diff --git a/vcell-core/src/main/java/cbit/util/kisao/KisaoOntology.java b/vcell-core/src/main/java/cbit/util/kisao/KisaoOntology.java index 203e0f96cd..83c6ff6d52 100644 --- a/vcell-core/src/main/java/cbit/util/kisao/KisaoOntology.java +++ b/vcell-core/src/main/java/cbit/util/kisao/KisaoOntology.java @@ -45,5 +45,12 @@ public void createRelations() { } } } + + public static void main(String[] args) { + + KisaoTerm sedmlSolverKisaoTerm = KisaoOntology.getInstance().getTermById("KISAO_0000027"); + System.out.println(sedmlSolverKisaoTerm); + System.out.println("Done"); + } } diff --git a/vcell-core/src/main/java/cbit/util/kisao/KisaoTerm.java b/vcell-core/src/main/java/cbit/util/kisao/KisaoTerm.java index 0db738a9db..ec72e19876 100644 --- a/vcell-core/src/main/java/cbit/util/kisao/KisaoTerm.java +++ b/vcell-core/src/main/java/cbit/util/kisao/KisaoTerm.java @@ -6,7 +6,7 @@ public class KisaoTerm { - private String id, name, def; + private String id, name; private List isaList = new ArrayList(); private List isaRef = new ArrayList(); // used only during parsing, as proxy for still unknown terms @@ -15,7 +15,7 @@ public class KisaoTerm { @Override public String toString() { - return "KisaoTerm [id=" + id + ", name=" + name + ", def=" + def + "]"; + return "KisaoTerm [id=" + id + ", name=" + name + "]"; } @Override public int hashCode() { @@ -61,13 +61,6 @@ void setName(String name) { this.name = name; } - public String getDefinition() { - return def; - } - void setDef(String def) { - this.def = def; - } - public List getIsa() { return Collections.unmodifiableList(isaList); } diff --git a/vcell-core/src/main/java/cbit/util/kisao/KisaoTermParser.java b/vcell-core/src/main/java/cbit/util/kisao/KisaoTermParser.java index d4f340fe05..14132f2294 100644 --- a/vcell-core/src/main/java/cbit/util/kisao/KisaoTermParser.java +++ b/vcell-core/src/main/java/cbit/util/kisao/KisaoTermParser.java @@ -1,7 +1,6 @@ package cbit.util.kisao; import java.io.BufferedReader; -import java.io.IOException; import java.io.InputStream; import java.io.InputStreamReader; import java.util.regex.Matcher; @@ -9,18 +8,18 @@ public class KisaoTermParser { + final String Kisao_OBO = "kisao_2020_12_13.obo"; + final String TERM_PATTERN = "\\[Term\\]"; final Pattern ID_PATTERN = Pattern.compile("id:\\s*(.+)"); final Pattern NAME_PATTERN = Pattern.compile("name:\\s*(.+)"); - final Pattern DEF_PATTERN = Pattern.compile("def:\\s*(.+)"); final Pattern ISA_PATTERN = Pattern.compile("is_a:\\s*(\\S+)"); KisaoOntology parse() { - InputStream is2 = KisaoTermParser.class.getClassLoader().getResourceAsStream(Kisao_OBO); - BufferedReader isr = new BufferedReader(new InputStreamReader(is2)); + InputStream is = KisaoTermParser.class.getClassLoader().getResourceAsStream(Kisao_OBO); + BufferedReader isr = new BufferedReader(new InputStreamReader(is)); String line = null; - boolean inPreamble = true; boolean inState = false; KisaoOntology ontology = new KisaoOntology(); KisaoTerm curr = null; @@ -34,10 +33,10 @@ KisaoOntology parse() { } if (line.matches("^$") && curr != null) { inState = false; - inPreamble = false; ontology.addTerm(curr); curr = null; } + if(inState) { Matcher matcher = ID_PATTERN.matcher(line); if (matcher.find()) { @@ -48,10 +47,6 @@ KisaoOntology parse() { if (matcher.find()) { curr.setName(matcher.group(1)); } - matcher = DEF_PATTERN.matcher(line); - if (matcher.find()) { - curr.setDef(matcher.group(1)); - } matcher = ISA_PATTERN.matcher(line); if (matcher.find()) { curr.addIsaRef(matcher.group(1));