From 3f1e56d185384f3b4008767f5d15258420472967 Mon Sep 17 00:00:00 2001
From: cfrainay <clement.frainay@inrae.fr>
Date: Tue, 10 May 2022 18:20:03 +0200
Subject: [PATCH 01/17] draft metanetwork creation
---
.../AbstractMetaNetworkBuilder.java | 209 ++++++++++++++++++
.../DefaultMetaEntityFactory.java | 42 ++++
.../multinetwork/MetaEntityFactory.java | 10 +
.../multinetwork/MetaNetworkBuilder.java | 45 ++++
.../multinetwork/MultiNetworkBuilder.java | 21 ++
.../MultiOrganNetworkBuilder.java | 57 +++++
.../multinetwork/NestedNetworkBuilder.java | 43 ++++
.../multinetwork/PanNetworkBuilder.java | 23 ++
8 files changed, 450 insertions(+)
create mode 100644 met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/AbstractMetaNetworkBuilder.java
create mode 100644 met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/DefaultMetaEntityFactory.java
create mode 100644 met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaEntityFactory.java
create mode 100644 met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaNetworkBuilder.java
create mode 100644 met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MultiNetworkBuilder.java
create mode 100644 met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MultiOrganNetworkBuilder.java
create mode 100644 met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/NestedNetworkBuilder.java
create mode 100644 met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/PanNetworkBuilder.java
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/AbstractMetaNetworkBuilder.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/AbstractMetaNetworkBuilder.java
new file mode 100644
index 000000000..64ddbcfe4
--- /dev/null
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/AbstractMetaNetworkBuilder.java
@@ -0,0 +1,209 @@
+package fr.inrae.toulouse.metexplore.met4j_core.biodata.multinetwork;
+
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.*;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.collection.BioCollection;
+import lombok.SneakyThrows;
+
+import java.lang.reflect.InvocationTargetException;
+import java.util.*;
+import java.util.function.Function;
+import java.util.function.Supplier;
+import java.util.stream.Collectors;
+
+public abstract class AbstractMetaNetworkBuilder implements MultiNetworkBuilder{
+
+ BioCollection<BioNetwork> networks;
+ Map<BioCompartment, Map<BioNetwork, BioCollection<BioMetabolite>>> metaCompComposition;
+ MetaEntityFactory entityFactory;
+
+ Boolean keepGPR = false;
+ Boolean flush;
+
+ public AbstractMetaNetworkBuilder(){
+ this.entityFactory= new DefaultMetaEntityFactory();
+ }
+
+ public AbstractMetaNetworkBuilder(MetaEntityFactory entityFactory){
+ this.entityFactory=entityFactory;
+ }
+
+ protected void addSharedCompartment(BioCompartment sc) {
+ metaCompComposition.put(sc,new HashMap<>());
+ }
+ protected void addSharedCompartment(BioCompartment sc, BioNetwork... bn) {
+ HashMap<BioNetwork, BioCollection<BioMetabolite>> map = Arrays.stream(bn).collect(Collectors.toMap(
+ x -> x,
+ x -> new BioCollection<BioMetabolite>(),
+ (prev, next) -> {prev.addAll(next);return prev;},
+ HashMap::new
+ ));
+ if(metaCompComposition.containsKey(sc)){
+ metaCompComposition.get(sc).putAll(map);
+ }else{
+ metaCompComposition.put(sc,map);
+ }
+ }
+
+ protected void fuseCompartmentIntoSharedCompartment(BioNetwork n, BioCompartment c, BioCompartment sc) {
+ //TODO
+ }
+
+ protected void bumpCompartmentIntoSharedCompartment(BioNetwork n, BioCompartment c, BioCompartment sc) {
+ Map<BioNetwork, BioCollection<BioMetabolite>> compartmentContent = metaCompComposition.get(sc);
+ if(compartmentContent==null) throw new IllegalArgumentException("Shared Compartment not found");
+ BioCollection<BioMetabolite> sharedContent = compartmentContent.get(n);
+ if(compartmentContent==null) throw new IllegalArgumentException("SubNetwork not in shared compartment");
+ BioCollection<BioMetabolite> toShare = n.getMetabolitesView().stream()
+ .filter(x -> n.getCompartmentsOf(x).contains(c))
+ .collect(BioCollection::new,BioCollection::add,BioCollection::addAll);
+ sharedContent.addAll(toShare);
+ }
+
+ protected void exchangeWithSharedCompartment(BioNetwork n, BioMetabolite m, BioCompartment sc) {
+ //todo
+ }
+
+ protected void exchangeWithSharedCompartment(BioNetwork n, BioCollection<BioMetabolite> m, BioCompartment sc) {
+ //todo
+ }
+
+ @Override
+ public void add(BioNetwork bn) {
+ networks.add(bn);
+ }
+
+ @Override
+ public abstract void merge();
+
+ @Override
+ public abstract BioNetwork build();
+
+
+ void populateMetaNetwork(BioNetwork meta){
+
+ for(BioNetwork sub : networks){
+
+ Map<BioMetabolite,BioMetabolite> metaboliteConversion = new HashMap<>();
+ Map<BioCompartment,BioCompartment> compartmentConversion = new HashMap<>();
+ Map<BioReaction,BioReaction> reactionConversion = new HashMap<>();
+ Map<BioProtein,BioProtein> proteinConversion = new HashMap<>();
+ Map<BioEnzyme,BioEnzyme> enzymeConversion = new HashMap<>();
+ Map<BioGene,BioGene> geneConversion = new HashMap<>();
+
+ for(BioMetabolite e : sub.getMetabolitesView()){
+ BioMetabolite e2 = entityFactory.copy(e,sub);
+ meta.add(e2);
+ metaboliteConversion.put(e,e2);
+ }
+ for(BioCompartment c : sub.getCompartmentsView()){
+ BioCompartment c2 = entityFactory.copy(c,sub);
+ meta.add(c2);
+ compartmentConversion.put(c,c2);
+ c.getComponentsView().stream().
+ filter((e) -> e.getClass().equals(BioMetabolite.class)).
+ forEach((m) -> {
+ BioMetabolite newMetabolite = metaboliteConversion.get(m);
+ meta.affectToCompartment(c, newMetabolite);
+ });
+ }
+
+ // Copy genes
+ if (keepGPR) {
+ //TODO case shared Genome
+ for (BioGene gene : sub.getGenesView()) {
+ BioGene newGene = entityFactory.copy(gene,sub);
+ meta.add(newGene);
+ geneConversion.put(gene,newGene);
+ }
+ for (BioProtein protein : sub.getProteinsView()) {
+ BioProtein newProtein = entityFactory.copy(protein,sub);
+ meta.add(newProtein);
+ proteinConversion.put(protein,newProtein);
+
+ if (protein.getGene() != null) {
+ BioGene newGene = geneConversion.get(protein.getGene());
+ meta.affectGeneProduct(newProtein, newGene);
+ }
+ }
+ for (BioEnzyme enzyme : sub.getEnzymesView()) {
+
+ BioEnzyme newEnzyme = entityFactory.copy(enzyme,sub);
+ meta.add(newEnzyme);
+ enzymeConversion.put(enzyme,newEnzyme);
+
+ BioCollection<BioEnzymeParticipant> participants = enzyme.getParticipantsView();
+
+ for (BioEnzymeParticipant participant : participants) {
+ Double quantity = participant.getQuantity();
+
+ if (participant.getPhysicalEntity().getClass().equals(BioMetabolite.class)) {
+ BioMetabolite metabolite = (BioMetabolite) participant.getPhysicalEntity();
+ BioMetabolite newMetabolite = metaboliteConversion.get(metabolite);
+ meta.affectSubUnit(newEnzyme, quantity, newMetabolite);
+ } else if (participant.getPhysicalEntity().getClass().equals(BioProtein.class)) {
+ BioProtein protein = (BioProtein) participant.getPhysicalEntity();
+ BioProtein newProtein = proteinConversion.get(protein);
+ meta.affectSubUnit(newEnzyme, quantity, newProtein);
+ }
+ }
+ }
+ }
+
+ for (BioReaction r : sub.getReactionsView()) {
+
+ BioReaction newReaction = entityFactory.copy(r,sub);;
+ newReaction.setSpontaneous(r.isSpontaneous());
+ newReaction.setReversible(r.isReversible());
+ newReaction.setEcNumber(r.getEcNumber());
+
+ meta.add(newReaction);
+
+ // Copy lefts
+ for (BioReactant reactant : r.getLeftReactantsView()) {
+ BioMetabolite newMetabolite = metaboliteConversion.get(reactant.getMetabolite());
+ BioCompartment newCpt = compartmentConversion.get(reactant.getLocation().getId());
+ Double sto = reactant.getQuantity();
+ meta.affectLeft(newReaction, sto, newCpt, newMetabolite);
+ }
+
+ // Copy rights
+ for (BioReactant reactant : r.getRightReactantsView()) {
+ BioMetabolite newMetabolite = metaboliteConversion.get(reactant.getMetabolite());
+ BioCompartment newCpt = compartmentConversion.get(reactant.getLocation().getId());
