+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ 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.schema.sources.CAPABILITY;
-import org.biodas.jdas.schema.sources.COORDINATES;
-import org.biodas.jdas.schema.sources.MAINTAINER;
-import org.biodas.jdas.schema.sources.PROP;
-import org.biodas.jdas.schema.sources.SOURCE;
-import org.biodas.jdas.schema.sources.VERSION;
-
-public class JalviewSource implements jalviewSourceI
-{
- SOURCE source;
-
- MultipleConnectionPropertyProviderI connprov;
-
- public JalviewSource(SOURCE local2,
- MultipleConnectionPropertyProviderI connprov, boolean local)
- {
- this.connprov = connprov;
- this.local = local;
- source = local2;
- }
-
- @Override
- public String getTitle()
- {
- return source.getTitle();
- }
-
- @Override
- public VERSION getVersion()
- {
-
- return getVersionFor(source);
- }
-
- @Override
- public String getDocHref()
- {
- return source.getDocHref();
- }
-
- @Override
- public String getDescription()
- {
- return source.getDescription();
- }
-
- @Override
- public String getUri()
- {
- return source.getUri();
- }
-
- @Override
- public MAINTAINER getMAINTAINER()
- {
- return source.getMAINTAINER();
- }
-
- @Override
- public String getEmail()
- {
- return (local) ? null : source.getMAINTAINER().getEmail();
- }
-
- boolean local = false;
-
- @Override
- public boolean isLocal()
- {
- return local;
- }
-
- @Override
- public boolean isSequenceSource()
- {
- String seqcap = "das1:" + Capabilities.SEQUENCE.getName();
- for (String cp : getCapabilityList(getVersionFor(source)))
- {
- if (cp.equals(seqcap))
- {
- return true;
-
- }
- }
- return false;
- }
-
- @Override
- public boolean isFeatureSource()
- {
- String seqcap = "das1:" + Capabilities.FEATURES.getName();
- for (String cp : getCapabilityList(getVersionFor(source)))
- {
- if (cp.equals(seqcap))
- {
- return true;
-
- }
- }
- return false;
- }
-
- private VERSION getVersionFor(SOURCE ds)
- {
- VERSION latest = null;
- for (VERSION v : ds.getVERSION())
- {
- if (latest == null
- || isLaterThan(latest.getCreated(), v.getCreated()))
- {
- // TODO: das 1.6 - should just get the first version - ignore other
- // versions since not specified how to construct URL from version's URI
- // + source URI
- latest = v;
- }
- }
- 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;
- if (ref != null && ref.trim().length() > 0)
- {
- try
- {
- refdate = DasTimeFormat.fromDASString(ref.trim());
-
- } catch (ParseException x)
- {
- }
- }
- if (newer != null && newer.trim().length() > 0)
- {
- try
- {
- newdate = DasTimeFormat.fromDASString(newer);
- } catch (ParseException e)
- {
- }
- }
- if (refdate != null)
- {
- if (newdate != null)
- {
- return refdate.before(newdate);
- }
- return false;
- }
- if (newdate != null)
- {
- return true;
- }
- // assume first instance of source is newest in list. - TODO: check if
- // natural ordering of source versions is newest first or oldest first
- return false;
- }
-
- public String[] getLabelsFor(VERSION v)
- {
- ArrayList<String> labels = new ArrayList<String>();
- for (PROP p : v.getPROP())
- {
- if (p.getName().equalsIgnoreCase("LABEL"))
- {
- labels.add(p.getValue());
- }
- }
- 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()))
- {
- return p;
- }
- }
- return null;
- }
-
- public String[] getCapabilityList(VERSION v)
- {
-
- ArrayList<String> labels = new ArrayList<String>();
- for (CAPABILITY p : v.getCAPABILITY())
- {
- // TODO: work out what to do with namespace prefix
- // does SEQUENCE == das1:SEQUENCE and das2:SEQUENCE ?
- // for moment, just show all capabilities...
- if (p.getType().startsWith("das1:"))
- {
- labels.add(p.getType());
- }
- }
- return labels.toArray(new String[0]);
- }
-
- @Override
- public List<DbSourceProxy> getSequenceSourceProxies()
- {
- if (!isSequenceSource())
- {
- return null;
- }
- ArrayList<DbSourceProxy> seqsources = new ArrayList<DbSourceProxy>();
- if (!local)
- {
- VERSION v = getVersion();
- Map<String, COORDINATES> latestc = new Hashtable<String, COORDINATES>();
- for (COORDINATES cs : v.getCOORDINATES())
- {
- 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())
- {
- 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
- {
- try
- {
- 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
- {
- // 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