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Commit c99df917 authored by Davide Lagoa's avatar Davide Lagoa
Browse files

generator for biochemical reactions improved

parent 45d7ef97
......@@ -41,9 +41,6 @@ public class GenerateTransportReactions {
int noMetabolitesNoReactionsCounter = 0;
// Map<String, TcdbMetabolitesContainer> tcdbMetabolites2 = new HashMap<>();
// tcdbMetabolites2.put("O07084", tcdbMetabolites2.get("O07084"));
for(String accession : tcdbMetabolites.keySet()) {
Map<String, TcNumberContainer> newContainers = new HashMap<>();
......@@ -2001,6 +1998,9 @@ public class GenerateTransportReactions {
if(uptake && efflux)
return null;
}
if(!uptake && !efflux)
return null;
if(uptake)
return true;
......
package pt.uminho.ceb.biosystems.transyt.scraper.tcdb.tcdbTransportTypesRetriever;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
......@@ -22,7 +23,7 @@ public class Retriever {
private static final Logger logger = LoggerFactory.getLogger(Retriever.class);
public static void runRetriever(boolean useCache) throws Exception {
public static void runRetriever(boolean useCache, boolean tests, String accTest) throws Exception {
try {
......@@ -79,7 +80,14 @@ public class Retriever {
List<String[]> excel = JSONFilesUtils.readTCDBScrapedInfo();
Map<String, TcdbMetabolitesContainer> tcdbMetabolites = ProcessTcdbMetabolitesExcel.processData(excel);
Map<String, TcdbMetabolitesContainer> tcdbMetabolitesAux = ProcessTcdbMetabolitesExcel.processData(excel);
Map<String, TcdbMetabolitesContainer> tcdbMetabolites = new HashMap<>();
if(tests)
tcdbMetabolites.put(accTest, tcdbMetabolitesAux.get(accTest));
else
tcdbMetabolites = tcdbMetabolitesAux;
Map<String, Map<String, TcNumberContainer>> transportReactions = GenerateTransportReactions.generateReactions(data2, tcdbMetabolites, proteinFamilyDescription);
......
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