+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * 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 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;
+
MultipleConnectionPropertyProviderI connprov;
- public JalviewSource(SOURCE local2, MultipleConnectionPropertyProviderI connprov, boolean local)
+
+ public JalviewSource(SOURCE local2,
+ MultipleConnectionPropertyProviderI connprov, boolean local)
{
- this.connprov=connprov;
+ this.connprov = connprov;
this.local = local;
source = local2;
}
{
try
{
- String url = new RegistrySourceAdapter(source)
- .getOriginalDataSourceUri();
- return url;
+ // 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 "
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;
+ }
}