Add sessionDelete

CHANGELOG.md

@@ -16,6 +16,8 @@ New in 1.19.0
 
   * `sessionList`
 
+  * `sessionDelete`
+
 * Move ASCIIGenome files and settings to `~/.asciigenome` directory.
 
 * `print` command does not decode the URL escapes for line feed and carriage

src/main/java/commandHelp/Command.java

@@ -46,6 +46,7 @@ public enum Command {
   sessionOpen("sessionOpen"),
   sessionSave("sessionSave"),
   sessionList("sessionList"),
+  sessionDelete("sessionDelete"),
   reload("reload"),
   recentlyOpened("recentlyOpened"),
   dropTracks("dropTracks"),

src/main/java/commandHelp/CommandList.java

@@ -1485,6 +1485,19 @@ public static final List<CommandHelp> commandHelpList()
             + "* :code:`-n` List up to this many sessions. Default 10");
     cmdList.add(cmd);
 
+    cmd = new CommandHelp();
+    cmd.setName("sessionDelete");
+    cmd.setArgs("[-f session.yml] <sessionName>");
+    cmd.inSection = Section.SESSION;
+    cmd.setBriefDescription("Delete session by name.");
+    cmd.setAdditionalDescription(
+        "\n"
+            + "* :code:`-f` List sessions in this file. Default: "
+            + " :code:`\\~/.asciigenome/session.yaml`\n"
+            + "\n"
+            + "* :code:`sessionName` Session name to delete");
+    cmdList.add(cmd);
+
     cmd = new CommandHelp();
     cmd.setName("reload");
     cmd.setArgs("[track_regex = .*]...");
@@ -1774,6 +1787,7 @@ public static final List<String> cmds() {
     paramList.add("sessionOpen");
     paramList.add("sessionSave");
     paramList.add("sessionList");
+    paramList.add("sessionDelete");
     paramList.add("reload");
     paramList.add("recentlyOpened");
     paramList.add("dropTracks");

src/main/java/samTextViewer/InteractiveInput.java

@@ -1,5 +1,7 @@
 package samTextViewer;
 
+import static session.SessionHandler.writeSessions;
+
 import colouring.Config;
 import colouring.ConfigKey;
 import com.google.common.base.Joiner;
@@ -180,7 +182,14 @@ protected TrackProcessor processInput(String cmdConcatInput, TrackProcessor proc
           System.out.print("\033[0m");
           console.clearScreen();
           console.flush();
-          SessionHandler.saveAs(SessionHandler.DEFAULT_SESSION_FILE, proc.toSession(), "");
+          try {
+            SessionHandler.saveAs(SessionHandler.DEFAULT_SESSION_FILE, proc.toSession(), "");
+          } catch (Exception e) {
+            System.err.println(
+                "Error saving session to file: " + SessionHandler.DEFAULT_SESSION_FILE);
+            System.err.println(e.getMessage());
+            System.exit(1);
+          }
           System.exit(0);
 
           // * These commands change the GenomicCoordinates (navigate) but do not touch the tracks.
@@ -290,6 +299,11 @@ protected TrackProcessor processInput(String cmdConcatInput, TrackProcessor proc
           args.remove(0);
           this.setInteractiveInputExitCode(this.listSessions(args, proc));
 
+        } else if (cmdTokens.get(0).equals("sessionDelete")) {
+          List<String> args = new ArrayList<>(cmdTokens);
+          args.remove(0);
+          this.setInteractiveInputExitCode(this.deleteSession(args, proc));
+
         } else if (cmdTokens.get(0).equals("setGenome")) {
           this.setGenome(cmdTokens, proc);
 
@@ -891,6 +905,51 @@ private ExitCode listSessions(List<String> args, TrackProcessor proc)
     return ExitCode.CLEAN_NO_FLUSH;
   }
 
