[DAS2] Human prototype server up
Allen Day
allenday at ucla.edu
Thu Apr 21 21:30:33 UTC 2005
Gregg,
Please post your instructions for how to use your server test application.
Thanks.
-Allen
On Thu, 21 Apr 2005, Helt,Gregg wrote:
> Cool, great to see a public server up and running!
>
> However, I'm having trouble with feature queries. For example:
> http://das.biopackages.net/das/genome/chado/chado-Hsa-17/feature?overlap
> s=chr21/21500000:22500000;type=0000110
>
> Which is an example of the most typical query IGB will be making -- one
> overlap filter combined with one type filter. But this query returns
> with a single <FEATURELIST> line, no <FEATURES>. I've tried it for
> every type returned by the type query and get the same results.
>
> Is there something wrong with my query syntax?
>
> If this is not a good region to test, can you send me an example feature
> query URL where you know what the response should be?
>
> thanks!
> gregg
>
> > -----Original Message-----
> > From: das2-bounces at portal.open-bio.org
> [mailto:das2-bounces at portal.open-
> > bio.org] On Behalf Of Allen Day
> > Sent: Wednesday, April 20, 2005 10:42 PM
> > To: das2 at portal.open-bio.org
> > Subject: [DAS2] Human prototype server up
> >
> > Contains UCSC Hg17 knownGene, as well as all Affymetrix "target"
> sequences
> > aligned to the genome w/ > 90% identity.
> >
> > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/region
> >
> > Here's a URL to get you going. This is running on 2 hosts: a dual
> > opteron/8GB webserver frontend and a dual opteron/16GB database
> backend.
> > There are no other applications on these hosts right now, so hammer
> away.
> >
> > You might want to use HTTP 1.1 keepalive though, the responses can be
> > *really* slow for /feature requests on large regions. The reason for
> this
> > is the feature/part subpart requests are done feature by feature due
> to
> > the 1-many relationship... I'm still trying to figure out how to
> improve
> > this.
> >
> > Components that aren't working in even a basic way:
> >
> > * alignments
> > * assemblies
> > * individual /feature/<id> requests
> > * versioned source response w/ supported formats
> > * most feature filters (overlaps, type, and exacttype work)
> >
> > -Allen
> > _______________________________________________
> > DAS2 mailing list
> > DAS2 at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/das2
>
On Thu, 21 Apr 2005, Allen Day wrote:
> This is a good region. I just realized the type ids coming back in the
> /type response don't match the type ids given in the /feature response.
> I'm in the process of switching over from using table PKs for types to
> using type names, so rather than using a filter "type=9770" you can
> instead us a filter "type=sofa.ontology:CDS" (the "sofa.ontology" string
> is the term's namespace. SO has already changed it to "SOFA" in their
> most recent SOFA file in CVS, but I haven't updated yet).
>
> So, sorry about that. I just change thed /type response back to give
> primary keys until I get names working. All the types should now work
> with the type= filter. Here's a quick document you can grab, a subregion
> of what you asked for in your request that has something interesting
> inside:
>
> http://das.biopackages.net/das/genome/chado/chado-Hsa-17/feature?overlaps=chr21/21292691:21324284;type=9688
>
> -Allen
>
>
>
> On Thu, 21 Apr 2005, Helt,Gregg wrote:
>
> > Cool, great to see a public server up and running!
> >
> > However, I'm having trouble with feature queries. For example:
> > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/feature?overlap
> > s=chr21/21500000:22500000;type=0000110
> >
> > Which is an example of the most typical query IGB will be making -- one
> > overlap filter combined with one type filter. But this query returns
> > with a single <FEATURELIST> line, no <FEATURES>. I've tried it for
> > every type returned by the type query and get the same results.
> >
> > Is there something wrong with my query syntax?
> >
> > If this is not a good region to test, can you send me an example feature
> > query URL where you know what the response should be?
> >
> > thanks!
