Change Log Report

Total number of changed sets: 1

Changes between 2015-07-21 and 2015-08-21

Total commits: 51
Total number of files changed: 80

Timestamp Author Details
2015-08-20 15:55:12 Jason Reilly <jdr0887@gmail.com> hearsay-dao/hearsay-dao-jpa/src/test/resources/META-INF/persistence.xml v 6bcfa1d0824ac93c407a1d7edb70ad530aa86f41

messing with query cache
2015-08-20 15:54:51 Jason Reilly <jdr0887@gmail.com> hearsay-dao/hearsay-dao-jpa/src/test/java/org/renci/hearsay/dao/jpa/ReferenceSequenceTest.java v d84f10dd3e906d47df34473abcec3dfdc2e150e6

adding time logging
2015-08-20 15:53:54 Jason Reilly <jdr0887@gmail.com> hearsay-dao/hearsay-dao-api/src/main/java/org/renci/hearsay/dao/model/Chromosome.java v 02e8112c63a33c06ee63a41af4db29a9e0aa33e7

moving constructor up
2015-08-20 15:53:36 Jason Reilly <jdr0887@gmail.com> hearsay-dao/hearsay-dao-api/src/main/java/org/renci/hearsay/dao/AlignmentDAO.java v af3d41b4cc7be50f7e34614efae7a5ddc4ad9322
hearsay-dao/hearsay-dao-api/src/main/java/org/renci/hearsay/dao/model/Alignment.java v af3d41b4cc7be50f7e34614efae7a5ddc4ad9322
hearsay-dao/hearsay-dao-jpa/src/main/java/org/renci/hearsay/dao/jpa/AlignmentDAOImpl.java v af3d41b4cc7be50f7e34614efae7a5ddc4ad9322
hearsay-dao/hearsay-dao-jpa/src/test/java/org/renci/hearsay/dao/jpa/AlignmentTest.java v af3d41b4cc7be50f7e34614efae7a5ddc4ad9322

adding findAll
2015-08-12 13:29:49 Jason Reilly <jdr0887@gmail.com> hearsay-dao/hearsay-dao-api/src/main/java/org/renci/hearsay/dao/model/CanonicalAllele.java v d3e609f8b97959bcd09830cd6b398d6c1fd4eeb4

adding getter/setters
2015-08-12 13:22:07 Jason Reilly <jdr0887@gmail.com> hearsay-dao/hearsay-dao-jpa/src/test/java/org/renci/hearsay/dao/jpa/IdentifierTest.java v f1550ddc41e57942beb9bf8f7db999b7af16fe00

initial add
2015-08-12 13:21:50 Jason Reilly <jdr0887@gmail.com> hearsay-server/pom.xml v 0dc7cbd71282c3eb12263db4e9f7bb53b9998605

incrementing version
2015-08-12 13:21:36 Jason Reilly <jdr0887@gmail.com> pom.xml v 729f3dca8dca54ba506738943a29264bfc95fc00

incrementing parent
2015-08-12 13:21:13 Jason Reilly <jdr0887@gmail.com> hearsay-dao/hearsay-dao-jpa/src/test/java/org/renci/hearsay/dao/jpa/CanonicalVariantTest.java v f42720694f2239e4c9e19776a23854aff108f4e3

organizing imports
2015-08-12 13:20:56 Jason Reilly <jdr0887@gmail.com> hearsay-dao/hearsay-dao-jpa/src/main/java/org/renci/hearsay/dao/jpa/RegionDAOImpl.java v 5164dede84eb8de21f13b8c91cd84aa5ebfd630b

removing logger
2015-08-12 13:20:45 Jason Reilly <jdr0887@gmail.com> hearsay-dao/hearsay-dao-jpa/src/main/java/org/renci/hearsay/dao/jpa/GeneSymbolDAOImpl.java v 912dec9556b3e8beb8419bc78bd02952e62cb254
hearsay-dao/hearsay-dao-jpa/src/main/java/org/renci/hearsay/dao/jpa/IntronOffsetDAOImpl.java v 912dec9556b3e8beb8419bc78bd02952e62cb254
hearsay-dao/hearsay-dao-jpa/src/main/java/org/renci/hearsay/dao/jpa/LocationDAOImpl.java v 912dec9556b3e8beb8419bc78bd02952e62cb254
hearsay-dao/hearsay-dao-jpa/src/main/java/org/renci/hearsay/dao/jpa/MolecularConsequenceDAOImpl.java v 912dec9556b3e8beb8419bc78bd02952e62cb254
hearsay-dao/hearsay-dao-jpa/src/main/java/org/renci/hearsay/dao/jpa/ReferenceCoordinateDAOImpl.java v 912dec9556b3e8beb8419bc78bd02952e62cb254

