Add possibility to add user defined resources

genepi · Sep 14, 2024 · e4fca96 · e4fca96
1 parent 53b2dcf
commit e4fca96
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Showing 9 changed files with 149 additions and 144 deletions.
diff --git a/src/main/html/webapp/components/admin/settings/server/server.stache b/src/main/html/webapp/components/admin/settings/server/server.stache
@@ -95,7 +95,9 @@
 						</div>
 					{{else}}
 						<h5 class="card-title"><i class="fas fa-times-circle text-danger"></i> {{name}}</h5>
-						{{{error}}}
+						<div class="log-pane">
+							<pre>{{error}}</pre>
+						</div>
 					{{/enabled}}
 				</div>
 			</div>

diff --git a/src/main/java/cloudgene/mapred/plugins/docker/DockerBinary.java b/src/main/java/cloudgene/mapred/plugins/docker/DockerBinary.java
@@ -38,12 +38,11 @@ public String getVersion() {
 		if (isInstalled()) {
 			String binary = getBinary();
 			Command command = new Command(binary, "version");
-			command.saveStdOut(FileUtil.path("docker-version.txt"));
+			StringBuffer stdout = new StringBuffer();
+			command.writeStdout(stdout);
 			command.setSilent(true);
 			command.execute();
-			String version = FileUtil.readFileAsString("docker-version.txt");
-			FileUtil.deleteFile("docker-version.txt");
-			return version;
+			return stdout.toString();
 		} else {
 			return "Docker not installed.";
 		}

diff --git a/src/main/java/cloudgene/mapred/plugins/nextflow/NextflowBinary.java b/src/main/java/cloudgene/mapred/plugins/nextflow/NextflowBinary.java
@@ -63,12 +63,11 @@ public boolean isInstalled() {
 	public String getVersion() {
 		if (isInstalled()) {
 			Command command = new Command(binary, "info");
-			command.saveStdOut(FileUtil.path("info-version.txt"));
+			StringBuffer stdout = new StringBuffer();
+			command.writeStdout(stdout);
 			command.setSilent(true);
 			command.execute();
-			String version = FileUtil.readFileAsString("info-version.txt");
-			FileUtil.deleteFile("info-version.txt");
-			return version;
+			return stdout.toString();
 		} else {
 			return "Nextflow not installed.";
 		}

diff --git a/src/main/java/cloudgene/mapred/server/controller/ServerAdminController.java b/src/main/java/cloudgene/mapred/server/controller/ServerAdminController.java
@@ -14,6 +14,7 @@
 import cloudgene.mapred.server.responses.ServerResponse;
 import cloudgene.mapred.server.responses.StatisticsResponse;
 import cloudgene.mapred.server.services.ServerService;
+import cloudgene.mapred.util.TextUtil;
 import genepi.io.FileUtil;
 import io.micronaut.core.annotation.Nullable;
 import io.micronaut.http.MediaType;
@@ -88,8 +89,7 @@ public String getDetails() {
 	public String getLogs() {
 		File file = new File(LOG_FILENAME);
 		if (file.exists()) {
-			String content = serverService.tail(file, 1000);
-			return content;
+			return TextUtil.tail(file, 1000);
 		} else {
 			return "No log file available.";
 		}

diff --git a/src/main/java/cloudgene/mapred/server/services/ServerService.java b/src/main/java/cloudgene/mapred/server/services/ServerService.java
@@ -3,15 +3,12 @@
 import java.io.File;
 import java.io.IOException;
 import java.net.URL;
-import java.util.Date;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Vector;
+import java.util.*;
 import java.util.jar.Attributes;
 import java.util.jar.Manifest;
 
 import cloudgene.mapred.plugins.nextflow.NextflowPlugin;
+import cloudgene.mapred.util.command.Command;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.fasterxml.jackson.databind.node.ArrayNode;
 import com.fasterxml.jackson.databind.node.ObjectNode;
@@ -211,6 +208,34 @@ public String getClusterDetails() {
 			plugins.add(pluginObject);
 		}
 
+		//check user defined resources
+		for (Map<String, String> resource: application.getSettings().getResources()){
+			String name = resource.get("name");
+			ObjectNode pluginObject = mapper.createObjectNode();
+			pluginObject.put("name", name);
+			if (!resource.containsKey("command")) {
+				pluginObject.put("error", "Command defined in resource '" + name + "'");
+			}
+			String cmd = resource.get("command");
+			String[] tiles = cmd.split(" ");
+			String[] params = Arrays.copyOfRange(tiles, 1, tiles.length);
+			Command command = new Command(tiles[0], params);
+			command.setSilent(true);
+			StringBuffer output = new StringBuffer();
+			StringBuffer error = new StringBuffer();
+			command.writeStdout(output);
+			command.writeStderr(error);
+			int exitCode = command.execute();
+			if (exitCode == 0) {
+				pluginObject.put("enabled", true);
+				pluginObject.put("details", output.toString());
+			}else {
+				pluginObject.put("enabled", false);
+				pluginObject.put("error",  output.toString()+ "\n" + error.toString());
+			}
+			plugins.add(pluginObject);
+		}
+
 		// database
 		object.put("db_max_active", application.getDatabase().getDataSource().getMaxActive());
 		object.put("db_active", application.getDatabase().getDataSource().getNumActive());
@@ -222,53 +247,6 @@ public String getClusterDetails() {
 		return object.toString();
 	}
 
