Data import

The source code repository contains a mysql data import script that loads loci from IMGT/HLA nomenclature version 3.18.0 (as hosted at gl.nmdp.org, e.g. https://gl.nmdp.org/imgt-hla/3.18.0/locus/0) and the Sequence Ontology as terms (e.g. http://purl.obolibrary.org/obo/SO:0000000).

The source code repository also contains a perl script that extracts the sequence features from the IMGT/HLA hla.xml file and registers them against the service.

To create the required database tables in feature database on host featuredb and populate run the following mysql commands.

mysql -u root -p -h featuredb feature < service-jdbi/src/main/sql/mysql-drop.sql
mysql -u root -p -h featuredb feature < service-jdbi/src/main/sql/mysql-create.sql
mysql -u root -p -h featuredb feature < service-jdbi/src/main/sql/mysql-load-imgt-hla.sql
mysql -u root -p -h featuredb feature < service-jdbi/src/main/sql/mysql-load-hgnc.sql
mysql -u root -p -h featuredb feature < service-jdbi/src/main/sql/mysql-load-sequence-ontology.sql 

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For Developers

Before you import the data you must have the feature service up and running. For instructions on how to get the service up and running refer to the Docker Depolyment page.

• The phpMyAdmin interface is should then be available on port 8080
  • http://localhost:8080

Logging In

Upon reaching the phpMyAdmin interface you will be prompted for a login.

The username = root
The password = supersecretpwd

Once logged in you will see the phpMyAdmin interface. You must click on feature seen in the sidebar on the left before you are able to import any data.

Importing Files

Importing files from here is really simple. Find the folder containing the sql files to import. They can be found here service-feature/service-jdbi/src/main/sql/ and drag the files into the phpMyAdmin window in the same order as seen in the above mysql commands.

You can also import files by selecting the import tab on the feature page and browsing for the sql files on your computer.