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From "Tim OConnell (JIRA)" <j...@apache.org>
Subject [jira] [Commented] (CTAKES-311) v_document_cui_sent View returns no results in cTAKES-YTEX
Date Wed, 10 Sep 2014 02:37:28 GMT

    [ https://issues.apache.org/jira/browse/CTAKES-311?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=14127963#comment-14127963
] 

Tim OConnell commented on CTAKES-311:
-------------------------------------

Hi Pei - here's my attempt at creating the patch.  I've just created it for the ytex scripts
- doing a search on the cTAKES project yielded 896 matches for 'edu.mayo.bmi.core' - I'm afraid
I don't have the fortitude to attempt to patch ~900 instances of this and risk causing some
serious issues.  I'm new to Eclipse, so please let me know if the syntax of this patch isn't
correct.  As well, as I don't have access to SQL server/Oracle systems (and I haven't set
up HSQL), I haven't had a chance to validate it outside of MySQL. 

Index: ctakes-ytex/scripts/data/hsql/uima/create_view.sql
===================================================================
--- ctakes-ytex/scripts/data/hsql/uima/create_view.sql	(revision 1620506)
+++ ctakes-ytex/scripts/data/hsql/uima/create_view.sql	(working copy)
@@ -57,7 +57,7 @@
 inner join anno_contain ac on da.anno_base_id = ac.child_anno_base_id
 INNER join anno_base s
   on ac.parent_anno_base_id = s.anno_base_id
-  and s.uima_type_id in (select uima_type_id from ref_uima_type where uima_type_name = 'edu.mayo.bmi.uima.core.type.textspan.Sentence')
+  and s.uima_type_id in (select uima_type_id from ref_uima_type where uima_type_name = 'org.apache.ctakes.typesystem.type.textspan.Sentence')
 INNER JOIN document d on da.document_id = d.document_id
 ;
 
Index: ctakes-ytex/scripts/data/mssql/uima/create_view.sql
===================================================================
--- ctakes-ytex/scripts/data/mssql/uima/create_view.sql	(revision 1620506)
+++ ctakes-ytex/scripts/data/mssql/uima/create_view.sql	(working copy)
@@ -59,8 +59,8 @@
   select ac.child_anno_base_id, s.span_begin, s.span_end
   from $(db_schema).anno_contain ac 
   INNER join $(db_schema).anno_base s on ac.parent_anno_base_id = s.anno_base_id
-  where s.uima_type_id in (select uima_type_id from $(db_schema).ref_uima_type where uima_type_name
= 'edu.mayo.bmi.uima.core.type.textspan.Sentence')
-  and ac.child_uima_type_id in (select uima_type_id from $(db_schema).ref_uima_type where
uima_type_name = 'edu.mayo.bmi.uima.core.type.textsem.EntityMention')
+  where s.uima_type_id in (select uima_type_id from $(db_schema).ref_uima_type where uima_type_name
= 'org.apache.ctakes.typesystem.type.textspan.Sentence')
+  and ac.child_uima_type_id in (select uima_type_id from $(db_schema).ref_uima_type where
uima_type_name = 'org.apache.ctakes.typesystem.type.textsem.EntityMention')
 ) s on da.anno_base_id = s.child_anno_base_id
 INNER JOIN $(db_schema).v_document d on da.document_id = d.document_id
 ;
Index: ctakes-ytex/scripts/data/mysql/uima/create_view.sql
===================================================================
--- ctakes-ytex/scripts/data/mysql/uima/create_view.sql	(revision 1620506)
+++ ctakes-ytex/scripts/data/mysql/uima/create_view.sql	(working copy)
@@ -57,7 +57,7 @@
 inner join anno_contain ac on da.anno_base_id = ac.child_anno_base_id
 INNER join anno_base s
   on ac.parent_anno_base_id = s.anno_base_id
-  and s.uima_type_id in (select uima_type_id from ref_uima_type where uima_type_name = 'edu.mayo.bmi.uima.core.type.textspan.Sentence')
+  and s.uima_type_id in (select uima_type_id from ref_uima_type where uima_type_name = 'org.apache.ctakes.typesystem.type.textspan.Sentence')
 INNER JOIN document d on da.document_id = d.document_id
 ;
 
Index: ctakes-ytex/scripts/data/orcl/uima/create_view.sql
===================================================================
--- ctakes-ytex/scripts/data/orcl/uima/create_view.sql	(revision 1620506)
+++ ctakes-ytex/scripts/data/orcl/uima/create_view.sql	(working copy)
@@ -58,8 +58,8 @@
   select ac.child_anno_base_id, s.span_begin, s.span_end
   from anno_contain ac 
   INNER join anno_base s on ac.parent_anno_base_id = s.anno_base_id
-  where s.uima_type_id in (select uima_type_id from ref_uima_type where uima_type_name =
'edu.mayo.bmi.uima.core.type.textspan.Sentence')
-  and ac.child_uima_type_id in (select uima_type_id from ref_uima_type where uima_type_name
= 'edu.mayo.bmi.uima.core.type.textsem.EntityMention')
+  where s.uima_type_id in (select uima_type_id from ref_uima_type where uima_type_name =
'org.apache.ctakes.typesystem.type.textspan.Sentence')
+  and ac.child_uima_type_id in (select uima_type_id from ref_uima_type where uima_type_name
= 'org.apache.ctakes.typesystem.type.textsem.EntityMention')
 ) s on da.anno_base_id = s.child_anno_base_id
 INNER JOIN v_document d on da.document_id = d.document_id
 ;




> v_document_cui_sent View returns no results in cTAKES-YTEX
> ----------------------------------------------------------
>
>                 Key: CTAKES-311
>                 URL: https://issues.apache.org/jira/browse/CTAKES-311
>             Project: cTAKES
>          Issue Type: Bug
>          Components: ctakes-ytex
>    Affects Versions: 3.2.1
>            Reporter: Tim OConnell
>            Priority: Minor
>              Labels: patch
>             Fix For: 3.2.1
>
>   Original Estimate: 168h
>  Remaining Estimate: 168h
>
> The script for the creation of ytex's v_document_cui_sent view contains an error - in
CTAKES_HOME\bin\ctakes-ytex\scripts\data\SQL_TYPE\uima\create_view.sql
> Where the script reads '....where (`ref_uima_type`.`uima_type_name` = 'edu.mayo.bmi.uima.core.type.textspan.Sentence')))))
join `document` `d` on((`da`.`document_id` = `d`.`document_id...', the 'edu.mayo.bmi.uima...'
is the old notation for the uima_type_name that this view depends on. It should be 'org.apache.ctakes.typesystem.type.textspan.Sentence'.

> On Mon, Sep 8, 2014 at 1:55 PM, Pei Chen <chenpei@apache.org> wrote:
> Hi Tim,
> Thanks for catching that- yes, would you mind creating a jira for that?
> Even better if you can attach a patch for it (perhaps a good idea to
> search/replace on the entire project) and we can include in the next
> 3.2.1 patch...
> --Pei



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