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MetaMap Transfer (MMTx) |
Rosetta Stone
MMTx Sample Installation Run:
This sample shows a successful installation of MMTx with
the Test and the 2001 strict databases being loaded. The install
program found several databases (old and new) already installed and
prompted our user with a choice of keeping or removing the old databases.
Our user elected to keep the old databases so they could continue to use
MMTx V2.0 for a while. The new databases that were found to be already
installed probably came from a failed installation and will be removed
before we add the new data. At the end, our user has decided not to install
the Data File Builder tools at this time.
Welcome to the MMTx Installation
We will be walking you through the following:
- Validating environment,
- Setting up config files, mmtxUser, and MySQL root user info,
- Creating & loading necessary databases,
- Running an initial test to verify operations,
- Optionally installing the Data File Builder.
------------------------------------
Validating environment ...
OS Info: SunOS 5.8 [sparc]
Valid version of Java found: 1.3.1_02
This script requires root privileges in MySQL!
Do you have access to these privileges[Y/y or N/n] [N]?
Verifying location of required commands ...
* shell - using /bin/sh
Done
Completed environment validation
-----------
Setting up the config files ...
Full pathname of the MMTx PARENT directory
[/net/skr1/ssa2/JGM/MMTX/new_distro/nls]:
Specify the Database Server Host name that you will be using.
The default database engine or server (MySQL or some other database)
will be located on the same machine that the MMTx sofware is on.
Database HostName [nls9]:
-- Updating hostname in config/mmtxRegistry.cfg ... Done
Completed config files setup ...
-----------
Checking for additional models to load ...
Searching for additional data models to load ...
-- No additional data models were found
Done
Completed additional models check
-----------
Setting up the mmtxUser and MySQL root user info ...
Do you wish to change the mmtxUser default password (Y/y or N/n) [N]?
-- You have elected to use the default password: 'defaultPass'
Database root user[root]:
Does MySQL have a password set for user root (Y/y or N/n) [N]?
-- Updating root info in config/mmtxRegistry.cfg ... Done
Completed mmtxUser and MySQL root user setup
-----------
Creating & loading necessary databases ...
Connection to MySQL established
- Searching for existing MMTx databases ...
-- found Old-Style 2001 strict model database (DB_01_strict)
-- found 01_custom lexicon database (MMTx_01_custom_lexicon)
-- found 01_custom strict model database (MMTx_01_custom_strict)
-- found 2001 lexicon database (MMTx_2001_lexicon)
-- found 2001 mmtx database (MMTx_2001_mmtx)
-- found 2001 strict model database (MMTx_2001_strict)
-- found 2002 lexicon database (MMTx_2002_lexicon)
-- found 2002 strict model database (MMTx_2002_strict)
-- found test lexicon database (MMTx_test_lexicon)
-- found test mmtx database (MMTx_test_mmtx)
-- found test strict model database (MMTx_test_strict)
-- found Old-Style MMTx Lexicon database (Static2001MMTxLexicon)
-- found Old-Style Basic Info database (mmtx)
Done
Databases from MMTx 2.0 have been found. We can drop them for you now
or you may drop them from MySQL later on your own.
Do you want the old style databased dropped [Y/y or N/n] [Y]?
- No Old-Style MMTx databases dropped.
Done
**************************************************************
NOTE: We will only alter remaining MMTx specific databases
if we are loading data into that specific database.
**************************************************************
- Creating new MMTx databases ...
-- Working on MMTx_test_mmtx ...
--- Dropping existing db ... Done
--- Creating and Loading db & tables ...
Wed Aug 21 03:35:17 EDT 2002 -
Creating table: semdef ... Finished in: 0:0:0.24
Loading semdef ... Finished in 0:0:0.01
Wed Aug 21 03:35:17 EDT 2002 -
Creating index: semdef_Indx
for table: semdef ... Finished in 0:0:0.23
Wed Aug 21 03:35:18 EDT 2002 -
Creating table: treecodes ... Finished in: 0:0:0.03
Loading treecodes ... Finished in 0:0:0.02
Wed Aug 21 03:35:18 EDT 2002 -
Creating index: treecodes_Indx
for table: treecodes ... Finished in 0:0:0.29
Completed Processing In: 0:0:0.83
Done
Finished - MMTx_test_mmtx
-- Working on MMTx_test_strict ...
--- Dropping existing db ... Done
--- Creating and Loading db & tables ...
