Timeline
08/03/10:
- 15:16 Changeset [20808] by contrino
- modmine release 17
07/03/10:
- 23:23 DraftReleaseNotes_0_93 edited by rns
- (diff)
- 23:16 DraftReleaseNotes_0_93 edited by rns
- (diff)
- 22:57 DraftReleaseNotes_0_93 edited by rns
- 21:20 BioSources edited by julie
- (diff)
05/03/10:
- 17:07 Changeset [20807] by rns
- Should have been in [20806].
- 17:06 Changeset [20806] by rns
- Temporary change to enable gzipping of gff output, exporters need some …
- 17:05 Changeset [20805] by rns
- Better display of protocol descriptions.
- 14:57 Changeset [20803] by julie
- put cytoscape web on the protein page instead of interaction page
- 14:55 Changeset [20802] by julie
- turn off debug mode for demo purposes. change name of mine.
- 13:53 Changeset [20800] by julie
- add directory temporarily to hold SIF files. this is going to be replaced …
- 13:52 Changeset [20799] by julie
- add cytoscapeweb
04/03/10:
- 17:28 Changeset [20798] by rns
- Fix eclipse warning.
- 16:58 Changeset [20797] by julie
- show linkouts on pathways page.
- 16:57 Changeset [20796] by julie
- display datasource name (kegg|reactome) next to logo
- 16:23 Changeset [20795] by julie
- put quotes around classnames in error messages to make it more obvious …
- 16:14 Changeset [20794] by julie
- add links to ratmine from pathway, GOTerm, protein domain
- 15:44 Changeset [20792] by rns
- Cleaned up test for primers, added DCCid to output.
- 15:09 Changeset [20791] by julie
- temporarily remove gridwidget config
- 14:36 Changeset [20790] by rns
- Make modMine experiment and feature pages valid entry points.
- 14:11 Changeset [20789] by julie
- temporarily check in a hack for ratmine. if gene.ensemblId exists, use …
- 13:21 Changeset [20788] by julie
- remove local webapp from list. add comment
03/03/10:
- 20:56 ItemsAPIPerl edited by julie
- (diff)
- 16:44 Changeset [20787] by julie
- log error and return null when error is encountered rendering a widget
- 16:16 Changeset [20786] by contrino
- modmine web: temporary fix for long list of primer (column made unsortable …
- 16:14 Changeset [20785] by julie
- make sure only non-null identifiers are returned. not all genes have a …
- 15:06 Changeset [20784] by julie
- javadoc
- 13:59 Changeset [20783] by julie
- put orthologue links back in the preview. turn debugging mode back on, …
- 13:57 Changeset [20782] by julie
- 23.0 branch
- 13:57 Changeset [20781] by julie
- 23.0 tag
- 13:56 Changeset [20780] by contrino
- modmine web: temporary fix until primers are taken out of exp. factors
- 13:54 Changeset [20779] by julie
- turn off debugging mode so that the cache is updated less frequently. …
- 11:55 Changeset [20778] by rns
- Fix GFF3 headers.
- 11:45 Changeset [20777] by julie
- remove debug code
- 11:45 Changeset [20776] by julie
- remove orthologue link outs temporarily.
- 11:30 Changeset [20775] by julie
- fix comma-adding. check appropriate radio button as the radio buttons …
- 11:05 Changeset [20774] by contrino
- modmine web: cleaned and improved feature location checking
- 10:57 Changeset [20773] by julie
- restore optimised method
- 10:40 Changeset [20772] by julie
- treat taxonId as a string
- 10:19 Changeset [20771] by rns
- Added FlyAtlas? links on gene pages.
- 10:15 Changeset [20770] by julie
- fixed bug which caused link outs configured using taxonId to not appear on …
- 09:56 Changeset [20769] by julie
- use new helper method
02/03/10:
- 16:25 Changeset [20768] by contrino
- modmine web: now the check about located features works also for …
- 15:56 Changeset [20767] by julie
- fixed null pointer error.
- 14:54 Changeset [20766] by julie
- only return orthologues
- 13:57 Changeset [20765] by rns
- Fix bug that set empty bag names if whitespace was entered as a bag name.
