Timeline



Sep 9, 2005:

8:28 PM Changeset [1329] by Nicklas Nordborg
Fixed bad link to installation document
4:40 PM Changeset [1328] by Gregory Vincic
2:14 PM Changeset [1327] by Nicklas Nordborg
The alpha 5 release
2:07 PM Changeset [1326] by Nicklas Nordborg
Released Base 2.0 alpha 5!!!!
2:04 PM Changeset [1325] by Gregory Vincic
Documenting
2:03 PM Changeset [1324] by Gregory Vincic
Added getPlateTypeById and documenting
1:56 PM Changeset [1323] by Nicklas Nordborg
ant dist now takes the correct base.config file
1:51 PM Changeset [1322] by Nicklas Nordborg
Updated installation instructions
1:47 PM Changeset [1321] by Nicklas Nordborg
Added TODO note for jarPath
1:44 PM Changeset [1320] by Gregory Vincic
LabeledExtract? now also sets Extract. Added getExtractById in …
1:25 PM Changeset [1319] by Gregory Vincic
MappedPlates? are working now
1:21 PM Changeset [1318] by Gregory Vincic
Added migration instructions
1:10 PM Changeset [1317] by Gregory Vincic
Activiated file removal
11:06 AM Changeset [1316] by Nicklas Nordborg
Added dist.migrate to ant dist
11:01 AM Changeset [1315] by Gregory Vincic
Documenting
11:01 AM Changeset [1314] by Gregory Vincic
createItem is now protected
11:00 AM Changeset [1313] by Nicklas Nordborg
Added installation instructions based on the old instructions for the …
10:47 AM Changeset [1312] by Nicklas Nordborg
ReporterBatcher? now evicts reporters returned by exists and getByExternalId
10:34 AM Changeset [1311] by Nicklas Nordborg
The PluginRequest? returned by Job.execute() now update the status of …
9:00 AM Changeset [1310] by Gregory Vincic
Status update 2005-09-08

Sep 8, 2005:

7:02 PM Changeset [1309] by Johan Enell
ReporterMap? test
4:47 PM Changeset [1308] by Gregory Vincic
Documenting
4:41 PM Changeset [1307] by Gregory Vincic
Documenting
4:34 PM Changeset [1306] by Gregory Vincic
Adding getProtocolTypeById and getPlateTypeById and documenting
4:22 PM Changeset [1305] by Gregory Vincic
Documenting
4:21 PM Changeset [1304] by Gregory Vincic
Documenting
3:44 PM Changeset [1303] by Gregory Vincic
Fixing bug for reporterId and wellId's
3:43 PM Changeset [1302] by Gregory Vincic
Changing createItem method to protected
3:43 PM Changeset [1301] by Gregory Vincic
Moving null value check into saveItem() in run() method
3:42 PM Changeset [1300] by Gregory Vincic
Documenting
3:40 PM Changeset [1299] by Nicklas Nordborg
Fixed bug where properties in ArrayDesignBlock:s didn't get updated
3:23 PM Changeset [1298] by Nicklas Nordborg
Fixed javadoc warnings
2:34 PM Changeset [1297] by Johan Enell
1:33 PM Changeset [1296] by Gregory Vincic
Documenting
1:01 PM Changeset [1295] by Gregory Vincic
Documenting
12:49 PM Changeset [1294] by Nicklas Nordborg
Added success parameter to AbstractFlatFileImporter?.end() method
12:42 PM Changeset [1293] by Nicklas Nordborg
Changed TestReporter? to display other columns.
12:31 PM Changeset [1292] by Nicklas Nordborg
Added "Update existing reporter" option to ReporterFlatFileParser?
12:07 PM Changeset [1291] by Gregory Vincic
Documenting
12:02 PM Changeset [1290] by Nicklas Nordborg
Added ConsoleProgressReporter? and updated test programs to use it
11:30 AM Changeset [1289] by Nicklas Nordborg
Fixed bug in FlatFileParser?
11:28 AM Changeset [1288] by Gregory Vincic
Fixing setArraySlide for Hybridizations
11:27 AM Changeset [1287] by Gregory Vincic
Fixing log output in the select method
11:20 AM Changeset [1286] by Nicklas Nordborg
Fixed ant dist to include documentation, etc.
10:41 AM Changeset [1285] by Nicklas Nordborg
Added JDOM
10:39 AM Changeset [1284] by Nicklas Nordborg
Added license texts and information about 3:rd-party components
10:35 AM Changeset [1283] by Gregory Vincic
Fixed new call to BlockInfo?
10:08 AM Changeset [1282] by Gregory Vincic
Fixed new call to BlockInfo?
10:05 AM Changeset [1281] by Gregory Vincic
Removing PhysicalFileTransfer?.java
10:03 AM Changeset [1280] by Gregory Vincic
ArrayDesignTransfer? now seems to work, transferring the basic data
10:01 AM Changeset [1279] by Gregory Vincic
Added getReporterById() method
10:00 AM Changeset [1278] by Gregory Vincic
Added a few columns to the sql query
9:59 AM Changeset [1277] by Gregory Vincic
Added getPlateById() method
9:58 AM Changeset [1276] by Gregory Vincic
Added getMaxId() method
9:35 AM Changeset [1275] by Nicklas Nordborg
Added support for min and max data columns parameters to …

