[DAS2] DAS/2 GET requests
dalke at dalkescientific.com
Sat Jan 28 00:46:47 UTC 2006
> i have gotten my apollo das/2 adapter to read das2xml, and now i want
> write the GET part. is the GET protocol now stable, and is there a
> reference server implementing it? i've been using the affy server
> because i couldn't get data from the biodas server (only metadata).
> if GET is not yet stable, can i have an estimate of when it will be?
I was out the last couple days for a local bioinformatics meeting
and not checking email. I think I caught you just before Friday 5pm.
There are no servers which support it. The spec is still being
written, including for the XML formats.
Today I worked on the stylesheet data. That's now in CVS.
My working data is in the
"scratch" because I'm likely to move things around and I don't
like CVS's filename delete support.
These formats are support with a nearly complete RNC
== "sources.rnc" is used for "application/x-das-sources+xml"
I expect at most minor changes (probably in the "ASSEMBLY"
field and perhaps an element or attribute name.
== "residues.rnc" is used for "application/x-das-residues+xml"
(I think this should be renamed "segments" since the it's hard
to make a plural of "residues".)
I expect no changes except perhaps to add extensibility.
== "types.rnc" is used for "application/x-das-types+xml"
I mostly have questions about how to refer to the ontology
(which ontology? what naming scheme?)
I also don't understand how the "source" attribute is used.
The one example uses "curated". Are there other properties?
== "feature.rnc" is used for "application/x-das-features+xml"
At most minor changes, probably a few attributes added
when people start use the features.
There will be some changes for the style information. These
will come up during the sprint. I think they can wait.
I have XML examples for the different data types. These are
made by hand and are scientifically non-realistic. They are
of the forms:
I worked on a test script to make sure these documents were
valid. It's a new (but simple) language to load an XML
file and verify it against the given type, then ask it
for some simple properties. The idea is that I or others
can reimplement the script commands in another language
and/or data structure and verify that the loaded data is
processed correctly. (For example, correct handling of Unicode)
The interpreter is named "verify_examples.py" (in the scratch
area). The commands are of the form "*_cmds.txt". For example,
here is part of "sources_cmds.txt"
# Simple maintainer, one genome, no versions
load SOURCES "sources2.xml"
attrib das:MAINTAINER name
= Yoyodyne DNA Systems
What remains is:
- the locking information (I'm waiting for the sprint for this)
- working more on the formal writeup (notes are
- updating the query interface
NOTE: the query interface is nearly unchanged. Well, except
for the "regions" and "properties" subtrees which no longer exist.
The feature filters should be unchanged.
dalke at dalkescientific.com
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