fix missing optional files exceptions in metaborank, precursor and scope network

met4j-io/src/main/resources/log4j2.properties

-#
-# Copyright INRAE (2022)
-#
-# contact-metexplore@inrae.fr
-#
-# This software is a computer program whose purpose is to [describe
-# functionalities and technical features of your software].
-#
-# This software is governed by the CeCILL license under French law and
-# abiding by the rules of distribution of free software.  You can  use,
-# modify and/ or redistribute the software under the terms of the CeCILL
-# license as circulated by CEA, CNRS and INRIA at the following URL
-# "https://cecill.info/licences/Licence_CeCILL_V2.1-en.html".
-#
-# As a counterpart to the access to the source code and  rights to copy,
-# modify and redistribute granted by the license, users are provided only
-# with a limited warranty  and the software's author,  the holder of the
-# economic rights,  and the successive licensors  have only  limited
-# liability.
-#
-# In this respect, the user's attention is drawn to the risks associated
-# with loading,  using,  modifying and/or developing or reproducing the
-# software by the user in light of its specific status of free software,
-# that may mean  that it is complicated to manipulate,  and  that  also
-# therefore means  that it is reserved for developers  and  experienced
-# professionals having in-depth computer knowledge. Users are therefore
-# encouraged to load and test the software's suitability as regards their
-# requirements in conditions enabling the security of their systems and/or
-# data to be ensured and,  more generally, to use and operate it in the
-# same conditions as regards security.
-#
-# The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL license and that you accept its terms.
-#
-#
-
-# Extra logging related to initialization of Log4j
-# Set to debug or trace if log4j initialization is failing
-status = error
-# Name of the configuration
-name = ConsoleLogConfigDemo
-
-# Console appender configuration
-appender.console.type = Console
-appender.console.name = consoleLogger
-appender.console.layout.type = PatternLayout
-appender.console.layout.pattern = %d{yyyy-MM-dd HH:mm:ss} %-5p %c{1}:%L - %m%n
-
-# Root logger level
-rootLogger.level = error
-# Root logger referring to console appender
-rootLogger.appenderRef.stdout.ref = consoleLogger
\ No newline at end of file

met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/MetaboRank.java

@@ -39,18 +39,17 @@ import fr.inrae.toulouse.metexplore.met4j_chemUtils.chemicalSimilarity.Fingerpri
 import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioMetabolite;
 import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
 import fr.inrae.toulouse.metexplore.met4j_graph.computation.analyze.centrality.EigenVectorCentrality;
-import fr.inrae.toulouse.metexplore.met4j_graph.computation.connect.weighting.ReactionProbabilityWeight;
-import fr.inrae.toulouse.metexplore.met4j_graph.computation.connect.weighting.SimilarityWeightPolicy;
-import fr.inrae.toulouse.metexplore.met4j_graph.computation.connect.weighting.WeightUtils;
-import fr.inrae.toulouse.metexplore.met4j_graph.computation.connect.weighting.WeightsFromFile;
+import fr.inrae.toulouse.metexplore.met4j_graph.computation.connect.weighting.*;
 import fr.inrae.toulouse.metexplore.met4j_graph.computation.transform.GraphFilter;
 import fr.inrae.toulouse.metexplore.met4j_graph.computation.utils.RankUtils;
 import fr.inrae.toulouse.metexplore.met4j_graph.core.GraphFactory;
+import fr.inrae.toulouse.metexplore.met4j_graph.core.WeightingPolicy;
 import fr.inrae.toulouse.metexplore.met4j_graph.core.compound.CompoundGraph;
 import fr.inrae.toulouse.metexplore.met4j_graph.core.compound.ReactionEdge;
 import fr.inrae.toulouse.metexplore.met4j_graph.io.Bionetwork2BioGraph;
 import fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.JsbmlReader;
 import fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.Met4jSbmlReaderException;
+import fr.inrae.toulouse.metexplore.met4j_io.utils.StringUtils;
 import fr.inrae.toulouse.metexplore.met4j_toolbox.generic.AbstractMet4jApplication;
 import fr.inrae.toulouse.metexplore.met4j_toolbox.generic.annotations.EnumFormats;
 import fr.inrae.toulouse.metexplore.met4j_toolbox.generic.annotations.Format;
@@ -228,15 +227,18 @@ public class MetaboRank extends AbstractMet4jApplication {
     }
 
