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Commit 189af95f authored by Davide Lagoa's avatar Davide Lagoa
Browse files

method to find same metabolites by name and formula modified

parent 9f18bd15
......@@ -19,6 +19,7 @@ import containers.TcNumberContainer;
import pt.uminho.sysbio.biosynth.integration.io.dao.neo4j.MetaboliteMajorLabel;
import pt.uminho.sysbio.biosynth.integration.neo4j.BiodbMetaboliteNode;
import pt.uminho.sysbio.biosynthframework.BiodbGraphDatabaseService;
import reactions.IdentifyReactionsMetabolites;
import reactions.ReactionsMetabolites;
import utilities.FileUtils;
import utilities.JSONfiles;
......@@ -46,8 +47,8 @@ public class WriteByMetabolitesID {
System.out.println("Retrieving data...");
// logger.trace("salfnafsn");
Map<String, BiosynthMetaboliteProperties> data = getBiosynthDBData(service);
// Map<String, BiosynthMetaboliteProperties> data = null;
// Map<String, BiosynthMetaboliteProperties> data = getBiosynthDBData(service);
Map<String, BiosynthMetaboliteProperties> data = null;
@SuppressWarnings("resource")
Scanner reader = new Scanner(System.in);
......@@ -82,6 +83,8 @@ public class WriteByMetabolitesID {
n = reader.nextInt();
} catch (Exception e) {
e.printStackTrace();
n = reader.nextInt();
}
}
......@@ -100,43 +103,44 @@ public class WriteByMetabolitesID {
try {
// Map<String, Set<TcNumberContainer>> reactionsData = JSONfiles.readJSONtcdbReactionsFile();
//
Map<String, Set<TcNumberContainer>> reactionsData = JSONfiles.readJSONtcdbReactionsFile();
// Set<String> tcdbMetabolites = ReactionsMetabolites.getMetabolitesFromReactions(reactionsData);
//
// System.out.println("TOTAL FOR SEARCH: " + tcdbMetabolites.size());
//
// Map<String, Map<String, MetaboliteMajorLabel>> tcdbMetabolitesIDs = ReactionsMetabolites.getMetabolitesIDs(tcdbMetabolites, namesAndIDsContainer, service);
//
// System.out.println("TOTAL FOUND: " + tcdbMetabolitesIDs.size());
//
//
// FileUtils.saveMapInFile2("C:\\Users\\Davide\\Documents\\InternalDB\\info\\getMetabolitesIDs.txt", namesAndIDsContainer.getMetabolitesIDs());
// FileUtils.saveMapInFile("C:\\Users\\Davide\\Documents\\InternalDB\\info\\getNamesLowerCase.txt", namesAndIDsContainer.getNamesLowerCase());
// FileUtils.saveMapInFile("C:\\Users\\Davide\\Documents\\InternalDB\\info\\getNamesLowerCaseWithoutSigns.txt", namesAndIDsContainer.getNamesLowerCaseWithoutSigns());
// FileUtils.saveMapInFile("C:\\Users\\Davide\\Documents\\InternalDB\\info\\getNamesWithoutSigns.txt", namesAndIDsContainer.getNamesWithoutSigns());
System.out.println(namesAndIDsContainer.getMetabolitesIDs().size());
new IdentifyReactionsMetabolites(reactionsData, data, namesAndIDsContainer, service);
// if(namesAndIDsContainer.getMetabolitesIDs().containsKey("polyol"))
// System.out.println(namesAndIDsContainer.getMetabolitesIDs());
// if(byName.containsKey("O2"))
// System.out.println(byName.get("O2"));
//
// if(byName.containsKey("oxygen"))
// System.out.println(byName.get("oxygen"));
// System.out.println("TOTAL FOUND: " + tcdbMetabolitesIDs.size());
//
// if(byName.containsKey("Oxygen"))
// System.out.println(byName.get("Oxygen"));
//
// if(byName.containsKey("OXYGEN-MOLECULE"))
// System.out.println(byName.get("OXYGEN-MOLECULE"));
// FileUtils.saveMapInFile2("C:\\Users\\Davide\\Documents\\InternalDB\\info\\getMetabolitesIDs2.txt", namesAndIDsContainer.getMetabolitesIDs());
// FileUtils.saveMapInFile("C:\\Users\\Davide\\Documents\\InternalDB\\info\\getNamesLowerCase2.txt", namesAndIDsContainer.getNamesLowerCase());
// FileUtils.saveMapInFile("C:\\Users\\Davide\\Documents\\InternalDB\\info\\getNamesLowerCaseWithoutSigns2.txt", namesAndIDsContainer.getNamesLowerCaseWithoutSigns());
