug, but I have no idea why this change fixes things, and
>>> what else might be broken now.
>>>
>>> Best
>>> Michael
>>>
>>>
>>> On Sep 25, 2013, at 11:58 AM, Michael Dondrup wrote:
>>>
>>>> I thought must have smth to do with the query SQL. I have tried several more simple queries to see if they work.
>>>>
>>>> So, I thought it might have something to do with the string literal, but it doesn't.
>>>> Now it's getting really weird ('works' means the query returns  non-empty result):
>>>>
>>>>     $cvtermsql = "SELECT CVT.cvterm_id FROM cvterm AS CVT WHERE CVT.name = 'glass'"; works! (cv_id = 2, local)
>>>>     $cvtermsql = "SELECT CVT.cvterm_id FROM cvterm AS CVT WHERE CVT.name = 'version'"; works! (cv_id = 6, chado_properties)
>>>> none of the following terms work:
>>>>    project_description (cv_id = 7, tripal),  analysis_type (cv_id = 27, tripal_analysis), accession (12, feature_property),   blastoutput, fraction_identical ,  variant_of (cv_id = 16, sequence) …, exon, CDS, etc.
>>>>
>>>> I didn't find any term with cvterm_id > 30 that worked (all queries work in psql). So it looked like something is really broken within that table.
>>>>
>>>> Finally I find that:
>>>> $cvtermsql = "SELECT CVT.cvterm_id FROM cvterm AS CVT WHERE CVT.cvterm_id = 29"; works
>>>> and
>>>> $cvtermsql = "SELECT CVT.cvterm_id FROM cvterm AS CVT WHERE CVT.cvterm_id = 30"; doesn't
>>>>
>>>> So it looks like these are the two entries, where 'in between' something breaks:
>>>>
>>>> licebase=> SELECT * from cvterm where cvterm_id >= 29 order by cvterm_id limit 2 ;
>>>> cvterm_id | cv_id |     name      |                                                                                         definition                                                                                          | dbxref_id | is_obsolete | is_relationshiptype
>>>> -----------+-------+---------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-----------+-------------+---------------------
>>>>         29 |     6 | version       | Chado schema version                                                                                                                                                                        |        29 |           0 |                   0
>>>>         30 |    27 | analysis_type | The type of analysis was performed. This value is automatically set by each Tripal Analysis module and should be equal to the module name (e.g. tripal_analysis_blast, tripal_analysis_go). |        30 |           0 |                   0
>>>> (2 rows)
>>>>
>>>> That means we have somehow established the fact that all entries in cvterm with id >=30 are invisible to db_query/pg_query. This is the oddest thing I have ever seen.
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On Sep 25, 2013, at 9:12 AM, Michael Dondrup wrote:
>>>>
>>>>> Here is the output:
>>>>>
>>>>> Array ( [0] => SELECT CVT.cvterm_id FROM {cvterm} CVT INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id LEFT JOIN {cvtermsynonym} CVTS on CVTS.cvterm_id = CVT.cvterm_id WHERE cv.name = '%s' and (CVT.name = '%s' or CVTS.synonym = '%s') [1] => CDS [2] => )
>>>>>
>>>>> The problem seems to be that db_query doesn't return something sensible, at least db_fetch_object  doesn't seem to know how to make an object out of it.
