command line interface added + README

map_generator/README.md

+# Map generator
+
+This code assemble resources into a single map.
+
+## Requirements
+
+* Java 8
+* Maven 3.6
+
+## Compilation
+
+```
+mvn -DskipTests=true clean install -pl biohackathon -am
+```
+
+The compiled runnable file will be located in biohackathon/target/biohackathon-1.0-jar-with-dependencies.jar.
+
+## Execution
+
+To get information about parameters just run:
+
+```
+java -jar biohackathon/target/biohackathon-1.0-jar-with-dependencies.jar
+```
+
+Sample usage:
+
+```
+java -jar biohackathon/target/biohackathon-1.0-jar-with-dependencies.jar --enrichr-file biohackathon/data/enrichr_output.txt --minerva-file  biohackathon/data/example_pathway_to_pull.txt --text-mining-file  biohackathon/data/brugada_output_file_omnipath.tsv --output-file output.xml
+```

map_generator/biohackathon/pom.xml

@@ -37,6 +37,13 @@
 			<artifactId>converter-sbml</artifactId>
 			<version>1.0</version>
 		</dependency>
+		<!-- https://mvnrepository.com/artifact/commons-cli/commons-cli -->
+		<dependency>
+			<groupId>commons-cli</groupId>
+			<artifactId>commons-cli</artifactId>
+			<version>1.4</version>
+		</dependency>
+
 	</dependencies>
 
 	<build>

map_generator/biohackathon/src/main/java/lcsb/mapviewer/Main.java

@@ -3,6 +3,7 @@ package lcsb.mapviewer;
 import java.io.ByteArrayInputStream;
 import java.util.*;
 
+import org.apache.commons.cli.*;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 
@@ -18,14 +19,31 @@ public class Main {
 
   public static void main(String[] args) {
 
-    logger.debug(Arrays.asList(args));
+    Options options = new Options();
+    Option enricherOption = new Option(null, "enrichr-file", true, "Enrichr output for wikipathway");
+    Option minervaOption = new Option(null, "minerva-file", true, "Minerva pathways");
+    Option outputOption = new Option(null, "output-file", true, "Output map in sbml format");
+    Option textMiningOption = new Option(null, "text-mining-file", true, "Text mining data");
+    enricherOption.setRequired(true);
+    minervaOption.setRequired(true);
+    outputOption.setRequired(true);
+    textMiningOption.setRequired(true);
 
-    String wikipathways = args[0];
-    String minervaPathways = args[1];
-    String network = args[2];
-    String output = args[3];
+    options.addOption(enricherOption)
+        .addOption(minervaOption)
+        .addOption(outputOption)
+        .addOption(textMiningOption);
 
+    HelpFormatter formatter = new HelpFormatter();
+
+    CommandLineParser parser = new DefaultParser();
     try {
+      // parse the command line arguments
+      CommandLine line = parser.parse(options, args);
+      String wikipathways = line.getOptionValue("enrichr-file");
+      String minervaPathways = line.getOptionValue("minerva-file");
+      String network = line.getOptionValue("text-mining-file");
+      String output = line.getOptionValue("output-file");
 
       PathwayMerger merger = new PathwayMerger();
       PathwayFetcher fetcher = new PathwayFetcher();
@@ -52,6 +70,9 @@ public class Main {
       new ApplySimpleLayoutModelCommand(modelWithTextMining, reactions).execute();
 
       new SbmlParser().model2File(modelWithTextMining, output);
+    } catch (ParseException exp) {
+      System.err.println("Parsing with input parameters: " + exp.getMessage());
+      formatter.printHelp("map_generator", options);
     } catch (Exception e) {
       e.printStackTrace();
       System.exit(-1);