Temp commit for session implementation

src/main/java/samTextViewer/InteractiveInput.java

@@ -22,6 +22,7 @@
 import net.sourceforge.argparse4j.inf.ArgumentParserException;
 import session.Session;
 import session.SessionHandler;
+import tracks.Track;
 import utils.Tokenizer;
 
 /** Class to process input from console */
@@ -33,8 +34,10 @@ public class InteractiveInput {
  private static int debug;
  private SAMSequenceDictionary samSeqDict;
  private String fasta;
- private String messages = ""; // Messages that may be sent from the various methods.
+ private List<String> messages =
+ new ArrayList<>(); // Messages that may be sent from the various methods.
  private SessionHandler sessionHandler;
+ private String currentSessionName;
 
  public InteractiveInput(ConsoleReader console, int debug) {
  InteractiveInput.debug = debug;
@@ -186,6 +189,7 @@ protected TrackProcessor processInput(String cmdConcatInput, TrackProcessor proc
  System.out.print("\033[0m");
  console.clearScreen();
  console.flush();
+ SessionHandler.saveAs(SessionHandler.DEFAULT_SESSION_FILE, proc.toSession(), "");
  System.exit(0);
 
  // * These commands change the GenomicCoordinates (navigate) but do not touch the tracks.
@@ -283,22 +287,21 @@ protected TrackProcessor processInput(String cmdConcatInput, TrackProcessor proc
  List<String> args = new ArrayList<>(cmdTokens);
  args.remove(0);
  if (args.isEmpty()) {
- this.messages +=
- "Provide a sub-command to handle a session. See `session -h` for details.";
+ this.messages.add(
+ "Provide a sub-command to handle a session. See `session -h` for details.");
  this.setInteractiveInputExitCode(ExitCode.ERROR);
  } else if (args.get(0).equals("open")) {
  args.remove(0);
  this.openSession(args, proc);
  } else if (args.get(0).equals("save")) {
  args.remove(0);
  this.saveSession(args, proc);
+ this.setInteractiveInputExitCode(ExitCode.CLEAN_NO_FLUSH);
  } else if (args.get(0).equals("list")) {
  args.remove(0);
- throw new RuntimeException("TODO");
- // this.listSessions(args, proc);
- // this.messages += Joiner.on("\n").join(this.session.getMessages());
+ this.setInteractiveInputExitCode(this.listSessions(args, proc));
  } else {
- this.messages += "Invalid sub-command. See `session -h` for details.";
+ this.messages.add("Invalid sub-command. See `session -h` for details.");
  this.setInteractiveInputExitCode(ExitCode.ERROR);
  }
  } else if (cmdTokens.get(0).equals("setGenome")) {
@@ -377,14 +380,14 @@ protected TrackProcessor processInput(String cmdConcatInput, TrackProcessor proc
  this.interactiveInputExitCode = ExitCode.ERROR;
  continue;
  }
- messages += proc.getTrackSet().dropTracksWithRegex(cmdTokens);
+ messages.add(proc.getTrackSet().dropTracksWithRegex(cmdTokens));
 
  } else if (cmdTokens.get(0).equals("orderTracks")) {
  cmdTokens.remove(0);
  proc.getTrackSet().orderTracks(cmdTokens);
 
  } else if (cmdTokens.get(0).equals("editNames")) {
- messages += proc.getTrackSet().editNamesForRegex(cmdTokens);
+ messages.add(proc.getTrackSet().editNamesForRegex(cmdTokens));
 
  } else if (cmdTokens.get(0).equals(Command.print.toString())) {
  proc.getTrackSet().setPrintModeAndPrintFeaturesForRegex(cmdTokens);
@@ -470,8 +473,8 @@ protected TrackProcessor processInput(String cmdConcatInput, TrackProcessor proc
  }
 
  } else if (cmdTokens.get(0).equals("bookmark")) {
- messages +=
- proc.getTrackSet().bookmark(proc.getGenomicCoordsHistory().current(), cmdTokens);
+ messages.add(
+ proc.getTrackSet().bookmark(proc.getGenomicCoordsHistory().current(), cmdTokens));
 
  } else {
  System.err.println(
@@ -550,10 +553,11 @@ protected TrackProcessor processInput(String cmdConcatInput, TrackProcessor proc
  break;
  }
  } // END OF LOOP THROUGH CHAIN OF INPUT COMMANDS
- if (!messages.isEmpty()) {
- System.err.println(Utils.padEndMultiLine(messages.trim(), proc.getWindowSize()));
+ if (!this.messages.isEmpty()) {
+ System.err.println(
+ Utils.padEndMultiLine(Joiner.on("\n").join(this.messages), proc.getWindowSize()));
  }
- messages = "";
+ this.messages = new ArrayList<>();
  return proc;
  }
 
