+++ /dev/null
-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;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.Enumeration;
-import java.util.HashMap;
-import java.util.List;
-import java.util.TreeMap;
-
-import org.testng.Assert;
-import org.testng.annotations.AfterClass;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
-public class BackupFilesTest
-{
- @BeforeClass(alwaysRun = true)
- public void setUpJvOptionPane()
- {
- JvOptionPane.setInteractiveMode(false);
- JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
- }
-
- private static boolean actuallyDeleteTmpFiles = true;
- private static String testDir = "examples";
-
- private static String testBasename = "backupfilestest";
-
- private static String testExt = ".fa";
-
- private static String testFilename = testBasename + testExt;
-
-
- private static String testFile = testDir + File.separatorChar
- + testFilename;
-
- private static String newBasename = testBasename + "Temp";
-
- private static String newFilename = newBasename + testExt;
-
- private static String newFile = testDir + File.separatorChar
- + newFilename;
-
- private static String sequenceName = "BACKUP_FILES";
-
- private static String sequenceDescription = "backupfiles";
-
- private static String sequenceData = "AAAARG";
-
- private static String suffix = "_BACKUPTEST-%n";
-
- private static int digits = 8;
-
- private static int rollMax = 2;
-
- private AlignFrame af;
-
- // read and save with backupfiles disabled
- @Test(groups = { "Functional" })
- public void noBackupsEnabledTest() throws Exception
- {
- // set BACKUPFILES_ENABLED to false (i.e. turn off BackupFiles feature -- no
- // backup files to be made when saving)
- setBackupFilesOptions(false, true, true);
-
- // init the newFile and backups (i.e. make sure newFile exists on its own
- // and has no backups
- initNewFileForTesting();
-
- // now save again
- save();
-
- // check no backup files
- File[] backupFiles = getBackupFiles();
- Assert.assertTrue(backupFiles.length == 0);
- }
-
- // save keeping all backup files
- @Test(groups = { "Functional" })
- public void backupsEnabledNoRollMaxTest() throws Exception
- {
- // Enable BackupFiles and set noMax so all backupfiles get kept
- setBackupFilesOptions(true, false, true);
-
- // init the newFile and backups (i.e. make sure newFile exists on its own
- // and has no backups)
- initNewFileForTesting();
-
- // now save a few times again. No rollMax so should have more than two
- // backup files
- int numSaves = 10;
- for (int i = 0; i < numSaves; i++)
- {
- save();
- }
-
- // check 10 backup files
- HashMap correctindexmap = new HashMap();
- correctindexmap.put(1, "backupfilestestTemp.fa_BACKUPTEST-00000001");
- correctindexmap.put(2, "backupfilestestTemp.fa_BACKUPTEST-00000002");
- correctindexmap.put(3, "backupfilestestTemp.fa_BACKUPTEST-00000003");
- correctindexmap.put(4, "backupfilestestTemp.fa_BACKUPTEST-00000004");
- correctindexmap.put(5, "backupfilestestTemp.fa_BACKUPTEST-00000005");
- correctindexmap.put(6, "backupfilestestTemp.fa_BACKUPTEST-00000006");
- correctindexmap.put(7, "backupfilestestTemp.fa_BACKUPTEST-00000007");
- correctindexmap.put(8, "backupfilestestTemp.fa_BACKUPTEST-00000008");
- correctindexmap.put(9, "backupfilestestTemp.fa_BACKUPTEST-00000009");
- correctindexmap.put(10, "backupfilestestTemp.fa_BACKUPTEST-00000010");
- HashMap wrongindexmap = new HashMap();
- wrongindexmap.put(1, "backupfilestestTemp.fa_BACKUPTEST-1");
- wrongindexmap.put(2, "backupfilestestTemp.fa_BACKUPTEST-00000002");
- wrongindexmap.put(3, "backupfilestestTemp.fa_BACKUPTEST-00000003");
- wrongindexmap.put(4, "backupfilestestTemp.fa_BACKUPTEST-00000004");
- wrongindexmap.put(5, "backupfilestestTemp.fa_BACKUPTEST-00000005");
- wrongindexmap.put(6, "backupfilestestTemp.fa_BACKUPTEST-00000006");
- wrongindexmap.put(7, "backupfilestestTemp.fa_BACKUPTEST-00000007");
- wrongindexmap.put(8, "backupfilestestTemp.fa_BACKUPTEST-00000008");
- wrongindexmap.put(9, "backupfilestestTemp.fa_BACKUPTEST-00000009");