- 13:55 Changeset [20764] by julie
- fix null pointer
- 13:50 Changeset [20763] by julie
- path fix
- 12:47 Changeset [20762] by julie
- fix query for local orthologues
- 12:18 Changeset [20761] by rachel
- updated for release 23.0
- 11:18 Changeset [20760] by julie
- fix path
- 11:02 Changeset [20759] by julie
- remove dataset, we're only going to constrain orthologues on organism. We …
- 11:01 Changeset [20758] by julie
- move methods to helper class as they are shared with the portal and ajax
01/03/10:
- 18:53 Changeset [20757] by rns
- Create indexes after all possible retrieve operations.
- 15:52 Changeset [20756] by rns
- Use standard chemical/x-fasta MIME type for sequence export.
- 14:21 Changeset [20755] by rns
- Export GFF3 as tab-separated-values mime type.
- 14:19 Changeset [20754] by julie
- portal bug fix
- 10:35 Changeset [20753] by julie
- added missing arguments
- 10:13 Changeset [20752] by julie
- added missing arguments
28/02/10:
- 16:26 Changeset [20751] by julie
- revert change made in [20719]
- 16:03 Changeset [20750] by rns
- Add Transcript to common features.
- 12:45 Changeset [20749] by rns
- Add another priority for length.
- 11:56 Changeset [20748] by rns
- Fix location priority mistake.
- 11:44 Changeset [20747] by rns
- Added Transcript location priority.
- 10:45 Changeset [20746] by rns
- Added featureType priority.
27/02/10:
- 12:32 Changeset [20745] by julie
- added some new class definitions for modmine
- 12:16 Changeset [20744] by julie
- updated data categories for 23.0
26/02/10:
- 20:56 Changeset [20743] by rns
- Add some workarounds for broken DAG structure, check for adding null …
- 18:14 Changeset [20742] by julie
- missing file from [20738]
- 16:54 Changeset [20741] by contrino
- modmine web: added check for submission for located features. TODO: add to …
- 16:15 Changeset [20740] by julie
- refactor portal to use new method that returns list of object IDs instead …
- 16:11 Changeset [20739] by julie
- don't display the dropdown select if there is only one option
- 16:10 Changeset [20738] by julie
- remove local version of StringUtils?.getEmpty(). we should use the apache …
- 13:11 Changeset [20737] by julie
- use correct default values
- 11:19 Changeset [20736] by julie
- remove duplicate config entry
- 10:25 Changeset [20735] by julie
- test fix
25/02/10:
- 17:34 Changeset [20734] by rns
- Fix gene identifiers before putting them in primaryIdentifier to item id …
- 16:00 Changeset [20733] by julie
- javadoc. checkstyle
- 13:50 Changeset [20732] by rns
- Add special case for creating DatabaseRecords? for broken SRA acc fields in …
- 12:21 Changeset [20729] by rns
- Try to make genes unique between created features and antibody/strain …
- 10:42 Changeset [20728] by julie
- use dropdown instead of boxy div. use same query as portal to convert …
- 09:09 Changeset [20727] by rns
- Add missing OrthologueEvidenceCode? key.
24/02/10:
- 17:44 Changeset [20726] by rns
- Add scoreProtocol and ResultFile? to model.
- 17:43 ReleaseProcedure edited by julie
- (diff)
- 17:43 ReleaseProcedure edited by julie
- (diff)
- 17:07 Changeset [20725] by contrino
- modmine: added also fastafor dpse
- 16:59 Changeset [20724] by contrino
- modmine: added dpse
- 16:59 Changeset [20723] by rns
- Add a collection of DatabaseRecords? to Submission and and extract GEO, …
- 15:30 Changeset [20722] by contrino
- modmine: noe update_publication after metadata
- 14:24 Changeset [20721] by contrino
- modmine meta: shortName -> name, fullName and correction of bug for …
- 10:47 Changeset [20720] by rns
- Removed unused code, fixed eclipse warnings.
- 10:06 Changeset [20719] by julie
- don't throw an exception if template has a list. this method is called on …
23/02/10:
- 17:19 Changeset [20717] by rns
- Fix bug with applied protocol outputs.
- 15:45 Changeset [20716] by julie
- make error msg more specific
- 14:43 Changeset [20715] by contrino
- modmine meta: added embargo date
- 14:25 Changeset [20714] by julie
- help msg
- 14:14 Changeset [20713] by rns
- Don't set RNA tiling array for some some experimentTypes.
