gusdev-gusdev

[GUSDEV] standardizing plugin cmd line args

[Steve F. <sfi...@pc...>]

folks-

there is at least one set of command line args that are used in the 
majority of plugins, those that get the name and version of the 
externalDatabaseRelease to tag the new data with.

many plugins have different names for these args.  here are some:
   --externalDatabase     and    --externalDatabaseVersion
   --externalDb  and -- externalDbRls
etc.

i'm getting a little tired of having to deal w/ the inconsistency.

i propose that we move to a new convention (slowly but surely).   i 
propose that plugins be upgraded to this when we get a chance, and, that 
we do not provide backward compatibility.   it just means a simple 
change to any script or pipeline that calls the plugin.

I think we should have this as the standard argument:
   --externalDatabaseSpec "Genbank|1.0.0"

In other words, we introduce a standard representation of a database 
name and version of the form:
    name|version

The plugin superclass method $self->getExtDbRlsId() will come in two 
forms.   The first would be new.  The second is already supported:
   $self->getExtDbRlsId($externalDatabaseSpec)
   $self->getExtDbRlsId($externalDatabaseName, $externalDatabaseVersion)

The additional advantage of introducing the standard format of 
name|version is that some plugins take two or more extDbRls's on the 
command line, and for each one there needs to be parallel args, one for 
the name and one for the version.   thus, this will simplify many plugin 
args.
   
Unless there are objections, new plugins will use this standard, and old 
ones will be upgraded sooner or later.

steve

Re: [GUSDEV] standardizing plugin cmd line args

[Aaron J. M. <am...@pc...>]

This is nice candy, but doesn't really solve the problem you've  
noticed, which is the non-canonicalization of argument names (-- 
seqTable, --subjectTable, etc. also come to mind).

On Nov 18, 2005, at 12:30 PM, Steve Fischer wrote:

> I think we should have this as the standard argument:
>   --externalDatabaseSpec "Genbank|1.0.0"

So now we can have --extDbSpec, --externalDatabaseSpecification, and  
everything in between.

-Aaron

--
Aaron J. Mackey, Ph.D.
Project Manager, ApiDB Bioinformatics Resource Center
Penn Genomics Institute, University of Pennsylvania
email:  am...@pc...
office: 215-898-1205 (Biology, 212 Goddard Labs)
         215-746-7018 (PCBI, 1428 Blockley Hall)
fax:    215-746-6697 (Penn Genomics Institute)
postal: Penn Genomics Institute
         Goddard Labs 212
         415 S. University Avenue
         Philadelphia, PA  19104-6017

Re: [GUSDEV] standardizing plugin cmd line args

[Steve F. <sfi...@pc...>]

i plan on converting all supported plugins to using 
--externalDatabaseSpec.   from there on out it will be a matter of 
people using the convention when they make a new plugin.



Aaron J. Mackey wrote:

> This is nice candy, but doesn't really solve the problem you've  
> noticed, which is the non-canonicalization of argument names (-- 
> seqTable, --subjectTable, etc. also come to mind).
>
> On Nov 18, 2005, at 12:30 PM, Steve Fischer wrote:
>
>> I think we should have this as the standard argument:
>>   --externalDatabaseSpec "Genbank|1.0.0"
>
>
> So now we can have --extDbSpec, --externalDatabaseSpecification, and  
> everything in between.
>
> -Aaron
>
> -- 
> Aaron J. Mackey, Ph.D.
> Project Manager, ApiDB Bioinformatics Resource Center
> Penn Genomics Institute, University of Pennsylvania
> email:  am...@pc...
> office: 215-898-1205 (Biology, 212 Goddard Labs)
>         215-746-7018 (PCBI, 1428 Blockley Hall)
> fax:    215-746-6697 (Penn Genomics Institute)
> postal: Penn Genomics Institute
>         Goddard Labs 212
>         415 S. University Avenue
>         Philadelphia, PA  19104-6017
>

Re: [GUSDEV] standardizing plugin cmd line args

[Elisabetta M. <man...@pc...>]