+ Double sto = reactant.getQuantity();
+ meta.affectRight(newReaction, sto, newCpt, newMetabolite);
+ }
+
+ // Copy enzymes
+ if (keepGPR) {
+ for (BioEnzyme enzyme : r.getEnzymesView()) {
+ BioEnzyme newEnzyme = enzymeConversion.get(enzyme);
+ meta.affectEnzyme(newReaction, newEnzyme);
+ }
+ }
+ }
+
+ for (BioPathway pathway : sub.getPathwaysView()) {
+ BioPathway newPathway = entityFactory.copy(pathway,sub);
+ meta.add(newPathway);
+ // Add reactions into pathway
+ BioCollection<BioReaction> reactions = sub.getReactionsFromPathways(pathway);
+
+ for (BioReaction reaction : reactions) {
+ BioReaction newReaction = reactionConversion.get(reaction);
+ meta.affectToPathway(newPathway, newReaction);
+ }
+ }
+ }
+ }
+
+
+ void initSharedComp(BioNetwork meta){
+ for(Map.Entry<BioCompartment, Map<BioNetwork, BioCollection<BioMetabolite>>> compDescriptor : metaCompComposition.entrySet()){
+ meta.addCompartment(compDescriptor.getKey());
+ for(Map.Entry<BioNetwork, BioCollection<BioMetabolite>> content : compDescriptor.getValue().entrySet()){
+ meta.affectToCompartment(compDescriptor.getKey(),content.getValue());
+ }
+ }
+ }
+}
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/DefaultMetaEntityFactory.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/DefaultMetaEntityFactory.java
new file mode 100644
index 000000000..ce5227046
--- /dev/null
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/DefaultMetaEntityFactory.java
@@ -0,0 +1,42 @@
+package fr.inrae.toulouse.metexplore.met4j_core.biodata.multinetwork;
+
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEntity;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
+import lombok.SneakyThrows;
+
+import java.lang.reflect.InvocationTargetException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.function.BiFunction;
+import java.util.function.Function;
+
+public class DefaultMetaEntityFactory implements MetaEntityFactory {
+
+ public BiFunction<BioEntity, BioNetwork, String> idSupplier = (e,bn) -> {
+ return e.getId()+"_"+bn.getId();
+ };
+
+ public BiFunction<BioEntity, BioNetwork, String> getIdSupplier() {
+ return idSupplier;
+ }
+
+ public void setIdSupplier(BiFunction<BioEntity, BioNetwork, String> idSupplier) {
+ this.idSupplier = idSupplier;
+ }
+
+ @SneakyThrows
+ @Override
+ public <E extends BioEntity> E copy(E entity, BioNetwork source) {
+ return newEntityInstance(entity, this.idSupplier.apply(entity,source));
+ }
+
+ public static <E extends BioEntity> E newEntityInstance(E entity, String newId) throws NoSuchMethodException, InvocationTargetException, InstantiationException, IllegalAccessException {
+ E newEntity = (E) entity.getClass().getDeclaredConstructor(String.class).newInstance(newId);
+ newEntity.setName(entity.getName());
+ newEntity.setSynonyms(new ArrayList<>(entity.getSynonyms()));
+ newEntity.setComment(entity.getComment());
+ newEntity.setRefs(new HashMap<>(entity.getRefs()));
+ newEntity.setAttributes(new HashMap<>(entity.getAttributes()));
+ return newEntity;
+ }
+}
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaEntityFactory.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaEntityFactory.java
new file mode 100644
index 000000000..554d7b182
--- /dev/null
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaEntityFactory.java
@@ -0,0 +1,10 @@
+package fr.inrae.toulouse.metexplore.met4j_core.biodata.multinetwork;
+
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEntity;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
+
+public interface MetaEntityFactory {
+
+ public <E extends BioEntity> E copy(E entity, BioNetwork source);
+
+}
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaNetworkBuilder.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaNetworkBuilder.java
new file mode 100644
index 000000000..7af6a2b5f
--- /dev/null
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaNetworkBuilder.java
@@ -0,0 +1,45 @@
+package fr.inrae.toulouse.metexplore.met4j_core.biodata.multinetwork;
+
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioCompartment;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioMetabolite;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.collection.BioCollection;
+
+import java.util.UUID;
+
+public class MetaNetworkBuilder extends AbstractMetaNetworkBuilder implements MultiNetworkBuilder{
+
+
+ private BioCompartment medium;
+
+ public MetaNetworkBuilder(BioNetwork superNetwork){
+ setMedium();
+ }
+
+ private void setMedium(){
+ this.medium = new BioCompartment(UUID.randomUUID().toString(),"medium");
+ this.addSharedCompartment(medium);
+ }
+
+ @Override
+ public void add(BioNetwork bn) {
+ super.add(bn);
+ this.addSharedCompartment(medium,this.networks.stream().toArray(BioNetwork[]::new));
+ }
+
+ @Override
+ public void merge() {
+ //todo
+ }
+
+ public void exchangeWithMedium(BioNetwork n, BioMetabolite m){
+ this.exchangeWithSharedCompartment(n, m, medium);
+ };
+
+ @Override
+ public BioNetwork build() {
+ //todo
+ return null;
+ }
+
+}
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MultiNetworkBuilder.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MultiNetworkBuilder.java
new file mode 100644
index 000000000..c17e2cadc
--- /dev/null
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MultiNetworkBuilder.java
@@ -0,0 +1,21 @@
+package fr.inrae.toulouse.metexplore.met4j_core.biodata.multinetwork;
+
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
+
+public interface MultiNetworkBuilder {
+
+ /**
+ * add network into meta-network
+ * @param bn
+ */
+ public void add(BioNetwork bn);
+
+ public void merge();
+
+ /**
+ * create a new network which encompass all added networks
+ * @return
+ */
+ public BioNetwork build();
+
+}
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MultiOrganNetworkBuilder.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MultiOrganNetworkBuilder.java
new file mode 100644
index 000000000..ae4c1b699
--- /dev/null
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MultiOrganNetworkBuilder.java
@@ -0,0 +1,57 @@
+package fr.inrae.toulouse.metexplore.met4j_core.biodata.multinetwork;
+
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioCompartment;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioMetabolite;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.collection.BioCollection;
+
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.stream.Collectors;
+
+public class MultiOrganNetworkBuilder extends AbstractMetaNetworkBuilder implements MultiNetworkBuilder{
+
+ @Override
+ public void merge() {
+ //TODO
+ }
+
+
+ @Override
+ public void addSharedCompartment(BioCompartment sc, BioNetwork... bn) {
+ super.addSharedCompartment(sc,bn);
+ }
+
+ @Override
+ public void fuseCompartmentIntoSharedCompartment(BioNetwork n, BioCompartment c, BioCompartment sc) {
+ super.fuseCompartmentIntoSharedCompartment(n,c,sc);
+ }
+
+ @Override
+ public void bumpCompartmentIntoSharedCompartment(BioNetwork n, BioCompartment c, BioCompartment sc) {
+ super.bumpCompartmentIntoSharedCompartment(n,c,sc);
+ }
+
+ @Override
+ public void exchangeWithSharedCompartment(BioNetwork n, BioMetabolite m, BioCompartment sc) {
+ super.exchangeWithSharedCompartment(n,m,sc);
+ }
+
+ @Override
+ public void exchangeWithSharedCompartment(BioNetwork n, BioCollection<BioMetabolite> m, BioCompartment sc) {
+ super.exchangeWithSharedCompartment(n,m,sc);
+ }
+
+ @Override
+ public BioNetwork build() {
+ //todo
+ //create empty meta network
+ BioNetwork meta = new BioNetwork();
+ //add each subnetwork content in dedicated compartment
+ this.populateMetaNetwork(meta);
+ //create shared compartment and the exchanged content
+ this.initSharedComp(meta);
+ return null;
+ }
+}
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/NestedNetworkBuilder.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/NestedNetworkBuilder.java