Sep 7, 2005:

5:17 PM Changeset [1274] by Johan Enell
ReporterMap? importer added
3:57 PM Changeset [1273] by Nicklas Nordborg
Added LineType? enum to FlatFileParser? instead of using int constants
3:28 PM Changeset [1272] by Nicklas Nordborg
Added more constructors to ParameterType:s
2:12 PM Changeset [1271] by Gregory Vincic
Initial revision
1:33 PM Changeset [1270] by Nicklas Nordborg
Documented Abstract- and ReporterFlatFileImporter?.
12:27 PM Changeset [1269] by Nicklas Nordborg
Added AbstractPlugin?.validateRequestParameters and javadoc
11:45 AM Changeset [1268] by Nicklas Nordborg
Fixed bad image
11:29 AM Changeset [1267] by Nicklas Nordborg
Added Plugin.getItems() method and changed about() and type() to …
9:06 AM Changeset [1266] by Nicklas Nordborg
Fixed problem with ItemParameterValue? mapping

Sep 6, 2005:

8:41 PM Changeset [1265] by Nicklas Nordborg
Fixed a NPE in ReporterFlatFileImporter? Added better constructors to …
4:53 PM Changeset [1264] by Johan Enell
Test job
4:11 PM Changeset [1263] by Nicklas Nordborg
Added import of extended columns to ReporterFlatFileImporter?
4:06 PM Changeset [1262] by Gregory Vincic
Removing verifyMappedIds()
4:00 PM Changeset [1261] by Gregory Vincic
Saving arrayDesign before adding block
3:50 PM Changeset [1260] by Gregory Vincic
Adding uggly fix to the problem of missing items from queries
2:44 PM Changeset [1259] by Gregory Vincic
Cleaning up requirements section
2:17 PM Changeset [1258] by Nicklas Nordborg
Test reporter import now delete it's job
2:07 PM Changeset [1257] by Johan Enell
create and delete in TestJob?
1:49 PM Changeset [1256] by Nicklas Nordborg
ReporterFlatFileImporter? now has a working skeleton. Added test class.
1:47 PM Changeset [1255] by Gregory Vincic
Fixed dependency check
1:02 PM Changeset [1254] by Gregory Vincic
Adding createItem and getPlateList
11:12 AM Changeset [1253] by Johan Enell
added ProgressReporter? parameter to Job.execute()
11:08 AM Changeset [1252] by Johan Enell
added ProgressReporter? parameter to Job.execute()
11:00 AM Changeset [1251] by Johan Enell
Plugin configuratin is tested
10:29 AM Changeset [1250] by Gregory Vincic
Documenting
10:28 AM Changeset [1249] by Gregory Vincic
Initial revision of ArraySlide? and ArrayBatchTransfer?
9:53 AM Changeset [1248] by Nicklas Nordborg
ReporterFlatFileImporter? is now ready to be tested
9:34 AM Changeset [1247] by Johan Enell
added throws baseexception in the interface

Sep 5, 2005:

