@@ -0,0 +1,1741 @@
+package org.mskcc.cbio.oncokb.importer;%0A%0Aimport org.json.JSONArray;%0Aimport org.json.JSONObject;%0Aimport org.mskcc.cbio.oncokb.model.Gene;%0Aimport org.mskcc.cbio.oncokb.util.ApplicationContextSingleton;%0Aimport org.mskcc.cbio.oncokb.util.FileUtils;%0Aimport org.mskcc.cbio.oncokb.util.GeneUtils;%0A%0Aimport java.io.IOException;%0Aimport java.util.ArrayList;%0Aimport java.util.HashSet;%0Aimport java.util.List;%0Aimport java.util.Set;%0A%0A/**%0A * @author Hongxin Zhang%0A */%0Apublic final class geneNamelImporter %7B%0A    private geneNamelImporter() %7B%0A        throw new AssertionError();%0A    %7D%0A%0A    private static String ALL_GENES_FILE = %22ftp://ftp.ebi.ac.uk/pub/databases/genenames/new/json/hgnc_complete_set.json%22;%0A%0A    public static void main(String%5B%5D args) throws IOException %7B%0A        String response = FileUtils.readRemote(ALL_GENES_FILE);%0A        JSONObject result = new JSONObject(response);%0A        JSONArray array = result.getJSONObject(%22response%22).getJSONArray(%22docs%22);%0A        Set%3CString%3E hugoSymbols = new HashSet%3C%3E();%0A%0A        for (int i = 0; i %3C array.length(); i++) %7B%0A            JSONObject object = array.getJSONObject(i);%0A            hugoSymbols.add(object.getString(%22symbol%22));%0A        %7D%0A%0A        Set%3CGene%3E genes = GeneUtils.getAllGenes();%0A%0A        for (Gene gene : genes) %7B%0A            List%3CString%3E aliases = new ArrayList%3C%3E(gene.getGeneAliases());%0A            for (String alias : aliases) %7B%0A                if (hugoSymbols.contains(alias)) %7B%0A                    gene.getGeneAliases().remove(alias);%0A                    System.out.println(%22Alias of %22 + gene.getHugoSymbol() + %22 has been removed: %22 + alias);%0A                %7D%0A            %7D%0A        %7D%0A%0A        ApplicationContextSingleton.getGeneBo().saveOrUpdateAll(new ArrayList%3C%3E(genes));%0A    %7D%0A%7D%0A

Add importer to remove current in use hugoSymbol from the alias list