+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.ws.dbsources.das.datamodel;
+import jalview.util.MessageManager;
+import jalview.ws.dbsources.das.api.jalviewSourceI;
+import jalview.ws.seqfetcher.DbSourceProxy;
+
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.client.threads.MultipleConnectionPropertyProviderI;
import org.biodas.jdas.dassources.Capabilities;
import org.biodas.jdas.dassources.utils.DasTimeFormat;
-import org.biodas.jdas.dassources.utils.RegistrySourceAdapter;
import org.biodas.jdas.schema.sources.CAPABILITY;
import org.biodas.jdas.schema.sources.COORDINATES;
import org.biodas.jdas.schema.sources.MAINTAINER;
import org.biodas.jdas.schema.sources.SOURCE;
import org.biodas.jdas.schema.sources.VERSION;
-import jalview.ws.dbsources.das.api.jalviewSourceI;
-import jalview.ws.seqfetcher.DbSourceProxy;
-
public class JalviewSource implements jalviewSourceI
{
SOURCE source;
- public JalviewSource(SOURCE local2, boolean local)
+ MultipleConnectionPropertyProviderI connprov;
+
+ public JalviewSource(SOURCE local2,
+ MultipleConnectionPropertyProviderI connprov, boolean local)
{
+ this.connprov = connprov;
this.local = local;
source = local2;
}
@Override
public VERSION getVersion()
{
-
+
return getVersionFor(source);
}
@Override
public String getEmail()
{
- return (local) ? null: source.getMAINTAINER().getEmail();
+ return (local) ? null : source.getMAINTAINER().getEmail();
}
boolean local = false;
}
return false;
}
+
@Override
public boolean isFeatureSource()
{
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
- {
- newdate = DasTimeFormat.fromDASString(newer);
- } catch (ParseException e)
+ if (newer != null && newer.trim().length() > 0)
{
- // TODO: handle exception
+ try
+ {
+ newdate = DasTimeFormat.fromDASString(newer);
+ } catch (ParseException e)
+ {
+ }
}
if (refdate != null)
{
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)
{
ArrayList<DbSourceProxy> seqsources = new ArrayList<DbSourceProxy>();
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<String, COORDINATES> latestc = new Hashtable<String, COORDINATES>();
+ for (COORDINATES cs : v.getCOORDINATES())
{
- seqsources.add(new DasSequenceSource("das:" + getTitle() + " ("
- + cs.getContent() + ")", cs.getContent(), 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, connprov));
+ 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, connprov));
} 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());
+ // kind of dumb, since
+ // org.biodas.jdas.dassources.utils.VersionAdapter.getSourceUriFromQueryUri()
+ // does this,
+ // but this way, we can access non DAS 1.6 compliant sources (which have
+ // to have a URL like <sourcename>/das/ and cause a validation exception)
+
+ for (CAPABILITY cap : getVersion().getCAPABILITY())
+ {
+ String capname = cap.getType().substring(
+ cap.getType().indexOf(":") + 1);
+ int p = cap.getQueryUri().lastIndexOf(capname);
+ if (p < -1)
+ {
+ throw new Exception(MessageManager.formatMessage(
+ "exception.invalid_das_source",
+ new String[] { source.getUri() }));
+ }
+ if (cap.getQueryUri().charAt(p) == '/')
+ {
+ p--;
+ }
+ return cap.getQueryUri().substring(0, p);
+ }
+ } 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());
+ }
+
+ @Override
+ public boolean isReferenceSource()
+ {
+ // TODO check source object for indication that we are the primary for a DAS
+ // coordinate system
+ return false;
+ }
}
git://source.jalview.org / jalview.git / blobdiff