Support browsing html files with relative links

src/main/html/webapp/components/core/job/detail/results/share-folder.stache

@@ -18,7 +18,7 @@
 {{/files}}</textarea><br>
 <small>Use the following command to download all results at once:</small>
   <div class="input-group mb-3">
-    <input id="curl" value="curl -sL {{hostname}}/get/{{id}}/{{hash}} | bash" class="form-control form-control-sm code-font" />
+    <input id="curl" value="curl -sL {{hostname}}/get/{{hash}} | bash" class="form-control form-control-sm code-font" />
     <div class="input-group-append">
       <button class="btn btn-outline-secondary btn-sm" id="btn-copy" type="button" data-toggle="tooltip" data-placement="bottom" title="Copy to clipboard"><i class="far fa-copy"></i></button>
     </div>

src/main/html/webapp/helpers/helpers.js

@@ -40,7 +40,7 @@ function renderTreeItem(jobId, items, level) {
       html += renderTreeItem(jobId, items[i].childs, level + 1);
     } else {
       html += '<i class="far fa-file-alt text-muted fa-fw file-item-icon""></i>&nbsp;'
-      html += '<a class="file-item" href="downloads/' + jobId + '/' + items[i].hash + '/' + items[i].name + '" target="_blank">' + items[i].name + '</a>';
+      html += '<a class="file-item" href="' + items[i].path + '" target="_blank">' + items[i].name + '</a>';
       html += '&nbsp;&nbsp;&nbsp;&nbsp;<span class="text-muted">(' + items[i].size + ")</span>";
     }
     html += "</li>";

src/main/java/cloudgene/mapred/CommandLineInterface.java

@@ -23,7 +23,7 @@ private void printHeader() {
 		System.out.println();
 		System.out.println("Cloudgene " + Application.VERSION);
 		System.out.println("http://www.cloudgene.io");
-		System.out.println("(c) 2009-2032 Lukas Forer and Sebastian Schoenherr");
+		System.out.println("(c) 2009-2024 Lukas Forer and Sebastian Schoenherr");
 		System.out.println();
 	}
 

src/main/java/cloudgene/mapred/database/DownloadDao.java

@@ -155,7 +155,35 @@ public Download findByJobAndPath(String job, String path) {
 		}
 	}
 
-	class DownloadMapper implements IRowMapper {
+    public Download findByParameterAndName(CloudgeneParameterOutput param, String filename) {
+		StringBuilder sql = new StringBuilder();
+		sql.append("select * ");
+		sql.append("from downloads ");
+		sql.append("where name = ? and parameter_id = ? ");
+		sql.append("order by path ");
+
+		Object[] params = new Object[2];
+		params[0] = filename;
+		params[1] = param.getId();
+
+		Download result = null;
+
+		try {
+
+			result = (Download) queryForObject(sql.toString(), params,
+					new DownloadMapper());
+
+			log.debug("find download by param " + param.getId() + " and path " + filename
+					+ " successful. results: " + result);
+
+			return result;
+		} catch (SQLException e) {
+			log.error("find download by job and path failed.", e);
+			return null;
+		}
+    }
+
+    class DownloadMapper implements IRowMapper {
 
 		@Override
 		public Object mapRow(ResultSet rs, int row) throws SQLException {

src/main/java/cloudgene/mapred/database/ParameterDao.java

@@ -28,12 +28,12 @@ public ParameterDao(Database database) {
 
 	public boolean insert(CloudgeneParameterInput parameter) {
 		StringBuilder sql = new StringBuilder();
-		sql.append("insert into parameter (name, `value`, input, job_id, type, variable, download, format, admin_only) ");
-		sql.append("values (?,?,?,?,?,?,?,?,?)");
+		sql.append("insert into parameter (name, `value`, input, job_id, type, variable, download, format, admin_only, hash) ");
+		sql.append("values (?,?,?,?,?,?,?,?,?,?)");
 
