public final class WebserviceUtil {
- public static final String PFAM_INST = "pfam";
- public static final String PFAM_NAME = "Pfam";
- public static final String PFAM_SERVER = "http://pfam.janelia.org";
- public static final String TOL_NAME = "Tree of Life";
- public static final String TOL_WEBSERVER = "http://tolweb.org/onlinecontributors/app?service=external&page=xml/TreeStructureService&node_id="
- + PhylogeniesWebserviceClient.QUERY_PLACEHOLDER;
- public static final String TREE_BASE_DESC = "This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment.";
- public static final String TREE_BASE_INST = "treebase";
- public static final String TREE_BASE_NAME = "TreeBASE";
- public static final String TREE_FAM_INST = "tree_fam";
- public static final String TREE_FAM_NAME = "TreeFam";
+ public static final String PFAM_INST = "pfam";
+ public static final String PFAM_NAME = "Pfam";
+ public static final String PFAM_SERVER = "http://pfam.janelia.org";
+ public static final String TOL_NAME = "Tree of Life (ToL)";
+ public static final String TOL_URL_BASE = "http://tolweb.org/onlinecontributors/app?service=external&page=xml/TreeStructureService&node_id=";
+ public static final String TOL_WEBSERVER = TOL_URL_BASE
+ + PhylogeniesWebserviceClient.QUERY_PLACEHOLDER;
+ public static final String TREE_BASE_DESC = "This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment.";
+ public static final String TREE_BASE_INST = "treebase";
+ public static final String TREE_BASE_NAME = "TreeBASE";
+ public static final String TREE_FAM_INST = "tree_fam";
+ public static final String TREE_FAM_NAME = "TreeFam";
+ public static final String TREE_FAM_URL_BASE = "http://www.treefam.org/family/TF";
+ public static final String TREEBASE_PHYLOWS_STUDY_URL_BASE = "http://purl.org/phylo/treebase/phylows/study/TB2:S";
+ public static final String TREEBASE_PHYLOWS_TREE_URL_BASE = "http://purl.org/phylo/treebase/phylows/tree/TB2:Tr";
public static List<PhylogeniesWebserviceClient> createDefaultClients() {
final List<PhylogeniesWebserviceClient> clients = new ArrayList<PhylogeniesWebserviceClient>();
clients.add( new BasicPhylogeniesWebserviceClient( TOL_NAME,
- "Read Tree from Tree of Life...",
+ "Read Tree from Tree of Life (ToL)...",
"Use ToL webservice to obtain a evolutionary tree",
"Please enter a Tree of Life node identifier\n(Examples: "
- + "19386 for Cephalopoda, 2461 for Cnidaria, 2466 for Deuterostomia)",
+ + "14923 for ray-finned fishes, 19386 for Cephalopoda, 2461 for Cnidaria)",
WsPhylogenyFormat.TOL_XML_RESPONSE,
PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
WebserviceUtil.TOL_WEBSERVER,
"http://tolweb.org",
null ) );
clients.add( new BasicPhylogeniesWebserviceClient( TREE_BASE_NAME,
- "Read Tree(s) from TreeBASE Study...",
+ "Read Tree(s) from TreeBASE study...",
"Use TreeBASE to obtain evolutionary tree(s) from a study",
"Please enter a TreeBASE study (\"S\") identifier (without the \"S\")\n(Examples: 15613, 15632, 14525, 14909)",
WsPhylogenyFormat.TREEBASE_STUDY,
null,
- "http://purl.org/phylo/treebase/phylows/study/TB2:S"
+ TREEBASE_PHYLOWS_STUDY_URL_BASE
+ PhylogeniesWebserviceClient.QUERY_PLACEHOLDER
+ "?format=nexus",
true,
"Please enter a TreeBASE tree (\"Tr\") identifier (without the \"Tr\")\n(Examples: 422, 2654, 825, 4931, 2518, 2406, 4934)",
WsPhylogenyFormat.TREEBASE_TREE,
null,
- "http://purl.org/phylo/treebase/phylows/tree/TB2:Tr"
+ TREEBASE_PHYLOWS_TREE_URL_BASE
+ PhylogeniesWebserviceClient.QUERY_PLACEHOLDER
+ "?format=nexus",
true,
"Please enter a TreeFam (TF) accession number\n(Examples: 101004 for Cyclin D, 315938 for Hox, 105310 for Wnt)",
WsPhylogenyFormat.NHX,
null,
- "http://www.treefam.org/family/TF"
+ TREE_FAM_URL_BASE
+ PhylogeniesWebserviceClient.QUERY_PLACEHOLDER
+ "/tree/newick",
true,
import org.forester.application.support_transfer;
import org.forester.archaeopteryx.TreePanelUtil;
+import org.forester.archaeopteryx.webservices.WebserviceUtil;
import org.forester.development.DevelopmentTools;
import org.forester.evoinference.TestPhylogenyReconstruction;
import org.forester.evoinference.matrix.character.CharacterStateMatrix;
+ ForesterUtil.getFileSeparator() + "test_data"
+ ForesterUtil.getFileSeparator();
private final static boolean PERFORM_DB_TESTS = false;
+ private static final boolean PERFORM_WEB_TREE_ACCESS = true;
private static final String PHYLOXML_LOCAL_XSD = PATH_TO_RESOURCES + "phyloxml_schema/"
+ ForesterConstants.PHYLO_XML_VERSION + "/"
+ ForesterConstants.PHYLO_XML_XSD;
System.out.println( "failed." );
failed++;
}
- if ( PERFORM_DB_TESTS ) {
- System.out.print( "Ebi Entry Retrieval: " );
- if ( Test.testEbiEntryRetrieval() ) {
- System.out.println( "OK." );
- succeeded++;
- }
- else {
- System.out.println( "failed." );
- failed++;
- }
- }
- // System.exit( 0 );
- if ( PERFORM_DB_TESTS ) {
- System.out.print( "Sequence DB tools 2: " );
- if ( testSequenceDbWsTools2() ) {
- System.out.println( "OK." );
- succeeded++;
- }
- else {
- System.out.println( "failed." );
- failed++;
- System.exit( -1 );
- }
- }
- // System.exit( 0 );
System.out.print( "Hmmscan output parser: " );
if ( testHmmscanOutputParser() ) {
System.out.println( "OK." );
System.out.println( "failed." );
failed++;
}
- //
System.out.print( "Overlap removal: " );
if ( !org.forester.test.Test.testOverlapRemoval() ) {
System.out.println( "failed." );
succeeded++;
}
System.out.println( "OK." );
- //
System.out.print( "Taxonomy code extraction: " );
if ( Test.testExtractTaxonomyCodeFromNodeName() ) {
System.out.println( "OK." );
System.out.println( "failed." );
failed++;
}
- if ( PERFORM_DB_TESTS ) {
- System.out.print( "Uniprot Entry Retrieval: " );
- if ( Test.testUniprotEntryRetrieval() ) {
- System.out.println( "OK." );
- succeeded++;
- }
- else {
- System.out.println( "failed." );
- failed++;
- }
- }
- if ( PERFORM_DB_TESTS ) {
- System.out.print( "Uniprot Taxonomy Search: " );
- if ( Test.testUniprotTaxonomySearch() ) {
- System.out.println( "OK." );
- succeeded++;
- }
- else {
- System.out.println( "failed." );
- failed++;
- }
- }
- //----
String path = "";
final String os = ForesterUtil.OS_NAME.toLowerCase();
if ( ( os.indexOf( "mac" ) >= 0 ) && ( os.indexOf( "os" ) > 0 ) ) {
System.out.println( "failed [will not count towards failed tests]" );
}
}
- //----
System.out.print( "Next nodes with collapsed: " );
if ( Test.testNextNodeWithCollapsing() ) {
System.out.println( "OK." );
System.out.println( "failed." );
failed++;
}
- System.out.print( "NHX parsing from URL: " );
- if ( Test.testNHXparsingFromURL() ) {
- System.out.println( "OK." );
- succeeded++;
- }
- else {
- System.out.println( "failed." );
- failed++;
- }
- System.out.print( "phyloXML parsing from URL: " );
- if ( Test.testPhyloXMLparsingFromURL() ) {
- System.out.println( "OK." );
- succeeded++;
- }
- else {
- System.out.println( "failed." );
- failed++;
- }
- System.out.print( "TreeBase parsing from URL: " );
- if ( Test.testTreeBaseReading() ) {
- System.out.println( "OK." );
- succeeded++;
+ if ( PERFORM_DB_TESTS ) {
+ System.out.print( "Uniprot Entry Retrieval: " );
+ if ( Test.testUniprotEntryRetrieval() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
+ System.out.print( "Ebi Entry Retrieval: " );
+ if ( Test.testEbiEntryRetrieval() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
+ System.out.print( "Sequence DB tools 2: " );
+ if ( testSequenceDbWsTools2() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ System.exit( -1 );
+ }
+ System.out.print( "Uniprot Taxonomy Search: " );
+ if ( Test.testUniprotTaxonomySearch() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
}
- else {
- System.out.println( "failed." );
- failed++;
+ if ( PERFORM_WEB_TREE_ACCESS ) {
+ System.out.print( "NHX parsing from URL: " );
+ if ( Test.testNHXparsingFromURL() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
+ System.out.print( "phyloXML parsing from URL: " );
+ if ( Test.testPhyloXMLparsingFromURL() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
+ System.out.print( "TreeBase acccess: " );
+ if ( Test.testTreeBaseReading() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
+ //
+ System.out.print( "ToL access: " );
+ if ( Test.testToLReading() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
+ //
+ System.out.print( "TreeFam access: " );
+ if ( Test.testTreeFamReading() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
+ //
+ //
+ System.out.print( "Pfam tree access: " );
+ if ( Test.testPfamTreeReading() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
}
System.out.println();
final Runtime rt = java.lang.Runtime.getRuntime();
return true;
}
- public static final boolean testPhyloXMLparsingFromURL() {
- try {
- final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/archaeopteryx_a/apaf_bcl2.xml";
- final URL u = new URL( s );
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final Phylogeny[] phys = factory.create( u.openStream(), PhyloXmlParser.createPhyloXmlParser() );
- if ( ( phys == null ) || ( phys.length != 2 ) ) {
