From 1180a0698d960a82093caac7b9f298aa1f29c619 Mon Sep 17 00:00:00 2001
From: Eric <emarinier@gmail.com>
Date: Mon, 3 Feb 2025 14:54:36 -0600
Subject: [PATCH] Adding tests.

---
 .../iridanext/SamplesheetParserTest.groovy    | 131 ++++++++++++++++++
 1 file changed, 131 insertions(+)
 create mode 100644 plugins/nf-iridanext/src/test/nextflow/iridanext/SamplesheetParserTest.groovy

diff --git a/plugins/nf-iridanext/src/test/nextflow/iridanext/SamplesheetParserTest.groovy b/plugins/nf-iridanext/src/test/nextflow/iridanext/SamplesheetParserTest.groovy
new file mode 100644
index 0000000..1d9d47a
--- /dev/null
+++ b/plugins/nf-iridanext/src/test/nextflow/iridanext/SamplesheetParserTest.groovy
@@ -0,0 +1,131 @@
+package nextflow.iridanext
+
+import java.nio.file.Paths
+import java.nio.file.FileSystems
+import nextflow.iridanext.SamplesheetParser
+
+import nextflow.Session
+import spock.lang.Specification
+import net.jimblackler.jsonschemafriend.Schema
+import net.jimblackler.jsonschemafriend.SchemaStore
+import groovy.util.logging.Slf4j
+import groovyx.gpars.dataflow.DataflowReadChannel
+
+import nextflow.iridanext.TestHelper
+
+import java.nio.file.Files
+import java.util.jar.Manifest
+
+import nextflow.Channel
+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.Dsl2Spec
+
+import java.nio.file.Path
+
+
+@Slf4j
+class SamplesheetParserTest extends Dsl2Spec {
+
+    @Shared String pluginsMode
+
+    // NOTE: This setup() may fail if updated to Nextflow v24.01.
+    //       Please refer to these changes for a possible fix:
+    //       https://github.com/nextflow-io/nf-hello/commit/f686fbcf2346f3fc02b2288f567c016ab6bf2e50#diff-ae2fcafb7e787d2831f4cc882f85884ac2a100c5183b014baee656e96ddd69a6
+    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)
+    }
+
+    def cleanup() {
+        Plugins.stop()
+        PluginExtensionProvider.reset()
+        pluginsMode ? System.setProperty('pf4j.mode',pluginsMode) : System.clearProperty('pf4j.mode')
+    }
+
+    def 'Test loadIridaSampleIds only metadata' () {
+        when:
+        def config = [
+            iridanext: [
+                enabled: true,
+                output: [
+                    path: "/tmp/output/output.json.gz"
+                ]
+            ]
+        ]
+        def session = Spy(Session) {
+            getConfig() >> config
+        }
+        def SCRIPT = '''
+            include { loadIridaSampleIds } from 'plugin/nf-iridanext'
+            channel
+                .of([["id":"sample1"]], [["id":"sample2"]], [["id":"sample3"]])
+                .loadIridaSampleIds()
+            '''
+        
+        final IridaNextJSONOutput iridaNextJSONOutput = IridaNextJSONOutput.getInstance()
+
+        and:
+        def result = new MockScriptRunner([:]).setScript(SCRIPT).execute()
+
+        then:
+        iridaNextJSONOutput.isValidId(iridaNextJSONOutput.SAMPLES, "sample1")
+        iridaNextJSONOutput.isValidId(iridaNextJSONOutput.SAMPLES, "sample2")
+        iridaNextJSONOutput.isValidId(iridaNextJSONOutput.SAMPLES, "sample3")
+        iridaNextJSONOutput.isValidId(iridaNextJSONOutput.SAMPLES, "sample4") == false
+    }
+
+    def 'Test loadIridaSampleIds metadata and data' () {
+        when:
+        def config = [
+            iridanext: [
+                enabled: true,
+                output: [
+                    path: "/tmp/output/output.json.gz"
+                ]
+            ]
+        ]
+        def session = Spy(Session) {
+            getConfig() >> config
+        }
+        def SCRIPT = '''
+            include { loadIridaSampleIds } from 'plugin/nf-iridanext'
+            channel
+                .of([["id":"sample1"], "data1"], [["id":"sample2"], "data2"], [["id":"sample3"], "data3"])
+                .loadIridaSampleIds()
+            '''
+        
+        final IridaNextJSONOutput iridaNextJSONOutput = IridaNextJSONOutput.getInstance()
+
+        and:
+        def result = new MockScriptRunner([:]).setScript(SCRIPT).execute()
+
+        then:
+        iridaNextJSONOutput.isValidId(iridaNextJSONOutput.SAMPLES, "sample1")
+        iridaNextJSONOutput.isValidId(iridaNextJSONOutput.SAMPLES, "sample2")
+        iridaNextJSONOutput.isValidId(iridaNextJSONOutput.SAMPLES, "sample3")
+        iridaNextJSONOutput.isValidId(iridaNextJSONOutput.SAMPLES, "sample4") == false
+    }
+}
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