@@ -827,37 +831,115 @@ private void setConfigOpt(List<String> cmdTokens)
 
  private void saveSession(List<String> args, TrackProcessor proc)
  throws InvalidCommandLineException, IOException, SessionException {
- String sessionYamlFile =
- Utils.getArgForParam(args, "-f", SessionHandler.DEFAULT_SESSION_FILE.getAbsolutePath());
- // if (args.isEmpty() && ) {}
- SessionHandler.saveAs(new File(sessionYamlFile), proc.toSession(), "stuff");
+ File sessionYamlFile;
+ String sf = Utils.getArgForParam(args, "-f", null);
+ if (sf == null && this.sessionHandler == null) {
+ sessionYamlFile = SessionHandler.DEFAULT_SESSION_FILE;
+ } else if (sf == null) {
+ sessionYamlFile = sessionHandler.getSessionFile();
+ } else {
+ sessionYamlFile = new File(sf);
+ }
+
+ if (!sessionYamlFile.getAbsoluteFile().getParentFile().exists()) {
+ this.messages.add("Directory '" + sessionYamlFile.getParentFile() + "' does not exist");
+ this.interactiveInputExitCode = ExitCode.ERROR;
+ return;
+ }
+ if (!sessionYamlFile.exists()) {
+ try {
+ sessionYamlFile.createNewFile();
+ sessionYamlFile.delete();
+ } catch (IOException e) {
+ this.messages.add("Cannot write to file '" + sessionYamlFile + "'");
+ this.interactiveInputExitCode = ExitCode.ERROR;
+ return;
+ }
+ } else if (!sessionYamlFile.canWrite()) {
+ this.messages.add("Cannot write to file '" + sessionYamlFile + "'");
+ this.interactiveInputExitCode = ExitCode.ERROR;
+ return;
+ }
+ String sessionName = this.getCurrentSessionName();
+ if (args.size() == 0 && sessionName == null) {
+ this.messages.add("Please provide a session name. See `session -h` for help");
+ this.interactiveInputExitCode = ExitCode.ERROR;
+ return;
+ } else if (args.size() > 1) {
+ this.messages.add("Too many arguments. See `session -h` for help");
+ this.interactiveInputExitCode = ExitCode.ERROR;
+ return;
+ } else if (args.size() == 1) {
+ sessionName = args.get(0);
+ }
+ SessionHandler.saveAs(sessionYamlFile, proc.toSession(), sessionName);
+ this.setCurrentSessionName(sessionName);
+ this.sessionHandler = new SessionHandler(sessionYamlFile);
+ this.messages.add(
+ "Session '" + sessionName + "' saved to '" + sessionYamlFile.getAbsolutePath() + "'");
+ }
+
+ private ExitCode listSessions(List<String> args, TrackProcessor proc)
+ throws InvalidGenomicCoordsException,
+ IOException,
+ SessionException,
+ 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;
+ }
+ int nsessions = Integer.parseInt(Utils.getArgForParam(args, "-n", "10"));
+ String sessionString = sh.print(nsessions);
+ System.err.println(Utils.padEndMultiLine(sessionString, proc.getWindowSize()));
+ return ExitCode.CLEAN_NO_FLUSH;
  }
 
  private void openSession(List<String> args, TrackProcessor proc)
- throws IOException,
-  InvalidCommandLineException,
-  InvalidGenomicCoordsException,
- InvalidTrackTypeException {
- String sessionYamlFile = Utils.getArgForParam(args, "-f", "");
+ throws IOException, InvalidCommandLineException {
+ File sessionYamlFile =
+ new File(
+  Utils.getArgForParam(
+  args, "-f", SessionHandler.DEFAULT_SESSION_FILE.getAbsolutePath()));
  String sessionNameOrIndex;
  if (args.isEmpty()) {
- this.messages +=
- "Please provide the name or number of the session to open. See `session -h` for details";
- this.interactiveInputExitCode = ExitCode.ERROR;
- return;
+ sessionNameOrIndex = "1";
  } else if (args.size() == 1) {
  sessionNameOrIndex = args.get(0);
  } else {
- this.messages += "Too many arguments. See `session -h` for details";
+ this.messages.add("Too many arguments. See `session -h` for details");
  this.interactiveInputExitCode = ExitCode.ERROR;
  return;
  }
  Session session;
  try {
- this.sessionHandler = new SessionHandler(new File(sessionYamlFile));
+ this.sessionHandler = new SessionHandler(sessionYamlFile);
  session = this.sessionHandler.get(sessionNameOrIndex);
+ if (session.getGenome().samSeqDictSource != null
+ && !new File(session.getGenome().samSeqDictSource).exists()) {
+ this.messages.add(
+ "Warning: Sequence dictionary file '"
+ + session.getGenome().samSeqDictSource
+ + "' does not exist");
+ }
+ if (session.getGenome().fastaFile != null
+ && !new File(session.getGenome().fastaFile).exists()) {
+ this.messages.add(
+ "Warning: Fasta file '" + session.getGenome().fastaFile + "' does not exist");
+ }
  } catch (SessionException e) {
- this.messages += e.getMessage();
+ this.messages.add(e.getMessage());
  this.interactiveInputExitCode = ExitCode.ERROR;
  return;
  }
@@ -866,9 +948,24 @@ private void openSession(List<String> args, TrackProcessor proc)
  proc.getGenomicCoordsHistory().setGenome(Collections.singletonList(gc.getFastaFile()));
  proc.getGenomicCoordsHistory().add(gc);
  proc.setTrackSet(session.toTrackSet());
+ this.setCurrentSessionName(session.getSessionName());
  } catch (Exception e) {
- this.messages +=
- "Unable to set genome for session " + sessionNameOrIndex + ". Session is:\n" + session;
+ this.messages.add(
+ "Unable to open session "
+ + sessionNameOrIndex
+ + ". Session is:\n"
+ + session
+ + "\n"
+ + e.getMessage());
+ }
+ List<String> passed = new ArrayList<>();
+ for (Track x : proc.getTrackSet().getTrackList()) {
+ passed.add(x.getTrackTag());
+ }
+ for (String tag : session.getTracks().keySet()) {
+ if (!passed.contains(tag)) {
+ this.messages.add("Warning: Failed to add track '" + tag + "'");
+ }
  }
  }
 
