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Upgrade nextflow version to 22.08.1-edge
Closes #8 Signed-off-by: Jorge Aguilera <[email protected]> Signed-off-by: Paolo Di Tommaso <[email protected]>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -19,28 +19,54 @@ package nextflow.sql | |
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| import groovy.sql.Sql | ||
| import nextflow.Channel | ||
| import nextflow.extension.ChannelExtensionProvider | ||
| import nextflow.plugin.Plugins | ||
| import nextflow.plugin.TestPluginDescriptorFinder | ||
| import nextflow.plugin.TestPluginManager | ||
| import nextflow.plugin.extension.PluginExtensionProvider | ||
| import org.pf4j.PluginDescriptorFinder | ||
| import spock.lang.Shared | ||
| import spock.lang.Timeout | ||
| import test.BaseSpec | ||
| import test.Dsl2Spec | ||
| import test.MockScriptRunner | ||
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| import java.nio.file.Path | ||
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| /** | ||
| * | ||
| * @author Paolo Di Tommaso <[email protected]> | ||
| */ | ||
| @Timeout(10) | ||
| class SqlDslTest extends BaseSpec { | ||
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| def setup () { | ||
| new ChannelExtensionProvider() | ||
| .install() | ||
| .loadPluginExtensionMethods(new ChannelSqlExtension(), ['fromQuery':'fromQuery', sqlInsert:'sqlInsert']) | ||
| class SqlDslTest extends Dsl2Spec { | ||
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| @Shared String pluginsMode | ||
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| def setup() { | ||
| // reset previous instances | ||
| PluginExtensionProvider.reset() | ||
| // this need to be set *before* the plugin manager class is created | ||
| pluginsMode = System.getProperty('pf4j.mode') | ||
| System.setProperty('pf4j.mode', 'dev') | ||
| // the plugin root should | ||
| def root = Path.of('.').toAbsolutePath().normalize() | ||
| def manager = new TestPluginManager(root){ | ||
| @Override | ||
| protected PluginDescriptorFinder createPluginDescriptorFinder() { | ||
| return new TestPluginDescriptorFinder(){ | ||
| @Override | ||
| protected Path getManifestPath(Path pluginPath) { | ||
| return pluginPath.resolve('build/resources/main/META-INF/MANIFEST.MF') | ||
| } | ||
| } | ||
| } | ||
| } | ||
| Plugins.init(root, 'dev', manager) | ||
| } | ||
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| def cleanup() { | ||
| ChannelExtensionProvider.reset() | ||
| Plugins.stop() | ||
| PluginExtensionProvider.reset() | ||
| pluginsMode ? System.setProperty('pf4j.mode',pluginsMode) : System.clearProperty('pf4j.mode') | ||
| } | ||
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| def 'should perform a query and create a channel' () { | ||
| given: | ||
| def JDBC_URL = 'jdbc:h2:mem:test_' + Random.newInstance().nextInt(1_000_000) | ||
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@@ -55,6 +81,7 @@ class SqlDslTest extends BaseSpec { | |
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| when: | ||
| def SCRIPT = ''' | ||
| include { fromQuery; sqlInsert } from 'plugin/nf-sqldb' | ||
| def table = 'FOO' | ||
| def sql = "select * from $table" | ||
| channel.fromQuery(sql, db: "test") | ||
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@@ -80,6 +107,7 @@ class SqlDslTest extends BaseSpec { | |
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| when: | ||
| def SCRIPT = ''' | ||
| include { fromQuery; sqlInsert } from 'plugin/nf-sqldb' | ||
| channel | ||
| .of(100,200,300) | ||
| .sqlInsert(into:"FOO", columns:'id', db:"ds1") | ||
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@@ -110,6 +138,7 @@ class SqlDslTest extends BaseSpec { | |
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| when: | ||
| def SCRIPT = ''' | ||
| include { fromQuery; sqlInsert } from 'plugin/nf-sqldb' | ||
| channel | ||
| .of(100,200,300,400,500) | ||
| .sqlInsert(into:'FOO', columns:'id', db:'ds1', batchSize: 2) | ||
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@@ -145,6 +174,7 @@ class SqlDslTest extends BaseSpec { | |
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| when: | ||
| def SCRIPT = ''' | ||
| include { fromQuery; sqlInsert } from 'plugin/nf-sqldb' | ||
| def table = 'FOO' | ||
| def sql = "select * from $table" | ||
| channel.fromQuery(sql, db: "test", emitColumns:true) | ||
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