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Commit 5fa17d2b authored by Davide Lagoa's avatar Davide Lagoa
Browse files

metabolites not being added to reactions fixed

parent b3fa48c4
......@@ -5,7 +5,7 @@
<groupId>pt.uminho.ceb.biosystems.transyt</groupId>
<artifactId>scraper</artifactId>
<version>0.0.11-SNAPSHOT</version>
<version>0.0.12-SNAPSHOT</version>
<packaging>jar</packaging>
<name>scraper</name>
......@@ -66,7 +66,7 @@
<dependency>
<groupId>pt.uminho.ceb.biosystems.transyt</groupId>
<artifactId>utilities</artifactId>
<version>0.0.11-SNAPSHOT</version>
<version>0.0.12-SNAPSHOT</version>
</dependency>
<dependency>
......
......@@ -43,7 +43,7 @@ public class GenerateTransportReactions {
int noMetabolitesNoReactionsCounter = 0;
// Map<String, TcdbMetabolitesContainer> tcdbMetabolites2 = new HashMap<>();
// tcdbMetabolites2.put("O06933", tcdbMetabolites2.get("O06933"));
// tcdbMetabolites2.put("P31801", tcdbMetabolites2.get("P31801"));
for(String accession : tcdbMetabolites.keySet()) {
......@@ -125,6 +125,8 @@ public class GenerateTransportReactions {
// System.out.println("AQUIII2" + "\t " + antiportOrSymport + " \t" + evidence + "\t" + reactionContainer.getTransportType().toString());
// }
int numberOfReactions = newTcContainer.getAllReactionsIds().size();
for(List<String> metabolites : tcdbMetContainer.getMetabolitesCombinations(tcNumber, antiportOrSymport, evidence, accession)) {
// if(accession.equalsIgnoreCase("P45539") && tcNumber.equals("2.A.3.8.17")) {
......@@ -136,8 +138,6 @@ public class GenerateTransportReactions {
// Set<String> metabolites = tcdbMetContainer.getMetabolites(tcNumber);
// System.out.println(reactionContainer.getTransportType());
if(evidence == null) {
if(reactionContainer.getTransportType().equals(TypeOfTransporter.PEPdependent))
newTcContainer = processPEPReactions(tcNumber+" "+accession, reactionContainer.getReaction(), "PEP-0" , reactionContainer.getProperties(), metabolites, newTcContainer);
......@@ -181,6 +181,13 @@ public class GenerateTransportReactions {
// System.out.println(tcNumber+" "+accession + " " + evidence + " " + reactionContainer.getTransportType() + " " + reactionContainer.getReaction() + "\t" + metabolites);
int currentCount = newTcContainer.getAllReactionsIds().size();
if((numberOfReactions == currentCount) && evidence != null && metabolites.size() == 1) {
newTcContainer = correctReaction(tcNumber+" "+accession, reactionContainer.getReaction(), "C-2" ,evidence, reactionContainer.getProperties(), metabolites, newTcContainer);
}
numberOfReactions = newTcContainer.getAllReactionsIds().size();;
}
}
}
......
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