+  private ExitCode deleteSession(List<String> args, TrackProcessor proc)
+      throws InvalidGenomicCoordsException, IOException, InvalidCommandLineException {
+    File sessionYamlFile =
+        new File(
+            Utils.getArgForParam(
+                args, "-f", SessionHandler.DEFAULT_SESSION_FILE.getAbsolutePath()));
+    SessionHandler sh;
+    if (this.sessionHandler == null) {
+      try {
+        sh = new SessionHandler(sessionYamlFile);
+      } catch (Exception e) {
+        this.messages.add(
+            "Failed to process session file '" + sessionYamlFile + "':\n" + e.getMessage());
+        return ExitCode.ERROR;
+      }
+    } else {
+      sh = this.sessionHandler;
+    }
+    if (args.size() == 0) {
+      this.messages.add("Please provide the name of the session to delete");
+      return ExitCode.ERROR;
+    }
+    if (args.size() > 1) {
+      this.messages.add("Please provide only one session to delete");
+      return ExitCode.ERROR;
+    }
+    String sessionName = args.get(0);
+    boolean found = sh.hasSessionName(sessionName);
+    if (!found) {
+      this.messages.add(
+          "No session with name '" + sessionName + "' found in file '" + sessionYamlFile + "'");
+      return ExitCode.ERROR;
+    }
+    boolean deleted = sh.deleteSession(sessionName);
+    if (deleted) {
+      System.err.println(
+          Utils.padEndMultiLine("Session '" + sessionName + "' deleted", proc.getWindowSize()));
+    } else {
+      this.messages.add("Failed to delete session '" + sessionName + "'");
+      return ExitCode.ERROR;
+    }
+    writeSessions(sh.getSessions(), sessionYamlFile);
+    return ExitCode.CLEAN_NO_FLUSH;
+  }
+
   private void openSession(List<String> args, TrackProcessor proc)
       throws IOException, InvalidCommandLineException {
     File sessionYamlFile =

src/main/java/session/SessionHandler.java

@@ -10,10 +10,7 @@
 import com.fasterxml.jackson.dataformat.yaml.YAMLMapper;
 import com.google.common.base.Joiner;
 import exceptions.SessionException;
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStream;
+import java.io.*;
 import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
 import java.nio.file.Paths;
@@ -75,6 +72,16 @@ private static void addOrReplaceSession(List<Session> sessions, Session session)
     sortSessionsByLastRead(sessions);
   }
 
+  public static void writeSessions(List<Session> sessions, File sessionFile) throws IOException {
+    YAMLFactory yf = new YAMLFactory();
+    yf.configure(WRITE_DOC_START_MARKER, false);
+    ObjectMapper mapper = new ObjectMapper(yf);
+    FileOutputStream fos = new FileOutputStream(sessionFile);
+    SequenceWriter sw = mapper.writerWithDefaultPrettyPrinter().writeValues(fos);
+    sw.write(sessions);
+    sw.close();
+  }
+
   public static void saveAs(File sessionFile, Session session, String sessionName)
       throws IOException, SessionException {
     session.setSessionName(sessionName);
@@ -83,13 +90,7 @@ public static void saveAs(File sessionFile, Session session, String sessionName)
       sessions = read(sessionFile);
     }
     addOrReplaceSession(sessions, session);
-    YAMLFactory yf = new YAMLFactory();
-    yf.configure(WRITE_DOC_START_MARKER, false);
-    ObjectMapper mapper = new ObjectMapper(yf);
-    FileOutputStream fos = new FileOutputStream(sessionFile);
-    SequenceWriter sw = mapper.writerWithDefaultPrettyPrinter().writeValues(fos);
-    sw.write(sessions);
-    sw.close();
+    writeSessions(sessions, sessionFile);
   }
 
   private static void sortSessionsByLastRead(List<Session> sessions) {
@@ -134,6 +135,15 @@ public void setSessionFile(File sessionFile) {
     this.sessionFile = sessionFile;
   }
 
