wenx999 / ytex Goto Github PK

What steps will reproduce the problem?
1. Download ytex
2. Unzip archive

What is the expected output? What do you see instead?
A top-level "ytex" directory should be created. Instead a number of directories 
are created that pollute the current directory where the zip archive is located

What version of the product are you using? On what operating system?
0.3

What steps will reproduce the problem?
1. Create UMLS MySql DB
2. Install ytex 0.5 per instructions
3. Script hangs at the setting up umls_aui_fword table. I have given it >2 days 
to run. When looking at mysql process list, the ytex user account only logs in 
once to create the table and doesn't login again. So the mysql settings are 
correct as the script can access the db but I can't seem to get it to progress.

What version of the product are you using? On what operating system?
0.5 on RedHat Enterprise Linux 6.2


Please provide any additional information below.

Of Note, I sucessfully installed this on Win7 machine without issue but I need 
this on the Linux server for further testing.

Any help would be greatly appreciated.

What steps will reproduce the problem?
1. Open CPE 
2. Set descriptor at 
yhome/config\desc\ytex\drugnerdesccollection_processing_engine/DrugNER_PlainText
_CPE.xml 
3. Set analysis_batch=“test” in Dbconsumer 
4. add analysis_engine DrugAggregatePlaintextProcessor Run.


What is the expected output? What do you see instead?
All CUIs including both medicalEventMention and  EntityMention should be seen 
in the database tables v_document_ontoanno and/or v_document_cui_sent. But only 
the latter were. 
For example, ibuprofen (C0020740), appeared in the text input file, cehcked and 
it is in my umls database, and it even also appeared  when view the analysis 
result in annotation viewer, but either of the two fore mentioned mysql tables 
contain this cui. 

What version of the product are you using? On what operating system?
Ytex0.8 and UMLS2012AB level 0. 

Please provide any additional information below.

Maybe it is hiding in some other tables that I did not go into. But I would 
rather them to be included in the above two tables too for ease of reference in 
future. 

ytex crashed on a set of notes because of out of range date times.  We changed 
the tstamp field in ytex.anno_date table from 'datetime' data type to 
'datetime2' data type.  Problem fixed.

What steps will reproduce the problem?
1.cd  YTEX_HOME\examples\fracture\cui
2 ..\..\..\setenv.cmd 
3 java %JAVA_OPTS% ytex.kernel.SparseDataExporterImpl -prop export.xml -type 
sparsematrix

What is the expected output? What do you see instead?

A non-null table from the export.xml operation in the cui folder. 

What version of the product are you using? On what operating system?

Ytex V08 on Window 7. 

Please provide any additional information below.

It turned out that in the export.xml file, there is mysql query with condition 
where certainty<>-1 but the table ytex.v_document_ontoanno does not have the 
column. Instead, the table has a polarity column. Change certainty to polarity 
can export a table correctly. 

Is this a bug?