Read

Vocabulary_ID=17

The following describes the procedure to update the READ 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/Read).

Script Name	Description
17_create_schema.sql	Create prestage-stage schema with tables and indexes
17_JJ_vocab_17.zip	JJ mapping sample data file
17_JJ_vocab_17.ctl	JJ mapping control file
17_transform_row_maps.sql	Convert and store in stage table SOURCE_TO_CONCEPT_MAP_STAGE
17_load_maps.sql	Load only new maps into SOURCE_TO_CONCEPT_MAP table, add invalid code information

1.2 Download data from source

1.2.1 Download data from JJ source

Usually a current internaitonal release is sent by e-mail by the analyst of the company JJ, responsible for the data.
File sample JJ_vocab_17.zip can be downloaded in the section «Add files» at the end of this page

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 (e.g. JJ_vocab_17.zip)

Transfer downloaded zip file to /data/Read directory.
Latest production zip file is ~1,6MB in size

Note: For the rest of the document we will be referring to current schema as READ_20140131 you would have to adjust this entry to correspond to current release date file.

1.3 Build Database Schema

All tables will be located in the schema READ_<DateOfSourceFile> as following: READ_20140131
The following steps will create a schema and will grant to a schema owner appropriate permissions.

In addition to the schema, it will create table to load raw data: JJ_VOCAB_17 as well as staging tables:

CONCEPT_STAGE, CONCEPT_ANCESTOR_STAGE,

CONCEPT_RELATIONSHIP_STAGE,
SOURCE_TO_CONCEPT_MAP_STAGE

$ sqlplus System/<SystemPass>@DEV_VOCAB @17_create_schema.sql <READ_Schema> <Pass_READ_Schema>

Format of READ_Schema should be READ_YYYYMMDD (e.g. READ_20140131 )

Staging tables match Vocabulary schema version 4.0 with slight modification. Modifications made to the tables are:

CONCEPT_STAGE.CONCEPT_ID is nullable

SOURCE_TO_CONCEPT_MAP_STAGE

.SOURCE_TO_CONCEPT_MAP_ID is nullable

CONCEPT_RELATIONSHIP_STAGE

.REL_ID is nullable

1.4 Raw data load into Oracle tables

1.4.1 Extract files from the zip archive into the current directory

$ unzip -u JJ_vocab_17.zip

1.4.2 Verify that the following file have been created:

JJ_vocab_17.csv (Latest file size ~4,7MB)

1.4.3 Load FDA raw data into Oracle.

This sqlldr process will run for about 1min.

$ sqlldr READ_20140131/myPass@DEV_VOCAB control=17_JJ_vocab_17.ctl

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

1.4.5 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/READ/*.zip /data/backup_area ; cp -Ru /data/READ/*.log /data/backup_area

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

$ sqlplus READ_20140131/myPass@DEV_VOCAB

Execute the following SQL commands:

SELECT count(*) FROM JJ_VOCAB_17;

Current production row count is: 8,3764 Rows

1.5 Loading Staging Tables from raw

1.5.1 Convert and store in staging table maps

Loaded from raw staged data JJ_VOCAB_17 into the staged data SOURCE_TO_CONCEPT_MAP_STAGE

$ sqlplus READ_20140131/myPass@DEV_VOCAB @17_transform_row_maps.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 READ_20140131/myPass@DEV_VOCAB

Execute the following SQL commands:

SELECT '- Num Rec in stage' AS scr, COUNT (8) cnt
FROM SOURCE_TO_CONCEPT_MAP_STAGE c
WHERE c.SOURCE_VOCABULARY_ID IN (17)
UNION ALL
SELECT '- Num Rec in DEV not deleted' AS scr, COUNT (8) cnt
FROM DEV.SOURCE_TO_CONCEPT_MAP d
WHERE     d.SOURCE_VOCABULARY_ID IN (17)
       AND D.TARGET_VOCABULARY_ID IN (01)
       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 SOURCE_TO_CONCEPT_MAP_STAGE c
WHERE c.SOURCE_VOCABULARY_ID IN (17) AND c.TARGET_VOCABULARY_ID IN (01)
       AND NOT EXISTS
                  (SELECT 1
                     FROM DEV.SOURCE_TO_CONCEPT_MAP d
                    WHERE     d.SOURCE_VOCABULARY_ID IN (17)
                          AND c.SOURCE_CODE = D.SOURCE_CODE
                          AND d.SOURCE_VOCABULARY_ID = c.SOURCE_VOCABULARY_ID
                          AND d.MAPPING_TYPE = c.MAPPING_TYPE
                          AND d.TARGET_CONCEPT_ID = c.TARGET_CONCEPT_ID
                          AND d.TARGET_VOCABULARY_ID = c.TARGET_VOCABULARY_ID)
UNION ALL
SELECT '- How many DEV active will be marked for deletion' AS scr,
       COUNT (8) cnt
FROM DEV.SOURCE_TO_CONCEPT_MAP d
WHERE     d.SOURCE_VOCABULARY_ID IN (17)
       AND D.TARGET_VOCABULARY_ID IN (01)
       AND NVL (d.INVALID_REASON, 'X') <> 'D'
       AND d.VALID_START_DATE <
              TO_DATE (
                 SUBSTR (USER, REGEXP_INSTR (USER, '_[[:digit:]]') + 1, 256),
                 'YYYYMMDD')
       AND NOT EXISTS
                  (SELECT 1
                     FROM SOURCE_TO_CONCEPT_MAP_STAGE c
                    WHERE     c.SOURCE_VOCABULARY_ID IN (17)
                          AND c.SOURCE_CODE = D.SOURCE_CODE
                          AND d.SOURCE_VOCABULARY_ID = c.SOURCE_VOCABULARY_ID
                          AND d.MAPPING_TYPE = c.MAPPING_TYPE
                          AND d.TARGET_CONCEPT_ID = c.TARGET_CONCEPT_ID
                          AND d.TARGET_VOCABULARY_ID = c.TARGET_VOCABULARY_ID)
       AND EXISTS
              (SELECT 1
                 FROM SOURCE_TO_CONCEPT_MAP_STAGE c
                WHERE     d.SOURCE_CODE = c.SOURCE_CODE
                      AND d.SOURCE_VOCABULARY_ID = c.SOURCE_VOCABULARY_ID
                      AND d.MAPPING_TYPE = c.MAPPING_TYPE
                      AND d.TARGET_VOCABULARY_ID = c.TARGET_VOCABULARY_ID);

Current Result:

- Num Rec in stage       62800

- Num Rec in DEV not deleted           54867

- How many records would be new in DEV added        3893

- How many DEV active will be marked for deletion    312

   1.5.3   Load new maps 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 SOURCE_TO_CONCEPT_MAP_STAGE to DEV.SOURCE_TO_CONCEPT_MAP table

   $ sqlplus READ_20140131/myPass@DEV_VOCAB @17_load_maps.sql