// FileUtils.saveMapInFile("C:\\Users\\Davide\\Documents\\InternalDB\\info\\getNamesWithoutSigns2.txt", namesAndIDsContainer.getNamesWithoutSigns());
// System.out.println(namesAndIDsContainer.getMetabolitesIDs().get("Cu2+"));
// if(namesAndIDsContainer.getMetabolitesIDs().containsKey("triose phosphate"))
// System.out.println(namesAndIDsContainer.getMetabolitesIDs().get("triose phosphate"));
// else
// System.out.println("nada");
// System.out.println(byName.containsKey("L-val"));
......@@ -208,16 +212,17 @@ public class WriteByMetabolitesID {
// MetabolitesChilds.getMetaboliteChilds("ECOLI:Sugar-alcohols", MetaboliteMajorLabel.MetaCyc, service);
// Node node = service.getNodeByEntryAndLabel("C19171", MetaboliteMajorLabel.LigandCompound);
// Node node2 = service.getNodeByEntryAndLabel("META:CU+2", MetaboliteMajorLabel.MetaCyc);
// if(byName.containsKey("Oxygen"))
// System.out.println(byName.get("oxygen"));
//
//
// Node node = service.getNodeByEntryAndLabel("C00007", MetaboliteMajorLabel.LigandCompound);
// Node node = service.getNodeByEntryAndLabel("ECOLI:Sugar-alcohols", MetaboliteMajorLabel.MetaCyc);
// System.out.println(node.getAllProperties());
// System.out.println(node2.getAllProperties());
//
// String names = (String) node.getAllProperties().get("name");
// String names = (String) node.getAllProperties().get("name");
......@@ -226,11 +231,11 @@ public class WriteByMetabolitesID {
// System.out.println(names);
//
//
// Map<String, Object> properties = node.getAllProperties();
// Map<String, Object> properties2 = node2.getAllProperties();
//
// System.out.println(properties);
// System.out.println(properties2);
// Map<String, Object> properties = node.getAllProperties();
// Map<String, Object> properties2 = node2.getAllProperties();
//
// System.out.println(properties);
// System.out.println(properties2);
//
// System.out.println();
//
......@@ -490,11 +495,11 @@ public class WriteByMetabolitesID {
if(useCache) {
namesLowerCaseWithoutSigns = FileUtils.readMapFromFile("C:\\Users\\Davide\\Documents\\InternalDB\\info\\getNamesLowerCaseWithoutSigns.txt");
namesWithoutSigns = FileUtils.readMapFromFile("C:\\Users\\Davide\\Documents\\InternalDB\\info\\getNamesWithoutSigns.txt");
namesLowerCase = FileUtils.readMapFromFile("C:\\Users\\Davide\\Documents\\InternalDB\\info\\getNamesLowerCase.txt");
namesLowerCaseWithoutSigns = FileUtils.readMapFromFile("C:\\Users\\Davide\\Documents\\InternalDB\\info\\getNamesLowerCaseWithoutSigns2.txt");
namesWithoutSigns = FileUtils.readMapFromFile("C:\\Users\\Davide\\Documents\\InternalDB\\info\\getNamesWithoutSigns2.txt");
namesLowerCase = FileUtils.readMapFromFile("C:\\Users\\Davide\\Documents\\InternalDB\\info\\getNamesLowerCase2.txt");
compounds = FileUtils.readMapFromFile2("C:\\Users\\Davide\\Documents\\InternalDB\\info\\getMetabolitesIDs.txt");
compounds = FileUtils.readMapFromFile2("C:\\Users\\Davide\\Documents\\InternalDB\\info\\getMetabolitesIDs2.txt");
return new BiosynthMetabolites(compounds, namesLowerCaseWithoutSigns, namesWithoutSigns, namesLowerCase);
}
......@@ -506,11 +511,11 @@ public class WriteByMetabolitesID {
Set<BiodbMetaboliteNode> allMetabolites = service.listMetabolites();
// Set<BiodbMetaboliteNode> allMetabolites = new HashSet<>();
//
// allMetabolites.add(service.getMetabolite("C00007", MetaboliteMajorLabel.LigandCompound));
// allMetabolites.add(service.getMetabolite("o2", MetaboliteMajorLabel.BiGG));
// allMetabolites.add(service.getMetabolite("ECOLI:OXYGEN-MOLECULE", MetaboliteMajorLabel.MetaCyc));
// allMetabolites.add(service.getMetabolite("cpd00007", MetaboliteMajorLabel.ModelSeed));
// allMetabolites.add(service.getMetabolite("C05359", MetaboliteMajorLabel.LigandCompound));
// allMetabolites.add(service.getMetabolite("glu-L", MetaboliteMajorLabel.BiGG));