new file mode 100644
index 000000000..aeca0c100
--- /dev/null
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/NestedNetworkBuilder.java
@@ -0,0 +1,43 @@
+package fr.inrae.toulouse.metexplore.met4j_core.biodata.multinetwork;
+
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioCompartment;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioMetabolite;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
+
+public class NestedNetworkBuilder extends AbstractMetaNetworkBuilder implements MultiNetworkBuilder{
+
+ private BioNetwork superNet;
+ private BioCompartment superNetComp;
+
+ public NestedNetworkBuilder(BioNetwork superNetwork){
+ setSuperNetwork(superNetwork);
+ }
+
+ private void setSuperNetwork(BioNetwork bn){
+ superNet=bn;
+ this.superNetComp = new BioCompartment(bn.getId());
+ this.addSharedCompartment(superNetComp,superNet);
+ }
+
+ @Override
+ public void add(BioNetwork bn) {
+ super.add(bn);
+ this.addSharedCompartment(superNetComp,this.networks.stream().toArray(BioNetwork[]::new));
+ }
+
+ @Override
+ public void merge() {
+ //todo
+ }
+
+ public void exchangeWithSuperNetwork(BioNetwork n, BioMetabolite m){
+ this.exchangeWithSharedCompartment(n, m, superNetComp);
+ };
+
+ @Override
+ public BioNetwork build() {
+ //todo
+ return null;
+ }
+
+}
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/PanNetworkBuilder.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/PanNetworkBuilder.java
new file mode 100644
index 000000000..346f71cbf
--- /dev/null
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/PanNetworkBuilder.java
@@ -0,0 +1,23 @@
+package fr.inrae.toulouse.metexplore.met4j_core.biodata.multinetwork;
+
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioMetabolite;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.collection.BioCollection;
+
+public class PanNetworkBuilder implements MultiNetworkBuilder {
+ @Override
+ public void add(BioNetwork bn) {
+ //todo
+ }
+
+ @Override
+ public void merge() {
+ //todo
+ }
+
+ @Override
+ public BioNetwork build() {
+ //todo
+ return null;
+ }
+}
--
GitLab
From 297b7681c25ed6758d203be91d54288ada8c42f4 Mon Sep 17 00:00:00 2001
From: cfrainay <clement.frainay@inrae.fr>
Date: Thu, 16 May 2024 16:29:19 +0200
Subject: [PATCH 02/17] finalize metanetwork creation
---
.../AbstractMetaNetworkBuilder.java | 209 ------------
.../multinetwork/CommunityNetworkBuilder.java | 49 +++
.../DefaultMetaEntityFactory.java | 42 ---
.../multinetwork/MetaBioMetabolite.java | 16 +
.../multinetwork/MetaEntityFactory.java | 8 +-
.../multinetwork/MetaNetworkBuilder.java | 313 ++++++++++++++++--
.../multinetwork/MultiNetworkBuilder.java | 3 +-
.../MultiOrganNetworkBuilder.java | 57 ----
.../multinetwork/NestedNetworkBuilder.java | 43 ---
.../multinetwork/PanNetworkBuilder.java | 23 --
.../PrefixedMetaEntityFactory.java | 86 +++++
.../multinetwork/TestMetaNetworkBuilder.java | 185 +++++++++++
12 files changed, 636 insertions(+), 398 deletions(-)
delete mode 100644 met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/AbstractMetaNetworkBuilder.java
create mode 100644 met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/CommunityNetworkBuilder.java
delete mode 100644 met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/DefaultMetaEntityFactory.java
create mode 100644 met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaBioMetabolite.java
delete mode 100644 met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MultiOrganNetworkBuilder.java
delete mode 100644 met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/NestedNetworkBuilder.java
delete mode 100644 met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/PanNetworkBuilder.java
create mode 100644 met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/PrefixedMetaEntityFactory.java
create mode 100644 met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/TestMetaNetworkBuilder.java
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/AbstractMetaNetworkBuilder.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/AbstractMetaNetworkBuilder.java
deleted file mode 100644
index 64ddbcfe4..000000000
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/AbstractMetaNetworkBuilder.java
+++ /dev/null
@@ -1,209 +0,0 @@
-package fr.inrae.toulouse.metexplore.met4j_core.biodata.multinetwork;
-
-import fr.inrae.toulouse.metexplore.met4j_core.biodata.*;
-import fr.inrae.toulouse.metexplore.met4j_core.biodata.collection.BioCollection;
-import lombok.SneakyThrows;
-
-import java.lang.reflect.InvocationTargetException;
-import java.util.*;
-import java.util.function.Function;
-import java.util.function.Supplier;
-import java.util.stream.Collectors;
-
-public abstract class AbstractMetaNetworkBuilder implements MultiNetworkBuilder{
-
- BioCollection<BioNetwork> networks;
- Map<BioCompartment, Map<BioNetwork, BioCollection<BioMetabolite>>> metaCompComposition;
- MetaEntityFactory entityFactory;
-
- Boolean keepGPR = false;
- Boolean flush;
-
- public AbstractMetaNetworkBuilder(){
- this.entityFactory= new DefaultMetaEntityFactory();
- }
-
- public AbstractMetaNetworkBuilder(MetaEntityFactory entityFactory){
- this.entityFactory=entityFactory;
- }
-
- protected void addSharedCompartment(BioCompartment sc) {
- metaCompComposition.put(sc,new HashMap<>());
- }
- protected void addSharedCompartment(BioCompartment sc, BioNetwork... bn) {
- HashMap<BioNetwork, BioCollection<BioMetabolite>> map = Arrays.stream(bn).collect(Collectors.toMap(
- x -> x,
- x -> new BioCollection<BioMetabolite>(),
- (prev, next) -> {prev.addAll(next);return prev;},
- HashMap::new
- ));
- if(metaCompComposition.containsKey(sc)){
- metaCompComposition.get(sc).putAll(map);
- }else{
- metaCompComposition.put(sc,map);
- }
- }
-
- protected void fuseCompartmentIntoSharedCompartment(BioNetwork n, BioCompartment c, BioCompartment sc) {
- //TODO
- }
-
- protected void bumpCompartmentIntoSharedCompartment(BioNetwork n, BioCompartment c, BioCompartment sc) {
- Map<BioNetwork, BioCollection<BioMetabolite>> compartmentContent = metaCompComposition.get(sc);
- if(compartmentContent==null) throw new IllegalArgumentException("Shared Compartment not found");
- BioCollection<BioMetabolite> sharedContent = compartmentContent.get(n);
- if(compartmentContent==null) throw new IllegalArgumentException("SubNetwork not in shared compartment");
- BioCollection<BioMetabolite> toShare = n.getMetabolitesView().stream()
- .filter(x -> n.getCompartmentsOf(x).contains(c))
- .collect(BioCollection::new,BioCollection::add,BioCollection::addAll);
- sharedContent.addAll(toShare);
- }
-
- protected void exchangeWithSharedCompartment(BioNetwork n, BioMetabolite m, BioCompartment sc) {
- //todo
- }
-
- protected void exchangeWithSharedCompartment(BioNetwork n, BioCollection<BioMetabolite> m, BioCompartment sc) {
- //todo
- }
-
- @Override
- public void add(BioNetwork bn) {
- networks.add(bn);
- }
-
- @Override
- public abstract void merge();
-
- @Override
- public abstract BioNetwork build();
-
-
- void populateMetaNetwork(BioNetwork meta){
-
- for(BioNetwork sub : networks){
-
- Map<BioMetabolite,BioMetabolite> metaboliteConversion = new HashMap<>();
- Map<BioCompartment,BioCompartment> compartmentConversion = new HashMap<>();
- Map<BioReaction,BioReaction> reactionConversion = new HashMap<>();
- Map<BioProtein,BioProtein> proteinConversion = new HashMap<>();
- Map<BioEnzyme,BioEnzyme> enzymeConversion = new HashMap<>();
- Map<BioGene,BioGene> geneConversion = new HashMap<>();
-
- for(BioMetabolite e : sub.getMetabolitesView()){
- BioMetabolite e2 = entityFactory.copy(e,sub);
- meta.add(e2);
- metaboliteConversion.put(e,e2);
- }
- for(BioCompartment c : sub.getCompartmentsView()){
- BioCompartment c2 = entityFactory.copy(c,sub);
- meta.add(c2);
- compartmentConversion.put(c,c2);
- c.getComponentsView().stream().
- filter((e) -> e.getClass().equals(BioMetabolite.class)).
