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 A.3 Instructions for Mac OS Users 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)
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.
Download and Run your Chosen MySQL Installer
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.
Select MySQL Server for Installation
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.
Checking Requirements
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 https://www.microsoft.com/en-us/download/details.aspx?id=48145 before proceeding.
Further notes on this process are provided on Meeting Requirements for MySQL Installation (Windows).
Continue with the Installation Process
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
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++
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 https://www.microsoft.com/en-us/download/details.aspx?id=48145.
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.
Set Required MySQL Configuration (Windows)
Open the Command Prompt in Administrator Mode
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.
Run the Following Commands from the Command Prompt
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
Install a Perl Processor
Download Strawberry Perl
Download either the appropriate version for your system (i.e. either 32-bit or 64-bit)
Install Strawberry Perl
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.
We recommend that you install in the default installation path (e.g. "C:\Strawberry)
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.
Check the Installation
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.
Tip
If the message above does not appear, check the following:
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.
Ensure that you have closed all open command line windows. Then open a new command line window and run the test command again.
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
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.
Change Directories to the SnomedRfsMySql Folder
You must change directories to the SnomedRfsMySql folder before starting the loader script.
Start the SNOMED CT Loader 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 (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.
Respond to Prompts from the Script
You will be prompted to enter the following data when the script is run.
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.
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. 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.
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.
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.
If the zip file is found it is unzipped and the resulting folder is used.
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.
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, 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.
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 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!
Now it is time to open MySQL Workbench to view your SNOMED CT database.
Troubleshooting (Windows)
MySQL Workbench Unable to Start or Stop MySQL Server (Windows)
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.
Check the Name of the Required Service
Open the Services Desktop app from the Windows menu.
Then search the list of services to identify the name of the MySQL service
Correct the Reference in MySQL Workbench
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.
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