From gbottu at ben.vub.ac.be Tue Aug 29 12:23:26 2006 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Tue, 29 Aug 2006 18:23:26 +0200 Subject: [emboss-dev] Questions about MRS and DbFetch - Checked by AntiVir DEMO version - Message-ID: <20060829162326.GA11317@bigben.ulb.ac.be> Dear developers, I am for the moment struggling to make MRS and DbFetch work as access methods. I installed the bug fixed from the ftp site. MRS works ! But I note that currently you are using the Web interface, not the Web services, and that access is only by ID (not AC or other fields). Are you considering further developements ? DbFetch does not work. I put in my .embossrc : DB testdbfetch [ type: N method: dbfetch format: embl dbalias: embl url: http://www.ebi.ac.uk/ws/services/Dbfetch ] Did I miss something ? By thz way, are there alternative DbFetch servers in the world ? If not, why not hard code the URL in the code, like you did for "entrez" ? Regards, Guy Bottu, BEN From rls at ebi.ac.uk Tue Aug 29 14:26:50 2006 From: rls at ebi.ac.uk (Rodrigo Lopez) Date: Tue, 29 Aug 2006 19:26:50 +0100 Subject: [emboss-dev] Questions about MRS and DbFetch - Checked by AntiVir DEMO version - In-Reply-To: <20060829162326.GA11317@bigben.ulb.ac.be> References: <20060829162326.GA11317@bigben.ulb.ac.be> Message-ID: <44F486EA.7070508@ebi.ac.uk> Don't quite know where that URL came from. If it is intended to point to the WSDL it should be: http://www.ebi.ac.uk/ws/services/urn:Dbfetch?wsdl If it is intended to point to the cgi it should be: http://www.ebi.ac.uk/cgi-bin/dbfetch Best to wait for the EMBOSS developers to explain where this is meant to go. Apologies for the inconvenience. R:) Guy Bottu wrote: > Dear developers, > > I am for the moment struggling to make MRS and DbFetch work as access > methods. I installed the bug fixed from the ftp site. > > MRS works ! But I note that currently you are using the Web interface, > not the Web services, and that access is only by ID (not AC or other > fields). Are you considering further developements ? > > DbFetch does not work. I put in my .embossrc : > > DB testdbfetch [ type: N method: dbfetch format: embl dbalias: embl > url: http://www.ebi.ac.uk/ws/services/Dbfetch ] > > Did I miss something ? > By thz way, are there alternative DbFetch servers in the world ? If not, > why not hard code the URL in the code, like you did for "entrez" ? > > Regards, > Guy Bottu, > BEN > > _______________________________________________ > emboss-dev mailing list > emboss-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss-dev From uludag at ebi.ac.uk Wed Aug 30 04:14:14 2006 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Wed, 30 Aug 2006 09:14:14 +0100 Subject: [emboss-dev] Questions about MRS and DbFetch - Checked by AntiVir DEMO version - In-Reply-To: <20060829162326.GA11317@bigben.ulb.ac.be> References: <20060829162326.GA11317@bigben.ulb.ac.be> Message-ID: <1156925654.8669.8.camel@emboss2.ebi.ac.uk> Hi Guy, > DbFetch does not work. I put in my .embossrc : > > DB testdbfetch [ type: N method: dbfetch format: embl dbalias: embl > url: http://www.ebi.ac.uk/ws/services/Dbfetch ] The following EMBOSS definition for dbfetch Peter gave me last week is working fine in my local EMBOSS installation. DB urldbfetch [ type: N methodentry: url format: embl url: http://www.ebi.ac.uk/cgi-bin/dbfetch?db=embl&id=%s&style=raw ] Regards, Mahmut From gbottu at ben.vub.ac.be Wed Aug 30 04:48:45 2006 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Wed, 30 Aug 2006 10:48:45 +0200 Subject: [emboss-dev] Questions about MRS and DbFetch - Checked by AntiVir D In-Reply-To: <1156925654.8669.8.camel@emboss2.ebi.ac.uk> References: <20060829162326.GA11317@bigben.ulb.ac.be> <1156925654.8669.8.camel@emboss2.ebi.ac.uk> Message-ID: <20060830084845.GB20376@bigben.ulb.ac.be> On Wed, Aug 30, 2006 at 09:14:14AM +0100, Mahmut Uludag wrote: > The following EMBOSS definition for dbfetch Peter gave me last week is > working fine in my local EMBOSS installation. > > DB urldbfetch [ type: N methodentry: url format: embl > url: http://www.ebi.ac.uk/cgi-bin/dbfetch?db=embl&id=%s&style=raw > ] But this is not using the method "dbfetch". There really seems to be a problem with it. I myself was already some time using the following : DB EBI_EMBL [ type: N methodquery: external format: embl app: '/opt/sw/EBIWS/WSDbfetchClient.pl fetchData embl:%s' ] where WSDbfetchClient.pl is the Perl SOAP client distributed by the EBI (http://www.ebi.ac.uk/Tools/webservices/WSDbfetch.html). regards, Guy Bottu From ajb at ebi.ac.uk Wed Aug 30 05:04:08 2006 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Wed, 30 Aug 2006 10:04:08 +0100 (BST) Subject: [emboss-dev] Questions about MRS and DbFetch - Checked by AntiVir D In-Reply-To: <20060830084845.GB20376@bigben.ulb.ac.be> References: <20060829162326.GA11317@bigben.ulb.ac.be> <1156925654.8669.8.camel@emboss2.ebi.ac.uk> <20060830084845.GB20376@bigben.ulb.ac.be> Message-ID: <37619.81.98.244.247.1156928648.squirrel@webmail.ebi.ac.uk> I believe the specification you need is, for example, DB dbfetchembl [ type: N comment: "EMBL dbfetch" methodentry: dbfetch dbalias: embl format: embl url: "http://www.ebi.ac.uk/cgi-bin/dbfetch" ] Alan From uludag at ebi.ac.uk Wed Aug 30 05:31:47 2006 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Wed, 30 Aug 2006 10:31:47 +0100 Subject: [emboss-dev] Questions about MRS and DbFetch - Checked by AntiVir D In-Reply-To: <20060830084845.GB20376@bigben.ulb.ac.be> References: <20060829162326.GA11317@bigben.ulb.ac.be> <1156925654.8669.8.camel@emboss2.ebi.ac.uk> <20060830084845.GB20376@bigben.ulb.ac.be> Message-ID: <1156930307.8669.18.camel@emboss2.ebi.ac.uk> > > DB urldbfetch [ type: N methodentry: url format: embl > > url: http://www.ebi.ac.uk/cgi-bin/dbfetch?db=embl&id=%s&style=raw > > ] > > But this is not using the method "dbfetch". There really seems to be a > problem with it. I myself was already some time using the following : You are right it doesn't use the method 'dbfetch'. I didn't know EMBOSS has the dbfetch method though it was apparent in your original message. However, the specification Alan just emailed is working fine, I have tested in my local installation. Regards, Mahmut