- wrongindexmap.put(10, "backupfilestestTemp.fa_BACKUPTEST-00000010");
- int[] indexes2 = { 3, 4, 5, 6, 7, 8, 9, 10 };
- int[] indexes3 = { 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 };
- Assert.assertTrue(checkBackupFiles(correctindexmap));
- Assert.assertFalse(checkBackupFiles(wrongindexmap));
- Assert.assertFalse(checkBackupFiles(indexes2));
- Assert.assertFalse(checkBackupFiles(indexes3));
- }
-
- // save keeping only the last rollMax (2) backup files
- @Test(groups = { "Functional" })
- public void backupsEnabledRollMaxTest() throws Exception
- {
- // Enable BackupFiles and set noMax so all backupfiles get kept
- setBackupFilesOptions(true, false, false);
-
- // init the newFile and backups (i.e. make sure newFile exists on its own
- // and has no backups)
- initNewFileForTesting();
-
- // now save a few times again. No rollMax so should have more than two
- // backup files
- int numSaves = 10;
- for (int i = 0; i < numSaves; i++)
- {
- save();
- }
-
- // check there are "rollMax" backup files and they are all saved correctly
- // check 10 backup files
- HashMap correctindexmap = new HashMap();
- correctindexmap.put(9, "backupfilestestTemp.fa_BACKUPTEST-00000009");
- correctindexmap.put(10, "backupfilestestTemp.fa_BACKUPTEST-00000010");
- int[] indexes2 = { 10 };
- int[] indexes3 = { 8, 9, 10 };
- Assert.assertTrue(checkBackupFiles(correctindexmap));
- Assert.assertFalse(checkBackupFiles(indexes2));
- Assert.assertFalse(checkBackupFiles(indexes3));
- }
-
- // save keeping only the last rollMax (2) backup files
- @Test(groups = { "Functional" })
- public void backupsEnabledReverseRollMaxTest() throws Exception
- {
- // Enable BackupFiles and set noMax so all backupfiles get kept
- setBackupFilesOptions(true, true, false);
-
- // init the newFile and backups (i.e. make sure newFile exists on its own
- // and has no backups)
- initNewFileForTesting();
-
- // now save a few times again. No rollMax so should have more than two
- // backup files
- int numSaves = 10;
- for (int i = 0; i < numSaves; i++)
- {
- save();
- }
-
- // check there are "rollMax" backup files and they are all saved correctly
- // check 10 backup files
- HashMap correctindexmap = new HashMap();
- correctindexmap.put(1, "backupfilestestTemp.fa_BACKUPTEST-00000001");
- correctindexmap.put(2, "backupfilestestTemp.fa_BACKUPTEST-00000002");
- int[] indexes2 = { 1 };
- int[] indexes3 = { 1, 2, 3 };
- Assert.assertTrue(checkBackupFiles(correctindexmap));
- Assert.assertFalse(checkBackupFiles(indexes2));
- Assert.assertFalse(checkBackupFiles(indexes3));
- }
-
- private void setBackupFilesOptions()
- {
- setBackupFilesOptions(true, false, false);
- }
-
- private void setBackupFilesOptions(boolean enabled, boolean reverse,
- boolean noMax)
- {
- Cache.loadProperties("test/jalview/io/testProps.jvprops");
-
- Cache.setPropertyNoSave(BackupFiles.ENABLED,
- Boolean.toString(enabled));
- Cache.setPropertyNoSave(BackupFiles.SUFFIX, suffix);
- Cache.setPropertyNoSave(BackupFiles.SUFFIX_DIGITS,
- Integer.toString(digits));
- Cache.setPropertyNoSave(BackupFiles.REVERSE_ORDER,
- Boolean.toString(reverse));
- Cache.setPropertyNoSave(BackupFiles.NO_MAX,
- Boolean.toString(noMax));
- Cache.setPropertyNoSave(BackupFiles.ROLL_MAX,
- Integer.toString(rollMax));
- Cache.setPropertyNoSave(BackupFiles.CONFIRM_DELETE_OLD,
- "false");
- }
-
- private void save()
- {
- if (af != null)
- {
- af.saveAlignment(newFile, jalview.io.FileFormat.Fasta);
- }
- }
-
- // this runs cleanTmpFiles and then writes the newFile once as a starting
- // point for all tests
- private void initNewFileForTesting() throws Exception
- {
- cleanupTmpFiles();
-
- AppletFormatAdapter afa = new AppletFormatAdapter();
- AlignmentI al = afa.readFile(testFile, DataSourceType.FILE,
- jalview.io.FileFormat.Fasta);
- List<SequenceI> l = al.getSequences();
-
- // check this is right
- if (l.size() != 1)
- {
- throw new Exception("single sequence from '" + testFile
- + "' not read in correctly (should be a single short sequence). List<SequenceI> size is wrong.");