// allMetabolites.add(service.getMetabolite("META:CU+2", MetaboliteMajorLabel.MetaCyc));
// allMetabolites.add(service.getMetabolite("cpd12713", MetaboliteMajorLabel.ModelSeed));
// allMetabolites.add(service.getMetabolite("glu__L", MetaboliteMajorLabel.BiGGMetabolite));
// Set<String> allDatabases = new HashSet<>();
......@@ -528,8 +533,8 @@ public class WriteByMetabolitesID {
Set<String> names = getSynonyms(node, nodeProperties, service);
// if(entryID.equals("ECOLI:VAL"))
// System.out.println("found ecoli >>>> " + names);
// if(entryID.equals("ECOLI:VAL"))
// System.out.println("found ecoli >>>> " + names);
if(!names.isEmpty()) {
......@@ -541,14 +546,24 @@ public class WriteByMetabolitesID {
// if(entryID.equals("META:OXYGEN-MOLECULE"))
// System.out.println(formula + "\t" + names);
names.remove("co2"); // to avoid errors with cobalt ions
for(String name : names) {
// System.out.println();
//
// System.out.println(name + " >>>>> " + formula);
for(String metab : formulas.keySet()) {
if(metab.equalsIgnoreCase(name)) {
// System.out.println("EQUALS NAME >>>>> " + metab + "\t" + name );
if(formula.equals(formulas.get(metab))) {
// System.out.println("EQUALS formula >>>>> " + formula + "\t" + formulas.get(metab) );
if(!formulas.containsKey(name))
formulas.put(name, formula);
......@@ -558,6 +573,9 @@ public class WriteByMetabolitesID {
newAlias.addAll(names);
// System.out.println(alias);
// System.out.println(newAlias);
for(String newEntry : newAlias)
alias.put(newEntry, newAlias);
......@@ -570,6 +588,11 @@ public class WriteByMetabolitesID {
for(String name : names) {
// if(name.equals("Cu2+"))
// System.out.println("coiso");
// System.out.println("name>>" + name);
if(!found) {
......@@ -584,6 +607,8 @@ public class WriteByMetabolitesID {
Map<MetaboliteMajorLabel, String> ids = new HashMap<>();
// System.out.println("alias>>> " + alias.get(name));
for(String name2 : alias.get(name)) {
if(compounds.containsKey(name2))
ids.putAll(compounds.get(name2));
......@@ -592,24 +617,35 @@ public class WriteByMetabolitesID {
ids.put(label, entryID);
for(String name2 : alias.get(name)) {
if(compounds.containsKey(name2)) {
for(MetaboliteMajorLabel key : ids.keySet()) {
if(!compounds.get(name2).containsKey(key))
compounds.get(name2).put(key, ids.get(key));
}
}
else
compounds.put(name2, ids);
namesWithoutSigns.put(name2, name2.replaceAll("[^A-Za-z0-9]", ""));
namesLowerCase.put(name2, name2.toLowerCase());
namesLowerCaseWithoutSigns.put(name2, name2.replaceAll("[^A-Za-z0-9]", "").toLowerCase());
}
}
}
}
}
// System.out.println(compounds.get("Electron"));
// FindMetabolitesID.saveMapInFile2("C:\\Users\\Davide\\Documents\\InternalDB\\DatabaseCompounds.txt", compounds);
// FindMetabolitesID.saveMapInFile2("C:\\Users\\Davide\\Documents\\InternalDB\\filtered.txt", filteredCompounds);
System.out.println("Number of compounds: " + compounds.size());
// System.out.println("Number of compounds: " + compounds.size());
// System.out.println(compounds);
// System.out.println("Number of filteredCompounds: " + filteredCompounds.size());
......@@ -663,6 +699,11 @@ public class WriteByMetabolitesID {
*/
private static Set<String> getSynonyms(Node node, Map<String, Object> nodeProperties, BiodbGraphDatabaseService service){
// if(node.getAllProperties().get("entry").equals("META:CU+2"))
// System.out.println("AQUIIII");
// else
// System.out.println("not found!!!!!!!!");
String names ="";
Set<String> synonyms = new HashSet<>();
......@@ -701,6 +742,7 @@ public class WriteByMetabolitesID {
}
for(String name : names.split(";")) {
if(!name.isEmpty()) {
synonyms.add(name.replaceAll("<i>", "").replaceAll("</i>", "").replaceAll("\\[", "")
.replaceAll("\\]", "").replaceAll("</sup>", "").replaceAll("<sup>", "").replaceAll("</I>", "").replaceAll("<I>", "")
......