- 11:52 Changeset [20712] by rns
- Make protocols unique, add wikiLink and version attributes.
- 10:39 Changeset [20711] by julie
- javadoc
- 10:39 Changeset [20710] by julie
- sp
22/02/10:
- 10:43 Changeset [20709] by contrino
- added natural transposable elements
- 10:37 Changeset [20708] by julie
- temporarily remove precompute table logging to help improve log …
- 10:37 Changeset [20707] by julie
- revert changes to checkstyle config made in [20691]
- 10:33 Changeset [20706] by julie
- checkstyle fix
- 10:33 Changeset [20705] by julie
- fix error msg
21/02/10:
- 16:38 Changeset [20704] by julie
- only link out to reactome with dmel proteins for now. we can link out on …
- 16:37 Changeset [20703] by julie
- add evidence code to objectstore summary config
- 15:07 Changeset [20702] by julie
- uniqueify evidence code
- 15:07 Changeset [20701] by julie
- add key for evidence code.
18/02/10:
- 11:23 Changeset [20699] by julie
- add list of friendly intermines
- 11:18 Changeset [20698] by julie
- link outs to other intermines
17/02/10:
- 17:29 Changeset [20697] by julie
- fix wildcard character in perl api example
- 16:41 Changeset [20696] by julie
- activate checkstyle
- 14:29 Changeset [20695] by julie
- fix regexp. correct pathquery constraint, datasets is a collection. …
12/02/10:
- 17:55 Changeset [20694] by mnw21
- Merged trunk
- 17:52 Changeset [20693] by mnw21
- PathQueryBinding? half finished
- 14:39 Changeset [20692] by julie
- remove link to ratmine.
- 14:34 Changeset [20691] by contrino
- modmine web: added genome and modmine versions to gff export
- 12:29 Changeset [20690] by julie
- get organism short name for genes in your list.
11/02/10:
- 14:13 Changeset [20689] by julie
- allow dataset to be an optional constraint when converting orthologues
- 14:10 Changeset [20688] by julie
- make a box for each bag displayer. need to not hardcode name
- 11:35 Changeset [20687] by julie
- add method to get organism shortname, eg. D. melanogaster
- 10:49 Changeset [20686] by julie
- remove duplicate method, use util method instead.
- 10:29 Changeset [20685] by julie
- eclipse warnings
- 07:49 Changeset [20684] by rns
- Add description for MiRNATarget and more fields to Transcript inline …
- 02:09 Changeset [20683] by rns
- Enable RESTful URLs for objects, e.g. /mine-name/rest/view/gene/eve
10/02/10:
- 16:40 Changeset [20682] by mnw21
- Add clone method
- 16:38 Changeset [20681] by julie
- move method to helper class.
- 15:57 Changeset [20680] by contrino
- modmine meta: now failing only if the target names are different (not only …
- 11:14 Changeset [20679] by julie
- restore features removed for debugging purposes. check for chromosome.
09/02/10:
- 17:51 Changeset [20678] by mnw21
- Merge in trunk
- 17:24 Changeset [20677] by mnw21
- Almost complete test coverage
- 16:59 Changeset [20676] by julie
- test fix
- 16:58 Changeset [20675] by julie
- add dataset to mapping query output
- 14:35 Changeset [20673] by julie
- test fix
- 14:28 Changeset [20672] by rachel
- Added stuff for >= and <=
- 13:56 Changeset [20671] by julie
- fix import
- 13:55 Changeset [20670] by julie
- update flybase chado query. get deletion locations from feature location …
- 13:35 Changeset [20669] by julie
- eclipse warning
- 13:35 Changeset [20668] by julie
- grammar
- 13:05 Changeset [20667] by julie
- move util to widget package
- 12:43 Changeset [20666] by julie
- rename class
- 12:42 Changeset [20665] by julie
- fixed eclipse warnings
- 01:22 Changeset [20663] by rns
- Branch for testing out clean/RESTful report page URLs
08/02/10:
- 15:03 Changeset [20662] by julie
- rename widgetutil, this isn't a Util class as we've redefined them during …
- 15:01 Changeset [20661] by julie
- typo. forgot space in query
- 10:51 Changeset [20659] by julie
- update deletion location query
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