 		try {
 
-			Object[] params = new Object[9];
+			Object[] params = new Object[10];
 			if (parameter.getDescription() != null) {
 				params[0] = parameter.getDescription().substring(0, Math.min(parameter.getDescription().length(), 100));
 			} else {
@@ -47,6 +47,7 @@ public boolean insert(CloudgeneParameterInput parameter) {
 			params[6] = false;
 			params[7] = "";
 			params[8] = parameter.isAdminOnly();
+			params[9] = parameter.getHash();
 
 			int paramId = insert(sql.toString(), params);
 			parameter.setId(paramId);
@@ -63,12 +64,12 @@ public boolean insert(CloudgeneParameterInput parameter) {
 
 	public boolean insert(CloudgeneParameterOutput parameter) {
 		StringBuilder sql = new StringBuilder();
-		sql.append("insert into parameter (name, `value`, input, job_id, type, variable, download, format, admin_only) ");
-		sql.append("values (?,?,?,?,?,?,?,?,?)");
+		sql.append("insert into parameter (name, `value`, input, job_id, type, variable, download, format, admin_only, hash) ");
+		sql.append("values (?,?,?,?,?,?,?,?,?,?)");
 
 		try {
 
-			Object[] params = new Object[9];
+			Object[] params = new Object[10];
 			params[0] = parameter.getDescription().substring(0, Math.min(parameter.getDescription().length(), 100));
 			params[1] = parameter.getValue();
 			params[2] = false;
@@ -78,6 +79,7 @@ public boolean insert(CloudgeneParameterOutput parameter) {
 			params[6] = parameter.isDownload();
 			params[7] = "";
 			params[8] = parameter.isAdminOnly();
+			params[9] = parameter.getHash();
 
 			int paramId = insert(sql.toString(), params);
 			parameter.setId(paramId);
@@ -180,6 +182,61 @@ public CloudgeneParameterOutput findById(int id) {
 		}
 	}
 
+    public CloudgeneParameterOutput findByHash(String hash) {
+		StringBuilder sql = new StringBuilder();
+		sql.append("select * ");
+		sql.append("from parameter ");
+		sql.append("where hash = ?");
+
+		Object[] params = new Object[1];
+		params[0] = hash;
+
+		CloudgeneParameterOutput result = null;
+
+		try {
+
+			result = (CloudgeneParameterOutput) queryForObject(sql.toString(), params, new ParameterOutputMapper());
+
+			DownloadDao downloadDao = new DownloadDao(database);
+			List<Download> downloads = downloadDao.findAllByParameter(result);
+			result.setFiles(downloads);
+
+			log.debug("find parameter by hash '" + hash + "' successful.");
+
+			return result;
+		} catch (SQLException e) {
+			log.error("find parameter by hash '" + hash + "' failed.", e);
+			return null;
+		}
+    }
+
+	public List<CloudgeneParameterOutput> findAllOutput() {
+		StringBuilder sql = new StringBuilder();
+		sql.append("select * ");
+		sql.append("from parameter ");
+		sql.append("where input = false");
+
+		List<CloudgeneParameterOutput> result = new Vector<CloudgeneParameterOutput>();
+
+		try {
+
+			result = query(sql.toString(), new ParameterOutputMapper());
+
+			DownloadDao downloadDao = new DownloadDao(database);
+			for (CloudgeneParameterOutput parameter : result) {
+				List<Download> downloads = downloadDao.findAllByParameter(parameter);
+				parameter.setFiles(downloads);
+			}
+
+			log.debug("find all output parameters  successful. results: " + result.size());
+
+			return result;
+		} catch (SQLException e) {
+			log.error("find all output parameters failed.", e);
+			return null;
+		}
+	}
+
 	class ParameterInputMapper implements IRowMapper {
 
 		@Override
@@ -192,6 +249,7 @@ public Object mapRow(ResultSet rs, int row) throws SQLException {
 			parameter.setType(WdlParameterInputType.getEnum(rs.getString("type")));
 			parameter.setId(rs.getInt("id"));
 			parameter.setAdminOnly(rs.getBoolean("admin_only"));
+			parameter.setHash(rs.getString("hash"));
 			return parameter;
 
