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From: <rv...@us...> - 2009-06-19 02:22:16
|
Revision: 69
http://treebase.svn.sourceforge.net/treebase/?rev=69&view=rev
Author: rvos
Date: 2009-06-19 02:22:14 +0000 (Fri, 19 Jun 2009)
Log Message:
-----------
Adding postgres TBASE2 creation script
Added Paths:
-----------
trunk/treebase-core/src/main/resources/TBASE2_POSTGRES_CREATION.sql
Added: trunk/treebase-core/src/main/resources/TBASE2_POSTGRES_CREATION.sql
===================================================================
--- trunk/treebase-core/src/main/resources/TBASE2_POSTGRES_CREATION.sql (rev 0)
+++ trunk/treebase-core/src/main/resources/TBASE2_POSTGRES_CREATION.sql 2009-06-19 02:22:14 UTC (rev 69)
@@ -0,0 +1,6545 @@
+/*
+--Script generated by Aqua Data Studio 6.5.12 on Jun-12-2009 12:30:24 AM
+--Database: TBASE2
+--Schema: JRUAN
+--Objects: TABLE
+*/
+-- ALTER TABLE JRUAN.USERTYPERRD_COLRANGE
+-- DROP CONSTRAINT FK405805DDC009330E
+-- GO
+-- ALTER TABLE JRUAN.USERTYPERRD_COLRANGE
+-- DROP CONSTRAINT FK405805DD79A523E6
+-- GO
+-- ALTER TABLE JRUAN.USERTYPERECORD
+-- DROP CONSTRAINT FK136AF61692E6A38E
+-- GO
+-- ALTER TABLE JRUAN.USERTYPERECORD
+-- DROP CONSTRAINT FK136AF6164D737E46
+-- GO
+-- ALTER TABLE JRUAN.USER
+-- DROP CONSTRAINT FK27E3CBF59DD12
+-- GO
+-- ALTER TABLE JRUAN.USER
+-- DROP CONSTRAINT FK27E3CBE3910672
+-- GO
+-- ALTER TABLE JRUAN.TYPESET
+-- DROP CONSTRAINT FKF7F2B6C8A414944F
+-- GO
+-- ALTER TABLE JRUAN.TREESET_PHYLOTREE
+-- DROP CONSTRAINT FK31FC19A7EC59B1E3
+-- GO
+-- ALTER TABLE JRUAN.TREESET_PHYLOTREE
+-- DROP CONSTRAINT FK31FC19A7B710CB23
+-- GO
+-- ALTER TABLE JRUAN.TREENODEEDGE
+-- DROP CONSTRAINT FK7767285D27FD0589
+-- GO
+-- ALTER TABLE JRUAN.TREENODEEDGE
+-- DROP CONSTRAINT FK7767285D1851763B
+-- GO
+-- ALTER TABLE JRUAN.TREEGROUP
+-- DROP CONSTRAINT FKA870258180CBD223
+-- GO
+-- ALTER TABLE JRUAN.TREEGROUP_PHYLOTREE
+-- DROP CONSTRAINT FKFB7D704B710CB23
+-- GO
+-- ALTER TABLE JRUAN.TREEGROUP_PHYLOTREE
+-- DROP CONSTRAINT FKFB7D7045E56A83
+-- GO
+-- ALTER TABLE JRUAN.TREEBLOCK
+-- DROP CONSTRAINT FKA826F38FE310471D
+-- GO
+-- ALTER TABLE JRUAN.TAXONVARIANT
+-- DROP CONSTRAINT FKEE3D127B1DE2FCDD
+-- GO
+-- ALTER TABLE JRUAN.TAXONSET_TAXON
+-- DROP CONSTRAINT FKC656C9031DE2FCDD
+-- GO
+-- ALTER TABLE JRUAN.TAXONSET_TAXON
+-- DROP CONSTRAINT FKC656C90313C28457
+-- GO
+-- ALTER TABLE JRUAN.TAXONLINK
+-- DROP CONSTRAINT FKC102D9A43BF5F2F7
+-- GO
+-- ALTER TABLE JRUAN.TAXONLINK
+-- DROP CONSTRAINT FKC102D9A41DE2FCDD
+-- GO
+-- ALTER TABLE JRUAN.TAXONLABELSET
+-- DROP CONSTRAINT FK28D3A5983C572C3C
+-- GO
+-- ALTER TABLE JRUAN.TAXONLABELSET_TAXONLABEL
+-- DROP CONSTRAINT FK2EB54B71E310471D
+-- GO
+-- ALTER TABLE JRUAN.TAXONLABELSET_TAXONLABEL
+-- DROP CONSTRAINT FK2EB54B7163AB9FD7
+-- GO
+-- ALTER TABLE JRUAN.TAXONLABELROUP_TAXONLABEL
+-- DROP CONSTRAINT FK4B1D0BC763AB9FD7
+-- GO
+-- ALTER TABLE JRUAN.TAXONLABELROUP_TAXONLABEL
+-- DROP CONSTRAINT FK4B1D0BC7294B993D
+-- GO
+-- ALTER TABLE JRUAN.TAXONLABELGROUP
+-- DROP CONSTRAINT FK4AE2663513A813DD
+-- GO
+-- ALTER TABLE JRUAN.TAXONLABEL
+-- DROP CONSTRAINT FK5F548A6A3C572C3C
+-- GO
+-- ALTER TABLE JRUAN.TAXONLABEL
+-- DROP CONSTRAINT FK5F548A6A3C1B6F7
+-- GO
+-- ALTER TABLE JRUAN.SUBMISSION
+-- DROP CONSTRAINT FKA120274CBEF300B2
+-- GO
+-- ALTER TABLE JRUAN.SUBMISSION
+-- DROP CONSTRAINT FKA120274C3C572C3C
+-- GO
+-- ALTER TABLE JRUAN.SUB_TREEBLOCK
+-- DROP CONSTRAINT FK94D50830BFD107C3
+-- GO
+-- ALTER TABLE JRUAN.SUB_TREEBLOCK
+-- DROP CONSTRAINT FK94D508308DFE4858
+-- GO
+-- ALTER TABLE JRUAN.SUB_TAXONLABEL
+-- DROP CONSTRAINT FK86909E98DFE4858
+-- GO
+-- ALTER TABLE JRUAN.SUB_TAXONLABEL
+-- DROP CONSTRAINT FK86909E963AB9FD7
+-- GO
+-- ALTER TABLE JRUAN.SUB_MATRIX
+-- DROP CONSTRAINT FK5F26A2C08DFE4858
+-- GO
+-- ALTER TABLE JRUAN.SUB_MATRIX
+-- DROP CONSTRAINT FK5F26A2C055961AEE
+-- GO
+-- ALTER TABLE JRUAN.STUDY
+-- DROP CONSTRAINT FK4B915A9BEF300B2
+-- GO
+-- ALTER TABLE JRUAN.STUDY
+-- DROP CONSTRAINT FK4B915A98E1E4DF8
+-- GO
+-- ALTER TABLE JRUAN.STUDY
+-- DROP CONSTRAINT FK4B915A9255A519C
+-- GO
+-- ALTER TABLE JRUAN.STUDY_NEXUSFILE
+-- DROP CONSTRAINT FK47FC1EE53C572C3C
+-- GO
+-- ALTER TABLE JRUAN.STEPMATRIXELEMENT
+-- DROP CONSTRAINT FK891100AF9E8198E
+-- GO
+-- ALTER TABLE JRUAN.STEPMATRIXELEMENT
+-- DROP CONSTRAINT FK891100AF6E979EE7
+-- GO
+-- ALTER TABLE JRUAN.STEPMATRIXELEMENT
+-- DROP CONSTRAINT FK891100AF6E972A88
+-- GO
+-- ALTER TABLE JRUAN.STATESET
+-- DROP CONSTRAINT FK7D38523150CBAB47
+-- GO
+-- ALTER TABLE JRUAN.STATEMODIFIER
+-- DROP CONSTRAINT FKD157BE48F4803CE6
+-- GO
+-- ALTER TABLE JRUAN.STATEMODIFIER
+-- DROP CONSTRAINT FKD157BE48BED40086
+-- GO
+-- ALTER TABLE JRUAN.STATEMODIFIER
+-- DROP CONSTRAINT FKD157BE48459091E5
+-- GO
+-- ALTER TABLE JRUAN.SPECIMENLABEL
+-- DROP CONSTRAINT FK1E8F38CCA2039B9D
+-- GO
+-- ALTER TABLE JRUAN.ROWSEGMENT
+-- DROP CONSTRAINT FKEE9AE819E7B3CDA6
+-- GO
+-- ALTER TABLE JRUAN.ROWSEGMENT
+-- DROP CONSTRAINT FKEE9AE81963AB9FD7
+-- GO
+-- ALTER TABLE JRUAN.RIGHTCHANGESET_CHARSTATE
+-- DROP CONSTRAINT FKC8AFC9F2F4803CE6
+-- GO
+-- ALTER TABLE JRUAN.RIGHTCHANGESET_CHARSTATE
+-- DROP CONSTRAINT FKC8AFC9F275763EAE
+-- GO
+-- ALTER TABLE JRUAN.PHYLOTREENODE
+-- DROP CONSTRAINT FK3EA79944B710CB23
+-- GO
+-- ALTER TABLE JRUAN.PHYLOTREENODE
+-- DROP CONSTRAINT FK3EA7994463AB9FD7
+-- GO
+-- ALTER TABLE JRUAN.PHYLOTREENODE
+-- DROP CONSTRAINT FK3EA799445BCC767D
+-- GO
+-- ALTER TABLE JRUAN.PHYLOTREENODE
+-- DROP CONSTRAINT FK3EA79944434FDCCB
+-- GO
+-- ALTER TABLE JRUAN.PHYLOTREENODE
+-- DROP CONSTRAINT FK3EA799443C348165
+-- GO
+-- ALTER TABLE JRUAN.PHYLOTREENODE
+-- DROP CONSTRAINT FK3EA79944271A5763
+-- GO
+-- ALTER TABLE JRUAN.PHYLOTREE
+-- DROP CONSTRAINT FK76F2E442FE2812F1
+-- GO
+-- ALTER TABLE JRUAN.PHYLOTREE
+-- DROP CONSTRAINT FK76F2E442F5AEA931
+-- GO
+-- ALTER TABLE JRUAN.PHYLOTREE
+-- DROP CONSTRAINT FK76F2E442F3D1CF03
+-- GO
+-- ALTER TABLE JRUAN.PHYLOTREE
+-- DROP CONSTRAINT FK76F2E442EA08B443
+-- GO
+-- ALTER TABLE JRUAN.PHYLOTREE
+-- DROP CONSTRAINT FK76F2E442BFD107C3
+-- GO
+-- ALTER TABLE JRUAN.PHYLOTREE
+-- DROP CONSTRAINT FK76F2E442A3015CE3
+-- GO
+-- ALTER TABLE JRUAN.PHYLOTREE
+-- DROP CONSTRAINT FK76F2E4423C572C3C
+-- GO
+-- ALTER TABLE JRUAN.MATRIXROW
+-- DROP CONSTRAINT FKE4688E59A414944F
+-- GO
+-- ALTER TABLE JRUAN.MATRIXROW
+-- DROP CONSTRAINT FKE4688E5963AB9FD7
+-- GO
+-- ALTER TABLE JRUAN.MATRIXELEMENT
+-- DROP CONSTRAINT FK90AE93FBF4803CE6
+-- GO
+-- ALTER TABLE JRUAN.MATRIXELEMENT
+-- DROP CONSTRAINT FK90AE93FBE7B3CDA6
+-- GO
+-- ALTER TABLE JRUAN.MATRIXELEMENT
+-- DROP CONSTRAINT FK90AE93FB8B2E884E
+-- GO
+-- ALTER TABLE JRUAN.MATRIXELEMENT
+-- DROP CONSTRAINT FK90AE93FB405A7CEE
+-- GO
+-- ALTER TABLE JRUAN.MATRIXDATATYPE
+-- DROP CONSTRAINT FKF054C4A5F5DECA46
+-- GO
+-- ALTER TABLE JRUAN.MATRIXCOLUMN
+-- DROP CONSTRAINT FK9B0BE57F5DECA46
+-- GO
+-- ALTER TABLE JRUAN.MATRIXCOLUMN
+-- DROP CONSTRAINT FK9B0BE57BED40086
+-- GO
+-- ALTER TABLE JRUAN.MATRIXCOLUMN
+-- DROP CONSTRAINT FK9B0BE57A414944F
+-- GO
+-- ALTER TABLE JRUAN.MATRIXCOLUMN_ITEMDEFINITION
+-- DROP CONSTRAINT FKB556F8E8B2E884E
+-- GO
+-- ALTER TABLE JRUAN.MATRIXCOLUMN_ITEMDEFINITION
+-- DROP CONSTRAINT FKB556F8E405A7CEE
+-- GO
+-- ALTER TABLE JRUAN.MATRIX
+-- DROP CONSTRAINT FK87208BC1E9B425A6
+-- GO
+-- ALTER TABLE JRUAN.MATRIX
+-- DROP CONSTRAINT FK87208BC1E310471D
+-- GO
+-- ALTER TABLE JRUAN.MATRIX
+-- DROP CONSTRAINT FK87208BC191BD3C8E
+-- GO
+-- ALTER TABLE JRUAN.MATRIX
+-- DROP CONSTRAINT FK87208BC1684F6406
+-- GO
+-- ALTER TABLE JRUAN.MATRIX
+-- DROP CONSTRAINT FK87208BC14D737E46
+-- GO
+-- ALTER TABLE JRUAN.MATRIX
+-- DROP CONSTRAINT FK87208BC14CE484AE
+-- GO
+-- ALTER TABLE JRUAN.MATRIX
+-- DROP CONSTRAINT FK87208BC1491DB20E
+-- GO
+-- ALTER TABLE JRUAN.MATRIX
+-- DROP CONSTRAINT FK87208BC145534A9C
+-- GO
+-- ALTER TABLE JRUAN.MATRIX
+-- DROP CONSTRAINT FK87208BC13C572C3C
+-- GO
+-- ALTER TABLE JRUAN.MATRIX_ITEMDEFINITION
+-- DROP CONSTRAINT FK5717E0E4AC5C19DD
+-- GO
+-- ALTER TABLE JRUAN.MATRIX_ITEMDEFINITION
+-- DROP CONSTRAINT FK5717E0E4405A7CEE
+-- GO
+-- ALTER TABLE JRUAN.LEFTCHANGESET_CHARSTATE
+-- DROP CONSTRAINT FKC8877207F4803CE6
+-- GO
+-- ALTER TABLE JRUAN.LEFTCHANGESET_CHARSTATE
+-- DROP CONSTRAINT FKC887720775763EAE
+-- GO
+-- ALTER TABLE JRUAN.ITEMVALUE
+-- DROP CONSTRAINT FK27B41A1E459091E5
+-- GO
+-- ALTER TABLE JRUAN.GENETICCODESET
+-- DROP CONSTRAINT FK6A12F7DCA414944F
+-- GO
+-- ALTER TABLE JRUAN.GENETICCODERECORD
+-- DROP CONSTRAINT FK237932B782D8ECCE
+-- GO
+-- ALTER TABLE JRUAN.GENETICCODERECORD
+-- DROP CONSTRAINT FK237932B76CB73FC6
+-- GO
+-- ALTER TABLE JRUAN.EXPLAIN_STREAM
+-- DROP CONSTRAINT SQL050919121811070
+-- GO
+-- ALTER TABLE JRUAN.EXPLAIN_STATEMENT
+-- DROP CONSTRAINT SQL050919121810950
+-- GO
+-- ALTER TABLE JRUAN.EXPLAIN_PREDICATE
+-- DROP CONSTRAINT SQL050919121811040
+-- GO
+-- ALTER TABLE JRUAN.EXPLAIN_OPERATOR
+-- DROP CONSTRAINT SQL050919121810970
+-- GO
+-- ALTER TABLE JRUAN.EXPLAIN_OBJECT
+-- DROP CONSTRAINT SQL050919121811000
+-- GO
+-- ALTER TABLE JRUAN.EXPLAIN_ARGUMENT
+-- DROP CONSTRAINT SQL050919121811060
+-- GO
+-- ALTER TABLE JRUAN.DISTANCEMATRIXELEMENT
+-- DROP CONSTRAINT FK92D3DDE6C1429863
+-- GO
+-- ALTER TABLE JRUAN.DISTANCEMATRIXELEMENT
+-- DROP CONSTRAINT FK92D3DDE64B8EF343
+-- GO
+-- ALTER TABLE JRUAN.DISTANCEMATRIXELEMENT
+-- DROP CONSTRAINT FK92D3DDE61F08BAE7
+-- GO
+-- ALTER TABLE JRUAN.DISCRETECHARSTATE
+-- DROP CONSTRAINT FK2EEF2802FE41A723
+-- GO
+-- ALTER TABLE JRUAN.DISCRETECHARSTATE
+-- DROP CONSTRAINT FK2EEF2802C7BEAAFE
+-- GO
+-- ALTER TABLE JRUAN.DISCRETECHARSTATE
+-- DROP CONSTRAINT FK2EEF2802163C67CE
+-- GO
+-- ALTER TABLE JRUAN.CSTREENODE
+-- DROP CONSTRAINT FK82B9AB10F572A92
+-- GO
+-- ALTER TABLE JRUAN.CSTREENODE
+-- DROP CONSTRAINT FK82B9AB10F4803CE6
+-- GO
+-- ALTER TABLE JRUAN.CSTREENODE
+-- DROP CONSTRAINT FK82B9AB10C6999FCE
+-- GO
+-- ALTER TABLE JRUAN.CONTANCSTATE_VALUE
+-- DROP CONSTRAINT FKA84B8C3FD450D2BD
+-- GO
+-- ALTER TABLE JRUAN.COMPOUND_ELEMENT
+-- DROP CONSTRAINT FK311830485F4F7CEB
+-- GO
+-- ALTER TABLE JRUAN.COMPOUND_ELEMENT
+-- DROP CONSTRAINT FK31183048459091E5
+-- GO
+-- ALTER TABLE JRUAN.CODONPOSITIONSET
+-- DROP CONSTRAINT FK4E501CC2A414944F
+-- GO
+-- ALTER TABLE JRUAN.CODONNONCODING_COLRANGE
+-- DROP CONSTRAINT FK307897FC79A523E6
+-- GO
+-- ALTER TABLE JRUAN.CODONNONCODING_COLRANGE
+-- DROP CONSTRAINT FK307897FC491DB20E
+-- GO
+-- ALTER TABLE JRUAN.CODONCHAR3_COLRANGE
+-- DROP CONSTRAINT FKC2EDB73679A523E6
+-- GO
+-- ALTER TABLE JRUAN.CODONCHAR3_COLRANGE
+-- DROP CONSTRAINT FKC2EDB736491DB20E
+-- GO
+-- ALTER TABLE JRUAN.CODONCHAR2_COLRANGE
+-- DROP CONSTRAINT FKCEA4461779A523E6
+-- GO
+-- ALTER TABLE JRUAN.CODONCHAR2_COLRANGE
+-- DROP CONSTRAINT FKCEA44617491DB20E
+-- GO
+-- ALTER TABLE JRUAN.CODONCHAR1_COLRANGE
+-- DROP CONSTRAINT FKDA5AD4F879A523E6
+-- GO
+-- ALTER TABLE JRUAN.CODONCHAR1_COLRANGE
+-- DROP CONSTRAINT FKDA5AD4F8491DB20E
+-- GO
+-- ALTER TABLE JRUAN.CODERECORD_COLRANGE
+-- DROP CONSTRAINT FKA3E6C61EDC51C546
+-- GO
+-- ALTER TABLE JRUAN.CODERECORD_COLRANGE
+-- DROP CONSTRAINT FKA3E6C61E79A523E6
+-- GO
+-- ALTER TABLE JRUAN.CITATION
+-- DROP CONSTRAINT FKD8A7FAE74C983658
+-- GO
+-- ALTER TABLE JRUAN.CITATION_EDITOR
+-- DROP CONSTRAINT FK2A8955C5EC93F501
+-- GO
+-- ALTER TABLE JRUAN.CITATION_EDITOR
+-- DROP CONSTRAINT FK2A8955C568F6F619
+-- GO
+-- ALTER TABLE JRUAN.CITATION_AUTHOR
+-- DROP CONSTRAINT FK24AA55E38E1E4DF8
+-- GO
+-- ALTER TABLE JRUAN.CITATION_AUTHOR
+-- DROP CONSTRAINT FK24AA55E36707573B
+-- GO
+-- ALTER TABLE JRUAN.CHARWEIGHTSET
+-- DROP CONSTRAINT FK99B8AC34A414944F
+-- GO
+-- ALTER TABLE JRUAN.CHARWEIGHT
+-- DROP CONSTRAINT FK8CC7694EE9B425A6
+-- GO
+-- ALTER TABLE JRUAN.CHARWEIGHT_COLRANGE
+-- DROP CONSTRAINT FK54CA674EF9A75EE
+-- GO
+-- ALTER TABLE JRUAN.CHARWEIGHT_COLRANGE
+-- DROP CONSTRAINT FK54CA674E79A523E6
+-- GO
+-- ALTER TABLE JRUAN.CHARSET
+-- DROP CONSTRAINT FK56D8ED2CA414944F
+-- GO
+-- ALTER TABLE JRUAN.CHARSET_COLRANGE
+-- DROP CONSTRAINT FK2CBD9079A523E6
+-- GO
+-- ALTER TABLE JRUAN.CHARSET_COLRANGE
+-- DROP CONSTRAINT FK2CBD90416D5B50
+-- GO
+-- ALTER TABLE JRUAN.CHARPARTITION
+-- DROP CONSTRAINT FKDEA9F834A414944F
+-- GO
+-- ALTER TABLE JRUAN.CHARGROUP
+-- DROP CONSTRAINT FK3AF18C91AA11DC6
+-- GO
+-- ALTER TABLE JRUAN.CHARGROUP_COLRANGE
+-- DROP CONSTRAINT FKB2D8C293971FFFA6
+-- GO
+-- ALTER TABLE JRUAN.CHARGROUP_COLRANGE
+-- DROP CONSTRAINT FKB2D8C29379A523E6
+-- GO
+-- ALTER TABLE JRUAN.ANCSTATESET
+-- DROP CONSTRAINT FK879339E7A414944F
+-- GO
+-- ALTER TABLE JRUAN.ANCESTRALSTATE
+-- DROP CONSTRAINT FK3FA14284F4803CE6
+-- GO
+-- ALTER TABLE JRUAN.ANCESTRALSTATE
+-- DROP CONSTRAINT FK3FA14284684F6406
+-- GO
+-- ALTER TABLE JRUAN.ANALYZEDDATA
+-- DROP CONSTRAINT FK8C961842B710CB23
+-- GO
+-- ALTER TABLE JRUAN.ANALYZEDDATA
+-- DROP CONSTRAINT FK8C96184255961AEE
+-- GO
+-- ALTER TABLE JRUAN.ANALYZEDDATA
+-- DROP CONSTRAINT FK8C9618424BA97F78
+-- GO
+-- ALTER TABLE JRUAN.ANALYSISSTEP