> > gregg
> >
> > > -----Original Message-----
> > > From: das2-bounces at portal.open-bio.org
> > [mailto:das2-bounces at portal.open-
> > > bio.org] On Behalf Of Allen Day
> > > Sent: Wednesday, April 20, 2005 10:42 PM
> > > To: das2 at portal.open-bio.org
> > > Subject: [DAS2] Human prototype server up
> > >
> > > Contains UCSC Hg17 knownGene, as well as all Affymetrix "target"
> > sequences
> > > aligned to the genome w/ > 90% identity.
> > >
> > > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/region
> > >
> > > Here's a URL to get you going. This is running on 2 hosts: a dual
> > > opteron/8GB webserver frontend and a dual opteron/16GB database
> > backend.
> > > There are no other applications on these hosts right now, so hammer
> > away.
> > >
> > > You might want to use HTTP 1.1 keepalive though, the responses can be
> > > *really* slow for /feature requests on large regions. The reason for
> > this
> > > is the feature/part subpart requests are done feature by feature due
> > to
> > > the 1-many relationship... I'm still trying to figure out how to
> > improve
> > > this.
> > >
> > > Components that aren't working in even a basic way:
> > >
> > > * alignments
> > > * assemblies
> > > * individual /feature/<id> requests
> > > * versioned source response w/ supported formats
> > > * most feature filters (overlaps, type, and exacttype work)
> > >
> > > -Allen
> > > _______________________________________________
> > > DAS2 mailing list
> > > DAS2 at portal.open-bio.org
> > > http://portal.open-bio.org/mailman/listinfo/das2
> >
> _______________________________________________
> DAS2 mailing list
> DAS2 at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/das2
>
On Thu, 21 Apr 2005, Ed Erwin wrote:
> That response comes back with some "%20" things in it. That seems like
> a bug to me, but is it?
>
> <PROP ptype="property/protein%20binding"/>
>
>
> Allen Day wrote:
> > This is a good region. I just realized the type ids coming back in the
> > /type response don't match the type ids given in the /feature response.
> > I'm in the process of switching over from using table PKs for types to
> > using type names, so rather than using a filter "type=9770" you can
> > instead us a filter "type=sofa.ontology:CDS" (the "sofa.ontology" string
> > is the term's namespace. SO has already changed it to "SOFA" in their
> > most recent SOFA file in CVS, but I haven't updated yet).
> >
> > So, sorry about that. I just change thed /type response back to give
> > primary keys until I get names working. All the types should now work
> > with the type= filter. Here's a quick document you can grab, a subregion
> > of what you asked for in your request that has something interesting
> > inside:
> >
> > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/feature?overlaps=chr21/21292691:21324284;type=9688
> >
> > -Allen
> >
> >
> >
> > On Thu, 21 Apr 2005, Helt,Gregg wrote:
> >
> >
> >>Cool, great to see a public server up and running!
> >>
> >>However, I'm having trouble with feature queries. For example:
> >>http://das.biopackages.net/das/genome/chado/chado-Hsa-17/feature?overlap
> >>s=chr21/21500000:22500000;type=0000110
> >>
> >>Which is an example of the most typical query IGB will be making -- one
> >>overlap filter combined with one type filter. But this query returns
> >>with a single <FEATURELIST> line, no <FEATURES>. I've tried it for
> >>every type returned by the type query and get the same results.
> >>
> >>Is there something wrong with my query syntax?
> >>
> >>If this is not a good region to test, can you send me an example feature
> >>query URL where you know what the response should be?
> >>
> >> thanks!
> >> gregg
> >>
> >>
> >>>-----Original Message-----
> >>>From: das2-bounces at portal.open-bio.org
> >>
> >>[mailto:das2-bounces at portal.open-
> >>
> >>>bio.org] On Behalf Of Allen Day
> >>>Sent: Wednesday, April 20, 2005 10:42 PM
> >>>To: das2 at portal.open-bio.org
> >>>Subject: [DAS2] Human prototype server up
> >>>
> >>>Contains UCSC Hg17 knownGene, as well as all Affymetrix "target"
> >>
> >>sequences
> >>
> >>>aligned to the genome w/ > 90% identity.