removing logger
2015-08-12 13:20:33 Jason Reilly <jdr0887@gmail.com> hearsay-dao/hearsay-dao-jpa/src/main/java/org/renci/hearsay/dao/jpa/CanonicalAlleleDAOImpl.java v ffaacb5431bbe8570fd1b01cc8470d3f7091f83e

removing logger
2015-08-12 13:20:22 Jason Reilly <jdr0887@gmail.com> hearsay-dao/hearsay-dao-api/src/main/java/org/renci/hearsay/dao/model/SimpleAllele.java v 51c198d94473acae5a56858cce4680fdd62f351a

making canonicalallele transient
2015-08-12 13:20:01 Jason Reilly <jdr0887@gmail.com> hearsay-dao/hearsay-dao-api/src/main/java/org/renci/hearsay/dao/model/CanonicalAllele.java v 8597e2d14784e7307d176ad4a1680ebaec021f17

removing parent/child relationship
2015-08-10 16:09:11 Jason Reilly <jdr0887@gmail.com> hearsay-commands/pom.xml v cab31a9a881c15fe4e56636f5019aa711df5f51c
hearsay-dao/hearsay-dao-api/pom.xml v cab31a9a881c15fe4e56636f5019aa711df5f51c
hearsay-dao/hearsay-dao-jpa/pom.xml v cab31a9a881c15fe4e56636f5019aa711df5f51c
hearsay-dao/pom.xml v cab31a9a881c15fe4e56636f5019aa711df5f51c
hearsay-datasource/pom.xml v cab31a9a881c15fe4e56636f5019aa711df5f51c
hearsay-features/pom.xml v cab31a9a881c15fe4e56636f5019aa711df5f51c
hearsay-web-service-api/pom.xml v cab31a9a881c15fe4e56636f5019aa711df5f51c
hearsay-web-services/hearsay-ws-alignment/pom.xml v cab31a9a881c15fe4e56636f5019aa711df5f51c
hearsay-web-services/hearsay-ws-canonical-allele/pom.xml v cab31a9a881c15fe4e56636f5019aa711df5f51c
hearsay-web-services/hearsay-ws-feature/pom.xml v cab31a9a881c15fe4e56636f5019aa711df5f51c
hearsay-web-services/hearsay-ws-gene-symbol/pom.xml v cab31a9a881c15fe4e56636f5019aa711df5f51c
hearsay-web-services/hearsay-ws-gene/pom.xml v cab31a9a881c15fe4e56636f5019aa711df5f51c
hearsay-web-services/hearsay-ws-genome-reference/pom.xml v cab31a9a881c15fe4e56636f5019aa711df5f51c
hearsay-web-services/hearsay-ws-identifier/pom.xml v cab31a9a881c15fe4e56636f5019aa711df5f51c
hearsay-web-services/hearsay-ws-intron-offset/pom.xml v cab31a9a881c15fe4e56636f5019aa711df5f51c
hearsay-web-services/hearsay-ws-molecular-consequence/pom.xml v cab31a9a881c15fe4e56636f5019aa711df5f51c
hearsay-web-services/hearsay-ws-population-frequency/pom.xml v cab31a9a881c15fe4e56636f5019aa711df5f51c
hearsay-web-services/hearsay-ws-reference-coordinate/pom.xml v cab31a9a881c15fe4e56636f5019aa711df5f51c
hearsay-web-services/hearsay-ws-reference-sequence/pom.xml v cab31a9a881c15fe4e56636f5019aa711df5f51c
hearsay-web-services/hearsay-ws-region/pom.xml v cab31a9a881c15fe4e56636f5019aa711df5f51c
hearsay-web-services/hearsay-ws-simple-allele/pom.xml v cab31a9a881c15fe4e56636f5019aa711df5f51c
hearsay-web-services/pom.xml v cab31a9a881c15fe4e56636f5019aa711df5f51c
hearsay-webapp/pom.xml v cab31a9a881c15fe4e56636f5019aa711df5f51c
pom.xml v cab31a9a881c15fe4e56636f5019aa711df5f51c

