The DAS Registry^{V2.8.5 02 09 2010}

DAS Registration Server Release History

V2.8.5 02 09 2010

* added "no caching" bug fix

V2.8.4 31 08 2010

* added search help (links to EBEye search examples to show use of boolean and defaults etc)
* added extra notes to coordinate system help page
* removed not local flag from mirrored sources from now on (doesn't apply to sources already mirrored as their unique id shouldn't change)
* added dsn to both 1.53E and 1.6 rngs so we don't complain if a server rightly lists dsn as a capability - the registry tolerates dsn as it's deprecated but does not wholly support it as it's been superseeded by the sources command 

V2.8.3 13 08 2010

* allows sources that are not overall valid to be updated
* now source updated page contains validation information (no extra step)
* gives warning for types response where attribute type is present but is deprecated for 1.6 sources - more deprecation warnings to come.

V2.8.2 09 08 2010

* added feature_by_id capabilities testing

V2.8.1 06 08 2010

* added example to testcode for validationa and put working examples in for protein and genomic sources
* altered version attributes in relaxng documents for 1.6 to make optional in error_segment, uknown_feature etc

V2.8.0 27 07 2010

* changed scheduling of chron like jobs to be done with quartz package instead of resin servlet configuration
* fixed bug with user settings page (loginSettings.jsp).

V2.7.9 19 07 2010

* added cors (Access-Control-Allow-Origin=*) to headers

V2.7.8 15 07 2010

* added CORS/cors to capabilities testing

V2.7.7 1 07 2010

* fixed light links in search results and types display
* added sanger sources document

V2.7.6 18 06 2010

* fixed test_ranges for UCSC mirror and added note to description about filtering by type
* UCSC mirror allows single das source query
* fixed single das source query for mirrored prefixes such ENSEMB_ sources.
* changed codebase for spice.jnlp

V2.7.5 16 06 2010

* changed version uri and source uri back to DS_ numbers
* changed query_uri for sources to the new 1.6 url for single source.

V2.7.4 16 06 2010

* spice client pages added
* UCSC mirroring via a proxy that guesses matching UCSC coordinate systems
* added types searching to the new search interface

V2.7.3 11 06 2010

* registry sources command accepts the typeskeywords parameter to filter sources on whether their types contain the keywords
* added .xsd for use with JAXB

V2.7.2 09 06 2010

* changed sanger search url for new searching requests
* changed mirroring to update all sources even if it thinks they have not changed

V2.7.2 01 06 2010

* fixed bug with registering a new coordinate system
* fixed colors on logged in background menus

V2.7.1 27 05 2010

* sources.xml displays days before deletion if source is scheduled for deletion and spec for all sources
* fixed search button to work with return button
* put in links to projects in new search results and many other tweeks

V2.7.0 20 05 2010

* menu highlights which page a user is on.
* search interface uses registry web service and lucene back end indexing
* search interface implemented in javascript so can be used by any other client in there interface - contact jw12@sanger.ac.uk for more information.
* added new css style and search button
* added new search page
* added multiple coordinates to sources output on new search/list page

V2.6.4 12 05 2010

* added keywords parameter to sources cmds e.g. http://www.dasregistry.org/das/sources?keywords=zebrafish
* added keywords parameter to coordinatesystem command http://www.dasregistry.org/das/coordinatesystem?keywords=gorilla
* added total, start, end attributes to coordinatesystem request response if rows specified http://www.dasregistry.org/das/coordinatesystem?keywords=gene&rows=1-10
* changed coordinate systems methods to be Lists not [] arrays
* fixed bugs with projects pages and assigning sources to projects
* changed prefix in mirroring to getId so that coorinate systems should be allocated to mirrored sources?

V2.6.3 04 05 2010

* sources document also displays the root uri of a source in the version uri attribute and the DS_ number in the source uri attribute
* added rows capability for the sources cmd http://www.dasregistry.org/das/sources?rows=1-2
* extra command for registry dasregistry/das/knownCapabilities
* dasobert library changed to use lists not arrays for DasSources

V2.6.2 22 04 2010

* added links to DAS 1.6 documentation
* removed necessity for version in entry_points responses that was in code.

