Trouble Report Ticket 28

Subject: word, strings, and concepts tables are empty (size 0)
Creator: 28
Created: 2012-09-26 20:44:59
Transaction: 324
Parent: 0
MessageId: [email redacted]
Filename: 
ContentType: text/plain
ContentEncoding: none

Content: 
         >Category: mmtxT
         >Synopsis: word, strings, and concepts tables are empty (size 0)
         >Confidential: no
         >Severity: serious
         >Priority: medium
         >Class: sw-bug
         >Submitter-Id: mmtxWeb
         >Release: 
         >Environment:
         >Operating System - MetaMap: 
         >OS Version - Leopard
         >Java Version - Java 1.6
         >MySQL Version - 
         >Description:
         Hi MetaMap Developers,
         
         I am making progress using the DFB for non UMLS ontologies. I am working on OSX 10.8.2. I have completed steps (from table 8 of the documentation) BuildDataFiles, 01CreateWorkFiles, 02Supress, 03FilterPrep, 04FilterStrict/Relaxed and I have having problems with 05GenerateMWIFiles.
         
         When I execute ./05GenerateMWIFiles, the files are created, but they are empty, nothing is inside them. It seems that this line in 0Generate2 isn't working for me.
         "glean_mrcon -csw $MRCON_FILTERED $PWD/0filter.0 $PWD/words.gleaned $PWD/strings.gleaned $PWD/concepts.gleaned" 
         
         0Generate1 works and the files contain what they are supposed to. Here is my command line going line by line through 0Generate2:
         
         After 0Generate1:
         [funky:SO/01metawordindex/model.relaxed] funky% pwd
         /Users/funky/Desktop/Code/public_mm_11/sourceData/SO/01metawordindex/model.relaxed
         [funky:SO/01metawordindex/model.relaxed] funky% ls -la
         total 1448
         drwxr-xr-x   8 funky  staff     272 Sep 24 12:03 .
         drwxr-xr-x  33 funky  staff    1122 Sep 24 11:47 ..
         -rw-r--r--@  1 funky  staff    6148 Sep 24 12:03 .DS_Store
         -rw-r--r--   1 funky  staff  142668 Sep 24 11:47 con_cui
         -rw-r--r--   1 funky  staff    5284 Sep 24 11:47 con_sui
         -rw-r--r--   1 funky  staff  142560 Sep 24 11:47 cui_sui.txt
         -rw-r--r--   1 funky  staff  285759 Sep 24 11:47 mrcon.filtered
         -rw-r--r--   1 funky  staff  147952 Sep 24 11:47 sui_cui.txt
         
         Starting line by line 0Generate2:
         [funky:SO/01metawordindex/model.relaxed] funky% touch 0filter.0
         
         [funky:SO/01metawordindex/model.relaxed] funky% glean_mrcon -csw /Users/funky/Desktop/Code/public_mm_11/sourceData/SO/01metawordindex/model.relaxed/mrcon.filtered /Users/funky/Desktop/Code/public_mm_11/sourceData/SO/01metawordindex/model.relaxed/0filter.0 /Users/funky/Desktop/Code/public_mm_11/sourceData/SO/01metawordindex/model.relaxed/words.gleaned /Users/funky/Desktop/Code/public_mm_11/sourceData/SO/01metawordindex/model.relaxed/strings.gleaned /Users/funky/Desktop/Code/public_mm_11/sourceData/SO/01metawordindex/model.relaxed/concepts.gleaned
         
         Glean mrcon
         
         glean_mrcon (2011AA)
         
         Control options:
           first_term_is_concept
           generate_CUIs
           generate_strings
           generate_words
         Processing /Users/funky/Desktop/Code/public_mm_11/sourceData/SO/01metawordindex/model.relaxed/mrcon.filtered and /Users/funky/Desktop/Code/public_mm_11/sourceData/SO/01metawordindex/model.relaxed/0filter.0 --> /Users/funky/Desktop/Code/public_mm_11/sourceData/SO/01metawordindex/model.relaxed/words.gleaned, /Users/funky/Desktop/Code/public_mm_11/sourceData/SO/01metawordindex/model.relaxed/strings.gleaned, and /Users/funky/Desktop/Code/public_mm_11/sourceData/SO/01metawordindex/model.relaxed/concepts.gleaned.
         Compiling file filter_pairs.pl
         
         
         ################################################################################
         ################################################################################
         
         Generating Concepts:  YES
         Generating Strings:   YES
         Generating Words:     YES
         
         ################################################################################
         ################################################################################
         
         
         After glean_mrcon (files created are empty):
         [funky:SO/01metawordindex/model.relaxed] funky% ls -la
         total 1448
         drwxr-xr-x  13 funky  staff     442 Sep 24 12:05 .
         drwxr-xr-x  33 funky  staff    1122 Sep 24 11:47 ..
         -rw-r--r--@  1 funky  staff    6148 Sep 24 12:03 .DS_Store
         -rw-r--r--   1 funky  staff       0 Sep 24 12:05 0filter.0
         -rw-r--r--   1 funky  staff  142668 Sep 24 11:47 con_cui
         -rw-r--r--   1 funky  staff    5284 Sep 24 11:47 con_sui
         -rw-r--r--   1 funky  staff       0 Sep 24 12:05 concepts.gleaned
         -rw-r--r--   1 funky  staff  142560 Sep 24 11:47 cui_sui.txt
         -rw-r--r--   1 funky  staff       0 Sep 24 12:05 filter_pairs.pl
         -rw-r--r--   1 funky  staff  285759 Sep 24 11:47 mrcon.filtered
         -rw-r--r--   1 funky  staff       0 Sep 24 12:05 strings.gleaned
         -rw-r--r--   1 funky  staff  147952 Sep 24 11:47 sui_cui.txt
         -rw-r--r--   1 funky  staff       0 Sep 24 12:05 words.gleaned
         
         Thanks,
         [User redacted]
         >How-To-Repeat:
         
         >Unformatted:

Subject: 
Creator: 28
Created: 2012-09-26 20:47:16
Transaction: 328
Parent: 0
MessageId: [email redacted]
Filename: 
ContentType: text/html
ContentEncoding: none

Content: 
         It looks like you need the GNU version of SED and GNU coreutils.  You
         can either download and compile the programs from source or get them
         from the FINK project (http://www.finkproject.org/) or Mac Ports
         (http://www.macports.org/).
         
         See also:
             http://metamap.nlm.nih.gov/README_macosx.html