ega-ingestion

Requirements

1. Java 8 (OpenJDK)
2. Maven
3. SAMLtools
4. Credentials

Installation of SAMtools

wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2
tar xjvf samtools-1.9.tar.bz2 && cd samtools-1.9
make && sudo make install

Credentials

We don't store credentials in our application.properties files. Credentials are instead stored in our ~/.m2/settings.xml file, for example, like this:

<profile>
  <id>localPostgresDatabase</id>
  <activation>
      <activeByDefault>true</activeByDefault>
  </activation>
  <properties>
      <ega.ukbb.temp.ingestion.datasource.re-encrypt.url>jdbc:postgresql://localhost:5432/...</ega.ukbb.temp.ingestion.datasource.re-encrypt.url>
      <ega.ukbb.temp.ingestion.datasource.re-encrypt.username>...</ega.ukbb.temp.ingestion.datasource.re-encrypt.username>
      <ega.ukbb.temp.ingestion.datasource.re-encrypt.password>...</ega.ukbb.temp.ingestion.datasource.re-encrypt.password>
  </properties>
</profile>

Most of the secret values (for the properties above) can be found in the credentials.txt file in the Vault.

Compile

mvn clean test install

Run

Currently, there are 4 "sub-projects": file-manager, file-discovery, file-encryption-processor, file-re-encryption-processor.
An example of running one of them:

cd file-re-encryption-processor
mvn spring-boot:run