From gbottu at vub.ac.be  Fri Jul  6 04:40:46 2007
From: gbottu at vub.ac.be (Guy Bottu)
Date: Fri, 06 Jul 2007 10:40:46 +0200
Subject: [emboss-dev] MRS 3 as EMBOSS sequence access mechanism
Message-ID: <468E000E.5020201@vub.ac.be>

	Dear all,

The MRS servers are shifting from version 2 to version 3. A result is that the 
EMBOSS sequence access mechanism "mrs" does not work anymore. The reason is that 
  the URL to be generated by the software is not anymore something like
http://mrs.cmbi.kun.nl/mrs/cgi-bin/mrs.cgi?db=sprot%2Btrembl&query=id:papa1_carpa&format=entry&exp=1&save_to=text/plain
but
http://mrs.cmbi.kun.nl/mrs-3/plain.do?db=uniprot&id=papa1_carpa
It is not possible to search several databanks at the same time, but MRS 3 has 
composite indexes for e.g. uniprot (=sprot+trembl) or embl (=nonredundant 
release + updates). It is also impossible to make a query with wild cards. A 
suppementary problem is that the MRS WWW server wants to set a cookie.

Do you think the next release of EMBOSS could support MRS 3 (maybe, in the 
tradition of backward compatibility, have both "mrs" and "mrs3" access methods)?

And are some of you really using MRS WWW as access sequence access mechanism for 
EMBOSS ?

	Regards,
	Guy Bottu,
	Belgian EMBnet Node

From pmr at ebi.ac.uk  Fri Jul  6 05:12:30 2007
From: pmr at ebi.ac.uk (Peter Rice)
Date: Fri, 06 Jul 2007 10:12:30 +0100
Subject: [emboss-dev] MRS 3 as EMBOSS sequence access mechanism
In-Reply-To: <468E000E.5020201@vub.ac.be>
References: <468E000E.5020201@vub.ac.be>
Message-ID: <468E077E.5080706@ebi.ac.uk>

Guy Bottu wrote:

> Do you think the next release of EMBOSS could support MRS 3 (maybe, in the 
> tradition of backward compatibility, have both "mrs" and "mrs3" access methods)?

Tricky - today is my last day for making changes before going on vacation until 
the release!

But yes I can do it. Is mrs3 the best name? Probably it is, because the URL now 
contains "mrs-3" :-)

Peter

From pmr at ebi.ac.uk  Fri Jul  6 05:20:47 2007
From: pmr at ebi.ac.uk (Peter Rice)
Date: Fri, 06 Jul 2007 10:20:47 +0100
Subject: [emboss-dev] MRS 3 as EMBOSS sequence access mechanism
In-Reply-To: <468E000E.5020201@vub.ac.be>
References: <468E000E.5020201@vub.ac.be>
Message-ID: <468E096F.70102@ebi.ac.uk>

Guy Bottu wrote:

> It is not possible to search several databanks at the same time, but MRS 3 has 
> composite indexes for e.g. uniprot (=sprot+trembl) or embl (=nonredundant 
> release + updates). It is also impossible to make a query with wild cards. A 
> suppementary problem is that the MRS WWW server wants to set a cookie.

We do not handle cookies. MRS3 will have to work without them. It appears it does.

How does MRS3 search for other fields (accession, etc.)?

Where is the MRS server documentation??? I found no documentation of the URL 
syntax or query fields at the CMBI server.

Peter

From pmr at ebi.ac.uk  Fri Jul  6 05:31:36 2007
From: pmr at ebi.ac.uk (Peter Rice)
Date: Fri, 06 Jul 2007 10:31:36 +0100
Subject: [emboss-dev] MRS 3 as EMBOSS sequence access mechanism
In-Reply-To: <468E000E.5020201@vub.ac.be>
References: <468E000E.5020201@vub.ac.be>
Message-ID: <468E0BF8.4030801@ebi.ac.uk>

Guy Bottu wrote:
> The MRS servers are shifting from version 2 to version 3. A result is that the 
> EMBOSS sequence access mechanism "mrs" does not work anymore. The reason is that 
>   the URL to be generated by the software is not anymore something like
> http://mrs.cmbi.kun.nl/mrs/cgi-bin/mrs.cgi?db=sprot%2Btrembl&query=id:papa1_carpa&format=entry&exp=1&save_to=text/plain
> but
> http://mrs.cmbi.kun.nl/mrs-3/plain.do?db=uniprot&id=papa1_carpa

Hah .. that works from wget but when I try that URL within EMBOSS I get nonsense 
back. The web page returns is a 302 error saying:

The document has moved <a 
href="http://mrs.cmbi.ru.nl/mrs-3/?db=embl&amp;id=x13776Host:">here</a>

with an href of http://mrs.cmbi.ru.nl/mrs-3/?db=embl&amp;id=x13776Host:
(yes, with Host: at the end)


> Do you think the next release of EMBOSS could support MRS 3 (maybe, in the 
> tradition of backward compatibility, have both "mrs" and "mrs3" access methods)?

