Return-Path: X-Original-To: apmail-ctakes-commits-archive@www.apache.org Delivered-To: apmail-ctakes-commits-archive@www.apache.org Received: from mail.apache.org (hermes.apache.org [140.211.11.3]) by minotaur.apache.org (Postfix) with SMTP id 5504710D98 for ; Wed, 8 Jan 2014 02:29:58 +0000 (UTC) Received: (qmail 56776 invoked by uid 500); 8 Jan 2014 02:29:58 -0000 Delivered-To: apmail-ctakes-commits-archive@ctakes.apache.org Received: (qmail 56742 invoked by uid 500); 8 Jan 2014 02:29:58 -0000 Mailing-List: contact commits-help@ctakes.apache.org; run by ezmlm Precedence: bulk List-Help: List-Unsubscribe: List-Post: List-Id: Reply-To: dev@ctakes.apache.org Delivered-To: mailing list commits@ctakes.apache.org Received: (qmail 56735 invoked by uid 99); 8 Jan 2014 02:29:58 -0000 Received: from nike.apache.org (HELO nike.apache.org) (192.87.106.230) by apache.org (qpsmtpd/0.29) with ESMTP; Wed, 08 Jan 2014 02:29:58 +0000 X-ASF-Spam-Status: No, hits=-2000.0 required=5.0 tests=ALL_TRUSTED X-Spam-Check-By: apache.org Received: from [140.211.11.4] (HELO eris.apache.org) (140.211.11.4) by apache.org (qpsmtpd/0.29) with ESMTP; Wed, 08 Jan 2014 02:29:53 +0000 Received: from eris.apache.org (localhost [127.0.0.1]) by eris.apache.org (Postfix) with ESMTP id 09026238889B; Wed, 8 Jan 2014 02:29:32 +0000 (UTC) Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Subject: svn commit: r1556425 - in /ctakes/branches/ytex/ctakes-ytex: scripts/data/ scripts/data/orcl/test/ scripts/data/orcl/uima/ scripts/data/orcl/umls/ src/test/java/org/apache/ctakes/ytex/ src/test/resources/org/apache/ctakes/ytex/ Date: Wed, 08 Jan 2014 02:29:31 -0000 To: commits@ctakes.apache.org From: vjapache@apache.org X-Mailer: svnmailer-1.0.9 Message-Id: <20140108022932.09026238889B@eris.apache.org> X-Virus-Checked: Checked by ClamAV on apache.org Author: vjapache Date: Wed Jan 8 02:29:31 2014 New Revision: 1556425 URL: http://svn.apache.org/r1556425 Log: oracle tests and scripts Added: ctakes/branches/ytex/ctakes-ytex/scripts/data/orcl/umls/index_view.sql ctakes/branches/ytex/ctakes-ytex/scripts/data/orcl/umls/insert_view.template.sql ctakes/branches/ytex/ctakes-ytex/src/test/resources/org/apache/ctakes/ytex/ytex.orcl.properties Removed: ctakes/branches/ytex/ctakes-ytex/scripts/data/orcl/umls/create_view.template.sql Modified: ctakes/branches/ytex/ctakes-ytex/scripts/data/build.xml ctakes/branches/ytex/ctakes-ytex/scripts/data/orcl/test/createdb.sql ctakes/branches/ytex/ctakes-ytex/scripts/data/orcl/uima/create_reference.sql ctakes/branches/ytex/ctakes-ytex/scripts/data/orcl/umls/create_view.sql ctakes/branches/ytex/ctakes-ytex/src/test/java/org/apache/ctakes/ytex/ConceptDaoTest.java Modified: ctakes/branches/ytex/ctakes-ytex/scripts/data/build.xml URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex/scripts/data/build.xml?rev=1556425&r1=1556424&r2=1556425&view=diff ============================================================================== --- ctakes/branches/ytex/ctakes-ytex/scripts/data/build.xml (original) +++ ctakes/branches/ytex/ctakes-ytex/scripts/data/build.xml Wed Jan 8 02:29:31 2014 @@ -349,8 +349,8 @@ Database connection parameters are taken - - + + execute ${sql.file} @@ -398,7 +398,7 @@ ${sql.delimiter} - + ALTER SESSION SET CURRENT_SCHEMA=${sql.schema} ${sql.delimiter} Modified: ctakes/branches/ytex/ctakes-ytex/scripts/data/orcl/test/createdb.sql URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex/scripts/data/orcl/test/createdb.sql?rev=1556425&r1=1556424&r2=1556425&view=diff ============================================================================== --- ctakes/branches/ytex/ctakes-ytex/scripts/data/orcl/test/createdb.sql (original) +++ ctakes/branches/ytex/ctakes-ytex/scripts/data/orcl/test/createdb.sql Wed Jan 8 02:29:31 2014 @@ -1,7 +1 @@ -alter session set container=PDBORCL; -create tablespace TBS_YTEX_TEST datafile 'C:/code/data/oradata/orcl/TBS_YTEX_TEST.dbf' size 1M autoextend on online; -create user ytex_test identified by ytex_test default tablespace TBS_YTEX_TEST; -grant connect, resource to ytex_test; -grant create materialized view to ytex_test; -grant create view to ytex_test; Modified: ctakes/branches/ytex/ctakes-ytex/scripts/data/orcl/uima/create_reference.sql URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex/scripts/data/orcl/uima/create_reference.sql?rev=1556425&r1=1556424&r2=1556425&view=diff ============================================================================== --- ctakes/branches/ytex/ctakes-ytex/scripts/data/orcl/uima/create_reference.sql (original) +++ ctakes/branches/ytex/ctakes-ytex/scripts/data/orcl/uima/create_reference.sql Wed Jan 8 02:29:31 2014 @@ -10,8 +10,8 @@ create table hibernate_sequences ( insert into hibernate_sequences(sequence_name, next_val) values ('document_id_sequence', 1); create table anno_base_sequence ( - sequence_name varchar(100) not null, - next_val int not null default 1, + sequence_name varchar2(100) not null, + next_val int default 1 not null, primary key (sequence_name) ); insert into anno_base_sequence(sequence_name, next_val) values ('anno_base_id_sequence', 1); Modified: ctakes/branches/ytex/ctakes-ytex/scripts/data/orcl/umls/create_view.sql URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex/scripts/data/orcl/umls/create_view.sql?rev=1556425&r1=1556424&r2=1556425&view=diff ============================================================================== --- ctakes/branches/ytex/ctakes-ytex/scripts/data/orcl/umls/create_view.sql (original) +++ ctakes/branches/ytex/ctakes-ytex/scripts/data/orcl/umls/create_view.sql Wed Jan 8 02:29:31 2014 @@ -1,37 +1,9 @@ -create table v_snomed_fword_lookup -as -select mrc.cui, t.tui, c.fword, c.fstem, c.tok_str, c.stem_str -from umls_aui_fword c -inner join ytex.MRCONSO mrc on c.aui = mrc.aui and mrc.SAB in ( 'SNOMEDCT', 'RXNORM') -inner join -( - select cui, min(tui) tui - from ytex.MRSTY sty - where sty.tui in - ( - /* diseasesAndDisordersTuis */ - 'T019', 'T020', 'T037', 'T046', 'T047', 'T048', 'T049', 'T050', - 'T190', 'T191', 'T033', - /* signAndSymptomTuis */ - 'T184', - /* anatomicalSitesTuis */ - 'T017', 'T029', 'T023', 'T030', 'T031', 'T022', 'T025', 'T026', - 'T018', 'T021', 'T024', - /* medicationsAndDrugsTuis */ - 'T116', 'T195', 'T123', 'T122', 'T118', 'T103', 'T120', 'T104', - 'T200', 'T111', 'T196', 'T126', 'T131', 'T125', 'T129', 'T130', - 'T197', 'T119', 'T124', 'T114', 'T109', 'T115', 'T121', 'T192', - 'T110', 'T127', - /* proceduresTuis */ - 'T060', 'T065', 'T058', 'T059', 'T063', 'T062', 'T061', - /* deviceTuis */ - 'T074', 'T075', - /* laboratoryTuis */ - 'T059' - ) - group by cui -) t on t.cui = mrc.cui +create table v_snomed_fword_lookup ( + cui char(8) not null, + tui char(8) null, + fword varchar2(70) not null, + fstem varchar2(70) null, + tok_str varchar2(250) not null, + stem_str varchar2(250) null +) ; -create index IX_vsnfl_cui on v_snomed_fword_lookup(cui); -create index IX_vsnfl_fword on v_snomed_fword_lookup(fword); -create index IX_vsnfl_fstem on v_snomed_fword_lookup(fstem); Added: ctakes/branches/ytex/ctakes-ytex/scripts/data/orcl/umls/index_view.sql URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex/scripts/data/orcl/umls/index_view.sql?rev=1556425&view=auto ============================================================================== --- ctakes/branches/ytex/ctakes-ytex/scripts/data/orcl/umls/index_view.sql (added) +++ ctakes/branches/ytex/ctakes-ytex/scripts/data/orcl/umls/index_view.sql Wed Jan 8 02:29:31 2014 @@ -0,0 +1,3 @@ +create index IX_vsnfl_fword on v_snomed_fword_lookup (fword); +create index IX_vsnfl_fstem on v_snomed_fword_lookup (fstem); +create index IX_vsnfl_cui on v_snomed_fword_lookup (cui); Added: ctakes/branches/ytex/ctakes-ytex/scripts/data/orcl/umls/insert_view.template.sql URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex/scripts/data/orcl/umls/insert_view.template.sql?rev=1556425&view=auto ============================================================================== --- ctakes/branches/ytex/ctakes-ytex/scripts/data/orcl/umls/insert_view.template.sql (added) +++ ctakes/branches/ytex/ctakes-ytex/scripts/data/orcl/umls/insert_view.template.sql Wed Jan 8 02:29:31 2014 @@ -0,0 +1,33 @@ +insert into v_snomed_fword_lookup +select mrc.cui, t.tui, c.fword, c.fstem, c.tok_str, c.stem_str +from umls_aui_fword c +inner join @UMLS_SCHEMA@.MRCONSO mrc on c.aui = mrc.aui and mrc.SAB in ( 'SNOMEDCT', 'RXNORM') +inner join +( + select cui, min(tui) tui + from @UMLS_SCHEMA@.MRSTY sty + where sty.tui in + ( + /* diseasesAndDisordersTuis */ + 'T019', 'T020', 'T037', 'T046', 'T047', 'T048', 'T049', 'T050', + 'T190', 'T191', 'T033', + /* signAndSymptomTuis */ + 'T184', + /* anatomicalSitesTuis */ + 'T017', 'T029', 'T023', 'T030', 'T031', 'T022', 'T025', 'T026', + 'T018', 'T021', 'T024', + /* medicationsAndDrugsTuis */ + 'T116', 'T195', 'T123', 'T122', 'T118', 'T103', 'T120', 'T104', + 'T200', 'T111', 'T196', 'T126', 'T131', 'T125', 'T129', 'T130', + 'T197', 'T119', 'T124', 'T114', 'T109', 'T115', 'T121', 'T192', + 'T110', 'T127', + /* proceduresTuis */ + 'T060', 'T065', 'T058', 'T059', 'T063', 'T062', 'T061', + /* deviceTuis */ + 'T074', 'T075', + /* laboratoryTuis */ + 'T059' + ) + group by cui +) t on t.cui = mrc.cui +; Modified: ctakes/branches/ytex/ctakes-ytex/src/test/java/org/apache/ctakes/ytex/ConceptDaoTest.java URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex/src/test/java/org/apache/ctakes/ytex/ConceptDaoTest.java?rev=1556425&r1=1556424&r2=1556425&view=diff ============================================================================== --- ctakes/branches/ytex/ctakes-ytex/src/test/java/org/apache/ctakes/ytex/ConceptDaoTest.java (original) +++ ctakes/branches/ytex/ctakes-ytex/src/test/java/org/apache/ctakes/ytex/ConceptDaoTest.java Wed Jan 8 02:29:31 2014 @@ -29,28 +29,39 @@ public class ConceptDaoTest { @Before public void setUp() throws Exception { -// ClassLoader cl = ClassLoader.getSystemClassLoader(); -// -// URL[] urls = ((URLClassLoader)cl).getURLs(); -// -// for(URL url: urls){ -// System.out.println(url.getFile()); -// } -// URL is = this.getClass().getClassLoader().getResource("org/apache/ctakes/ytex/kernelBeanRefContext.xml"); -// System.out.println(is); + // ClassLoader cl = ClassLoader.getSystemClassLoader(); + // + // URL[] urls = ((URLClassLoader)cl).getURLs(); + // + // for(URL url: urls){ + // System.out.println(url.getFile()); + // } + // URL is = + // this.getClass().getClassLoader().getResource("org/apache/ctakes/ytex/kernelBeanRefContext.xml"); + // System.out.println(is); appCtx = (ApplicationContext) ContextSingletonBeanFactoryLocator - .getInstance("classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml") + .getInstance( + "classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml") .useBeanFactory("kernelApplicationContext").getFactory(); conceptDao = appCtx.getBean(ConceptDao.class); JdbcTemplate jdbcTemplate = new JdbcTemplate(); jdbcTemplate.setDataSource(appCtx.getBean(DataSource.class)); - Properties ytexProperties = (Properties)appCtx.getBean("ytexProperties"); + Properties ytexProperties = (Properties) appCtx + .getBean("ytexProperties"); String dbtype = ytexProperties.getProperty("db.type"); - if("hsql".equals(dbtype) || "mysql".equals(dbtype)) + if ("hsql".equals(dbtype) || "mysql".equals(dbtype)) jdbcTemplate.execute("drop table if exists test_concepts"); - if("mssql".equals(dbtype)) - jdbcTemplate.execute("if exists(select * from sys.objects where object_id = object_id('test_concepts')) drop table test_concepts"); - //TODO if("orcl".equals(dbtype))) + if ("mssql".equals(dbtype)) + jdbcTemplate + .execute("if exists(select * from sys.objects where object_id = object_id('test_concepts')) drop table test_concepts"); + if ("orcl".equals(dbtype)) { + // just try dropping the table, catch exception and hope all is well + try { + jdbcTemplate.execute("drop table test_concepts"); + } catch (Exception ignore) { + + } + } jdbcTemplate .execute("create table test_concepts(parent varchar(20), child varchar(20))"); jdbcTemplate @@ -65,13 +76,13 @@ public class ConceptDaoTest { .execute("insert into test_concepts values ('root', 'bacteria')"); jdbcTemplate .execute("insert into test_concepts values ('bacteria', 'e coli')"); - System.out.println("Create concept graph"); + System.out.println("Create concept graph"); conceptDao.createConceptGraph(null, "test", "select child, parent from test_concepts", true, Collections.EMPTY_SET); ConceptGraph cg = conceptDao.getConceptGraph("test"); Assert.notNull(cg); - ((ConfigurableApplicationContext)appCtx).close(); + ((ConfigurableApplicationContext) appCtx).close(); } @Test Added: ctakes/branches/ytex/ctakes-ytex/src/test/resources/org/apache/ctakes/ytex/ytex.orcl.properties URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex/src/test/resources/org/apache/ctakes/ytex/ytex.orcl.properties?rev=1556425&view=auto ============================================================================== --- ctakes/branches/ytex/ctakes-ytex/src/test/resources/org/apache/ctakes/ytex/ytex.orcl.properties (added) +++ ctakes/branches/ytex/ctakes-ytex/src/test/resources/org/apache/ctakes/ytex/ytex.orcl.properties Wed Jan 8 02:29:31 2014 @@ -0,0 +1,31 @@ +# jdbc url for database. +# Replace localhost:1521:orcl with the host, port and service name/SID of your database +# another format that works is e.g.: jdbc:oracle:thin:ytex/ytex@localhost:1521:orcl +db.url=jdbc:oracle:thin:@localhost:1521:orcl + +# oracle username and password +# user needs connect, resource, and create view privileges +db.username=ytex_test +db.password=ytex_test + +# database schema +# typically identical to username +# alternatively, the user must have access to the schema +db.schema=ytex_test + +# the schema where umls is installed +# if not specified, will default to schema from ytex +#umls.schema=umls + + +# you should not have to modify anything below +# hibernate database dialect +# specify Oracle8iDialect, Oracle9iDialect, or Oracle10gDialect +# can use Oracle10gDialect for Oracle11 +hibernate.dialect=org.hibernate.dialect.Oracle10gDialect + +db.type=orcl +db.driver=oracle.jdbc.driver.OracleDriver + +# transaction isolation level +db.isolationLevel=READ_COMMITTED