Add testcases for dependency resolver

src/test/java/com/askimed/nf/test/lang/dependencies/DependencyResolverTest.java

@@ -0,0 +1,192 @@
+package com.askimed.nf.test.lang.dependencies;
+
+import org.junit.jupiter.api.Test;
+
+import java.io.*;
+import java.net.HttpURLConnection;
+import java.net.URL;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.nio.file.StandardCopyOption;
+import java.util.List;
+import java.util.Vector;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipInputStream;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+class DependencyResolverTest {
+
+    public File getNfGwas() throws IOException {
+        String url = "https://github.com/genepi/nf-gwas/archive/refs/tags/v1.0.7.zip";
+        return downloadAndExtractZip(url, "temp", "nf-gwas-1.0.7");
+    }
+
+    public File getFetchNgs() throws IOException {
+        String url = "https://github.com/nf-core/fetchngs/archive/refs/tags/1.12.0.zip";
+        return downloadAndExtractZip(url, "temp", "fetchngs-1.12.0");
+    }
+
+    @Test
+    void findAllTests() throws Exception {
+        File root = getNfGwas();
+        DependencyResolver resolver = new DependencyResolver(root);
+        resolver.buildGraph();
+        assertEquals(10, resolver.findAllTests().size());
+
+        Coverage coverage = new Coverage(resolver);
+        assertEquals(10, coverage.getAll().getCoveredItems());
+        assertEquals(39, coverage.getAll().getItems().size());
+    }
+
+    @Test
+    void findRelatedTests() throws Exception {
+
+        File root = getNfGwas();
+        DependencyResolver resolver = new DependencyResolver(root);
+        resolver.buildGraph();
+        assertEquals(2, resolver.findRelatedTestsByFiles(
+                new File(root, "modules/../modules/local/regenie/regenie_step1_run.nf"),
+                new File(root, "nextflow.config")
+        ).size());
+
+        assertEquals(3, resolver.findRelatedTestsByFiles(
+                new File(root, "modules/../modules/local/regenie/regenie_step1_run.nf"),
+                new File(root, "modules/../modules/local/regenie/regenie_step2_run.nf")
+        ).size());
+    }
+
+    @Test
+    void findRelatedTestAndFollowDependencies() throws Exception {
+
+        File root = getFetchNgs();
+
+        DependencyResolver resolver = new DependencyResolver(root);
+        resolver.setFollowingDependencies(false);
+
+        resolver.buildGraph();
+        assertEquals(10, resolver.findRelatedTestsByFiles(
+                new File(root, "modules/local/sra_to_samplesheet/main.nf")
+        ).size());
+
+        resolver = new DependencyResolver(root);
+        resolver.setFollowingDependencies(true);
+
+        resolver.buildGraph();
+        assertEquals(11, resolver.findRelatedTestsByFiles(
+                new File(root, "modules/local/sra_to_samplesheet/main.nf")
+        ).size());
+
+        Coverage coverage = new Coverage(resolver);
+        assertEquals(17, coverage.getAll().getCoveredItems());
+        assertEquals(17, coverage.getAll().getItems().size());
+    }
+
+    @Test
+    void findRelatedTestsWithTrigger() throws Exception {
+
+        File root = getNfGwas();
+        DependencyResolver resolver = new DependencyResolver(root);
+        List<String> triggers = new Vector<String>();
+        triggers.add("nextflow.config");
+        resolver.buildGraph(new Vector<>(), triggers);
+
+        assertEquals(10, resolver.findRelatedTestsByFiles(
+                new File(root, "modules/../modules/local/regenie/regenie_step1_run.nf"),
+                new File(root, "nextflow.config")
+        ).size());
+
+    }
+
+    @Test
+    void findRelatedTestsWithTriggerAndPattern() throws Exception {
+
+        File root = getNfGwas();
+        DependencyResolver resolver = new DependencyResolver(root);
+        List<String> triggers = new Vector<String>();
+        triggers.add("*.config");
+        resolver.buildGraph(new Vector<>(), triggers);
+
+        assertEquals(10, resolver.findRelatedTestsByFiles(
+                new File(root, "modules/../modules/local/regenie/regenie_step1_run.nf"),
+                new File(root, "nextflow.config")
+        ).size());
+
+    }
+
+    @Test
+    void findRelatedTestsWithTriggerAndTestDataPattern() throws Exception {
+
+        File root = getNfGwas();
+        DependencyResolver resolver = new DependencyResolver(root);
+        List<String> triggers = new Vector<String>();
+        triggers.add("tests/input/**/*");
+        resolver.buildGraph(new Vector<>(), triggers);
+
+        assertEquals(10, resolver.findRelatedTestsByFiles(
+                new File(root, "tests/input/filter_results/regenie_step2_example_Y1.regenie.gz")
+        ).size());
+
+        resolver = new DependencyResolver(root);
+        resolver.buildGraph();
+
+        assertEquals(0, resolver.findRelatedTestsByFiles(
+                new File(root, "tests/input/filter_results/regenie_step2_example_Y1.regenie.gz")
+        ).size());
+
+    }
+
+    private File downloadAndExtractZip(String url, String destinationFolder, String name) throws IOException {
+        // Check if destination folder exists
+        File destFolder = new File(destinationFolder);
+        if (!new File(destFolder, name).exists()) {
+            // Create destination folder if it doesn't exist
+            destFolder.mkdirs();
+
+            // Download the zip file
+            URL zipUrl = new URL(url);
+            HttpURLConnection connection = (HttpURLConnection) zipUrl.openConnection();
+            try (InputStream inputStream = connection.getInputStream()) {
+                Path zipFilePath = Paths.get(destinationFolder, "temp.zip");
+                Files.copy(inputStream, zipFilePath, StandardCopyOption.REPLACE_EXISTING);
+            }
+
+            // Extract the contents of the zip file
+            File extractedFolder = new File(destinationFolder, name);
+            try (ZipInputStream zipInputStream = new ZipInputStream(new FileInputStream(new File(destinationFolder, "temp.zip")))) {
+                ZipEntry entry = zipInputStream.getNextEntry();
+                while (entry != null) {
+                    Path filePath = Paths.get(destinationFolder, entry.getName());
+                    if (!entry.isDirectory()) {
+                        // Create parent directories if they don't exist
+                        Files.createDirectories(filePath.getParent());
+                        // Write file content
+                        try (OutputStream outputStream = new FileOutputStream(filePath.toFile())) {
+                            byte[] buffer = new byte[1024];
+                            int length;
+                            while ((length = zipInputStream.read(buffer)) > 0) {
+                                outputStream.write(buffer, 0, length);
+                            }
+                        }
+                    } else {
+                        // Create directory if it doesn't exist
+                        Files.createDirectories(filePath);
+                    }
+                    zipInputStream.closeEntry();
+                    entry = zipInputStream.getNextEntry();
+                }
+            }
+
+            // Clean up: Delete the temporary zip file
+            Files.deleteIfExists(Paths.get(destinationFolder, "temp.zip"));
+
+            return extractedFolder;
+        } else {
+            // If the destination folder already exists, return it without downloading
+            return new File(destinationFolder, name);
+        }
+    }
+
+
+}