Note that there are situations in which more than one ExtDbRelId needs to 
be passed in to the plugin, for different databases: e.g. RefSeq, DBTSS, 
etc. Don't know if the plugins currently in Supported have examples of 
this, but there are certainly plugins that we are writing at CBIL that 
have this and some of these might one day be moved to GUS::Supported.
What should the convention be in this case?
I'm currently using things like:

--refSeqExternalDatabaseSpec
--dbtssExternalDatabaseSpec

etc.
Elisabetta

---

On Fri, 18 Nov 2005, Steve Fischer wrote:

> i plan on converting all supported plugins to using 
> --externalDatabaseSpec.   from there on out it will be a matter of people 
> using the convention when they make a new plugin.
>
>
>
> Aaron J. Mackey wrote:
>
>> This is nice candy, but doesn't really solve the problem you've 
>> noticed, which is the non-canonicalization of argument names (-- 
>> seqTable, --subjectTable, etc. also come to mind).
>> 
>> On Nov 18, 2005, at 12:30 PM, Steve Fischer wrote:
>> 
>>> I think we should have this as the standard argument:
>>>   --externalDatabaseSpec "Genbank|1.0.0"
>> 
>> 
>> So now we can have --extDbSpec, --externalDatabaseSpecification, and 
>> everything in between.
>> 
>> -Aaron
>> 
>> -- 
>> Aaron J. Mackey, Ph.D.
>> Project Manager, ApiDB Bioinformatics Resource Center
>> Penn Genomics Institute, University of Pennsylvania
>> email:  am...@pc...
>> office: 215-898-1205 (Biology, 212 Goddard Labs)
>>         215-746-7018 (PCBI, 1428 Blockley Hall)
>> fax:    215-746-6697 (Penn Genomics Institute)
>> postal: Penn Genomics Institute
>>         Goddard Labs 212
>>         415 S. University Avenue
>>         Philadelphia, PA  19104-6017
>> 
>
>
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Re: [GUSDEV] standardizing plugin cmd line args

[Steve F. <sfi...@pc...>]

yes, that seems fine.   they can take either one value, or they can be 
list arguments

steve

Elisabetta Manduchi wrote:

>
> Note that there are situations in which more than one ExtDbRelId needs 
> to be passed in to the plugin, for different databases: e.g. RefSeq, 
> DBTSS, etc. Don't know if the plugins currently in Supported have 
> examples of this, but there are certainly plugins that we are writing 
> at CBIL that have this and some of these might one day be moved to 
> GUS::Supported.
> What should the convention be in this case?
> I'm currently using things like:
>
> --refSeqExternalDatabaseSpec
> --dbtssExternalDatabaseSpec
>
> etc.
> Elisabetta
>
> ---
>
> On Fri, 18 Nov 2005, Steve Fischer wrote:
>
>> i plan on converting all supported plugins to using 
>> --externalDatabaseSpec.   from there on out it will be a matter of 
>> people using the convention when they make a new plugin.
>>
>>
>>
>> Aaron J. Mackey wrote:
>>
>>> This is nice candy, but doesn't really solve the problem you've 
>>> noticed, which is the non-canonicalization of argument names (-- 
>>> seqTable, --subjectTable, etc. also come to mind).
>>>
>>> On Nov 18, 2005, at 12:30 PM, Steve Fischer wrote:
>>>
>>>> I think we should have this as the standard argument:
>>>>   --externalDatabaseSpec "Genbank|1.0.0"
>>>
>>>
>>>
>>> So now we can have --extDbSpec, --externalDatabaseSpecification, and 
>>> everything in between.
>>>
>>> -Aaron
>>>
>>> -- 
>>> Aaron J. Mackey, Ph.D.
>>> Project Manager, ApiDB Bioinformatics Resource Center
>>> Penn Genomics Institute, University of Pennsylvania
>>> email:  am...@pc...
>>> office: 215-898-1205 (Biology, 212 Goddard Labs)
>>>         215-746-7018 (PCBI, 1428 Blockley Hall)
>>> fax:    215-746-6697 (Penn Genomics Institute)
>>> postal: Penn Genomics Institute
>>>         Goddard Labs 212
>>>         415 S. University Avenue
>>>         Philadelphia, PA  19104-6017
>>>
>>
>>
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