> >>>
> >>>http://das.biopackages.net/das/genome/chado/chado-Hsa-17/region
> >>>
> >>>Here's a URL to get you going. This is running on 2 hosts: a dual
> >>>opteron/8GB webserver frontend and a dual opteron/16GB database
> >>
> >>backend.
> >>
> >>>There are no other applications on these hosts right now, so hammer
> >>
> >>away.
> >>
> >>>You might want to use HTTP 1.1 keepalive though, the responses can be
> >>>*really* slow for /feature requests on large regions. The reason for
> >>
> >>this
> >>
> >>>is the feature/part subpart requests are done feature by feature due
> >>
> >>to
> >>
> >>>the 1-many relationship... I'm still trying to figure out how to
> >>
> >>improve
> >>
> >>>this.
> >>>
> >>>Components that aren't working in even a basic way:
> >>>
> >>> * alignments
> >>> * assemblies
> >>> * individual /feature/<id> requests
> >>> * versioned source response w/ supported formats
> >>> * most feature filters (overlaps, type, and exacttype work)
> >>>
> >>>-Allen
> >>>_______________________________________________
> >>>DAS2 mailing list
> >>>DAS2 at portal.open-bio.org
> >>>http://portal.open-bio.org/mailman/listinfo/das2
> >>
> > _______________________________________________
> > DAS2 mailing list
> > DAS2 at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/das2
>
On Thu, 21 Apr 2005, Ed Erwin wrote:
>
> This is a question for Andrew Dalke.
>
>
> Allen Day wrote:
> > I don't know, is it? I have found the description of properties and the
> > /property response document examples to be extremely unclear. I opted to
> > URI escape here, but maybe it's not the right thing to do.
> >
> > -Allen
> >
> >
> > On Thu, 21 Apr 2005, Ed Erwin wrote:
> >
> >
> >>That response comes back with some "%20" things in it. That seems like
> >>a bug to me, but is it?
> >>
> >> <PROP ptype="property/protein%20binding"/>
> >>
> >>
> >>Allen Day wrote:
> >>
> >>>This is a good region. I just realized the type ids coming back in the
> >>>/type response don't match the type ids given in the /feature response.
> >>>I'm in the process of switching over from using table PKs for types to
> >>>using type names, so rather than using a filter "type=9770" you can
> >>>instead us a filter "type=sofa.ontology:CDS" (the "sofa.ontology" string
> >>>is the term's namespace. SO has already changed it to "SOFA" in their
> >>>most recent SOFA file in CVS, but I haven't updated yet).
> >>>
> >>>So, sorry about that. I just change thed /type response back to give
> >>>primary keys until I get names working. All the types should now work
> >>>with the type= filter. Here's a quick document you can grab, a subregion
> >>>of what you asked for in your request that has something interesting
> >>>inside:
> >>>
> >>>http://das.biopackages.net/das/genome/chado/chado-Hsa-17/feature?overlaps=chr21/21292691:21324284;type=9688
> >>>
> >>>-Allen
> >>>
> >>>
> >>>
> >>>On Thu, 21 Apr 2005, Helt,Gregg wrote:
> >>>
> >>>
> >>>
> >>>>Cool, great to see a public server up and running!
> >>>>
> >>>>However, I'm having trouble with feature queries. For example:
> >>>>http://das.biopackages.net/das/genome/chado/chado-Hsa-17/feature?overlap
> >>>>s=chr21/21500000:22500000;type=0000110
> >>>>
> >>>>Which is an example of the most typical query IGB will be making -- one
> >>>>overlap filter combined with one type filter. But this query returns
> >>>>with a single <FEATURELIST> line, no <FEATURES>. I've tried it for
> >>>>every type returned by the type query and get the same results.
> >>>>
> >>>>Is there something wrong with my query syntax?
> >>>>
> >>>>If this is not a good region to test, can you send me an example feature
> >>>>query URL where you know what the response should be?
> >>>>
> >>>> thanks!
