Ace-MODS urgent help!!

Saurav Mohanty saurav at algodon.tamu.edu
Fri Dec 3 03:25:41 EST 2004


Hello Dave,

Thanks again for your help.I think I will take my chances and test
everything on a seperate copy of the database.In case of issues   I
would need  further technical clarifications..

thank you 
Saurav

On Thu, 2 Dec 2004, Dave Matthews wrote:

> Hi Saurav,
> 
> Yes, this modification is well tested and quite stable.  But you're right,
> you need some documentation to use it.  What's available is sketchy and
> dispersed.  
> 
> First, you don't have to make any changes in your models.wrm or your .ace
> data.  What you do is create a rule in wspec/markup.pl that is used by
> AceBrowser to parse the data and create the href link if there is a match
> to the rule.  
> 
> This example,
> http://www.graingenes.org/cgi-bin/ace/tree/graingenes?name=BE403741&class=Sequence
> has several links to external databases.  Let's look just at the DB_info
> line.
> 
> The ACEDB data for this is:
> 
> Sequence : "BE403741"
> DB_info External_DB "GenBank" "BE403741"
> 
> AceBrowser has added the href links "[DDBJ|EMBL|GenBank]" according to the
> rule in wspec/markup.pl.
> 
> The model for class Sequence is:
> 
> ?Sequence ...
>           DB_info External_DB Text Text
> 
> The rule in markup.pl is:
> 
> ##########################################
> # Connection to external DB for Sequence #
> ##########################################
> {'root'=> {'cl'=>'Sequence'},
>  'branch' => [{ty=>tg,va=>'DB_info'},
>               {ty=>tg,va=>'External_DB'},
>               {ty=>tx,va=>'GenBank'},
>               {ty=>tx}],
>  'urls' => [{'name'=>'EMBL', 'URL'=>'http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-e+[embl-acc:$keys[0]]'},'GenBankAC',{'name'=>'DDBJ', 'URL'=>'http://getentry.ddbj.nig.ac.jp/cgi-bin/get_entry.pl?$keys[0]'}],
> },
> #
> 
> Documentation on writing these rules is given in
> http://www.acedb.org/Cornell/ace95/nalwww.html#appendix3.  Briefly,
> "cl" means class, "ty" means type, "tg" means tag, "va" means value, and
> "tx" means text.  The value of that final ty=>tx field will be substituted
> in for the variable $keys[0].  
> 
> In this rule, 'GenBankAC' is the name for an URL that is defined in another
> file, externalURLs, which is located in the AceBrowser configuration 
> directory.  The GenBankAC line in this file should currently say:
> GenBankAC:GenBank:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Nucleotide&doptcmdl=GenBank&term=$keys[0]
> 
> Writing these rules is actually easier than it looks, and there are a
> lot of examples in the distributed markup.pl file.
> 
> > 2) is the release stable and has it been tested??If not what type of
> > support can I expect in case of urgent malfunctioning if I decide to
> > incorporate the new set of scripts into my database.
> 
> I would counsel some caution, e.g. setting it up on a test machine first.
> Hugh himself has been able to install it on two other servers but I don't 
> know if anyone has done it using only the instructions provided.
> 
> best,
> - Dave
> 
> > From saurav at algodon.tamu.edu  Thu Dec  2 13:40:52 2004
> > 
> > Hello Dave,
> > 
> > Thank you for your reply.
> > I have some queries reagrding the Ace-Mods
> > 
> > 1) what changes needs to
> > be done in the
> > .ace files slurped by AceDB and to the corresponding class in the 
> > wspec/models.wrm .In short what modifications(tag addition for external
> > Url linking) need to be done to the
> > concerned class defination in the models.wrm to make the whole thing work.
> > 
> > 2) is the release stable and has it been tested??If not what type of
> > support can I expect in case of urgent malfunctioning if I decide to
> > incorporate the new set of scripts into my database.
> > 
> > 
> > 
> > 3)If possible can you please send me just the class definition and one
> > data
> > object of the .ace file of the graingenes database for reference where
> > you have implemented this feature..
> > 
> > 4) Is there any sort of comprehensive documentation..which I guess is not
> > necessary for me  if you can send me just an example as requested in 3
> > ,but anyway
> > necessary for any one who would really like to be completely sure  
> >  Thank you for your help in advance..I would be really thankful of you can
> > help me out of this.
> > 
> > regards
> > Saurav
> 
> 

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