[DAS] maxbins in DAS1.6?
Jonathan Warren
jw12 at sanger.ac.uk
Wed Sep 16 09:28:13 UTC 2009
I think Thomas is right in that we can't change the das1 base url
principle at least for 1.6 anyway, as it is supposed to be a
consolidation.
As there have been no objections to using for example http://www.ebi.ac.uk/das-srv/genomicdas/das/eqtl_rat_cis_fat
as a single source request we can put that into 1.6. The only real
change would need to be in the registry. See explanation below. But we
can get around that.
> What I meant was that the root URI isn't actually used for anything,
> at best it's just the location of the description you're already
> reading.
Except for the registry sources command where there is then no link
back to where the server you are talking about is (as you are not at
the server) apart from the query_uri's (example 1 below).
das2 has "xml:base", but that is then for all sources so wouldn't work
for the registry see example 2 below. We could always add another prop
to the registry I guess ;)
example1 registry sources:
<SOURCES>
<SOURCE uri="DS_109" title="uniprot aristotle" doc_href="http://www.ebi.ac.uk/uniprot-das/
" description="This datasource (aristotle) is a legacy datasource
that comprises the new 'uniprot', 'ipi' and 'uniparc' datasources
that are available from the http://www.ebi.ac.uk/das-srv/uniprot/das
server. Despite being a legacy dsn, there are no plans to remove
this DAS datasource from service.">
<MAINTAINER email="rantunes at ebi.ac.uk" />
<VERSION uri="DS_109" created="2005-03-21T16:26:03+0000">
<COORDINATES uri="http://www.dasregistry.org/dasregistry/coordsys/CS_DS93
" source="Protein Sequence" authority="UniParc"
test_range="UPI00000017EA">UniParc,Protein Sequence</COORDINATES>
<COORDINATES uri="http://www.dasregistry.org/dasregistry/coordsys/CS_DS35
" source="Protein Sequence" authority="IPI"
test_range="IPI00000021">IPI,Protein Sequence</COORDINATES>
<COORDINATES uri="http://www.dasregistry.org/dasregistry/coordsys/CS_DS6
" source="Protein Sequence" authority="UniProt"
test_range="P00280">UniProt,Protein Sequence</COORDINATES>
<CAPABILITY type="das1:stylesheet" query_uri="http://www.ebi.ac.uk/das-srv/uniprot/das/aristotle/stylesheet
" />
<CAPABILITY type="das1:features" query_uri="http://www.ebi.ac.uk/das-srv/uniprot/das/aristotle/features
" />
<CAPABILITY type="das1:types" query_uri="http://www.ebi.ac.uk/das-srv/uniprot/das/aristotle/types
" />
<CAPABILITY type="das1:sequence" query_uri="http://www.ebi.ac.uk/das-srv/uniprot/das/aristotle/sequence
" />
<CAPABILITY type="das1:entry_points" query_uri="http://www.ebi.ac.uk/das-srv/uniprot/das/aristotle/entry_points
" />
<CAPABILITY type="das1:unknown_segment" query_uri="http://www.ebi.ac.uk/das-srv/uniprot/das/aristotle/unknown_segment
" />
<CAPABILITY type="das1:error_segment" query_uri="http://www.ebi.ac.uk/das-srv/uniprot/das/aristotle/error_segment
" />
<PROP name="label" value="Predicted" />
<PROP name="label" value="Manually curated" />
<PROP name="label" value="ENSEMBL" />
<PROP name="leaseTime" value="2009-09-15T11:00:15+0000" />
<PROP name="projectHome" value="http://www.biosapiens.info" />
<PROP name="projectIcon" value="http://www.dasregistry.org/ProjectIcon?id=74
" />
<PROP name="projectDesc" value="BioSapiens is a Network of
Excellence, funded by the European Union's 6th Framework Programme,
and made up of bioinformatics researchers from 25 institutions based
in 14 countries throughout Europe.