>>>>>
>>>>> On Sep 24, 2013, at 2:29 PM, Stephen Ficklin wrote:
>>>>>
>>>>>> Hi Michael,
>>>>>>
>>>>>> Would you mind adding this code to line 91 of the
>>>>>> tripal_feature-delete.inc and running it again and tell me what the
>>>>>> output is that you see when you try to delete  a feature of a given type:
>>>>>>
>>>>>> print_r(array($cvtermsql, $seq_type, $cvterm));
>>>>>>
>>>>>> So, the code should look like this:
>>>>>>
>>>>>> // check to make sure the types exists
>>>>>> if ($seq_type) {
>>>>>>    $cvtermsql = "SELECT CVT.cvterm_id
>>>>>>                  FROM {cvterm} CVT
>>>>>>                     INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
>>>>>>                     LEFT JOIN {cvtermsynonym} CVTS on CVTS.cvterm_id =
>>>>>> CVT.cvterm_id
>>>>>>                  WHERE cv.name = '%s' and (CVT.name = '%s' or
>>>>>> CVTS.synonym = '%s')";
>>>>>>    $cvterm = db_fetch_object(db_query($cvtermsql, 'sequence',
>>>>>> $seq_type, $seq_type));
>>>>>>    print_r(array($cvtermsql, $seq_type, $cvterm));
>>>>>>    if (!$cvterm) {
>>>>>>      form_set_error('seq_type', t("The Sequence Ontology (SO) term
>>>>>> selected for the sequence type is not available in the database. Please
>>>>>> check spelling or select another."));
>>>>>>    }
>>>>>> }
>>>>>>
>>>>>> Thanks,
>>>>>> Stephen
>>>>>>
>>>>>> On 9/24/2013 6:05 AM, Michael Dondrup wrote:
>>>>>>> Hi Stephen,
>>>>>>>
>>>>>>> I have now tried to follow this up a bit more, but things seem really weird. I really have no clue what could be going here,
>>>>>>> so I am about to give up, which means I will leave the form validation disabled.
>>>>>>>
>>>>>>> I am trying to use the feature delete form. The error seems is raised in function tripal_feature_delete_form_validate.
>>>>>>>
>>>>>>> The processed SQL sent to db_query is the following:
>>>>>>>
>>>>>>> SELECT CVT.cvterm_id FROM cvterm CVT INNER JOIN cv CV on CVT.cv_id = CV.cv_id LEFT JOIN cvtermsynonym CVTS on CVTS.cvterm_id = CVT.cvterm_id WHERE cv.name = 'sequence' and (CVT.name = 'CDS' or CVTS.synonym = 'CDS')
>>>>>>>
>>>>>>> The result of this query is the following as given by var_dump:
>>>>>>> resource(264) of type (pgsql result)
>>>>>>> or "Resource id #264" via print_r
>>>>>>>
>>>>>>> When I enter the exact SQL via psql using the same user account as the server user, I get a valid result as expected:
>>>>>>>
>>>>>>> licebase=> SELECT CVT.cvterm_id FROM cvterm CVT INNER JOIN cv CV on CVT.cv_id = CV.cv_id LEFT JOIN cvtermsynonym CVTS on CVTS.cvterm_id = CVT.cvterm_id WHERE cv.name = 'sequence' and (CVT.name = 'CDS' or CVTS.synonym = 'CDS')
>>>>>>> licebase-> ;
>>>>>>> cvterm_id
>>>>>>> -----------
>>>>>>>       387
>>>>>>> (1 row)
>>>>>>>
>>>>>>> Also the CV term listing is able to find terms containing CDS, so am really sure it is there.
>>>>>>> I have also checked pg_last_error() and pg_result_status() but there is no error message all together.  By disabling the form validation, I was able to get a delete job submitted, which is running just fine:
>>>>>>> alling: tripal_feature_delete_features(, , CDS, 0, , 159)
>>>>>>> Deleting 56954 features
>>>>>>> Removing orphaned feature pages
>>>>>>> Getting nodes
>>>>>>> Getting chado_feature
>>>>>>> Verifying all chado_feature Entries
>>>>>>> ...
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Aug 26, 2013, at 5:26 PM, Michael Dondrup wrote:
>>>>>>>
>>>>>>>> Hi Stephen,
>>>>>>>>
>>>>>>>> I tried again, but the error persists. No output in the dblog, nor server logs. Maybe I have fallen victim
>>>>>>>> to some lagacy code, I will check that first.
>>>>>>>>
>>>>>>>> thank you
>>>>>>>> Michael
>>>>>>>>
>>>>>>>> On Aug 26, 2013, at 3:25 PM, Stephen Ficklin wrote:
>>>>>>>>
>>>>>>>>> Hi Michael,
>>>>>>>>>
>>>>>>>>> That is the SQL statement that gets executed in the form validate
>>>>>>>>> function checking to see if the sequence type exists.  So, if that SQL
>>>>>>>>> fails then it gives the error message that you saw (if interested, see
>>>>>>>>> line 72 of the tripal/tripal_feature/includes/tripal_feature-delete.inc
>>>>>>>>> file). You were able to execute the SQL just fine through psql, so I'm
>>>>>>>>> not sure why it would have failed inside of Tripal. It's the same SQL
>>>>>>>>> statement.  The only thing I can think of is that the term may have been
>>>>>>>>> misspelled?
