Move repository location to configuration

genepi · Jun 5, 2024 · e179c71 · e179c71
1 parent cf1b784
commit e179c71
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Showing 6 changed files with 19 additions and 20 deletions.
diff --git a/src/main/java/genepi/haplogrep3/App.java b/src/main/java/genepi/haplogrep3/App.java
@@ -82,7 +82,7 @@ public void loadConfiguration(String configFilename) {
 
 			configuration = Configuration.loadFromFile(configFile, parent);
 			treeRepository = new PhylotreeRepository();
-			treeRepository.loadFromConfiguration(configuration, parent);
+			treeRepository.loadFromConfiguration(configuration);
 
 			jobQueue = new JobQueue(configuration.getThreads());
 

diff --git a/src/main/java/genepi/haplogrep3/commands/ClusterHaplogroupsCommand.java b/src/main/java/genepi/haplogrep3/commands/ClusterHaplogroupsCommand.java
@@ -56,8 +56,7 @@ public Integer call() throws Exception {
 	public Phylotree loadPhylotree(String id) throws FileNotFoundException, IOException {
 		PhylotreeRepository repository = new PhylotreeRepository();
 		Configuration configuration = Configuration.loadFromFile(new File(CONFIG_FILE), "");
-		String parent = ".";
-		repository.loadFromConfiguration(configuration, parent);
+		repository.loadFromConfiguration(configuration);
 		return repository.getById(id);
 	}
 

diff --git a/src/main/java/genepi/haplogrep3/config/Configuration.java b/src/main/java/genepi/haplogrep3/config/Configuration.java
@@ -37,6 +37,8 @@ public class Configuration {
 
 	private List<NavbarLink> navbar = new Vector<NavbarLink>();
 
+	private String parent = "";
+
 	public Configuration() {
 
 	}
@@ -146,6 +148,8 @@ public static Configuration loadFromFile(File file, String parent) throws IOExce
 		Configuration configuration = reader.read(Configuration.class);
 		reader.close();
 
+		configuration.parent = parent;
+
 		for (Dataset dataset : configuration.getExamples()) {
 			dataset.updateParent(parent);
 		}
@@ -163,4 +167,7 @@ public void save(File file) throws IOException {
 
 	}
 
+    public File getPluginsLocation() {
+		return new File(parent, "trees");
+    }
 }
diff --git a/src/main/java/genepi/haplogrep3/model/PhylotreeRepository.java b/src/main/java/genepi/haplogrep3/model/PhylotreeRepository.java
@@ -27,12 +27,12 @@ public PhylotreeRepository() {
 		trees = new Vector<Phylotree>();
 	}
 
-	public synchronized void loadFromConfiguration(Configuration configuration, String parent)
+	public synchronized void loadFromConfiguration(Configuration configuration)
 			throws FileNotFoundException, IOException {
 
 		trees = new Vector<Phylotree>();
 
-		PluginRepository repository = new PluginRepository(configuration.getRepositories(), forceUpdate, parent);
+		PluginRepository repository = new PluginRepository(configuration.getRepositories(), forceUpdate, configuration.getPluginsLocation());
 
 		for (String id : configuration.getPhylotrees()) {
 
@@ -61,9 +61,7 @@ public synchronized void loadFromConfiguration(Configuration configuration, Stri
 
 	public void install(String id, Configuration configuration) throws IOException {
 
-		String parent = ".";
-
-		PluginRepository repository = new PluginRepository(configuration.getRepositories(), forceUpdate, parent);
+		PluginRepository repository = new PluginRepository(configuration.getRepositories(), forceUpdate, configuration.getPluginsLocation());
 
 		Phylotree phylotree = null;
 

diff --git a/src/main/java/genepi/haplogrep3/plugins/PluginRepository.java b/src/main/java/genepi/haplogrep3/plugins/PluginRepository.java
@@ -22,17 +22,13 @@ public class PluginRepository {
 
 	public static String LATEST_VERSION = null;
 
-	public File plugins_location = new File("trees");
+	public File pluginsLocation = new File("trees");
 
 	private List<List<Plugin>> repositories = new Vector<List<Plugin>>();
 
-	public PluginRepository(List<String> urls, boolean forceUpdate, String parent) throws IOException {
-
-		if (!parent.equals(".")) {
-			plugins_location = new File(FileUtil.path(parent, "trees"));
-		}
-
-		plugins_location.mkdirs();
+	public PluginRepository(List<String> urls, boolean forceUpdate, File pluginsLocation) throws IOException {
+		this.pluginsLocation = pluginsLocation;
+		pluginsLocation.mkdirs();
 
 		for (String url : urls) {
 			repositories.add(loadFromUrl(url, forceUpdate));
@@ -90,7 +86,7 @@ public InstalledPlugin resolveRelease(PluginRelease release) throws IOException
 
 		String filename = "tree.yaml";
 
-		File pluginPath = new File(plugins_location, FileUtil.path(id, release.getVersion()));
+		File pluginPath = new File(pluginsLocation, FileUtil.path(id, release.getVersion()));
 		InstalledPlugin plugin = new InstalledPlugin();
 		plugin.setRelease(release);
 		plugin.setPath(new File(pluginPath.getAbsolutePath(), filename));
@@ -132,7 +128,7 @@ private List<Plugin> loadFromUrl(String url, boolean forceUpdate) throws IOExcep
 		File indexFile = null;
 
 		if (isHttpProtocol(url)) {
-			indexFile = new File(plugins_location, getNameForUrl(url) + ".yaml");
+			indexFile = new File(pluginsLocation, getNameForUrl(url) + ".yaml");
 			if (!indexFile.exists() || forceUpdate) {
 				download(url, indexFile);
 			}

diff --git a/src/test/java/genepi/haplogrep3/tasks/ClassificationTaskTest.java b/src/test/java/genepi/haplogrep3/tasks/ClassificationTaskTest.java
@@ -29,8 +29,7 @@ public class ClassificationTaskTest {
 	public Phylotree loadPhylotree(String id) throws FileNotFoundException, IOException {
 		PhylotreeRepository repository = new PhylotreeRepository();
 		Configuration configuration = Configuration.loadFromFile(new File(CONFIG_FILE), "");
-		String parent = ".";
-		repository.loadFromConfiguration(configuration, parent);
+		repository.loadFromConfiguration(configuration);
 		return repository.getById(id);
 	}