> >>>> gregg
> >>>>
> >>>>
> >>>>
> >>>>>-----Original Message-----
> >>>>>From: das2-bounces at portal.open-bio.org
> >>>>
> >>>>[mailto:das2-bounces at portal.open-
> >>>>
> >>>>
> >>>>>bio.org] On Behalf Of Allen Day
> >>>>>Sent: Wednesday, April 20, 2005 10:42 PM
> >>>>>To: das2 at portal.open-bio.org
> >>>>>Subject: [DAS2] Human prototype server up
> >>>>>
> >>>>>Contains UCSC Hg17 knownGene, as well as all Affymetrix "target"
> >>>>
> >>>>sequences
> >>>>
> >>>>
> >>>>>aligned to the genome w/ > 90% identity.
> >>>>>
> >>>>>http://das.biopackages.net/das/genome/chado/chado-Hsa-17/region
> >>>>>
> >>>>>Here's a URL to get you going. This is running on 2 hosts: a dual
> >>>>>opteron/8GB webserver frontend and a dual opteron/16GB database
> >>>>
> >>>>backend.
> >>>>
> >>>>
> >>>>>There are no other applications on these hosts right now, so hammer
> >>>>
> >>>>away.
> >>>>
> >>>>
> >>>>>You might want to use HTTP 1.1 keepalive though, the responses can be
> >>>>>*really* slow for /feature requests on large regions. The reason for
> >>>>
> >>>>this
> >>>>
> >>>>
> >>>>>is the feature/part subpart requests are done feature by feature due
> >>>>
> >>>>to
> >>>>
> >>>>
> >>>>>the 1-many relationship... I'm still trying to figure out how to
> >>>>
> >>>>improve
> >>>>
> >>>>
> >>>>>this.
> >>>>>
> >>>>>Components that aren't working in even a basic way:
> >>>>>
> >>>>> * alignments
> >>>>> * assemblies
> >>>>> * individual /feature/<id> requests
> >>>>> * versioned source response w/ supported formats
> >>>>> * most feature filters (overlaps, type, and exacttype work)
> >>>>>
> >>>>>-Allen
> >>>>>_______________________________________________
> >>>>>DAS2 mailing list
> >>>>>DAS2 at portal.open-bio.org
> >>>>>http://portal.open-bio.org/mailman/listinfo/das2
> >>>>
> >>>_______________________________________________
> >>>DAS2 mailing list
> >>>DAS2 at portal.open-bio.org
> >>>http://portal.open-bio.org/mailman/listinfo/das2
> >>
>
On Thu, 21 Apr 2005, Ed Erwin wrote:
> My reasoning is that it ISN'T a URL yet, so you don't escape it until
> you turn it into a URL. But Andrew can figure out which is right and
> document it.
>
> Allen Day wrote:
> > exactly. my reasoning was that it was a relative url and needed to be
> > escaped.
> >
> > On Thu, 21 Apr 2005, Ed Erwin wrote:
> >
> >
> >>This is a question for Andrew Dalke.
> >>
> >>
> >>Allen Day wrote:
> >>
> >>>I don't know, is it? I have found the description of properties and the
> >>>/property response document examples to be extremely unclear. I opted to
> >>>URI escape here, but maybe it's not the right thing to do.
> >>>
> >>>-Allen
> >>>
> >>>
> >>>On Thu, 21 Apr 2005, Ed Erwin wrote:
> >>>
> >>>
> >>>
> >>>>That response comes back with some "%20" things in it. That seems like
> >>>>a bug to me, but is it?
> >>>>
> >>>> <PROP ptype="property/protein%20binding"/>
> >>>>
> >>>>
> >>>>Allen Day wrote:
> >>>>
> >>>>
> >>>>>This is a good region. I just realized the type ids coming back in the
> >>>>>/type response don't match the type ids given in the /feature response.
> >>>>>I'm in the process of switching over from using table PKs for types to
> >>>>>using type names, so rather than using a filter "type=9770" you can
> >>>>>instead us a filter "type=sofa.ontology:CDS" (the "sofa.ontology" string
> >>>>>is the term's namespace. SO has already changed it to "SOFA" in their
> >>>>>most recent SOFA file in CVS, but I haven't updated yet).