+  public boolean hasSessionName(String sessionName) {
+    for (Session x : this.getSessions()) {
+      if (x.getSessionName().equals(sessionName)) {
+        return true;
+      }
+    }
+    return false;
+  }
+
   public String print(int upto, boolean mostRecentLast) throws IOException {
     List<String> out = new ArrayList<>();
     int i = 0;
@@ -155,4 +165,15 @@ public String print(int upto, boolean mostRecentLast) throws IOException {
     out.add("Session file: " + this.getSessionFile());
     return Joiner.on("\n").join(out);
   }
+
+  public boolean deleteSession(String sessionName) {
+    Session ss;
+    try {
+      ss = this.get(sessionName);
+    } catch (SessionException e) {
+      return false;
+    }
+    this.getSessions().remove(ss);
+    return true;
+  }
 }

src/test/java/samTextViewer/InteractiveInputTest.java

@@ -36,12 +36,7 @@ public static class ProcessInput {
   }
 
   public ProcessInput processInput(InteractiveInput ip, String cmd, TrackProcessor p)
-      throws SQLException,
-          InvalidGenomicCoordsException,
-          InvalidCommandLineException,
-          IOException,
-          ClassNotFoundException,
-          InvalidRecordException {
+      throws InvalidGenomicCoordsException, IOException {
     ByteArrayOutputStream err = new ByteArrayOutputStream();
     System.setErr(new PrintStream(err));
     ip.processInput(cmd, p);
@@ -116,6 +111,42 @@ public void canListCurrentSessionNameAndFile()
     assertTrue(pi.stderr.contains("Current session: no-fastafile"));
   }
 
+  @Test
+  public void canDeleteSession()
+      throws IOException,
+          InvalidConfigException,
+          SQLException,
+          InvalidGenomicCoordsException,
+          ClassNotFoundException,
+          InvalidRecordException,
+          InvalidCommandLineException {
+    new Config(null);
+    TrackProcessor proc = gimmeTrackProcessor("chr7:1001-1800", 80);
+    InteractiveInput ip = new InteractiveInput(new ConsoleReader(), 1);
+
+    ProcessInput pi = processInput(ip, "sessionDelete", proc);
+    pi = processInput(ip, "sessionDelete -f test_data/session.yaml", proc);
+    assertEquals(ExitCode.ERROR, ip.getInteractiveInputExitCode());
+    assertEquals("Please provide the name of the session to delete", pi.stderr.trim());
+
+    pi = processInput(ip, "sessionDelete", proc);
+    assertEquals(ExitCode.ERROR, ip.getInteractiveInputExitCode());
+    assertEquals("Please provide the name of the session to delete", pi.stderr.trim());
+
+    File f = new File("tmp.yml");
+    f.delete();
+    Files.copy(Paths.get("test_data/session.yaml"), Paths.get("tmp.yml"));
+
+    processInput(ip, "sessionDelete -f tmp.yml newSession", proc);
+    assertEquals(ExitCode.CLEAN_NO_FLUSH, ip.getInteractiveInputExitCode());
+    String txt = new String(Files.readAllBytes(Paths.get("tmp.yml")));
+    assertTrue(!txt.contains("newSession"));
+
+    processInput(ip, "sessionDelete -f tmp.yml newSession", proc);
+    assertEquals(ExitCode.ERROR, ip.getInteractiveInputExitCode());
+    f.delete();
+  }
+
   @Test
   public void canSaveCurrentSessionInPlace()
       throws IOException,
@@ -124,7 +155,6 @@ public void canSaveCurrentSessionInPlace()
           InvalidGenomicCoordsException,
           ClassNotFoundException,
           InvalidRecordException,
-          InvalidCommandLineException,
           SessionException {
     new Config(null);
     TrackProcessor proc = gimmeTrackProcessor("chr7:1001-1800", 80);
@@ -165,7 +195,6 @@ public void canReplaceGenome()
           IOException,
           ClassNotFoundException,
           InvalidRecordException,
-          InvalidCommandLineException,
           InvalidConfigException {
     new Config(null);
     TrackProcessor proc = gimmeTrackProcessor("chr7:1001-1800", 80);
@@ -187,8 +216,7 @@ public void canOpenSessionWithFileMissing()
           SQLException,
           InvalidGenomicCoordsException,
           ClassNotFoundException,
-          InvalidRecordException,
-          InvalidCommandLineException {
+          InvalidRecordException {
     new Config(null);
     TrackProcessor proc = gimmeTrackProcessor("chr7:1001-1800", 80);
 
