Git Lab CI for docker build enabled! You can enable it using .gitlab-ci.yml in your project. Check file template at https://gitlab.bio.di.uminho.pt/snippets/5

Commit 6b6507a1 authored by Davide Lagoa's avatar Davide Lagoa
Browse files

minor bug fix

parent ca93f33c
......@@ -4,7 +4,7 @@
<modelVersion>4.0.0</modelVersion>
<groupId>pt.uminho.ceb.biosystems.transyt</groupId>
<artifactId>service</artifactId>
<version>0.0.11-SNAPSHOT</version>
<version>0.0.12-SNAPSHOT</version>
<properties>
......@@ -111,7 +111,7 @@
<dependency>
<groupId>pt.uminho.ceb.biosystems.transyt</groupId>
<artifactId>utilities</artifactId>
<version>0.0.11-SNAPSHOT</version>
<version>0.0.12-SNAPSHOT</version>
<exclusions>
<exclusion>
<groupId>ch.qos.logback</groupId>
......@@ -141,7 +141,7 @@
<dependency>
<groupId>pt.uminho.ceb.biosystems.transyt</groupId>
<artifactId>scraper</artifactId>
<version>0.0.11-SNAPSHOT</version>
<version>0.0.12-SNAPSHOT</version>
<exclusions>
<exclusion>
<groupId>uk.ac.ebi.uniprot</groupId>
......
......@@ -84,28 +84,28 @@ public class WriteByMetabolitesID {
// Map<String, String[]> forChildsSearch = metabolitesIdentification.getforChildsSearch();
int n = 1;
while (n != 99) {
n = 99;
// int n = 1;
//
// while (n != 99) {
//
// n = 99;
Map<String, Set<TcNumberContainer2>> newData = test(namesAndIDsContainer, data, service, reactionsData, properties); //uncomment
// test2(service, data, namesAndIDsContainer);
// new PopulateTransytNeo4jDatabase(data, newData, properties); //uncomment
System.out.println("Enter a random number to repeat (100 to repeat data retrieval) or 99 to finish: ");
new PopulateTransytNeo4jDatabase(data, newData, properties); //uncomment
try {
n = reader.nextInt();
} catch (Exception e) {
e.printStackTrace();
n = reader.nextInt();
}
}
// System.out.println("Enter a random number to repeat (100 to repeat data retrieval) or 99 to finish: ");
//
// try {
// n = reader.nextInt();
// } catch (Exception e) {
// e.printStackTrace();
//
// n = reader.nextInt();
// }
//
// }
dataTx.failure();
dataTx.close();
service.shutdown();
......@@ -240,38 +240,38 @@ public class WriteByMetabolitesID {
try {
Map<String, Set<TcNumberContainer2>> reactionsData2 = new HashMap<>();
String[] accessions = new String[] {"O06933"};
for(String acc : accessions)
reactionsData2.put(acc, reactionsData.get(acc));
// Map<String, Set<TcNumberContainer2>> reactionsData2 = new HashMap<>();
// String[] accessions = new String[] {"P31801"};
//
// for(String acc : accessions)
// reactionsData2.put(acc, reactionsData.get(acc));
/////TRANSYT
Map<String, Set<TcNumberContainer2>> newData = new TransportReactionsBuilder(reactionsData2, service, data, namesAndIDsContainer, properties).getResults(); //uncomment
for(TcNumberContainer2 container : newData.get("O06933")) {
System.out.println(container.getTcNumber());
Map<String, Set<TcNumberContainer2>> newData = new TransportReactionsBuilder(reactionsData, service, data, namesAndIDsContainer, properties).getResults(); //uncomment
for( Integer id : container.getAllReactionsIds()) {
System.out.println();
System.out.println(container.getReactionContainer(id).getReactionID());
System.out.println(container.getReactionContainer(id).getMetaReactionID());
System.out.println(container.getReactionContainer(id).getCompartmentalizedReactionID());
System.out.println(container.getReactionContainer(id).getReaction());
System.out.println(container.getReactionContainer(id).getReactionBase());
System.out.println(container.getReactionContainer(id).getReactionKEGG());
System.out.println(container.getReactionContainer(id).getReactionBiGG());
System.out.println(container.getReactionContainer(id).getReactionMetaCyc());
System.out.println(container.getReactionContainer(id).getReactionModelSEED());
System.out.println(container.getReactionContainer(id).getOriginalReaction());
}
System.out.println();
}
// for(TcNumberContainer2 container : newData.get("P31801")) {
//
// System.out.println(container.getTcNumber());
//
// for( Integer id : container.getAllReactionsIds()) {
// System.out.println();
//
// System.out.println(container.getReactionContainer(id).getReactionID());
// System.out.println(container.getReactionContainer(id).getMetaReactionID());
// System.out.println(container.getReactionContainer(id).getCompartmentalizedReactionID());
// System.out.println(container.getReactionContainer(id).getReaction());
// System.out.println(container.getReactionContainer(id).getReactionBase());
// System.out.println(container.getReactionContainer(id).getReactionKEGG());
// System.out.println(container.getReactionContainer(id).getReactionBiGG());
// System.out.println(container.getReactionContainer(id).getReactionMetaCyc());
// System.out.println(container.getReactionContainer(id).getReactionModelSEED());
// System.out.println(container.getReactionContainer(id).getOriginalReaction());
// }
//
//
// System.out.println();
// }
......
......@@ -74,6 +74,8 @@ public class IdentifyReactionsMetabolites {
this.allMetabolitesByName = new HashMap<>(this.namesAndIDsContainer.getMetabolitesIDs());
System.out.println(this.allMetabolitesByName.containsKey("undecaprenyl phosphate-4-amino-4-deoxy-L-arabinose"));
// System.out.println("MET>>>>> " + allMetabolitesByName.get("Electron"));
//
// System.out.println("metabolites >>>" + metabolites.size()); //2078
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment