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="[email protected]" />
<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="[email protected]" />
<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
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Jonathan Warren
Senior Developer and DAS coordinator
[email protected]
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
[email protected]
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
[email protected]
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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