[maven-release-plugin] prepare for next development iteration
2015-08-10 16:09:10 Jason Reilly <jdr0887@gmail.com> hearsay-commands/pom.xml v 6a21c4add79152ad15b3f81099df0900519841d2
hearsay-dao/hearsay-dao-api/pom.xml v 6a21c4add79152ad15b3f81099df0900519841d2
hearsay-dao/hearsay-dao-jpa/pom.xml v 6a21c4add79152ad15b3f81099df0900519841d2
hearsay-dao/pom.xml v 6a21c4add79152ad15b3f81099df0900519841d2
hearsay-datasource/pom.xml v 6a21c4add79152ad15b3f81099df0900519841d2
hearsay-features/pom.xml v 6a21c4add79152ad15b3f81099df0900519841d2
hearsay-web-service-api/pom.xml v 6a21c4add79152ad15b3f81099df0900519841d2
hearsay-web-services/hearsay-ws-alignment/pom.xml v 6a21c4add79152ad15b3f81099df0900519841d2
hearsay-web-services/hearsay-ws-canonical-allele/pom.xml v 6a21c4add79152ad15b3f81099df0900519841d2
hearsay-web-services/hearsay-ws-feature/pom.xml v 6a21c4add79152ad15b3f81099df0900519841d2
hearsay-web-services/hearsay-ws-gene-symbol/pom.xml v 6a21c4add79152ad15b3f81099df0900519841d2
hearsay-web-services/hearsay-ws-gene/pom.xml v 6a21c4add79152ad15b3f81099df0900519841d2
hearsay-web-services/hearsay-ws-genome-reference/pom.xml v 6a21c4add79152ad15b3f81099df0900519841d2
hearsay-web-services/hearsay-ws-identifier/pom.xml v 6a21c4add79152ad15b3f81099df0900519841d2
hearsay-web-services/hearsay-ws-intron-offset/pom.xml v 6a21c4add79152ad15b3f81099df0900519841d2
hearsay-web-services/hearsay-ws-molecular-consequence/pom.xml v 6a21c4add79152ad15b3f81099df0900519841d2
hearsay-web-services/hearsay-ws-population-frequency/pom.xml v 6a21c4add79152ad15b3f81099df0900519841d2
hearsay-web-services/hearsay-ws-reference-coordinate/pom.xml v 6a21c4add79152ad15b3f81099df0900519841d2
hearsay-web-services/hearsay-ws-reference-sequence/pom.xml v 6a21c4add79152ad15b3f81099df0900519841d2
hearsay-web-services/hearsay-ws-region/pom.xml v 6a21c4add79152ad15b3f81099df0900519841d2
hearsay-web-services/hearsay-ws-simple-allele/pom.xml v 6a21c4add79152ad15b3f81099df0900519841d2
hearsay-web-services/pom.xml v 6a21c4add79152ad15b3f81099df0900519841d2
hearsay-webapp/pom.xml v 6a21c4add79152ad15b3f81099df0900519841d2
pom.xml v 6a21c4add79152ad15b3f81099df0900519841d2

[maven-release-plugin] prepare release hearsay-0.0.45
2015-08-10 16:07:59 Jason Reilly <jdr0887@gmail.com> src/site/fml/manual/faq.fml v b3d5560c11b62c854f7195e32b120e7b8baa9494

initial commit
2015-08-10 16:07:44 Jason Reilly <jdr0887@gmail.com> src/site/site.xml v 9d400475f5971c3caaf6bf58159bf517864df65c

adding faq
2015-08-10 16:06:57 Jason Reilly <jdr0887@gmail.com> hearsay-dao/hearsay-dao-api/src/test/java/org/renci/hearsay/dao/model/TestSerialization.java v 6ebca41505ab6330d0780931ac178cdafae5f75f

removing
2015-08-10 16:06:05 Jason Reilly <jdr0887@gmail.com> hearsay-dao/hearsay-dao-jpa/src/test/java/org/renci/hearsay/dao/jpa/CanonicalVariantTest.java v 88d20190322bf8dc6ab5dd6b47934b97f1301312

