Add triggers

docs/docs/configuration.md

@@ -14,7 +14,8 @@ The `nf-test.config` file is a configuration file used to customize settings and
 | `withTrace`  | Enable or disable tracing options during testing. Disable tracing if your containers don't include the `procps` tool.                                              | `true`                    |
 | `autoSort`   | Enable or disable sorted channels by default when running tests.                                                                                                   | `true`                    |
 | `options`    | Custom Nextflow command-line options to be applied when running tests. For example `"-dump-channels -stub-run"`                                                    |                           |
-| `ignore`     | List of filenames or patterns that should be ignored when building the dependency graph. For example: `ignore ['folder/**/*.nf', 'modules/module.nf']`             | ``                        |
+| `ignore`     | List of filenames or patterns that should be ignored when building the dependency graph. For example: `ignore 'folder/**/*.nf', 'modules/module.nf'`               | ``                        |
+| `triggers`   | List of filenames or patterns that should be trigger a full test run. For example: `triggers 'nextflow.config', 'test-data/**/*'`                                  | ``                        |
 | `requires`   | Can be used to specify the minimum required version of nf-test. Requires nf-test > 0.9.0                                                                           | ``                        |
 
 Here's an example of what an `nf-test.config` file could look like:

src/main/java/com/askimed/nf/test/commands/ListTestsCommand.java

@@ -71,7 +71,7 @@ public Integer execute() throws Exception {
 
 			DependencyResolver resolver = new DependencyResolver(new File(new File("").getAbsolutePath()));
 			if (config != null) {
-				resolver.buildGraph(config.getIgnore());
+				resolver.buildGraph(config.getIgnore(), config.getTriggers());
 			} else {
 				resolver.buildGraph();
 			}

src/main/java/com/askimed/nf/test/commands/RunTestsCommand.java

@@ -213,7 +213,7 @@ public Integer execute() throws Exception {
 
 			if (findRelatedTests) {
 
-				resolver.buildGraph(config.getIgnore());
+				resolver.buildGraph(config.getIgnore(), config.getTriggers());
 				scripts = resolver.findRelatedTestsByFiles(testPaths);
 				System.out.println("Found " + scripts.size() + " related test(s)");
 				if (scripts.isEmpty()) {
@@ -229,7 +229,7 @@ public Integer execute() throws Exception {
 
 			} else {
 				if (config != null) {
-					resolver.buildGraph(config.getIgnore());
+					resolver.buildGraph(config.getIgnore(), config.getTriggers());
 				} else {
 					resolver.buildGraph();
 				}

src/main/java/com/askimed/nf/test/config/Config.java

@@ -1,9 +1,7 @@
 package com.askimed.nf.test.config;
 
 import java.io.File;
-import java.util.List;
-import java.util.Vector;
-import java.util.Map;
+import java.util.*;
 
 import com.askimed.nf.test.App;
 import com.askimed.nf.test.nextflow.NextflowCommand;
@@ -52,6 +50,8 @@ public class Config {
 
 	private Map<String, Object> requires = null;
 
+	private List<String> triggers = new Vector<String>();
+
 	public void testsDir(String testsDir) {
 		this.testsDir = testsDir;
 	}
@@ -160,14 +160,42 @@ public List<String> getIgnore() {
 		return ignore;
 	}
 
-	public void ignore(List<String> ignores) {
-		this.ignore.addAll(ignores);
+	public void ignore(List<Object> ignores) {
+		for (Object ignore: ignores) {
+			this.ignore.add(ignore.toString());
+		}
 	}
 
 	public void ignore(String ignore) {
 		this.ignore.add(ignore);
 	}
 
+	public void ignore(String ... ignore) {
+		this.ignore.addAll(Arrays.asList(ignore));
+	}
+
+	public void setTriggers(List<String> triggers) {
+		this.triggers = triggers;
+	}
+
+	public List<String> getTriggers() {
+		return triggers;
+	}
+
+	public void triggers(List<Object> triggers) {
+		for (Object trigger: triggers) {
+			this.triggers.add(trigger.toString());
+		}
+	}
+
+	public void triggers(String ... triggers) {
+		this.triggers.addAll(Arrays.asList(triggers));
+	}
+
+	public void trigger(String trigger) {
+		this.triggers.add(trigger);
+	}
+
 	public void stage(Closure closure) {
 		closure.setDelegate(stageBuilder);
 		closure.setResolveStrategy(Closure.DELEGATE_ONLY);		

src/main/java/com/askimed/nf/test/lang/dependencies/DependencyResolver.java

@@ -16,6 +16,8 @@ public class DependencyResolver {
 
     private DependencyGraph graph = new DependencyGraph();
 
+    private List<PathMatcher> triggerPatterns = new Vector<PathMatcher>();
+
     private boolean followingDependencies = false;
 
     private static Logger log = LoggerFactory.getLogger(DependencyResolver.class);
@@ -89,6 +91,13 @@ public List<File> findRelatedTestsByFiles(List<File> files) throws Exception {
 
     public List<File> findRelatedTestsByFiles(File ... files) throws Exception {
 
+        for (File file: files) {
+            if (matches2(file.toPath(), triggerPatterns)) {
+                log.info("File " + file.getAbsolutePath() + " triggers full test run.");
+                return findAllTests();
+            }
+        }
+
         Set<File> results = new HashSet<File>();
 
         long time0 = System.currentTimeMillis();
@@ -149,16 +158,20 @@ private Set<File> findRelatedTestsByFile(File file, boolean followingDependencie
 
 
     public void buildGraph() throws Exception {
-        buildGraph(new Vector<String>());
+        buildGraph(new Vector<String>(), new Vector<String>());
     }
 
     public void buildGraph(String ... ignoreGlobs) throws Exception {
         List<String> list = new Vector<>();
         Collections.addAll(list, ignoreGlobs);
-        buildGraph(list);
+        buildGraph(list, new Vector<>());
     }
 
-    public void buildGraph(List<String> ignoreGlobs) throws Exception {
+    public void buildGraph(List<String> ignoreGlobs, List<String> triggerPatterns) throws Exception {
+
+        for (String glob: triggerPatterns) {
+            this.triggerPatterns.add(pathMatcher("glob:" + baseDir.getAbsolutePath() + "/" + glob));
+        }
 
         List<TestFilePattern> ignorePatterns = new Vector<TestFilePattern>();
         ignorePatterns.add(fileToPathMatcher(".nf-test/**"));
@@ -230,6 +243,7 @@ public TestFilePattern fileToPathMatcher(File file) {
 
 
     public PathMatcher pathMatcher(String pattern) {
+        System.out.println(pattern);
         return FileSystems.getDefault().getPathMatcher(pattern);
     }
 
@@ -243,4 +257,15 @@ public TestFilePattern matches(Path path, List<TestFilePattern> ignorePatterns)
         return null;
     }
 
+    public boolean matches2(Path path, List<PathMatcher> ignorePatterns) {
+        PathMatcher pathMatcher;
+        for (PathMatcher pattern : ignorePatterns) {
+            if (pattern.matches(path)) {
+                return true;
+            }
+        }
+        return false;
+    }
+
+
 }