 		}
@@ -211,6 +269,7 @@ public Object mapRow(ResultSet rs, int row) throws SQLException {
 			parameter.setDownload(rs.getBoolean("download"));
 			parameter.setId(rs.getInt("id"));
 			parameter.setAdminOnly(rs.getBoolean("admin_only"));
+			parameter.setHash(rs.getString("hash"));
 			return parameter;
 
 		}

src/main/java/cloudgene/mapred/jobs/CloudgeneJob.java

@@ -59,6 +59,7 @@ public CloudgeneJob(User user, String id, WdlApp app, Map<String, String> params
 		outputParams = new Vector<CloudgeneParameterOutput>();
 		for (WdlParameterOutput output : app.getWorkflow().getOutputs()) {
 			CloudgeneParameterOutput newOutput = new CloudgeneParameterOutput(output);
+			newOutput.initHash();
 			newOutput.setJob(this);
 			outputParams.add(newOutput);
 		}
@@ -93,6 +94,7 @@ protected void initLogOutput() {
 		logOutput.setName(CLOUDGENE_LOGS_PARAM);
 		logOutput.setType(WdlParameterOutputType.LOCAL_FOLDER);
 		logOutput.setJob(this);
+		logOutput.initHash();
 	}
 
 	@Override

src/main/java/cloudgene/mapred/jobs/CloudgeneParameterInput.java

@@ -21,6 +21,8 @@ public class CloudgeneParameterInput {
 
 	private boolean adminOnly = false;
 
+	private String hash = "";
+
 	public CloudgeneParameterInput() {
 
 	}
@@ -97,4 +99,11 @@ public boolean isAdminOnly() {
 		return adminOnly;
 	}
 
+	public void setHash(String hash) {
+		this.hash = hash;
+	}
+
+	public String getHash() {
+		return hash;
+	}
 }

src/main/java/cloudgene/mapred/jobs/CloudgeneParameterOutput.java

@@ -1,11 +1,13 @@
 package cloudgene.mapred.jobs;
 
 import java.util.List;
+import java.util.Random;
 import java.util.Vector;
 
 import cloudgene.mapred.util.HashUtil;
 import cloudgene.mapred.wdl.WdlParameterOutput;
 import cloudgene.mapred.wdl.WdlParameterOutputType;
+import org.apache.commons.math3.random.RandomGenerator;
 
 public class CloudgeneParameterOutput {
 
@@ -141,13 +143,17 @@ public void setHash(String hash) {
 	public String getHash() {
 		return hash;
 	}
-
-	public String createHash() {
-		String hash = "";
-		for (Download download: files) {
-			hash += download.getHash();
+
+	public void initHash() {
+		String alphabet = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789";
+		hash = "";
+		Random random = new Random();
+		int length = 40;
+		for (int i = 0; i < length; i++) {
+			int index = random.nextInt(alphabet.length());
+			char randomChar = alphabet.charAt(index);
+			hash += randomChar;
 		}
-		return HashUtil.getSha256(hash);
 	}
 
 }

src/main/java/cloudgene/mapred/server/Application.java

@@ -27,7 +27,7 @@
 @Context
 public class Application {
 
-	public static final String VERSION = "3.0.0-beta4";
+	public static final String VERSION = "3.0.0-beta5";
 
 	private Database database;
 

src/main/java/cloudgene/mapred/server/controller/DownloadController.java

@@ -82,26 +82,36 @@ public MutableHttpResponse<InputStream> downloadPublicLink(String hash, String f
 
 	}
 
-	@Get("/get/{paramId}/{hash}")
+	@Get("/browse/{hash}/{filename:.+}")
 	@Secured(SecurityRule.IS_ANONYMOUS)
-	public String downloadScript(String paramId, String hash) {
-
-		int id = -1;
-		try {
-			id = Integer.parseInt(paramId);
-		} catch (NumberFormatException e) {
-			throw new JsonHttpStatusException(HttpStatus.BAD_REQUEST, "Parameter ID is not numeric.");
-		}
+	public MutableHttpResponse<InputStream> downloadByParamHash(String hash, String filename)
+			throws URISyntaxException, IOException {
 
