UCUM

Vocabulary_ID=11

The following describes the procedure to update the UCUM vocabulary  with the latest release of the source.

The load process is a complete refresh of data. All new vocabulary entieties will be added. All vocabulary entities that do not exist in the latest files set will be marked as deprecated.


1.1 Scripts Transfer

All scripts and files listed at the bottom of this page should be transferred to specially created directory (eg /data/UCUM).

 Script Name Description
11_create_schema.sql Create prestage-stage schema with tables and indexes
11_load_to_prestage_concepts.ctl  Concepts control file
11_load_concepts.sql
 Load only new concepts into concept table, add invalid code information
11_transform_row_concepts.sql   
 Convert and store in stage table concept_stage


1.2 Download data from source

            1.2.1 Download data from UCUM source

                    The most current international release is located at the following URL: http://aurora.regenstrief.org/~ucum/ucum.html

                    Note: Make sure you perform updates in chronological order. So, if you want to process a January and April release, execute the below steps for January, and after successful completion, for April.

                    Download the latest release file
                     Transfer downloaded zip file to /data/UCUM directory.

                     Latest production zip file is ~1MB in size


1.3 Build Database Schema

All tables will be located in the schema UCUM_<DateOfSourceFile> as following: UCUM_20120131
The following steps will create a schema and will grant to a schema owner appropriate permissions. 


In addition to the schema, it will create tables to load raw data:  UCUM_CONCEPTS as well as staging tables: 

CONCEPT_STAGE, CONCEPT_ANCESTOR_STAGE, 

 

CONCEPT_RELATIONSHIP_STAGE, 

 

SOURCE_TO_CONCEPT_MAP_STAGE



$ sqlplus System/<SystemPass>@DEV_VOCAB @11_create_schema.sql <UCUM_Schema> <Pass_UCUM_Schema>

Format of  UCUM_Schema should be  UCUM_YYYYMMDD (e.g.  UCUM_20120918)


1.4 Raw data load into Oracle tables


 1.4.1 Extract files from the zip archive into the current directory

        $ unzip -u UCUM.zip
      

1.4.2 Verify that the following 2 files have been created:

     UCUM_CONCEPTS.txt               (Latest file size ~1MB)

   

            1.4.3   
Load CMS raw data into Oracle. 

            Each sqlldr process will run for about 1min.

             $ sqlldr UCUM_20120918/myPass@DEV_VOCAB control=11_load_to_prestage_concepts.ctl


            1.4.5 Verify that files with extension .bad are empty, no records have been rejected.


            1.4.6 Copy data and intermediate files to backup area In this step, downloaded files will be archived to preserve source of the data. Discuss a location of backup area with your system administrator.         

                $ cp -Ru /data/UCUM/*.zip /data/backup_area ; cp -Ru /data/UCUM/*.log /data/backup_area

            1.4.7  Verify that number of records loaded is equivalent to prior production load

                     sqlplus UCUM_20120918/myPass@DEV_VOCAB

            Execute the following SQL commands:

    SELECT count(*) FROM UCUM_CONCEPTS;
            Current production row count is:     766 Rows


1.5 Loading Staging Tables from raw


1.5.1 Convert and store in staging table concepts

Loaded from raw staged data RXNCONSO into the staged data CONCEPT_STAGE

In this step we will perform substitute GUID identifiers into numerical format.

 

$  sqlplus UCUM_20120918/myPass@DEV_VOCAB @11_transform_row_concepts.sql

1.5.2  Verify that number of records loaded is equivalent to prior production load

    In this step we will verify that number of active records in staging tables is valid prior to transfer data to historical DEV schema. 

    a. Number of Records in stage table

    b. Number of records in DEV schema not deleted (active, prior load production)

    c. How many records would be added to DEV schema table

            d. How many active DEV records will be marked for deletion


    In most cases  number of records in stage (a) should be greater than number of active records in production (b) 
    In rare occasion that might not be the case. It is responsibility of the developer running the scripts to verify that that is the the valid.



     $ sqlplus  UCUM_20120918/myPass@DEV_VOCAB

 Execute the following SQL commands:

SELECT '- Num Rec in stage' AS scr, COUNT (8) cnt
  FROM CONCEPT_STAGE c
 WHERE C.VOCABULARY_ID IN (11)
UNION ALL
SELECT '- Num Rec in DEV not deleted' AS scr, COUNT (8) cnt
  FROM DEV.CONCEPT d
 WHERE d.VOCABULARY_ID IN (11) AND NVL (d.INVALID_REASON, 'X') <> 'D'
UNION ALL
SELECT '- How many records would be new in DEV added' AS scr, COUNT (8) cnt
  FROM CONCEPT_STAGE c
 WHERE C.VOCABULARY_ID IN (11)
       AND NOT EXISTS
              (SELECT 1
                 FROM DEV.CONCEPT d
                WHERE d.VOCABULARY_ID IN (11) AND c.CONCEPT_CODE = D.CONCEPT_CODE)
UNION ALL
SELECT '- How many DEV active will be marked for deletion' AS scr,
       COUNT (8) cnt
  FROM DEV.CONCEPT d
 WHERE     d.VOCABULARY_ID IN (11)
       AND NVL (d.INVALID_REASON, 'X') <> 'D'
       AND NOT EXISTS
              (SELECT 1
                 FROM CONCEPT_STAGE c
                WHERE c.VOCABULARY_ID IN (11) AND c.CONCEPT_CODE = D.CONCEPT_CODE);

Current Result:
- Num Rec in stage                                                   766
- Num Rec in DEV not deleted                                     766
- How many records would be new in DEV added            0
- How many DEV active will be marked for deletion          0

       1.5.3    Load new concepts into DEV schema concept table,mark deprecated concepts as deleted.

          Valid start date, valid end date and invalid reason are left empty for now.
          Transfer records from CONCEPT_STAGE to DEV.CONCEPT table


    $  sqlplus UCUM_20120918/myPass@DEV_VOCAB @11_load_concepts.sql




ċ
11_create_schema.sql
(7k)
Serg Vereshagin,
Oct 24, 2013, 5:17 AM
ċ
11_load_concepts.sql
(3k)
Serg Vereshagin,
Oct 24, 2013, 5:17 AM
ċ
11_load_to_prestage_concepts.ctl
(1k)
Serg Vereshagin,
Oct 24, 2013, 5:17 AM
ċ
11_transform_row_concepts.sql
(2k)
Serg Vereshagin,
Oct 24, 2013, 5:17 AM
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