Wed Aug 21 03:35:18 EDT 2002 -
Creating table: all_words ... Finished in: 0:0:0.08
Loading all_words ... Finished in 0:0:0.03
Wed Aug 21 03:35:18 EDT 2002 -
Creating index: all_words_Indx
for table: all_words ... Finished in 0:0:0.30
Wed Aug 21 03:35:19 EDT 2002 -
Creating table: concept_cui ... Finished in: 0:0:0.04
Loading concept_cui ... Finished in 0:0:0.01
Wed Aug 21 03:35:19 EDT 2002 -
Creating index: concept_cui_concept_Indx
for table: concept_cui ... Finished in 0:0:0.25
Wed Aug 21 03:35:19 EDT 2002 -
Creating index: concept_cui_cui_Indx
for table: concept_cui ... Finished in 0:0:0.22
Wed Aug 21 03:35:19 EDT 2002 -
Creating table: concept_st ... Finished in: 0:0:0.05
Loading concept_st ... Finished in 0:0:0.01
Wed Aug 21 03:35:19 EDT 2002 -
Creating index: concept_st_Indx
for table: concept_st ... Finished in 0:0:0.27
Wed Aug 21 03:35:20 EDT 2002 -
Creating table: first_words ... Finished in: 0:0:0.04
Loading first_words ... Finished in 0:0:0.01
Wed Aug 21 03:35:20 EDT 2002 -
Creating index: first_words_Indx
for table: first_words ... Finished in 0:0:0.27
Wed Aug 21 03:35:20 EDT 2002 -
Creating table: first_words_of_one ... Finished in: 0:0:0.04
Loading first_words_of_one ... Finished in 0:0:0.00
Wed Aug 21 03:35:20 EDT 2002 -
Creating index: first_words_of_one_Indx
for table: first_words_of_one ... Finished in 0:0:0.27
Wed Aug 21 03:35:20 EDT 2002 -
Creating table: first_words_of_two ... Finished in: 0:0:0.04
Loading first_words_of_two ... Finished in 0:0:0.01
Wed Aug 21 03:35:20 EDT 2002 -
Creating index: first_words_of_two_Indx
for table: first_words_of_two ... Finished in 0:0:0.24
Wed Aug 21 03:35:20 EDT 2002 -
Creating table: sui_nmstr_str ... Finished in: 0:0:0.04
Loading sui_nmstr_str ... Finished in 0:0:0.07
Wed Aug 21 03:35:21 EDT 2002 -
Creating index: sui_nmstr_str_Indx
for table: sui_nmstr_str ... Finished in 0:0:0.35
Completed Processing In: 0:0:2.62
Done
Finished - MMTx_test_strict
-- Working on MMTx_test_lexicon ...
--- Dropping existing db ... Done
--- Creating and Loading db & tables ...
Wed Aug 21 03:35:21 EDT 2002 -
Creating table: fullVars ... Finished in: 0:0:0.06
Loading fullVars ... Finished in 0:0:42.32
Wed Aug 21 03:36:03 EDT 2002 -
Creating index: varsFullIndex
for table: fullVars ... Finished in 0:1:45.04
Completed Processing In: 0:2:27.42
Done
Finished - MMTx_test_lexicon
-- Working on MMTx_2001_lexicon ...
--- Dropping existing db ... Done
--- Creating and Loading db & tables ...
Wed Aug 21 03:37:49 EDT 2002 -
Creating table: fullVars ... Finished in: 0:0:0.05
Loading fullVars ... Finished in 0:0:40.58
Wed Aug 21 03:38:29 EDT 2002 -
Creating index: varsFullIndex
for table: fullVars ... Finished in 0:1:41.91
Completed Processing In: 0:2:22.54
Done
Finished - MMTx_2001_lexicon
-- Working on MMTx_2001_mmtx ...
--- Dropping existing db ... Done
--- Creating and Loading db & tables ...
Wed Aug 21 03:40:11 EDT 2002 -
Creating table: semdef ... Finished in: 0:0:0.05
Loading semdef ... Finished in 0:0:0.01
Wed Aug 21 03:40:11 EDT 2002 -
Creating index: semdef_Indx
for table: semdef ... Finished in 0:0:0.25
Wed Aug 21 03:40:12 EDT 2002 -
Creating table: treecodes ... Finished in: 0:0:0.04
Loading treecodes ... Finished in 0:0:4.59
Wed Aug 21 03:40:16 EDT 2002 -
Creating index: treecodes_Indx
for table: treecodes ... Finished in 0:0:12.29
Completed Processing In: 0:0:17.24
Done
Finished - MMTx_2001_mmtx
-- Working on MMTx_2001_strict ...