adding testCanonicalAlleleSerialization
2015-08-10 16:05:08 Jason Reilly <jdr0887@gmail.com> hearsay-dao/hearsay-dao-jpa/src/test/java/org/renci/hearsay/dao/jpa/AlignmentTest.java v dc48149cdd37adb683b90c8f37dcc5fb71eb43e4

messing around
2015-08-10 16:04:54 Jason Reilly <jdr0887@gmail.com> hearsay-dao/hearsay-dao-api/src/main/java/org/renci/hearsay/dao/model/SimpleAllele.java v 0956782256aa8a65ec2345af6771d95857b9d3c5

adding canonicalAllele
2015-08-10 16:04:20 Jason Reilly <jdr0887@gmail.com> hearsay-dao/hearsay-dao-api/src/main/java/org/renci/hearsay/dao/model/CanonicalAllele.java v 18661a62b15fcde780e9f4a5bc23f5a86faf1206

fixing bug
2015-08-10 16:04:07 Jason Reilly <jdr0887@gmail.com> hearsay-dao/hearsay-dao-api/src/main/java/org/renci/hearsay/dao/SimpleAlleleDAO.java v 7927f385c7a1942fc6f55ebb8fdd129e1ec7994d
hearsay-dao/hearsay-dao-jpa/src/main/java/org/renci/hearsay/dao/jpa/SimpleAlleleDAOImpl.java v 7927f385c7a1942fc6f55ebb8fdd129e1ec7994d
hearsay-web-service-api/src/main/java/org/renci/hearsay/ws/SimpleAlleleService.java v 7927f385c7a1942fc6f55ebb8fdd129e1ec7994d

adding findByName
2015-08-10 16:03:51 Jason Reilly <jdr0887@gmail.com> hearsay-web-services/hearsay-ws-simple-allele/src/main/java/org/renci/hearsay/ws/impl/SimpleAlleleServiceImpl.java v 78ba395531af0446c07baaa760019ff21dbe5b3f

adding findByName
2015-08-10 15:11:47 Bradford Powell <bpow@drpowell.org> hearsay-server/src/main/assembly/bin/setenv v 13b79bc65db3372907ae627ce3d17a3ca13e17b0

check if ~/.hearsayrc exists before sourcing
2015-08-05 10:49:53 Jason Reilly <jdr0887@gmail.com> hearsay-dao/hearsay-dao-jpa/src/test/java/org/renci/hearsay/dao/jpa/AlignmentTest.java v b8b80a4519c82927a0fadf8be0c8898db316f97c

messing with null alignment regions
2015-08-05 10:49:45 Jason Reilly <jdr0887@gmail.com> hearsay-dao/hearsay-dao-jpa/src/main/java/org/renci/hearsay/dao/jpa/AlignmentDAOImpl.java v 67da5e840eee8320fd11f1602cacc529be8aa43e

messing with null alignment regions
2015-08-04 10:26:34 Jason Reilly <jdr0887@gmail.com> hearsay-dao/hearsay-dao-api/src/main/java/org/renci/hearsay/dao/model/Alignment.java v 6dd550aeee628a7197b8f551c9ffb98c1b43eb62

cleaning imports
2015-08-04 10:25:44 Jason Reilly <jdr0887@gmail.com> hearsay-commands/src/main/java/org/renci/hearsay/commands/ListReferenceSequencesAction.java v 5873028ae8026643803961692b1a8e0287ac24f2
hearsay-dao/hearsay-dao-jpa/src/main/java/org/renci/hearsay/dao/jpa/GeneDAOImpl.java v 5873028ae8026643803961692b1a8e0287ac24f2
hearsay-dao/hearsay-dao-jpa/src/main/java/org/renci/hearsay/dao/jpa/ReferenceSequenceDAOImpl.java v 5873028ae8026643803961692b1a8e0287ac24f2
hearsay-dao/hearsay-dao-jpa/src/test/java/org/renci/hearsay/dao/jpa/CanonicalVariantTest.java v 5873028ae8026643803961692b1a8e0287ac24f2
hearsay-dao/hearsay-dao-jpa/src/test/java/org/renci/hearsay/dao/jpa/GeneTest.java v 5873028ae8026643803961692b1a8e0287ac24f2
hearsay-dao/hearsay-dao-jpa/src/test/java/org/renci/hearsay/dao/jpa/ReferenceSequenceTest.java v 5873028ae8026643803961692b1a8e0287ac24f2

