Connect to Thrift
Learn about the DNAnexus Thrift server, a service that allows JDBC and ODBC clients to run Spark SQL queries.
About the DNAnexus Thrift Server
The DNAnexus Thrift server connects to a high availability Apache Spark cluster integrated with the platform. It leverages the same security, permissions, and sharing features built into DNAnexus.
Connecting to Thrift Server
To connect to the Thrift server, we need the following:
The JDBC URL:
AWS US (East): jdbc:hive2://query.us-east-1.apollo.dnanexus.com:10000/;ssl=true AWS London (UKB): jdbc:hive2://query.eu-west-2.apollo.dnanexus.com:10000/;ssl=true Azure US (West): jdbc:hive2://query.westus.apollo.dnanexus.com:10001/;ssl=true;transportMode=http;httpPath=cliservice AWS Frankfurt (General): jdbc:hive2://query.eu-central-1.apollo.dnanexus.com:10000/;ssl=trueNote: Azure UK South (OFH) region does not support access to Thrift.
We support the following format of the username:
TOKEN__PROJECTID : TOKEN is DNAnexus user generated token and PROJECTID is a DNAnexus project ID used as the project context (when you create databases). Note the double underscore between the token and the project ID.
Both the Thrift server that the user wants to connect to and the project must be from the same region.
Generate a DNAnexus Platform Authentication Token
See the Authentication tokens page.
Getting the Project ID
Navigate to https://platform.dnanexus.com and login using your username and password.
Go to Projects -> your project -> Settings -> Project ID and click on Copy to Clipboard.
Using Beeline
Beeline is a JDBC client bundled with Apache Spark that can be used to run interactive queries on the command line.
Installing Apache Spark
You can download Apache Spark 3.5.2 for Hadoop 3.x from here.
tar -zxvf spark-3.5.2-bin-hadoop3.tgzYou need to have Java installed in your system PATH, or the JAVA_HOME environment variable pointing to a Java installation.
Single Command Connection
If you already have beeline installed and all the credentials, you can quickly connect with the following command:
<beeline> -u <thrift path> -n <token>__<project-id>In the following AWS example, note that some characters are escaped (; with \)
$SPARK_HOME/bin/beeline -u jdbc:hive2://query.us-east-1.apollo.dnanexus.com:10000/\;ssl=true -n yourToken__project-xxxxNote that the command for connecting to Thrift is different for Azure, as seen below:
$SPARK_HOME/bin/beeline -u jdbc:hive2://query.westus.apollo.dnanexus.com:10001/\;ssl=true\;transportMode=http\;httpPath=cliservice -n yourToken__project-xxxxRunning Beeline Guided Connection
The beeline client is located under $SPARK_HOME/bin/.
cd spark-3.5.2-bin-hadoop3/bin
./beelineConnect to beeline using the JDBC URL:
$ beeline> !connect jdbc:hive2://query.us-east-1.apollo.dnanexus.com:10000/;ssl=true
Enter username: <TOKEN__PROJECTID>
Enter password: <empty - press RETURN>Once successfully connected, you should see the message:
Connected to: Spark SQL (version 3.5.2)
Driver: Hive JDBC (version 2.3.9)
Transaction isolation: TRANSACTION_REPEATABLE_READQuerying in Beeline
You are now connected to the Thrift server using your credentials and will be able to see all databases to which you have access to within your current region.
0: jdbc:hive2://query.us-east-1.apollo.dnanex> show databases;
+---------------------------------------------------------+--+
| databaseName |
+---------------------------------------------------------+--+
| database_fj7q18009xxzzzx0gjfk6vfz__genomics_180718_01 |
| database_fj8gygj0v10vj50j0gyfqk1x__af_result_180719_01 |
| database_fj96qx00v10vj50j0gyfv00z__af_result2 |
| database_fjf3y28066y5jxj2b0gz4g85__metabric_data |
| database_fjj1jkj0v10p8pvx78vkkpz3__pchr1_test |
| database_fjpz6fj0v10fjy3fjy282ybz__af_result1 |
+---------------------------------------------------------+--+You can query using the unique database name including the lowercase database ID, for example, database_fjf3y28066y5jxj2b0gz4g85__metabric_data. If the database is within the same username and project you used to connect to the Thrift server, you can query using only the database name, for example, metabric_data. If the database is located outside the project, you will need to use the unique database name.
0: jdbc:hive2://query.us-east-1.apollo.dnanex> use metabric_data;You may also find databases stored in other projects if you specify the project context in the LIKE option of SHOW DATABASES using the format '<project-id>:<database pattern>' like so:
0: jdbc:hive2://query.us-east-1.apollo.dnanex> SHOW DATABASES LIKE 'project-xxx:af*';
+---------------------------------------------------------+--+
| databaseName |
+---------------------------------------------------------+--+
| database_fj8gygj0v10vj50j0gyfqk1x__af_result_180719_01 |
| database_fj96qx00v10vj50j0gyfv00z__af_result2 |
| database_fjpz6fj0v10fjy3fjy282ybz__af_result1 |
+---------------------------------------------------------+--+Now you can run SQL queries.
0: jdbc:hive2://query.us-east-1.apollo.dnanex> select * from cna limit 10;
+--------------+-----------------+------------+--------+--+
| hugo_symbol | entrez_gene_id | sample_id | value |
+--------------+-----------------+------------+--------+--+
| MIR3675 | NULL | MB-6179 | -1 |
| MIR3675 | NULL | MB-6181 | 0 |
| MIR3675 | NULL | MB-6182 | 0 |
| MIR3675 | NULL | MB-6183 | 0 |
| MIR3675 | NULL | MB-6184 | 0 |
| MIR3675 | NULL | MB-6185 | -1 |
| MIR3675 | NULL | MB-6187 | 0 |
| MIR3675 | NULL | MB-6188 | 0 |
| MIR3675 | NULL | MB-6189 | 0 |
| MIR3675 | NULL | MB-6190 | 0 |
+--------------+-----------------+------------+--------+--+Last updated
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