Thread: [Gusdev-gusdev] Re: plugin

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Steve, Jonathan,

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);

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?

Also, could you pass this on to debbie please, although she may already know?

make step 2 of the conversion guide to include;

  "@ISA = qw(GUS::PluginMgr::Plugin); #defines what is inherited"

Paul.

steve fischer wrote:
> yes, gus 3.0.
> 
> can we set a time for tuesday?  i think an hour will more than do it. 
> we are 5 hours behind you. i get in around 10:30.
> 
> meanwhile, i have attached debbie's notes on how to convert a plugin, 
> and a canonical plugin so you can get a start.
> 
> steve
> 
> pjm wrote:
> 
>> steve fischer wrote:
>>  
>>
>>> paul-
>>>
>>> finally got the GUS grant out the door.
>>>
>>> still waiting for James Cuff to move the gus cvs to sanger.  i sent it
>>> to him more than a week ago.  i just reminded him again today.
>>>
>>> so, early next week will be a good time to go over the plugin stuff.
>>>
>>> i have a meeting monday morning, so maybe tuesday?
>>>
>>> steve
>>>   
>>
>>
>> Tuesday will be good. I have a couple of smaller jobs to do but we are 
>> all keen
>> to get hacking, err, writing code for GUS30!
>>
>> I take it you mean you sent a GUS30 tar ball to James?
>>
>>
>>  
>>
> 
> 
> ------------------------------------------------------------------------
> 
> 1) Give the package name a complete path 
>    e.g.package DoTS::DotsBuild::Plugin::ExtractAndBlockAssemblySequences;
> 
> 2) Give all of our 'use' objects full paths
>    e.g.use GUS::Model::DoTS::AssemblySequence;
>        use CBIL::Bio::SequenceUtils;
> 
> 3) Change 'sub new'
>    a. Copy new from template:
> 
> sub new {
>   my $Class = shift;
>   my $self = {};
>   bless($self,$class);
>   my $usage = 'Extract unprocessed AssembySequences........';
>   my $easycsp =
>     [
>      {o => 'testnumber',
>       t => 'int',
>       h => 'number of iterations for testing',
>      }];
>   $self->initialize({requiredDbVersion => {},
> 		  cvsRevision => '$Revision: 1.6 $', # cvs fills this in!
> 		  cvsTag => '$Name:  $', # cvs fills this in!
> 		  name => ref($m),
> 		  revisionNotes => 'make consistent with GUS 3.0',
> 		  easyCspOptions => $easycsp,
> 		  usage => $usage
> 		 });
>   return $self;
> }
>    b. Replace usage string with string in original usage sub, delete usage sub
> 
>    c. replace easycsp hashes with original EasyCspOptions hash, delete keys 
>       and conform to above model
> 
> 4) put $self = shift at beginning of all subs  
> 
> 5) call all subs with $self->subname (search for & and replace with $self->)
> 
> 6) replace $ctx->{cla}-> with $self->getCla
> 
> 7) replace $ctx->{'self_inv'}->getQueryHandle with $self->getQueryHandle
> 
> 8) use $self->getQueryHandle instead of passing a database handle or using a 
>    global database handle
> 
> 9) avoid use DBI or DbiDatabase
> 
> 10) search for 'new' (instantiating new database objects) and add the full 
>     path for objects e.g. GUS::Model::DoTS::AssemblySequence-> 
>     new( { 'assembly_sequence_id' => $id } );
> 
> 11) use $self->undefPointerCache instead of newObject->undefPointerCache
> 
> 12) substitute 'sub run' for 'sub Run'
> 
> 
> ------------------------------------------------------------------------
> 
> package GUS::Common::Plugin::UpdateGusFromXML;
> 
> @ISA = qw(GUS::PluginMgr::Plugin);
> use strict;
> 
> use FileHandle;
> 
> # ----------------------------------------------------------------------
> # create and initalize new plugin instance.
> 
> sub new {
>   my ($class) = @_;
> 
>   my $self = {};
>   bless($self, $class);
> 
>   my $usage = 'update GUS from an XML file. ("// on newline delimits submits)';
> 
>   my $easycsp =
