From saurav at algodon.tamu.edu Thu Dec 2 03:38:32 2004 From: saurav at algodon.tamu.edu (Saurav Mohanty) Date: Mon Mar 7 01:06:45 2005 Subject: acedb to netscape Message-ID: Hello, If I want to make a link from the Genebank accession number from my Acedb objects to the NCBI website showing the same Accession number with its corresponding data ...then how do I go about it? Some objects in my database has a genebank number.I want the users to be redirected to the NCBI website from my Acebrowser (without leaving my site) feeding in the query to the NCBI website and throwing out the results into my Acebrowser. Can I do it using ?Url tag Pls enlighten me. Thnak you in advance Saurav On -1 xxx -1, it was written: > the document /acedocs/ace97/ACEDB_2_WWW.html > does NOT YET corresponds to the distributed acedb > > upto and including acedb.4_5, use the generic external > call mechanism > > in any class, add a line > Pick_me_to_call Text Text > > and in the object > Pick_me_to_call Mosaic "http:\/\/www.truc.fr/ici/machin.html" > > en cliquant Pick_me_to_call il y a lancement de l'exe > wscripts/Mosaic avec le param "http:\/\/www.truc.fr/ici/machin.html" > > an peut de cette amniere appleler n'importe quoi > text1; nom du script > text2 = ligne de commande du script > > > > -------------------------------------------------------------------------------- > > > ------=_NextPart_000_95b_5aa0_5ae0-- > --- From matthews at greengenes.cit.cornell.edu Fri Dec 3 03:25:32 2004 From: matthews at greengenes.cit.cornell.edu (Dave Matthews) Date: Mon Mar 7 01:06:45 2005 Subject: Ace-MODS urgent help!! Message-ID: <200412022002.iB2K2fmu016548@greengenes.cit.cornell.edu> 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@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 --- From matthews at greengenes.cit.cornell.edu Fri Dec 3 03:25:37 2004 From: matthews at greengenes.cit.cornell.edu (Dave Matthews) Date: Mon Mar 7 01:06:45 2005 Subject: acedb to netscape Message-ID: <200412021753.iB2HrlhK015826@greengenes.cit.cornell.edu> Hi Saurav, As far as I know AceBrowser doesn't normally have a feature to make specific links to external Web databases. We've modified our version of AceBrowser to do this, and the modification is available. See http://www.graingenes.org/acebrowser_mods/ and "Hyperlink AceDB objects to external databases" at http://www.graingenes.org/acebrowser_mods/features.html. This isn't completely supported, as Hugh Edwards has another job now, but we'll do what we can if you have problems. best, - Dave > To: bionet-software-acedb@net.bio.net > From: saurav@algodon.tamu.edu (Saurav Mohanty) > Subject: Re: acedb to netscape > Date: Thu, 2 Dec 2004 08:38:32 +0000 (GMT) > > Hello, > > If I want to make a link from the Genebank accession number from my Acedb > objects to the NCBI website showing the same Accession number with its > corresponding data ...then how do I go about it? > Some objects in my database has a genebank number.I want the users to be > redirected to the NCBI website from my Acebrowser (without leaving my > site) feeding in the query to the NCBI website and throwing out the > results into my Acebrowser. > > Can I do it using ?Url tag > > Pls enlighten me. > > Thnak you in advance > Saurav --- From saurav at algodon.tamu.edu Fri Dec 3 03:25:41 2004 From: saurav at algodon.tamu.edu (Saurav Mohanty) Date: Mon Mar 7 01:06:46 2005 Subject: Ace-MODS urgent help!! References: <200412022002.iB2K2fmu016548@greengenes.cit.cornell.edu> Message-ID: 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@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 > > --- From saurav at algodon.tamu.edu Fri Dec 3 03:25:42 2004 From: saurav at algodon.tamu.edu (Saurav Mohanty) Date: Mon Mar 7 01:06:46 2005 Subject: Ace-MODS urgent help!! References: <200412021753.iB2HrlhK015826@greengenes.cit.cornell.edu> Message-ID: 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 On Thu, 2 Dec 2004, Dave Matthews wrote: > Hi Saurav, > > As far as I know AceBrowser doesn't normally have a feature to make specific > links to external Web databases. We've modified our version of AceBrowser to > do this, and the modification is available. See > http://www.graingenes.org/acebrowser_mods/ and "Hyperlink AceDB objects to > external databases" at > http://www.graingenes.org/acebrowser_mods/features.html. > > This isn't completely supported, as Hugh Edwards has another job now, but > we'll do what we can if you have problems. > > best, > - Dave > > > To: bionet-software-acedb@net.bio.net > > From: saurav@algodon.tamu.edu (Saurav Mohanty) > > Subject: Re: acedb to netscape > > Date: Thu, 2 Dec 2004 08:38:32 +0000 (GMT) > > > > Hello, > > > > If I want to make a link from the Genebank accession number from my Acedb > > objects to the NCBI website showing the same Accession number with its > > corresponding data ...then how do I go about it? > > Some objects in my database has a genebank number.I want the users to be > > redirected to the NCBI website from my Acebrowser (without leaving my > > site) feeding in the query to the NCBI website and throwing out the > > results into my Acebrowser. > > > > Can I do it using ?Url tag > > > > Pls enlighten me. > > > > Thnak you in advance > > Saurav > ---