From: tcofoegbu Date: Thu, 7 Jan 2016 14:50:06 +0000 (+0000) Subject: JAL-1479 implemented timestamp based caching of SIFTS by providing code which checks... X-Git-Tag: Release_2_10_0~332 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=6971cef43ca33a794aef8e8493ba7301d921444e;p=jalview.git JAL-1479 implemented timestamp based caching of SIFTS by providing code which checks if an already downloaded SIFTS file has exceeded a certain threshold upon processing. Also added a method to handle SIFTS entries for cases when an 'entityId' is NOT EQUAL TO 'chainId', this is a heuristic measure achieved using greedy search. --- diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java index 00da2fc..7d5ae2e 100644 --- a/src/jalview/ws/sifts/SiftsClient.java +++ b/src/jalview/ws/sifts/SiftsClient.java @@ -47,9 +47,14 @@ import java.io.InputStream; import java.io.PrintStream; import java.net.URL; import java.net.URLConnection; +import java.nio.file.Files; +import java.nio.file.Path; +import java.nio.file.attribute.BasicFileAttributes; import java.util.ArrayList; import java.util.Arrays; import java.util.Collection; +import java.util.Collections; +import java.util.Date; import java.util.HashMap; import java.util.HashSet; import java.util.List; @@ -98,6 +103,8 @@ public class SiftsClient implements SiftsClientI private final static String NEWLINE = System.lineSeparator(); + private final static int THRESHOLD_IN_DAYS = 2; + private String curSourceDBRef; private HashSet curDBRefAccessionIdsString; @@ -180,7 +187,7 @@ public class SiftsClient implements SiftsClientI try (InputStream in = new FileInputStream(siftFile); GZIPInputStream gzis = new GZIPInputStream(in);) { - System.out.println("File : " + siftFile.getAbsolutePath()); + // System.out.println("File : " + siftFile.getAbsolutePath()); JAXBContext jc = JAXBContext.newInstance("jalview.xml.binding.sifts"); XMLStreamReader streamReader = XMLInputFactory.newInstance() .createXMLStreamReader(gzis); @@ -220,14 +227,17 @@ public class SiftsClient implements SiftsClientI public static File getSiftsFile(String pdbId) throws SiftsException { File siftsFile = new File(SiftsSettings.getSiftDownloadDirectory() - + pdbId.toLowerCase() - + ".xml.gz"); + + pdbId.toLowerCase() + ".xml.gz"); if (siftsFile.exists()) { - // TODO it may be worth performing an age check to determine if a - // new SIFTs file should be re-downloaded as SIFTs entries are usually - // updated weekly + // The line below is required for unit testing... don't comment it out!!! System.out.println(">>> SIFTS File already downloaded for " + pdbId); + + if (isFileOlderThanThreshold(siftsFile, THRESHOLD_IN_DAYS)) + { + // System.out.println("Downloaded file is out of date, hence re-downloading..."); + siftsFile = downloadSiftsFile(pdbId.toLowerCase()); + } return siftsFile; } siftsFile = downloadSiftsFile(pdbId.toLowerCase()); @@ -235,6 +245,34 @@ public class SiftsClient implements SiftsClientI } /** + * This method enables checking if a cached file has exceeded a certain + * threshold(in days) + * + * @param file + * the cached file + * @param noOfDays + * the threshold in days + * @return + */ + public static boolean isFileOlderThanThreshold(File file, int noOfDays) + { + Path filePath = file.toPath(); + BasicFileAttributes attr; + int diffInDays = 0; + try + { + attr = Files.readAttributes(filePath, BasicFileAttributes.class); + diffInDays = (int) ((new Date().getTime() - attr.lastModifiedTime() + .toMillis()) / (1000 * 60 * 60 * 24)); + // System.out.println("Diff in days : " + diffInDays); + } catch (IOException e) + { + e.printStackTrace(); + } + return noOfDays <= diffInDays; + } + + /** * Download a SIFTs XML file for a given PDB Id from an FTP repository * * @param pdbId @@ -255,7 +293,7 @@ public class SiftsClient implements SiftsClientI } try { - System.out.println(">> Download ftp url : " + siftsFileFTPURL); + // System.out.println(">> Download ftp url : " + siftsFileFTPURL); URL url = new URL(siftsFileFTPURL); URLConnection conn = url.openConnection(); InputStream inputStream = conn.getInputStream(); @@ -269,7 +307,7 @@ public class SiftsClient implements SiftsClientI } outputStream.close(); inputStream.close(); - System.out.println(">>> File downloaded : " + downloadedSiftsFile); + // System.out.println(">>> File downloaded : " + downloadedSiftsFile); } catch (IOException ex) { throw new SiftsException(ex.getMessage()); @@ -287,8 +325,7 @@ public class SiftsClient implements SiftsClientI public static boolean deleteSiftsFileByPDBId(String pdbId) { File siftsFile = new File(SiftsSettings.getSiftDownloadDirectory() - + pdbId.toLowerCase() - + ".xml.gz"); + + pdbId.toLowerCase() + ".xml.gz"); if (siftsFile.exists()) { return siftsFile.delete(); @@ -296,7 +333,6 @@ public class SiftsClient implements SiftsClientI return true; } - /** * Get a valid SIFTs DBRef for the given sequence current SIFTs entry * @@ -345,7 +381,6 @@ public class SiftsClient implements SiftsClientI throw new SiftsException("Could not get source DB Ref"); } - /** * Check that the DBRef Entry is properly populated and is available in this * SiftClient instance @@ -408,15 +443,13 @@ public class SiftsClient implements SiftsClientI String mappingOutput = mappingDetails.toString(); StructureMapping siftsMapping = new StructureMapping(seq, pdbFile, - pdbId, chain, mapping, - mappingOutput); + pdbId, chain, mapping, mappingOutput); return siftsMapping; } @Override - public HashMap getGreedyMapping(String entityId, SequenceI seq, - java.io.PrintStream os) - throws SiftsException + public HashMap getGreedyMapping(String entityId, + SequenceI seq, java.io.PrintStream os) throws SiftsException { ArrayList omitNonObserved = new ArrayList(); int nonObservedShiftIndex = 0; @@ -424,8 +457,7 @@ public class SiftsClient implements SiftsClientI Entity entity = null; entity = getEntityById(entityId); String originalSeq = AlignSeq.extractGaps( - jalview.util.Comparison.GapChars, - seq.getSequenceAsString()); + jalview.util.Comparison.GapChars, seq.getSequenceAsString()); HashMap mapping = new HashMap(); DBRefEntryI sourceDBRef = seq.getSourceDBRef(); if (sourceDBRef == null) @@ -477,7 +509,14 @@ public class SiftsClient implements SiftsClientI String resNumIndexString = cRefDb.getDbResNum() .equalsIgnoreCase("None") ? String.valueOf(UNASSIGNED) : cRefDb.getDbResNum(); - currSeqIndex = Integer.valueOf(resNumIndexString); + try + { + currSeqIndex = Integer.valueOf(resNumIndexString); + } catch (NumberFormatException nfe) + { + currSeqIndex = Integer.valueOf(resNumIndexString + .split("[a-zA-Z]")[0]); + } if (pdbRefDb != null) { break;// exit loop if pdb and uniprot are already found @@ -494,7 +533,8 @@ public class SiftsClient implements SiftsClientI try { resNum = (pdbRefDb == null) ? Integer.valueOf(residue - .getDbResNum()) : Integer.valueOf(pdbRefDb.getDbResNum()); + .getDbResNum()) : Integer.valueOf(pdbRefDb + .getDbResNum()); } catch (NumberFormatException nfe) { resNum = (pdbRefDb == null) ? Integer.valueOf(residue @@ -526,7 +566,10 @@ public class SiftsClient implements SiftsClientI { e.printStackTrace(); } - padWithGaps(resNumMap, omitNonObserved); + if (seqCoordSys == CoordinateSys.UNIPROT) + { + padWithGaps(resNumMap, omitNonObserved); + } int seqStart = UNASSIGNED; int seqEnd = UNASSIGNED; int pdbStart = UNASSIGNED; @@ -662,7 +705,6 @@ public class SiftsClient implements SiftsClientI } } - /** * * @param chainId @@ -727,9 +769,94 @@ public class SiftsClient implements SiftsClientI } return entity; } + Entity entity = getEntityByMostOptimalMatchedId(id); + if (entity != null) + { + return entity; + } throw new SiftsException("Entity " + id + " not found"); } + /** + * This method was added because EntityId is NOT always equal to ChainId. + * Hence, it provides the logic to greedily detect the "true" Entity for a + * given chainId where discrepancies exist. + * + * @param chainId + * @return + */ + public Entity getEntityByMostOptimalMatchedId(String chainId) + { + System.out + .println("--------------> advanced greedy entityId matching block entered.."); + List entities = siftsEntry.getEntity(); + SiftsEntitySortPojo[] sPojo = new SiftsEntitySortPojo[entities.size()]; + int count = 0; + for (Entity entity : entities) + { + sPojo[count] = new SiftsEntitySortPojo(); + sPojo[count].entityId = entity.getEntityId(); + + List segments = entity.getSegment(); + for (Segment segment : segments) + { + List residues = segment.getListResidue().getResidue(); + for (Residue residue : residues) + { + List cRefDbs = residue.getCrossRefDb(); + for (CrossRefDb cRefDb : cRefDbs) + { + if (!cRefDb.getDbSource().equalsIgnoreCase("PDB")) + { + continue; + } + ++sPojo[count].resCount; + if (cRefDb.getDbChainId().equalsIgnoreCase(chainId)) + { + ++sPojo[count].chainIdFreq; + } + } + } + } + sPojo[count].pid = 100 * (sPojo[count].chainIdFreq / sPojo[count].resCount); + ++count; + } + Arrays.sort(sPojo, Collections.reverseOrder()); + System.out.println("highest matched entity : " + sPojo[0].entityId); + System.out.println("highest matched pid : " + sPojo[0].pid); + + if (sPojo[0].entityId != null) + { + for (Entity entity : entities) + { + if (!entity.getEntityId().equalsIgnoreCase(sPojo[0].entityId)) + { + continue; + } + return entity; + } + } + return null; + } + + public class SiftsEntitySortPojo implements + Comparable + { + public String entityId; + + public int chainIdFreq; + + public int pid; + + public int resCount; + + @Override + public int compareTo(SiftsEntitySortPojo o) + { + return this.pid - o.pid; + } + } + @Override public String[] getEntryDBs() { @@ -757,9 +884,9 @@ public class SiftsClient implements SiftsClientI String strName = mp.getStrName(); int pdbStart = mp.getStrStart(); int pdbEnd = mp.getStrEnd(); - + String type = mp.getType(); - + int maxid = (seqName.length() >= strName.length()) ? seqName.length() : strName.length(); int len = 72 - maxid - 1; @@ -786,7 +913,7 @@ public class SiftsClient implements SiftsClientI output.append(" - "); output.append(String.valueOf(pdbEnd)); output.append(NEWLINE).append(NEWLINE); - + int matchedSeqCount = 0; for (int j = 0; j < nochunks; j++) { @@ -810,32 +937,33 @@ public class SiftsClient implements SiftsClientI { try { - if ((i + (j * len)) < seqRes.length()) - { - if (seqRes.charAt(i + (j * len)) == strRes.charAt(i + (j * len)) - && !jalview.util.Comparison.isGap(seqRes.charAt(i - + (j * len)))) + if ((i + (j * len)) < seqRes.length()) { + if (seqRes.charAt(i + (j * len)) == strRes + .charAt(i + (j * len)) + && !jalview.util.Comparison.isGap(seqRes.charAt(i + + (j * len)))) + { matchedSeqCount++; - output.append("|"); - } - else if (type.equals("pep")) - { - if (ResidueProperties.getPAM250(seqRes.charAt(i + (j * len)), - strRes.charAt(i + (j * len))) > 0) + output.append("|"); + } + else if (type.equals("pep")) { - output.append("."); + if (ResidueProperties.getPAM250(seqRes.charAt(i + (j * len)), + strRes.charAt(i + (j * len))) > 0) + { + output.append("."); + } + else + { + output.append(" "); + } } else { output.append(" "); } } - else - { - output.append(" "); - } - } } catch (IndexOutOfBoundsException e) { continue; @@ -859,13 +987,13 @@ public class SiftsClient implements SiftsClientI { throw new SiftsException("Low PID detected for SIFTs mapping..."); } - output.append("Length of alignment = " + seqRes.length()) - .append(NEWLINE); + output.append("Length of alignment = " + seqRes.length()).append( + NEWLINE); output.append(new Format("Percentage ID = %2.2f").form(pid)); output.append(NEWLINE); return output; } - + @Override public int getEntityCount() { @@ -901,4 +1029,5 @@ public class SiftsClient implements SiftsClientI { return siftsEntry.getDbVersion(); } + } diff --git a/test/jalview/ws/sifts/SiftsClientTest.java b/test/jalview/ws/sifts/SiftsClientTest.java index 24c6751..28b44e1 100644 --- a/test/jalview/ws/sifts/SiftsClientTest.java +++ b/test/jalview/ws/sifts/SiftsClientTest.java @@ -41,6 +41,11 @@ public class SiftsClientTest { private final ByteArrayOutputStream outContent = new ByteArrayOutputStream(); + public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System + .getProperty("user.home") + + File.separatorChar + + ".sifts_downloads" + File.separatorChar; + private String testPDBId = "1a70"; private SiftsClient siftsClient = null; @@ -69,9 +74,13 @@ public class SiftsClientTest { // SIFTs entries are updated weekly - so use saved SIFTs file to enforce // test reproducibility + SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache.getDefault( + "sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR)); + File testSiftsFile = new File("test/jalview/io/" + testPDBId + ".xml.gz"); PDBfile pdbFile = new PDBfile(false, false, false); + pdbFile.id = testPDBId; siftsClient = new SiftsClient(pdbFile, testSiftsFile); }