JAL-3628 Test for doubly saved single backup file scheme

diff --git a/test/jalview/io/BackupFilesTest.java b/test/jalview/io/BackupFilesTest.java
index 64cf902..e735ef6 100644 (file)
--- a/test/jalview/io/BackupFilesTest.java
+++ b/test/jalview/io/BackupFilesTest.java
@@ -1,12 +1,5 @@
 package jalview.io;
 
-import jalview.bin.Cache;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceI;
-import jalview.gui.AlignFrame;
-import jalview.gui.JvOptionPane;
-
 import java.io.File;
 import java.io.IOException;
 import java.nio.file.Files;
@@ -24,6 +17,13 @@ import org.testng.annotations.AfterClass;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
+
 public class BackupFilesTest
 {
   @BeforeClass(alwaysRun = true)
@@ -43,7 +43,6 @@ public class BackupFilesTest
 
   private static String testFilename = testBasename + testExt;
 
-
   private static String testFile = testDir + File.separatorChar
           + testFilename;
 
@@ -88,6 +87,33 @@ public class BackupFilesTest
     Assert.assertTrue(backupFiles.length == 0);
   }
 
+  // save with no numbers in the backup file names
+  @Test(groups = { "Functional" })
+  public void backupsEnabledSingleFileBackupTest() throws Exception
+  {
+    // Enable BackupFiles and set noMax so all backupfiles get kept
+    String mysuffix = "~";
+    BackupFilesPresetEntry bfpe = new BackupFilesPresetEntry(mysuffix, 1,
+            false, true, 1, false);
+    setBackupFilesOptions(true, false, true,
+            "test/jalview/io/testProps_singlefilebackup.jvprops", bfpe);
+
+    // init the newFile and backups (i.e. make sure newFile exists on its own
+    // and has no backups)
+    initNewFileForTesting();
+    HashMap<Integer, String> correctindexmap = new HashMap<>();
+    correctindexmap.put(0, "backupfilestestTemp.fa~");
+
+    save();
+    Assert.assertTrue(checkBackupFiles(correctindexmap, newFile, "~", 1));
+
+    // and a second time -- see JAL-3628
+    save();
+    Assert.assertTrue(checkBackupFiles(correctindexmap, newFile, "~", 1));
+
+    cleanupTmpFiles(newFile, "~", 1);
+  }
+
   // save keeping all backup files
   @Test(groups = { "Functional" })
   public void backupsEnabledNoRollMaxTest() throws Exception
@@ -208,10 +234,16 @@ public class BackupFilesTest
   private void setBackupFilesOptions(boolean enabled, boolean reverse,
           boolean noMax)
   {
-    Cache.loadProperties("test/jalview/io/testProps.jvprops");
-
     BackupFilesPresetEntry bfpe = new BackupFilesPresetEntry(suffix, digits,
             reverse, noMax, rollMax, false);
+    setBackupFilesOptions(enabled, reverse, noMax,
+            "test/jalview/io/testProps.jvprops", bfpe);
+  }
+
+  private void setBackupFilesOptions(boolean enabled, boolean reverse,
+          boolean noMax, String propsFile, BackupFilesPresetEntry bfpe)
+  {
+    Cache.loadProperties(propsFile);
 
     Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
             Boolean.toString(enabled));
@@ -238,7 +270,7 @@ public class BackupFilesTest
   {
     if (af != null)
     {
-    af.saveAlignment(newFile, jalview.io.FileFormat.Fasta);
+      af.saveAlignment(newFile, jalview.io.FileFormat.Fasta);
     }
   }
 
@@ -277,12 +309,17 @@ public class BackupFilesTest
   @AfterClass(alwaysRun = true)
   private void cleanupTmpFiles()
   {
-    File newfile = new File(newFile);
+    cleanupTmpFiles(newFile, suffix, digits);
+  }
+
+  private void cleanupTmpFiles(String file, String mysuffix, int mydigits)
+  {
+    File newfile = new File(file);
     if (newfile.exists())
     {
       newfile.delete();
     }
-    File[] tmpFiles = getBackupFiles(newFile, suffix, digits);
+    File[] tmpFiles = getBackupFiles(file, mysuffix, mydigits);
     for (int i = 0; i < tmpFiles.length; i++)
     {
       if (actuallyDeleteTmpFiles)
@@ -298,8 +335,8 @@ public class BackupFilesTest
 
