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Rev Chgset Date Author Log Message
(edit) @327 [327] 6 months martijn 1.0 release branch
(edit) @326 [326] 6 months martijn Fixed: complains about schemaversion for completely unrelated errors
(edit) @325 [325] 6 months martijn Fix classpath in jUnit testing
(edit) @324 [324] 6 months martijn Fixes NPE in DataSource?.isMetabolite()
(edit) @323 [323] 6 months martijn Added WikiPathways?, removed urn:bridgedb urns. Fixes #46 and #50.
(edit) @322 [322] 6 months martijn Added contents page, to get a list of available organisms. Fixes #37
(edit) @321 [321] 6 months martijn New HMDB maker and Quality Control script
(edit) @320 [320] 6 months martijn Tweaked rdb.construct package for coming HMDB update
(edit) @319 [319] 6 months martijn Integrated o.b.rdb.construct in global build
(edit) @318 [318] 6 months martijn Made SimpleGdb? thread-safe. Instantiate with con- nection string instead …
(edit) @317 [317] 6 months martijn Refactoring dead code: Removed all methods pertaining to constructing …
(edit) @316 [316] 6 months martijn refactor LazyPst? to also handle resultset and connection
(edit) @315 [315] 7 months martijn Accidentally checked in old version of GdbProvider?, reverted. Adjusted …
(edit) @314 [314] 7 months thomas added script to copy derby database to mysql
(edit) @313 [313] 7 months martijn Various fixes to buildsystem
(edit) @312 [312] 7 months martijn update cronos to jar reorg
(edit) @311 [311] 7 months martijn Check axis code in, to be able to build offline
(edit) @310 [310] 7 months martijn Removed empty directories
(edit) @309 [309] 7 months martijn Removed empty direcotory
(edit) @308 [308] 7 months martijn Big project Reogranization: - all modules are named with their main …
(edit) @307 [307] 7 months jgao Add isFreeAttributeSearchSupported() to AttributeMapper?
(edit) @306 [306] 7 months martijn Replaced spaces with tab in datasources.txt
(edit) @305 [305] 7 months AlexanderPico added EnZm? for Maize
(edit) @304 [304] 7 months AlexanderPico modified linkout to gramene for EnAt?
(edit) @303 [303] 7 months AlexanderPico adding datasource for WikiGene? (already in databases and causing "null" in …
(edit) @302 [302] 7 months AlexanderPico removing temp fixes from repo
(edit) @301 [301] 7 months AlexanderPico modified to distinguish derby productions from web service
(edit) @300 [300] 7 months AlexanderPico added DataSources? for WikiGene?, GOSlim, and Symbols
(edit) @299 [299] 7 months jgao BioMart?: do not print the url when retrieve attributes for a dataset.
(edit) @298 [298] 7 months jgao BridgeRest?: cache supportedSrc/TgtDataSources and attributeSet; support …
(edit) @297 [297] 7 months martijn Nicer error message in IDMapperBiomart
(edit) @296 [296] 7 months jgao filterconversion move to webservice/biomart/util
(edit) @295 [295] 7 months jgao BiomartClient?: using absolute path of filterconversion.txt
(edit) @294 [294] 7 months martijn Checkstyle header rule isn't behaving right, disabled
(edit) @293 [293] 7 months martijn Upgraded to checkstyle 5.0
(edit) @292 [292] 8 months AlexanderPico updated to produce sql files for database reconstruction (bridedbrest + …
(edit) @291 [291] 8 months martijn Fixed Transitivity OutOfMemory? exception
(edit) @290 [290] 8 months martijn Throw checked exception with faulty connection string
(edit) @289 [289] 8 months martijn Bug fixed: SimpleGdbImpl?2 didn't store database name
(edit) @288 [288] 8 months martijn Coding style and warnings
(edit) @287 [287] 8 months martijn Refactoring of Biomart client. Fixes spurious errors in BioMart? in java 6
(edit) @286 [286] 8 months martijn Better error reporting in Biomart test
(edit) @285 [285] 8 months AlexanderPico added dump of table structure for 2-step reconstruction later
(edit) @284 [284] 8 months AlexanderPico fixed index creation on MySQLDerby attributes table
(edit) @283 [283] 8 months martijn Allow freeAttributeSearch to be used for id search as well
(edit) @282 [282] 8 months AlexanderPico indexing Derby version of mysql dbs for bridgedb rest server performance
(edit) @281 [281] 8 months AlexanderPico added Oj
(edit) @280 [280] 8 months AlexanderPico documented API solution for efg extraction
(edit) @279 [279] 8 months AlexanderPico added Zea mays (corn)