- forEach((m) -> {
- BioMetabolite newMetabolite = metaboliteConversion.get(m);
- meta.affectToCompartment(c, newMetabolite);
- });
- }
-
- // Copy genes
- if (keepGPR) {
- //TODO case shared Genome
- for (BioGene gene : sub.getGenesView()) {
- BioGene newGene = entityFactory.copy(gene,sub);
- meta.add(newGene);
- geneConversion.put(gene,newGene);
- }
- for (BioProtein protein : sub.getProteinsView()) {
- BioProtein newProtein = entityFactory.copy(protein,sub);
- meta.add(newProtein);
- proteinConversion.put(protein,newProtein);
-
- if (protein.getGene() != null) {
- BioGene newGene = geneConversion.get(protein.getGene());
- meta.affectGeneProduct(newProtein, newGene);
- }
- }
- for (BioEnzyme enzyme : sub.getEnzymesView()) {
-
- BioEnzyme newEnzyme = entityFactory.copy(enzyme,sub);
- meta.add(newEnzyme);
- enzymeConversion.put(enzyme,newEnzyme);
-
- BioCollection<BioEnzymeParticipant> participants = enzyme.getParticipantsView();
-
- for (BioEnzymeParticipant participant : participants) {
- Double quantity = participant.getQuantity();
-
- if (participant.getPhysicalEntity().getClass().equals(BioMetabolite.class)) {
- BioMetabolite metabolite = (BioMetabolite) participant.getPhysicalEntity();
- BioMetabolite newMetabolite = metaboliteConversion.get(metabolite);
- meta.affectSubUnit(newEnzyme, quantity, newMetabolite);
- } else if (participant.getPhysicalEntity().getClass().equals(BioProtein.class)) {
- BioProtein protein = (BioProtein) participant.getPhysicalEntity();
- BioProtein newProtein = proteinConversion.get(protein);
- meta.affectSubUnit(newEnzyme, quantity, newProtein);
- }
- }
- }
- }
-
- for (BioReaction r : sub.getReactionsView()) {
-
- BioReaction newReaction = entityFactory.copy(r,sub);;
- newReaction.setSpontaneous(r.isSpontaneous());
- newReaction.setReversible(r.isReversible());
- newReaction.setEcNumber(r.getEcNumber());
-
- meta.add(newReaction);
-
- // Copy lefts
- for (BioReactant reactant : r.getLeftReactantsView()) {
- BioMetabolite newMetabolite = metaboliteConversion.get(reactant.getMetabolite());
- BioCompartment newCpt = compartmentConversion.get(reactant.getLocation().getId());
- Double sto = reactant.getQuantity();
- meta.affectLeft(newReaction, sto, newCpt, newMetabolite);
- }
-
- // Copy rights
- for (BioReactant reactant : r.getRightReactantsView()) {
- BioMetabolite newMetabolite = metaboliteConversion.get(reactant.getMetabolite());
- BioCompartment newCpt = compartmentConversion.get(reactant.getLocation().getId());
- Double sto = reactant.getQuantity();
- meta.affectRight(newReaction, sto, newCpt, newMetabolite);
- }
-
- // Copy enzymes
- if (keepGPR) {
- for (BioEnzyme enzyme : r.getEnzymesView()) {
- BioEnzyme newEnzyme = enzymeConversion.get(enzyme);
- meta.affectEnzyme(newReaction, newEnzyme);
- }
- }
- }
-
- for (BioPathway pathway : sub.getPathwaysView()) {
- BioPathway newPathway = entityFactory.copy(pathway,sub);
- meta.add(newPathway);
- // Add reactions into pathway
- BioCollection<BioReaction> reactions = sub.getReactionsFromPathways(pathway);
-
- for (BioReaction reaction : reactions) {
- BioReaction newReaction = reactionConversion.get(reaction);
- meta.affectToPathway(newPathway, newReaction);
- }
- }
- }
- }
-
-
- void initSharedComp(BioNetwork meta){
- for(Map.Entry<BioCompartment, Map<BioNetwork, BioCollection<BioMetabolite>>> compDescriptor : metaCompComposition.entrySet()){
- meta.addCompartment(compDescriptor.getKey());
- for(Map.Entry<BioNetwork, BioCollection<BioMetabolite>> content : compDescriptor.getValue().entrySet()){
- meta.affectToCompartment(compDescriptor.getKey(),content.getValue());
- }
- }
- }
-}
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/CommunityNetworkBuilder.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/CommunityNetworkBuilder.java
new file mode 100644
index 000000000..c14270c6d
--- /dev/null
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/CommunityNetworkBuilder.java
@@ -0,0 +1,49 @@
+package fr.inrae.toulouse.metexplore.met4j_core.biodata.multinetwork;
+
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioCompartment;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioMetabolite;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
+
+import java.util.Map;
+import java.util.Set;
+import java.util.UUID;
+import java.util.stream.Collectors;
+
+public class CommunityNetworkBuilder extends MetaNetworkBuilder implements MultiNetworkBuilder{
+
+ private BioCompartment medium;
+
+ public CommunityNetworkBuilder(){
+ setMedium();
+ }
+
+ public CommunityNetworkBuilder(BioCompartment medium){
+ this.medium=medium;
+ this.addNewSharedCompartment(medium);
+ }
+
+ public CommunityNetworkBuilder(Set<BioNetwork> networks){
+ setMedium();
+ Map<BioNetwork,String> prefixes = networks.stream()
+ .collect(Collectors.toMap(n->n,n->n.getId()+"_"));
+ this.setEntityFactory(new PrefixedMetaEntityFactory(prefixes,"pool"));
+ for(BioNetwork bn : networks){
+ this.add(bn);
+ }
+ }
+
+ private void setMedium(){
+ this.medium = new BioCompartment(UUID.randomUUID().toString(),"medium");
+ this.addNewSharedCompartment(medium);
+ }
+
+ public void exchangeWithMedium(BioNetwork sourceNetwork, BioCompartment sourceCompartment, BioMetabolite metabolite){
+ this.exchangeWithSharedCompartment(sourceNetwork, sourceCompartment, metabolite, medium);
+ };
+
+ public void add(BioNetwork bn, BioCompartment externalComp) {
+ super.add(bn);
+ this.fuseCompartmentIntoSharedCompartment(bn,externalComp,medium);
+ }
+
+}
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/DefaultMetaEntityFactory.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/DefaultMetaEntityFactory.java
deleted file mode 100644
index ce5227046..000000000
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/DefaultMetaEntityFactory.java
+++ /dev/null
@@ -1,42 +0,0 @@
-package fr.inrae.toulouse.metexplore.met4j_core.biodata.multinetwork;
-
-import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEntity;
-import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
-import lombok.SneakyThrows;
-
-import java.lang.reflect.InvocationTargetException;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.function.BiFunction;
-import java.util.function.Function;
-
-public class DefaultMetaEntityFactory implements MetaEntityFactory {
-
- public BiFunction<BioEntity, BioNetwork, String> idSupplier = (e,bn) -> {
- return e.getId()+"_"+bn.getId();
- };
-
- public BiFunction<BioEntity, BioNetwork, String> getIdSupplier() {
- return idSupplier;
- }
-
- public void setIdSupplier(BiFunction<BioEntity, BioNetwork, String> idSupplier) {
- this.idSupplier = idSupplier;
- }
-
- @SneakyThrows
- @Override
- public <E extends BioEntity> E copy(E entity, BioNetwork source) {
- return newEntityInstance(entity, this.idSupplier.apply(entity,source));
- }
-
- public static <E extends BioEntity> E newEntityInstance(E entity, String newId) throws NoSuchMethodException, InvocationTargetException, InstantiationException, IllegalAccessException {
- E newEntity = (E) entity.getClass().getDeclaredConstructor(String.class).newInstance(newId);
- newEntity.setName(entity.getName());
- newEntity.setSynonyms(new ArrayList<>(entity.getSynonyms()));
- newEntity.setComment(entity.getComment());
- newEntity.setRefs(new HashMap<>(entity.getRefs()));
- newEntity.setAttributes(new HashMap<>(entity.getAttributes()));
- return newEntity;
- }
-}
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaBioMetabolite.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaBioMetabolite.java
new file mode 100644
index 000000000..4d3bfce22
--- /dev/null
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaBioMetabolite.java
@@ -0,0 +1,16 @@
+package fr.inrae.toulouse.metexplore.met4j_core.biodata.multinetwork;
+
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioCompartment;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioMetabolite;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
+
+public record MetaBioMetabolite(BioMetabolite metabolite, BioCompartment sourceCompartment, BioNetwork sourceNetwork) {
+ public MetaBioMetabolite(BioMetabolite metabolite, BioCompartment sourceCompartment, BioNetwork sourceNetwork){
+ if(!sourceNetwork.containsMetabolite(metabolite.getId())) throw new IllegalArgumentException("Source network does not contains metabolites");
+ if(!sourceNetwork.containsCompartment(sourceCompartment.getId())) throw new IllegalArgumentException("Source network does not contains source compartment");
+ if(sourceCompartment.getComponentsView().get(metabolite.getId())==null) throw new IllegalArgumentException("Source compartment does not contains metabolites");
+ this.metabolite = metabolite;
+ this.sourceCompartment = sourceCompartment;
+ this.sourceNetwork = sourceNetwork;
+ }
+}
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaEntityFactory.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaEntityFactory.java
index 554d7b182..c7254a7cf 100644
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaEntityFactory.java
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaEntityFactory.java
@@ -1,10 +1,16 @@
package fr.inrae.toulouse.metexplore.met4j_core.biodata.multinetwork;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioCompartment;
import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEntity;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioMetabolite;
import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
+import java.util.Collection;
+
public interface MetaEntityFactory {
- public <E extends BioEntity> E copy(E entity, BioNetwork source);
+ <E extends BioEntity> E createMetaEntity(E originalEntity, BioNetwork source);
+ BioMetabolite createSharedCompound(BioMetabolite originalEntity, BioCompartment sharedComp);
+ BioMetabolite createPoolCompound (Collection<BioMetabolite> entities, BioCompartment sharedComp);
}
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaNetworkBuilder.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaNetworkBuilder.java
index 7af6a2b5f..b5b5b2958 100644
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaNetworkBuilder.java
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaNetworkBuilder.java
@@ -1,45 +1,316 @@
package fr.inrae.toulouse.metexplore.met4j_core.biodata.multinetwork;
-import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioCompartment;
-import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioMetabolite;
-import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.*;
import fr.inrae.toulouse.metexplore.met4j_core.biodata.collection.BioCollection;
+import lombok.Getter;
+import lombok.Setter;
-import java.util.UUID;
+import java.util.*;
+import java.util.function.BiFunction;
+import java.util.function.Function;
+import java.util.stream.Collectors;
-public class MetaNetworkBuilder extends AbstractMetaNetworkBuilder implements MultiNetworkBuilder{
+/**
+ * A class that creates a meta-networks from multiple sub-networks. A meta-network is a single model which contains several
+ * sub-networks that remains individualized within the meta-network (as opposed to models fusion), but which can share
+ * some of their components with other sub-networks through shared compartments.
