Tmp commit

src/main/java/exceptions/InvalidTrackTypeException.java

@@ -0,0 +1,13 @@
+package exceptions;
+
+public class InvalidTrackTypeException extends Exception {
+    public InvalidTrackTypeException() {
+
+    }
+    public InvalidTrackTypeException(String message)
+    {
+        super(message);
+    }
+    /** */
+    private static final long serialVersionUID = 1L;
+}

src/main/java/exceptions/SessionException.java

@@ -0,0 +1,12 @@
+package exceptions;
+
+public class SessionException extends Exception {
+    public SessionException() {
+
+    }
+    public SessionException(String message)
+    {
+        super(message);
+    }
+    private static final long serialVersionUID = 1L;
+}

src/main/java/samTextViewer/ASCIIGenomeHistory.java

@@ -127,7 +127,7 @@ public void setCommands(List<String> commands) {
     this.commands = commands;
   }
 
-  private void write(File outYaml) throws IOException {
+  protected void write(File outYaml) throws IOException {
     Map<String, Object> asciigenome_history = new HashMap<String, Object>();
 
     // List of commands

src/main/java/samTextViewer/InteractiveInput.java

@@ -8,22 +8,14 @@
 import com.google.common.collect.Lists;
 import commandHelp.Command;
 import commandHelp.CommandList;
-import exceptions.InvalidColourException;
-import exceptions.InvalidCommandLineException;
-import exceptions.InvalidConfigException;
-import exceptions.InvalidGenomicCoordsException;
-import exceptions.InvalidRecordException;
+import exceptions.*;
 import htsjdk.samtools.SAMSequenceDictionary;
 import java.io.BufferedReader;
 import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.InputStreamReader;
 import java.sql.SQLException;
-import java.util.ArrayList;
-import java.util.LinkedHashMap;
-import java.util.LinkedHashSet;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
 import java.util.regex.Pattern;
 import java.util.regex.PatternSyntaxException;
 import jline.console.ConsoleReader;
@@ -41,6 +33,7 @@ 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.
 
   public InteractiveInput(ConsoleReader console, int debug) {
     InteractiveInput.debug = debug;
@@ -89,7 +82,6 @@ protected TrackProcessor processInput(String cmdConcatInput, TrackProcessor proc
     this.fasta = proc.getGenomicCoordsHistory().current().getFastaFile();
     this.samSeqDict = proc.getGenomicCoordsHistory().current().getSamSeqDict();
 
-    String messages = ""; // Messages that may be sent from the various methods.
     for (String cmdString : cmdInputChainList) {
 
       List<String> cmdTokens = new Tokenizer(cmdString).tokenize();
@@ -812,15 +804,22 @@ private void setConfigOpt(List<String> cmdTokens)
     }
   }
 
-  private void openSession(String sessionYamlFile, String session, TrackProcessor proc) throws IOException, InvalidGenomicCoordsException, InvalidCommandLineException {
-    Session ss = new Session(sessionYamlFile, session, Utils.getTerminalWidth());
-    GenomicCoords testSeqDict = new GenomicCoords(ss.getRegion(), Utils.getTerminalWidth(), null, null);
-    List<String> genomeFile = new ArrayList<String>();
-    genomeFile.add(ss.getGenomeFile());
-    testSeqDict.setGenome(genomeFile, true);
-    proc.getGenomicCoordsHistory().setGenome(genomeFile);
-    proc.getGenomicCoordsHistory()
-            .add(testSeqDict);
+  private void openSession(String sessionYamlFile, String session, TrackProcessor proc) throws IOException {
+      Session ss = null;
+      try {
+          ss = new Session(sessionYamlFile, session);
+      } catch (SessionException e) {
+          this.messages += e.getMessage();
+          this.interactiveInputExitCode = ExitCode.ERROR;
+          return;
+      }
+      try {
+        GenomicCoords gc = ss.getGenome();
+        proc.getGenomicCoordsHistory().setGenome(Collections.singletonList(gc.getFastaFile()));
+        proc.getGenomicCoordsHistory().add(gc);
+      } catch (Exception e) {
+        this.messages += "Unable to set genome for session " + session;
+    }
   }
 
   private void setGenome(List<String> cmdTokens, TrackProcessor proc)

src/main/java/session/Session.java

@@ -4,7 +4,9 @@
 import com.esotericsoftware.yamlbeans.YamlReader;
 import exceptions.InvalidGenomicCoordsException;
 import exceptions.InvalidRecordException;
+import exceptions.InvalidTrackTypeException;
 import samTextViewer.GenomicCoords;
+import samTextViewer.Utils;
 import tracks.Track;
 import tracks.TrackPileup;
 import tracks.TrackReads;
@@ -15,26 +17,36 @@
 import java.io.IOException;
 import java.sql.SQLException;
 import java.util.*;
+import exceptions.SessionException;
 
 public class Session {
   private ArrayList<Map<String, Object>> sessionList;
   private Map<String, Object> session;
 
-  public Session(String sessionYamlFile, String session, int terminalWidth) throws FileNotFoundException, YamlException {
+  public Session(String sessionYamlFile, String session) throws FileNotFoundException, YamlException, SessionException {
     // Read yaml file
     // Get genome file if set and parse it into genomicCoords
     // For each track populate trackSet
     YamlReader reader = new YamlReader(new FileReader(sessionYamlFile));
     this.sessionList = (ArrayList<Map<String, Object>>) reader.read();
     this.sortListSessionsLastRead(this.sessionList);
-    this.session = this.sessionList.get(0);
+    for (Map<String, Object> ss : this.sessionList) {
+      if (((String) ss.get("name")).equals(session)) {
+        this.session = ss;
+        break;
+      }
+    }
+    if (this.session == null) {
+      throw new SessionException("Session '" + session + "' not found in file " + sessionYamlFile);
+    }
   }
 