+-- DROP CONSTRAINT FK21F853A8D1884DD8
+-- GO
+-- ALTER TABLE JRUAN.ANALYSISSTEP
+-- DROP CONSTRAINT FK21F853A865EDD5F8
+-- GO
+-- ALTER TABLE JRUAN.ANALYSISSTEP
+-- DROP CONSTRAINT FK21F853A848A2817C
+-- GO
+-- ALTER TABLE JRUAN.ANALYSIS
+-- DROP CONSTRAINT FKF19622DC3C572C3C
+-- GO
+-- ALTER TABLE JRUAN.ALGORITHM
+-- DROP CONSTRAINT FKB388C44FC6E814E6
+-- GO
+-- ALTER TABLE JRUAN.ALGORITHM
+-- DROP CONSTRAINT FKB388C44F9698D32E
+-- GO
+-- ALTER TABLE JRUAN.ALGORITHM
+-- DROP CONSTRAINT FKB388C44F92E6A38E
+-- GO
+-- ALTER TABLE JRUAN.USERTYPERRD_COLRANGE
+-- DROP CONSTRAINT SQL081219134227270
+-- GO
+-- ALTER TABLE JRUAN.USER
+-- DROP CONSTRAINT SQL081219134226851
+-- GO
+-- ALTER TABLE JRUAN.SUBMISSION
+-- DROP CONSTRAINT SQL081219134223811
+-- GO
+-- ALTER TABLE JRUAN.SUB_TREEBLOCK
+-- DROP CONSTRAINT SQL081219134224130
+-- GO
+-- ALTER TABLE JRUAN.SUB_TAXONLABEL
+-- DROP CONSTRAINT SQL081219134224030
+-- GO
+-- ALTER TABLE JRUAN.SUB_MATRIX
+-- DROP CONSTRAINT SQL081219134223920
+-- GO
+-- ALTER TABLE JRUAN.COMPOUND_ELEMENT
+-- DROP CONSTRAINT SQL081219134219010
+-- GO
+-- ALTER TABLE JRUAN.CODONNONCODING_COLRANGE
+-- DROP CONSTRAINT SQL081219134220010
+-- GO
+-- ALTER TABLE JRUAN.CODONCHAR3_COLRANGE
+-- DROP CONSTRAINT SQL081219134219910
+-- GO
+-- ALTER TABLE JRUAN.CODONCHAR2_COLRANGE
+-- DROP CONSTRAINT SQL081219134219810
+-- GO
+-- ALTER TABLE JRUAN.CODONCHAR1_COLRANGE
+-- DROP CONSTRAINT SQL081219134219710
+-- GO
+-- ALTER TABLE JRUAN.CODERECORD_COLRANGE
+-- DROP CONSTRAINT SQL081219134219610
+-- GO
+-- ALTER TABLE JRUAN.CHARWEIGHT_COLRANGE
+-- DROP CONSTRAINT SQL081219134219510
+-- GO
+-- ALTER TABLE JRUAN.CHARSET_COLRANGE
+-- DROP CONSTRAINT SQL081219134219400
+-- GO
+-- ALTER TABLE JRUAN.CHARGROUP_COLRANGE
+-- DROP CONSTRAINT SQL081219134219300
+-- GO
+-- ALTER TABLE JRUAN.USERTYPERECORD
+-- DROP CONSTRAINT SQL081219134227170
+-- GO
+-- ALTER TABLE JRUAN.USERTYPE
+-- DROP CONSTRAINT SQL081219134227060
+-- GO
+-- ALTER TABLE JRUAN.USERROLE
+-- DROP CONSTRAINT SQL081219134226960
+-- GO
+-- ALTER TABLE JRUAN.USER
+-- DROP CONSTRAINT SQL081219134226850
+-- GO
+-- ALTER TABLE JRUAN.TYPESET
+-- DROP CONSTRAINT SQL081219134226550
+-- GO
+-- ALTER TABLE JRUAN.TREETYPE
+-- DROP CONSTRAINT SQL081219134226440
+-- GO
+-- ALTER TABLE JRUAN.TREESET
+-- DROP CONSTRAINT SQL081219134226240
+-- GO
+-- ALTER TABLE JRUAN.TREESET_PHYLOTREE
+-- DROP CONSTRAINT SQL081219134226340
+-- GO
+-- ALTER TABLE JRUAN.TREEQUALITY
+-- DROP CONSTRAINT SQL081219134226140
+-- GO
+-- ALTER TABLE JRUAN.TREEPARTITION
+-- DROP CONSTRAINT SQL081219134226040
+-- GO
+-- ALTER TABLE JRUAN.TREENODEEDGE
+-- DROP CONSTRAINT SQL081219134225930
+-- GO
+-- ALTER TABLE JRUAN.TREEKIND
+-- DROP CONSTRAINT SQL081219134225820
+-- GO
+-- ALTER TABLE JRUAN.TREEGROUP
+-- DROP CONSTRAINT SQL081219134225620
+-- GO
+-- ALTER TABLE JRUAN.TREEGROUP_PHYLOTREE
+-- DROP CONSTRAINT SQL081219134225720
+-- GO
+-- ALTER TABLE JRUAN.TREEBLOCK
+-- DROP CONSTRAINT SQL081219134225510
+-- GO
+-- ALTER TABLE JRUAN.TREEATTRIBUTE
+-- DROP CONSTRAINT SQL081219134225410
+-- GO
+-- ALTER TABLE JRUAN.TAXONVARIANT
+-- DROP CONSTRAINT SQL081219134225250
+-- GO
+-- ALTER TABLE JRUAN.TAXONSET
+-- DROP CONSTRAINT SQL081219134225050
+-- GO
+-- ALTER TABLE JRUAN.TAXONSET_TAXON
+-- DROP CONSTRAINT SQL081219134225150
+-- GO
+-- ALTER TABLE JRUAN.TAXONLINK
+-- DROP CONSTRAINT SQL081219134224950
+-- GO
+-- ALTER TABLE JRUAN.TAXONLABELSET
+-- DROP CONSTRAINT SQL081219134226650
+-- GO
+-- ALTER TABLE JRUAN.TAXONLABELSET_TAXONLABEL
+-- DROP CONSTRAINT SQL081219134226750
+-- GO
+-- ALTER TABLE JRUAN.TAXONLABELPARTITION
+-- DROP CONSTRAINT SQL081219134224760
+-- GO
+-- ALTER TABLE JRUAN.TAXONLABELGROUP
+-- DROP CONSTRAINT SQL081219134224650
+-- GO
+-- ALTER TABLE JRUAN.TAXONLABEL
+-- DROP CONSTRAINT SQL081219134224550
+-- GO
+-- ALTER TABLE JRUAN.TAXONAUTHORITY
+-- DROP CONSTRAINT SQL081219134224450
+-- GO
+-- ALTER TABLE JRUAN.TAXON
+-- DROP CONSTRAINT SQL081219134224350
+-- GO
+-- ALTER TABLE JRUAN.SUBMISSION
+-- DROP CONSTRAINT SQL081219134223810
+-- GO
+-- ALTER TABLE JRUAN.SUB_TREEBLOCK
+-- DROP CONSTRAINT SQL081219134224120
+-- GO
+-- ALTER TABLE JRUAN.SUB_TAXONLABEL
+-- DROP CONSTRAINT SQL081219134224020
+-- GO
+-- ALTER TABLE JRUAN.SUB_MATRIX
+-- DROP CONSTRAINT SQL081219134223910
+-- GO
+-- ALTER TABLE JRUAN.STUDYSTATUS
+-- DROP CONSTRAINT SQL081219134223710
+-- GO
+-- ALTER TABLE JRUAN.STUDY
+-- DROP CONSTRAINT SQL081219134223600
+-- GO
+-- ALTER TABLE JRUAN.STUDY_NEXUSFILE
+-- DROP CONSTRAINT SQL081219134224240
+-- GO
+-- ALTER TABLE JRUAN.STEPMATRIXELEMENT
+-- DROP CONSTRAINT SQL081219134223500
+-- GO
+-- ALTER TABLE JRUAN.STATESET
+-- DROP CONSTRAINT SQL081219134223390
+-- GO
+-- ALTER TABLE JRUAN.STATEMODIFIER
+-- DROP CONSTRAINT SQL081219134223290
+-- GO
+-- ALTER TABLE JRUAN.STATEFORMAT
+-- DROP CONSTRAINT SQL081219134223190
+-- GO
+-- ALTER TABLE JRUAN.STATECHANGESET
+-- DROP CONSTRAINT SQL081219134223070
+-- GO
+-- ALTER TABLE JRUAN.SPECIMENLABEL
+-- DROP CONSTRAINT SQL080428163906480
+-- GO
+-- ALTER TABLE JRUAN.SOFTWARE
+-- DROP CONSTRAINT SQL081219134222960
+-- GO
+-- ALTER TABLE JRUAN.ROWSEGMENT
+-- DROP CONSTRAINT SQL081219134222850
+-- GO
+-- ALTER TABLE JRUAN.POLYTCOUNT
+-- DROP CONSTRAINT SQL081219134222660
+-- GO
+-- ALTER TABLE JRUAN.PHYLOTREENODE
+-- DROP CONSTRAINT SQL081219134222560
+-- GO
+-- ALTER TABLE JRUAN.PHYLOTREE
+-- DROP CONSTRAINT SQL081219134222440
+-- GO
+-- ALTER TABLE JRUAN.PHYLOCHAR
+-- DROP CONSTRAINT SQL081219134222330
+-- GO
+-- ALTER TABLE JRUAN.PERSON
+-- DROP CONSTRAINT SQL081219134222230
+-- GO
+-- ALTER TABLE JRUAN.NODEATTRIBUTE
+-- DROP CONSTRAINT SQL081219134222120
+-- GO
+-- ALTER TABLE JRUAN.MATRIXROW
+-- DROP CONSTRAINT SQL081219134221900
+-- GO
+-- ALTER TABLE JRUAN.MATRIXKIND
+-- DROP CONSTRAINT SQL081219134221790
+-- GO
+-- ALTER TABLE JRUAN.MATRIXELEMENT
+-- DROP CONSTRAINT SQL081219134221690
+-- GO
+-- ALTER TABLE JRUAN.MATRIXDATATYPE
+-- DROP CONSTRAINT SQL081219134221580
+-- GO
+-- ALTER TABLE JRUAN.MATRIXCOLUMN
+-- DROP CONSTRAINT SQL081219134221370
+-- GO
+-- ALTER TABLE JRUAN.MATRIXCOLUMN_ITEMDEFINITION
+-- DROP CONSTRAINT SQL081219134221470
+-- GO
+-- ALTER TABLE JRUAN.MATRIX
+-- DROP CONSTRAINT SQL081219134221270
+-- GO
+-- ALTER TABLE JRUAN.MATRIX_ITEMDEFINITION
+-- DROP CONSTRAINT SQL081219134222010
+-- GO
+-- ALTER TABLE JRUAN.ITEMVALUE
+-- DROP CONSTRAINT SQL081219134221080
+-- GO
+-- ALTER TABLE JRUAN.ITEMDEFINITION
+-- DROP CONSTRAINT SQL081219134220970
+-- GO
+-- ALTER TABLE JRUAN.HELP
+-- DROP CONSTRAINT SQL081219134220860
+-- GO
+-- ALTER TABLE JRUAN.GEOSPOT
+-- DROP CONSTRAINT SQL080428163906080
+-- GO
+-- ALTER TABLE JRUAN.GENETICCODESET
+-- DROP CONSTRAINT SQL081219134220550
+-- GO
+-- ALTER TABLE JRUAN.GENETICCODERECORD
+-- DROP CONSTRAINT SQL081219134220760
+-- GO
+-- ALTER TABLE JRUAN.GENETICCODE
+-- DROP CONSTRAINT SQL081219134220650
+-- GO
+-- ALTER TABLE JRUAN.GAPMODE
+-- DROP CONSTRAINT SQL081219134220440
+-- GO
+-- ALTER TABLE JRUAN.EXPLAIN_STATEMENT
+-- DROP CONSTRAINT SQL050919121810940
+-- GO
+-- ALTER TABLE JRUAN.EXPLAIN_INSTANCE
+-- DROP CONSTRAINT SQL050919121810910
+-- GO
+-- ALTER TABLE JRUAN.DISTANCEMATRIXELEMENT
+-- DROP CONSTRAINT SQL081219134220330
+-- GO
+-- ALTER TABLE JRUAN.DISCRETECHARSTATE
+-- DROP CONSTRAINT SQL081219134220230
+-- GO
+-- ALTER TABLE JRUAN.CSTREENODE
+-- DROP CONSTRAINT SQL081219134219200
+-- GO
+-- ALTER TABLE JRUAN.COMPOUND_ELEMENT
+-- DROP CONSTRAINT SQL081219134219000
+-- GO
+-- ALTER TABLE JRUAN.COLUMNRANGE
+-- DROP CONSTRAINT SQL081219134218890
+-- GO
+-- ALTER TABLE JRUAN.CODONPOSITIONSET
+-- DROP CONSTRAINT SQL081219134220130
+-- GO
+-- ALTER TABLE JRUAN.CITATIONSTATUS
+-- DROP CONSTRAINT SQL081219134218570
+-- GO
+-- ALTER TABLE JRUAN.CITATION
+-- DROP CONSTRAINT SQL081219134218470
+-- GO
+-- ALTER TABLE JRUAN.CITATION_EDITOR
+-- DROP CONSTRAINT SQL081219134218780
+-- GO
+-- ALTER TABLE JRUAN.CITATION_AUTHOR
+-- DROP CONSTRAINT SQL081219134218670
+-- GO
+-- ALTER TABLE JRUAN.CHARWEIGHTSET
+-- DROP CONSTRAINT SQL081219134218310
+-- GO
+-- ALTER TABLE JRUAN.CHARWEIGHT
+-- DROP CONSTRAINT SQL081219134218200
+-- GO
+-- ALTER TABLE JRUAN.CHARSET
+-- DROP CONSTRAINT SQL081219134218100
+-- GO
+-- ALTER TABLE JRUAN.CHARPARTITION
+-- DROP CONSTRAINT SQL081219134217990
+-- GO
+-- ALTER TABLE JRUAN.CHARGROUP
+-- DROP CONSTRAINT SQL081219134217890
+-- GO
+-- ALTER TABLE JRUAN.ANCSTATESET
+-- DROP CONSTRAINT SQL081219134217770
+-- GO
+-- ALTER TABLE JRUAN.ANCESTRALSTATE
+-- DROP CONSTRAINT SQL081219134217670
+-- GO
+-- ALTER TABLE JRUAN.ANALYZEDDATA
+-- DROP CONSTRAINT SQL081219134217570
+-- GO
+-- ALTER TABLE JRUAN.ANALYSISSTEP
+-- DROP CONSTRAINT SQL081219134217470
+-- GO
+-- ALTER TABLE JRUAN.ANALYSIS
+-- DROP CONSTRAINT SQL081219134217310
+-- GO
+-- ALTER TABLE JRUAN.ALGORITHM
+-- DROP CONSTRAINT SQL081219134217210
+-- GO
+/*
+ALTER TABLE USERTYPERRD_COLRANGE
+ DROP CONSTRAINT FK405805DDC009330E;
+ALTER TABLE USERTYPERRD_COLRANGE
+ DROP CONSTRAINT FK405805DD79A523E6;
+ALTER TABLE USERTYPERECORD
+ DROP CONSTRAINT FK136AF61692E6A38E;
+ALTER TABLE USERTYPERECORD
+ DROP CONSTRAINT FK136AF6164D737E46;
+ALTER TABLE "user"
+ DROP CONSTRAINT FK27E3CBF59DD12;
+ALTER TABLE "user"
+ DROP CONSTRAINT FK27E3CBE3910672;
+ALTER TABLE TYPESET
+ DROP CONSTRAINT FKF7F2B6C8A414944F;
+ALTER TABLE TREESET_PHYLOTREE
+ DROP CONSTRAINT FK31FC19A7EC59B1E3;
+ALTER TABLE TREESET_PHYLOTREE
+ DROP CONSTRAINT FK31FC19A7B710CB23;
+ALTER TABLE TREENODEEDGE
+ DROP CONSTRAINT FK7767285D27FD0589;
+ALTER TABLE TREENODEEDGE
+ DROP CONSTRAINT FK7767285D1851763B;
+ALTER TABLE TREEGROUP
+ DROP CONSTRAINT FKA870258180CBD223;
+ALTER TABLE TREEGROUP_PHYLOTREE
+ DROP CONSTRAINT FKFB7D704B710CB23;
+ALTER TABLE TREEGROUP_PHYLOTREE
+ DROP CONSTRAINT FKFB7D7045E56A83;
+ALTER TABLE TREEBLOCK
+ DROP CONSTRAINT FKA826F38FE310471D;
+ALTER TABLE TAXONVARIANT
+ DROP CONSTRAINT FKEE3D127B1DE2FCDD;
+ALTER TABLE TAXONSET_TAXON
+ DROP CONSTRAINT FKC656C9031DE2FCDD;
+ALTER TABLE TAXONSET_TAXON
+ DROP CONSTRAINT FKC656C90313C28457;
+ALTER TABLE TAXONLINK
+ DROP CONSTRAINT FKC102D9A43BF5F2F7;
+ALTER TABLE TAXONLINK
+ DROP CONSTRAINT FKC102D9A41DE2FCDD;
+ALTER TABLE TAXONLABELSET
+ DROP CONSTRAINT FK28D3A5983C572C3C;
+ALTER TABLE TAXONLABELSET_TAXONLABEL
+ DROP CONSTRAINT FK2EB54B71E310471D;
+ALTER TABLE TAXONLABELSET_TAXONLABEL
+ DROP CONSTRAINT FK2EB54B7163AB9FD7;
+ALTER TABLE TAXONLABELROUP_TAXONLABEL
+ DROP CONSTRAINT FK4B1D0BC763AB9FD7;
+ALTER TABLE TAXONLABELROUP_TAXONLABEL
+ DROP CONSTRAINT FK4B1D0BC7294B993D;
+ALTER TABLE TAXONLABELGROUP
+ DROP CONSTRAINT FK4AE2663513A813DD;
+ALTER TABLE TAXONLABEL
+ DROP CONSTRAINT FK5F548A6A3C572C3C;
+ALTER TABLE TAXONLABEL
+ DROP CONSTRAINT FK5F548A6A3C1B6F7;
+ALTER TABLE SUBMISSION
+ DROP CONSTRAINT FKA120274CBEF300B2;
+ALTER TABLE SUBMISSION
+ DROP CONSTRAINT FKA120274C3C572C3C;
+ALTER TABLE SUB_TREEBLOCK
+ DROP CONSTRAINT FK94D50830BFD107C3;
+ALTER TABLE SUB_TREEBLOCK
+ DROP CONSTRAINT FK94D508308DFE4858;
+ALTER TABLE SUB_TAXONLABEL
+ DROP CONSTRAINT FK86909E98DFE4858;
+ALTER TABLE SUB_TAXONLABEL
+ DROP CONSTRAINT FK86909E963AB9FD7;
+ALTER TABLE SUB_MATRIX
+ DROP CONSTRAINT FK5F26A2C08DFE4858;
+ALTER TABLE SUB_MATRIX
+ DROP CONSTRAINT FK5F26A2C055961AEE;
+ALTER TABLE STUDY
+ DROP CONSTRAINT FK4B915A9BEF300B2;
+ALTER TABLE STUDY
+ DROP CONSTRAINT FK4B915A98E1E4DF8;
+ALTER TABLE STUDY
+ DROP CONSTRAINT FK4B915A9255A519C;
+ALTER TABLE STUDY_NEXUSFILE
+ DROP CONSTRAINT FK47FC1EE53C572C3C;
+ALTER TABLE STEPMATRIXELEMENT
+ DROP CONSTRAINT FK891100AF9E8198E;
+ALTER TABLE STEPMATRIXELEMENT
+ DROP CONSTRAINT FK891100AF6E979EE7;
+ALTER TABLE STEPMATRIXELEMENT
+ DROP CONSTRAINT FK891100AF6E972A88;
+ALTER TABLE STATESET
+ DROP CONSTRAINT FK7D38523150CBAB47;
+ALTER TABLE STATEMODIFIER
+ DROP CONSTRAINT FKD157BE48F4803CE6;
+ALTER TABLE STATEMODIFIER
+ DROP CONSTRAINT FKD157BE48BED40086;
+ALTER TABLE STATEMODIFIER
+ DROP CONSTRAINT FKD157BE48459091E5;
+ALTER TABLE SPECIMENLABEL
+ DROP CONSTRAINT FK1E8F38CCA2039B9D;
+ALTER TABLE ROWSEGMENT
+ DROP CONSTRAINT FKEE9AE819E7B3CDA6;
+ALTER TABLE ROWSEGMENT
+ DROP CONSTRAINT FKEE9AE81963AB9FD7;
+ALTER TABLE RIGHTCHANGESET_CHARSTATE
+ DROP CONSTRAINT FKC8AFC9F2F4803CE6;
+ALTER TABLE RIGHTCHANGESET_CHARSTATE
+ DROP CONSTRAINT FKC8AFC9F275763EAE;
+ALTER TABLE PHYLOTREENODE
+ DROP CONSTRAINT FK3EA79944B710CB23;
+ALTER TABLE PHYLOTREENODE
+ DROP CONSTRAINT FK3EA7994463AB9FD7;
+ALTER TABLE PHYLOTREENODE
+ DROP CONSTRAINT FK3EA799445BCC767D;
+ALTER TABLE PHYLOTREENODE
+ DROP CONSTRAINT FK3EA79944434FDCCB;
+ALTER TABLE PHYLOTREENODE
+ DROP CONSTRAINT FK3EA799443C348165;
+ALTER TABLE PHYLOTREENODE
+ DROP CONSTRAINT FK3EA79944271A5763;
+ALTER TABLE PHYLOTREE
+ DROP CONSTRAINT FK76F2E442FE2812F1;
+ALTER TABLE PHYLOTREE
+ DROP CONSTRAINT FK76F2E442F5AEA931;
+ALTER TABLE PHYLOTREE
+ DROP CONSTRAINT FK76F2E442F3D1CF03;
+ALTER TABLE PHYLOTREE
+ DROP CONSTRAINT FK76F2E442EA08B443;
+ALTER TABLE PHYLOTREE
+ DROP CONSTRAINT FK76F2E442BFD107C3;