- return false;
- }
- }
- catch ( final Exception e ) {
- e.printStackTrace();
- }
- return true;
- }
-
- public static final boolean testTreeBaseReading() {
- try {
- final String s = "http://purl.org/phylo/treebase/phylows/tree/TB2:Tr825?format=nexus";
- final URL u = new URL( s );
- final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
- parser.setReplaceUnderscores( true );
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final Phylogeny[] phys = factory.create( u.openStream(), parser );
- if ( ( phys == null ) || ( phys.length != 1 ) ) {
- return false;
- }
- }
- catch ( final Exception e ) {
- e.printStackTrace();
- }
- return true;
- }
-
public static final boolean testNHXparsingFromURL() {
try {
final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/simple/simple_1.nh";
return true;
}
+ public static final boolean testPfamTreeReading() {
+ try {
+ final URL u = new URL( WebserviceUtil.PFAM_SERVER + "/family/PF" + "01849" + "/tree/download" );
+ final NHXParser parser = new NHXParser();
+ parser.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ parser.setReplaceUnderscores( false );
+ parser.setGuessRootedness( true );
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final Phylogeny[] phys = factory.create( u.openStream(), parser );
+ if ( ( phys == null ) || ( phys.length != 1 ) ) {
+ return false;
+ }
+ if ( phys[ 0 ].getNumberOfExternalNodes() < 10 ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace();
+ }
+ return true;
+ }
+
+ public static final boolean testPhyloXMLparsingFromURL() {
+ try {
+ final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/archaeopteryx_a/apaf_bcl2.xml";
+ final URL u = new URL( s );
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final Phylogeny[] phys = factory.create( u.openStream(), PhyloXmlParser.createPhyloXmlParser() );
+ if ( ( phys == null ) || ( phys.length != 2 ) ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace();
+ }
+ return true;
+ }
+
+ public static final boolean testToLReading() {
+ try {
+ final URL u = new URL( WebserviceUtil.TOL_URL_BASE + "15079" );
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final Phylogeny[] phys = factory.create( u.openStream(), new TolParser() );
+ if ( ( phys == null ) || ( phys.length != 1 ) ) {
+ return false;
+ }
+ if ( !phys[ 0 ].getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "15079" ) ) {
+ return false;
+ }
+ if ( !phys[ 0 ].getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Protacanthopterygii" ) ) {
+ return false;
+ }
+ if ( phys[ 0 ].getNumberOfExternalNodes() < 5 ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace();
+ }
+ return true;
+ }
+
+ public static final boolean testTreeBaseReading() {
+ try {
+ final URL u = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "825?format=nexus" );
+ final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
+ parser.setReplaceUnderscores( true );
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final Phylogeny[] phys = factory.create( u.openStream(), parser );
+ if ( ( phys == null ) || ( phys.length != 1 ) ) {
+ return false;
+ }
+ final URL u2 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "15613?format=nexus" );
+ final NexusPhylogeniesParser parser2 = new NexusPhylogeniesParser();
+ parser2.setReplaceUnderscores( true );
+ final PhylogenyFactory factory2 = ParserBasedPhylogenyFactory.getInstance();
+ final Phylogeny[] phys2 = factory2.create( u2.openStream(), parser2 );
+ if ( ( phys2 == null ) || ( phys2.length != 9 ) ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace();
+ }
+ return true;
+ }
+
+ public static final boolean testTreeFamReading() {
+ try {
+ final URL u = new URL( WebserviceUtil.TREE_FAM_URL_BASE + "101004" + "/tree/newick" );
+ final NHXParser parser = new NHXParser();
+ parser.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
+ parser.setReplaceUnderscores( false );
+ parser.setGuessRootedness( true );
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final Phylogeny[] phys = factory.create( u.openStream(), parser );
+ if ( ( phys == null ) || ( phys.length != 1 ) ) {
+ return false;
+ }
+ if ( phys[ 0 ].getNumberOfExternalNodes() < 10 ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace();
+ }
+ return true;
+ }
+
private final static Phylogeny createPhylogeny( final String nhx ) throws IOException {
final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ];
return p;
git://source.jalview.org / jalview.git / commitdiff