From be78a936034455f8ab1be4df53736000631d87ff Mon Sep 17 00:00:00 2001 From: jprocter Date: Tue, 24 Apr 2012 15:31:53 +0100 Subject: [PATCH] JAL-972 - test to distinguish sources based on age - used to select one of duplicate sources in registry --- .../ws/dbsources/das/api/jalviewSourceI.java | 7 + .../dbsources/das/datamodel/DasSourceRegistry.java | 18 ++- .../ws/dbsources/das/datamodel/JalviewSource.java | 155 ++++++++++++++------ 3 files changed, 135 insertions(+), 45 deletions(-) diff --git a/src/jalview/ws/dbsources/das/api/jalviewSourceI.java b/src/jalview/ws/dbsources/das/api/jalviewSourceI.java index fef6a0b..7c36ddb 100644 --- a/src/jalview/ws/dbsources/das/api/jalviewSourceI.java +++ b/src/jalview/ws/dbsources/das/api/jalviewSourceI.java @@ -46,4 +46,11 @@ public interface jalviewSourceI */ String getSourceURL(); + /** + * test to see if this source's latest version is older than the given source + * @param jalviewSourceI + * @return true if newer than given source + */ + boolean isNewerThan(jalviewSourceI jalviewSourceI); + } diff --git a/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java b/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java index 07a8656..6d62d97 100644 --- a/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java +++ b/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java @@ -10,6 +10,7 @@ import java.util.ArrayList; import java.util.Collection; import java.util.Enumeration; import java.util.HashMap; +import java.util.HashSet; import java.util.Hashtable; import java.util.List; import java.util.Map; @@ -103,9 +104,24 @@ public class DasSourceRegistry implements DasSourceRegistryI, List dassources = sources.getSOURCE(); ArrayList dsrc = new ArrayList(); + HashMap latests=new HashMap(); + Integer latest; for (SOURCE src : dassources) { - dsrc.add(new JalviewSource(src, false)); + JalviewSource jsrc=new JalviewSource(src, false); + latest=latests.get(jsrc.getSourceURL()); + if (latest!=null) + { + if (jsrc.isNewerThan(dsrc.get(latest.intValue()))) + { + dsrc.set(latest.intValue(), jsrc); + } else { + System.out.println("Debug: Ingored older source "+jsrc.getTitle()); + } + } else { + latests.put(jsrc.getSourceURL(), Integer.valueOf(dsrc.size())); + dsrc.add(jsrc); + } } return dsrc; } catch (Exception ex) diff --git a/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java b/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java index c5b1fed..c9caf6e 100644 --- a/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java +++ b/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java @@ -3,7 +3,9 @@ package jalview.ws.dbsources.das.datamodel; import java.text.ParseException; import java.util.ArrayList; import java.util.Date; +import java.util.Hashtable; import java.util.List; +import java.util.Map; import org.biodas.jdas.dassources.Capabilities; import org.biodas.jdas.dassources.utils.DasTimeFormat; @@ -37,7 +39,7 @@ public class JalviewSource implements jalviewSourceI @Override public VERSION getVersion() { - + return getVersionFor(source); } @@ -68,7 +70,7 @@ public class JalviewSource implements jalviewSourceI @Override public String getEmail() { - return (local) ? null: source.getMAINTAINER().getEmail(); + return (local) ? null : source.getMAINTAINER().getEmail(); } boolean local = false; @@ -93,6 +95,7 @@ public class JalviewSource implements jalviewSourceI } return false; } + @Override public boolean isFeatureSource() { @@ -125,23 +128,34 @@ public class JalviewSource implements jalviewSourceI return latest; } + /** + * compare date strings. null or unparseable dates are assumed to be oldest + * + * @param ref + * @param newer + * @return true iff ref comes before newer + */ private boolean isLaterThan(String ref, String newer) { Date refdate = null, newdate = null; - try + if (ref != null && ref.trim().length() > 0) { - refdate = DasTimeFormat.fromDASString(ref); + try + { + refdate = DasTimeFormat.fromDASString(ref.trim()); - } catch (ParseException x) - { - return false; + } catch (ParseException x) + { + } } - try + if (newer != null && newer.trim().length() > 0) { - newdate = DasTimeFormat.fromDASString(newer); - } catch (ParseException e) - { - // TODO: handle exception + try + { + newdate = DasTimeFormat.fromDASString(newer); + } catch (ParseException e) + { + } } if (refdate != null) { @@ -173,15 +187,20 @@ public class JalviewSource