Re: [Gusdev-gusdev] Re: plugin

[Jonathan C. <cra...@sn...>]

Paul-

> when doing a `ga +create GUS::Common::Plugin::LoadPfam --commit`
> it complained because my plugin did not match anything from
> AlgorithmParamKeyType table. This was because it ws empty.
>
> Finding this in the code;
>
>      $RV = { 'str' => 0,
> 	    'flo' => 1,
> 	    'int' => 2,
> 	    'ref' => 3,
> 	    'boo' => 4,
>
> I did this;
>
> insert into AlgorithmParamKeyType
> VALUES (0, 'string',sysdate, 1,1,1,1,1,1,1,1,1,1);
> insert into AlgorithmParamKeyType
> VALUES (1, 'float',sysdate, 1,1,1,1,1,1,1,1,1,1);
> insert into AlgorithmParamKeyType
> VALUES (2, 'integer',sysdate, 1,1,1,1,1,1,1,1,1,1);
> insert into AlgorithmParamKeyType
> VALUES (3, 'ref',sysdate, 1,1,1,1,1,1,1,1,1,1);
> insert into AlgorithmParamKeyType
> VALUES (4, 'boolean',sysdate, 1,1,1,1,1,1,1,1,1,1);

This definitely looks like an omission on my part; I'll look into it and
add a file to the schema create scripts if necessary.

> After doing this I found the original string in ImportPfam describing the flat
> file argument was too big! AlgorithmParamKey.DESCRIPTION
>
> h => ("Flat file containing the release of Pfam to load.  Expects\n" .
>        "\t\t\tthe file containing the annotation and full alignments in Pfam\n" .
>        "\t\t\tformat of all Pfam-A families (called \"Pfam-A.full\" in release
> 5.2)\n" .
>        "\t\t\tThe specified file may be in gzip (.gz) or compressed (.Z) format."),
>
> This string is 280 characters! Does anyone mind if I change the length to 512
> and do a cvs commit?

Hmm, I don't know when this column would have been shortened, but yes, we
can definitely make it larger.  The only thing to remember is that
whenever the schema is modified we also have to modify the appropriate
migration script (in this case the 3.0 -> 3.1 migration script.)  I
haven't created these yet, but will get to it shortly.  So for now just
make sure that you let me know if you've made a schema change so that I
can include it in the script.  The way I've been keeping track of this so
far is by creating items in the SourceForge schema (change request)
tracker; I'll assign them to myself and make the changes but then I'll
have a record of what I've done and why that I can then transfer into the
schema change log.

Jonathan