+ALTER TABLE PHYLOTREE
+ DROP CONSTRAINT FK76F2E442A3015CE3;
+ALTER TABLE PHYLOTREE
+ DROP CONSTRAINT FK76F2E4423C572C3C;
+ALTER TABLE MATRIXROW
+ DROP CONSTRAINT FKE4688E59A414944F;
+ALTER TABLE MATRIXROW
+ DROP CONSTRAINT FKE4688E5963AB9FD7;
+ALTER TABLE MATRIXELEMENT
+ DROP CONSTRAINT FK90AE93FBF4803CE6;
+ALTER TABLE MATRIXELEMENT
+ DROP CONSTRAINT FK90AE93FBE7B3CDA6;
+ALTER TABLE MATRIXELEMENT
+ DROP CONSTRAINT FK90AE93FB8B2E884E;
+ALTER TABLE MATRIXELEMENT
+ DROP CONSTRAINT FK90AE93FB405A7CEE;
+ALTER TABLE MATRIXDATATYPE
+ DROP CONSTRAINT FKF054C4A5F5DECA46;
+ALTER TABLE MATRIXCOLUMN
+ DROP CONSTRAINT FK9B0BE57F5DECA46;
+ALTER TABLE MATRIXCOLUMN
+ DROP CONSTRAINT FK9B0BE57BED40086;
+ALTER TABLE MATRIXCOLUMN
+ DROP CONSTRAINT FK9B0BE57A414944F;
+ALTER TABLE MATRIXCOLUMN_ITEMDEFINITION
+ DROP CONSTRAINT FKB556F8E8B2E884E;
+ALTER TABLE MATRIXCOLUMN_ITEMDEFINITION
+ DROP CONSTRAINT FKB556F8E405A7CEE;
+ALTER TABLE MATRIX
+ DROP CONSTRAINT FK87208BC1E9B425A6;
+ALTER TABLE MATRIX
+ DROP CONSTRAINT FK87208BC1E310471D;
+ALTER TABLE MATRIX
+ DROP CONSTRAINT FK87208BC191BD3C8E;
+ALTER TABLE MATRIX
+ DROP CONSTRAINT FK87208BC1684F6406;
+ALTER TABLE MATRIX
+ DROP CONSTRAINT FK87208BC14D737E46;
+ALTER TABLE MATRIX
+ DROP CONSTRAINT FK87208BC14CE484AE;
+ALTER TABLE MATRIX
+ DROP CONSTRAINT FK87208BC1491DB20E;
+ALTER TABLE MATRIX
+ DROP CONSTRAINT FK87208BC145534A9C;
+ALTER TABLE MATRIX
+ DROP CONSTRAINT FK87208BC13C572C3C;
+ALTER TABLE MATRIX_ITEMDEFINITION
+ DROP CONSTRAINT FK5717E0E4AC5C19DD;
+ALTER TABLE MATRIX_ITEMDEFINITION
+ DROP CONSTRAINT FK5717E0E4405A7CEE;
+ALTER TABLE LEFTCHANGESET_CHARSTATE
+ DROP CONSTRAINT FKC8877207F4803CE6;
+ALTER TABLE LEFTCHANGESET_CHARSTATE
+ DROP CONSTRAINT FKC887720775763EAE;
+ALTER TABLE ITEMVALUE
+ DROP CONSTRAINT FK27B41A1E459091E5;
+ALTER TABLE GENETICCODESET
+ DROP CONSTRAINT FK6A12F7DCA414944F;
+ALTER TABLE GENETICCODERECORD
+ DROP CONSTRAINT FK237932B782D8ECCE;
+ALTER TABLE GENETICCODERECORD
+ DROP CONSTRAINT FK237932B76CB73FC6;
+--ALTER TABLE EXPLAIN_STREAM
+-- DROP CONSTRAINT SQL050919121811070;
+--ALTER TABLE EXPLAIN_STATEMENT
+-- DROP CONSTRAINT SQL050919121810950;
+--ALTER TABLE EXPLAIN_PREDICATE
+-- DROP CONSTRAINT SQL050919121811040;
+--ALTER TABLE EXPLAIN_OPERATOR
+-- DROP CONSTRAINT SQL050919121810970;
+--ALTER TABLE EXPLAIN_OBJECT
+-- DROP CONSTRAINT SQL050919121811000;
+--ALTER TABLE EXPLAIN_ARGUMENT
+-- DROP CONSTRAINT SQL050919121811060;
+ALTER TABLE DISTANCEMATRIXELEMENT
+ DROP CONSTRAINT FK92D3DDE6C1429863;
+ALTER TABLE DISTANCEMATRIXELEMENT
+ DROP CONSTRAINT FK92D3DDE64B8EF343;
+ALTER TABLE DISTANCEMATRIXELEMENT
+ DROP CONSTRAINT FK92D3DDE61F08BAE7;
+ALTER TABLE DISCRETECHARSTATE
+ DROP CONSTRAINT FK2EEF2802FE41A723;
+ALTER TABLE DISCRETECHARSTATE
+ DROP CONSTRAINT FK2EEF2802C7BEAAFE;
+ALTER TABLE DISCRETECHARSTATE
+ DROP CONSTRAINT FK2EEF2802163C67CE;
+ALTER TABLE CSTREENODE
+ DROP CONSTRAINT FK82B9AB10F572A92;
+ALTER TABLE CSTREENODE
+ DROP CONSTRAINT FK82B9AB10F4803CE6;
+ALTER TABLE CSTREENODE
+ DROP CONSTRAINT FK82B9AB10C6999FCE;
+ALTER TABLE CONTANCSTATE_VALUE
+ DROP CONSTRAINT FKA84B8C3FD450D2BD;
+ALTER TABLE COMPOUND_ELEMENT
+ DROP CONSTRAINT FK311830485F4F7CEB;
+ALTER TABLE COMPOUND_ELEMENT
+ DROP CONSTRAINT FK31183048459091E5;
+ALTER TABLE CODONPOSITIONSET
+ DROP CONSTRAINT FK4E501CC2A414944F;
+ALTER TABLE CODONNONCODING_COLRANGE
+ DROP CONSTRAINT FK307897FC79A523E6;
+ALTER TABLE CODONNONCODING_COLRANGE
+ DROP CONSTRAINT FK307897FC491DB20E;
+ALTER TABLE CODONCHAR3_COLRANGE
+ DROP CONSTRAINT FKC2EDB73679A523E6;
+ALTER TABLE CODONCHAR3_COLRANGE
+ DROP CONSTRAINT FKC2EDB736491DB20E;
+ALTER TABLE CODONCHAR2_COLRANGE
+ DROP CONSTRAINT FKCEA4461779A523E6;
+ALTER TABLE CODONCHAR2_COLRANGE
+ DROP CONSTRAINT FKCEA44617491DB20E;
+ALTER TABLE CODONCHAR1_COLRANGE
+ DROP CONSTRAINT FKDA5AD4F879A523E6;
+ALTER TABLE CODONCHAR1_COLRANGE
+ DROP CONSTRAINT FKDA5AD4F8491DB20E;
+ALTER TABLE CODERECORD_COLRANGE
+ DROP CONSTRAINT FKA3E6C61EDC51C546;
+ALTER TABLE CODERECORD_COLRANGE
+ DROP CONSTRAINT FKA3E6C61E79A523E6;
+ALTER TABLE CITATION
+ DROP CONSTRAINT FKD8A7FAE74C983658;
+ALTER TABLE CITATION_EDITOR
+ DROP CONSTRAINT FK2A8955C5EC93F501;
+ALTER TABLE CITATION_EDITOR
+ DROP CONSTRAINT FK2A8955C568F6F619;
+ALTER TABLE CITATION_AUTHOR
+ DROP CONSTRAINT FK24AA55E38E1E4DF8;
+ALTER TABLE CITATION_AUTHOR
+ DROP CONSTRAINT FK24AA55E36707573B;
+ALTER TABLE CHARWEIGHTSET
+ DROP CONSTRAINT FK99B8AC34A414944F;
+ALTER TABLE CHARWEIGHT
+ DROP CONSTRAINT FK8CC7694EE9B425A6;
+ALTER TABLE CHARWEIGHT_COLRANGE
+ DROP CONSTRAINT FK54CA674EF9A75EE;
+ALTER TABLE CHARWEIGHT_COLRANGE
+ DROP CONSTRAINT FK54CA674E79A523E6;
+ALTER TABLE CHARSET
+ DROP CONSTRAINT FK56D8ED2CA414944F;
+ALTER TABLE CHARSET_COLRANGE
+ DROP CONSTRAINT FK2CBD9079A523E6;
+ALTER TABLE CHARSET_COLRANGE
+ DROP CONSTRAINT FK2CBD90416D5B50;
+ALTER TABLE CHARPARTITION
+ DROP CONSTRAINT FKDEA9F834A414944F;
+ALTER TABLE CHARGROUP
+ DROP CONSTRAINT FK3AF18C91AA11DC6;
+ALTER TABLE CHARGROUP_COLRANGE
+ DROP CONSTRAINT FKB2D8C293971FFFA6;
+ALTER TABLE CHARGROUP_COLRANGE
+ DROP CONSTRAINT FKB2D8C29379A523E6;
+ALTER TABLE ANCSTATESET
+ DROP CONSTRAINT FK879339E7A414944F;
+ALTER TABLE ANCESTRALSTATE
+ DROP CONSTRAINT FK3FA14284F4803CE6;
+ALTER TABLE ANCESTRALSTATE
+ DROP CONSTRAINT FK3FA14284684F6406;
+ALTER TABLE ANALYZEDDATA
+ DROP CONSTRAINT FK8C961842B710CB23;
+ALTER TABLE ANALYZEDDATA
+ DROP CONSTRAINT FK8C96184255961AEE;
+ALTER TABLE ANALYZEDDATA
+ DROP CONSTRAINT FK8C9618424BA97F78;
+ALTER TABLE ANALYSISSTEP
+ DROP CONSTRAINT FK21F853A8D1884DD8;
+ALTER TABLE ANALYSISSTEP
+ DROP CONSTRAINT FK21F853A865EDD5F8;
+ALTER TABLE ANALYSISSTEP
+ DROP CONSTRAINT FK21F853A848A2817C;
+ALTER TABLE ANALYSIS
+ DROP CONSTRAINT FKF19622DC3C572C3C;
+ALTER TABLE ALGORITHM
+ DROP CONSTRAINT FKB388C44FC6E814E6;
+ALTER TABLE ALGORITHM
+ DROP CONSTRAINT FKB388C44F9698D32E;
+ALTER TABLE ALGORITHM
+ DROP CONSTRAINT FKB388C44F92E6A38E;
+ALTER TABLE USERTYPERRD_COLRANGE
+ DROP CONSTRAINT SQL081219134227270;
+ALTER TABLE "user"
+ DROP CONSTRAINT SQL081219134226851;
+ALTER TABLE SUBMISSION
+ DROP CONSTRAINT SQL081219134223811;
+ALTER TABLE SUB_TREEBLOCK
+ DROP CONSTRAINT SQL081219134224130;
+ALTER TABLE SUB_TAXONLABEL
+ DROP CONSTRAINT SQL081219134224030;
+ALTER TABLE SUB_MATRIX
+ DROP CONSTRAINT SQL081219134223920;
+ALTER TABLE COMPOUND_ELEMENT
+ DROP CONSTRAINT SQL081219134219010;
+ALTER TABLE CODONNONCODING_COLRANGE
+ DROP CONSTRAINT SQL081219134220010;
+ALTER TABLE CODONCHAR3_COLRANGE
+ DROP CONSTRAINT SQL081219134219910;
+ALTER TABLE CODONCHAR2_COLRANGE
+ DROP CONSTRAINT SQL081219134219810;
+ALTER TABLE CODONCHAR1_COLRANGE
+ DROP CONSTRAINT SQL081219134219710;
+ALTER TABLE CODERECORD_COLRANGE
+ DROP CONSTRAINT SQL081219134219610;
+ALTER TABLE CHARWEIGHT_COLRANGE
+ DROP CONSTRAINT SQL081219134219510;
+ALTER TABLE CHARSET_COLRANGE
+ DROP CONSTRAINT SQL081219134219400;
+ALTER TABLE CHARGROUP_COLRANGE
+ DROP CONSTRAINT SQL081219134219300;
+ALTER TABLE USERTYPERECORD
+ DROP CONSTRAINT SQL081219134227170;
+ALTER TABLE USERTYPE
+ DROP CONSTRAINT SQL081219134227060;
+ALTER TABLE USERROLE
+ DROP CONSTRAINT SQL081219134226960;
+ALTER TABLE "user"
+ DROP CONSTRAINT SQL081219134226850;
+ALTER TABLE TYPESET
+ DROP CONSTRAINT SQL081219134226550;
+ALTER TABLE TREETYPE
+ DROP CONSTRAINT SQL081219134226440;
+ALTER TABLE TREESET
+ DROP CONSTRAINT SQL081219134226240;
+ALTER TABLE TREESET_PHYLOTREE
+ DROP CONSTRAINT SQL081219134226340;
+ALTER TABLE TREEQUALITY
+ DROP CONSTRAINT SQL081219134226140;
+ALTER TABLE TREEPARTITION
+ DROP CONSTRAINT SQL081219134226040;
+ALTER TABLE TREENODEEDGE
+ DROP CONSTRAINT SQL081219134225930;
+ALTER TABLE TREEKIND
+ DROP CONSTRAINT SQL081219134225820;
+ALTER TABLE TREEGROUP
+ DROP CONSTRAINT SQL081219134225620;
+ALTER TABLE TREEGROUP_PHYLOTREE
+ DROP CONSTRAINT SQL081219134225720;
+ALTER TABLE TREEBLOCK
+ DROP CONSTRAINT SQL081219134225510;
+ALTER TABLE TREEATTRIBUTE
+ DROP CONSTRAINT SQL081219134225410;
+ALTER TABLE TAXONVARIANT
+ DROP CONSTRAINT SQL081219134225250;
+ALTER TABLE TAXONSET
+ DROP CONSTRAINT SQL081219134225050;
+ALTER TABLE TAXONSET_TAXON
+ DROP CONSTRAINT SQL081219134225150;
+ALTER TABLE TAXONLINK
+ DROP CONSTRAINT SQL081219134224950;
+ALTER TABLE TAXONLABELSET
+ DROP CONSTRAINT SQL081219134226650;
+ALTER TABLE TAXONLABELSET_TAXONLABEL
+ DROP CONSTRAINT SQL081219134226750;
+ALTER TABLE TAXONLABELPARTITION
+ DROP CONSTRAINT SQL081219134224760;
+ALTER TABLE TAXONLABELGROUP
+ DROP CONSTRAINT SQL081219134224650;
+ALTER TABLE TAXONLABEL
+ DROP CONSTRAINT SQL081219134224550;
+ALTER TABLE TAXONAUTHORITY
+ DROP CONSTRAINT SQL081219134224450;
+ALTER TABLE TAXON
+ DROP CONSTRAINT SQL081219134224350;
+ALTER TABLE SUBMISSION
+ DROP CONSTRAINT SQL081219134223810;
+ALTER TABLE SUB_TREEBLOCK
+ DROP CONSTRAINT SQL081219134224120;
+ALTER TABLE SUB_TAXONLABEL
+ DROP CONSTRAINT SQL081219134224020;
+ALTER TABLE SUB_MATRIX
+ DROP CONSTRAINT SQL081219134223910;
+ALTER TABLE STUDYSTATUS
+ DROP CONSTRAINT SQL081219134223710;
+ALTER TABLE STUDY
+ DROP CONSTRAINT SQL081219134223600;
+ALTER TABLE STUDY_NEXUSFILE
+ DROP CONSTRAINT SQL081219134224240;
+ALTER TABLE STEPMATRIXELEMENT
+ DROP CONSTRAINT SQL081219134223500;
+ALTER TABLE STATESET
+ DROP CONSTRAINT SQL081219134223390;
+ALTER TABLE STATEMODIFIER
+ DROP CONSTRAINT SQL081219134223290;
+ALTER TABLE STATEFORMAT
+ DROP CONSTRAINT SQL081219134223190;
+ALTER TABLE STATECHANGESET
+ DROP CONSTRAINT SQL081219134223070;
+ALTER TABLE SPECIMENLABEL
+ DROP CONSTRAINT SQL080428163906480;
+ALTER TABLE SOFTWARE
+ DROP CONSTRAINT SQL081219134222960;
+ALTER TABLE ROWSEGMENT
+ DROP CONSTRAINT SQL081219134222850;
+ALTER TABLE POLYTCOUNT
+ DROP CONSTRAINT SQL081219134222660;
+ALTER TABLE PHYLOTREENODE
+ DROP CONSTRAINT SQL081219134222560;
+ALTER TABLE PHYLOTREE
+ DROP CONSTRAINT SQL081219134222440;
+ALTER TABLE PHYLOCHAR
+ DROP CONSTRAINT SQL081219134222330;
+ALTER TABLE PERSON
+ DROP CONSTRAINT SQL081219134222230;
+ALTER TABLE NODEATTRIBUTE
+ DROP CONSTRAINT SQL081219134222120;
+ALTER TABLE MATRIXROW
+ DROP CONSTRAINT SQL081219134221900;
+ALTER TABLE MATRIXKIND
+ DROP CONSTRAINT SQL081219134221790;
+ALTER TABLE MATRIXELEMENT
+ DROP CONSTRAINT SQL081219134221690;
+ALTER TABLE MATRIXDATATYPE
+ DROP CONSTRAINT SQL081219134221580;
+ALTER TABLE MATRIXCOLUMN
+ DROP CONSTRAINT SQL081219134221370;
+ALTER TABLE MATRIXCOLUMN_ITEMDEFINITION
+ DROP CONSTRAINT SQL081219134221470;
+ALTER TABLE MATRIX
+ DROP CONSTRAINT SQL081219134221270;
+ALTER TABLE MATRIX_ITEMDEFINITION
+ DROP CONSTRAINT SQL081219134222010;
+ALTER TABLE ITEMVALUE
+ DROP CONSTRAINT SQL081219134221080;
+ALTER TABLE ITEMDEFINITION
+ DROP CONSTRAINT SQL081219134220970;
+ALTER TABLE HELP
+ DROP CONSTRAINT SQL081219134220860;
+ALTER TABLE GEOSPOT
+ DROP CONSTRAINT SQL080428163906080;
+ALTER TABLE GENETICCODESET
+ DROP CONSTRAINT SQL081219134220550;
+ALTER TABLE GENETICCODERECORD
+ DROP CONSTRAINT SQL081219134220760;
+ALTER TABLE GENETICCODE
+ DROP CONSTRAINT SQL081219134220650;
+ALTER TABLE GAPMODE
+ DROP CONSTRAINT SQL081219134220440;
+--ALTER TABLE EXPLAIN_STATEMENT
+-- DROP CONSTRAINT SQL050919121810940;
+--ALTER TABLE EXPLAIN_INSTANCE
+-- DROP CONSTRAINT SQL050919121810910;
+ALTER TABLE DISTANCEMATRIXELEMENT
+ DROP CONSTRAINT SQL081219134220330;
+ALTER TABLE DISCRETECHARSTATE
+ DROP CONSTRAINT SQL081219134220230;
+ALTER TABLE CSTREENODE
+ DROP CONSTRAINT SQL081219134219200;
+ALTER TABLE COMPOUND_ELEMENT
+ DROP CONSTRAINT SQL081219134219000;
+ALTER TABLE COLUMNRANGE
+ DROP CONSTRAINT SQL081219134218890;
+ALTER TABLE CODONPOSITIONSET
+ DROP CONSTRAINT SQL081219134220130;
+ALTER TABLE CITATIONSTATUS
+ DROP CONSTRAINT SQL081219134218570;
+ALTER TABLE CITATION
+ DROP CONSTRAINT SQL081219134218470;
+ALTER TABLE CITATION_EDITOR
+ DROP CONSTRAINT SQL081219134218780;
+ALTER TABLE CITATION_AUTHOR
+ DROP CONSTRAINT SQL081219134218670;
+ALTER TABLE CHARWEIGHTSET
+ DROP CONSTRAINT SQL081219134218310;
+ALTER TABLE CHARWEIGHT
+ DROP CONSTRAINT SQL081219134218200;
+ALTER TABLE CHARSET
+ DROP CONSTRAINT SQL081219134218100;
+ALTER TABLE CHARPARTITION
+ DROP CONSTRAINT SQL081219134217990;
+ALTER TABLE CHARGROUP
+ DROP CONSTRAINT SQL081219134217890;
+ALTER TABLE ANCSTATESET
+ DROP CONSTRAINT SQL081219134217770;
+ALTER TABLE ANCESTRALSTATE
+ DROP CONSTRAINT SQL081219134217670;
+ALTER TABLE ANALYZEDDATA
+ DROP CONSTRAINT SQL081219134217570;
+ALTER TABLE ANALYSISSTEP
+ DROP CONSTRAINT SQL081219134217470;
+ALTER TABLE ANALYSIS
+ DROP CONSTRAINT SQL081219134217310;
+ALTER TABLE ALGORITHM
+ DROP CONSTRAINT SQL081219134217210;
+*/
+-- DROP INDEX JRUAN.TVARI_NBID_IDX
+-- GO
+-- DROP INDEX JRUAN.TVARI_TAXON_IDX
+-- GO
+-- DROP INDEX JRUAN.TVARI_FNAME_IDX
+-- GO
+-- DROP INDEX JRUAN.TLABEL_STUDY_IDX
+-- GO
+-- DROP INDEX JRUAN.TAXON_NAME_IDX
+-- GO
+-- DROP INDEX JRUAN.STUDY_NAME_IDX
+-- GO
+-- DROP INDEX JRUAN.SPECIM_INST_IDX
+-- GO
+-- DROP INDEX JRUAN.TNODE_TREE_IDX
+-- GO
+-- DROP INDEX JRUAN.TNODE_TAXLABEL_IDX
+-- GO