 		ParameterDao parameterDao = new ParameterDao(application.getDatabase());
-		CloudgeneParameterOutput param = parameterDao.findById(id);
+		CloudgeneParameterOutput param = parameterDao.findByHash(hash);
 
 		if (param == null) {
-			throw new JsonHttpStatusException(HttpStatus.NOT_FOUND, "Param " + param + " not found.");
+			throw new JsonHttpStatusException(HttpStatus.NOT_FOUND, "Param for hash " + hash + " not found.");
 		}
 
-		if (!hash.equals(param.createHash())) {
-			throw new JsonHttpStatusException(HttpStatus.FORBIDDEN, "Download forbidden.");
+		DownloadDao dao = new DownloadDao(application.getDatabase());
+		Download download = dao.findByParameterAndName(param, filename);
+
+		String message = String.format("Job: Anonymously downloading file '%s' (hash %s)", filename, hash);
+		log.info(message);
+		return downloadService.download(download);
+
+	}
+
+	@Get("/get/{hash}")
+	@Secured(SecurityRule.IS_ANONYMOUS)
+	public String downloadScript(String hash) {
+
+		ParameterDao parameterDao = new ParameterDao(application.getDatabase());
+		CloudgeneParameterOutput param = parameterDao.findByHash(hash);
+
+		if (param == null) {
+			throw new JsonHttpStatusException(HttpStatus.NOT_FOUND, "Param for hash " + hash + " not found.");
 		}
 
 		DownloadDao dao = new DownloadDao(application.getDatabase());

src/main/java/cloudgene/mapred/server/responses/JobResponse.java

@@ -169,9 +169,7 @@ public static JobResponse build(AbstractJob job, User user) {
 
 		// create tree
 		for (CloudgeneParameterOutput param : job.getOutputParams()) {
-			String hash = param.createHash();
-			param.setHash(hash);
-			param.setTree(JobResultsTreeUtil.createTree(param.getFiles()));
+			param.setTree(JobResultsTreeUtil.createTree(param));
 		}
 
 		// removes outputs that are for admin only

src/main/java/cloudgene/mapred/util/JobResultsTreeUtil.java

@@ -4,14 +4,15 @@
 import java.util.List;
 import java.util.Vector;
 
+import cloudgene.mapred.jobs.CloudgeneParameterOutput;
 import cloudgene.mapred.jobs.Download;
 import cloudgene.mapred.jobs.JobResultsTreeItem;
 
 public class JobResultsTreeUtil {
 
-	public static List<JobResultsTreeItem> createTree(List<Download> files) {
+	public static List<JobResultsTreeItem> createTree(CloudgeneParameterOutput param) {
 		List<JobResultsTreeItem> items = new Vector<JobResultsTreeItem>();
-		for (Download file : files) {
+		for (Download file : param.getFiles()) {
 			String[] tiles = file.getName().split("/");
 			JobResultsTreeItem root = null;
 			for (int i = 0; i < tiles.length - 1; i++) {
@@ -32,7 +33,11 @@ public static List<JobResultsTreeItem> createTree(List<Download> files) {
 			}
 			JobResultsTreeItem item = new JobResultsTreeItem();
 			item.setName(tiles[tiles.length - 1]);
-			item.setPath(file.getPath());
+			if (param.getHash() != null) {
+				item.setPath("/browse/" + param.getHash() + "/" + file.getName());
+			} else {
+				item.setPath("/share/results/" + file.getHash() + "/" + file.getName());
+			}
 			item.setHash(file.getHash());
 			item.setSize(file.getSize());
 			item.setFolder(false);

src/main/sql/updates.sql

@@ -168,3 +168,6 @@ alter table job add column user_agent VARCHAR (400);
 
 -- 3.0.0-beta1
 alter table `user` add column api_token_expires_on timestamp null default null;
+
+-- 3.0.0-beta5
+alter table `parameter` add column hash varchar(300) null default null;