> >>>>>
> >>>>>So, sorry about that. I just change thed /type response back to give
> >>>>>primary keys until I get names working. All the types should now work
> >>>>>with the type= filter. Here's a quick document you can grab, a subregion
> >>>>>of what you asked for in your request that has something interesting
> >>>>>inside:
> >>>>>
> >>>>>http://das.biopackages.net/das/genome/chado/chado-Hsa-17/feature?overlaps=chr21/21292691:21324284;type=9688
> >>>>>
> >>>>>-Allen
> >>>>>
> >>>>>
> >>>>>
> >>>>>On Thu, 21 Apr 2005, Helt,Gregg wrote:
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>>Cool, great to see a public server up and running!
> >>>>>>
> >>>>>>However, I'm having trouble with feature queries. For example:
> >>>>>>http://das.biopackages.net/das/genome/chado/chado-Hsa-17/feature?overlap
> >>>>>>s=chr21/21500000:22500000;type=0000110
> >>>>>>
> >>>>>>Which is an example of the most typical query IGB will be making -- one
> >>>>>>overlap filter combined with one type filter. But this query returns
> >>>>>>with a single <FEATURELIST> line, no <FEATURES>. I've tried it for
> >>>>>>every type returned by the type query and get the same results.
> >>>>>>
> >>>>>>Is there something wrong with my query syntax?
> >>>>>>
> >>>>>>If this is not a good region to test, can you send me an example feature
> >>>>>>query URL where you know what the response should be?
> >>>>>>
> >>>>>> thanks!
> >>>>>> gregg
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>>-----Original Message-----
> >>>>>>>From: das2-bounces at portal.open-bio.org
> >>>>>>
> >>>>>>[mailto:das2-bounces at portal.open-
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>>bio.org] On Behalf Of Allen Day
> >>>>>>>Sent: Wednesday, April 20, 2005 10:42 PM
> >>>>>>>To: das2 at portal.open-bio.org
> >>>>>>>Subject: [DAS2] Human prototype server up
> >>>>>>>
> >>>>>>>Contains UCSC Hg17 knownGene, as well as all Affymetrix "target"
> >>>>>>
> >>>>>>sequences
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>>aligned to the genome w/ > 90% identity.
> >>>>>>>
> >>>>>>>http://das.biopackages.net/das/genome/chado/chado-Hsa-17/region
> >>>>>>>
> >>>>>>>Here's a URL to get you going. This is running on 2 hosts: a dual
> >>>>>>>opteron/8GB webserver frontend and a dual opteron/16GB database
> >>>>>>
> >>>>>>backend.
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>>There are no other applications on these hosts right now, so hammer
> >>>>>>
> >>>>>>away.
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>>You might want to use HTTP 1.1 keepalive though, the responses can be
> >>>>>>>*really* slow for /feature requests on large regions. The reason for
> >>>>>>
> >>>>>>this
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>>is the feature/part subpart requests are done feature by feature due
> >>>>>>
> >>>>>>to
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>>the 1-many relationship... I'm still trying to figure out how to
> >>>>>>
> >>>>>>improve
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>>this.
> >>>>>>>
> >>>>>>>Components that aren't working in even a basic way:
> >>>>>>>
> >>>>>>>* alignments
> >>>>>>>* assemblies
> >>>>>>>* individual /feature/<id> requests
> >>>>>>>* versioned source response w/ supported formats
> >>>>>>>* most feature filters (overlaps, type, and exacttype work)
> >>>>>>>
> >>>>>>>-Allen
> >>>>>>>_______________________________________________
> >>>>>>>DAS2 mailing list
> >>>>>>>DAS2 at portal.open-bio.org
> >>>>>>>http://portal.open-bio.org/mailman/listinfo/das2
> >>>>>>
> >>>>>_______________________________________________
> >>>>>DAS2 mailing list
> >>>>>DAS2 at portal.open-bio.org
> >>>>>http://portal.open-bio.org/mailman/listinfo/das2
> >>>>
>
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