+ */
+public class MetaNetworkBuilder implements MultiNetworkBuilder{
+ private Map<BioMetabolite,BioMetabolite> metaboliteConversion;
+ private Map<BioCompartment,BioCompartment> compartmentConversion;
+ private Map<BioReaction,BioReaction> reactionConversion;
+ private Map<BioProtein,BioProtein> proteinConversion;
+ private Map<BioEnzyme,BioEnzyme> enzymeConversion;
+ private Map<BioGene,BioGene> geneConversion;
- private BioCompartment medium;
+ protected BioCollection<BioNetwork> networks = new BioCollection<>();
+ private Map<BioCompartment, Set<MetaBioMetabolite>> metaCompComposition = new HashMap<>();
- public MetaNetworkBuilder(BioNetwork superNetwork){
- setMedium();
+ @Setter
+ protected Function<BioMetabolite,String> getSharedIdFunction = BioEntity::getName;
+ @Setter
+ private String poolReactionPrefix = "poolReaction_";
+ @Setter
+ private String sharedTransportPrefix = "transport_";
+ @Setter
+ protected BiFunction<BioMetabolite, BioMetabolite, BioReaction> createLinkWithSharedPool = (m, pool) -> {
+ BioReaction r=new BioReaction(poolReactionPrefix+ m.getId());
+ r.setReversible(true);
+ return r;
+ };
+ @Setter
+ protected BiFunction<BioMetabolite, BioCompartment, BioReaction> createTransportWithSharedComp = (m, comp) -> {
+ BioReaction r=new BioReaction(sharedTransportPrefix+ m.getId()+"_to_"+comp.getId());
+ r.setReversible(true);
+ return r;
+ };
+ @Setter
+ @Getter
+ protected MetaEntityFactory entityFactory;
+ protected HashMap<BioCompartment,BioCompartment> fuseMap= new HashMap<>();
+ protected Boolean keepGPR = false;
+
+ /**
+ * enable a compartment to be shared between multiple organisms
+ * @param sc
+ */
+ public void addNewSharedCompartment(BioCompartment sc) {
+ metaCompComposition.put(sc,new HashSet<>());
+ }
+
+ /**
+ * Fuse a sub-network's compartment into a meta-network's shared compartment. The former will be replaced by the latter during build.
+ * All compartment's component will be added to the shared compartment
+ * @param n
+ * @param c
+ * @param sc
+ */
+ public void fuseCompartmentIntoSharedCompartment(BioNetwork n, BioCompartment c, BioCompartment sc) {
+ if(!metaCompComposition.containsKey(sc)) throw new IllegalArgumentException("Shared meta-compartment "+sc.getId()+" not found in network");
+ fuseMap.put(c,sc);
}
- private void setMedium(){
- this.medium = new BioCompartment(UUID.randomUUID().toString(),"medium");
- this.addSharedCompartment(medium);
+ /**
+ * Bump a sub-network's compartment into a meta-network's shared compartment. For each compartment's component,
+ * a copy is created within the shared compartment
+ * @param n
+ * @param c
+ * @param sc
+ */
+ public void bumpCompartmentIntoSharedCompartment(BioNetwork n, BioCompartment c, BioCompartment sc) {
+ BioCollection<BioMetabolite> toShare = n.getMetabolitesView().stream()
+ .filter(x -> n.getCompartmentsOf(x).contains(c))
+ .collect(BioCollection::new,BioCollection::add,BioCollection::addAll);
+ this.exchangeWithSharedCompartment(n,c,toShare,sc);
+ }
+
+ /**
+ *
+ * @param sourceNetwork the original subnetwork of the compound
+ * @param sourceCompartment the original compartment of the compound in the subnetwork
+ * @param metabolite the compound
+ * @param sc the target shared meta-compartment that will receive the compound
+ */
+ public void exchangeWithSharedCompartment(BioNetwork sourceNetwork, BioCompartment sourceCompartment, BioMetabolite metabolite, BioCompartment sc) {
+ if(!metaCompComposition.containsKey(sc)) throw new IllegalArgumentException("Shared meta-compartment "+sc.getId()+" not found in network");
+ metaCompComposition.get(sc).add(new MetaBioMetabolite(metabolite,sourceCompartment,sourceNetwork));
+ }
+
+ /**
+ *
+ * @param sourceNetwork the original subnetwork of the compounds
+ * @param sourceCompartment the original compartment of the compounds in the subnetwork
+ * @param metabolites the compounds
+ * @param sc the target shared meta-compartment that will receive the compounds
+ */
+ public void exchangeWithSharedCompartment(BioNetwork sourceNetwork, BioCompartment sourceCompartment, BioCollection<BioMetabolite> metabolites, BioCompartment sc) {
+ if(!metaCompComposition.containsKey(sc)) throw new IllegalArgumentException("Shared meta-compartment "+sc.getId()+" not found in network");
+ Set<MetaBioMetabolite> scCompo = metaCompComposition.get(sc);
+ for(BioMetabolite m : metabolites ){
+ scCompo.add(new MetaBioMetabolite(m,sourceCompartment,sourceNetwork));
+ }
}
@Override
public void add(BioNetwork bn) {
- super.add(bn);
- this.addSharedCompartment(medium,this.networks.stream().toArray(BioNetwork[]::new));
+ networks.add(bn);
}
- @Override
- public void merge() {
- //todo
+ protected BioNetwork initMetaNetwork(){
+ this.metaboliteConversion = new HashMap<>();
+ this.compartmentConversion = new HashMap<>();
+ this.reactionConversion = new HashMap<>();
+ this.proteinConversion = new HashMap<>();
+ this.enzymeConversion = new HashMap<>();
+ this.geneConversion = new HashMap<>();
+ return new BioNetwork();
}
- public void exchangeWithMedium(BioNetwork n, BioMetabolite m){
- this.exchangeWithSharedCompartment(n, m, medium);
- };
+ protected void populateMetaNetwork(BioNetwork meta){
+
+ for(BioNetwork sub : networks){
+
+ for(BioMetabolite e : sub.getMetabolitesView()){
+ BioMetabolite e2 = entityFactory.createMetaEntity(e,sub);
+ meta.add(e2);
+ metaboliteConversion.put(e,e2);