V2.6.1 15 04 2010

* fixed bug with Ontology validation for 1.6 and cvId checking
* added ontology checking for method tag cvId attribute in 1.6
* added option of text in target tag for features with 1.6 spec 

V2.6.0 19 03 2010

* added das 1.6 sources to the main listings as part of shifting to new 1.6 specification
* added geo3D to alignment.rng
* changed spec dropdown so any should come up at initial listings
* fixed bug with updateBean usage and added 1.6 spec option for updates 

V2.5.9 10 03 2010

* added caching of sources so sources.xml only updated when the database sources or coordinate systems are updated
* changed structure.rng

V2.5.8 4 03 2010

* altered entry_points.rng to meet 1.6 spec and tolerate deprecated version tag
* fixed email subject header

V2.5.7 2 03 2010

* added some gramene sources to mirroring
* fixed email bug where repeat sending

V2.5.6 1 03 2010

* altered sources.rng to allow for multiple versions
* turned email notification back on

V2.5.5 15 02 2010

* added version parameter for filtering sources in sources requests e.g. can do this now http://www.dasregistry/das1/sources?organism=9606&authority=NCBI&type=chromosome&version=36

V2.5.4 15 02 2010

* changed html in registration to for spec to be correct

V2.5.3 05 02 2010

* altered deletion by admins through interface to archive servers as well.
* added multi alignment to 1.6 alignment rng as well.

V2.5.2 02 02 2010

* added list of archived sources
* email notifications should be sent a week before deletion as well as 2 days after invalid and after deletion.

V2.5.1 27 01 2010

* altered course2010 page to point to EBI 
* added some documentation on scripting validation

V2.5.0 25 01 2010

* added new 1.6 spec way of getting single source http://www.dasregistry.org/das/DS_blah 
* added ability for programmatic validation of das sources via www.dasregistry.org/validate/ e.g. http://www.dasregistry.org/validate/?url=http://das.sanger.ac.uk/das/otter_das/&testcode=22:19173435,19372173
minumum parameters needed are the url and the testcode
* archive servers now implemented - so total number of servers will be reduced

V2.4.9 14 01 2010

* changed renewlease to be renewed when any valid capabilities found set to 0
* changed renewlease to be 1 when all valid
* deleting/archiving available but not initiated yet. 

V2.4.8 6 01 2010

* added request support for sources document for 1.6E compliant sources http://www.dasregistry/das1.6/sources as posed to 1.5* sources http://www.dasregistry/das/sources
* filter by specification 1.5E or 1.6E or get all from the web interface
* put types counts in statistics page
* put quicker statistics page up
* put specification as displayed by headers response by servers
* fixed bug where autovalidation said capability was valid if no testcode was available
* fixed bug where lights links were not specified correctly when a testcode was not provided (old ensembl sources)

V2.4.7 20 11 2009

* fixed bug where owner was not automatically set when a source was registered.

V2.4.6 20 11 2009

* fixed relaxng document for alignments with block as oneOrMore not one.
* added periodic indexing for future lucene and current sanger search
* fixed bug where validation would throw 500 error if form input not correct
* removed statistics pages temporarily until re-written as taking too long
* temporarily disabled organism requests url

V2.4.5 13 11 2009

* storage of types and number of types info
* display of types info in list services page using ajax with popout
* re-written validation code

V2.4.4 29 09 2009

* put a reset button on listServices page

V2.4.3 25 09 2009

* altered validation pages to show more informative responses
* all capabilities even if invalid are clickable for testing in listservices and validation pages
* fixed so query_uri is not necessary for certain capabilities such as feature_by_id
* cleaned up command generation using capabilities enum so we can just loop through all commands (using public Abstract getCommandString(String testcode) method.

V2.4.2 18 09 2009

* fixed bug with updating a registered server
* put more appropriate messages in mouse over of lights on listServer.jsp 
* fixed bug with maxbins validation so now only validates if features responses are valid!!

V2.4.1 07 09 2009

* added full stylesheet validation using http://www.dasregistry.org/validation/stylesheet.rng
* tests that servers have a unique id for each feature returned
* validation now validates most commands known to the registry for every server and produces probably valid for capablilites not stated by source provider but that appear to be valid = amber light
* put sorting by number of valid capabilities into the listservers.jsp page
* fixed example validation to work again
* changed capabilities to enums java 5 feature
* added error_segment, unknown_segment, unknown_feature, maxbins and next_feature (1.6 only) testing and support
* altered some caching? usage chart on stats page
* re-factored 1.6 and 1.5 validation so use same code
* more efficient getting of sources for list of servers sql.
* fixed bug with registering a new source so that if validation fails notify the user.
* added delete capability for prefixed sources for admins

V2.3.07 03 08 2009

* fizxed a bug with validating sources.xml as the url is set by the capabilities and randomly if sources is specified last it would use the wrong url resulting in a false duplicate entry.
* fixed bug when reading a sources document and a newline after string in an element the variables are trimmed so coordinate systems will match.

