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Add the AWS Athena JDBC driver for nf-sqldb plugin #2500

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Merged
merged 6 commits into from
Feb 1, 2022
Merged

Add the AWS Athena JDBC driver for nf-sqldb plugin #2500

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49fdf39
Add the local AWS Athena JDBC file
abhi18av Dec 17, 2021
aa61418
Add gradle tasks for downloading the Athena JDBC driver
abhi18av Dec 19, 2021
d84e602
Update the driver - use the AWS included SDK
abhi18av Dec 19, 2021
b5c7325
Simplify build for Athena support
pditommaso Dec 21, 2021
0ea5f8c
Fix Athena download tasks order
pditommaso Dec 21, 2021
4b078ae
Add athena tasks
pditommaso Dec 21, 2021
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31 changes: 31 additions & 0 deletions plugins/nf-sqldb/build.gradle
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Original file line number Diff line number Diff line change
Expand Up @@ -13,11 +13,17 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/

plugins {
id 'de.undercouch.download' version '4.1.2'
}

apply plugin: 'java'
apply plugin: 'java-test-fixtures'
apply plugin: 'idea'
apply plugin: 'groovy'


sourceSets {
main.java.srcDirs = []
main.groovy.srcDirs = ['src/main']
Expand All @@ -36,17 +42,42 @@ dependencies {
compileOnly project(':nextflow')
compileOnly 'org.slf4j:slf4j-api:1.7.10'
compileOnly 'org.pf4j:pf4j:3.4.1'
compileOnly "org.slf4j:log4j-over-slf4j:1.7.32"
api("org.codehaus.groovy:groovy-sql:3.0.9") { transitive = false }
api 'com.h2database:h2:1.4.200'
api 'mysql:mysql-connector-java:8.0.22'
api 'org.mariadb.jdbc:mariadb-java-client:2.7.0'
api 'org.postgresql:postgresql:42.2.23'
api 'org.xerial:sqlite-jdbc:3.36.0.3'
api 'org.duckdb:duckdb_jdbc:0.3.0'
api files('downloads/unzip/AthenaJDBC42_2.0.25.1001.jar')

testImplementation(testFixtures(project(":nextflow")))
testImplementation project(':nextflow')
testImplementation "org.codehaus.groovy:groovy:3.0.9"
testImplementation "org.codehaus.groovy:groovy-nio:3.0.9"
}


/**
* The following tasks download and confirm the MD5 checksum of the ZIP archive
* for Simba Athena JDBC driver and extract its contents to the build directory
*/
task downloadAthenDep(type: Download) {
src 'https://s3.amazonaws.com/athena-downloads/drivers/JDBC/SimbaAthenaJDBC-2.0.25.1001/SimbaAthenaJDBC-2.0.25.1001.zip'
dest new File(buildDir, 'downloads/SimbaAthenaJDBC-2.0.25.1001.zip')
overwrite false
}

task verifyAthenDep(type: Verify, dependsOn: downloadAthenDep) {
src new File(buildDir, 'downloads/SimbaAthenaJDBC-2.0.25.1001.zip')
algorithm 'MD5'
checksum '71504d0317656d790978363358d0c068'
}

task unzipAthenDep(dependsOn: verifyAthenDep, type: Copy) {
from zipTree(new File(buildDir, 'downloads/SimbaAthenaJDBC-2.0.25.1001.zip'))
into "${buildDir}/downloads/unzip"
}

project.compileGroovy.dependsOn('unzipAthenDep')
1 change: 1 addition & 0 deletions plugins/nf-sqldb/src/main/nextflow/sql/config/SqlDataSource.groovy
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Expand Up @@ -65,6 +65,7 @@ class SqlDataSource {
case 'mariadb': return 'org.mariadb.jdbc.Driver'
case 'postgresql': return 'org.postgresql.Driver'
case 'duckdb': return 'org.duckdb.DuckDBDriver'
case 'awsathena': return 'com.simba.athena.jdbc.Driver'
}
return null
}
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1 change: 1 addition & 0 deletions plugins/nf-sqldb/src/test/nextflow/sql/config/SqlDataSourceTest.groovy
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Expand Up @@ -69,6 +69,7 @@ class SqlDataSourceTest extends Specification {
'jdbc:mysql:some-host' | 'com.mysql.cj.jdbc.Driver'
'jdbc:mariadb:other-host' | 'org.mariadb.jdbc.Driver'
'jdbc:duckdb:' | 'org.duckdb.DuckDBDriver'
'jdbc:awsathena:' | 'com.simba.athena.jdbc.Driver'
}

def 'should get default config' () {
Expand Down