+ }
+ for(BioCompartment c : sub.getCompartmentsView()){
+ BioCompartment c2 = fuseMap.get(c);
+ if(c2==null){
+ c2 = entityFactory.createMetaEntity(c,sub);
+ meta.add(c2);
+ }
+ compartmentConversion.put(c,c2);
+ BioCollection<BioMetabolite> content = c.getComponentsView().stream()
+ .filter((e) -> e.getClass().equals(BioMetabolite.class))
+ .map(metaboliteConversion::get)
+ .collect(BioCollection::new,BioCollection::add,BioCollection::addAll);
+
+ meta.affectToCompartment(c2, content);
+ }
+
+ // Copy genes
+ if (keepGPR) {
+ //TODO case shared Genome
+ for (BioGene gene : sub.getGenesView()) {
+ BioGene newGene = entityFactory.createMetaEntity(gene,sub);
+ meta.add(newGene);
+ geneConversion.put(gene,newGene);
+ }
+ for (BioProtein protein : sub.getProteinsView()) {
+ BioProtein newProtein = entityFactory.createMetaEntity(protein,sub);
+ meta.add(newProtein);
+ proteinConversion.put(protein,newProtein);
+
+ if (protein.getGene() != null) {
+ BioGene newGene = geneConversion.get(protein.getGene());
+ meta.affectGeneProduct(newProtein, newGene);
+ }
+ }
+ for (BioEnzyme enzyme : sub.getEnzymesView()) {
+
+ BioEnzyme newEnzyme = entityFactory.createMetaEntity(enzyme,sub);
+ meta.add(newEnzyme);
+ enzymeConversion.put(enzyme,newEnzyme);
+
+ BioCollection<BioEnzymeParticipant> participants = enzyme.getParticipantsView();
+
+ for (BioEnzymeParticipant participant : participants) {
+ Double quantity = participant.getQuantity();
+
+ if (participant.getPhysicalEntity().getClass().equals(BioMetabolite.class)) {
+ BioMetabolite metabolite = (BioMetabolite) participant.getPhysicalEntity();
+ BioMetabolite newMetabolite = metaboliteConversion.get(metabolite);
+ meta.affectSubUnit(newEnzyme, quantity, newMetabolite);
+ } else if (participant.getPhysicalEntity().getClass().equals(BioProtein.class)) {
+ BioProtein protein = (BioProtein) participant.getPhysicalEntity();
+ BioProtein newProtein = proteinConversion.get(protein);
+ meta.affectSubUnit(newEnzyme, quantity, newProtein);
+ }
+ }
+ }
+ }
+
+ for (BioReaction r : sub.getReactionsView()) {
+
+ BioReaction newReaction = entityFactory.createMetaEntity(r,sub);
+ newReaction.setSpontaneous(r.isSpontaneous());
+ newReaction.setReversible(r.isReversible());
+ newReaction.setEcNumber(r.getEcNumber());
+
+ meta.add(newReaction);
+ reactionConversion.put(r,newReaction);
+
+ // Copy lefts
+ for (BioReactant reactant : r.getLeftReactantsView()) {
+ BioMetabolite newMetabolite = metaboliteConversion.get(reactant.getMetabolite());
+ BioCompartment newCpt = compartmentConversion.get(reactant.getLocation());
+ Double sto = reactant.getQuantity();
+ meta.affectLeft(newReaction, sto, newCpt, newMetabolite);
+ }
+
+ // Copy rights
+ for (BioReactant reactant : r.getRightReactantsView()) {
+ BioMetabolite newMetabolite = metaboliteConversion.get(reactant.getMetabolite());
+ BioCompartment newCpt = compartmentConversion.get(reactant.getLocation());
+ Double sto = reactant.getQuantity();
+ meta.affectRight(newReaction, sto, newCpt, newMetabolite);
+ }
+
+ // Copy enzymes
+ if (keepGPR) {
+ for (BioEnzyme enzyme : r.getEnzymesView()) {
+ BioEnzyme newEnzyme = enzymeConversion.get(enzyme);
+ meta.affectEnzyme(newReaction, newEnzyme);
+ }
+ }
+ }
+
+ for (BioPathway pathway : sub.getPathwaysView()) {
+ BioPathway newPathway = entityFactory.createMetaEntity(pathway,sub);
+ meta.add(newPathway);
+ // Add reactions into pathway
+ BioCollection<BioReaction> reactions = sub.getReactionsFromPathways(pathway);
+
+ for (BioReaction reaction : reactions) {
+ BioReaction newReaction = reactionConversion.get(reaction);
+ meta.affectToPathway(newPathway, newReaction);
+ }
+ }
+ }
+ }
+
+ public void setAliasPrefixes(Map<BioNetwork,String> aliases, String poolPrefix){
+ this.setEntityFactory(new PrefixedMetaEntityFactory(aliases, poolPrefix));
+ }
@Override
public BioNetwork build() {
- //todo
- return null;
+ BioNetwork meta = this.initMetaNetwork();
+ //create shared compartment
+ this.initSharedComp(meta);
+ //add each subnetwork content
+ this.populateMetaNetwork(meta);
+ //add shared compartment components and exchanges
+ this.populateSharedComp(meta);
+ //link compounds in shared compartment
+ this.linkCompoundsInSharedComp(meta);
+ return meta;
+ }
+ protected void initSharedComp(BioNetwork meta) {
+ for (Map.Entry<BioCompartment, Set<MetaBioMetabolite>> compDescriptor : metaCompComposition.entrySet()) {
+ BioCompartment sc = compDescriptor.getKey();
+ meta.addCompartment(sc);
+ }
}
+ protected void populateSharedComp(BioNetwork meta){
+ for(Map.Entry<BioCompartment, Set<MetaBioMetabolite>> compDescriptor : metaCompComposition.entrySet()){
+ for(MetaBioMetabolite m : compDescriptor.getValue()){
+ BioMetabolite m1 = metaboliteConversion.get(m.metabolite());
+ BioMetabolite m2 = entityFactory.createSharedCompound(m1,compDescriptor.getKey());
+ meta.add(m2);
+ meta.affectToCompartment(compDescriptor.getKey(),m2);
+ BioReaction t = createTransportWithSharedComp.apply(m1,compDescriptor.getKey());
+ meta.add(t);
+ meta.affectLeft(t,1.0,compartmentConversion.get(m.sourceCompartment()),metaboliteConversion.get(m.metabolite()));
+ meta.affectLeft(t,1.0,compDescriptor.getKey(),m2);
+ }
+ }
+ }
+
+ /**
+ * Links the source-specific metabolites representing the same compounds in the shared compartments, by creating a shared "pool" entity
+ * alongside their interconversion reactions.
