DAS Workshop 2011

thickbugΛογισμικό & κατασκευή λογ/κού

28 Οκτ 2013 (πριν από 3 χρόνια και 7 μήνες)

76 εμφανίσεις

Update on the DAS Registry

DAS Workshop 2011

Jonathan Warren

>50,000

-
~1300 sources currently


-
break sources up by genome, work soon?

-
Increasing:


-
Next Gen files in DAS


-
multiple genomes per organism


-
many different organisms and genomes
sequenced.




Content

-
General updates

-
Interface/web service improvements


-
List Sources


-
List Servers


-
Search

-
To Do In the Future



General Updates

-
Moved to new VMs.. and Tomcat6

-
sources now become inactive rather than archived

-
registered servers have their sources document auto
updated in the registry

-
added .xsd for use with JAXB

-
changed coordinate system urls to xml response for
clients rather than html for browsers
http://www.dasregistry.org/coordsys/CS_DS6

-
The regsitry web service accepts ; and &

-
UCSC mirroring via a proxy that guesses matching UCSC
coordinate systems
http://www.dasregistry.org/ucsc/das/sources

-
sources and coordinatesystem caching

-
extra command for registry
dasregistry/das/knownCapabilities

General continued:

-
rows support for sources, coordinatesystems requests

-
Web Service examples
http://www.dasregistry.org/DASCommandExamples.jsp

-
validate command can be used to validate a server using
the das registry and get back an xml sources response
containing extra properties pertaining to the validity of
specific capabilities:

http://www.dasregistry.org/validate?url=http://das.sanger.
ac.uk/das/otter_das/&testcode=22:19173435,19372173


List Sources:

-
list sources view

-
updated list sources page uses the registry web
service

-
old page still available for direct access to
database.

List Sources web service:

-
http://www.dasregistry.org/das/sources?serverUrl=http
://www.ensembl.org/das&rows=1
-
10

-
request support for sources document for 1.6E
compliant sources
http://www.dasregistry.org/das1.6/sources as apposed
to 1.5 sources
http://www.dasregistry.org/das1.5/sources

-
sources.xml displays days before deletion if source is
scheduled for deletion and spec for all sources

-
filter sources based on validcapability as well as
capability.

Sources Web Service:

-
sorting added to sources web service


-
id


-
nickname or title


-
status (ie. uses leasedate)


-
registerdate


-
leasedate


-
url


-
adminemail


-
description


-
capabilities (user/server specified)


-
validcapabilities (sorts on valid capabilities determined
by the registry not user/server selected)


-
coordinatesystem (sorts by the number of coordinate
systems a source specifies).

-
reverse=true parameter reverses the order of the above
sorts.

-
sorts on listSources.jsp


List Servers:

-
servers listing capability
http://www.dasregistry.org/das/servers

-

see listSources.jsp

Search:

-
search interface


-
registry web service


-
lucene back end indexing

-
search interface implemented in javascript so
can be used by any other client in their
interface

-
added search help (links to EBEye search
examples to show use of boolean and defaults
etc)

-
added types searching to the new search
interface

Scripting for Searching:


keywords parameter
http://www.dasregistry.org/das/sources?keywords=zebrafis
h


typeskeywords
http://www.dasregistry.org/das/sources?typeskeyword
s=gene


keywords parameter
http://www.dasregistry.org/das/coordinatesystem?key
words=gorilla

Scripting Continued:

-

knownCapabilities (responds with the DAS
capabilities that the registry is aware of and
supports):

http://www.dasregistry.org/das/knownCapabilities

-
validate command can be used to validate a
server using the das registry and get back an
xml sources response containing extra
properties pertaining to the validity of specific
capabilities:

http://www.dasregistry.org/validate?url=http://das.
sanger.ac.uk/das/otter_das/&testcode=22:19173
435,19372173

Archiving:

-
Sources are archived/ labelled inactive if non of
the specified capabilities are valid.

-

If server controlled archived if not in the
sources.xml

To do:

-
Get rid of Prefixes for mirrored sources
completely

-
header validation?

-
smoother validation interface with helpful tips
and more meaningful validation error
messages.

-
ping sources to see if responding at all
separately



Should the DAS registry say list all sources and
just give information on their validity rather
than archiving sources. Should clients do all
they can to accommodate poor data sources or
should they link to validation data and
encourage correct data source
compliance?(JW)

Day 3 topic :

Acknowledgments:

Andy Jenkinson (EBI)

Rafael Jiminez

Bernat Gel

Jose Villaveces

Gustavo Salazar

James Smith

Andreas Prlic

Gregg Helt

Lincoln Stein

Tim Hubbard

The DAS community