@@ -1222,4 +1319,12 @@ public ExitCode getInteractiveInputExitCode() {
  public void setInteractiveInputExitCode(ExitCode exitCode) {
  this.interactiveInputExitCode = exitCode;
  }
+
+ public String getCurrentSessionName() {
+ return currentSessionName;
+ }
+
+ public void setCurrentSessionName(String currentSessionName) {
+ this.currentSessionName = currentSessionName;
+ }
 }

src/main/java/session/Session.java

@@ -1,8 +1,5 @@
 package session;
 
-import exceptions.InvalidGenomicCoordsException;
-import exceptions.InvalidTrackTypeException;
-import java.io.IOException;
 import java.time.LocalDateTime;
 import java.time.format.DateTimeFormatter;
 import java.util.ArrayList;
@@ -12,28 +9,30 @@
 import tracks.TrackSet;
 
 public class Session {
- private final ArrayList<String> messages = new ArrayList<>();
  private String sessionName;
  private String lastRead;
  private SessionGenome genome;
  private Map<String, SessionTrack> tracks;
 
  public Session() {}
 
- public Session(SessionGenome gc, Map<String, SessionTrack> tracks) {
+ public Session(SessionGenome sessionGenome, Map<String, SessionTrack> tracks) {
  LocalDateTime date = LocalDateTime.now();
  this.setLastRead(date.format(DateTimeFormatter.ISO_LOCAL_DATE_TIME));
- this.genome = gc;
+ this.genome = sessionGenome;
  this.tracks = tracks;
  }
 
- public TrackSet toTrackSet()
- throws InvalidGenomicCoordsException, IOException, InvalidTrackTypeException {
+ public TrackSet toTrackSet() {
  List<Track> trackList = new ArrayList<>();
  for (String trackName : tracks.keySet()) {
- SessionTrack st = tracks.get(trackName);
- Track tr = st.toTrack(trackName, this.getGenome().toGenomicCoords());
- trackList.add(tr);
+ try {
+ SessionTrack st = tracks.get(trackName);
+ Track tr = st.toTrack(trackName, this.getGenome().toGenomicCoords());
+ trackList.add(tr);
+ } catch (Exception e) {
+ //
+ }
  }
  return new TrackSet(trackList);
  }
@@ -70,10 +69,6 @@ public void setTracks(Map<String, SessionTrack> track) {
  this.tracks = track;
  }
 
- public ArrayList<String> getMessages() {
- return this.messages;
- }
-
  @Override
  public boolean equals(Object o) {
  if (o == this) {

src/main/java/session/SessionGenome.java

@@ -23,7 +23,7 @@ public SessionGenome() {}
  public SessionGenome(GenomicCoords gc) {
  this.chrom = gc.getChrom();
  this.from = gc.getFrom();
- this.to = gc.getTerminalWidth();
+ this.to = gc.getTo();
  this.fastaFile =
  gc.getFastaFile() == null ? null : new File(gc.getFastaFile()).getAbsolutePath();
  this.samSeqDictSource = gc.getSamSeqDictSource();
@@ -38,8 +38,9 @@ public GenomicCoords toGenomicCoords() throws InvalidGenomicCoordsException, IOE
  SAMSequenceDictionary samSeqDict = null;
  if (this.samSeqDictSource != null && new File(this.samSeqDictSource).exists()) {
  SamReaderFactory srf = SamReaderFactory.make();
- SamReader samReader = srf.open(new File(this.samSeqDictSource));
- samSeqDict = samReader.getFileHeader().getSequenceDictionary();
+ try (SamReader samReader = srf.open(new File(this.samSeqDictSource))) {
+ samSeqDict = samReader.getFileHeader().getSequenceDictionary();
+ }
  }
  return new GenomicCoords(region, Utils.getTerminalWidth(), samSeqDict, ff);
  }