I will add an MRS3 method. Whether it will work before EMBOSS 5.1.0 is another 
question :-)

Peter

From pmr at ebi.ac.uk  Fri Jul  6 06:13:58 2007
From: pmr at ebi.ac.uk (Peter Rice)
Date: Fri, 06 Jul 2007 11:13:58 +0100
Subject: [emboss-dev] MRS 3 as EMBOSS sequence access mechanism
In-Reply-To: <468E000E.5020201@vub.ac.be>
References: <468E000E.5020201@vub.ac.be>
Message-ID: <468E15E6.1030609@ebi.ac.uk>

Guy Bottu wrote:
> 	Dear all,
> 
> The MRS servers are shifting from version 2 to version 3. A result is that the 
> EMBOSS sequence access mechanism "mrs" does not work anymore. The reason is that 
>   the URL to be generated by the software is not anymore something like
> http://mrs.cmbi.kun.nl/mrs/cgi-bin/mrs.cgi?db=sprot%2Btrembl&query=id:papa1_carpa&format=entry&exp=1&save_to=text/plain
> but
> http://mrs.cmbi.kun.nl/mrs-3/plain.do?db=uniprot&id=papa1_carpa

Hmmm ... I have something working.

The MRS3 server absolutely requires HTTP/1.x on the GET line.

The MRS2 server was happy without it (though I am not sure why it was the only 
EMBOSS method that did not use it)

Peter

From gbottu at vub.ac.be  Mon Jul  9 03:53:25 2007
From: gbottu at vub.ac.be (Guy Bottu)
Date: Mon, 09 Jul 2007 09:53:25 +0200
Subject: [emboss-dev] MRS 3 as EMBOSS sequence access mechanism
In-Reply-To: <468E096F.70102@ebi.ac.uk>
References: <468E000E.5020201@vub.ac.be> <468E096F.70102@ebi.ac.uk>
Message-ID: <4691E975.7050500@vub.ac.be>

Peter Rice wrote:
> How does MRS3 search for other fields (accession, etc.)

Alas, with MRS2 you could write a single URL to perform a query and then
retrieve the result as plain text. With MRS3 this has become impossible,
because there are now separate programs. Could EMBOSS eventually first
ask for a query.do, parse the reply and then ask for a plain.do ?
Or you could consider using the Web services instead. I have no 
experience with the Web services under MRS3 ; I will in the coming weeks 
try to get informed.

> Where is the MRS server documentation??? I found no documentation of the URL 
> syntax or query fields at the CMBI server.

There is no documentation for the moment. Well, let's not blame dear 
Maarten, he is alone in his corner with a big development project...

You can however find a list of available databanks, with for each 
databank the available field shortnames. It is possible to write an URL
like ..../mrs-3/query.do?db=uniprot&query=id:papa?_carpa|ac:papa?_carpa

	Guy



From pmr at ebi.ac.uk  Sun Jul  8 10:22:00 2007
From: pmr at ebi.ac.uk (Peter Rice)
Date: Sun, 08 Jul 2007 15:22:00 +0100
Subject: [emboss-dev] MRS 3 as EMBOSS sequence access mechanism
In-Reply-To: <4691E975.7050500@vub.ac.be>
References: <468E000E.5020201@vub.ac.be> <468E096F.70102@ebi.ac.uk>
	<4691E975.7050500@vub.ac.be>
Message-ID: <4690F308.2000108@ebi.ac.uk>

Guy Bottu wrote:
> Alas, with MRS2 you could write a single URL to perform a query and then
> retrieve the result as plain text. With MRS3 this has become impossible,
> because there are now separate programs. Could EMBOSS eventually first
> ask for a query.do, parse the reply and then ask for a plain.do ?
> Or you could consider using the Web services instead. I have no 
> experience with the Web services under MRS3 ; I will in the coming weeks 
> try to get informed.

Yes ... we already do something like that for Entrez.

