Merge branch 'master' into StringDoubleMap

.github/workflows/code-coverage.yaml

@@ -26,7 +26,7 @@ jobs:
         run: mvn verify -P jacoco --batch-mode --also-make --projects matsim -Dmaven.test.redirectTestOutputToFile -Dmatsim.preferLocalDtds=true
 
       - name: Push coverage to CodeCov
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
         with:
           files: ./matsim/target/site/jacoco/jacoco.xml
 

contribs/application/pom.xml

@@ -79,6 +79,7 @@
 			<artifactId>gtfs2matsim</artifactId>
 			<version>master-33809c4f0f-1</version>
 			<exclusions>
+				<!-- Exclude unneeded dependencies and these with known CVE -->
 				<exclusion>
 					<groupId>org.geotools</groupId>
 					<artifactId>*</artifactId>
@@ -87,6 +88,18 @@
 					<groupId>org.matsim</groupId>
 					<artifactId>*</artifactId>
 				</exclusion>
+				<exclusion>
+					<groupId>com.amazonaws</groupId>
+					<artifactId>*</artifactId>
+				</exclusion>
+				<exclusion>
+					<groupId>com.graphql-java</groupId>
+					<artifactId>*</artifactId>
+				</exclusion>
+				<exclusion>
+					<groupId>org.postgresql</groupId>
+					<artifactId>*</artifactId>
+				</exclusion>
 			</exclusions>
 		</dependency>
 

contribs/application/src/main/java/org/matsim/application/ApplicationUtils.java

@@ -1,17 +1,24 @@
 package org.matsim.application;
 
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.dataformat.yaml.YAMLFactory;
+import com.fasterxml.jackson.dataformat.yaml.YAMLGenerator;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.matsim.api.core.v01.Scenario;
 import org.matsim.application.options.CrsOptions;
 import org.matsim.application.options.InputOptions;
 import org.matsim.application.options.OutputOptions;
 import org.matsim.core.config.Config;
+import org.matsim.core.config.ConfigAliases;
+import org.matsim.core.config.ConfigGroup;
 import org.matsim.core.config.ConfigUtils;
 import org.matsim.core.scenario.ScenarioUtils;
 import org.matsim.core.utils.io.IOUtils;
 import picocli.CommandLine;
 
+import java.io.BufferedReader;
 import java.io.File;
 import java.io.IOException;
 import java.io.UncheckedIOException;
@@ -21,13 +28,20 @@
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.PathMatcher;
-import java.util.Optional;
+import java.util.*;
+import java.util.stream.Collectors;
 import java.util.stream.Stream;
+import java.util.stream.StreamSupport;
 
 public class ApplicationUtils {
 
 	private static final Logger log = LogManager.getLogger(ApplicationUtils.class);
 
+	/**
+	 * This encoding indicates command line was used to start the jar.
+	 */
+	private static final String WIN_CLI_ENCODING = "cp850";
+
 	private ApplicationUtils() {
 	}
 
@@ -46,7 +60,197 @@ public static String[] mergeArgs(String[] args, String... defaultArgs) {
 	}
 
