private static void initGlossary(IGlossary glossary, IInflector inflector, TaxonGroup taxonGroup)
throws IOException {
OTOClient otoClient = new OTOClient("http://biosemantics.arizona.edu:8080/OTO");
GlossaryDownload glossaryDownload = new GlossaryDownload();
String glossaryVersion = "latest";
otoClient.open();
Future<GlossaryDownload> futureGlossaryDownload =
otoClient.getGlossaryDownload(taxonGroup.getDisplayName(), glossaryVersion);
try {
glossaryDownload = futureGlossaryDownload.get();
} catch (Exception e) {
otoClient.close();
e.printStackTrace();
}
otoClient.close();
// add the syn set of the glossary
HashSet<Term> gsyns = new HashSet<Term>();
for (TermSynonym termSyn : glossaryDownload.getTermSynonyms()) {
// if(termSyn.getCategory().compareTo("structure")==0){
if (termSyn.getCategory().matches("structure|taxon_name|substance")) {
// take care of singular and plural forms
String syns = "";
String synp = "";
String terms = "";
String termp = "";
if (inflector.isPlural(
termSyn
.getSynonym()
.replaceAll(
"_",
"-"))) { // must convert _ to -, as matching entity phrases will be converted
// from leg iii to leg-iii in the sentence.
synp = termSyn.getSynonym().replaceAll("_", "-");
syns = inflector.getSingular(synp);
} else {
syns = termSyn.getSynonym().replaceAll("_", "-");
synp = inflector.getPlural(syns);
}
if (inflector.isPlural(termSyn.getTerm().replaceAll("_", "-"))) {
termp = termSyn.getTerm().replaceAll("_", "-");
terms = inflector.getSingular(termp);
} else {
terms = termSyn.getTerm().replaceAll("_", "-");
termp = inflector.getPlural(terms);
}
glossary.addSynonym(syns, termSyn.getCategory(), terms);
glossary.addSynonym(synp, termSyn.getCategory(), termp);
gsyns.add(new Term(syns, termSyn.getCategory()));
gsyns.add(new Term(synp, termSyn.getCategory()));
} else {
// glossary.addSynonym(termSyn.getSynonym().replaceAll("_", "-"), "arrangement",
// termSyn.getTerm());
glossary.addSynonym(
termSyn.getSynonym().replaceAll("_", "-"), termSyn.getCategory(), termSyn.getTerm());
gsyns.add(new Term(termSyn.getSynonym().replaceAll("_", "-"), termSyn.getCategory()));
// gsyns.add(new Term(termSyn.getSynonym().replaceAll("_", "-"), "arrangement"));
}
}
// the glossary, excluding gsyns
for (TermCategory termCategory : glossaryDownload.getTermCategories()) {
if (!gsyns.contains(
new Term(termCategory.getTerm().replaceAll("_", "-"), termCategory.getCategory())))
glossary.addEntry(
termCategory.getTerm().replaceAll("_", "-"),
termCategory.getCategory()); // primocane_foliage =>primocane-foliage Hong 3/2014
}
List<Synonym> synonyms = new LinkedList<Synonym>();
CSVReader reader =
new CSVReader(
new FileReader(
"C:\\Users\\rodenhausen\\Desktop\\test-enhance\\"
+ "Gordon_complexity_term_review\\category_mainterm_synonymterm-task-Gordon_complexity.csv"));
List<String[]> lines = reader.readAll();
int i = 0;
Set<String> hasSynonym = new HashSet<String>();
for (String[] line : lines) {
synonyms.add(new Synonym(String.valueOf(i), line[1], line[0], line[2]));
hasSynonym.add(line[1]);
}
reader =
new CSVReader(
new FileReader(
"C:\\Users\\rodenhausen\\Desktop\\test-enhance\\"
+ "Gordon_complexity_term_review\\category_term-task-Gordon_complexity.csv"));
lines = reader.readAll();
List<Decision> decisions = new LinkedList<Decision>();
i = 0;
for (String[] line : lines) {
decisions.add(
new Decision(String.valueOf(i), line[1], line[0], hasSynonym.contains(line[1]), ""));
}
Download download = new Download(true, decisions, synonyms);
// add syn set of term_category
HashSet<Term> dsyns = new HashSet<Term>();
if (download != null) {
for (Synonym termSyn : download.getSynonyms()) {
// Hong TODO need to add category info to synonym entry in OTOLite
// if(termSyn.getCategory().compareTo("structure")==0){
if (termSyn.getCategory().matches("structure|taxon_name|substance")) {
// take care of singular and plural forms
String syns = "";
String synp = "";
String terms = "";
String termp = "";
if (inflector.isPlural(termSyn.getSynonym().replaceAll("_", "-"))) {
synp = termSyn.getSynonym().replaceAll("_", "-");
syns = inflector.getSingular(synp);
} else {
syns = termSyn.getSynonym().replaceAll("_", "-");
synp = inflector.getPlural(syns);
}
if (inflector.isPlural(termSyn.getTerm().replaceAll("_", "-"))) {
termp = termSyn.getTerm().replaceAll("_", "-");
terms = inflector.getSingular(termp);
} else {
terms = termSyn.getTerm().replaceAll("_", "-");
termp = inflector.getPlural(terms);
}
// glossary.addSynonym(syns, termSyn.getCategory(), terms);
// glossary.addSynonym(synp, termSyn.getCategory(), termp);
// dsyns.add(new Term(syns, termSyn.getCategory());
// dsyns.add(new Term(synp, termSyn.getCategory());
glossary.addSynonym(syns, termSyn.getCategory(), terms);
glossary.addSynonym(synp, termSyn.getCategory(), termp);
dsyns.add(new Term(syns, termSyn.getCategory()));
dsyns.add(new Term(synp, termSyn.getCategory()));
} else { // forking_1 and forking are syns 5/5/14 hong test, shouldn't _1 have already been
// removed?
glossary.addSynonym(
termSyn.getSynonym().replaceAll("_", "-"), termSyn.getCategory(), termSyn.getTerm());
dsyns.add(new Term(termSyn.getSynonym().replaceAll("_", "-"), termSyn.getCategory()));
}
}
// term_category from OTO, excluding dsyns
for (Decision decision : download.getDecisions()) {
if (!dsyns.contains(
new Term(
decision.getTerm().replaceAll("_", "-"),
decision.getCategory()))) // calyx_tube => calyx-tube
glossary.addEntry(decision.getTerm().replaceAll("_", "-"), decision.getCategory());
}
}
}