- }
- SequenceI s = l.get(0);
- Sequence ref = new Sequence(sequenceName, sequenceData);
- ref.setDescription(sequenceDescription);
- if (!sequencesEqual(s, ref))
- {
- throw new Exception("single sequence from '" + testFile
- + "' not read in correctly (should be a single short sequence). SequenceI name, description or data is wrong.");
- }
- // save alignment file to new filename -- this doesn't test backups disabled
- // yet as this file shouldn't already exist
- af = new AlignFrame(al, 0, 0);
- af.saveAlignment(newFile, jalview.io.FileFormat.Fasta);
- }
-
- // this deletes the newFile (if it exists) and any saved backup file for it
- @AfterClass(alwaysRun = true)
- private void cleanupTmpFiles()
- {
- File newfile = new File(newFile);
- if (newfile.exists())
- {
- newfile.delete();
- }
- File[] tmpFiles = getBackupFiles(newFile, suffix, digits);
- for (int i = 0; i < tmpFiles.length; i++)
- {
- if (actuallyDeleteTmpFiles)
- {
- tmpFiles[i].delete();
- }
- else
- {
- System.out.println("Pretending to delete " + tmpFiles[i].getPath());
- }
- }
- }
-
- private static File[] getBackupFiles(String f, String s, int i)
- {
- TreeMap<Integer, File> bfTreeMap = BackupFiles.getBackupFilesAsTreeMap(f,
- s, i);
- File[] backupFiles = new File[bfTreeMap.size()];
- bfTreeMap.values().toArray(backupFiles);
- return backupFiles;
- }
-
- private static File[] getBackupFiles()
- {
- return getBackupFiles(newFile, suffix, digits);
- }
-
- private static boolean checkBackupFiles(HashMap<Integer, String> indexmap)
- throws IOException
- {
- TreeMap<Integer, File> map = BackupFiles.getBackupFilesAsTreeMap(newFile,
- suffix, digits);
- Enumeration<Integer> indexesenum = Collections
- .enumeration(indexmap.keySet());
- while (indexesenum.hasMoreElements())
- {
- int i = indexesenum.nextElement();
- String indexfilename = indexmap.get(i);
- if (!map.containsKey(i))
- {
- return false;
- }
- File f = map.get(i);
- if (!filesContentEqual(newFile, f.getPath()))
- {
- return false;
- }
- map.remove(i);
- if (f == null)
- {
- return false;
- }
- if (!f.getName().equals(indexfilename))
- {
- return false;
- }
- }
- // should be nothing left in map
- if (map.size() > 0)
- {
- return false;
- }
-
- return true;
- }
-
- private static boolean checkBackupFiles(int[] indexes) throws IOException
- {
- TreeMap<Integer, File> map = BackupFiles.getBackupFilesAsTreeMap(newFile,
- suffix, digits);
- for (int m = 0; m < indexes.length; m++)
- {
- int i = indexes[m];
- if (!map.containsKey(i))
- {
- return false;
- }
- File f = map.get(i);
- if (!filesContentEqual(newFile, f.getPath()))
- {
- return false;
- }
- map.remove(i);
- if (f == null)
- {
- return false;
- }
- // 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()))
- {
- System.out.println("Supposed filename '" + filename
- + "' not equal to actual filename '" + f.getName() + "'");
- return false;
- }
- }
- // should be nothing left in map
- if (map.size() > 0)
- {
- return false;
- }
-
- return true;
- }
-
- private static String[] getBackupFilesAsStrings()
- {
- File[] files = getBackupFiles(newFile, suffix, digits);
- String[] filenames = new String[files.length];
- for (int i = 0; i < files.length; i++)
- {
- filenames[i] = files[i].getPath();
- }
- return filenames;
- }
-
- public static boolean sequencesEqual(SequenceI s1, SequenceI s2) {
- if (s1 == null && s2 == null) {
- return true;
- } else if (s1 == null || s2 == null) {
- return false;
- }
- return (s1.getName().equals(s2.getName())
- && s1.getDescription().equals(s2.getDescription())
- && Arrays.equals(s1.getSequence(), s2.getSequence()));
- }
-
- public static boolean filesContentEqual(String fileName1,
- String fileName2) throws IOException
- {
- Path file1 = Paths.get(fileName1);
- Path file2 = Paths.get(fileName2);
- byte[] bytes1 = Files.readAllBytes(file1);
- byte[] bytes2 = Files.readAllBytes(file2);
- return Arrays.equals(bytes1, bytes2);
- }
-
-}
git://source.jalview.org / jalview.git / blobdiff