     public void setEdgeWeights(CompoundGraph graph, String localFilePath) {
+        Boolean defaultWeight = (localFilePath==null || localFilePath.isEmpty() || localFilePath.isBlank());
         //import weights from file
-        WeightsFromFile<BioMetabolite, ReactionEdge, CompoundGraph> wp = new WeightsFromFile<>(localFilePath, true);
+        WeightingPolicy wp = (defaultWeight) ? new DefaultWeightPolicy() : new WeightsFromFile<>(localFilePath, true);
         //set weights to edges
         wp.setWeight(graph);
-        //remove weights below 0.0
-        int nb = GraphFilter.weightFilter(graph, 0.0, "<=");
-        System.err.println(nb + " edges removed");
-        //remove edges without NaN weight
-        WeightUtils.removeEdgeWithNaNWeight(graph);
+        if (!defaultWeight) {
+            //remove weights below 0.0
+            int nb = GraphFilter.weightFilter(graph, 0.0, "<=");
+            System.err.println(nb + " edges removed");
+            //remove edges without NaN weight
+            WeightUtils.removeEdgeWithNaNWeight(graph);
+        }
         //remove disconnected nodes
         graph.removeIsolatedNodes();
         System.err.println("weights computed.");

met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/PrecursorNetwork.java

@@ -41,12 +41,12 @@ public class PrecursorNetwork extends AbstractMet4jApplication {
     @Option(name = "-o", usage = "output file: path to the .gml file where the results precursor network will be exported", required = true)
     public String output;
 
-    //oprtions
+    //options
     @ParameterType(name = InputFile)
     @Option(name = "-sc", aliases = {"--sides"}, usage = "an optional file containing list of ubiquitous compounds to be considered already available")
     public String sideCompoundFile = null;
     @ParameterType(name = InputFile)
-    @Option(name = "-ir", aliases = {"--ignore"}, usage = "an optional file containing list of reaction to ignore (forbid inclusion in scope")
+    @Option(name = "-ir", aliases = {"--ignore"}, usage = "an optional file containing list of reaction to ignore (forbid inclusion in scope)")
     public String reactionToIgnoreFile = null;
 
     public static void main(String[] args) throws IOException, Met4jSbmlReaderException {
@@ -64,10 +64,10 @@ public class PrecursorNetwork extends AbstractMet4jApplication {
         BioCollection<BioMetabolite> targets = mapper.map(targetsFilePath).stream()
                 .map(BioMetabolite.class::cast)
                 .collect(BioCollection::new, BioCollection::add, BioCollection::addAll);
-        BioCollection<BioMetabolite> bootstraps = mapper.map(sideCompoundFile).stream()
+        BioCollection<BioMetabolite> bootstraps = (sideCompoundFile==null) ? new BioCollection<>() : mapper.map(sideCompoundFile).stream()
                 .map(BioMetabolite.class::cast)
                 .collect(BioCollection::new, BioCollection::add, BioCollection::addAll);
-        BioCollection<BioReaction> forbidden = mapper.map(reactionToIgnoreFile).stream()
+        BioCollection<BioReaction> forbidden = (reactionToIgnoreFile==null) ? new BioCollection<>() : mapper.map(reactionToIgnoreFile).stream()
                 .map(BioReaction.class::cast)
                 .collect(BioCollection::new, BioCollection::add, BioCollection::addAll);
 

met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/ScopeNetwork.java

@@ -72,17 +72,12 @@ public class ScopeNetwork extends AbstractMet4jApplication {
         BioCollection<BioMetabolite> seeds = mapper.map(seedsFilePath).stream()
                 .map(BioMetabolite.class::cast)
                 .collect(BioCollection::new, BioCollection::add, BioCollection::addAll);
-        BioCollection<BioMetabolite> bootstraps = mapper.map(sideCompoundFile).stream()
+        BioCollection<BioMetabolite> bootstraps = (sideCompoundFile==null) ? new BioCollection<>() : mapper.map(sideCompoundFile).stream()
                 .map(BioMetabolite.class::cast)
                 .collect(BioCollection::new, BioCollection::add, BioCollection::addAll);
-
-        BioCollection<BioReaction> forbidden = new BioCollection<>();
-
-        if (reactionToIgnoreFile != null) {
-            forbidden = mapper.map(reactionToIgnoreFile).stream()
+        BioCollection<BioReaction> forbidden = (reactionToIgnoreFile==null) ? new BioCollection<>() : mapper.map(reactionToIgnoreFile).stream()
                     .map(BioReaction.class::cast)
                     .collect(BioCollection::new, BioCollection::add, BioCollection::addAll);
-        }
 
         ScopeCompounds scopeComp = new ScopeCompounds(graph, seeds, bootstraps, forbidden);
         if (includeSides) scopeComp.includeBootstrapsInScope();