8:34 PM Changeset [1246] by Gregory Vincic
Removing @author statements from methods
7:50 PM Changeset [1245] by Gregory Vincic
Adding dependency checking
4:09 PM Changeset [1244] by Nicklas Nordborg
Readded AbstractFlatFileImporter? and ReporterFlatFileImporter?.
3:56 PM Changeset [1243] by Johan Enell
added the build folder to svn:ignore
3:53 PM Changeset [1242] by Johan Enell
PluginDefinition? tested
3:40 PM Changeset [1241] by Johan Enell
id tag updated
3:38 PM Changeset [1240] by Johan Enell
NullPlugin? created
2:14 PM Changeset [1239] by Johan Enell
AbstractPlugin? created
1:57 PM Changeset [1238] by Nicklas Nordborg
Implemented core part of the plugin system
1:42 PM Changeset [1237] by Gregory Vincic
Adding SampleTissue?
12:11 PM Changeset [1236] by Gregory Vincic
Documenting
12:10 PM Changeset [1235] by Gregory Vincic
Initial revision
12:09 PM Changeset [1234] by Gregory Vincic
Initial revision
12:08 PM Changeset [1233] by Gregory Vincic
Renamming getSelects to countRows
11:56 AM Changeset [1232] by Gregory Vincic
Documenting
11:55 AM Changeset [1231] by Gregory Vincic
Documenting
11:54 AM Changeset [1230] by Gregory Vincic
Documenting
11:54 AM Changeset [1229] by Gregory Vincic
Documenting
11:53 AM Changeset [1228] by Gregory Vincic
Using setCommonData
11:53 AM Changeset [1227] by Gregory Vincic
Documenting
11:52 AM Changeset [1226] by Gregory Vincic
Documenting
11:36 AM Changeset [1225] by Gregory Vincic
Using incode class in quickstart
11:24 AM Changeset [1224] by Gregory Vincic
Adding requirements and clarifying quickstart
11:21 AM Changeset [1223] by Gregory Vincic
Documenting
9:49 AM Changeset [1222] by Gregory Vincic
Documenting
9:27 AM Changeset [1221] by Gregory Vincic
Fixing stop call
9:26 AM Changeset [1220] by Gregory Vincic
Documenting
9:02 AM Changeset [1219] by Nicklas Nordborg
Removed PluginJobData? and made JobData? have a type and optional …
8:49 AM Changeset [1218] by Gregory Vincic
Documenting
8:23 AM Changeset [1217] by Gregory Vincic
Set MappedPlates? to no, it's not working properly
8:01 AM Changeset [1216] by Gregory Vincic
Added ArrayBatch?- and ArrayDesignTransfer? classes

Sep 2, 2005:

5:05 PM Changeset [1215] by Johan Enell
getters in About
5:03 PM Changeset [1214] by Johan Enell
updated plugin design
4:51 PM Changeset [1213] by Johan Enell
just a small syntax update
4:04 PM Changeset [1212] by Nicklas Nordborg
Begin implementation of new plugin system
3:55 PM Changeset [1211] by Johan Enell
updated plugin design
1:56 PM Changeset [1210] by Gregory Vincic
Initial revision
1:56 PM Changeset [1209] by Gregory Vincic
Including Array*
1:54 PM Changeset [1208] by Gregory Vincic
Bug fix, Protocols do not have to have a file associated to them
1:54 PM Changeset [1207] by Gregory Vincic
Adding ArrayBatch? and ArrayDesign? Transfer
1:53 PM Changeset [1206] by Gregory Vincic
Initial revision
1:50 PM Changeset [1205] by Nicklas Nordborg
New design of the plugin system
1:25 PM Changeset [1204] by Johan Enell
updated plugin design
1:04 PM Changeset [1203] by Gregory Vincic
Fixing bug in chown
1:03 PM Changeset [1202] by Gregory Vincic
Saving file within createItem
1:03 PM Changeset [1201] by Gregory Vincic
Added some logging
1:02 PM Changeset [1200] by Gregory Vincic
Using DELIMITER for separation of data in the description
1:01 PM Changeset [1199] by Gregory Vincic
Commenting
1:01 PM Changeset [1198] by Gregory Vincic
Nicer tissue string
1:00 PM Changeset [1197] by Gregory Vincic
Only transfer files that are of size 0
1:00 PM Changeset [1196] by Gregory Vincic
Added filechecking through md5
12:59 PM Changeset [1195] by Gregory Vincic
Added a PhysicalFileTransfer? after UploadTransfer? is done
12:58 PM Changeset [1194] by Gregory Vincic
Initial revision
11:49 AM Changeset [1193] by Gregory Vincic
Plates are now destroyed after transfer