-  public String getGenomeFile() {
+  public GenomicCoords getGenome() throws IOException, InvalidGenomicCoordsException {
     Map<String, Object> genome = (Map<String, Object>) this.session.get("genome");
-    return (String) genome.get("file");
+    return new GenomicCoords((String) genome.get("region"), Utils.getTerminalWidth(),null, (String) genome.get("fasta"));
   }
-  public String getRegion() {
+
+  private String getRegion() {
     Map<String, Object> genome = (Map<String, Object>) this.session.get("genome");
     return (String) genome.get("region");
   }
@@ -43,11 +55,11 @@ private void sortListSessionsLastRead(List<Map<String, Object>> ss) {
     ss.sort((o1, o2) -> ((String) o2.get("lastRead")).compareTo((String) o1.get("lastRead")));
   }
 
-  public TrackSet getTrackSet() throws Exception {
+  public TrackSet getTrackSet() throws SQLException, InvalidGenomicCoordsException, IOException, InvalidRecordException, ClassNotFoundException, InvalidTrackTypeException {
     List<Map<String, Object>> tracks = (List<Map<String, Object>>) this.session.get("tracks");
     List<String> tl = new ArrayList<String>();
     TrackSet trackSet = new TrackSet(tl, null);
-    GenomicCoords gc = new GenomicCoords(this.getRegion(), 80, null, null);
+    GenomicCoords gc = new GenomicCoords(this.getRegion(), Utils.getTerminalWidth(), null, null);
     for (Map<String, Object> map : tracks) {
       Track tr;
       String type = (String) map.get("type");
@@ -56,7 +68,7 @@ public TrackSet getTrackSet() throws Exception {
       } else if (type.equals("TrackReads")) {
         tr = new TrackReads((String) map.get("source"), gc);
       } else {
-        throw new Exception("Invalid type: " + type);
+        throw new InvalidTrackTypeException("Invalid type: " + type);
       }
       trackSet.addTrack(tr, (String) map.get("name"));
     }

src/test/java/session/SessionTest.java

@@ -1,20 +1,31 @@
 package session;
 
 import coloring.Config;
-import com.esotericsoftware.yamlbeans.YamlException;
+import exceptions.InvalidConfigException;
 import exceptions.InvalidGenomicCoordsException;
-import exceptions.InvalidRecordException;
+import exceptions.SessionException;
 import org.junit.Test;
+import samTextViewer.GenomicCoords;
 
-import java.io.FileNotFoundException;
 import java.io.IOException;
-import java.sql.SQLException;
+
+import static org.junit.Assert.assertEquals;
 
 public class SessionTest {
+    /** TESTS:
+        * genome.file not found
+        * genome.file not valid
+        * genome.file empty or not present (session doesn't have a genome)
+        * genome.region Invalid (malformed, extending beyond contig, contig not found in genome.file)
+        * genome.region empty or not present
+     */
     @Test
-    public void canReadSession() throws Exception {
+    public void canReadValidGenome() throws IOException, InvalidConfigException, SessionException, InvalidGenomicCoordsException {
         new Config(null);
-        Session session = new Session("test_data/session.yaml", "last", 80);
-        System.err.println(session.getTrackSet().getTrackList());
+        Session session = new Session("test_data/session.yaml", "S2");
+        GenomicCoords gc = session.getGenome();
+        assertEquals((long)gc.getFrom(), 1);
+        assertEquals((long)gc.getTo(), 10000);
+        assertEquals(gc.getSamSeqDict().getSequence("chr7").getSequenceName(), "chr7");
     }
 }

test_data/session.yaml

@@ -3,7 +3,7 @@
     name: mysession,
     lastRead: "2024-01-01T20:40:00",
     genome: {
-      file: "test_data/chr7.fa",
+      fasta: "test_data/chr7.fa",
       region: "chr7:1-1000",
     },
     tracks: [
@@ -14,25 +14,46 @@
       }
     ]
   },
-    {
-        name: mysession2,
-        lastRead: "2024-01-02T20:40:00",
-        genome: {
-            file: "test_data/chr7.fa",
-            region: "chr7:1-10000",
-        },
-        tracks: [
-          {
-                name: "ds051#1",
-                source: "test_data/ds051.actb.bam",
-                type: "TrackPileup",
-          },
-          {
-            name: "ds051#2",
+  {
+    name: S2,
+    lastRead: "2024-01-02T20:40:00",
+    genome: {
+        fasta: "test_data/chr7.fa",
+        region: "chr7:1-10000",
+    },
+    tracks: [
+      {
+            name: "ds051#1",
             source: "test_data/ds051.actb.bam",
-            type: "TrackReads",
-          }
+            type: "TrackPileup",
+      },
+      {
+        name: "ds051#2",
+        source: "test_data/ds051.actb.bam",
+        type: "TrackReads",
+      }
 
-        ]
-    }
+    ]
+  },
+  {
+    name: genome-not-found,
+    lastRead: "2024-01-03T20:40:00",
+    genome: {
+      fasta: "notfound.fasta",
+      region: "chr7:1-10000",
+    },
+    tracks: [
+      {
+        name: "ds051#1",
+        source: "test_data/ds051.actb.bam",
+        type: "TrackPileup",
+      },
+      {
+        name: "ds051#2",
+        source: "test_data/ds051.actb.bam",
+        type: "TrackReads",
+      }
+
+    ]
+  }
 ]