> There is no documentation for the moment. Well, let's not blame dear 
> Maarten, he is alone in his corner with a big development project...
> 
> You can however find a list of available databanks, with for each 
> databank the available field shortnames. It is possible to write an URL
> like ..../mrs-3/query.do?db=uniprot&query=id:papa?_carpa|ac:papa?_carpa

Thanks. The query access will now have to wait for EMBOSS 5.1.0. The 
basic ID retrieval is in the 5.0.0 release.

regards,

Peter

From gbottu at vub.ac.be  Fri Jul  6 08:40:46 2007
From: gbottu at vub.ac.be (Guy Bottu)
Date: Fri, 06 Jul 2007 10:40:46 +0200
Subject: [emboss-dev] MRS 3 as EMBOSS sequence access mechanism
Message-ID: <468E000E.5020201@vub.ac.be>

	Dear all,

The MRS servers are shifting from version 2 to version 3. A result is that the 
EMBOSS sequence access mechanism "mrs" does not work anymore. The reason is that 
  the URL to be generated by the software is not anymore something like
http://mrs.cmbi.kun.nl/mrs/cgi-bin/mrs.cgi?db=sprot%2Btrembl&query=id:papa1_carpa&format=entry&exp=1&save_to=text/plain
but
http://mrs.cmbi.kun.nl/mrs-3/plain.do?db=uniprot&id=papa1_carpa
It is not possible to search several databanks at the same time, but MRS 3 has 
composite indexes for e.g. uniprot (=sprot+trembl) or embl (=nonredundant 
release + updates). It is also impossible to make a query with wild cards. A 
suppementary problem is that the MRS WWW server wants to set a cookie.

Do you think the next release of EMBOSS could support MRS 3 (maybe, in the 
tradition of backward compatibility, have both "mrs" and "mrs3" access methods)?

And are some of you really using MRS WWW as access sequence access mechanism for 
EMBOSS ?

	Regards,
	Guy Bottu,
	Belgian EMBnet Node


From pmr at ebi.ac.uk  Fri Jul  6 09:12:30 2007
From: pmr at ebi.ac.uk (Peter Rice)
Date: Fri, 06 Jul 2007 10:12:30 +0100
Subject: [emboss-dev] MRS 3 as EMBOSS sequence access mechanism
In-Reply-To: <468E000E.5020201@vub.ac.be>
References: <468E000E.5020201@vub.ac.be>
Message-ID: <468E077E.5080706@ebi.ac.uk>

Guy Bottu wrote:

> Do you think the next release of EMBOSS could support MRS 3 (maybe, in the 
> tradition of backward compatibility, have both "mrs" and "mrs3" access methods)?

Tricky - today is my last day for making changes before going on vacation until 
the release!

But yes I can do it. Is mrs3 the best name? Probably it is, because the URL now 
contains "mrs-3" :-)

Peter


From pmr at ebi.ac.uk  Fri Jul  6 09:20:47 2007
From: pmr at ebi.ac.uk (Peter Rice)
Date: Fri, 06 Jul 2007 10:20:47 +0100
Subject: [emboss-dev] MRS 3 as EMBOSS sequence access mechanism
In-Reply-To: <468E000E.5020201@vub.ac.be>
References: <468E000E.5020201@vub.ac.be>
Message-ID: <468E096F.70102@ebi.ac.uk>

Guy Bottu wrote:

> It is not possible to search several databanks at the same time, but MRS 3 has 
> composite indexes for e.g. uniprot (=sprot+trembl) or embl (=nonredundant 
> release + updates). It is also impossible to make a query with wild cards. A 
> suppementary problem is that the MRS WWW server wants to set a cookie.

We do not handle cookies. MRS3 will have to work without them. It appears it does.

How does MRS3 search for other fields (accession, etc.)?

Where is the MRS server documentation??? I found no documentation of the URL 
syntax or query fields at the CMBI server.

Peter


From pmr at ebi.ac.uk  Fri Jul  6 09:31:36 2007
From: pmr at ebi.ac.uk (Peter Rice)
Date: Fri, 06 Jul 2007 10:31:36 +0100
Subject: [emboss-dev] MRS 3 as EMBOSS sequence access mechanism
In-Reply-To: <468E000E.5020201@vub.ac.be>
References: <468E000E.5020201@vub.ac.be>
Message-ID: <468E0BF8.4030801@ebi.ac.uk>

Guy Bottu wrote:
> The MRS servers are shifting from version 2 to version 3. A result is that the 
> EMBOSS sequence access mechanism "mrs" does not work anymore. The reason is that 
>   the URL to be generated by the software is not anymore something like
> http://mrs.cmbi.kun.nl/mrs/cgi-bin/mrs.cgi?db=sprot%2Btrembl&query=id:papa1_carpa&format=entry&exp=1&save_to=text/plain
> but
> http://mrs.cmbi.kun.nl/mrs-3/plain.do?db=uniprot&id=papa1_carpa

Hah .. that works from wget but when I try that URL within EMBOSS I get nonsense 
back. The web page returns is a 302 error saying:

The document has moved <a 
href="http://mrs.cmbi.ru.nl/mrs-3/?db=embl&amp;id=x13776Host:">here</a>

with an href of http://mrs.cmbi.ru.nl/mrs-3/?db=embl&amp;id=x13776Host:
(yes, with Host: at the end)


> Do you think the next release of EMBOSS could support MRS 3 (maybe, in the 
> tradition of backward compatibility, have both "mrs" and "mrs3" access methods)?