+-- DROP INDEX JRUAN.PERSON_EMAIL_IDX
+-- GO
+-- DROP INDEX JRUAN.PERSON_LNAME_IDX
+-- GO
+-- DROP INDEX JRUAN.ROW_M_IDX
+-- GO
+-- DROP INDEX JRUAN.ELEMENT_COL_IDX
+-- GO
+-- DROP INDEX JRUAN.ELEMENT_ROW_IDX
+-- GO
+-- DROP INDEX JRUAN.COLUMN_M_IDX
+-- GO
+/*
+DROP INDEX TVARI_NBID_IDX;
+DROP INDEX TVARI_TAXON_IDX;
+DROP INDEX TVARI_FNAME_IDX;
+DROP INDEX TLABEL_STUDY_IDX;
+DROP INDEX TAXON_NAME_IDX;
+DROP INDEX STUDY_NAME_IDX;
+DROP INDEX SPECIM_INST_IDX;
+DROP INDEX TNODE_TREE_IDX;
+DROP INDEX TNODE_TAXLABEL_IDX;
+DROP INDEX PERSON_EMAIL_IDX;
+DROP INDEX PERSON_LNAME_IDX;
+DROP INDEX ROW_M_IDX;
+DROP INDEX ELEMENT_COL_IDX;
+DROP INDEX ELEMENT_ROW_IDX;
+DROP INDEX COLUMN_M_IDX;
+*/
+-- DROP TABLE JRUAN.USERTYPERRD_COLRANGE
+-- GO
+-- DROP TABLE JRUAN.USERTYPERECORD
+-- GO
+-- DROP TABLE JRUAN.USERTYPE
+-- GO
+-- DROP TABLE JRUAN.USERROLE
+-- GO
+-- DROP TABLE JRUAN.USER
+-- GO
+-- DROP TABLE JRUAN.TYPESET
+-- GO
+-- DROP TABLE JRUAN.TREETYPE
+-- GO
+-- DROP TABLE JRUAN.TREESET
+-- GO
+-- DROP TABLE JRUAN.TREESET_PHYLOTREE
+-- GO
+-- DROP TABLE JRUAN.TREEQUALITY
+-- GO
+-- DROP TABLE JRUAN.TREEPARTITION
+-- GO
+-- DROP TABLE JRUAN.TREENODEEDGE
+-- GO
+-- DROP TABLE JRUAN.TREEKIND
+-- GO
+-- DROP TABLE JRUAN.TREEGROUP
+-- GO
+-- DROP TABLE JRUAN.TREEGROUP_PHYLOTREE
+-- GO
+-- DROP TABLE JRUAN.TREEBLOCK
+-- GO
+-- DROP TABLE JRUAN.TREEATTRIBUTE
+-- GO
+-- DROP TABLE JRUAN.TAXONVARIANT
+-- GO
+-- DROP TABLE JRUAN.TAXONSET
+-- GO
+-- DROP TABLE JRUAN.TAXONSET_TAXON
+-- GO
+-- DROP TABLE JRUAN.TAXONLINK
+-- GO
+-- DROP TABLE JRUAN.TAXONLABELSET
+-- GO
+-- DROP TABLE JRUAN.TAXONLABELSET_TAXONLABEL
+-- GO
+-- DROP TABLE JRUAN.TAXONLABELROUP_TAXONLABEL
+-- GO
+-- DROP TABLE JRUAN.TAXONLABELPARTITION
+-- GO
+-- DROP TABLE JRUAN.TAXONLABELGROUP
+-- GO
+-- DROP TABLE JRUAN.TAXONLABEL
+-- GO
+-- DROP TABLE JRUAN.TAXONAUTHORITY
+-- GO
+-- DROP TABLE JRUAN.TAXON
+-- GO
+-- DROP TABLE JRUAN.SUBMISSION
+-- GO
+-- DROP TABLE JRUAN.SUB_TREEBLOCK
+-- GO
+-- DROP TABLE JRUAN.SUB_TAXONLABEL
+-- GO
+-- DROP TABLE JRUAN.SUB_MATRIX
+-- GO
+-- DROP TABLE JRUAN.STUDYSTATUS
+-- GO
+-- DROP TABLE JRUAN.STUDY
+-- GO
+-- DROP TABLE JRUAN.STUDY_NEXUSFILE
+-- GO
+-- DROP TABLE JRUAN.STEPMATRIXELEMENT
+-- GO
+-- DROP TABLE JRUAN.STATESET
+-- GO
+-- DROP TABLE JRUAN.STATEMODIFIER
+-- GO
+-- DROP TABLE JRUAN.STATEFORMAT
+-- GO
+-- DROP TABLE JRUAN.STATECHANGESET
+-- GO
+-- DROP TABLE JRUAN.SPECIMENLABEL
+-- GO
+-- DROP TABLE JRUAN.SOFTWARE
+-- GO
+-- DROP TABLE JRUAN.ROWSEGMENT
+-- GO
+-- DROP TABLE JRUAN.RIGHTCHANGESET_CHARSTATE
+-- GO
+-- DROP TABLE JRUAN.POLYTCOUNT
+-- GO
+-- DROP TABLE JRUAN.PHYLOTREENODE
+-- GO
+-- DROP TABLE JRUAN.PHYLOTREE
+-- GO
+-- DROP TABLE JRUAN.PHYLOCHAR
+-- GO
+-- DROP TABLE JRUAN.PERSON
+-- GO
+-- DROP TABLE JRUAN.NODEATTRIBUTE
+-- GO
+-- DROP TABLE JRUAN.MATRIXROW
+-- GO
+-- DROP TABLE JRUAN.MATRIXKIND
+-- GO
+-- DROP TABLE JRUAN.MATRIXELEMENT
+-- GO
+-- DROP TABLE JRUAN.MATRIXDATATYPE
+-- GO
+-- DROP TABLE JRUAN.MATRIXCOLUMN
+-- GO
+-- DROP TABLE JRUAN.MATRIXCOLUMN_ITEMDEFINITION
+-- GO
+-- DROP TABLE JRUAN.MATRIX
+-- GO
+-- DROP TABLE JRUAN.MATRIX_ITEMDEFINITION
+-- GO
+-- DROP TABLE JRUAN.LEFTCHANGESET_CHARSTATE
+-- GO
+-- DROP TABLE JRUAN.ITEMVALUE
+-- GO
+-- DROP TABLE JRUAN.ITEMDEFINITION
+-- GO
+-- DROP TABLE JRUAN.HELP
+-- GO
+-- DROP TABLE JRUAN.GEOSPOT
+-- GO
+-- DROP TABLE JRUAN.GENETICCODESET
+-- GO
+-- DROP TABLE JRUAN.GENETICCODERECORD
+-- GO
+-- DROP TABLE JRUAN.GENETICCODE
+-- GO
+-- DROP TABLE JRUAN.GAPMODE
+-- GO
+-- DROP TABLE JRUAN.EXPLAIN_STREAM
+-- GO
+-- DROP TABLE JRUAN.EXPLAIN_STATEMENT
+-- GO
+-- DROP TABLE JRUAN.EXPLAIN_PREDICATE
+-- GO
+-- DROP TABLE JRUAN.EXPLAIN_OPERATOR
+-- GO
+-- DROP TABLE JRUAN.EXPLAIN_OBJECT
+-- GO
+-- DROP TABLE JRUAN.EXPLAIN_INSTANCE
+-- GO
+-- DROP TABLE JRUAN.EXPLAIN_ARGUMENT
+-- GO
+-- DROP TABLE JRUAN.DISTANCEMATRIXELEMENT
+-- GO
+-- DROP TABLE JRUAN.DISCRETECHARSTATE
+-- GO
+-- DROP TABLE JRUAN.CSTREENODE
+-- GO
+-- DROP TABLE JRUAN.CONTANCSTATE_VALUE
+-- GO
+-- DROP TABLE JRUAN.COMPOUND_ELEMENT
+-- GO
+-- DROP TABLE JRUAN.COLUMNRANGE
+-- GO
+-- DROP TABLE JRUAN.CODONPOSITIONSET
+-- GO
+-- DROP TABLE JRUAN.CODONNONCODING_COLRANGE
+-- GO
+-- DROP TABLE JRUAN.CODONCHAR3_COLRANGE
+-- GO
+-- DROP TABLE JRUAN.CODONCHAR2_COLRANGE
+-- GO
+-- DROP TABLE JRUAN.CODONCHAR1_COLRANGE
+-- GO
+-- DROP TABLE JRUAN.CODERECORD_COLRANGE
+-- GO
+-- DROP TABLE JRUAN.CITATIONSTATUS
+-- GO
+-- DROP TABLE JRUAN.CITATION
+-- GO
+-- DROP TABLE JRUAN.CITATION_EDITOR
+-- GO
+-- DROP TABLE JRUAN.CITATION_AUTHOR
+-- GO
+-- DROP TABLE JRUAN.CHARWEIGHTSET
+-- GO
+-- DROP TABLE JRUAN.CHARWEIGHT
+-- GO
+-- DROP TABLE JRUAN.CHARWEIGHT_COLRANGE
+-- GO
+-- DROP TABLE JRUAN.CHARSET
+-- GO
+-- DROP TABLE JRUAN.CHARSET_COLRANGE
+-- GO
+-- DROP TABLE JRUAN.CHARPARTITION
+-- GO
+-- DROP TABLE JRUAN.CHARGROUP
+-- GO
+-- DROP TABLE JRUAN.CHARGROUP_COLRANGE
+-- GO
+-- DROP TABLE JRUAN.ANCSTATESET
+-- GO
+-- DROP TABLE JRUAN.ANCESTRALSTATE
+-- GO
+-- DROP TABLE JRUAN.ANALYZEDDATA
+-- GO
+-- DROP TABLE JRUAN.ANALYSISSTEP
+-- GO
+-- DROP TABLE JRUAN.ANALYSIS
+-- GO
+-- DROP TABLE JRUAN.ALGORITHM
+-- GO
+-- DROP TABLE JRUAN.ADVISE_WORKLOAD
+-- GO
+-- DROP TABLE JRUAN.ADVISE_INDEX
+-- GO
+/*
+DROP TABLE USERTYPERRD_COLRANGE;
+DROP TABLE USERTYPERECORD;
+DROP TABLE USERTYPE;
+DROP TABLE USERROLE;
+DROP TABLE "user";
+DROP TABLE TYPESET;
+DROP TABLE TREETYPE;
+DROP TABLE TREESET;
+DROP TABLE TREESET_PHYLOTREE;
+DROP TABLE TREEQUALITY;
+DROP TABLE TREEPARTITION;
+DROP TABLE TREENODEEDGE;
+DROP TABLE TREEKIND;
+DROP TABLE TREEGROUP;
+DROP TABLE TREEGROUP_PHYLOTREE;
+DROP TABLE TREEBLOCK;
+DROP TABLE TREEATTRIBUTE;
+DROP TABLE TAXONVARIANT;
+DROP TABLE TAXONSET;
+DROP TABLE TAXONSET_TAXON;
+DROP TABLE TAXONLINK;
+DROP TABLE TAXONLABELSET;
+DROP TABLE TAXONLABELSET_TAXONLABEL;
+DROP TABLE TAXONLABELROUP_TAXONLABEL;
+DROP TABLE TAXONLABELPARTITION;
+DROP TABLE TAXONLABELGROUP;
+DROP TABLE TAXONLABEL;
+DROP TABLE TAXONAUTHORITY;
+DROP TABLE TAXON;
+DROP TABLE SUBMISSION;
+DROP TABLE SUB_TREEBLOCK;
+DROP TABLE SUB_TAXONLABEL;
+DROP TABLE SUB_MATRIX;
+DROP TABLE STUDYSTATUS;
+DROP TABLE STUDY;
+DROP TABLE STUDY_NEXUSFILE;
+DROP TABLE STEPMATRIXELEMENT;
+DROP TABLE STATESET;
+DROP TABLE STATEMODIFIER;
+DROP TABLE STATEFORMAT;
+DROP TABLE STATECHANGESET;
+DROP TABLE SPECIMENLABEL;
+DROP TABLE SOFTWARE;
+DROP TABLE ROWSEGMENT;
+DROP TABLE RIGHTCHANGESET_CHARSTATE;
+DROP TABLE POLYTCOUNT;
+DROP TABLE PHYLOTREENODE;
+DROP TABLE PHYLOTREE;
+DROP TABLE PHYLOCHAR;
+DROP TABLE PERSON;
+DROP TABLE NODEATTRIBUTE;
+DROP TABLE MATRIXROW;
+DROP TABLE MATRIXKIND;
+DROP TABLE MATRIXELEMENT;
+DROP TABLE MATRIXDATATYPE;
+DROP TABLE MATRIXCOLUMN;
+DROP TABLE MATRIXCOLUMN_ITEMDEFINITION;
+DROP TABLE MATRIX;
+DROP TABLE MATRIX_ITEMDEFINITION;
+DROP TABLE LEFTCHANGESET_CHARSTATE;
+DROP TABLE ITEMVALUE;
+DROP TABLE ITEMDEFINITION;
+DROP TABLE HELP;
+DROP TABLE GEOSPOT;
+DROP TABLE GENETICCODESET;
+DROP TABLE GENETICCODERECORD;
+DROP TABLE GENETICCODE;
+DROP TABLE GAPMODE;
+--DROP TABLE EXPLAIN_STREAM;
+--DROP TABLE EXPLAIN_STATEMENT;
+--DROP TABLE EXPLAIN_PREDICATE;
+--DROP TABLE EXPLAIN_OPERATOR;
+--DROP TABLE EXPLAIN_OBJECT;
+--DROP TABLE EXPLAIN_INSTANCE;
+--DROP TABLE EXPLAIN_ARGUMENT;
+DROP TABLE DISTANCEMATRIXELEMENT;
+DROP TABLE DISCRETECHARSTATE;
+DROP TABLE CSTREENODE;
+DROP TABLE CONTANCSTATE_VALUE;
+DROP TABLE COMPOUND_ELEMENT;
+DROP TABLE COLUMNRANGE;
+DROP TABLE CODONPOSITIONSET;
+DROP TABLE CODONNONCODING_COLRANGE;
+DROP TABLE CODONCHAR3_COLRANGE;
+DROP TABLE CODONCHAR2_COLRANGE;
+DROP TABLE CODONCHAR1_COLRANGE;
+DROP TABLE CODERECORD_COLRANGE;
+DROP TABLE CITATIONSTATUS;
+DROP TABLE CITATION;
+DROP TABLE CITATION_EDITOR;
+DROP TABLE CITATION_AUTHOR;
+DROP TABLE CHARWEIGHTSET;
+DROP TABLE CHARWEIGHT;
+DROP TABLE CHARWEIGHT_COLRANGE;
+DROP TABLE CHARSET;
+DROP TABLE CHARSET_COLRANGE;
+DROP TABLE CHARPARTITION;
+DROP TABLE CHARGROUP;
+DROP TABLE CHARGROUP_COLRANGE;
+DROP TABLE ANCSTATESET;
+DROP TABLE ANCESTRALSTATE;
+DROP TABLE ANALYZEDDATA;
+DROP TABLE ANALYSISSTEP;
+DROP TABLE ANALYSIS;
+DROP TABLE ALGORITHM;
+--DROP TABLE ADVISE_WORKLOAD;
+--DROP TABLE ADVISE_INDEX;
+*/
+-- CREATE TABLE JRUAN.ADVISE_INDEX (
+-- EXPLAIN_REQUESTER VARCHAR(128) NOT NULL DEFAULT '',
+-- EXPLAIN_TIME TIMESTAMP NOT NULL DEFAULT CURRENT TIMESTAMP,
+-- SOURCE_NAME VARCHAR(128) NOT NULL DEFAULT '',
+-- SOURCE_SCHEMA VARCHAR(128) NOT NULL DEFAULT '',
+-- SOURCE_VERSION VARCHAR(64) NOT NULL DEFAULT '',
+-- EXPLAIN_LEVEL CHARACTER(1) NOT NULL DEFAULT '',
+-- STMTNO INTEGER NOT NULL DEFAULT 0,
+-- SECTNO INTEGER NOT NULL DEFAULT 0,
+-- QUERYNO INTEGER NOT NULL DEFAULT 0,
+-- QUERYTAG CHARACTER(20) NOT NULL DEFAULT '',
+-- NAME VARCHAR(128) NOT NULL,
+-- CREATOR VARCHAR(128) NOT NULL DEFAULT '',
+-- TBNAME VARCHAR(128) NOT NULL,
+-- TBCREATOR VARCHAR(128) NOT NULL DEFAULT '',
+-- COLNAMES CLOB(2097152) NOT NULL,
+-- UNIQUERULE CHARACTER(1) NOT NULL DEFAULT '',
+-- COLCOUNT SMALLINT NOT NULL DEFAULT 0,
+-- IID SMALLINT NOT NULL DEFAULT 0,
+-- NLEAF INTEGER NOT NULL DEFAULT 0,
+-- NLEVELS SMALLINT NOT NULL DEFAULT 0,
+-- FIRSTKEYCARD BIGINT NOT NULL DEFAULT 0,
+-- FULLKEYCARD BIGINT NOT NULL DEFAULT 0,
+-- CLUSTERRATIO SMALLINT NOT NULL DEFAULT 0,
+-- CLUSTERFACTOR DOUBLE NOT NULL DEFAULT 0,
+-- USERDEFINED SMALLINT NOT NULL DEFAULT 0,
+-- SYSTEM_REQUIRED SMALLINT NOT NULL DEFAULT 0,
+-- CREATE_TIME TIMESTAMP NOT NULL DEFAULT CURRENT TIMESTAMP,
+-- STATS_TIME TIMESTAMP DEFAULT CURRENT TIMESTAMP,
+-- PAGE_FETCH_PAIRS VARCHAR(254) NOT NULL DEFAULT '',
+-- REMARKS VARCHAR(254) DEFAULT '',
+-- DEFINER VARCHAR(128) NOT NULL DEFAULT '',
+-- CONVERTED CHARACTER(1) NOT NULL DEFAULT '',
+-- SEQUENTIAL_PAGES INTEGER NOT NULL DEFAULT 0,
+-- DENSITY INTEGER NOT NULL DEFAULT 0,
+-- FIRST2KEYCARD BIGINT NOT NULL DEFAULT 0,
+-- FIRST3KEYCARD BIGINT NOT NULL DEFAULT 0,
+-- FIRST4KEYCARD BIGINT NOT NULL DEFAULT 0,
+-- PCTFREE SMALLINT NOT NULL DEFAULT -1,
+-- UNIQUE_COLCOUNT SMALLINT NOT NULL DEFAULT -1,
+-- MINPCTUSED SMALLINT NOT NULL DEFAULT 0,
+-- REVERSE_SCANS CHARACTER(1) NOT NULL DEFAULT 'N',
+-- USE_INDEX CHARACTER(1),
+-- CREATION_TEXT CLOB(2097152) NOT NULL DEFAULT '',
+-- PACKED_DESC BLOB(1048576)
+-- )
+-- GO
+-- CREATE TABLE JRUAN.ADVISE_WORKLOAD (
+-- WORKLOAD_NAME CHARACTER(128) NOT NULL DEFAULT 'WK0',
+-- STATEMENT_NO INTEGER NOT NULL DEFAULT 1,
+-- STATEMENT_TEXT CLOB(2097152) NOT NULL,
+-- STATEMENT_TAG VARCHAR(256) NOT NULL DEFAULT '',
+-- FREQUENCY INTEGER NOT NULL DEFAULT 1,
+-- IMPORTANCE DOUBLE NOT NULL DEFAULT 1,
+-- WEIGHT DOUBLE NOT NULL DEFAULT 1,
+-- COST_BEFORE DOUBLE,
+-- COST_AFTER DOUBLE,
+-- COMPILABLE CHARACTER(17)
+-- )
+-- GO
+-- CREATE TABLE JRUAN.ALGORITHM (
+-- TYPE CHARACTER(1) NOT NULL,
+-- ALGORITHM_ID BIGINT GENERATED BY DEFAULT AS IDENTITY (START WITH 1, INCREMENT BY 1, CACHE 20) NOT NULL,
+-- VERSION INTEGER,
+-- DESCRIPTION VARCHAR(2000),
+-- PROPERTYNAME VARCHAR(255),
+-- PROPERTYVALUE VARCHAR(255),
+-- USERTYPE_ID BIGINT,
+-- GAPMODE_ID BIGINT,
+-- POLYTCOUNT_ID BIGINT
+-- )
+-- GO
+CREATE TABLE algorithm
+(
+ "type" character(1) NOT NULL,
+ algorithm_id bigint NOT NULL,
+ "version" integer,
+ description character varying(2000),
+ propertyname character varying(255),
+ propertyvalue character varying(255),
+ usertype_id bigint,
+ gapmode_id bigint,
+ polytcount_id bigint
+)
+WITH (OIDS=FALSE);
+ALTER TABLE algorithm OWNER TO postgres;
+
+-- CREATE TABLE JRUAN.ANALYSIS (
+-- ANALYSIS_ID BIGINT GENERATED BY DEFAULT AS IDENTITY (START WITH 1, INCREMENT BY 1, CACHE 20) NOT NULL,
+-- VERSION INTEGER,
+-- NAME VARCHAR(255),
+-- NOTES VARCHAR(2000),
+-- VALIDATED SMALLINT,
+-- STUDY_ID BIGINT,
+-- ANALYSIS_ORDER INTEGER
+-- )
+-- GO
+CREATE TABLE analysis
+(
+ analysis_id bigint NOT NULL,
+ "version" integer,
+ "name" character varying(255),
+ notes character varying(2000),
+ validated smallint,
+ study_id bigint,
+ analysis_order integer
+)
+WITH (OIDS=FALSE);
+ALTER TABLE analysis OWNER TO postgres;
+
+-- CREATE TABLE JRUAN.ANALYSISSTEP (
+-- ANALYSISSTEP_ID BIGINT GENERATED BY DEFAULT AS IDENTITY (START WITH 1, INCREMENT BY 1, CACHE 20) NOT NULL,
+-- VERSION INTEGER,
+-- COMMANDS VARCHAR(2000),
+-- NAME VARCHAR(255),
+-- NOTES VARCHAR(2000),
+-- ALGORITHM_ID BIGINT,
+-- ANALYSIS_ID BIGINT,
+-- SOFTWARE_ID BIGINT,
+-- STEP_ORDER INTEGER,
+-- TB_ANALYSISID VARCHAR(34)
+-- )
+-- GO
+CREATE TABLE analysisstep
+(
+ analysisstep_id bigint NOT NULL,
+ "version" integer,
+ commands character varying(2000),
+ "name" character varying(255),
+ notes character varying(2000),
+ algorithm_id bigint,
+ analysis_id bigint,
+ software_id bigint,
+ step_order integer,
+ tb_analysisid character varying(34)
+)
+WITH (OIDS=FALSE);
+ALTER TABLE analysisstep OWNER TO postgres;
+
+-- CREATE TABLE JRUAN.ANALYZEDDATA (
+-- TYPE CHARACTER(1) NOT NULL,
+-- ANALYZEDDATA_ID BIGINT GENERATED BY DEFAULT AS IDENTITY (START WITH 1, INCREMENT BY 1, CACHE 20) NOT NULL,
+-- VERSION INTEGER,
+-- INPUT SMALLINT,