Sep 1, 2005:

1:40 PM Changeset [1192] by Nicklas Nordborg
Added missing parameter types and renamed TextParameterType? to …
1:30 PM Changeset [1191] by Nicklas Nordborg
Removed unneccessary code from Type
1:23 PM Changeset [1190] by Nicklas Nordborg
Changed ParameterType? (and subclasses) to use the new Values class. …
12:23 PM Changeset [1189] by Gregory Vincic
removed value is now set
11:11 AM Changeset [1188] by Nicklas Nordborg
Added Values class and made Annotation and AnnotationType? use it.
10:31 AM Changeset [1187] by Gregory Vincic
Removing TODO comments
8:57 AM Changeset [1186] by Nicklas Nordborg
Updated development status. Made Parameters (9) and Plugins execution …

Aug 31, 2005:

8:35 PM Changeset [1185] by Nicklas Nordborg
Updated development status
6:08 PM Changeset [1184] by Gregory Vincic
Adding Protocols section
3:54 PM Changeset [1183] by Gregory Vincic
Fixing stop statement
3:44 PM Changeset [1182] by Nicklas Nordborg
Added Directory.exists() method
3:42 PM Changeset [1181] by Gregory Vincic
Fixing stop statement
3:24 PM Changeset [1180] by Nicklas Nordborg
Added Job and made lots of changes to the ParameterType? and …
1:33 PM Changeset [1179] by Nicklas Nordborg
Changes to the plugin/jobs diagram
11:28 AM Changeset [1178] by Gregory Vincic
Added uploadFT to ProtocolFileTransfer?
11:27 AM Changeset [1177] by Gregory Vincic
Added uploadFT to ProtocolFileTransfer?
11:25 AM Changeset [1176] by Gregory Vincic
Added getFileByName
9:55 AM Changeset [1175] by Gregory Vincic
Fixed missing externalId
9:12 AM Changeset [1174] by Gregory Vincic
Fixed stop() call

Aug 30, 2005:

4:56 PM Changeset [1173] by Gregory Vincic
Added setDescription
4:05 PM Changeset [1172] by Nicklas Nordborg
Oops, here is the new JobData? also
4:04 PM Changeset [1171] by Nicklas Nordborg
First version of JobData?
3:18 PM Changeset [1170] by Gregory Vincic
Major rewrite and bug fix
3:18 PM Changeset [1169] by Gregory Vincic
Added some logging
3:17 PM Changeset [1168] by Gregory Vincic
3:16 PM Changeset [1167] by Gregory Vincic
Changing connect() and configure() to protected methods for …
3:15 PM Changeset [1166] by Gregory Vincic
Major rewrite, using run() in Transfer.java
3:14 PM Changeset [1165] by Gregory Vincic
Major rewrite, using run() in Transfer.java
3:13 PM Changeset [1164] by Gregory Vincic
Rewrote output decisions in run()
3:12 PM Changeset [1163] by Gregory Vincic
Added check for protocolFileTransfer in constructor
3:11 PM Changeset [1162] by Gregory Vincic
Adding logging of which users are created
3:10 PM Changeset [1161] by Gregory Vincic
Initial revision
3:10 PM Changeset [1160] by Gregory Vincic
Fixing stop call
3:09 PM Changeset [1159] by Gregory Vincic
Documenting
3:08 PM Changeset [1158] by Gregory Vincic
Adding stop(method, str) and log(method,e)
2:51 PM Changeset [1157] by Nicklas Nordborg
Fixed javadoc warnings
2:12 PM Changeset [1156] by Nicklas Nordborg
Implemented methods for inheriting annotations and fixed some errors …
11:53 AM Changeset [1155] by Nicklas Nordborg
Removed an old TODO
11:52 AM Changeset [1154] by Nicklas Nordborg
Finished isUsed() method for Protocol
11:48 AM Changeset [1153] by Nicklas Nordborg
Fixed error in Array slides diagram
11:45 AM Changeset [1152] by Nicklas Nordborg
Fixed isUsed method in Hardware and inverse mappings for ArrayDesign?
11:22 AM Changeset [1151] by Nicklas Nordborg
Removed an old TODO
11:21 AM Changeset [1150] by Nicklas Nordborg
Removed unused code
11:19 AM Changeset [1149] by Nicklas Nordborg
Fixed isUsed and getReporter in Well
11:06 AM Changeset [1148] by Nicklas Nordborg
Fixed mappings for Plate, PlateParents? and PlateMapping?
9:08 AM Changeset [1147] by Nicklas Nordborg
Added getAnnotatableParents to Annotatable interface