I will add an MRS3 method. Whether it will work before EMBOSS 5.1.0 is another 
question :-)

Peter


From pmr at ebi.ac.uk  Fri Jul  6 10:13:58 2007
From: pmr at ebi.ac.uk (Peter Rice)
Date: Fri, 06 Jul 2007 11:13:58 +0100
Subject: [emboss-dev] MRS 3 as EMBOSS sequence access mechanism
In-Reply-To: <468E000E.5020201@vub.ac.be>
References: <468E000E.5020201@vub.ac.be>
Message-ID: <468E15E6.1030609@ebi.ac.uk>

Guy Bottu wrote:
> 	Dear all,
> 
> The MRS servers are shifting from version 2 to version 3. A result is that the 
> EMBOSS sequence access mechanism "mrs" does not work anymore. The reason is that 
>   the URL to be generated by the software is not anymore something like
> http://mrs.cmbi.kun.nl/mrs/cgi-bin/mrs.cgi?db=sprot%2Btrembl&query=id:papa1_carpa&format=entry&exp=1&save_to=text/plain
> but
> http://mrs.cmbi.kun.nl/mrs-3/plain.do?db=uniprot&id=papa1_carpa

Hmmm ... I have something working.

The MRS3 server absolutely requires HTTP/1.x on the GET line.

The MRS2 server was happy without it (though I am not sure why it was the only 
EMBOSS method that did not use it)

Peter


From gbottu at vub.ac.be  Mon Jul  9 07:53:25 2007
From: gbottu at vub.ac.be (Guy Bottu)
Date: Mon, 09 Jul 2007 09:53:25 +0200
Subject: [emboss-dev] MRS 3 as EMBOSS sequence access mechanism
In-Reply-To: <468E096F.70102@ebi.ac.uk>
References: <468E000E.5020201@vub.ac.be> <468E096F.70102@ebi.ac.uk>
Message-ID: <4691E975.7050500@vub.ac.be>

Peter Rice wrote:
> How does MRS3 search for other fields (accession, etc.)

Alas, with MRS2 you could write a single URL to perform a query and then
retrieve the result as plain text. With MRS3 this has become impossible,
because there are now separate programs. Could EMBOSS eventually first
ask for a query.do, parse the reply and then ask for a plain.do ?
Or you could consider using the Web services instead. I have no 
experience with the Web services under MRS3 ; I will in the coming weeks 
try to get informed.

> Where is the MRS server documentation??? I found no documentation of the URL 
> syntax or query fields at the CMBI server.

There is no documentation for the moment. Well, let's not blame dear 
Maarten, he is alone in his corner with a big development project...

You can however find a list of available databanks, with for each 
databank the available field shortnames. It is possible to write an URL
like ..../mrs-3/query.do?db=uniprot&query=id:papa?_carpa|ac:papa?_carpa

	Guy




From pmr at ebi.ac.uk  Sun Jul  8 14:22:00 2007
From: pmr at ebi.ac.uk (Peter Rice)
Date: Sun, 08 Jul 2007 15:22:00 +0100
Subject: [emboss-dev] MRS 3 as EMBOSS sequence access mechanism
In-Reply-To: <4691E975.7050500@vub.ac.be>
References: <468E000E.5020201@vub.ac.be> <468E096F.70102@ebi.ac.uk>
	<4691E975.7050500@vub.ac.be>
Message-ID: <4690F308.2000108@ebi.ac.uk>

Guy Bottu wrote:
> Alas, with MRS2 you could write a single URL to perform a query and then
> retrieve the result as plain text. With MRS3 this has become impossible,
> because there are now separate programs. Could EMBOSS eventually first
> ask for a query.do, parse the reply and then ask for a plain.do ?
> Or you could consider using the Web services instead. I have no 
> experience with the Web services under MRS3 ; I will in the coming weeks 
> try to get informed.

Yes ... we already do something like that for Entrez.

> There is no documentation for the moment. Well, let's not blame dear 
> Maarten, he is alone in his corner with a big development project...
> 
> You can however find a list of available databanks, with for each 
> databank the available field shortnames. It is possible to write an URL
> like ..../mrs-3/query.do?db=uniprot&query=id:papa?_carpa|ac:papa?_carpa

Thanks. The query access will now have to wait for EMBOSS 5.1.0. The 
basic ID retrieval is in the 5.0.0 release.

regards,

Peter