RE: [Gusdev-gusdev] Problem building WDK on Fedora

[Dave B. <db...@pc...>]

Hey Alberto,

Here is what I have so far.  Sorry I don't have the complete solution but 
I don't have any sort of setup yet on a Postgres instance, I will see what 
I can do about getting that set up on our side for better debugging.

First of all, your assertion here:

> In the "PostgreSQL.java" file we edited:
>
> line 117:
> String alterSql = "alter table " + tableName + " add i varchar(100)";
>
> We changed "number(12)" to "varchar(100)" because in the next line it makes an update and try to insert characters in that field that was "number(12)" then it was only accepting numbers.
   >

The next line you mention (line 123) is

String rownumSql = "update " + tableName + " set i = " + tableName + 
"_sq.nextval";

Now that should evaluate to "update query_result_2 set i = 
query_result_2_sq.nextval"

and query_result_2_sq.nextval is the proper way to call the next value 
in the primary key sequence for that table, right?  So that should 
evaluate to a number, not a string.  I am not sure why it is evaluating to 
"query_result_2_sq" as it seems to be in your code...where did the 
".nextval" go??

Can you make sure that line 123 is what I think it should be above?  Sorry 
to be obtuse about this, but just make sure you are using WDK version 1.1 
or later for this, I remember we made some PostGres upgrades at some point 
and they were all incorporated into 1.1.  (as a side note, we have 1.2 out 
if you want to work with that instead).

Regardless, that column should remain a number, not the string it is 
above.

Let us handle the ResultFactory issue after we solve this one because they 
might be related.  I will continute to investigate.

Dave
>
> In "ResultFactory.java", lines 312 until 346:
>
> In the following error, it assumes the "nextID" variable as being
> "gus.QueryInstance_pkseq" and returns the error because this field should receive a numeric value: we changed the variable to a numeric value (in the script) to test and the data were inserted with success.
>
> [poliana@phytomonas gus_home]$ wdkQuery -model toyModel -query
> RnaIds.ByDbESTLib -params NumEstLibs 6 AssemblyConsistency 80
> Failed executing sql:
> insert into gus.QueryInstance (query_instance_id, query_name, cached,
> session_id, dataset_name, start_time, param0, param1) values
> (gus.QueryInstance_pkseq, 'RnaIds.ByDbESTLib', 1, null, null, now(),
> '6', '80')
>
> org.gusdb.wdk.model.WdkModelException:
> org.postgresql.util.PSQLException: ERROR: relation "gus" does not
> exist


>
> -----------------------------------------------------------------------------------------------------------
> After debugging that, we got this:
>
> [poliana@phytomonas gus_home]$ wdkQuery -model toyModel -query
> RnaIds.ByDbESTLib -params NumEstLibs 6 AssemblyConsistency 80
> 92484435         query_result_2_sq
> 92484471         query_result_2_sq
> 92484523         query_result_2_sq
> 92484578         query_result_2_sq
> 92484601         query_result_2_sq
> 92484678         query_result_2_sq
> 92484682         query_result_2_sq
> 92484686         query_result_2_sq
> 92484695         query_result_2_sq
> 92484703         query_result_2_sq
> 92484708         query_result_2_sq
> 92484710         query_result_2_sq
> 92484731         query_result_2_sq
> 92484741         query_result_2_sq
> 92484752         query_result_2_sq
> 92484755         query_result_2_sq
> 92484758         query_result_2_sq
> 92484764         query_result_2_sq
> 92484767         query_result_2_sq
> 92484768         query_result_2_sq
> 92484772         query_result_2_sq
> 92484779         query_result_2_sq
> 92484780         query_result_2_sq
> 92484801         query_result_2_sq
> 92484835         query_result_2_sq
> 92484836         query_result_2_sq
> 101853404        query_result_2_sq
>
> So... is the latter the expected output for "wdkQuery" ? If so, then looks like we have lot of debugging to do, if not maybe we are just not invoking/using the commands properly... as usual, any further suggestions are greatly appreciated ;-)
>
> Alberto
>
>