   private static File[] getBackupFiles(String f, String s, int i)
   {
-    TreeMap<Integer, File> bfTreeMap = BackupFiles.getBackupFilesAsTreeMap(f,
-            s, i);
+    TreeMap<Integer, File> bfTreeMap = BackupFiles
+            .getBackupFilesAsTreeMap(f, s, i);
     File[] backupFiles = new File[bfTreeMap.size()];
     bfTreeMap.values().toArray(backupFiles);
     return backupFiles;
@@ -313,8 +350,14 @@ public class BackupFilesTest
   private static boolean checkBackupFiles(HashMap<Integer, String> indexmap)
           throws IOException
   {
-    TreeMap<Integer, File> map = BackupFiles.getBackupFilesAsTreeMap(newFile,
-            suffix, digits);
+    return checkBackupFiles(indexmap, newFile, suffix, digits);
+  }
+
+  private static boolean checkBackupFiles(HashMap<Integer, String> indexmap,
+          String file, String mysuffix, int mydigits) throws IOException
+  {
+    TreeMap<Integer, File> map = BackupFiles.getBackupFilesAsTreeMap(file,
+            mysuffix, mydigits);
     Enumeration<Integer> indexesenum = Collections
             .enumeration(indexmap.keySet());
     while (indexesenum.hasMoreElements())
@@ -351,8 +394,8 @@ public class BackupFilesTest
 
   private static boolean checkBackupFiles(int[] indexes) throws IOException
   {
-    TreeMap<Integer, File> map = BackupFiles.getBackupFilesAsTreeMap(newFile,
-            suffix, digits);
+    TreeMap<Integer, File> map = BackupFiles
+            .getBackupFilesAsTreeMap(newFile, suffix, digits);
     for (int m = 0; m < indexes.length; m++)
     {
       int i = indexes[m];
@@ -370,7 +413,8 @@ public class BackupFilesTest
       {
         return false;
       }
-      // check the filename -- although this uses the same code to forumulate the filename so not much of a test!
+      // check the filename -- although this uses the same code to forumulate
+      // the filename so not much of a test!
       String filename = BackupFilenameParts.getBackupFilename(i,
               newBasename + testExt, suffix, digits);
       if (!filename.equals(f.getName()))
@@ -400,10 +444,14 @@ public class BackupFilesTest
     return filenames;
   }
 
-  public static boolean sequencesEqual(SequenceI s1, SequenceI s2) {
-    if (s1 == null && s2 == null) {
+  public static boolean sequencesEqual(SequenceI s1, SequenceI s2)
+  {
+    if (s1 == null && s2 == null)
+    {
       return true;
-    } else if (s1 == null || s2 == null) {
+    }
+    else if (s1 == null || s2 == null)
+    {
       return false;
     }
     return (s1.getName().equals(s2.getName())