implements jalviewSourceI return labels.toArray(new String[0]); } - private CAPABILITY getCapability(Capabilities capability) { - for (CAPABILITY p: getVersion().getCAPABILITY()) { - if (p.getType().equalsIgnoreCase(capability.getName()) || p.getType().equalsIgnoreCase("das1:"+capability.getName())) + private CAPABILITY getCapability(Capabilities capability) + { + for (CAPABILITY p : getVersion().getCAPABILITY()) + { + if (p.getType().equalsIgnoreCase(capability.getName()) + || p.getType().equalsIgnoreCase( + "das1:" + capability.getName())) { return p; } } return null; } + public String[] getCapabilityList(VERSION v) { @@ -209,55 +228,103 @@ public class JalviewSource implements jalviewSourceI ArrayList seqsources = new ArrayList(); if (!local) { - VERSION v = getVersion(); - for (COORDINATES cs : v.getCOORDINATES()) - { - - /* - * if (css == null || css.length == 0) { // TODO: query das source - * directly to identify coordinate system... or // have to make up a - * coordinate system css = new DasCoordinateSystem[] { new - * DasCoordinateSystem() }; css[0].setName(d1s.getNickname()); - * css[0].setUniqueId(d1s.getNickname()); } for (int c = 0; c < - * css.length; c++) { - */ - try + VERSION v = getVersion(); + Map latestc = new Hashtable(); + for (COORDINATES cs : v.getCOORDINATES()) { - seqsources.add(new DasSequenceSource("das:" + getTitle() + " (" - + cs.getAuthority()+" "+cs.getSource() + ")", cs.getAuthority(), source, v, cs)); - } catch (Exception e) + COORDINATES ltst = latestc.get(cs.getUri()); + if (ltst == null + || ltst.getVersion() == null + || (ltst.getVersion() != null && cs.getVersion() != null && isLaterThan( + ltst.getVersion(), cs.getVersion()))) + { + latestc.put(cs.getUri(), cs); + } + } + for (COORDINATES cs : latestc.values()) { - System.err.println("Ignoring sequence coord system " + cs + " (" - + cs.getContent() + ") for source " + getTitle() - + "- threw exception when constructing fetcher.\n"); - e.printStackTrace(); + DasSequenceSource ds; + /* + * if (css == null || css.length == 0) { // TODO: query das source + * directly to identify coordinate system... or // have to make up a + * coordinate system css = new DasCoordinateSystem[] { new + * DasCoordinateSystem() }; css[0].setName(d1s.getNickname()); + * css[0].setUniqueId(d1s.getNickname()); } for (int c = 0; c < + * css.length; c++) { + */ + try + { + seqsources.add(ds = new DasSequenceSource(getTitle() + " (" + + cs.getAuthority() + " " + cs.getSource() + + (cs.getVersion() != null ? " " + cs.getVersion() : "") + + ")", cs.getAuthority(), source, v, cs)); + if (seqsources.size() > 1) + { + System.err.println("Added another sequence DB source for " + + getTitle() + " (" + ds.getDbName() + ")"); + } + } catch (Exception e) + { + System.err.println("Ignoring sequence coord system " + cs + " (" + + cs.getContent() + ") for source " + getTitle() + + "- threw exception when constructing fetcher.\n"); + e.printStackTrace(); + } } } - } else { + else + { try { - seqsources.add(new DasSequenceSource("das:"+getTitle(), getTitle(), source, getVersion(), null)); + seqsources.add(new DasSequenceSource(getTitle(), getTitle(), + source, getVersion(), null)); } catch (Exception e) { // TODO Auto-generated catch block e.printStackTrace(); } - + + } + if (seqsources.size() > 1) + { + // sort by name + DbSourceProxy[] tsort = seqsources.toArray(new DasSequenceSource[0]); + String[] nm = new String[tsort.length]; + for (int i = 0; i < nm.length; i++) + { + nm[i] = tsort[i].getDbName().toLowerCase(); + } + jalview.util.QuickSort.sort(nm, tsort); + seqsources.clear(); + for (DbSourceProxy ssrc : tsort) + { + seqsources.add(ssrc); + } } return seqsources; } + @Override public String getSourceURL() { - try { - String url = new RegistrySourceAdapter(source).getOriginalDataSourceUri(); - return url; - } - catch (Exception x) + try { - System.err.println("Serious: Couldn't get the URL for source "+source.getTitle()); + String url = new RegistrySourceAdapter(source) + .getOriginalDataSourceUri(); + return url; + } catch (Exception x) + { + System.err.println("Serious: Couldn't get the URL for source " + + source.getTitle()); x.printStackTrace(); } return null; } + + @Override + public boolean isNewerThan(jalviewSourceI other) + { + return isLaterThan(getVersion().getCreated(), other.getVersion() + .getCreated()); + } } -- 1.7.10.2