V2.3.06 - 29 07 2009

* error message from ontology validation only comes back when errors not just info so validation works.
* put traffic lights on project pages

V2.3.05 - 23 07 2009

* fixed bug so when updating validation status of a known source by web page or registration it should update status of lights instantly
* fixed bug with lights so when stated capability is not valid it shows it as red not clear for optional capabilities

V2.3.04 - 21 07 2009

* updated alignment.rng to comply with spec

V2.3.03 - 15 07 2009

* added send to a friend functionality with restricted input from form.

Version 2.3.0.2 - 2009 07 07

* added more complex checking of validation for lights status e.g if features specified then types must be implemented and if not therefor it's red
* valid capabilities can also be found using the SOAP service see http://www.biodas.org/wiki/Everything_DAS#Discovering_DAS_sources_programmatically
* fixed bug in validated_capabilities so now straight after registering a new source the valid sources will show green.

Version 2.3.0.1 - 2009 06 30

* Added support for client scripting to check on validity of sources: prop element with attribute value of "valid" in sources.xml response.
* Added lesser used capabilities to sources validation
* made changes to caching mechanism so sources and coordinates.xml responses should get updated more frequently??

Version 2.3 - 2009 06 30

* Traffic lights to show actual validation status of sources (not stated capabilities) in the list services page.
* relaxng validation enabled so only sources that comply are considered valid

Version 2.2.9.2 - 2009 06 10

* alphabetical list of organisms
* keyup event for ajax dropdown in admin pages
* fixed alignment relaxng validation bugs and schema

Version 2.2.9.1 - 2009 06 5

* changed ontology validation to check current ontologies using EBI web service
* forced compliance with validation and relaxng for newly registered servers and servers that are edited.
* added support for validating servers for up and coming 1.6 spec.
* updated ensembl default autoactivation links to new urls.

Version 2.2.9 - 2009 03 3

* added extra coordinate system (checks against registry and own sources) and capabilities validation to sources xml response validation.
* altered relaxng validation so doesn't complain about namespaces for interaction and structure DAS. Also fixed "Target" tag validation for features.
* added detailed schedule information for workshop 2009

Version 2.2.8 - 2009 02 5

* closed registration and updated web pages to reflect this.
* added extra documentation under "everything.. das" page.

Version 2.2.7 - 2008 01 30

* added extra validation to sources cmd response checking that checks if the coordinate systems returned in each source is
in the registry and uses all fields of the coordinate system i.e. unique Id and organism name need to match as well as category, version and taxid.
* added extra documentation with links to general DAS info on the help pages.

Version 2.2.6 - 2008 01 23

* added sources cmd support for das servers capabilities with relaxNG validation
* sources cmd response gets coordinate system and checks it exists in the registry
* mirroring is turned off until ensembl works nicely with registry
* admin users can now add new organisms through the interface.
* added structured documentation for DAS "everything you'll ever need to know about das" (link needs to be added

Version 2.2.5 - 2008 12 22

* added relaxNG validation with warnings for features, types, entry_points, alignments, sequence, interaction, structure.

Version 2.2.4 - TBC

* fixed a bug related to deleting of DAS sources
* improved stylesheet
 

Version 2.2.3 - 2008 01 29

* added the possibility to validate the BioSapiens Feature ontology
* fixed a bug during creation of projects
 

Version 2.2.2 - 2007 12 11

* added the ontology documentation
* fixed some bugs with validation of Interaction DAS servers.

Version 2.2.1 - 2007 11 30

* updated the course schedule
* some docu improvements

Version 2.2 - 2007 10 23

* new publication on DAS-registry and extensions (see http://www.biomedcentral.com/1471-2105/8/333)
* bundled the supported DAS extensions to the new spec DAS 1.53E (E for Extension)
* improved the user interface, now easier selection of DAS 
  sources by organism, authority and type
* added support for Interaction DAS extension
* added several new documentation pages
* added release history page
* new lastModified functionality
* re-enabled user configuration of auto-activation URLs
* updated to latest openid4java library and resolved several login issues

Version 2.1.1 - 2007 08 10

* fixed the broken validation mechanism

Version 2.1 - 2007 08 02

* log into the registry using OpenID - a free and decentralized  
  single sign on system
* share ownership of DAS sources between multiple users
* give reference to the funding of a DAS source by creating  
  "projects" and adding your DAS sources to them