The objective of the BioSapiens is to provide a large" />
<PROP name="projectName" value="BioSapiens" />
<PROP name="valid" value="stylesheet" />
<PROP name="valid" value="features" />
<PROP name="valid" value="types" />
<PROP name="valid" value="sequence" />
<PROP name="valid" value="entry_points" />
<PROP name="valid" value="error_segment" />
</VERSION>
</SOURCE>
das2 has xml:base, but that is then for all sources so wouldn't work
for the registry:
xml:base="http://bioserver.hci.utah.edu:8080/DAS2/das2/" >
<MAINTAINER email="david.nix at hci.utah.edu" />
<SOURCE uri="H_sapiens" title="H_sapiens" >
<VERSION uri="H_sapiens_Mar_2006" title="H_sapiens_Mar_2006"
created="2008-01-03 14:39:44" >
<COORDINATES uri="http://www.ncbi.nlm.nih.gov/genome/H_sapiens/B36.1/
" authority="NCBI" taxid="9606" version="36" source="Chromosome" />
<CAPABILITY type="segments" query_uri="H_sapiens_Mar_2006/
segments" />
<CAPABILITY type="types" query_uri="H_sapiens_Mar_2006/
types" />
<CAPABILITY type="features" query_uri="H_sapiens_Mar_2006/
features" />
</VERSION>
</SOURCE>
On 16 Sep 2009, at 09:25, Andy Jenkinson wrote:
> What I meant was that the root URI isn't actually used for anything,
> at best it's just the location of the description you're already
> reading. That would mean that adding another field to capture it
> wouldn't be of particular benefit.
>
> Whether we can easily remove the 'paradigm' of server/das/source/
> command without confusing people is something else!
>
> On 15 Sep 2009, at 18:11, Jonathan Warren wrote:
>
>> Andy I wasn't suggesting we get rid of query_uri - quite the
>> opposite in fact. just that the single source uri would have to be
>> specified with a uri as conceptually all other commands may not
>> contain the root uri. This also seems to me means we will have to
>> update das1 code to cope with multiple query uris.
>>
>> On 15 Sep 2009, at 17:56, Andy Jenkinson wrote:
>>
>>> On 15 Sep 2009, at 16:35, Jonathan Warren wrote:
>>>
>>>> I agree with Andy on both these (we talked about versioning
>>>> before).
>>>> The version numbers really have no meaning at the moment (no web
>>>> pages anywhere actually explain what a different version means)
>>>> and don't seem to be used at all in data sources ( I'm guessing
>>>> people end up just copying the version numbers from examples given.
>>>>
>>>> I've always had an issue with the commands like this http://www.ebi.ac.uk/das-srv/genomicdas/das/eqtl_rat_cis_fat
>>>> not being a valid das command as it's the most natural request
>>>> for a person new to das to make. So giving it a specific purpose
>>>> and response is a good idea.
>>>>
>>>> My only concern is how to handle these if we start using the
>>>> power of multiple query_uri s per das source (inherited from
>>>> DAS2, which we have started to talk about, rather than the das1
>>>> style where all urls have a root) as currently there is no "root"
>>>> url specified in the DAS2 spec in the sources document...?? So
>>>> this would have to be specified as another capability? or you
>>>> could infer it from the features command, but obviously not the
>>>> sources cmd!!!
>>>
>>> My take on this is that the root URI identifies the source. In a
>>> conceptual sense the definition of a source is merely a
>>> combination of commands acting on a common set of data. It is not
>>> really important where that information comes from (a registry, a
>>> server, a flat file...) because a server by itself does not really
>>> mean anything. So the URI http://www.ebi.ac.uk/das-srv/genomicdas/das/eqtl_rat_cis_fat
>>> is not actually meaningful, even less so given it is not even a
>>> resolvable URL.
>>>
>>> The query URI system inherited from DAS/2 has the potential to
>>> allow the commands to be served from different locations on the
>>> web. It is not something we have needed up to now (all query URIs
>>> start with the same path), and does add confusion but I can see it
>>> being used for stylesheets. For example a "sequence ontology
>>> stylesheet" served from a single location.
>>>
>>> But the biggest reason to have it is because of the registry. The
>>> registry assigns its own root URIs for a DAS source (e.g.
>>> DS_1234), which means it is necessary to provide another URI used
>>> to actually query it. Since we already have a way of doing it in
>>> the sources document, I don't really want to change it now. It
>>> seems we might as well just embrace the extra flexibility and
>>> merely describe it better.
>>>
>>>> On 15 Sep 2009, at 15:47, Andy Jenkinson wrote:
>>>>
>>>>> On 15 Sep 2009, at 15:19, Thomas Down wrote:
>>>>>> Capabilities are stated in the sources document:
>>>>>> <CAPABILITY type="das1:maxbins" />
>>>>>>
>>>>>> Ah, interesting. I'd seen that, of course, but hadn't
>>>>>> explicitly linked this with the idea of capabilities as listed
>>>>>> in the X-DAS-Capabilities header (although of course it makes a
>>>>>> lot more sense to have one set of capability metadata, rather
>>>>>> than two!). There are a couple of issues here:
>>>>>>
>>>>>> 1. The SOURCES examples all say "das command" in the
>>>>>> type attribute of the CAPABILITY element, whereas many of the
>>>>>> capabilities don't actually map to commands. I notice that the
>>>>>> latest DAS1.6 draft does give an example to clarify this.