>     [
>      { h => 'if true then will update the row with new modification data and algorithmInvocation regardless if has changed from the database',
>        t => 'boolean',
>        o => 'refresh',
>      },
>      { h => 'name of file containing XML',
>        t => 'string',
>        d => '-',
>        o => 'filename',
>      },
>     ];
> 
>   $self->initialize({requiredDbVersion => {},
> 		     cvsRevision => '$Revision: 1.8 $', # cvs fills this in!
> 		     cvsTag => '$Name:  $', # cvs fills this in!
> 		     name => ref($self),
> 		     revisionNotes => 'make consistent with GUS 3.0',
> 		     easyCspOptions => $easycsp,
> 		     usage => $usage
> 		 });
> 
>   return $self;
> }
> 
> # ----------------------------------------------------------------------
> # plugin-global variables.
> 
> my $countObjs = 0;
> my $countUpdates = 0;
> 
> # ----------------------------------------------------------------------
> # run method to do the work
> 
> sub run {
>   my $self   = shift;
> 
>   my $RV;
> 
>   my $fh = FileHandle->new('<'.$self->getCla->{'filename'});
>   if ($fh) {
> 
>     $self->logAlert('COMMIT', $self->getCla->{commit} ? 'ON' : 'OFF' );
> 
>     ##testing exitOnFailure...
>     $self->getDb()->setExitOnSQLFailure(0);
> 
>     # process XML file.
>     my @xml;
>     while (<$fh>) {
>       if (/^\/\/\s*$/) {	##"//" on a newline defines entry
> 	$self->process(\@xml) if scalar(@xml) > 1; ##must be at least 3 actually to be valid...
> 	undef @xml;		##reset for the new one...
>       } else {
> 	push(@xml,$_);
>       }
>     }
>     $self->process(\@xml) if scalar(@xml) > 1; ##must be at least 3 actually to be valid...
>     $fh->close;
> 
>     # create, log, and return result string.
>     $RV = join(' ',
> 	       "processed $countObjs objects, inserted",
> 	       $self->getSelfInv->getTotalInserts(),
> 	       'and updated',
> 	       $self->getSelfInv->getTotalUpdates() || 0,
> 	      );
>   }
> 
>   # no file.
>   else {
>     $RV = join(' ',
> 	       'a valid --filename <filename> must be on the commandline',
> 	       $self->getCla->{filename},
> 	       $!);
>   }
> 
>   $self->logAlert('RESULT', $RV);
>   return $RV;
> }
> 
> # ----------------------------------------------------------------------
> # do the real work.
> sub process {
>   my $self    = shift;
>   my($xml) = @_;
> 
>   $self->getSelfInv->parseXML($xml);
>   $self->countChangedObjs($self->getSelfInv);
> 
>   ##now submit the sucker...
>   ##must first remove invocation parent before submitting immediate children
>   $self->getSelfInv->manageTransaction(undef,'begin');
>   foreach my $c ($self->getSelfInv->getAllChildren()) {
>     $c->removeParent($self->getSelfInv);
>     $c->submit(undef,1);
>     $c->setParent($self->getSelfInv); ##add back so can see at the end...
>   }
>   $self->getSelfInv->manageTransaction(undef,'commit');
>   if (!$self->getCla->{commit}) {
>     $self->logAlert('ERROR', "XML that was not committed to the database\n\n");
>     foreach my $c ($self->getSelfInv->getAllChildren()) {
>       $self->logAlert('BAD-XML', $c->toXML());
>     }
>   }
>   $self->getSelfInv->removeAllChildren();
>   $self->getSelfInv->undefPointerCache();
> }
> 
> sub countChangedObjs {
>   my $self = shift;
>   my($par) = @_;
> 
>   foreach my $c ($par->getAllChildren()) {
>     $self->logAlert('DEBUG',
> 	    "Checking to see if has changed attributes\n".$c->toXML()) if $self->getCla->{debug};
>     $countObjs++;
>     $countUpdates++;
>     if (!$self->getCla->{refresh} && !$c->hasChangedAttributes()) {
>       $self->logAlert('DEBUG','There are no changed attributes') if $self->getCla->{debug};
>       $countUpdates--;
>     }
>     $self->countChangedObjs($c);
>   }
> }
> 
> 1;
> 

Thread: [Gusdev-gusdev] Re: plugin

gusdev-gusdev