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Re: [Gusdev-gusdev] Re: plugin
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From: Arnaud K. <ax...@sa...> - 2003-02-24 16:51:18
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Pjm wrote:
> 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.
I think I deleted them, sorry!! Can anyone confirm that they are
generated during the build process ?
Arnaud
>
> 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;
>>
>
>
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