+-- NOTES VARCHAR(2000),
+-- TREELENGTH INTEGER,
+-- ANALYSISSTEP_ID BIGINT NOT NULL,
+-- MATRIX_ID BIGINT,
+-- PHYLOTREE_ID BIGINT
+-- )
+-- GO
+CREATE TABLE analyzeddata
+(
+ "type" character(1) NOT NULL,
+ analyzeddata_id bigint NOT NULL,
+ "version" integer,
+ "input" smallint,
+ notes character varying(2000),
+ treelength integer,
+ analysisstep_id bigint NOT NULL,
+ matrix_id bigint,
+ phylotree_id bigint
+)
+WITH (OIDS=FALSE);
+ALTER TABLE analyzeddata OWNER TO postgres;
+
+-- CREATE TABLE JRUAN.ANCESTRALSTATE (
+-- TYPE CHARACTER(1) NOT NULL,
+-- ANCESTRALSTATE_ID BIGINT GENERATED BY DEFAULT AS IDENTITY (START WITH 1, INCREMENT BY 1, CACHE 20) NOT NULL,
+-- VERSION INTEGER,
+-- TITLE VARCHAR(255),
+-- ANCVALUE VARCHAR(255),
+-- DISCRETECHARSTATE_ID BIGINT,
+-- ANCSTATESET_ID BIGINT
+-- )
+-- GO
+CREATE TABLE ancestralstate
+(
+ "type" character(1) NOT NULL,
+ ancestralstate_id bigint NOT NULL,
+ "version" integer,
+ title character varying(255),
+ ancvalue character varying(255),
+ discretecharstate_id bigint,
+ ancstateset_id bigint
+)
+WITH (OIDS=FALSE);
+ALTER TABLE ancestralstate OWNER TO postgres;
+
+-- CREATE TABLE JRUAN.ANCSTATESET (
+-- ANCSTATESET_ID BIGINT GENERATED BY DEFAULT AS IDENTITY (START WITH 1, INCREMENT BY 1, CACHE 20) NOT NULL,
+-- VERSION INTEGER,
+-- TITLE VARCHAR(255),
+-- MATRIX_ID BIGINT
+-- )
+-- GO
+CREATE TABLE ancstateset
+(
+ ancstateset_id bigint NOT NULL,
+ "version" integer,
+ title character varying(255),
+ matrix_id bigint
+)
+WITH (OIDS=FALSE);
+ALTER TABLE ancstateset OWNER TO postgres;
+
+-- CREATE TABLE JRUAN.CHARGROUP_COLRANGE (
+-- CHARGROUP_ID BIGINT NOT NULL,
+-- COLUMNRANGE_ID BIGINT NOT NULL
+-- )
+-- GO
+CREATE TABLE chargroup_colrange
+(
+ chargroup_id bigint NOT NULL,
+ columnrange_id bigint NOT NULL
+)
+WITH (OIDS=FALSE);
+ALTER TABLE chargroup_colrange OWNER TO postgres;
+
+-- CREATE TABLE JRUAN.CHARGROUP (
+-- CHARGROUP_ID BIGINT GENERATED BY DEFAULT AS IDENTITY (START WITH 1, INCREMENT BY 1, CACHE 20) NOT NULL,
+-- VERSION INTEGER,
+-- TITLE VARCHAR(255),
+-- CHARPARTITION_ID BIGINT
+-- )
+-- GO
+CREATE TABLE chargroup
+(
+ chargroup_id bigint NOT NULL,
+ "version" integer,
+ title character varying(255),
+ charpartition_id bigint
+)
+WITH (OIDS=FALSE);
+ALTER TABLE chargroup OWNER TO postgres;
+
+-- CREATE TABLE JRUAN.CHARPARTITION (
+-- CHARPARTITION_ID BIGINT GENERATED BY DEFAULT AS IDENTITY (START WITH 1, INCREMENT BY 1, CACHE 20) NOT NULL,
+-- VERSION INTEGER,
+-- TITLE VARCHAR(255),
+-- MATRIX_ID BIGINT
+-- )
+-- GO
+CREATE TABLE charpartition
+(
+ charpartition_id bigint NOT NULL,
+ "version" integer,
+ title character varying(255),
+ matrix_id bigint
+)
+WITH (OIDS=FALSE);
+ALTER TABLE charpartition OWNER TO postgres;
+
+-- CREATE TABLE JRUAN.CHARSET_COLRANGE (
+-- CHARSET_ID BIGINT NOT NULL,
+-- COLUMNRANGE_ID BIGINT NOT NULL
+-- )
+-- GO
+CREATE TABLE charset_colrange
+(
+ charset_id bigint NOT NULL,
+ columnrange_id bigint NOT NULL
+)
+WITH (OIDS=FALSE);
+ALTER TABLE charset_colrange OWNER TO postgres;
+
+-- CREATE TABLE JRUAN.CHARSET (
+-- TYPE CHARACTER(1) NOT NULL,
+-- CHARSET_ID BIGINT GENERATED BY DEFAULT AS IDENTITY (START WITH 1, INCREMENT BY 1, CACHE 20) NOT NULL,
+-- VERSION INTEGER,
+-- TITLE VARCHAR(255),
+-- MATRIX_ID BIGINT
+-- )
+-- GO
+CREATE TABLE charset
+(
+ "type" character(1) NOT NULL,
+ charset_id bigint NOT NULL,
+ "version" integer,
+ title character varying(255),
+ matrix_id bigint
+)
+WITH (OIDS=FALSE);
+ALTER TABLE charset OWNER TO postgres;
+
+-- CREATE TABLE JRUAN.CHARWEIGHT_COLRANGE (
+-- CHARWEIGHT_ID BIGINT NOT NULL,
+-- COLUMNRANGE_ID BIGINT NOT NULL
+-- )
+-- GO
+CREATE TABLE charweight_colrange
+(
+ charweight_id bigint NOT NULL,
+ columnrange_id bigint NOT NULL
+)
+WITH (OIDS=FALSE);
+ALTER TABLE charweight_colrange OWNER TO postgres;
+
+-- CREATE TABLE JRUAN.CHARWEIGHT (
+-- TYPE CHARACTER(1) NOT NULL,
+-- CHARWEIGHT_ID BIGINT GENERATED BY DEFAULT AS IDENTITY (START WITH 1, INCREMENT BY 1, CACHE 20) NOT NULL,
+-- VERSION INTEGER,
+-- WEIGHT INTEGER,
+-- REALWEIGHT DOUBLE,
+-- CHARWEIGHTSET_ID BIGINT
+-- )
+-- GO
+CREATE TABLE charweight
+(
+ "type" character(1) NOT NULL,
+ charweight_id bigint NOT NULL,
+ "version" integer,
+ weight integer,
+ realweight double precision,
+ charweightset_id bigint
+)
+WITH (OIDS=FALSE);
+ALTER TABLE charweight OWNER TO postgres;
+
+-- CREATE TABLE JRUAN.CHARWEIGHTSET (
+-- CHARWEIGHTSET_ID BIGINT GENERATED BY DEFAULT AS IDENTITY (START WITH 1, INCREMENT BY 1, CACHE 20) NOT NULL,
+-- VERSION INTEGER,
+-- TITLE VARCHAR(255),
+-- MATRIX_ID BIGINT
+-- )
+-- GO
+CREATE TABLE charweightset
+(
+ charweightset_id bigint NOT NULL,
+ "version" integer,
+ title character varying(255),
+ matrix_id bigint
+)
+WITH (OIDS=FALSE);
+ALTER TABLE charweightset OWNER TO postgres;
+
+-- CREATE TABLE JRUAN.CITATION_AUTHOR (
+-- CITATION_ID BIGINT NOT NULL,
+-- AUTHORS_PERSON_ID BIGINT NOT NULL,
+-- AUTHOR_ORDER INTEGER NOT NULL
+-- )
+-- GO
+CREATE TABLE citation_author
+(
+ citation_id bigint NOT NULL,
+ authors_person_id bigint NOT NULL,
+ author_order integer NOT NULL
+)
+WITH (OIDS=FALSE);
+ALTER TABLE citation_author OWNER TO postgres;
+
+-- CREATE TABLE JRUAN.CITATION_EDITOR (
+-- CITATION_ID BIGINT NOT NULL,
+-- EDITORS_PERSON_ID BIGINT NOT NULL,
+-- EDITOR_ORDER INTEGER NOT NULL
+-- )
+-- GO
+CREATE TABLE citation_editor
+(
+ citation_id bigint NOT NULL,
+ editors_person_id bigint NOT NULL,
+ editor_order integer NOT NULL
+)
+WITH (OIDS=FALSE);
+ALTER TABLE citation_editor OWNER TO postgres;
+
+-- CREATE TABLE JRUAN.CITATION (
+-- TYPE CHARACTER(1) NOT NULL,
+-- CITATION_ID BIGINT GENERATED BY DEFAULT AS IDENTITY (START WITH 1, INCREMENT BY 1, CACHE 20) NOT NULL,
+-- VERSION INTEGER,
+-- PMID VARCHAR(255),
+-- URL VARCHAR(255),
+-- ABSTRACT VARCHAR(10000),
+-- DOI VARCHAR(255),
+-- KEYWORDS VARCHAR(255),
+-- PAGES VARCHAR(255),
+-- PUBLISHYEAR INTEGER,
+-- PUBLISHED SMALLINT,
+-- TITLE VARCHAR(500),
+-- ISSUE VARCHAR(255),
+-- JOURNAL VARCHAR(255),
+-- VOLUME VARCHAR(255),
+-- ISBN VARCHAR(255),
+-- BOOKTITLE VARCHAR(255),
+-- CITY VARCHAR(255),
+-- PUBLISHER VARCHAR(255),
+-- CITATIONSTATUS_ID BIGINT,
+-- TB_STUDYID VARCHAR(30)
+-- )
+-- GO
+CREATE TABLE citation
+(
+ "type" character(1) NOT NULL,
+ citation_id bigint NOT NULL,
+ "version" integer,
+ pmid character varying(255),
+ url character varying(255),
+ abstract character varying(10000),
+ doi character varying(255),
+ keywords character varying(255),
+ pages character varying(255),
+ publishyear integer,
+ published smallint,
+ title character varying(500),
+ issue character varying(255),
+ journal character varying(255),
+ volume character varying(255),
+ isbn character varying(255),
+ booktitle character varying(255),
+ city character varying(255),
+ publisher character varying(255),
+ citationstatus_id bigint,
+ tb_studyid character varying(30)
+)
+WITH (OIDS=FALSE);
+ALTER TABLE citation OWNER TO postgres;
+
+-- CREATE TABLE JRUAN.CITATIONSTATUS (
+-- CITATIONSTATUS_ID BIGINT GENERATED BY DEFAULT AS IDENTITY (START WITH 1, INCREMENT BY 1, CACHE 20) NOT NULL,
+-- VERSION INTEGER,
+-- DESCRIPTION VARCHAR(50)
+-- )
+-- GO
+CREATE TABLE citationstatus
+(
+ citationstatus_id bigint NOT NULL,
+ "version" integer,
+ description character varying(50)
+)
+WITH (OIDS=FALSE);
+ALTER TABLE citationstatus OWNER TO postgres;
+
+-- CREATE TABLE JRUAN.CODERECORD_COLRANGE (
+-- GENETICCODERECORD_ID BIGINT NOT NULL,
+-- COLUMNRANGE_ID BIGINT NOT NULL
+-- )
+-- GO
+CREATE TABLE coderecord_colrange
+(
+ geneticcoderecord_id bigint NOT NULL,
+ columnrange_id ...
[truncated message content] |
|
From: <rv...@us...> - 2009-06-19 02:18:22
|
Revision: 68
http://treebase.svn.sourceforge.net/treebase/?rev=68&view=rev
Author: rvos
Date: 2009-06-19 02:18:21 +0000 (Fri, 19 Jun 2009)
Log Message:
-----------
Added nexmlService bean configuration.
Modified Paths:
--------------
trunk/treebase-core/src/main/resources/applicationContext-service.xml
Modified: trunk/treebase-core/src/main/resources/applicationContext-service.xml
===================================================================
--- trunk/treebase-core/src/main/resources/applicationContext-service.xml 2009-06-19 02:17:12 UTC (rev 67)
+++ trunk/treebase-core/src/main/resources/applicationContext-service.xml 2009-06-19 02:18:21 UTC (rev 68)
@@ -143,6 +143,11 @@
<property name="taxonLabelHome" ref="taxonLabelHome"/>
<property name="itemDefinitionHome" ref="itemDefinitionHome"/>
<property name="mesquiteFolderDir" value="${mesquite.folder_dir}"/>
+ </bean>
+
+ <bean id="nexmlService" class = "org.cipres.treebase.service.nexus.NexusServiceNexml">
+ <property name="domainHome" ref="domainHome"/>
+ <property name="taxonLabelHome" ref="taxonLabelHome"/>
</bean>
<!-- package: org.cipres.treebase.domain.study -->
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|
|
From: <rv...@us...> - 2009-06-19 02:17:13
|
Revision: 67
http://treebase.svn.sourceforge.net/treebase/?rev=67&view=rev
Author: rvos
Date: 2009-06-19 02:17:12 +0000 (Fri, 19 Jun 2009)
Log Message:
-----------
Implemented serialize() methods.
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNexml.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNexml.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNexml.java 2009-06-19 02:16:12 UTC (rev 66)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNexml.java 2009-06-19 02:17:12 UTC (rev 67)
@@ -3,18 +3,25 @@
import java.io.File;
import java.util.Collection;
+import javax.xml.parsers.ParserConfigurationException;
+
import org.apache.log4j.Logger;
import org.cipres.treebase.domain.DomainHome;
import org.cipres.treebase.domain.nexus.NexusDataSet;
import org.cipres.treebase.domain.nexus.NexusService;
import org.cipres.treebase.domain.nexus.nexml.NexmlConverter;
+import org.cipres.treebase.domain.nexus.nexml.NexmlDocumentConverter;
import org.cipres.treebase.domain.study.Study;
+import org.cipres.treebase.domain.taxon.TaxonLabelHome;
import org.cipres.treebase.event.ProgressionListener;
import org.cipres.treebase.service.AbstractServiceImpl;
+import org.nexml.model.Document;
+import org.nexml.model.DocumentFactory;
public class NexusServiceNexml extends AbstractServiceImpl implements NexusService {
private static final Logger LOGGER = Logger.getLogger(NexusServiceNexml.class);
private DomainHome mDomainHome;
+ private TaxonLabelHome mTaxonLabelHome;
@Override
public Class defaultResultClass() {
@@ -32,8 +39,12 @@
public NexusDataSet parseNexus(Study study, Collection<File> nexusFiles,
ProgressionListener listener) {
- // TODO Auto-generated method stub
- return null;
+ NexusDataSet data = new NexusDataSet();
+ NexmlConverter converter = new NexmlConverter();
+ for ( File nexusFile : nexusFiles ) {
+ converter.parseOneFile(nexusFile, study, data);
+ }
+ return data;
}
public NexusDataSet parseNexus(Study study, File nexusFile) {
@@ -49,4 +60,34 @@
return data;
}
+ public String serialize(NexusDataSet nexusDataSet) {
+ Document document = null;
+ try {
+ document = DocumentFactory.createDocument();
+ } catch (ParserConfigurationException e) {
+ e.printStackTrace();
+ }
+ NexmlDocumentConverter ndc = new NexmlDocumentConverter(null,getTaxonLabelHome(),document);
+ return ndc.fromTreeBaseToXml(nexusDataSet).getXmlString();
+ }
+
+ public String serialize(Study study) {
+ Document document = null;
+ try {
+ document = DocumentFactory.createDocument();
+ } catch (ParserConfigurationException e) {
+ e.printStackTrace();
+ }
+ NexmlDocumentConverter ndc = new NexmlDocumentConverter(study,getTaxonLabelHome(),document);
+ return ndc.fromTreeBaseToXml(study).getXmlString();
+ }
+
+ public TaxonLabelHome getTaxonLabelHome() {
+ return mTaxonLabelHome;
+ }
+
+ public void setTaxonLabelHome(TaxonLabelHome taxonLabelHome) {
+ mTaxonLabelHome = taxonLabelHome;
+ }
+
}
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|
|
From: <rv...@us...> - 2009-06-19 02:16:17
|
Revision: 66
http://treebase.svn.sourceforge.net/treebase/?rev=66&view=rev
Author: rvos
Date: 2009-06-19 02:16:12 +0000 (Fri, 19 Jun 2009)
Log Message:
-----------
Added serialize() stubs.
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNCL.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNCL.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNCL.java 2009-06-19 02:15:55 UTC (rev 65)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNCL.java 2009-06-19 02:16:12 UTC (rev 66)
@@ -164,4 +164,14 @@
return null;
}
+ public String serialize(NexusDataSet nexusDataSet) {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ public String serialize(Study study) {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
}
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|
|
From: <rv...@us...> - 2009-06-19 02:15:56
|
Revision: 65
http://treebase.svn.sourceforge.net/treebase/?rev=65&view=rev
Author: rvos
Date: 2009-06-19 02:15:55 +0000 (Fri, 19 Jun 2009)
Log Message:
-----------
Added serialize() stubs.
