SQL Practical Guide

Search

SNOMED CT Document Library

    Loading...

Page tree

You are viewing an old version of this page. View the current version.

Compare with Current View Page History

Version 1 Current »

Disk Space

Before running the SNOMED CT load script, ensure you have at least 10Gb of free disk space. Once the load is completed 4Gb can be released by deleting the Release package folder and zip file.

The following figures apply to the SNOMED CT International Release package 2019-07-31.

  • Release Package zip file: 0.5 Gb
  • Release Package folder: 3.5 Gb
  • Installed database up to: 5.5 Gb

Open the Terminal Application

Change Directories to the SnomedRfsMySql Folder

You must change directories to the SnomedRfsMySql folder before starting the loader script.

cd "$HOME/SnomedRfsMySql"

Start the SNOMED CT Loaded Script for MySQL

As shown above you must be in the SnomedRfsMySql folder to run the loader script. Additionally as shown below you must include the name of the subfolder (bash) when running the loader script. The script may not run correctly if called from a different current folder or without the including the subfolder name.

bash/snomed_load_mysql

Respond to Prompts from the Script

You will be prompted to enter the following data when the script is run.

PromptResponse optionsNotes

Release folder path

As noted above the prompt the release folder can be specified in any of the following ways:

  • Full path to release package zip archive (or unzipped folder)
  • Name of release package zip archive (or unzipped folder) in: $HOME/SnomedCT_ReleaseFiles
  • Blank for most recent previously loaded release file

The path specified must point to a release package zip archive or an unzipped release package folder.

  • There is no need to include the .zip extension when referring to a release package archive or folder.
    • The script first looks for an unzipped release folder with the relevant name.
    • If the folder is not found the script looks for a zip archive with the same name plus the .zip extension.
    • If the zip file is found it is unzipped and the resulting folder is used.

Database name

Leave blank

Default option

  • Uses the database name snomedct.
  • If the snomedct database already exists, it will be dropped (deleted) and recreated.
Specify a name (must begin with the letter s followed by lowercase letters and/or digits)

Uses the database name provided.

  • Using different names allows several SNOMED CT databases to co-exist (e.g. for different Editions)
  • Each SNOMED CT database will use about 5Gb of disk space ... so using different names may fill your available disk space!
  • If the named database already exists, it will be dropped (deleted) and recreated.

Loader script identifying tag

Leave blankRecommended option
Uses the default VP_latest script in the SnomedRfsMySql package.
Enter the name of one of the available scripts (these are listed above the prompt)Uses the specified script to control the process of loading the SNOMED CT data into the database.
In future, the SnomedRfsMySql package may include several scripts to support different features or different SNOMED CT Editions.
MySQL usernameLeave blank to accept the default

The first time you use the script the default is root.
After that the default is the most recent MySQL user name that you specified when running the script.

Enter your MySQL usernameThe username chosen must be an account with administrator access rights enabling database creation.

Wait for the Database Password Prompt

Before the creating the database the script generates an additional release file containing the transitive closure (this is used to optimize testing and listing of subtypes). This may take between 2 and 5 minutes to complete.

  • If you rerun the loader script again on the same release, the script will reuse the existing transitive closure. If you accept the options, there will be no delay while the rebuild occurs.

Respond to the Database Password Prompt

When the script starts to access MySQL you will then be prompted for your database password.

  • Note that the required password here is the password associated with your MySQL account. 

  • As noted earlier the account used for the SNOMED CT load process must have appropriate access permissions and its username should match your Mac login name.

Wait for the Load Process to Complete

  • Depending on system performance the process may take between 20 and 45 minutes to complete. It may take longer with National Editions that contain additional content.
    • As the MySQL script runs it will report progress on the screen. Some steps take much longer than others. For example, loading data into the database tables and adding or building indexes take much longer than any of the other steps. So if the message about these steps are showing for a long time don't worry. Let the process continue.
  • When the script completes, scroll back up the command window to check for any ERROR reports for MySQL ... there should not be any!
  • Now it is time to open MySQL Workbench to view your SNOMED CT database.




Feedback
  • No labels