@@ -213,8 +241,7 @@ public void canOpenSessionWithFastaFileMissing()
           SQLException,
           InvalidGenomicCoordsException,
           ClassNotFoundException,
-          InvalidRecordException,
-          InvalidCommandLineException {
+          InvalidRecordException {
     new Config(null);
     TrackProcessor proc = gimmeTrackProcessor("chr7:1001-1800", 80);
 
@@ -275,8 +302,7 @@ public void canOpenSession()
           SQLException,
           InvalidGenomicCoordsException,
           ClassNotFoundException,
-          InvalidRecordException,
-          InvalidCommandLineException {
+          InvalidRecordException {
     new Config(null);
     TrackProcessor proc = gimmeTrackProcessor("chr7:1001-1800", 80);
     InteractiveInput ip = new InteractiveInput(new ConsoleReader(), 1);
@@ -321,7 +347,6 @@ public void canSaveSession()
           InvalidGenomicCoordsException,
           ClassNotFoundException,
           InvalidRecordException,
-          InvalidCommandLineException,
           SessionException {
     new Config(null);
     TrackProcessor proc = gimmeTrackProcessor("chr7:1001-1800", 80);
@@ -341,8 +366,7 @@ public void canPrintGenome()
           ClassNotFoundException,
           InvalidGenomicCoordsException,
           InvalidRecordException,
-          SQLException,
-          InvalidCommandLineException {
+          SQLException {
     new Config(null);
     TrackProcessor proc;
     InteractiveInput ip = new InteractiveInput(new ConsoleReader(), 1);
@@ -358,7 +382,6 @@ public void canMovePositionByColumn()
           InvalidRecordException,
           ClassNotFoundException,
           SQLException,
-          InvalidCommandLineException,
           InvalidConfigException {
 
     new Config(null);
@@ -422,12 +445,7 @@ public void canMovePositionByColumn()
 
   @Test
   public void canPrintHelp()
-      throws InvalidGenomicCoordsException,
-          IOException,
-          ClassNotFoundException,
-          InvalidRecordException,
-          SQLException,
-          InvalidCommandLineException {
+      throws InvalidGenomicCoordsException, IOException, InvalidRecordException {
 
     InteractiveInput ip = new InteractiveInput(null, 1);
 

src/test/java/session/SessionHandlerTest.java

@@ -1,7 +1,6 @@
 package session;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.*;
 
 import colouring.Config;
 import exceptions.InvalidColourException;
@@ -27,11 +26,19 @@
 public class SessionHandlerTest {
 
   @Test
-  public void testGetSessionByNameOrIndex()
-      throws IOException,
-          SessionException,
-          InvalidGenomicCoordsException,
-          InvalidTrackTypeException {
+  public void canDeleteSession() throws IOException, SessionException {
+    InputStream yaml = Files.newInputStream(Paths.get("test_data/session.yaml"));
+    SessionHandler sh = new SessionHandler(new File("test_data/session.yaml"));
+    sh.get("newSession");
+    boolean deleted = sh.deleteSession("newSession");
+    assertTrue(deleted);
+
+    deleted = sh.deleteSession("newSession");
+    assertFalse(deleted);
+  }
+
+  @Test
+  public void testGetSessionByNameOrIndex() throws IOException, SessionException {
     InputStream yaml = Files.newInputStream(Paths.get("test_data/session.yaml"));
     SessionHandler sh = new SessionHandler(new File("test_data/session.yaml"));
     assertEquals("no-fastafile", sh.get("1").getSessionName());