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceMesquite.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceMesquite.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceMesquite.java 2009-06-19 02:15:10 UTC (rev 64)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceMesquite.java 2009-06-19 02:15:55 UTC (rev 65)
@@ -212,4 +212,14 @@
return null;
}
+ public String serialize(NexusDataSet nexusDataSet) {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ public String serialize(Study study) {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
}
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|
|
From: <rv...@us...> - 2009-06-19 02:15:52
|
Revision: 62
http://treebase.svn.sourceforge.net/treebase/?rev=62&view=rev
Author: rvos
Date: 2009-06-19 02:12:51 +0000 (Fri, 19 Jun 2009)
Log Message:
-----------
Adding NexmlDocumentConverter class
Added Paths:
-----------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentConverter.java
Added: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentConverter.java (rev 0)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentConverter.java 2009-06-19 02:12:51 UTC (rev 62)
@@ -0,0 +1,149 @@
+package org.cipres.treebase.domain.nexus.nexml;
+
+import org.cipres.treebase.domain.admin.Person;
+import org.cipres.treebase.domain.nexus.NexusDataSet;
+import org.cipres.treebase.domain.study.ArticleCitation;
+import org.cipres.treebase.domain.study.Citation;
+import org.cipres.treebase.domain.study.Study;
+import org.cipres.treebase.domain.taxon.TaxonLabelHome;
+import org.cipres.treebase.domain.taxon.TaxonLabelSet;
+import org.nexml.model.Document;
+import org.nexml.model.Matrix;
+import org.nexml.model.OTUs;
+import org.nexml.model.TreeBlock;
+
+public class NexmlDocumentConverter extends NexmlObjectConverter {
+
+ /**
+ *
+ * @param study
+ * @param taxonLabelHome
+ * @param document
+ */
+ public NexmlDocumentConverter(Study study, TaxonLabelHome taxonLabelHome,
+ Document document) {
+ super(study, taxonLabelHome, document);
+ }
+
+ /**
+ *
+ * @param pDocument
+ * @return
+ */
+ public NexusDataSet fromXmlToTreeBase(Document pDocument) {
+ NexusDataSet nexusDataSet = new NexusDataSet();
+ nexusDataSet.setNexmlProject(pDocument);
+
+ NexmlOTUConverter noc = new NexmlOTUConverter(getStudy(),getTaxonLabelHome(),pDocument);
+ for ( OTUs xmlOTUs : pDocument.getOTUsList() ) {
+ TaxonLabelSet taxonLabelSet = noc.fromXmlToTreeBase(xmlOTUs);
+ nexusDataSet.addTaxonLabelSet(xmlOTUs, taxonLabelSet);
+ }
+
+ NexmlMatrixConverter nmc = new NexmlMatrixConverter(getStudy(),getTaxonLabelHome(),pDocument);
+ for ( Matrix<?> xmlMatrix : pDocument.getMatrices() ) {
+ org.cipres.treebase.domain.matrix.Matrix matrix = nmc.fromXmlToTreeBase(xmlMatrix);
+ nexusDataSet.getMatrices().add(matrix);
+ }
+
+ NexmlTreeBlockConverter ntc = new NexmlTreeBlockConverter(getStudy(),getTaxonLabelHome(),pDocument);
+ for ( TreeBlock xmlTreeBlock : pDocument.getTreeBlockList() ) {
+ org.cipres.treebase.domain.tree.TreeBlock treeBlock = ntc.fromXmlToTreeBase(xmlTreeBlock);
+ nexusDataSet.getTreeBlocks().add(treeBlock);
+ }
+
+ return nexusDataSet;
+ }
+
+ /**
+ *
+ * @param pNexusDataSet
+ * @return
+ */
+ public Document fromTreeBaseToXml(NexusDataSet pNexusDataSet) {
+
+ NexmlOTUConverter noc = new NexmlOTUConverter(getStudy(),getTaxonLabelHome(),getDocument());
+ for ( TaxonLabelSet taxonLabelSet : pNexusDataSet.getTaxonLabelSets() ) {
+ noc.fromTreeBaseToXml(taxonLabelSet);
+ }
+
+ NexmlMatrixConverter nmc = new NexmlMatrixConverter(getStudy(),getTaxonLabelHome(),getDocument());
+ for (org.cipres.treebase.domain.matrix.Matrix matrix : pNexusDataSet.getMatrices() ) {
+ nmc.fromTreeBaseToXml(matrix);
+ }
+
+ NexmlTreeBlockConverter ntc = new NexmlTreeBlockConverter(getStudy(),getTaxonLabelHome(),getDocument());
+ for ( org.cipres.treebase.domain.tree.TreeBlock treeBlock : pNexusDataSet.getTreeBlocks() ) {
+ ntc.fromTreeBaseToXML(treeBlock);
+ }
+
+ return getDocument();
+
+ }
+
+ /**
+ *
+ * @param citation
+ * @param document
+ */
+ private void copyCitationMetadata(Citation citation,Document document) {
+ attachAnnotation("prism:publicationDate",citation.getPublishYear().toString(),mPrismURI,document);
+ attachAnnotation("prism:doi",citation.getDoi(),mPrismURI,document);
+ String[] pages = citation.getPages().split("-");
+ if ( pages.length > 2 ) {
+ attachAnnotation("prism:startingPage",pages[0],mPrismURI,document);
+ attachAnnotation("prism:endingPage",pages[1],mPrismURI,document);
+ attachAnnotation("prism:pageRange",citation.getPages(),mPrismURI,document);
+ }
+ String[] keywords = citation.getKeywords().split(", ");
+ for ( int i = 0; i < keywords.length; i++ ) {
+ attachAnnotation("prism:keyword",keywords[i],mPrismURI,document);
+ }
+ if ( citation instanceof ArticleCitation ) {
+ attachAnnotation("prism:publicationName",((ArticleCitation)citation).getJournal(),mPrismURI,document);
+ attachAnnotation("prism:volume",((ArticleCitation)citation).getVolume(),mPrismURI,document);
+ attachAnnotation("prism:number",((ArticleCitation)citation).getIssue(),mPrismURI,document);
+ }
+ }
+
+ /**
+ *
+ * @param pStudy
+ * @return
+ */
+ public Document fromTreeBaseToXml(Study pStudy) {
+ attachTreeBaseID(getDocument(), pStudy);
+ attachAnnotation("dc:title", pStudy.getName(), mDCURI, getDocument());
+ attachAnnotation("dc:abstract",pStudy.getCitation().getAbstract(), mDCURI,getDocument());
+ attachAnnotation(
+ "dc:creator",
+ pStudy.getSubmission().getSubmitter().getPerson().getFullNameCitationStyle(),
+ mDCURI,
+ getDocument()
+ );
+ for ( Person person : pStudy.getAuthors() ) {
+ String personName = person.getFullNameCitationStyle();
+ attachAnnotation("dc:contributor",personName,mDCURI,getDocument());
+ }
+ attachAnnotation("prism:creationDate",pStudy.getSubmission().getCreateDate().toString(),mPrismURI,getDocument());
+ attachAnnotation("prism:embargoDate",pStudy.getReleaseDate().toString(),mPrismURI,getDocument());
+ copyCitationMetadata(pStudy.getCitation(),getDocument());
+
+ NexmlOTUConverter noc = new NexmlOTUConverter(getStudy(),getTaxonLabelHome(),getDocument());
+ for ( TaxonLabelSet taxonLabelSet : pStudy.getTaxonLabelSets() ) {
+ noc.fromTreeBaseToXml(taxonLabelSet);
+ }
+
+ NexmlMatrixConverter nmc = new NexmlMatrixConverter(getStudy(),getTaxonLabelHome(),getDocument());
+ for (org.cipres.treebase.domain.matrix.Matrix matrix : pStudy.getMatrices() ) {
+ nmc.fromTreeBaseToXml(matrix);
+ }
+
+ NexmlTreeBlockConverter ntc = new NexmlTreeBlockConverter(getStudy(),getTaxonLabelHome(),getDocument());
+ for ( org.cipres.treebase.domain.tree.TreeBlock treeBlock : pStudy.getTreeBlocks() ) {
+ ntc.fromTreeBaseToXML(treeBlock);
+ }
+ return getDocument();
+ }
+
+}
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|
|
From: <rv...@us...> - 2009-06-19 02:15:51
|
Revision: 60
http://treebase.svn.sourceforge.net/treebase/?rev=60&view=rev
Author: rvos
Date: 2009-06-19 02:10:56 +0000 (Fri, 19 Jun 2009)
Log Message:
-----------
Added @Transient getTreeBlocks() method
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Study.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Study.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Study.java 2009-06-18 09:40:42 UTC (rev 59)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Study.java 2009-06-19 02:10:56 UTC (rev 60)
@@ -59,6 +59,7 @@
import org.cipres.treebase.domain.taxon.TaxonLabelSet;
import org.cipres.treebase.domain.taxon.TaxonVariant;
import org.cipres.treebase.domain.tree.PhyloTree;
+import org.cipres.treebase.domain.tree.TreeBlock;
import org.hibernate.annotations.BatchSize;
import org.hibernate.annotations.Cache;
import org.hibernate.annotations.CacheConcurrencyStrategy;
@@ -690,4 +691,20 @@
}
return trees;
}
+
+ /**
+ * @return all the treeblocks for all the trees from getTrees();
+ * @author rvosa
+ */
+ @Transient
+ public Set<TreeBlock> getTreeBlocks() {
+ Set<TreeBlock> treeBlocks = new HashSet<TreeBlock>();
+ for ( PhyloTree tree : getTrees() ) {
+ TreeBlock treeBlock = tree.getTreeBlock();
+ if ( ! treeBlocks.contains(treeBlock) ) {
+ treeBlocks.add(treeBlock);
+ }
+ }
+ return treeBlocks;
+ }
}
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|
|
From: <rv...@us...> - 2009-06-19 02:15:47
|
Revision: 64
http://treebase.svn.sourceforge.net/treebase/?rev=64&view=rev
Author: rvos
Date: 2009-06-19 02:15:10 +0000 (Fri, 19 Jun 2009)
Log Message:
-----------
Added NCBI taxonID and uBio namebankID serialization (to metadata attachments)
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlOTUConverter.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlOTUConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlOTUConverter.java 2009-06-19 02:14:12 UTC (rev 63)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlOTUConverter.java 2009-06-19 02:15:10 UTC (rev 64)
@@ -4,6 +4,7 @@
import org.cipres.treebase.domain.taxon.TaxonLabel;
import org.cipres.treebase.domain.taxon.TaxonLabelHome;
import org.cipres.treebase.domain.taxon.TaxonLabelSet;
+import org.cipres.treebase.domain.taxon.TaxonVariant;
import org.nexml.model.Document;
import org.nexml.model.OTU;
import org.nexml.model.OTUs;
@@ -74,6 +75,15 @@
OTU xmlOTU = xmlOTUs.createOTU();
xmlOTU.setLabel(taxonLabel.getTaxonLabel());
attachTreeBaseID(xmlOTU,taxonLabel);
+ if ( null != taxonLabel.getNcbiTaxID() ) {
+ attachAnnotation("dc:identifier", "NCBI:" + taxonLabel.getNcbiTaxID(), mDCURI, xmlOTU);
+ }
+ TaxonVariant tv = taxonLabel.getTaxonVariant();
+ if ( null != tv ) {
+ if ( null != tv.getNamebankID() ) {
+ attachAnnotation("dc:identifier", "uBio:" + tv.getNamebankID(), mDCURI, xmlOTU);
+ }
+ }
return xmlOTU;
}
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|
|
From: <rv...@us...> - 2009-06-19 02:15:46
|
Revision: 61
http://treebase.svn.sourceforge.net/treebase/?rev=61&view=rev
Author: rvos
Date: 2009-06-19 02:11:48 +0000 (Fri, 19 Jun 2009)
Log Message:
-----------
Added serialize(NexusDataSet) and serialize(Study) interface methods
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/NexusService.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/NexusService.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/NexusService.java 2009-06-19 02:10:56 UTC (rev 60)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/NexusService.java 2009-06-19 02:11:48 UTC (rev 61)
@@ -56,5 +56,25 @@
* @return
*/
NexusDataSet parseNexus(Study pStudy, File pNexusFile);
+
+ /**
+ * Write the NexusDataSet to a string that represents the object.
+ * The exact output format is up to the implementing service, i.e.
+ * this can either be nexus or nexml.
+ *
+ * @param pNexusDataSet
+ * @return a serialization of the supplied NexusDataSet
+ */
+ String serialize(NexusDataSet pNexusDataSet);
+
+ /**
+ * Write the NexusDataSet to a string that represents the object.
+ * The exact output format is up to the implementing service, i.e.
+ * this can either be nexus or nexml.
+ *
+ * @param pStudy
+ * @return a serialization of the supplied Study
+ */
+ String serialize(Study pStudy);
}
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|
|
From: <rv...@us...> - 2009-06-19 02:15:46
|
Revision: 63
http://treebase.svn.sourceforge.net/treebase/?rev=63&view=rev
Author: rvos
Date: 2009-06-19 02:14:12 +0000 (Fri, 19 Jun 2009)
Log Message:
-----------
Added attachAnnotation(String key,String value,URI,Annotatable) method and mPrismURI static field.
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java 2009-06-19 02:12:51 UTC (rev 62)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java 2009-06-19 02:14:12 UTC (rev 63)
@@ -15,7 +15,9 @@
public class NexmlObjectConverter extends AbstractNexusConverter {
protected static URI mDCURI;
+ protected static URI mPrismURI;
private static String mDCURIString = "http://purl.org/dc/elements/1.1/";
+ private static String mPrismURIString = "http://prismstandard.org/namespaces/1.2/basic/";
private static String mDCIdentifier = "dc:identifier";
public static String TreeBASE2Prefix = "TreeBASE2";
private Document mDocument;
@@ -28,9 +30,10 @@
public NexmlObjectConverter(Study study, TaxonLabelHome taxonLabelHome, Document document) {
try {
mDCURI = new URI(mDCURIString);
+ mPrismURI = new URI(mPrismURIString);
} catch (URISyntaxException e) {
e.printStackTrace();
- }
+ }
setTaxonLabelHome(taxonLabelHome);
setStudy(study);
setDocument(document);
@@ -57,12 +60,23 @@
* @param tbPersistable
*/
protected void attachTreeBaseID(Annotatable annotatable,TBPersistable tbPersistable) {
- annotatable.addAnnotationValue(mDCIdentifier, mDCURI, makeNamespacedID(tbPersistable));
+ attachAnnotation(mDCIdentifier,makeNamespacedID(tbPersistable),mDCURI,annotatable);
}
/**
*
+ * @param key
+ * @param value
+ * @param namespace
* @param annotatable
+ */
+ protected void attachAnnotation(String key,String value,URI namespace,Annotatable annotatable) {
+ annotatable.addAnnotationValue(key, namespace, value);
+ }
+
+ /**
+ *
+ * @param annotatable
* @param persistableClass
* @return
*/
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|
|
From: SourceForge.net <no...@so...> - 2009-06-18 18:26:52
|
Bugs item #2808561, was opened at 2009-06-18 14:26 Message generated for change (Tracker Item Submitted) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2808561&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None Status: Open Priority: 6 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: Nobody/Anonymous (nobody) Summary: Admin study update ergonomics Initial Comment: We will soon start having workstudy students improve TreeBASE data records (e.g. updating citations, DOIs, etc). This means that admin users and associate editors, etc, need efficient interactivity with the database. I've noticed two problems in this regard: (1) an admin person who clicks "Search Submission" under "Study Management" can only search by legacy study id, not the new study id. An easy solution is to have this search for (Legacy_ID OR Study_ID). An alternative solution is to provide the user with a choice between specifying either type of ID. The second problem (2) is that the Admin user has to start by toggling the study from "Published" to "In Progress" before he can edit the citation, and then after editing the citation, the Admin user has to toggle the study from "In Progress" back to "Published" (via "Ready"). The problem is that after editing a citation, there is no link to take the admin person back to the screen where the status can be toggled -- the only solution that I can find is that the admin person has to search for the study all over again ("Search Submission" under "Study Management"). It would be better to either provide a link to return to this page where status can be toggled OR give the admin person the ability to edit a Published study without having to toggle it to "In Progress" (i.e. keep the study as "Published" throughout the citation editing process -- currently this is not allowed). ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2808561&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2009-06-18 18:15:36
|
Bugs item #2808555, was opened at 2009-06-18 14:15 Message generated for change (Tracker Item Submitted) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2808555&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None Status: Open Priority: 4 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: Nobody/Anonymous (nobody) Summary: DOI column in study list takes up too much space Initial Comment: When a DOI is available for a study, it forces the table to allocate lots of space for the DOI column, causing the Title column (which is the more important one) to be squashed and multi-line. It would be better if we did not even show the whole DOI in the study summary list, but rather just offered the mini-icon with an active DOI resolver link. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2808555&group_id=248804 |
|
From: <rv...@us...> - 2009-06-18 09:40:44
|
Revision: 59
http://treebase.svn.sourceforge.net/treebase/?rev=59&view=rev
Author: rvos
Date: 2009-06-18 09:40:42 +0000 (Thu, 18 Jun 2009)
Log Message:
-----------
Added NexusService for NeXML
Added Paths:
-----------
trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNexml.java
Added: trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNexml.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNexml.java (rev 0)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceNexml.java 2009-06-18 09:40:42 UTC (rev 59)
@@ -0,0 +1,52 @@
+package org.cipres.treebase.service.nexus;
+
+import java.io.File;
+import java.util.Collection;
+
+import org.apache.log4j.Logger;
+import org.cipres.treebase.domain.DomainHome;
+import org.cipres.treebase.domain.nexus.NexusDataSet;
+import org.cipres.treebase.domain.nexus.NexusService;
+import org.cipres.treebase.domain.nexus.nexml.NexmlConverter;
+import org.cipres.treebase.domain.study.Study;
+import org.cipres.treebase.event.ProgressionListener;
+import org.cipres.treebase.service.AbstractServiceImpl;
+
+public class NexusServiceNexml extends AbstractServiceImpl implements NexusService {
+ private static final Logger LOGGER = Logger.getLogger(NexusServiceNexml.class);
+ private DomainHome mDomainHome;
+
+ @Override
+ public Class defaultResultClass() {
+ return null;
+ }
+
+ @Override
+ protected DomainHome getDomainHome() {
+ return mDomainHome;
+ }
+
+ public void setDomainHome(DomainHome domainHome) {
+ mDomainHome = domainHome;
+ }
+
+ public NexusDataSet parseNexus(Study study, Collection<File> nexusFiles,
+ ProgressionListener listener) {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ public NexusDataSet parseNexus(Study study, File nexusFile) {
+ if (study == null) {
+ if (LOGGER.isInfoEnabled()) {
+ LOGGER.info("parseNexus - Study is null"); //$NON-NLS-1$
+ }
+ return null;
+ }
+ NexusDataSet data = new NexusDataSet();
+ NexmlConverter converter = new NexmlConverter();
+ converter.parseOneFile(nexusFile, study, data);
+ return data;
+ }
+
+}
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|
|
From: <rv...@us...> - 2009-06-18 09:38:55
|
Revision: 58
http://treebase.svn.sourceforge.net/treebase/?rev=58&view=rev
Author: rvos
Date: 2009-06-18 09:38:54 +0000 (Thu, 18 Jun 2009)
Log Message:
-----------
Added getters/setters for NeXML objects
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/ContinuousMatrixJDBC.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/DiscreteMatrixJDBC.java
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/MatrixJDBC.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/ContinuousMatrixJDBC.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/ContinuousMatrixJDBC.java 2009-06-18 09:34:25 UTC (rev 57)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/ContinuousMatrixJDBC.java 2009-06-18 09:38:54 UTC (rev 58)
@@ -39,6 +39,7 @@
import org.cipres.treebase.domain.matrix.ContinuousMatrix;
import org.cipres.treebase.domain.matrix.ItemDefinition;
import org.cipres.treebase.domain.nexus.mesquite.MesquiteMatrixConverter;
+import org.cipres.treebase.domain.nexus.nexml.NexmlMatrixConverter;
/**
* Helper class for direct Matrix related SQL operations. Bypass the hibernate framework for high
@@ -83,6 +84,10 @@
private Map<String, Long> mItemDefNameToIDMap;
+ private org.nexml.model.ContinuousMatrix mNexmlCharacterData;
+
+ private NexmlMatrixConverter mNexmlMatrixConverter;
+
// Note: currently we support only one set of item definitions for the entire matrix.
// It is modeled in continuousMatrix.itemDefinitions.
// The matrixColumn.itemDefinitions are not supported at this time since Mesquite (and Nexus)
@@ -117,6 +122,15 @@
}
+ public ContinuousMatrixJDBC(ContinuousMatrix tbMatrix,
+ org.nexml.model.ContinuousMatrix xmlMatrix,
+ NexmlMatrixConverter nexmlMatrixConverter) {
+ this();
+ setCharacterMatrix(tbMatrix);
+ setNexmlCharacterData(xmlMatrix);
+ setNexmlMatrixConverter(nexmlMatrixConverter);
+ }
+
// /**
// * Return the ItemDefJDBCs field.
// *
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/DiscreteMatrixJDBC.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/DiscreteMatrixJDBC.java 2009-06-18 09:34:25 UTC (rev 57)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/DiscreteMatrixJDBC.java 2009-06-18 09:38:54 UTC (rev 58)
@@ -38,9 +38,11 @@
import org.springframework.jdbc.UncategorizedSQLException;
import org.cipres.treebase.domain.matrix.CharacterMatrix;
+import org.cipres.treebase.domain.matrix.ContinuousMatrix;
import org.cipres.treebase.domain.matrix.DiscreteChar;
import org.cipres.treebase.domain.matrix.DiscreteCharState;
import org.cipres.treebase.domain.nexus.mesquite.MesquiteMatrixConverter;
+import org.cipres.treebase.domain.nexus.nexml.NexmlMatrixConverter;
/**
* Helper class for direct Matrix related SQL operations. Bypass the hibernate framework for high
@@ -121,6 +123,15 @@
mRowSymbolBufs.add(new StringBuffer());
}
}
+
+ public DiscreteMatrixJDBC(CharacterMatrix tbMatrix,
+ org.nexml.model.CategoricalMatrix xmlMatrix,
+ NexmlMatrixConverter nexmlMatrixConverter) {
+ this();
+ setCharacterMatrix(tbMatrix);
+ setNexmlCharacterData(xmlMatrix);
+ setNexmlMatrixConverter(nexmlMatrixConverter);
+ }
/**
* Return the RowSymbolBufs field.
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/MatrixJDBC.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/MatrixJDBC.java 2009-06-18 09:34:25 UTC (rev 57)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/MatrixJDBC.java 2009-06-18 09:38:54 UTC (rev 58)
@@ -32,11 +32,13 @@
import org.apache.log4j.Logger;
import org.hibernate.Query;
import org.hibernate.Session;
+import org.nexml.model.Matrix;
import org.springframework.jdbc.UncategorizedSQLException;
import org.cipres.treebase.domain.matrix.CharacterMatrix;
import org.cipres.treebase.domain.matrix.ContinuousMatrix;
import org.cipres.treebase.domain.nexus.mesquite.MesquiteMatrixConverter;
+import org.cipres.treebase.domain.nexus.nexml.NexmlMatrixConverter;
/**
* Helper class for direct Matrix related SQL operations. Bypass the hibernate framework for high
@@ -86,6 +88,8 @@
private List<MatrixColumnJDBC> mMatrixColumnJDBCs;
private MesquiteMatrixConverter mMesqMatrixConverter;
+ private NexmlMatrixConverter mNexmlMatrixConverter;
+ private Matrix mNexmlCharacterData;
/**
* Factory methods for creating a new MatrixJDBC instance based on the CharacterMatrix type.