......@@ -40,8 +40,16 @@ public class IdentifyReactionsMetabolites {
Set<String> tcdbMetabolites = getMetabolitesFromReactions(reactionsData);
System.out.println("TOTAL FOR SEARCH: " + tcdbMetabolites.size());
getMetabolitesIDs(tcdbMetabolites, namesAndIDsContainer, service);
System.out.println("TOTAL FOUND: " + tcdbMetabolitesIDs.size()); //1103
// for(String metabolite : metabolites)
// System.out.println(metabolite);
//
// System.out.println(metabolites.size());
}
......@@ -62,42 +70,41 @@ public class IdentifyReactionsMetabolites {
namesAndIDsContainer = standardizationOfNames2(namesAndIDsContainer);
System.out.println("metabolites >>>" + metabolites.size());
// System.out.println("MET>>>>> " + allMetabolitesByName.get("Electron"));
System.out.println("metabolites >>>" + metabolites.size()); //2078
System.out.println("allmetabolites >>>" + namesAndIDsContainer.getMetabolitesIDs().size());
System.out.println("allmetabolites >>>" + namesAndIDsContainer.getMetabolitesIDs().size()); //154224
identificationByDirectMatch();
System.out.println("FOUND1: " + tcdbMetabolitesIDs.size());
System.out.println("FOUND1: " + tcdbMetabolitesIDs.size()); //911
identificationDeletingStoichiometry();
System.out.println("FOUND2: " + tcdbMetabolitesIDs.size());
System.out.println("FOUND2: " + tcdbMetabolitesIDs.size()); //975
identificationInLowerCase();
System.out.println("FOUND3: " + tcdbMetabolitesIDs.size());
System.out.println("FOUND3: " + tcdbMetabolitesIDs.size()); //1089
identificationReplacingNonAlphanumeric();
System.out.println("FOUND4: " + tcdbMetabolitesIDs.size());
System.out.println("FOUND4: " + tcdbMetabolitesIDs.size()); //1095
identificationIntroducingDandL();
System.out.println("FOUND5: " + tcdbMetabolitesIDs.size());
System.out.println("FOUND5: " + tcdbMetabolitesIDs.size()); //1103
identificationReplacingNonAlphanumericAndInLowercase();
System.out.println("FOUND6: " + tcdbMetabolitesIDs.size());
System.out.println("FOUND6: " + tcdbMetabolitesIDs.size()); //1109
......@@ -112,7 +119,7 @@ public class IdentifyReactionsMetabolites {
private void saveMetabolite(String metabolite, Map<MetaboliteMajorLabel, String> ids) {
MetaboliteMajorLabel id = selectMetaboliteMajorLabel(ids);
MetaboliteMajorLabel id = selectMetaboliteMajorLabel(metabolite, ids);
if(id != null) {
Map<String, MetaboliteMajorLabel> map = new HashMap<>();
......@@ -132,6 +139,16 @@ public class IdentifyReactionsMetabolites {
for(String metabolite : new HashSet<>(metabolites)) {
if(metabolite.matches("^(D*L*-+).+")){
if(namesAndIDsContainer.getNamesWithoutSigns().containsKey(metabolite.replaceAll("^(D*L*-+)", ""))) {
Map<MetaboliteMajorLabel, String> ids = allMetabolitesByName.get(metabolite.replaceAll("^(D*L*-+)", ""));
saveMetabolite(metabolite, ids);
}
}
else {
if(namesAndIDsContainer.getNamesWithoutSigns().containsKey("D-"+metabolite)) {
Map<MetaboliteMajorLabel, String> ids = allMetabolitesByName.get("D-"+metabolite);
......@@ -144,7 +161,7 @@ public class IdentifyReactionsMetabolites {
Map<MetaboliteMajorLabel, String> ids = allMetabolitesByName.get("L-"+metabolite);
saveMetabolite(metabolite, ids);
}
}
}
}
......@@ -161,6 +178,8 @@ public class IdentifyReactionsMetabolites {