--- Dropping existing db ... Done
--- Creating and Loading db & tables ...
Wed Aug 21 03:40:29 EDT 2002 -
Creating table: all_words ... Finished in: 0:0:0.03
Loading all_words ... Finished in 0:0:23.11
Wed Aug 21 03:40:52 EDT 2002 -
Creating index: all_words_Indx
for table: all_words ... Finished in 0:1:8.71
Wed Aug 21 03:42:01 EDT 2002 -
Creating table: concept_cui ... Finished in: 0:0:0.03
Loading concept_cui ... Finished in 0:0:6.01
Wed Aug 21 03:42:07 EDT 2002 -
Creating index: concept_cui_concept_Indx
for table: concept_cui ... Finished in 0:0:19.30
Wed Aug 21 03:42:26 EDT 2002 -
Creating index: concept_cui_cui_Indx
for table: concept_cui ... Finished in 0:0:27.95
Wed Aug 21 03:42:54 EDT 2002 -
Creating table: concept_st ... Finished in: 0:0:0.04
Loading concept_st ... Finished in 0:0:6.68
Wed Aug 21 03:43:01 EDT 2002 -
Creating index: concept_st_Indx
for table: concept_st ... Finished in 0:0:25.16
Wed Aug 21 03:43:26 EDT 2002 -
Creating table: first_words ... Finished in: 0:0:0.06
Loading first_words ... Finished in 0:0:6.77
Wed Aug 21 03:43:33 EDT 2002 -
Creating index: first_words_Indx
for table: first_words ... Finished in 0:0:19.84
Wed Aug 21 03:43:53 EDT 2002 -
Creating table: first_words_of_one ... Finished in: 0:0:0.04
Loading first_words_of_one ... Finished in 0:0:0.96
Wed Aug 21 03:43:54 EDT 2002 -
Creating index: first_words_of_one_Indx
for table: first_words_of_one ... Finished in 0:0:2.21
Wed Aug 21 03:43:56 EDT 2002 -
Creating table: first_words_of_two ... Finished in: 0:0:0.03
Loading first_words_of_two ... Finished in 0:0:3.23
Wed Aug 21 03:43:59 EDT 2002 -
Creating index: first_words_of_two_Indx
for table: first_words_of_two ... Finished in 0:0:8.29
Wed Aug 21 03:44:07 EDT 2002 -
Creating table: sui_nmstr_str ... Finished in: 0:0:0.04
Loading sui_nmstr_str ... Finished in 0:0:14.00
Wed Aug 21 03:44:22 EDT 2002 -
Creating index: sui_nmstr_str_Indx
for table: sui_nmstr_str ... Finished in 0:0:18.14
Completed Processing In: 0:4:10.70
Done
Finished - MMTx_2001_strict
Done
- Adding mmtxUser grants ... Done
Completed creating & loading necessary databases
-----------
Creating MMTx Executable ... Done
-----------
Creating BuildDataFiles Shell Script ... Done
-----------
Creating LoadDataFiles Shell Script ... Done
+--------------------------------------------+
| OPTIONAL DATA FILE BUILDER |
| |
| The DFBuilder is a component of the MMTx |
| that generates MMTx source data files |
| from raw UMLS data files which have been |
| customized either by MetaMorphysis or |
| by the addition of local data. DFBuilder |
| is needed only if you will be crafting |
| customized versions of the UMLS. |
| |
| This optional install is going to install |
| a third party package called |
| The Java Lexical Tools. |
| |
| It will ask you to confirm the |
| installation. |
| This portion of the install will take |
| a significant amount of time.(~40 minutes) |
+--------------------------------------------+
Do you want to install the Data File Builder?[Y/y or N/n] [N]?
-----------
Verifying MMTx Installation ...
CONGRATULATIONS!! You have successfully installed MMTx
Completed MMTx Validation
---------------------------------------------------------------
MMTx exists as a program at:
${MMTX_PATH}/mmtx/bin/MMTx
You have two options for running the MMTx program:
1) Add the ${MMTX_PATH}/mmtx/bin to your $PATH
environment. You can then run the MMTx program
from any location
I.e.,
> MMTx --fileName=inputFile
2) You can run the 'MMTx' program by invoking the
its absolute path
I.e.,
> /aux6/nls/mmtx_v1.1.a/mmtx/bin/MMTx --fileName=inputFile