@@ -287,6 +291,16 @@
mMesquiteCharacterData = pNewMesquiteCharacterData;
}
+ protected void setNexmlMatrixConverter(
+ NexmlMatrixConverter nexmlMatrixConverter) {
+ mNexmlMatrixConverter = nexmlMatrixConverter;
+ }
+
+ protected void setNexmlCharacterData(
+ org.nexml.model.Matrix xmlMatrix) {
+ mNexmlCharacterData = xmlMatrix;
+ }
+
/**
* Return the discriminator value for the sub classes in MatrixElement class hierarchy.
*
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|
|
From: <rv...@us...> - 2009-06-18 09:34:26
|
Revision: 57
http://treebase.svn.sourceforge.net/treebase/?rev=57&view=rev
Author: rvos
Date: 2009-06-18 09:34:25 +0000 (Thu, 18 Jun 2009)
Log Message:
-----------
Added getters/setters for NeXML objects
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/NexusDataSet.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/NexusDataSet.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/NexusDataSet.java 2009-06-18 09:33:26 UTC (rev 56)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/NexusDataSet.java 2009-06-18 09:34:25 UTC (rev 57)
@@ -39,6 +39,8 @@
import org.cipres.treebase.domain.taxon.TaxonLabelSet;
import org.cipres.treebase.domain.tree.PhyloTree;
import org.cipres.treebase.domain.tree.TreeBlock;
+import org.nexml.model.Document;
+import org.nexml.model.OTUs;
/**
* Contains nexus data set after a nexus file is parsed.
@@ -54,9 +56,11 @@
private List<TaxonLabel> mTaxonLabels;
private List<TaxonLabelSet> mTaxonLabelSets;
private Map<Taxa, TaxonLabelSet> mTaxonLabelSetMap;
+ private Map<OTUs, TaxonLabelSet> mTaxonLabelSetMapNexml;
private NexusDataSetJDBC mDataJDBC = new NexusDataSetJDBC();
private MesquiteProject mMesqProject;
+ private Document mNexmlDocument;
/**
@@ -126,6 +130,18 @@
}
return mTaxonLabelSetMap;
}
+
+ /**
+ * Return the TaxonLabelSetMapNexml field. Uses lazy initialization.
+ *
+ * @return Map<Taxa, TaxonLabelSet> mTaxonLabelSetMapNexml
+ */
+ private Map<OTUs, TaxonLabelSet> getTaxonLabelSetMapNexml() {
+ if (mTaxonLabelSetMapNexml == null) {
+ mTaxonLabelSetMapNexml = new HashMap<OTUs, TaxonLabelSet>();
+ }
+ return mTaxonLabelSetMapNexml;
+ }
/**
* Add a Taxon label set.
@@ -140,6 +156,20 @@
}
}
}
+
+ /**
+ * Add a Taxon label set.
+ *
+ * @param pSet
+ */
+ public void addTaxonLabelSet(OTUs pTaxa, TaxonLabelSet pSet) {
+ if (pSet != null) {
+ if (getTaxonLabelSetMapNexml().put(pTaxa, pSet) == null) {
+ // it is a new entry:
+ getTaxonLabelSets().add(pSet);
+ }
+ }
+ }
/**
* Find a taxon label set based on the taxa.
@@ -150,6 +180,16 @@
public TaxonLabelSet getTaxonLabelSet(Taxa pTaxa) {
return getTaxonLabelSetMap().get(pTaxa);
}
+
+ /**
+ * Find a taxon label set based on the nexml OTUs.
+ *
+ * @param xmlOTUs
+ * @return
+ */
+ public TaxonLabelSet getTaxonLabelSet(OTUs xmlOTUs) {
+ return getTaxonLabelSetMapNexml().get(xmlOTUs);
+ }
/**
* Return the PhyloTrees field. Uses lazy initialization.
@@ -266,4 +306,13 @@
return treeTaxonLabels;
}
+ /**
+ * Set the NexmlProject field.
+ */
+ public void setNexmlProject(Document document) {
+ mNexmlDocument = document;
+
+ }
+
+
}
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|
|
From: <rv...@us...> - 2009-06-18 09:33:27
|
Revision: 56
http://treebase.svn.sourceforge.net/treebase/?rev=56&view=rev
Author: rvos
Date: 2009-06-18 09:33:26 +0000 (Thu, 18 Jun 2009)
Log Message:
-----------
JavaDoc typo correction
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/mesquite/MesquiteMatrixConverter.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/mesquite/MesquiteMatrixConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/mesquite/MesquiteMatrixConverter.java 2009-06-18 09:32:34 UTC (rev 55)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/mesquite/MesquiteMatrixConverter.java 2009-06-18 09:33:26 UTC (rev 56)
@@ -156,7 +156,7 @@
/**
* First convert matrixElements for saving to database using direct JDBC, then batch insert the
- * elements to datbase.
+ * elements to database.
*
* For memory considerations, the large matrix elementJDBC list is returned, while the compound
* elements are created and stored inside the MatrixJDBC.
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|
|
From: <rv...@us...> - 2009-06-18 09:32:37
|
Revision: 55
http://treebase.svn.sourceforge.net/treebase/?rev=55&view=rev
Author: rvos
Date: 2009-06-18 09:32:34 +0000 (Thu, 18 Jun 2009)
Log Message:
-----------
Adding NeXML conversion classes.
Added Paths:
-----------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlConverter.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlOTUConverter.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlTreeBlockConverter.java
Added: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlConverter.java (rev 0)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlConverter.java 2009-06-18 09:32:34 UTC (rev 55)
@@ -0,0 +1,72 @@
+package org.cipres.treebase.domain.nexus.nexml;
+
+import java.io.File;
+import java.util.Collection;
+
+import org.cipres.treebase.domain.matrix.Matrix;
+import org.cipres.treebase.domain.nexus.AbstractNexusConverter;
+import org.cipres.treebase.domain.nexus.NexusDataSet;
+import org.cipres.treebase.domain.nexus.NexusParserConverter;
+import org.cipres.treebase.domain.study.Study;
+import org.cipres.treebase.domain.tree.PhyloTree;
+import org.cipres.treebase.domain.tree.TreeBlock;
+import org.cipres.treebase.event.ProgressionListener;
+import org.nexml.model.Document;
+import org.nexml.model.DocumentFactory;
+import org.nexml.model.OTUs;
+
+public class NexmlConverter extends AbstractNexusConverter implements
+ NexusParserConverter {
+
+ /**
+ *
+ */
+ public void processLoadFile(Collection<File> nexusFiles, Study study,
+ NexusDataSet dataSet, ProgressionListener listener) {
+ // TODO Auto-generated method stub
+
+ }
+
+ /**
+ *
+ * @param pFile
+ * @param pStudy
+ * @param pDataSet
+ */
+ public void parseOneFile(File pFile, Study pStudy, NexusDataSet pDataSet) {
+ Document document = null;
+ try {
+ document = DocumentFactory.parse(pFile);
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ // Taxa
+ NexmlOTUConverter noc = new NexmlOTUConverter(pStudy,getTaxonLabelHome(),document);
+ for ( OTUs xmlOTUs : document.getOTUsList() ) {
+ pDataSet.addTaxonLabelSet(xmlOTUs, noc.fromXmlToTreeBase(xmlOTUs));
+ }
+
+ // Matrices
+ NexmlMatrixConverter nmc = new NexmlMatrixConverter(pStudy,getTaxonLabelHome(),document);
+ for ( org.nexml.model.Matrix<?> xmlMatrix : document.getMatrices() ) {
+ Matrix tbMatrix = nmc.fromXmlToTreeBase(xmlMatrix);
+ tbMatrix.setNexusFileName(pFile.getName());
+ pDataSet.getMatrices().add(tbMatrix);
+ }
+
+ // Trees
+ NexmlTreeBlockConverter ntbc = new NexmlTreeBlockConverter(pStudy,getTaxonLabelHome(),document);
+ for ( org.nexml.model.TreeBlock xmlTreeBlock : document.getTreeBlockList() ) {
+ TreeBlock tbTreeBlock = ntbc.fromXmlToTreeBase(xmlTreeBlock);
+ for ( PhyloTree phyloTree : tbTreeBlock.getTreeList() ) {
+ phyloTree.setNexusFileName(pFile.getName());
+ }
+ pDataSet.getTreeBlocks().add(tbTreeBlock);
+ }
+
+ // Store document
+ pDataSet.setNexmlProject(document);
+ }
+
+}
Added: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java (rev 0)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java 2009-06-18 09:32:34 UTC (rev 55)
@@ -0,0 +1,162 @@
+package org.cipres.treebase.domain.nexus.nexml;
+
+import java.util.ArrayList;
+import java.util.List;
+import org.cipres.treebase.dao.jdbc.ContinuousMatrixElementJDBC;
+import org.cipres.treebase.dao.jdbc.ContinuousMatrixJDBC;
+import org.cipres.treebase.dao.jdbc.DiscreteMatrixElementJDBC;
+import org.cipres.treebase.dao.jdbc.DiscreteMatrixJDBC;
+import org.cipres.treebase.dao.jdbc.MatrixColumnJDBC;
+import org.cipres.treebase.domain.matrix.ContinuousChar;
+import org.cipres.treebase.domain.matrix.DiscreteChar;
+import org.cipres.treebase.domain.matrix.DiscreteMatrix;
+import org.cipres.treebase.domain.matrix.Matrix;
+import org.cipres.treebase.domain.study.Study;
+import org.cipres.treebase.domain.taxon.TaxonLabelHome;
+import org.cipres.treebase.domain.taxon.TaxonLabelSet;
+import org.nexml.model.Annotatable;
+import org.nexml.model.CategoricalMatrix;
+import org.nexml.model.CharacterState;
+import org.nexml.model.ContinuousMatrix;
+import org.nexml.model.Document;
+import org.nexml.model.MatrixCell;
+import org.nexml.model.OTUs;
+import org.nexml.model.OTU;
+
+public class NexmlMatrixConverter extends NexmlObjectConverter {
+
+ /**
+ *
+ * @param study
+ * @param taxonLabelHome
+ */
+ public NexmlMatrixConverter(Study study,TaxonLabelHome taxonLabelHome,Document document) {
+ super(study,taxonLabelHome,document);
+ }
+
+ /**
+ *
+ * @param xmlMatrix
+ * @return
+ */
+ public Matrix fromXmlToTreeBase(CategoricalMatrix xmlMatrix) {
+ DiscreteMatrix tbMatrix = new DiscreteMatrix();
+ DiscreteMatrixJDBC matrixJDBC = new DiscreteMatrixJDBC(tbMatrix, xmlMatrix, this);
+ List<MatrixColumnJDBC> columnJDBCs = new ArrayList<MatrixColumnJDBC>();
+ long[] colIds = matrixJDBC.getColIDs();
+ long[] rowIds = matrixJDBC.getRowIDs();
+ List<DiscreteMatrixElementJDBC> elements = new ArrayList<DiscreteMatrixElementJDBC>();
+ int colIndex = 0;
+ for ( org.nexml.model.Character xmlCharacter : xmlMatrix.getCharacters() ) {
+ String charName = xmlCharacter.getLabel();
+ DiscreteChar tbChar = new DiscreteChar();
+ tbChar.setDescription(charName);
+ MatrixColumnJDBC aColumnJDBC = new MatrixColumnJDBC();
+ aColumnJDBC.setPhyloChar(tbChar);
+ columnJDBCs.add(aColumnJDBC);
+ int rowIndex = 0;
+ for ( OTU xmlOTU : xmlMatrix.getOTUs().getAllOTUs() ) {
+ MatrixCell<CharacterState> xmlCell = xmlMatrix.getCell(xmlOTU, xmlCharacter);
+ DiscreteMatrixElementJDBC element = new DiscreteMatrixElementJDBC();
+ //element.setValue(xmlCell.getValue()); // XXX nested stateset lookup song & dance here
+ element.setElementOrder(colIndex);
+ element.setMatrixRowID(rowIds[rowIndex]);
+ element.setMatrixColID(colIds[colIndex]);
+ elements.add(element);
+ rowIndex++;
+ }
+ colIndex++;
+ }
+ DiscreteMatrixElementJDBC.batchDiscreteElements(elements, getTaxonLabelHome().getConnection());
+ return tbMatrix;
+ }
+
+ /**
+ *
+ * @param xmlMatrix
+ * @return
+ */
+ public Matrix fromXmlToTreeBase(ContinuousMatrix xmlMatrix) {
+ org.cipres.treebase.domain.matrix.ContinuousMatrix tbMatrix =
+ new org.cipres.treebase.domain.matrix.ContinuousMatrix();
+ ContinuousMatrixJDBC matrixJDBC = new ContinuousMatrixJDBC(tbMatrix, xmlMatrix, this);
+ List<MatrixColumnJDBC> columnJDBCs = new ArrayList<MatrixColumnJDBC>();
+ long[] colIds = matrixJDBC.getColIDs();
+ long[] rowIds = matrixJDBC.getRowIDs();
+ List<ContinuousMatrixElementJDBC> elements = new ArrayList<ContinuousMatrixElementJDBC>();
+
+ int colIndex = 0;
+ for ( org.nexml.model.Character xmlCharacter : xmlMatrix.getCharacters() ) {
+ String charName = xmlCharacter.getLabel();
+ ContinuousChar tbChar = new ContinuousChar();
+ tbChar.setDescription(charName);
+ MatrixColumnJDBC aColumnJDBC = new MatrixColumnJDBC();
+ aColumnJDBC.setPhyloChar(tbChar);
+ columnJDBCs.add(aColumnJDBC);
+ int rowIndex = 0;
+ for ( OTU xmlOTU : xmlMatrix.getOTUs().getAllOTUs() ) {
+ MatrixCell<Double> xmlCell = xmlMatrix.getCell(xmlOTU, xmlCharacter);
+ ContinuousMatrixElementJDBC element = new ContinuousMatrixElementJDBC();
+ element.setValue(xmlCell.getValue());
+ element.setElementOrder(colIndex);
+ element.setMatrixRowID(rowIds[rowIndex]);
+ element.setMatrixColID(colIds[colIndex]);
+ elements.add(element);
+ rowIndex++;
+ }
+ colIndex++;
+ }
+ ContinuousMatrixElementJDBC.batchContinuousElements(elements, getTaxonLabelHome().getConnection());
+ return tbMatrix;
+ }
+
+ /**
+ *
+ * @param xmlMatrix
+ * @return
+ */
+ public Matrix fromXmlToTreeBase(org.nexml.model.Matrix<?> xmlMatrix) {
+ OTUs xmlOTUs = xmlMatrix.getOTUs();
+ Matrix tbMatrix = null;
+ TaxonLabelSet tbTaxa = null;
+ Long tbTaxonLabelSetID = readTreeBaseID((Annotatable) xmlOTUs,TaxonLabelSet.class);
+ if ( null != tbTaxonLabelSetID ) {
+ tbTaxa = getTaxonLabelHome()
+ .findPersistedObjectByID(TaxonLabelSet.class, tbTaxonLabelSetID);
+ }
+ if ( xmlMatrix instanceof CategoricalMatrix ) {
+ tbMatrix = fromXmlToTreeBase((CategoricalMatrix) xmlMatrix);
+ }
+ else if ( xmlMatrix instanceof ContinuousMatrix ) {
+ tbMatrix = fromXmlToTreeBase((ContinuousMatrix) xmlMatrix);
+ }
+ if ( null != tbMatrix ) {
+ attachTreeBaseID((Annotatable) xmlMatrix, tbMatrix);
+ if ( null != tbTaxa ) {
+ tbMatrix.setTaxa(tbTaxa);
+ }
+ tbMatrix.setStudy(getStudy());
+ tbMatrix.setTitle(xmlMatrix.getLabel());
+ tbMatrix.setPublished(false);
+ }
+ return tbMatrix;
+ }
+
+ public org.nexml.model.Matrix<?> fromTreeBaseToXml(Matrix tbMatrix) {
+ TaxonLabelSet taxonLabelSet = tbMatrix.getTaxa();
+ Long taxonLabelSetId = taxonLabelSet.getId();
+ OTUs xmlOTUs = null;
+ for ( OTUs otus : getDocument().getOTUsList() ) {
+ Long annotatedID = readTreeBaseID(otus, TaxonLabelSet.class);
+ if ( taxonLabelSetId == annotatedID ) {
+ xmlOTUs = otus;
+ break;
+ }
+ }
+ org.nexml.model.Matrix<?> xmlMatrix = getDocument().createCategoricalMatrix(xmlOTUs);
+ xmlMatrix.setLabel(tbMatrix.getTitle());
+ attachTreeBaseID((Annotatable)xmlMatrix, tbMatrix);
+ return xmlMatrix;
+ }
+
+}
Added: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlOTUConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlOTUConverter.java (rev 0)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlOTUConverter.java 2009-06-18 09:32:34 UTC (rev 55)
@@ -0,0 +1,80 @@
+package org.cipres.treebase.domain.nexus.nexml;
+
+import org.cipres.treebase.domain.study.Study;
+import org.cipres.treebase.domain.taxon.TaxonLabel;
+import org.cipres.treebase.domain.taxon.TaxonLabelHome;
+import org.cipres.treebase.domain.taxon.TaxonLabelSet;
+import org.nexml.model.Document;
+import org.nexml.model.OTU;
+import org.nexml.model.OTUs;
+
+public class NexmlOTUConverter extends NexmlObjectConverter {
+
+ /**
+ *
+ * @param study
+ * @param taxonLabelHome
+ */
+ public NexmlOTUConverter(Study study,TaxonLabelHome taxonLabelHome,Document document) {
+ super(study,taxonLabelHome,document);
+ }
+
+ /**
+ *
+ * @param xmlOTUs
+ * @return
+ */
+ public TaxonLabelSet fromXmlToTreeBase (OTUs xmlOTUs) {
+ TaxonLabelSet labelSet = new TaxonLabelSet();
+ attachTreeBaseID(xmlOTUs,labelSet);
+ labelSet.setStudy(getStudy());
+ labelSet.setTitle(xmlOTUs.getLabel());
+ labelSet.setTaxa(true);
+ for ( OTU xmlOTU : xmlOTUs.getAllOTUs() ) {
+ TaxonLabel taxonLabel = fromXmlToTreeBase(xmlOTU);
+ labelSet.addPhyloTaxonLabel(taxonLabel);
+ }
+ return labelSet;
+ }
+
+ /**
+ *
+ * @param taxonLabelSet
+ * @return
+ */
+ public OTUs fromTreeBaseToXml(TaxonLabelSet taxonLabelSet) {
+ OTUs xmlOTUs = getDocument().createOTUs();
+ xmlOTUs.setLabel(taxonLabelSet.getTitle());
+ attachTreeBaseID(xmlOTUs,taxonLabelSet);
+ for ( TaxonLabel taxonLabel : taxonLabelSet.getTaxonLabelsReadOnly() ) {
+ fromTreeBaseToXml(taxonLabel,xmlOTUs);
+ }
+ return xmlOTUs;
+ }
+
+ /**
+ *
+ * @param xmlOTU
+ * @return
+ */
+ public TaxonLabel fromXmlToTreeBase(OTU xmlOTU) {
+ TaxonLabel taxonLabel = getTaxonLabelHome().getByDescriptionAndStudy(xmlOTU.getLabel(), getStudy());
+ taxonLabel.setStudy(getStudy());
+ attachTreeBaseID(xmlOTU,taxonLabel);
+ return taxonLabel;
+ }
+
+ /**
+ *
+ * @param taxonLabel
+ * @param xmlOTUs
+ * @return
+ */
+ public OTU fromTreeBaseToXml(TaxonLabel taxonLabel,OTUs xmlOTUs) {
+ OTU xmlOTU = xmlOTUs.createOTU();
+ xmlOTU.setLabel(taxonLabel.getTaxonLabel());
+ attachTreeBaseID(xmlOTU,taxonLabel);
+ return xmlOTU;
+ }
+
+}
Added: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java (rev 0)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java 2009-06-18 09:32:34 UTC (rev 55)
@@ -0,0 +1,93 @@
+package org.cipres.treebase.domain.nexus.nexml;
+
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.util.Iterator;
+import java.util.Set;
+
+import org.cipres.treebase.TreebaseIDString;
+import org.cipres.treebase.domain.TBPersistable;
+import org.cipres.treebase.domain.nexus.AbstractNexusConverter;
+import org.cipres.treebase.domain.study.Study;
+import org.cipres.treebase.domain.taxon.TaxonLabelHome;
+import org.nexml.model.Annotatable;
+import org.nexml.model.Document;
+
+public class NexmlObjectConverter extends AbstractNexusConverter {
+ protected static URI mDCURI;
+ private static String mDCURIString = "http://purl.org/dc/elements/1.1/";
+ private static String mDCIdentifier = "dc:identifier";
+ public static String TreeBASE2Prefix = "TreeBASE2";
+ private Document mDocument;
+
+ /**
+ *
+ * @param study
+ * @param taxonLabelHome
+ */
+ public NexmlObjectConverter(Study study, TaxonLabelHome taxonLabelHome, Document document) {
+ try {
+ mDCURI = new URI(mDCURIString);
+ } catch (URISyntaxException e) {
+ e.printStackTrace();
+ }
+ setTaxonLabelHome(taxonLabelHome);
+ setStudy(study);
+ setDocument(document);
+ }
+
+ /**
+ *
+ * @param tbPersistable
+ * @return
+ */
+ public String makeNamespacedID (TBPersistable tbPersistable) {
+ StringBuilder sb = new StringBuilder();
+ sb
+ .append(TreeBASE2Prefix)
+ .append(':')
+ .append(TreebaseIDString.getPrefixForClass(tbPersistable.getClass()))
+ .append(tbPersistable.getId());
+ return sb.toString();
+ }
+
+ /**
+ *
+ * @param annotatable
+ * @param tbPersistable
+ */
+ protected void attachTreeBaseID(Annotatable annotatable,TBPersistable tbPersistable) {
+ annotatable.addAnnotationValue(mDCIdentifier, mDCURI, makeNamespacedID(tbPersistable));
+ }
+
+ /**
+ *
+ * @param annotatable
+ * @param persistableClass