Aug 29, 2005:

9:03 PM Changeset [1146] by Nicklas Nordborg
Check that the database supports transactions at startup
3:46 PM Changeset [1145] by Nicklas Nordborg
Updated raw data uml diagram
3:45 PM Changeset [1144] by Nicklas Nordborg
Updated batching documentation
1:36 PM Changeset [1143] by Nicklas Nordborg
Fixed batching of Features and AffyFeatures?
9:20 AM Changeset [1142] by Nicklas Nordborg
Added RawDataUtil? and documented some methods for raw data and reporters

Aug 26, 2005:

8:17 PM Changeset [1141] by Nicklas Nordborg
Updated development status
3:37 PM Changeset [1140] by Nicklas Nordborg
Added fetching of spot images and test program for it
2:23 PM Changeset [1139] by Nicklas Nordborg
Added SpotImages? and test program to create spot images
11:37 AM Changeset [1138] by Johan Enell
Major changes to the plugin system
9:16 AM Changeset [1137] by Nicklas Nordborg
PlateMapping? can now take empty source plates in the apply() method

Aug 25, 2005:

3:35 PM Changeset [1136] by Nicklas Nordborg
Fixed javadoc warnings
2:59 PM Changeset [1135] by Nicklas Nordborg
Raw data is not checked agains arraydesign of raw bioassay Added test …
11:41 AM Changeset [1134] by Nicklas Nordborg
More redesign of the BasicBatcher? to make it more like the BasicItem?
10:40 AM Changeset [1133] by Gregory Vincic
Splitting Plate into Unmapped and Mapped PlateTransfers?
10:39 AM Changeset [1132] by Gregory Vincic
Initial revision
10:38 AM Changeset [1131] by Gregory Vincic
Renaming class properly
10:36 AM Changeset [1130] by Gregory Vincic
Splitting PlateTransfer? into Mapped and Unmapped PlateTransfer?
10:36 AM Changeset [1129] by Gregory Vincic
Adding resetItemsCounter()
10:33 AM Changeset [1128] by Gregory Vincic
Removing use of COMMIT_SIZE
10:32 AM Changeset [1127] by Gregory Vincic
Removing use of COMMIT_SIZE

Aug 24, 2005:

4:06 PM Changeset [1126] by Gregory Vincic
Adding createItem method and using Transfer.run( sql ) run eash transfer
3:32 PM Changeset [1125] by Nicklas Nordborg
Updated hybridizations diagram
3:27 PM Changeset [1124] by Nicklas Nordborg
Minor redesign of the batch classes First version of actually batching …
12:26 PM Changeset [1123] by Nicklas Nordborg
Removed some unnecessary code and comments from ReporterData?
12:21 PM Changeset [1122] by Nicklas Nordborg
Fixed permission problems and security holes with reporters
11:01 AM Changeset [1121] by Nicklas Nordborg
Implemented RawBioAssay? and added test class Some code for batching …
8:53 AM Changeset [1120] by Gregory Vincic
Renamed buildItem to createItem

Aug 23, 2005:

5:22 PM Changeset [1119] by Gregory Vincic
Using run() and buildItem() methods
5:22 PM Changeset [1118] by Gregory Vincic
Transfer now handles BasicItem? transfers through run()
4:04 PM Changeset [1117] by Nicklas Nordborg
Added Scan, Image and test classes
2:04 PM Changeset [1116] by Nicklas Nordborg
Implemented the rest of Hybridization and added test class for it
2:04 PM Changeset [1115] by Johan Enell
added testfiles to testflatfileparser
12:27 PM Changeset [1114] by Johan Enell
more tests
12:21 PM Changeset [1113] by Johan Enell
added default constructor for hibernate proxies
12:17 PM Changeset [1112] by Gregory Vincic
Removing id mapping through extra information in the description
11:28 AM Changeset [1111] by Gregory Vincic
Migrater now also reads base.config, removing redundant configuration …
11:26 AM Changeset [1110] by Johan Enell
changed constructor to ParameterValueData?
10:59 AM Changeset [1109] by Nicklas Nordborg
Fixed a mapping problem in PlateData?
10:50 AM Changeset [1108] by Nicklas Nordborg
First implementation of RawBioAssay? and some raw data support
10:37 AM Changeset [1107] by Johan Enell
added constructor to ParameterValueData?
10:16 AM Changeset [1106] by Johan Enell
FlatFileParser? tested

Aug 22, 2005:

8:26 PM Changeset [1105] by Nicklas Nordborg
Updated development status
3:38 PM Changeset [1104] by Gregory Vincic
Added read access to Hardware/Software? Administrator for HARDWARE and …
3:37 PM Changeset [1103] by Gregory Vincic
Seperated version from description
3:27 PM Changeset [1102] by Nicklas Nordborg
Added most data classes for the "Hybridzations and raw data" section
1:15 PM Changeset [1101] by Nicklas Nordborg
Added Hybridizations diagram
10:55 AM Changeset [1100] by Gregory Vincic
Tested and fixed role assignment in RoleTransfer?.getRoleIds()
10:30 AM Changeset [1099] by Gregory Vincic
Described how base 1 permissions are mapped to roles in BASE 2
10:12 AM Changeset [1098] by Nicklas Nordborg
Clarified the comments
9:10 AM Changeset [1097] by Gregory Vincic
Removed isPropertyTrue usage
9:08 AM Changeset [1096] by Gregory Vincic
Major rewrite of id mapping between base 1 and base 2 ids.
9:05 AM Changeset [1095] by Gregory Vincic
Initial revision
8:03 AM Changeset [1094] by Nicklas Nordborg
Removed migrate compilation from ant dist since there is a compile error

Aug 19, 2005:

6:38 PM Changeset [1093] by Johan Enell
weekend commit
5:26 PM Changeset [1092] by Johan Enell
minor update to generic in methods replaceValues and setSingleValues
5:15 PM Changeset [1091] by Johan Enell
minor update to generic in methods replaceValues and setSingleValues

Aug 18, 2005:

2:43 PM Changeset [1090] by Johan Enell
added setDefaultValue(Object defaultValue) to ParameterType?

Aug 17, 2005:

10:19 AM Changeset [1089] by Johan Enell
changed variablenames in ArrayDesignBlock?

Aug 16, 2005:

1:02 PM Changeset [1088] by Gregory Vincic
Documenting
1:01 PM Changeset [1087] by Gregory Vincic
Moved Reporter transfer prior to Plate transfer
1:00 PM Changeset [1086] by Gregory Vincic
Added id mapping for reporters
12:59 PM Changeset [1085] by Gregory Vincic
mapIds() now warns if the query is emtpy
10:49 AM Changeset [1084] by Gregory Vincic
Fixed bug in setCommonItemData(), setName was not set correctly
8:56 AM Changeset [1083] by Gregory Vincic
Added output to mapIds() and documentation
8:54 AM Changeset [1082] by Gregory Vincic
Added stop method which outputs the SELECT statement of a specific …

Aug 11, 2005:

3:25 PM Changeset [1081] by Gregory Vincic
PlateMappings? are now created and shared to everyone

Aug 10, 2005:

5:01 PM Changeset [1080] by Gregory Vincic
Documenting and cleaning up code
4:23 PM Changeset [1079] by Gregory Vincic
Documenting
4:22 PM Changeset [1078] by Gregory Vincic
Made the start() method abstract
2:40 PM Changeset [1077] by Gregory Vincic
Initial revision of PlateEventTypeTransfer?.java
2:39 PM Changeset [1076] by Gregory Vincic
Added id mapping
10:46 AM Changeset [1075] by Gregory Vincic
Sperating class inheritance from dependcy
Note: See TracTimeline for information about the timeline view.