>>>>>>>>>
>>>>>>>>> Are there any error messages in your Drupal 'recent logs'?
>>>>>>>>>
>>>>>>>>> Stephen
>>>>>>>>>
>>>>>>>>> On 8/26/2013 9:19 AM, Michael Dondrup wrote:
>>>>>>>>>> Hi,
>>>>>>>>>> the output is
>>>>>>>>>> 283 and 285. So they seem to be there. Also, SELECT count(*) FROM cvterm
>>>>>>>>>> gives 4544.
>>>>>>>>>>
>>>>>>>>>> also:
>>>>>>>>>>
>>>>>>>>>> licebase=> SELECT CVT.*
>>>>>>>>>> FROM cvterm CVT
>>>>>>>>>> INNER JOIN cv CV ON CVT.cv_id = CV.cv_id
>>>>>>>>>> LEFT JOIN cvtermsynonym CVTS ON CVTS.cvterm_id = CVT.cvterm_id
>>>>>>>>>> WHERE cv.name = 'sequence' AND (CVT.name = 'match' or CVTS.synonym =
>>>>>>>>>> 'match')
>>>>>>>>>>
>>>>>>>>>> cvterm_id | cv_id | name  |                                                               definition                                                                | dbxref_id | is_obsolete | is_relationshiptype
>>>>>>>>>> -----------+-------+-------+-----------------------------------------------------------------------------------------------------------------------------------------+-----------+-------------+---------------------
>>>>>>>>>>      285 |    16 | match | A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4. [SO:ke] |       321 |           0 |                   0
>>>>>>>>>> (1 row)
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Aug 26, 2013, at 2:53 PM, Stephen Ficklin wrote:
>>>>>>>>>>
>>>>>>>>>>> Hi Michael,
>>>>>>>>>>>
>>>>>>>>>>> I tested deleting features of type 'match' and then 'match_part' on my
>>>>>>>>>>> end without any troubles.   Can you run these SQL statements and tell me
>>>>>>>>>>> what you get:
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> SELECT CVT.cvterm_id
>>>>>>>>>>> FROM cvterm CVT
>>>>>>>>>>> INNER JOIN cv CV ON CVT.cv_id = CV.cv_id
>>>>>>>>>>> LEFT JOIN cvtermsynonym CVTS ON CVTS.cvterm_id = CVT.cvterm_id
>>>>>>>>>>> WHERE cv.name = 'sequence' AND (CVT.name = 'match' or CVTS.synonym =
>>>>>>>>>>> 'match')
>>>>>>>>>>>
>>>>>>>>>>> SELECT CVT.cvterm_id
>>>>>>>>>>> FROM cvterm CVT
>>>>>>>>>>> INNER JOIN cv CV ON CVT.cv_id = CV.cv_id
>>>>>>>>>>> LEFT JOIN cvtermsynonym CVTS ON CVTS.cvterm_id = CVT.cvterm_id
>>>>>>>>>>> WHERE cv.name = 'sequence' AND (CVT.name = 'match_part' or CVTS.synonym
>>>>>>>>>>> = 'match_part')
>>>>>>>>>>>
>>>>>>>>>>> Thanks,
>>>>>>>>>>> Stephen
>>>>>>>>>>>
>>>>>>>>>>> On 8/24/2013 6:27 AM, Michael Dondrup wrote:
>>>>>>>>>>>> Hi again,
>>>>>>>>>>>> I have made a new GFF file of blast results and therefore I am trying to delete all features of
>>>>>>>>>>>> type 'match' and 'match_part' via the Feature->Delete page for a fresh start. I get an error saying
>>>>>>>>>>>> "The Sequence Ontology (SO) term selected for the sequence type is not available in the database. Please check spelling or select another."
>>>>>>>>>>>> for both types, but I can see the features of this type in the feature view. The delete feature option works for a list of Feature Names entered into the
>>>>>>>>>>>> text area of the same page.
>>>>>>>>>>>>
>>>>>>>>>>>> Regards
>>>>>>>>>>>> Michael
>>>>>>>>>>>>
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