UberphenoOboParserTest.java 文件源码

@Test
public void testParseUberphenoHead() throws IOException {
  final UberphenoOboParser parser = new UberphenoOboParser(uberphenoHeadFile, true);
  final UberphenoOntology ontology = parser.parse();

  assertEquals(
      "ImmutableDirectedGraph [edgeLists={ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000001]=ImmutableVertexEdgeList [inEdges=[], outEdges=[ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000001], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=UBERPHENO], id=00000001], id=2]]], ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0000001]=ImmutableVertexEdgeList [inEdges=[ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0001186], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0000001], id=4]], outEdges=[ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0000001], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=UBERPHENO], id=00000001], id=1]]], ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0001186]=ImmutableVertexEdgeList [inEdges=[], outEdges=[ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0001186], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0000001], id=4]]], ImmutableTermId [prefix=ImmutableTermPrefix [value=UBERPHENO], id=00000001]=ImmutableVertexEdgeList [inEdges=[ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000001], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=UBERPHENO], id=00000001], id=2], ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0000001], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=UBERPHENO], id=00000001], id=1], ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=ZP], id=0000001], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=UBERPHENO], id=00000001], id=3]], outEdges=[]], ImmutableTermId [prefix=ImmutableTermPrefix [value=ZP], id=0000001]=ImmutableVertexEdgeList [inEdges=[], outEdges=[ImmutableEdge [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=ZP], id=0000001], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=UBERPHENO], id=00000001], id=3]]]}, edgeCount=4]",
      ontology.getGraph().toString());
  assertEquals(
      "[ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000001], ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0000001], ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0001186], ImmutableTermId [prefix=ImmutableTermPrefix [value=UBERPHENO], id=00000001], ImmutableTermId [prefix=ImmutableTermPrefix [value=ZP], id=0000001]]",
      ImmutableSortedSet.copyOf(ontology.getAllTermIds()).toString());
  assertEquals(
      "{ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000001]=UberphenoTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000001], altTermIds=[], name=All, definition=null, comment=null, subsets=[], synonyms=[], obsolete=false, createdBy=null, creationDate=null, xrefs=[]], ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0000001]=UberphenoTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0000001], altTermIds=[], name=mammalian phenotype, definition=null, comment=null, subsets=[], synonyms=[], obsolete=false, createdBy=null, creationDate=null, xrefs=[]], ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0001186]=UberphenoTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0001186], altTermIds=[], name=pigmentation phenotype, definition=null, comment=null, subsets=[], synonyms=[], obsolete=false, createdBy=null, creationDate=null, xrefs=[]], ImmutableTermId [prefix=ImmutableTermPrefix [value=UBERPHENO], id=00000001]=UberphenoTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=UBERPHENO], id=00000001], altTermIds=[], name=UBERPHENO_ROOT, definition=null, comment=null, subsets=[], synonyms=[], obsolete=false, createdBy=null, creationDate=null, xrefs=[]], ImmutableTermId [prefix=ImmutableTermPrefix [value=ZP], id=0000001]=UberphenoTerm [id=ImmutableTermId [prefix=ImmutableTermPrefix [value=ZP], id=0000001], altTermIds=[], name=abnormal(ly) quality zebrafish anatomical entity, definition=null, comment=null, subsets=[], synonyms=[], obsolete=false, createdBy=null, creationDate=null, xrefs=[]]}",
      ImmutableSortedMap.copyOf(ontology.getTermMap()).toString());
  assertEquals(
      "{1=UberphenoTermRelation [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0000001], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=UBERPHENO], id=00000001], id=1, relationQualifier=IS_A], 2=UberphenoTermRelation [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000001], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=UBERPHENO], id=00000001], id=2, relationQualifier=IS_A], 3=UberphenoTermRelation [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=ZP], id=0000001], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=UBERPHENO], id=00000001], id=3, relationQualifier=IS_A], 4=UberphenoTermRelation [source=ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0001186], dest=ImmutableTermId [prefix=ImmutableTermPrefix [value=MP], id=0000001], id=4, relationQualifier=IS_A]}",
      ImmutableSortedMap.copyOf(ontology.getRelationMap()).toString());
  assertEquals("ImmutableTermId [prefix=ImmutableTermPrefix [value=UBERPHENO], id=00000001]",
      ontology.getRootTermId().toString());
  assertEquals("{date=20:01:2012 06:00}", ontology.getMetaInfo().toString());
}