+ * @param meta
+ */
+ protected void linkCompoundsInSharedComp(BioNetwork meta) {
+ //loop over each shared compartment
+ for(BioCompartment sharedComp : metaCompComposition.keySet()){
+ //retrieve all metabolite components that has been previously set, using whole compartment fusing or individual additions
+ BioCollection<BioMetabolite> content = sharedComp.getComponentsView().stream()
+ .filter((e) -> e.getClass().equals(BioMetabolite.class))
+ .map(o -> (BioMetabolite)o)
+ .collect(BioCollection::new,BioCollection::add,BioCollection::addAll);
+
+ //all entities that represent the same compounds from different source are grouped
+ Map<String, List<BioMetabolite>> compoundGroups = content.stream().collect(Collectors.groupingBy(getSharedIdFunction));
+
+ //for each group, create a "pool" metabolite that represent them
+ for(Map.Entry<String, List<BioMetabolite>> group : compoundGroups.entrySet()){
+ BioMetabolite pool = this.entityFactory.createPoolCompound(group.getValue(),sharedComp);
+ meta.add(pool);
+ meta.affectToCompartment(sharedComp,pool);
+ //for each member of the group, create a reversible reaction linking them to their "pool" counterpart
+ for(BioMetabolite e : group.getValue()){
+ BioReaction r = this.createLinkWithSharedPool.apply(e,pool);
+ meta.add(r);
+ meta.affectRight(r,1.0, sharedComp,e);
+ meta.affectLeft(r,1.0, sharedComp,pool);
+ }
+ }
+ }
+ }
}
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MultiNetworkBuilder.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MultiNetworkBuilder.java
index c17e2cadc..12f084efa 100644
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MultiNetworkBuilder.java
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MultiNetworkBuilder.java
@@ -10,12 +10,11 @@ public interface MultiNetworkBuilder {
*/
public void add(BioNetwork bn);
- public void merge();
-
/**
* create a new network which encompass all added networks
* @return
*/
public BioNetwork build();
+
}
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MultiOrganNetworkBuilder.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MultiOrganNetworkBuilder.java
deleted file mode 100644
index ae4c1b699..000000000
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MultiOrganNetworkBuilder.java
+++ /dev/null
@@ -1,57 +0,0 @@
-package fr.inrae.toulouse.metexplore.met4j_core.biodata.multinetwork;
-
-import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioCompartment;
-import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioMetabolite;
-import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
-import fr.inrae.toulouse.metexplore.met4j_core.biodata.collection.BioCollection;
-
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.stream.Collectors;
-
-public class MultiOrganNetworkBuilder extends AbstractMetaNetworkBuilder implements MultiNetworkBuilder{
-
- @Override
- public void merge() {
- //TODO
- }
-
-
- @Override
- public void addSharedCompartment(BioCompartment sc, BioNetwork... bn) {
- super.addSharedCompartment(sc,bn);
- }
-
- @Override
- public void fuseCompartmentIntoSharedCompartment(BioNetwork n, BioCompartment c, BioCompartment sc) {
- super.fuseCompartmentIntoSharedCompartment(n,c,sc);
- }
-
- @Override
- public void bumpCompartmentIntoSharedCompartment(BioNetwork n, BioCompartment c, BioCompartment sc) {
- super.bumpCompartmentIntoSharedCompartment(n,c,sc);
- }
-
- @Override
- public void exchangeWithSharedCompartment(BioNetwork n, BioMetabolite m, BioCompartment sc) {
- super.exchangeWithSharedCompartment(n,m,sc);
- }
-
- @Override
- public void exchangeWithSharedCompartment(BioNetwork n, BioCollection<BioMetabolite> m, BioCompartment sc) {
- super.exchangeWithSharedCompartment(n,m,sc);
- }
-
- @Override
- public BioNetwork build() {
- //todo
- //create empty meta network
- BioNetwork meta = new BioNetwork();
- //add each subnetwork content in dedicated compartment
- this.populateMetaNetwork(meta);
- //create shared compartment and the exchanged content
- this.initSharedComp(meta);
- return null;
- }
-}
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/NestedNetworkBuilder.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/NestedNetworkBuilder.java
deleted file mode 100644
index aeca0c100..000000000
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/NestedNetworkBuilder.java
+++ /dev/null
@@ -1,43 +0,0 @@
-package fr.inrae.toulouse.metexplore.met4j_core.biodata.multinetwork;
-
-import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioCompartment;
-import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioMetabolite;
-import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
-
-public class NestedNetworkBuilder extends AbstractMetaNetworkBuilder implements MultiNetworkBuilder{
-
- private BioNetwork superNet;
- private BioCompartment superNetComp;
-
- public NestedNetworkBuilder(BioNetwork superNetwork){
- setSuperNetwork(superNetwork);
- }
-
- private void setSuperNetwork(BioNetwork bn){
- superNet=bn;
- this.superNetComp = new BioCompartment(bn.getId());
- this.addSharedCompartment(superNetComp,superNet);
- }
-
- @Override
- public void add(BioNetwork bn) {
- super.add(bn);
- this.addSharedCompartment(superNetComp,this.networks.stream().toArray(BioNetwork[]::new));
- }
-
- @Override
- public void merge() {
- //todo
- }
-
- public void exchangeWithSuperNetwork(BioNetwork n, BioMetabolite m){
- this.exchangeWithSharedCompartment(n, m, superNetComp);
- };
-
- @Override
- public BioNetwork build() {
- //todo
- return null;
- }
-
-}
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/PanNetworkBuilder.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/PanNetworkBuilder.java
deleted file mode 100644
index 346f71cbf..000000000
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/PanNetworkBuilder.java
+++ /dev/null
@@ -1,23 +0,0 @@
-package fr.inrae.toulouse.metexplore.met4j_core.biodata.multinetwork;
-
-import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioMetabolite;
-import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
-import fr.inrae.toulouse.metexplore.met4j_core.biodata.collection.BioCollection;
-
-public class PanNetworkBuilder implements MultiNetworkBuilder {
- @Override
- public void add(BioNetwork bn) {
- //todo
- }
-
- @Override
- public void merge() {
- //todo
- }
-
- @Override
- public BioNetwork build() {
- //todo
- return null;
- }
-}
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/PrefixedMetaEntityFactory.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/PrefixedMetaEntityFactory.java
new file mode 100644
index 000000000..3137021eb
--- /dev/null
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/PrefixedMetaEntityFactory.java
@@ -0,0 +1,86 @@
+package fr.inrae.toulouse.metexplore.met4j_core.biodata.multinetwork;
+
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioCompartment;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEntity;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioMetabolite;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
+import lombok.SneakyThrows;
+
+import java.lang.reflect.InvocationTargetException;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.function.BiFunction;
+import java.util.function.Function;
+
+public class PrefixedMetaEntityFactory implements MetaEntityFactory {
+
+ Map<BioNetwork,String> sourcePrefixMap;
+ String poolPrefix;
+
+ public PrefixedMetaEntityFactory(Map<BioNetwork,String> sourcePrefixMap, String poolPrefix){
+ this.sourcePrefixMap=sourcePrefixMap;
+ this.poolPrefix=poolPrefix;
+ }
+
+ /**
+ * create prefix-id from network alias
+ */
+ public BiFunction<String, BioNetwork, String> addSourcePrefix = (id, bn) -> sourcePrefixMap.get(bn)+"_"+id;
+
+ /**
+ * create sharedCompartment-suffix id
+ */
+ public BiFunction<String, BioCompartment, String> addCompSuffix = (id, comp) -> id+"_"+comp.getId();
+ public BiFunction<String, BioCompartment, String> addCompPreffix = (id, comp) -> comp.getId()+"_"+id;
+
+
+ /**
+ * remove prefix-id from network alias
+ */
+ public Function<String, String> removeSourceSuffix = id -> {
+ for(String s : sourcePrefixMap.values()) {
+ id = id.replaceAll("^" + s + "_","");
+ };
+ return id;
+ };
+
+ /**
+ * create pool-prefix id
+ */
+ public Function<String, String> addPoolFlag = (id) -> poolPrefix+"_"+id;
+
+
+ @SneakyThrows
+ @Override
+ public <E extends BioEntity> E createMetaEntity(E originalEntity, BioNetwork source) {
+ return newEntityInstance(originalEntity, this.addSourcePrefix.apply(originalEntity.getId(),source));
+ }
+
+ @SneakyThrows
+ @Override
+ public BioMetabolite createSharedCompound(BioMetabolite entity, BioCompartment sharedCompartment) {
+ return newEntityInstance(entity, this.addCompSuffix.apply(entity.getId(),sharedCompartment));