 	/**
-	 * Extends a context (usually config location) with an relative filename.
+	 * Utility method to check if a jar might be run from the desktop (using double-click).
+	 */
+	public static boolean isRunFromDesktop() {
+
+		// check if gui was explicitly enabled
+		String env = System.getenv().getOrDefault("RUN_GUI", "undefined");
+		if (env.equalsIgnoreCase("true") || env.equals("1"))
+			return true;
+		else if (env.equalsIgnoreCase("false") || env.equals("0"))
+			return false;
+
+		String property = System.getProperty("RUN_GUI", "undefined");
+		if (property.equalsIgnoreCase("true") || property.equals("1"))
+			return true;
+		else if (property.equalsIgnoreCase("false") || property.equals("0"))
+			return false;
+
+		String macIdentifier = System.getenv().getOrDefault("__CFBundleIdentifier", "none");
+
+		if (macIdentifier.equals("com.apple.java.JarLauncher") || macIdentifier.equals("com.apple.JavaLauncher"))
+			return true;
+
+		String os = System.getProperty("os.name");
+
+		if (os.toLowerCase().startsWith("windows")) {
+
+			// presence of the prompt variable indicates that the jar was run from the command line
+			boolean hasPrompt = System.getenv().containsKey("PROMPT");
+
+			// this prompt is not set in PowerShell, so we need another check
+			if (hasPrompt)
+				return false;
+
+			// stdout.encoding from CLI are usually cp850
+			String encoding = System.getProperty("stdout.encoding", "none");
+			String sunEncoding = System.getProperty("sun.stdout.encoding", "none");
+
+			if (encoding.equals(WIN_CLI_ENCODING) || sunEncoding.equals(WIN_CLI_ENCODING))
+				return false;
+
+			// Run from intelij, will not start the gui by default
+			if (System.getenv().containsKey("IDEA_INITIAL_DIRECTORY"))
+				return false;
+			// also file.encoding=UTF-8, seems to be set by default in IntelliJ
+
+			// if no other cli indicators are present, we have to assume that the jar was run from the desktop
+			return true;
+		}
+
+		return false;
+
+	}
+
+	/**
+	 * Apply run configuration in yaml format.
+	 */
+	public static void applyConfigUpdate(Config config, Path yaml) {
+
+		if (!Files.exists(yaml)) {
+			throw new IllegalArgumentException("Given config yaml does not exist: " + yaml);
+		}
+
+		ObjectMapper mapper = new ObjectMapper(new YAMLFactory()
+			.enable(YAMLGenerator.Feature.MINIMIZE_QUOTES));
+
+		ConfigAliases aliases = new ConfigAliases();
+		Deque<String> emptyStack = new ArrayDeque<>();
+
+		try (BufferedReader reader = Files.newBufferedReader(yaml)) {
+
+			JsonNode node = mapper.readTree(reader);
+
+			Iterator<Map.Entry<String, JsonNode>> fields = node.fields();
+
+			while (fields.hasNext()) {
+				Map.Entry<String, JsonNode> field = fields.next();
+				String configGroupName = aliases.resolveAlias(field.getKey(), emptyStack);
+				ConfigGroup group = config.getModules().get(configGroupName);
+				if (group == null) {
+					group = new ConfigGroup(configGroupName);
+					config.addModule(group);
+				}
+
+				applyNodeToConfigGroup(field.getValue(), group);
+			}
+
+		} catch (IOException e) {
+			throw new UncheckedIOException(e);
+		}
+
+	}
+
+	/**
+	 * Sets the json config into
+	 */
+	private static void applyNodeToConfigGroup(JsonNode node, ConfigGroup group) {
+
+		Iterator<Map.Entry<String, JsonNode>> fields = node.fields();
+
+		while (fields.hasNext()) {
+			Map.Entry<String, JsonNode> field = fields.next();
+
+			if (isParameterSet(field.getValue())) {
+
+				// store the current parameters sets, newly added sets are not merged with each other
+				List<? extends ConfigGroup> params = new ArrayList<>(group.getParameterSets(field.getKey()));
+
+				for (JsonNode item : field.getValue()) {
+
+
+					// Special case of parameter sets that have only one entry
+					if (field.getValue().size() == 1 && params.size() == 1 && field.getValue().get(0).isObject()) {
+
+						applyNodeToConfigGroup(field.getValue().get(0), params.get(0));
+
+					} else {
+
+						applyNodeAsParameterSet(field.getKey(), item, group, params);
+					}
+				}
+			} else {
+
+				if (field.getValue().isTextual())
+					group.addParam(field.getKey(), field.getValue().textValue());
+				else if (field.getValue().isArray()) {
+					// arrays are joined using ","
+					Stream<JsonNode> stream = StreamSupport.stream(field.getValue().spliterator(), false);
+					String string = stream.map(n -> n.isTextual() ? n.textValue() : n.toString()).collect(Collectors.joining(","));
+					group.addParam(field.getKey(), string);
+				} else
+					group.addParam(field.getKey(), field.getValue().toString());
+			}
+		}
+	}
+
+	/**
+	 * Any array of complex object can be considered a config group.
+	 */
+	private static boolean isParameterSet(JsonNode node) {
+
+		if (!node.isArray())
+			return false;
+
+		// any object can be assigned as parameter set
+		for (JsonNode el : node) {
+			if (!el.isObject())
+				return false;
+		}
+
+		return true;
+	}
+
+	/**
+	 * Handle possible update and creation of parameter sets within a config group.
+	 */
+	private static void applyNodeAsParameterSet(String groupName, JsonNode item, ConfigGroup group, List<? extends ConfigGroup> params) {
+
+		Iterator<Map.Entry<String, JsonNode>> it = item.fields();
+
+		// There was at least one matching group
+		boolean matched = false;
+
+		while (!params.isEmpty() && it.hasNext()) {
+
+			Map.Entry<String, JsonNode> attr = it.next();
+			List<? extends ConfigGroup> candidates = params.stream()
+				.filter(p -> p.getParams().containsKey(attr.getKey()))
+				.filter(p -> p.getParams().get(attr.getKey())
+					.equals(attr.getValue().isTextual() ? attr.getValue().textValue() : attr.getValue().toString()))
+				.toList();
+
+			if (candidates.isEmpty())
+				break;
+
+			matched = true;
+			params = candidates;
+		}
+
+		if (params.size() > 1) {
+			throw new IllegalArgumentException("Ambiguous parameter set: " + item);
+		} else if (params.size() == 1 && matched) {
+			applyNodeToConfigGroup(item, params.get(0));
+		} else {
+			ConfigGroup newGroup = group.createParameterSet(groupName);
+			group.addParameterSet(newGroup);
+			applyNodeToConfigGroup(item, newGroup);
+		}
+	}
+
+	/**
+	 * Extends a context (usually config location) with a relative filename.
 	 * If the results is a local file, the path will be returned. Otherwise, it will be an url.
 	 * The results can be used as input for command line parameter or {@link IOUtils#resolveFileOrResource(String)}.
 	 *
@@ -75,10 +279,11 @@ public static Path globFile(Path path, String pattern) {
 		PathMatcher m = path.getFileSystem().getPathMatcher("glob:" + pattern);
 
 		try {
-			return Files.list(path)
-				.filter(p -> m.matches(p.getFileName()))
-				.findFirst()
-				.orElseThrow(() -> new IllegalStateException("No " + pattern + " file found."));
+			try (Stream<Path> list = Files.list(path)) {
+				return list.filter(p -> m.matches(p.getFileName()))
+					.findFirst()
+					.orElseThrow(() -> new IllegalStateException("No " + pattern + " file found."));
+			}
 		} catch (IOException e) {
 			throw new RuntimeException(e);
 		}