Map<MetaboliteMajorLabel, String> ids = allMetabolitesByName.get(metabolite.replaceAll("[^A-Za-z0-9]", "").toLowerCase());
// System.out.println(metabolite + ids);
saveMetabolite(metabolite, ids);
}
else if(String.valueOf(metabolite.charAt(metabolite.length()-1)).equals(s)) {
......@@ -168,6 +187,9 @@ public class IdentifyReactionsMetabolites {
Map<MetaboliteMajorLabel, String> ids = allMetabolitesByName.get(metabolite.substring(0, metabolite.length()-1).replaceAll("[^A-Za-z0-9]", ""));
// System.out.println(metabolite + ids);
saveMetabolite(metabolite, ids);
}
}
......@@ -185,6 +207,8 @@ public class IdentifyReactionsMetabolites {
Map<MetaboliteMajorLabel, String> ids = allMetabolitesByName.get(metabolite.replaceAll("[^A-Za-z0-9]", ""));
// System.out.println(metabolite + ids);
saveMetabolite(metabolite, ids);
}
else if(String.valueOf(metabolite.charAt(metabolite.length()-1)).equals(s)) {
......@@ -192,6 +216,8 @@ public class IdentifyReactionsMetabolites {
Map<MetaboliteMajorLabel, String> ids = allMetabolitesByName.get(metabolite.substring(0, metabolite.length()-1).replaceAll("[^A-Za-z0-9]", ""));
// System.out.println(metabolite + ids);
saveMetabolite(metabolite, ids);
}
}
......@@ -209,6 +235,8 @@ public class IdentifyReactionsMetabolites {
Map<MetaboliteMajorLabel, String> ids = allMetabolitesByName.get(metabolite.toLowerCase());
// System.out.println(metabolite + ids);
saveMetabolite(metabolite, ids);
}
else if(String.valueOf(metabolite.charAt(metabolite.length()-1)).equals(s)) {
......@@ -217,6 +245,8 @@ public class IdentifyReactionsMetabolites {
Map<MetaboliteMajorLabel, String> ids = allMetabolitesByName.get(metabolite.substring(0, metabolite.length()-1).toLowerCase());
// System.out.println(metabolite + ids);
saveMetabolite(metabolite, ids);
}
}
......@@ -249,6 +279,9 @@ public class IdentifyReactionsMetabolites {
*/
private void identificationDeletingStoichiometryAux(String metabolite, boolean correctName) {
// if(metabolite.equals("nCo2+"))
// System.out.println("metaboliteFound!!!");
String metabolite2 = metabolite;
if(correctName)
......@@ -268,14 +301,24 @@ public class IdentifyReactionsMetabolites {
met = met.replaceAll(REGEX_STOICHIOMETRY[i], "");
// if(metabolite.equals("nCo2+"))
// System.out.println("met >>>> " + met);
if(allMetabolitesByName.containsKey(met)) {
key = met;
}
// if(metabolite.equals("nCo2+"))
// System.out.println("key >>>> " + key);
if(key == null ) {
String alias = dictionary.getSynonym(met.replace("\\s+", "").toLowerCase());
// if(metabolite.equals("nCo2+"))
// System.out.println("alias >>>> " + alias);
if(alias != null) {
if(allMetabolitesByName.containsKey(alias))
......@@ -286,8 +329,13 @@ public class IdentifyReactionsMetabolites {
if(key != null) {
// if(metabolite.equals("nCo2+"))
// System.out.println("ids >>>> " + allMetabolitesByName.get(key));
Map<MetaboliteMajorLabel, String> ids = allMetabolitesByName.get(key);
// System.out.println(metabolite + ids);
saveMetabolite(metabolite2, ids);
}
}
......@@ -310,6 +358,8 @@ public class IdentifyReactionsMetabolites {
Map<MetaboliteMajorLabel, String> ids = allMetabolitesByName.get(metabolite);
// System.out.println(metabolite + ids);
saveMetabolite(metabolite, ids);
}