diff --git a/test/jalview/io/testProps_singlefilebackup.jvprops b/test/jalview/io/testProps_singlefilebackup.jvprops
new file mode 100644 (file)
index 0000000..dea7713
--- /dev/null
+++ b/test/jalview/io/testProps_singlefilebackup.jvprops
@@ -0,0 +1,112 @@
+#---JalviewX Properties File---
+#Mon Dec 14 16:32:45 GMT 2020
+BACKUPFILES_CUSTOM=_BACKUPFILESTESTTMP%n\t6\tfalse\tfalse\t2\tfalse
+BACKUPFILES_ENABLED=true
+BACKUPFILES_PRESET=2
+BACKUPFILES_SAVED=~\t1\tfalse\tfalse\t1\tfalse
+ADD_SS_ANN=false
+ADD_TEMPFACT_ANN=false
+ANNOTATIONCOLOUR_MAX=ff0000
+ANNOTATIONCOLOUR_MIN=ffc800
+ANTI_ALIAS=false
+AUTHORFNAMES=Jim Procter, Mungo Carstairs, Ben Soares, Kira Mourao, Tochukwu 'Charles' Ofoegbu, Andrew Waterhouse, Jan Engelhardt, Lauren Lui, Anne Menard, Daniel Barton, Natasha Sherstnev, David Roldan-Martinez, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton
+AUTHORS=J Procter, M Carstairs, B Soares, K Mourao, TC Ofoegbu, AM Waterhouse, J Engelhardt, LM Lui, A Menard, D Barton, N Sherstnev, D Roldan-Martinez, M Clamp, S Searle, G Barton
+AUTO_CALC_CONSENSUS=true
+BLC_JVSUFFIX=true
+BUILD_DATE=20\:10\:14 10 December 2020
+CLUSTAL_JVSUFFIX=true
+DAS_ACTIVE_SOURCE=uniprot\t
+DAS_LOCAL_SOURCE=
+DAS_REGISTRY_URL=http\://www.ebi.ac.uk/das-srv/registry/das/
+DEFAULT_COLOUR=None
+DEFAULT_COLOUR_NUC=None
+DEFAULT_COLOUR_PROT=None
+DEFAULT_FILE_FORMAT=FASTA
+DEFAULT_URL=EMBL-EBI Search
+EPS_RENDERING=Prompt each time
+EXPORT_EMBBED_BIOJSON=true
+FASTA_JVSUFFIX=true
+FIGURE_AUTOIDWIDTH=false
+FIGURE_FIXEDIDWIDTH=
+FIGURE_USERIDWIDTH=
+FONT_NAME=SansSerif
+FONT_SIZE=10
+FONT_STYLE=plain
+GAP_COLOUR=c0c0c0
+GAP_SYMBOL=-
+HIDDEN_COLOUR=2c2c2c
+HTML_RENDERING=Prompt each time
+ID_ITALICS=true
+INSTALLATION=Source git-commit\:225f7f621b [develop]
+JALVIEW_NEWS_RSS_LASTMODIFIED=29 Oct 2020, 21\:44\:11
+JALVIEW_RSS_WINDOW_SCREEN_HEIGHT=301
+JALVIEW_RSS_WINDOW_SCREEN_WIDTH=550
+JALVIEW_RSS_WINDOW_SCREEN_X=0
+JALVIEW_RSS_WINDOW_SCREEN_Y=0
+JAVA_CONSOLE_SCREEN_HEIGHT=250
+JAVA_CONSOLE_SCREEN_WIDTH=337
+JAVA_CONSOLE_SCREEN_X=622
+JAVA_CONSOLE_SCREEN_Y=320
+JWS2HOSTURLS=http\://www.compbio.dundee.ac.uk/jabaws
+LAST_DIRECTORY=/Volumes/Data/Users/jimp/Documents/testing/Jalview/examples
+logs.Jalview.level=DEBUG
+MAP_WITH_SIFTS=false
+MSF_JVSUFFIX=true
+NOQUESTIONNAIRES=true
+PAD_GAPS=false
+PFAM_JVSUFFIX=true
+PILEUP_JVSUFFIX=true
+PIR_JVSUFFIX=true
+PIR_MODELLER=false
+PROXY_AUTH=false
+RECENT_FILE=examples/uniref50.fa\t/Volumes/Data/Users/jimp/Documents/testing/Jalview/examples/RF00031_folded.stk\t/Volumes/Data/Users/jimp/bs_ig_mult.out
+RECENT_URL=http\://www.jalview.org/examples/exampleFile_2_7.jar
+RIGHT_ALIGN_IDS=false
+RSBS_SERVICES=|Multi-Harmony|Analysis|Sequence Harmony and Multi-Relief (Brandt et al. 2010)|hseparable,gapCharacter\='-',returns\='ANNOTATION'|?tool\=jalview|http\://zeus.few.vu.nl/programs/shmrwww/index.php?tool\=jalview&groups\=$PARTITION\:min\='2',minsize\='2',sep\=' '$&ali_file\=$ALIGNMENT\:format\='Fasta',writeasfile$
+SCALE_PROTEIN_TO_CDNA=false
+SCREENGEOMETRY_HEIGHT=1080
+SCREENGEOMETRY_WIDTH=1920
+SCREEN_HEIGHT=1018
+SCREEN_WIDTH=1920
+SCREEN_X=0
+SCREEN_Y=0
+SEQUENCE_LINKS=EMBL-EBI Search|https\://www.ebi.ac.uk/ebisearch/search.ebi?db\=allebi&query\=$SEQUENCE_ID$
+SHOW_ANNOTATIONS=true
+SHOW_AUTOCALC_ABOVE=true
+SHOW_CONSENSUS_HISTOGRAM=true
+SHOW_CONSENSUS_LOGO=false
+SHOW_CONSERVATION=true
+SHOW_DBREFS_TOOLTIP=true
+SHOW_ENFIN_SERVICES=true
+SHOW_FULLSCREEN=false
+SHOW_GROUP_CONSENSUS=false
+SHOW_GROUP_CONSERVATION=false
+SHOW_IDENTITY=true
+SHOW_JAVA_CONSOLE=false
+SHOW_JVSUFFIX=true
+SHOW_JWS2_SERVICES=true
+SHOW_NPFEATS_TOOLTIP=true
+SHOW_OCCUPANCY=true
+SHOW_OVERVIEW=false
+SHOW_OV_HIDDEN_AT_START=false
+SHOW_QUALITY=true
+SHOW_STARTUP_FILE=false
+SHOW_UNCONSERVED=false
+SHOW_WSDISCOVERY_ERRORS=true
+SORT_ALIGNMENT=No sort
+SORT_ANNOTATIONS=NONE
+SORT_BY_TREE=false
+STARTUP_FILE=http\://www.jalview.org/examples/exampleFile_2_3.jar
+STRUCT_FROM_PDB=false
+STRUCTURE_DISPLAY=JMOL
+SVG_RENDERING=Prompt each time
+USAGESTATS=false
+USE_LEGACY_GAP=false
+USE_PROXY=false
+USE_RNAVIEW=false
+VERSION=2.11.2.0-develop
+VERSION_CHECK=false
+WRAP_ALIGNMENT=false
+WSMENU_BYHOST=false
+WSMENU_BYTYPE=false
+YEAR=2018