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A.4 Instructions for Windows Users

The instructions in this section are specific to users of Windows systems.

Users of Mac OS systems should refer A.3 Instructions for Mac OS Users.

Users of other Unix based system such as Linux or Ubuntu may also find useful. However, the location of MySQL configuration files may differ and as a result some aspects of the configuration process may need to be altered.

MySQL Installation (Windows)

Info

The instruction in this section assume you are installing MySQL for the first time or have fully uninstalled an earlier installation. If MySQL is already installed you may choose to skip this section.

Note

If MySQL was installed using a different installation package, some of the configuration steps described in later sections may need to be modified.

Please refer to for detailed information about MySQL.

Install the MySQL Windows MSI installer

This is available as a free download from: https://dev.mysql.com/downloads/installer/

Note

Although the installers are 32-bit software, they will install the 64-bit version of MySQL if you are using a 64-bit system.

You can use either of the installers listed here:

  • The first installer option downloads a small package and then gets the other packages during the installation process.

  • The second installer downloads all the packages and can then continue the installation without an internet connection.

During the installation process you will be prompted to choose the setup type. The minimum recommended installation for the SNOMED CT database only required MySQL Server and MySQL Workbench so (unless you have additional requirements) select the Custom option as shown below.

Continue the process by clicking the next button.

  • You will then be prompted to specify the products and features to be installed.

  • Expand the nested list under MySQL Servers

  • Select the MySQL Server 8.0.17 (or a higher version if one is shown)

  • Click the arrow pointing to the right

  • This will add the MySQL Server to the list of Products/Features To Be Installed.

  • When both Server and Workbench are in the right-hand list, click the Next button.

At this point you may see a message indicating a requirement for a Visual C++ Redistributable package as shown below.

If you see this message you should download and install the required package from before proceeding.

  • Further notes on this process are provided on .

  • Select the Standalone MySQL Server option.

  • Select the Development Computer option

  • Select the Legacy Authentication Method unless you will be using the database for other purposes that require greater security.

  • Accept or apply the following Server Connection settings

During the installation of MySQL 8.0.x on Windows you may see a message indicating that you need to install or update to the Microsoft Visual C++ 2015 Redistributable package.

  • If required this can be obtained as a free download from .

  • Click the Download button.

  • Choose the x64 version if you have a 64-bit computer or the x86 if you have an older 32-bit computer.

  • Continue an install the package.

  • The return to the MySQL installation process.

  • In the main Window menu locate the Command Prompt Desktop app.

  • Right-click on this item to show the drop down menu

  • Select the Run as administrator option.

    • This is necessary as some steps below require administrator status.

  • Adjust the path as necessary if you have not installed the SnomedRfsMySql folder in the root folder on drive C.

  • Type the following command to stop the MySQL server (if it is running).

  • Type the following command to run the configuration process. This command runs a script that updates the MySQL server configuration.

  • Type the following command to restart the MySQL server

  • Go to

  • Download either the appropriate version for your system (i.e. either 32-bit or 64-bit)

  • Open and run the downloaded file

    • This will have a name like "strawberry-perl-5.30.0.1-64bit.msi" (version numbers may differ).

  • Go through the installation process

    • Read and accept the license.

  • When the installation is complete, you can test the installation by running the following command in a newly opened Command Prompt.

  • If Strawberry Perl is correctly installed the result should the following message.

  • In the main Window menu locate the Command Prompt Desktop app.

  • Right-click on this item to show the drop down menu

  • Select the Run as administrator option.

    • This is necessary as some steps below require adminstrator status.

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

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 (win) 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.

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

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, you will be offered the option to reuse the existing transitive closure. If you accept the options, there will be no delay while the rebuild occurs.

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.

  • Depending on system performance the process may take between 20 and 90 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!

This issue usually results from an incorrect service name reference. This arises when the MySQL Workbench contains a reference to an older service name (e.g. mysql), whereas MySQL Server 8.0.x uses the service name MySQL80.

  • Open the Services Desktop app from the Windows menu.

  • Then search the list of services to identify the name of the MySQL service

  • Open MySQL Workbench.

  • In the Server menu select Management Access Settings.

  • In the Manage Server Connections dialog update the Window Service Name to match the service name identified earlier.

We recommend that you install in the default installation path (e.g. "C:\Strawberry)

Uses the specified script to control the process of loading the SNOMED CT data into the database. Scripts keys have two parts a prefix and suffix separated by an underscore. The prefix indicates the kind of action:

  • create : Create a new database and load the data from the specified version.