......@@ -319,6 +369,8 @@ public class IdentifyReactionsMetabolites {
Map<MetaboliteMajorLabel, String> ids = allMetabolitesByName.get(metabolite.substring(0, metabolite.length()-1));
// System.out.println(metabolite + ids);
saveMetabolite(metabolite, ids);
}
}
......@@ -351,8 +403,16 @@ public class IdentifyReactionsMetabolites {
String[] metabs = reaction.split(" \\+ ");
for(String metab : metabs)
for(String metab : metabs) {
metab = metab.replaceAll("^(\\+\\s)", "");
// if(metab.trim().equals("+ Fe2+"))
// System.out.println(reactionContainer.getReaction() + "\t" + tcContainer.getTcNumber());
metabolites.add(metab.trim());
}
}
}
......@@ -376,10 +436,19 @@ public class IdentifyReactionsMetabolites {
for(String metabolite : metabolites) {
metabolite = metabolite.replaceAll("ic acid", "ate");
// if(metabolite.equals("Monocarboxylic Acids"))
// System.out.println("sim");
if(metabolite.matches("(?i).+(-P)$"))
metabolite = metabolite.replaceAll("(?i)(-P)$", "\\sphosphate");
metabolite = metabolite.replaceAll("(?i)(ic acids*)", "ate");
String word = dictionary.getSynonym(metabolite.replaceAll("\\s+", "").toLowerCase());
// if(metabolite.equals("Monocarboxylic Acids"))
// System.out.println(word + "\t" + metabolite);
if(word != null)
standardNames.add(word);
else
......@@ -430,8 +499,6 @@ public class IdentifyReactionsMetabolites {
if(word.matches("ic acids*"))
word = word.replaceAll("ic acids*", "ate");
else if(word.matches("(ates*)$"))
word = word.replaceAll("(ates*)$", "ic acid");
if(!word.equals(originalWord)) {
namesAndIDsContainer.getMetabolitesIDs().put(word, namesAndIDsContainer.getMetabolitesIDs().get(metabolite));
......@@ -452,7 +519,9 @@ public class IdentifyReactionsMetabolites {
* @param ids
* @return
*/
private static MetaboliteMajorLabel selectMetaboliteMajorLabel(Map<MetaboliteMajorLabel, String> ids){
private static MetaboliteMajorLabel selectMetaboliteMajorLabel(String metabolite, Map<MetaboliteMajorLabel, String> ids){
try {
if(ids.containsKey(MetaboliteMajorLabel.ModelSeed))
return MetaboliteMajorLabel.ModelSeed;
......@@ -470,6 +539,13 @@ public class IdentifyReactionsMetabolites {
for(MetaboliteMajorLabel key : ids.keySet())
return key;
}
}
catch (Exception e) {
System.out.println("[ERROR] while selecting best metabolite major label for: " + metabolite);
System.out.println(ids);
e.printStackTrace();
}
return null;
}
......
......@@ -12,6 +12,11 @@ import dictionary.Synonyms;
import pt.uminho.sysbio.biosynth.integration.io.dao.neo4j.MetaboliteMajorLabel;
import pt.uminho.sysbio.biosynthframework.BiodbGraphDatabaseService;
/**
*
* @deprecated Use class IdentifyReactionsMetabolites.java instead
*/
@Deprecated
public class ReactionsMetabolites {
public static final String[] REGEX_STOICHIOMETRY = {"^(\\s*n\\s*)", "^(\\d+\\/*\\d*\\s*)"};
......
......@@ -15,6 +15,7 @@ import java.util.Map;
import java.util.Set;
import java.util.TreeMap;
import dictionary.Synonyms;
import pt.uminho.sysbio.biosynth.integration.io.dao.neo4j.MetaboliteMajorLabel;
import pt.uminho.sysbio.common.bioapis.externalAPI.ebi.uniprot.UniProtAPI;
import uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry;
......@@ -139,14 +140,21 @@ class Test {
@org.junit.jupiter.api.Test