>>>>>>
>>>>>> 2. X-DAS-Capabilities entries are versioned whereas
>>>>>> SOURCES capabilities aren't, which makes them look rather
>>>>>> different. (and I note that the 1.6 spec is bumping up the
>>>>>> version numbers on some of the existing capabilities...)
>>>>>>
>>>>>> How about versioning capabilities in SOURCES, e.g.:
>>>>>>
>>>>>> <CAPABILITY type="features" version="1.1" query_uri="http://noranti.derkholm.net/das/mydata/features
>>>>>> " />
>>>>>> <CAPABILITY type="maxbins" version="1.0" />
>>>>>>
>>>>>> Assume any missing version attributes are "1.0" and everything
>>>>>> should be backwards compatible.
>>>>>
>>>>> Indeed I did increment the version, just because it seemed the
>>>>> right thing to do. However as far as I am aware these per-
>>>>> capability versions are totally superfluous when taken in
>>>>> context with the X-DAS-Version header, i.e. we do NOT want to
>>>>> make it possible to implement DAS 1.6 and features 1.0, for
>>>>> example. This could create a whole world of pain!
>>>>>
>>>>> IMO the per-capability version is unnecessary and confusing.
>>>>> ProServer does use it internally, but that can be easily
>>>>> changed. Getting rid of it would make the spec less confusing,
>>>>> but will of course break things that depend on the current
>>>>> format (if there are any).
>>>>>
>>>>> What do others think?
>>>>>
>>>>>> The only snag is that right now you have to parse all sources.
>>>>>> Technically both the registry and proserver allow you do do:
>>>>>> http://www.ebi.ac.uk/das-srv/genomicdas/das/sources/eqtl_rat_cis_fat
>>>>>>
>>>>>> But IIRC I didn't include this in the spec to keep things simple.
>>>>>>
>>>>>> If this isn't specified yet, how about allowing:
>>>>>>
>>>>>> http://www.ebi.ac.uk/das-srv/genomicdas/das/eqtl_rat_cis_fat/sources
>>>>>>
>>>>>> ?
>>>>>>
>>>>>> Then it's possible to stick with the model of passing a single
>>>>>> URI around to refer to a "DAS datasource", and stick a command
>>>>>> on the end of it to get the data you're after.
>>>>>
>>>>> Well, the reason we didn't use this format is simply that it
>>>>> doesn't "read" well, if only because "sources" is plural. What
>>>>> would perhaps make sense, and which would allow for quickly
>>>>> 'pinging' a source for other similar uses, is to use this URL
>>>>> format:
>>>>> http://www.ebi.ac.uk/das-srv/genomicdas/das/eqtl_rat_cis_fat
>>>>>
>>>>> Again, this is what seems most 'sensible' to me but I am happy
>>>>> to go with the consensus.
>>>>> _______________________________________________
>>>>> DAS mailing list
>>>>> DAS at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/das
>>>>
>>>> Jonathan Warren
>>>> Senior Developer and DAS coordinator
>>>> jw12 at sanger.ac.uk
>>>> Ext: 2314
>>>> Telephone: 01223 492314
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> The Wellcome Trust Sanger Institute is operated by Genome
>>>> ResearchLimited, a charity registered in England with number
>>>> 1021457 and acompany registered in England with number 2742969,
>>>> whose registeredoffice is 215 Euston Road, London, NW1 2BE.
>>>
>>
>> Jonathan Warren
>> Senior Developer and DAS coordinator
>> jw12 at sanger.ac.uk
>> Ext: 2314
>> Telephone: 01223 492314
>>
>>
>>
>>
>>
>>
>>
>> --
>> The Wellcome Trust Sanger Institute is operated by Genome
>> ResearchLimited, a charity registered in England with number
>> 1021457 and acompany registered in England with number 2742969,
>> whose registeredoffice is 215 Euston Road, London, NW1 2BE.
>
Jonathan Warren
Senior Developer and DAS coordinator
jw12 at sanger.ac.uk
Ext: 2314
Telephone: 01223 492314
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
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