  • update : Update the views and procedures in the database without recreating the database or reloading the the tables.

  • extend : Extend the database by loading data from another package to the existing database.

Release package path

You must enter the full path of the release package folder or release package zip archive.

You will not be prompted for this if you select an update script option.

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.

Database name

Leave blank to accept the default

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.

MySQL username

Leave blank to accept the default

The default is root.

Enter your MySQL username

The username chosen must be an account with administrator access rights enabling database creation.

Now it is time to open MySQL Workbench to view your SNOMED CT database.

Prompt

Response options

Notes

Loader script identifying tag

Leave blank to accept the default

Recommended option Uses the default create_latest script in the SnomedRfsMySql package.

Download and Run your Chosen MySQL Installer

Select MySQL Server for Installation

Checking Requirements

Continue with the Installation Process

Note

The Configuration File setting must refer to: C:\ProgramData\MySQL\MySQL Server 8.0\my.ini

  • This is a file that will be modified in the to configure the server so that it will correctly load the SNOMED CT release files.

Warning

Be sure to remember your root password this as you will need it for access to the database.

Meeting Requirements for MySQL Installation (Windows)

Installing or Updating Microsoft Visual C++

Set Required MySQL Configuration (Windows)

Open the Command Prompt in Administrator Mode

Run the Following Commands from the Command Prompt

Install a Perl Processor

Before importing the SNOMED CT data the import process creates a "transitive closure file". This allows this file to imported to create a transitive closure table that supports rapid subtype testing. The process that creates the transitive closure file from other release files uses the Perl language. Windows does not include a Perl language interpreter. Strawberry Perl is a widely used free Perl environment for Window and this should be installed on your computer before running the import script.

Download Strawberry Perl

Install Strawberry Perl

Warnings

Do not install Strawberry Perl within the SnomedRfsMySql folder as the installation will be removed by future updates to the SnomedRfsMySql package. Ideally you should install Strawberry Perl on drive C.

If you need to install Perl on another disk or network drive (click here)

If Perl is installed on a network or a secondary drive (i.e. not drive C), you need to specify that location. To do this create (or edit) a plain text file called perlPath.cfg file in the SnomedRfsMySql\win folder. This file must contain a single line of text specifying the full path of the perl.exe file (for example the file might contain the text "D:\AddedSoftware\Strawberry\perl\bin\perl.exe")

If the import script cannot find perl.exe at the location specified in the perlPath.cfg file, that configuration file will be deleted and will need to be recreated with the correct full path to perl.exe.

Check the Installation

Tip

If the message above does not appear, check the following:

  1. The command line above assumes that SnomedRfsMySql is installed in the C:\ root folder. If this is not the case, repeat the test with the correct path to SnomedRdsMySql.

  2. Ensure that you have closed all open command line windows. Then open a new command line window and run the test command again.

  3. If neither of the above steps corrects corrects the issue, it suggest a problem with the installation. Consider uninstalling and reinstalling Strawberry Perl to correct the issue.

Load Release Package into MySQL (Windows)

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 Command Prompt in Administrator Mode

Change Directories to the SnomedRfsMySql Folder

Start the SNOMED CT Loader Script for MySQL

Respond to Prompts from the Script

Wait for the Database Password Prompt

Respond to the Database Password Prompt

Wait for the Load Process to Complete

Troubleshooting (Windows)

This section contains notes on some known issues with configuration of MySQL for use with Windows and the actions required to resolve them.

MySQL Workbench Unable to Start or Stop MySQL Server (Windows)

Check the Name of the Required Service

Correct the Reference in MySQL Workbench

https://www.microsoft.com/en-us/download/details.aspx?id=48145
Meeting Requirements for MySQL Installation (Windows)
https://www.microsoft.com/en-us/download/details.aspx?id=48145
http://strawberryperl.com
Provide Feedback
A.3 Instructions for Mac OS Users
https://www.mysql.com/products/community/

Enter the name of one of the available scripts (these are listed above the prompt)

The suffix indicates the edition and version to which this applies:
  • latest : The most recent International Edition package

  • yyyymmdd: The International Edition for the stated year month and day

  • packageyyyymmdd: The identified Edition or Package for the stated year month and day.

If the zip file is found it is unzipped and the resulting folder is used.