using collectionutils
2015-08-04 10:25:00 Jason Reilly <jdr0887@gmail.com> hearsay-web-service-api/src/main/java/org/renci/hearsay/ws/AlignmentService.java v 9f6f61514c11821e59ae4301e4fd2d24a36ee582

adding pathparam
2015-08-04 10:24:48 Jason Reilly <jdr0887@gmail.com> hearsay-web-service-api/src/main/java/org/renci/hearsay/ws/FeatureService.java v 327e46e59568a0a22506baa4d28059483afb9b27

adding pathparam
2015-08-04 10:24:27 Jason Reilly <jdr0887@gmail.com> hearsay-web-services/hearsay-ws-alignment/src/main/java/org/renci/hearsay/ws/impl/AlignmentServiceImpl.java v 4aa4f7ae4977d7e558ea0e4bcfd0ba9ddfd5a064

sorting regions
2015-08-04 10:23:53 Jason Reilly <jdr0887@gmail.com> hearsay-dao/hearsay-dao-jpa/src/test/java/org/renci/hearsay/dao/jpa/AlignmentTest.java v e52100b199626e8fc9797bb0167256d9f405ba6c

initial commit
2015-07-30 16:13:00 Jason Reilly <jdr0887@gmail.com> hearsay-server/src/site/resources/css/site.css v 717371722373e661ddb8c57051f8817f33188ab2
hearsay-server/src/site/site.xml v 717371722373e661ddb8c57051f8817f33188ab2
hearsay-server/src/site/xdoc/index.xml v 717371722373e661ddb8c57051f8817f33188ab2
hearsay-server/src/site/xdoc/usage.xml v 717371722373e661ddb8c57051f8817f33188ab2

removing
2015-07-28 09:16:36 Jason Reilly <jdr0887@gmail.com> hearsay-web-service-api/src/main/java/org/renci/hearsay/ws/AlignmentService.java v a2d76893fb669656c3f75c4b9760a555dcf3beb4
hearsay-web-service-api/src/main/java/org/renci/hearsay/ws/FeatureService.java v a2d76893fb669656c3f75c4b9760a555dcf3beb4
hearsay-web-services/hearsay-ws-alignment/src/main/java/org/renci/hearsay/ws/impl/AlignmentServiceImpl.java v a2d76893fb669656c3f75c4b9760a555dcf3beb4
hearsay-web-services/hearsay-ws-feature/src/main/java/org/renci/hearsay/ws/impl/FeatureServiceImpl.java v a2d76893fb669656c3f75c4b9760a555dcf3beb4

adding findByReferenceSequenceId
2015-07-27 14:32:18 Jason Reilly <jdr0887@gmail.com> src/site/site.xml v dfe23420babdcb9b11d06b98d31dd6810752b510
src/site/xdoc/index.xml v dfe23420babdcb9b11d06b98d31dd6810752b510
src/site/xdoc/manual/server.xml v dfe23420babdcb9b11d06b98d31dd6810752b510

updating docs
2015-07-27 14:32:02 Jason Reilly <jdr0887@gmail.com> hearsay-server/pom.xml v ca7c3fb4bd1425357d5eb56bc39abbbb751457b3

incrementing version
2015-07-27 14:31:25 Jason Reilly <jdr0887@gmail.com> hearsay-dao/hearsay-dao-jpa/src/test/java/org/renci/hearsay/dao/jpa/ReferenceSequenceTest.java v d768f0246a51c79bd859a1a9893a47e037df9922

adding findAll
2015-07-27 14:30:40 Jason Reilly <jdr0887@gmail.com> hearsay-dao/hearsay-dao-api/src/main/resources/META-INF/persistence.xml v 183841c2f1a1dafb84820a0cef4372552bc96546
hearsay-dao/hearsay-dao-jpa/src/test/resources/META-INF/persistence.xml v 183841c2f1a1dafb84820a0cef4372552bc96546

removing dictionaryentity
2015-07-27 14:30:17 Jason Reilly <jdr0887@gmail.com> hearsay-dao/hearsay-dao-api/src/main/java/org/renci/hearsay/dao/model/Region.java v 04a457fb4727dce9a6ae4fca8c05a9edc70a0a30