+ * @return
+ */
+ protected Long readTreeBaseID(Annotatable annotatable, Class<? extends TBPersistable> persistableClass) {
+ Set<Object> values = annotatable.getAnnotationValues(mDCIdentifier);
+ Iterator<Object> objectIterator = values.iterator();
+ while ( objectIterator.hasNext() ) {
+ String namespacedId = objectIterator.next().toString();
+ StringBuffer prefix = new StringBuffer();
+ prefix
+ .append(TreeBASE2Prefix)
+ .append(':')
+ .append(TreebaseIDString.getPrefixForClass(persistableClass));
+ if ( namespacedId.startsWith(prefix.toString()) ) {
+ return Long.parseLong(namespacedId.substring(prefix.length()));
+ }
+ }
+ return null;
+ }
+
+ public Document getDocument() {
+ return mDocument;
+ }
+
+ public void setDocument(Document document) {
+ mDocument = document;
+ }
+}
Added: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlTreeBlockConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlTreeBlockConverter.java (rev 0)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlTreeBlockConverter.java 2009-06-18 09:32:34 UTC (rev 55)
@@ -0,0 +1,226 @@
+package org.cipres.treebase.domain.nexus.nexml;
+
+import java.util.Iterator;
+import java.util.Set;
+
+import org.cipres.treebase.domain.study.Study;
+import org.cipres.treebase.domain.taxon.TaxonLabel;
+import org.cipres.treebase.domain.taxon.TaxonLabelHome;
+import org.cipres.treebase.domain.taxon.TaxonLabelSet;
+import org.cipres.treebase.domain.tree.PhyloTree;
+import org.cipres.treebase.domain.tree.PhyloTreeNode;
+import org.cipres.treebase.domain.tree.TreeBlock;
+import org.nexml.model.Annotatable;
+import org.nexml.model.Document;
+import org.nexml.model.Edge;
+import org.nexml.model.FloatEdge;
+import org.nexml.model.IntEdge;
+import org.nexml.model.Network;
+import org.nexml.model.Node;
+import org.nexml.model.OTUs;
+import org.nexml.model.Tree;
+
+public class NexmlTreeBlockConverter extends NexmlObjectConverter {
+
+ /**
+ *
+ * @param study
+ * @param taxonLabelHome
+ */
+ public NexmlTreeBlockConverter(Study study,TaxonLabelHome taxonLabelHome,Document document) {
+ super(study,taxonLabelHome,document);
+ }
+
+ /**
+ *
+ * @param xmlTreeBlock
+ * @return
+ */
+ public TreeBlock fromXmlToTreeBase(org.nexml.model.TreeBlock xmlTreeBlock) {
+ OTUs xmlOTUs = xmlTreeBlock.getOTUs();
+ Long tbTaxonLabelSetId = readTreeBaseID(xmlOTUs,TaxonLabelSet.class);
+ TreeBlock tbTreeBlock = new TreeBlock();
+ tbTreeBlock.setTitle(xmlTreeBlock.getLabel());
+ if ( null != tbTaxonLabelSetId ) {
+ TaxonLabelSet tbTaxonLabelSet = getTaxonLabelHome()
+ .findPersistedObjectByID(TaxonLabelSet.class, tbTaxonLabelSetId);
+ tbTreeBlock.setTaxonLabelSet(tbTaxonLabelSet);
+ }
+ Iterator<Network<?>> xmlNetworkIterator = xmlTreeBlock.iterator();
+ while ( xmlNetworkIterator.hasNext() ) {
+ Network<?> xmlNetwork = xmlNetworkIterator.next();
+ if ( xmlNetwork instanceof Tree ) {
+ PhyloTree tbPhyloTree = fromXmlToTreeBase((Tree<?>) xmlNetwork);
+ tbPhyloTree.setStudy(getStudy());
+ tbTreeBlock.addPhyloTree(tbPhyloTree);
+ }
+ }
+ return tbTreeBlock;
+ }
+
+ /**
+ *
+ * @param xmlTree
+ * @return
+ */
+ public PhyloTree fromXmlToTreeBase(Tree<?> xmlTree) {
+ PhyloTree tbPhyloTree = new PhyloTree();
+ tbPhyloTree.setLabel(xmlTree.getLabel());
+ tbPhyloTree.setPublished(false);
+ tbPhyloTree.setRootedTree(((Node)xmlTree.getRoot()).isRoot());
+ copyXmlTree(xmlTree, tbPhyloTree);
+ tbPhyloTree.updateSubtreeBounds();
+ return tbPhyloTree;
+ }
+
+ /**
+ *
+ * @param phyloTree
+ * @return
+ */
+ public Tree<?> fromTreeBaseToXml(PhyloTree phyloTree,org.nexml.model.TreeBlock xmlTreeBlock) {
+ Tree<FloatEdge> xmlTree = xmlTreeBlock.createFloatTree();
+ xmlTree.setLabel(phyloTree.getLabel());
+ attachTreeBaseID(xmlTree, phyloTree);
+ copyTreeBaseTree(phyloTree, xmlTree);
+ return xmlTree;
+ }
+
+ /**
+ *
+ * @param treeBlock
+ * @return
+ */
+ public org.nexml.model.TreeBlock fromTreeBaseToXML(TreeBlock treeBlock) {
+ TaxonLabelSet taxonLabelSet = treeBlock.getTaxonLabelSet();
+ OTUs xmlOTUs = null;
+ Long taxonLabelSetId = taxonLabelSet.getId();
+ for ( OTUs otus : getDocument().getOTUsList() ) {
+ Long otusId = readTreeBaseID(otus, TaxonLabelSet.class);
+ if ( taxonLabelSetId == otusId ) {
+ xmlOTUs = otus;
+ break;
+ }
+ }
+ org.nexml.model.TreeBlock xmlTreeBlock = getDocument().createTreeBlock(xmlOTUs);
+ xmlTreeBlock.setLabel(treeBlock.getTitle());
+ attachTreeBaseID((Annotatable)xmlTreeBlock,treeBlock);
+ for ( PhyloTree phyloTree : treeBlock.getTreeList() ) {
+ fromTreeBaseToXml(phyloTree,xmlTreeBlock);
+ }
+ return xmlTreeBlock;
+ }
+
+ /**
+ *
+ * @param phyloTree
+ * @param xmlTree
+ */
+ private void copyTreeBaseTree(PhyloTree phyloTree,Tree<FloatEdge> xmlTree) {
+ traverseTreeBaseTree(phyloTree,phyloTree.getRootNode(),xmlTree.createNode(),xmlTree);
+ }
+
+ /**
+ *
+ * @param tbTree
+ * @param tbNode
+ * @param xmlNode
+ * @param xmlTree
+ */
+ private void traverseTreeBaseTree(PhyloTree tbTree,PhyloTreeNode tbNode,Node xmlNode,Tree<FloatEdge> xmlTree) {
+ xmlNode.setLabel(tbNode.getName());
+ attachTreeBaseID(xmlNode, tbNode);
+ TaxonLabel taxonLabel = tbNode.getTaxonLabel();
+ if ( null != taxonLabel ) {
+ Long taxonId = taxonLabel.getId();
+ for ( OTUs xmlOTUs : getDocument().getOTUsList() ) {
+ for ( org.nexml.model.OTU xmlOTU : xmlOTUs.getAllOTUs() ) {
+ Long currentTaxonId = readTreeBaseID(xmlOTU, TaxonLabel.class);
+ if ( taxonId == currentTaxonId ) {
+ xmlNode.setOTU(xmlOTU);
+ break;
+ }
+ }
+ }
+ }
+ for ( PhyloTreeNode tbChildNode : tbNode.getChildNodes() ) {
+ Node xmlChildNode = xmlTree.createNode();
+ FloatEdge xmlEdge = xmlTree.createEdge(xmlNode, xmlChildNode);
+ xmlEdge.setLength(tbChildNode.getBranchLength());
+ traverseTreeBaseTree(tbTree, tbChildNode, xmlChildNode, xmlTree);
+ }
+ }
+
+ /**
+ *
+ * @param xmlTree
+ * @param tbPhyloTree
+ */
+ private void copyXmlTree(Tree<?> xmlTree, PhyloTree tbPhyloTree) {
+ StringBuilder sb = new StringBuilder();
+ PhyloTreeNode tbRoot = new PhyloTreeNode();
+ traverseXmlTree(xmlTree,sb,xmlTree.getRoot(), tbRoot, tbPhyloTree);
+ tbPhyloTree.setRootNode(tbRoot);
+ sb.append(';');
+ tbPhyloTree.setNewickString(sb.toString());
+ }
+
+ /**
+ *
+ * @param xmlTree
+ * @param sb
+ * @param xmlNode
+ * @param tbNode
+ * @param tbTree
+ */
+ private void traverseXmlTree(Tree<?> xmlTree, StringBuilder sb, Node xmlNode, PhyloTreeNode tbNode, PhyloTree tbTree) {
+ tbTree.addTreeNode(tbNode);
+ if ( null != xmlNode.getOTU() ) {
+ Long tbTaxonLabelId = readTreeBaseID(xmlNode.getOTU(),TaxonLabel.class);
+ if ( null != tbTaxonLabelId ) {
+ TaxonLabel tbTaxonLabel = getTaxonLabelHome()
+ .findPersistedObjectByID(TaxonLabel.class, tbTaxonLabelId);
+ tbNode.setTaxonLabel(tbTaxonLabel);
+ }
+ }
+
+ Set<Node> xmlChildren = xmlTree.getOutNodes(xmlNode);
+ if ( ! xmlChildren.isEmpty() ) {// xmlNode is internal
+ sb.append('(');
+ }
+ int currentChild = 1;
+ for ( Node child : xmlChildren ) {
+ PhyloTreeNode tbChild = new PhyloTreeNode();
+ tbNode.addChildNode(tbChild);
+ traverseXmlTree(xmlTree,sb,child,tbChild,tbTree);
+ if ( currentChild < xmlChildren.size() ) {
+ sb.append(',');
+ }
+ currentChild++;
+ }
+ if ( ! xmlChildren.isEmpty() ) {// xmlNode is internal
+ sb.append(')');
+ }
+ String label = xmlNode.getLabel();
+ if ( null != label ) {
+ sb.append(label);
+ tbNode.setName(label);
+ }
+
+ Set<Node> xmlParents = xmlTree.getInNodes(xmlNode);
+ if ( ! xmlParents.isEmpty() ) { // xmlNode is not topological root
+ Edge xmlEdge = xmlTree.getEdge(xmlParents.iterator().next(), xmlNode);
+ if ( xmlEdge instanceof FloatEdge ) {
+ Double length = ((FloatEdge)xmlEdge).getLength();
+ sb.append(':').append(length);
+ tbNode.setBranchLength(length);
+ }
+ else if ( xmlEdge instanceof IntEdge ) {
+ Integer length = ((IntEdge)xmlEdge).getLength();
+ sb.append(':').append(length);
+ tbNode.setBranchLength(length.doubleValue());
+ }
+ }
+ }
+
+}
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From: <rv...@us...> - 2009-06-16 00:10:45
|
Revision: 54
http://treebase.svn.sourceforge.net/treebase/?rev=54&view=rev
Author: rvos
Date: 2009-06-16 00:10:30 +0000 (Tue, 16 Jun 2009)
Log Message:
-----------
Some code formatting.
Modified Paths:
--------------
trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/RecDumper.pm
Modified: trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/RecDumper.pm
===================================================================
--- trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/RecDumper.pm 2009-06-15 23:38:04 UTC (rev 53)
+++ trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/RecDumper.pm 2009-06-16 00:10:30 UTC (rev 54)
@@ -80,16 +80,14 @@
}
}
elsif ($t eq 'DATE'){
- my ( $day, $month, $year );
+ my ( $day, $month, $year );
if ( m|(\d{1,2})/(\d{1,2})/(\d{4})| ) {
- ( $day, $month, $year ) =
- ( $1, $2, $3 );
+ ( $day, $month, $year ) = ( $1, $2, $3 );
}
- if ( m|(\d{4})-(\d{1,2})-(\d{1,2})| ) {
- ( $year, $month, $day ) =
- ( $1, $2, $3 );
- }
- $_ = "'${year}-${month}-${day}'";
+ if ( m|(\d{4})-(\d{1,2})-(\d{1,2})| ) {
+ ( $year, $month, $day ) = ( $1, $2, $3 );
+ }
+ $_ = "'${year}-${month}-${day}'";
}
else {
croak("Unknown field type '$t'; aborting");
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From: <mjd...@us...> - 2009-06-15 23:38:56
|
Revision: 53
http://treebase.svn.sourceforge.net/treebase/?rev=53&view=rev
Author: mjdominus
Date: 2009-06-15 23:38:04 +0000 (Mon, 15 Jun 2009)
Log Message:
-----------
Added handler for ISO 8601 dates
Modified Paths:
--------------
trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/RecDumper.pm
Modified: trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/RecDumper.pm
===================================================================
--- trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/RecDumper.pm 2009-06-15 23:31:27 UTC (rev 52)
+++ trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/RecDumper.pm 2009-06-15 23:38:04 UTC (rev 53)
@@ -80,11 +80,16 @@
}
}
elsif ($t eq 'DATE'){
+ my ( $day, $month, $year );
if ( m|(\d{1,2})/(\d{1,2})/(\d{4})| ) {
- my ( $day, $month, $year ) =
- ( $1, $2, $3 );
- $_ = "'${year}-${month}-${day}'";
+ ( $day, $month, $year ) =
+ ( $1, $2, $3 );
}
+ if ( m|(\d{4})-(\d{1,2})-(\d{1,2})| ) {
+ ( $year, $month, $day ) =
+ ( $1, $2, $3 );
+ }
+ $_ = "'${year}-${month}-${day}'";
}
else {
croak("Unknown field type '$t'; aborting");
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|
From: <rv...@us...> - 2009-06-15 23:32:05
|
Revision: 52
http://treebase.svn.sourceforge.net/treebase/?rev=52&view=rev
Author: rvos
Date: 2009-06-15 23:31:27 +0000 (Mon, 15 Jun 2009)
Log Message:
-----------
Added single quotes around date and timestamp reformatted strings
Modified Paths:
--------------
trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/RecDumper.pm
Modified: trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/RecDumper.pm
===================================================================
--- trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/RecDumper.pm 2009-06-15 23:24:14 UTC (rev 51)
+++ trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/RecDumper.pm 2009-06-15 23:31:27 UTC (rev 52)
@@ -76,14 +76,14 @@
if ( m|(\d{1,2})/(\d{1,2})/(\d{4})\s+(\d{2}):(\d{2}):(\d{2})| ) {
my ( $day, $month, $year, $hour, $minute, $second ) =
( $1, $2, $3, $4, $5, $6 );
- $_ = "${year}-${month}-${day} ${hour}:${minute}:${second}";
+ $_ = "'${year}-${month}-${day} ${hour}:${minute}:${second}'";
}
}
elsif ($t eq 'DATE'){
if ( m|(\d{1,2})/(\d{1,2})/(\d{4})| ) {
my ( $day, $month, $year ) =
( $1, $2, $3 );
- $_ = "${year}-${month}-${day}";
+ $_ = "'${year}-${month}-${day}'";
}
}
else {
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|
From: <rv...@us...> - 2009-06-15 23:24:16
|
Revision: 51
http://treebase.svn.sourceforge.net/treebase/?rev=51&view=rev
Author: rvos
Date: 2009-06-15 23:24:14 +0000 (Mon, 15 Jun 2009)
Log Message:
-----------
Added DATE handler
Modified Paths:
--------------
trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/RecDumper.pm
Modified: trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/RecDumper.pm
===================================================================
--- trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/RecDumper.pm 2009-06-12 07:08:24 UTC (rev 50)
+++ trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/RecDumper.pm 2009-06-15 23:24:14 UTC (rev 51)
@@ -79,6 +79,13 @@
$_ = "${year}-${month}-${day} ${hour}:${minute}:${second}";
}
}
+ elsif ($t eq 'DATE'){
+ if ( m|(\d{1,2})/(\d{1,2})/(\d{4})| ) {
+ my ( $day, $month, $year ) =
+ ( $1, $2, $3 );
+ $_ = "${year}-${month}-${day}";
+ }
+ }
else {
croak("Unknown field type '$t'; aborting");
}
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|
From: SourceForge.net <no...@so...> - 2009-06-12 22:17:34
|
Bugs item #2805720, was opened at 2009-06-12 18:16 Message generated for change (Tracker Item Submitted) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2805720&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: performance Group: None Status: Open Priority: 5 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: Nobody/Anonymous (nobody) Summary: slow join from taxa to trees Initial Comment: If I do a taxon variant search on "Metepeira*" I get 7 items. If I then click on the "Tree" tab, it takes 1 minute and 20 seconds to get a list of trees. That strikes me as quite slow for a join with only 7 taxa. I tried searching on "Mara*" and got a significantly longer list, then clicking on the Tree tab took a very long time (I gave up after six minutes). Ideally this join should be better optimized. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2805720&group_id=248804 |
|
From: <rv...@us...> - 2009-06-12 07:09:25
|
Revision: 50
http://treebase.svn.sourceforge.net/treebase/?rev=50&view=rev
Author: rvos
Date: 2009-06-12 07:08:24 +0000 (Fri, 12 Jun 2009)
Log Message:
-----------
Fixed typo in regex
Modified Paths:
--------------
trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/RecDumper.pm
Modified: trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/RecDumper.pm
===================================================================
--- trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/RecDumper.pm 2009-06-12 07:04:33 UTC (rev 49)
+++ trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/RecDumper.pm 2009-06-12 07:08:24 UTC (rev 50)
@@ -73,7 +73,7 @@
# do nothing
}
elsif ($t eq 'TIMESTMP'){
- if ( m|(\d+)/(\d+)/(\d+)\s+(\d+{2}):(\d+{2}):(\d+{2})| ) {
+ if ( m|(\d{1,2})/(\d{1,2})/(\d{4})\s+(\d{2}):(\d{2}):(\d{2})| ) {
my ( $day, $month, $year, $hour, $minute, $second ) =
( $1, $2, $3, $4, $5, $6 );
$_ = "${year}-${month}-${day} ${hour}:${minute}:${second}";
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|
From: <mjd...@us...> - 2009-06-12 07:06:20
|
Revision: 49
http://treebase.svn.sourceforge.net/treebase/?rev=49&view=rev
Author: mjdominus
Date: 2009-06-12 07:04:33 +0000 (Fri, 12 Jun 2009)
Log Message:
-----------
Added test mode
Modified Paths:
--------------
trunk/treebase-core/src/main/perl/dump/sqldump
Modified: trunk/treebase-core/src/main/perl/dump/sqldump
===================================================================
--- trunk/treebase-core/src/main/perl/dump/sqldump 2009-06-12 07:02:15 UTC (rev 48)
+++ trunk/treebase-core/src/main/perl/dump/sqldump 2009-06-12 07:04:33 UTC (rev 49)
@@ -14,6 +14,7 @@
my $name_file_after_table = 0; # name output file after table
my $schema = 'TBASE2'; # name of schema to analyze
my $zip = 0; # zip output
+my $test = 0; # test run: delete produced files
# get command line options, see Getopt::Long
GetOptions(
@@ -26,6 +27,7 @@
'dsn=s' => \$ENV{'TREEBASE_DB_DSN'},
'table=s' => \@tables,
'zip' => \$zip,
+ 'test' => \$test,
'all' => sub { @tables = get_all_tables() },
'help|?' => sub { pod2usage( '-verbose' => 0 ) }, # see Pod::Usage
'man' => sub { pod2usage( '-verbose' => 1 ) }, # see Pod::Usage
@@ -97,10 +99,18 @@
# write insert statements
if ( $with_inserts ) {
eval {
- print_insert_statements ($dumper, $dbh, $table)
+ print_insert_statements ($dumper, $dbh, $table);
+ if ( $test ) {
+ for ( qw(gz sql) ) {
+ if ( -e "${table}.${_}" ) {
+ unlink "${table}.${_}";
+ }
+ }
+ }
};
if ( $@ ) {
print STDERR "Table ${table} failed: $@\n";
+ $dumper->dump_create;
}
}
}
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|
From: <rv...@us...> - 2009-06-12 07:04:00
|
Revision: 48
http://treebase.svn.sourceforge.net/treebase/?rev=48&view=rev
Author: rvos
Date: 2009-06-12 07:02:15 +0000 (Fri, 12 Jun 2009)
Log Message:
-----------
Added TIMESTMP handler
Modified Paths:
--------------
trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/RecDumper.pm
Modified: trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/RecDumper.pm
===================================================================
--- trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/RecDumper.pm 2009-06-12 06:14:21 UTC (rev 47)
+++ trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/RecDumper.pm 2009-06-12 07:02:15 UTC (rev 48)
@@ -72,6 +72,13 @@
elsif ($t =~ /^(BIG|SMALL|)INT$/ || $t eq 'INTEGER' || $t eq 'DOUBLE') {
# do nothing
}
+ elsif ($t eq 'TIMESTMP'){
+ if ( m|(\d+)/(\d+)/(\d+)\s+(\d+{2}):(\d+{2}):(\d+{2})| ) {
+ my ( $day, $month, $year, $hour, $minute, $second ) =
+ ( $1, $2, $3, $4, $5, $6 );
+ $_ = "${year}-${month}-${day} ${hour}:${minute}:${second}";
+ }
+ }
else {
croak("Unknown field type '$t'; aborting");
}
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