(edit) @278 [278] 8 months martijn Optimization: use dataSource parameter when targeting a single dataSource
(edit) @277 [277] 8 months martijn Optimization: rewrite of Xref stream parser
(edit) @276 [276] 8 months martijn Optimization: don't copy objects needlessly
(edit) @275 [275] 8 months martijn Allow code 204, now sometimes returned by new restlet
(edit) @274 [274] 8 months martijn Create new BridgeRest? url to show server configuration
(edit) @273 [273] 9 months thomas REST webservice: - updated restlet to latest version - added ant task to …
(edit) @272 [272] 9 months martijn GdbProvider? uses generic IDMapper, not IDMapperRdb. Makes it possible to …
(edit) @271 [271] 9 months martijn Added mysql driver
(edit) @270 [270] 9 months martijn New idmapper-jdbc driver for e.g. MySQL
(edit) @269 [269] 9 months martijn Allow using sql.Connection directly instead of using DBConnector wrapper, …
(edit) @268 [268] 9 months martijn Example and counter example for supplemental data
(edit) @267 [267] 10 months thomas fixed nugo linkout (fixes #39)
(edit) @266 [266] 10 months thomas fixed concurrentmodification exceptions when performing parallel requests
(edit) @265 [265] 10 months thomas - refactored rest service code (reuse common code patterns) - added url …
(edit) @264 [264] 10 months thomas added direct cronos mapping example
(edit) @263 [263] 10 months martijn Added a few examples to demonstrate the working of the API
(edit) @262 [262] 10 months martijn Get more affy out of CRONOS
(edit) @261 [261] 10 months martijn Updated README.txt
(edit) @260 [260] 10 months martijn Updated ComparisonScript?, with new 1000 affy id list
(edit) @259 [259] 10 months martijn tweak to build file
(edit) @258 [258] 10 months martijn Updated tar.gz target in build file
(edit) @257 [257] 10 months martijn Fixed 100% success bug in comparison script
(edit) @256 [256] 10 months martijn Comparison script, benchmarks and compares a number of idmappers
(edit) @255 [255] 10 months martijn Bunch of small fixes: * idmapper-derbyclient now creates connection with …
(edit) @254 [254] 10 months thomas updated bridgedb webservice examples to new url structure
(edit) @253 [253] 10 months martijn Fixed some jar references in build files
(edit) @252 [252] 10 months martijn Made Picr and PicrRest? comply with basic unit tests
(edit) @251 [251] 10 months AlexanderPico modifications to workaround new Funcgen database for probe annotations
(edit) @250 [250] 10 months AlexanderPico adapted for gathering probes and goslim
(edit) @249 [249] 10 months martijn Finalized build file for cronos
(edit) @248 [248] 10 months martijn tweaks: * picr: cache loadDatabases call * prefer named exception in …
(edit) @247 [247] 10 months martijn Refactoring of Biomart to get rid of all the map-in-map's. Fixed biomart …
(edit) @246 [246] 10 months martijn Cleanup of BrigeRest? IDMapper, make sure all arguments are URLEncoded.
(edit) @245 [245] 10 months martijn Cleanup of IDMapperFile
(edit) @244 [244] 10 months martijn Implemented unsupported operations in IDMapperPicr
(edit) @243 [243] 10 months martijn Added multiMap methods to internalUtils
(edit) @242 [242] 10 months martijn Simplified config parsing of IDMapperSynergizer
(edit) @241 [241] 10 months martijn Moved redundant getInputStream implementations to InternalUtils?
(edit) @240 [240] 10 months martijn Cleanup of IDMapperPicrRest
(edit) @239 [239] 10 months martijn Simplified config parsing of IDMapperPicr and IDMapperPicrRest
(edit) @238 [238] 10 months martijn Simplified argument parsing for Biomart driver
(edit) @237 [237] 10 months martijn Simplified signature of parseLocation helper
(edit) @236 [236] 10 months AlexanderPico fix #31
(edit) @235 [235] 10 months AlexanderPico fix #32
(edit) @234 [234] 10 months martijn New IDMapperCronos, see …
(edit) @233 [233] 10 months martijn Created InternalUtils? class to reduce redundancy
(edit) @232 [232] 10 months martijn Fix wrong overloaded mapID method signature in IDMapperPicrRest
(edit) @231 [231] 10 months martijn Added tests for Picr-rest and biomart
(edit) @230 [230] 10 months martijn Better JUnit test for BioMart?
(edit) @229 [229] 10 months martijn Change Set to Collection. API change, backwards compatible
(edit) @228 [228] 10 months martijn Make IDMapperFile comply to standard unit test
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