making region type an attribute
2015-07-27 14:30:00 Jason Reilly <jdr0887@gmail.com> hearsay-dao/hearsay-dao-api/src/main/java/org/renci/hearsay/dao/model/ReferenceSequence.java v 5d279bf90b843e6459da428186529944fc8464ac

making features and alignments lazy
2015-07-27 14:28:55 Jason Reilly <jdr0887@gmail.com> hearsay-dao/hearsay-dao-api/src/main/java/org/renci/hearsay/dao/model/GeneSymbol.java v 63d899613e13add441495b4cb35b143f6bf979d7

adding id
2015-07-27 14:28:42 Jason Reilly <jdr0887@gmail.com> hearsay-dao/hearsay-dao-api/src/main/java/org/renci/hearsay/dao/model/Chromosome.java v ee2b35ef7e10caf9d0cf1ee570d03eb109e9183d

adding id
2015-07-27 14:28:26 Jason Reilly <jdr0887@gmail.com> hearsay-dao/hearsay-dao-api/src/main/java/org/renci/hearsay/dao/model/Alignment.java v 3f84d197e0449d73626137ea3aa46b4927a30720

adding wrapper to regions
2015-07-27 14:27:44 Jason Reilly <jdr0887@gmail.com> hearsay-dao/hearsay-dao-jpa/src/main/java/org/renci/hearsay/dao/jpa/ReferenceSequenceDAOImpl.java v 3e386fd94a72d4d45b79aecfec983036bf23815b

adding findByExample & findByIdentifiers
2015-07-27 14:27:36 Jason Reilly <jdr0887@gmail.com> hearsay-dao/hearsay-dao-api/src/main/java/org/renci/hearsay/dao/ReferenceSequenceDAO.java v 3dad0faaa00ca7f7a03d4608649c8e8917c2ae67

adding findByExample & findByIdentifiers
2015-07-27 14:26:16 Jason Reilly <jdr0887@gmail.com> hearsay-dao/hearsay-dao-api/src/main/java/org/renci/hearsay/dao/AlignmentDAO.java v 6bd3c65a71256ea5bb4e1493bab30c37032a8654
hearsay-dao/hearsay-dao-api/src/main/java/org/renci/hearsay/dao/FeatureDAO.java v 6bd3c65a71256ea5bb4e1493bab30c37032a8654
hearsay-dao/hearsay-dao-jpa/src/main/java/org/renci/hearsay/dao/jpa/AlignmentDAOImpl.java v 6bd3c65a71256ea5bb4e1493bab30c37032a8654
hearsay-dao/hearsay-dao-jpa/src/main/java/org/renci/hearsay/dao/jpa/FeatureDAOImpl.java v 6bd3c65a71256ea5bb4e1493bab30c37032a8654

findByReferenceSequenceId(Long)
2015-07-27 14:25:19 Jason Reilly <jdr0887@gmail.com> hearsay-dao/hearsay-dao-jpa/src/test/java/org/renci/hearsay/dao/jpa/GeneTest.java v c39e2b993b930cc1434ba0f1fee7423b06d7639b
src/site/xdoc/manual/commands.xml v c39e2b993b930cc1434ba0f1fee7423b06d7639b
src/site/xdoc/manual/download.xml v c39e2b993b930cc1434ba0f1fee7423b06d7639b

initial commit
2015-07-27 14:24:51 Jason Reilly <jdr0887@gmail.com> src/site/xdoc/code-format.xml v 80d0dd163cddb82434c36c8592ea183a43468d04
src/site/xdoc/download.xml v 80d0dd163cddb82434c36c8592ea183a43468d04
src/site/xdoc/faq.xml v 80d0dd163cddb82434c36c8592ea183a43468d04
src/site/xdoc/manual/client.xml v 80d0dd163cddb82434c36c8592ea183a43468d04
src/site/xdoc/manual/index.xml v 80d0dd163cddb82434c36c8592ea183a43468d04

removing
2015-07-27 14:24:31 Jason Reilly <jdr0887@gmail.com> hearsay-dao/hearsay-dao-api/src/main/java/org/renci/hearsay/dao/model/DictionaryEntity.java v 436cd9ffe512f61fd5c811e1cb3194c287d628df

removing