-	public String tail(File file, int lines) {
-		java.io.RandomAccessFile fileHandler = null;
-		try {
-			fileHandler = new java.io.RandomAccessFile(file, "r");
-			long fileLength = fileHandler.length() - 1;
-			StringBuilder sb = new StringBuilder();
-			int line = 0;
-
-			for (long filePointer = fileLength; filePointer != -1; filePointer--) {
-				fileHandler.seek(filePointer);
-				int readByte = fileHandler.readByte();
-
-				if (readByte == 0xA) {
-					line = line + 1;
-					if (line == lines) {
-						if (filePointer == fileLength) {
-							continue;
-						}
-						break;
-					}
-				} else if (readByte == 0xD) {
-					line = line + 1;
-					if (line == lines) {
-						if (filePointer == fileLength - 1) {
-							continue;
-						}
-						break;
-					}
-				}
-				sb.append((char) readByte);
-			}
-
-			String lastLine = sb.reverse().toString();
-			return lastLine;
-		} catch (java.io.IOException e) {
-			log.error("Parsing log file failed.", e);
-			return null;
-		} finally {
-			if (fileHandler != null)
-				try {
-					fileHandler.close();
-				} catch (IOException e) {
-					log.error("Parsing log file failed.", e);
-				}
-		}
-	}
-
 	public void updateNextflowConfig(String content) {
 		NextflowPlugin plugin = (NextflowPlugin) PluginManager.getInstance().getPlugin(NextflowPlugin.ID);
 		String filename = plugin.getNextflowConfig();

diff --git a/src/main/java/cloudgene/mapred/util/Settings.java b/src/main/java/cloudgene/mapred/util/Settings.java
@@ -48,6 +48,8 @@ public class Settings {
 
 	private List<Map<String, String>> errorHandlers = new Vector<Map<String, String>>();
 
+	private List<Map<String, String>> resources = new Vector<>();
+
 	private int autoRetireInterval = 5;
 
 	private int retireAfter = 6;
@@ -389,6 +391,14 @@ public List<Map<String, String>> getErrorHandlers() {
 		return errorHandlers;
 	}
 
+	public void setResources(List<Map<String, String>> resources) {
+		this.resources = resources;
+	}
+
+	public List<Map<String, String>> getResources() {
+		return resources;
+	}
+
 	public void setRepository(ApplicationRepository repository) {
 		this.repository = repository;
 	}

diff --git a/src/main/java/cloudgene/mapred/util/TextUtil.java b/src/main/java/cloudgene/mapred/util/TextUtil.java
@@ -0,0 +1,59 @@
+package cloudgene.mapred.util;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.File;
+import java.io.IOException;
+
+public class TextUtil {
+
+    private static final Logger log = LoggerFactory.getLogger(TextUtil.class);
+
+    public static String tail(File file, int lines) {
+        java.io.RandomAccessFile fileHandler = null;
+        try {
+            fileHandler = new java.io.RandomAccessFile(file, "r");
+            long fileLength = fileHandler.length() - 1;
+            StringBuilder sb = new StringBuilder();
+            int line = 0;
+
+            for (long filePointer = fileLength; filePointer != -1; filePointer--) {
+                fileHandler.seek(filePointer);
+                int readByte = fileHandler.readByte();
+
+                if (readByte == 0xA) {
+                    line = line + 1;
+                    if (line == lines) {
+                        if (filePointer == fileLength) {
+                            continue;
+                        }
+                        break;
+                    }
+                } else if (readByte == 0xD) {
+                    line = line + 1;
+                    if (line == lines) {
+                        if (filePointer == fileLength - 1) {
+                            continue;
+                        }
+                        break;
+                    }
+                }
+                sb.append((char) readByte);
+            }
+
+            String lastLine = sb.reverse().toString();
+            return lastLine;
+        } catch (java.io.IOException e) {
+            log.error("Parsing log file failed.", e);
+            return null;
+        } finally {
+            if (fileHandler != null)
+                try {
+                    fileHandler.close();
+                } catch (IOException e) {
+                    log.error("Parsing log file failed.", e);
+                }
+        }
+    }
+}