+ }
+
+ @SneakyThrows
+ @Override
+ public BioMetabolite createPoolCompound(Collection<BioMetabolite> entities, BioCompartment sharedCompartment) {
+ BioMetabolite entity = entities.iterator().next();
+ return newEntityInstance(entity, removeSourceSuffix
+ .andThen(s -> addCompPreffix.apply(s,sharedCompartment))
+ .andThen(addPoolFlag)
+ .apply(entity.getId()));
+ }
+
+ private static <E extends BioEntity> E newEntityInstance(E entity, String newId) throws NoSuchMethodException, InvocationTargetException, InstantiationException, IllegalAccessException {
+ E newEntity = (E) entity.getClass().getDeclaredConstructor(String.class).newInstance(newId);
+ newEntity.setName(entity.getName());
+ newEntity.setSynonyms(new ArrayList<>(entity.getSynonyms()));
+ newEntity.setComment(entity.getComment());
+ newEntity.setRefs(new HashMap<>(entity.getRefs()));
+ newEntity.setAttributes(new HashMap<>(entity.getAttributes()));
+ return newEntity;
+ }
+}
diff --git a/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/TestMetaNetworkBuilder.java b/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/TestMetaNetworkBuilder.java
new file mode 100644
index 000000000..75a02f9fb
--- /dev/null
+++ b/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/TestMetaNetworkBuilder.java
@@ -0,0 +1,185 @@
+package fr.inrae.toulouse.metexplore.met4j_core.biodata.multinetwork;
+
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.*;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+import java.util.HashMap;
+
+import static org.junit.Assert.*;
+
+public class TestMetaNetworkBuilder {
+
+
+ public static BioNetwork bn1, bn2, bn3, bn4;
+ public static BioMetabolite a1,b1,c1,c1ex,c2,c2ex,d3, d3ex, f3, d4, d4ex;
+ public static BioCompartment co1in, co1ex, co2in, co2ex, co3in, co3ex,co4in, co4ex,medium,medium2;
+ public static BioReaction r1, r3, tc1, tc2, td3,td4;
+
+
+ public static BioNetwork initBump() {
+ HashMap<BioNetwork,String> alias = new HashMap<>();
+ alias.put(bn1,"model1");
+ alias.put(bn2,"model2");
+ alias.put(bn3,"model3");
+ alias.put(bn4,"model4");
+ medium=new BioCompartment("medium");
+ medium2=new BioCompartment("medium2");
+ CommunityNetworkBuilder builder = new CommunityNetworkBuilder(medium);
+ builder.addNewSharedCompartment(medium2);
+ builder.setEntityFactory(new PrefixedMetaEntityFactory(alias,"pool"));
+ builder.add(bn1);
+ builder.add(bn2);
+ builder.add(bn3);
+ builder.add(bn4);
+ builder.bumpCompartmentIntoSharedCompartment(bn1,co1ex,medium);
+ builder.bumpCompartmentIntoSharedCompartment(bn2,co2ex,medium);
+ builder.bumpCompartmentIntoSharedCompartment(bn3,co3ex,medium);
+ builder.bumpCompartmentIntoSharedCompartment(bn4,co4ex,medium2);
+ builder.bumpCompartmentIntoSharedCompartment(bn4,co4ex,medium);
+ return builder.build();
+ }
+
+ public static BioNetwork initFuse() {
+ HashMap<BioNetwork,String> alias = new HashMap<>();
+ alias.put(bn1,"model1");
+ alias.put(bn2,"model2");
+ alias.put(bn3,"model3");
+ alias.put(bn4,"model4");
+ medium=new BioCompartment("medium");
+ medium2=new BioCompartment("medium2");
+ CommunityNetworkBuilder builder = new CommunityNetworkBuilder(medium);
+ builder.addNewSharedCompartment(medium2);
+ builder.setEntityFactory(new PrefixedMetaEntityFactory(alias,"pool"));
+ builder.add(bn1,co1ex);
+ builder.add(bn2,co2ex);
+ builder.add(bn3,co3ex);
+ builder.add(bn4);
+ builder.fuseCompartmentIntoSharedCompartment(bn4,co4ex,medium2);
+ return builder.build();
+ }
+
+ @BeforeClass
+ public static void beforeClass() {
+ bn1 = new BioNetwork("bn1");
+ bn2 = new BioNetwork("bn2");
+ bn3 = new BioNetwork("bn3");
+ bn4 = new BioNetwork("bn4");
+ a1 = new BioMetabolite("a_in","a");
+ b1 = new BioMetabolite("b_in","b");
+ c1 = new BioMetabolite("c_in","c");
+ c1ex = new BioMetabolite("c_ex","c");
+ r1 = new BioReaction("r1");
+ tc1 = new BioReaction("tc");
+ co1in = new BioCompartment("in");
+ co1ex = new BioCompartment("ex");
+ bn1.add(a1,b1,c1,c1ex,r1,tc1,co1in,co1ex);
+ bn1.affectToCompartment(co1in,a1,b1,c1);
+ bn1.affectToCompartment(co1ex,c1ex);
+ bn1.affectLeft(r1,1.0,co1in,a1);
+ bn1.affectLeft(r1,1.0,co1in,b1);
+ bn1.affectRight(r1,2.0,co1in,c1);
+ bn1.affectLeft(tc1,1.0,co1in,c1);
+ bn1.affectRight(tc1,1.0,co1ex,c1ex);
+ c2 = new BioMetabolite("c_in","c");
+ c2ex = new BioMetabolite("c_ex","c");
+ tc2 = new BioReaction("tc");
+ co2in = new BioCompartment("in");
+ co2ex = new BioCompartment("ex");
+ bn2.add(c2,c2ex,tc2,co2in,co2ex);
+ bn2.affectToCompartment(co2in,c2);
+ bn2.affectToCompartment(co2ex,c2ex);
+ bn2.affectLeft(tc2,1.0,co2in,c2);
+ bn2.affectRight(tc2,1.0,co2ex,c2ex);
+ d3ex = new BioMetabolite("d_ex","d");
+ d3 = new BioMetabolite("d_in","d");
+ f3 = new BioMetabolite("f_in","f");
+ r3 = new BioReaction("r2");
+ td3 = new BioReaction("td");
+ co3in = new BioCompartment("in");
+ co3ex = new BioCompartment("ex");
+ bn3.add(d3ex,d3,f3,r3,td3,co3in,co3ex);
+ bn3.affectToCompartment(co3in,d3,f3);
+ bn3.affectToCompartment(co3ex,d3ex);
+ bn3.affectLeft(td3,1.0,co3in,d3);
+ bn3.affectRight(td3,1.0,co3ex,d3ex);
+ bn3.affectLeft(r3,1.0,co3in,d3);
+ bn3.affectRight(r3,1.0,co3in,f3);
+ d4 = new BioMetabolite("d_in","d");
+ d4ex = new BioMetabolite("d_ex","d");
+ td4 = new BioReaction("td");
+ co4in = new BioCompartment("in");
+ co4ex = new BioCompartment("ex");
+ bn4.add(d4,d4ex,td4,co4in,co4ex);
+ bn4.affectToCompartment(co4in,d4);
+ bn4.affectToCompartment(co4ex,d4ex);
+ bn4.affectLeft(td4,1.0,co4in,d4);
+ bn4.affectRight(td4,1.0,co4ex,d4ex);
+ }
+
+ @Test
+ public void testCompoundsFuse(){
+ BioNetwork meta = initFuse();
+ assertEquals(14,meta.getMetabolitesView().size());
+ assertNotNull(meta.getMetabolite("model1_a_in"));
+ assertNotNull(meta.getMetabolite("model1_c_in"));
+ assertNotNull(meta.getMetabolite("model1_c_ex"));
+ assertNotNull(meta.getMetabolite("model2_c_ex"));
+ assertNotNull(meta.getMetabolite("model2_c_in"));
+
+ assertNotNull(meta.getMetabolite("pool_medium_c_ex"));
+ assertNotNull(meta.getMetabolite("pool_medium_d_ex"));
+ assertNotNull(meta.getMetabolite("pool_medium2_d_ex"));
+ }
+
+ @Test
+ public void testReactionsFuse() {
+ BioNetwork meta = initFuse();
+ assertEquals(10, meta.getReactionsView().size());
+ assertNotNull(meta.getReaction("poolReaction_model2_c_ex"));
+ assertNotNull(meta.getReaction("poolReaction_model1_c_ex"));
+ assertNotNull(meta.getReaction("poolReaction_model3_d_ex"));
+ }
+
+ @Test
+ public void testCompartmentFuse(){
+ BioNetwork meta = initFuse();
+ assertEquals(6,meta.getCompartmentsView().size());
+ }
+
+
+ @Test
+ public void testCompoundsBump(){
+ BioNetwork meta = initBump();
+ assertEquals(19,meta.getMetabolitesView().size());
+ assertNotNull(meta.getMetabolite("model1_a_in"));
+ assertNotNull(meta.getMetabolite("model1_c_in"));
+ assertNotNull(meta.getMetabolite("model1_c_ex"));
+ assertNotNull(meta.getMetabolite("model2_c_ex"));
+ assertNotNull(meta.getMetabolite("model2_c_in"));
+
+ assertNotNull(meta.getMetabolite("pool_medium_c_ex_medium"));
+ assertNotNull(meta.getMetabolite("pool_medium_d_ex_medium"));
+ assertNotNull(meta.getMetabolite("pool_medium2_d_ex_medium2"));
+ }
+
+ @Test
+ public void testReactionsBump() {
+ BioNetwork meta = initBump();
+ assertEquals(16, meta.getReactionsView().size());
+ assertNotNull(meta.getReaction("poolReaction_model2_c_ex_medium"));
+ assertNotNull(meta.getReaction("poolReaction_model1_c_ex_medium"));
+ assertNotNull(meta.getReaction("poolReaction_model3_d_ex_medium"));
+ assertNotNull(meta.getReaction("transport_model1_c_ex_to_medium"));
+ assertNotNull(meta.getReaction("poolReaction_model4_d_ex_medium2"));
+ assertNotNull(meta.getReaction("poolReaction_model4_d_ex_medium"));
+ assertNotNull(meta.getReaction("transport_model4_d_ex_to_medium2"));
+ assertNotNull(meta.getReaction("transport_model4_d_ex_to_medium"));
+ }
+
+ @Test
+ public void testCompartmentBump(){
+ BioNetwork meta = initBump();
+ assertEquals(10,meta.getCompartmentsView().size());
+ }
+}
--
GitLab
From 168bf2c6f61555711a38857a48649133bea7df2c Mon Sep 17 00:00:00 2001
From: cfrainay <clement.frainay@inrae.fr>
Date: Wed, 18 Sep 2024 00:03:18 +0200
Subject: [PATCH 03/17] app stub
---
.../reconstruction/CreateMetaNetwork.java | 173 ++++++++++++++++++
1 file changed, 173 insertions(+)
create mode 100644 met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/reconstruction/CreateMetaNetwork.java
diff --git a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/reconstruction/CreateMetaNetwork.java b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/reconstruction/CreateMetaNetwork.java
new file mode 100644
index 000000000..d5767c203
--- /dev/null
+++ b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/reconstruction/CreateMetaNetwork.java
@@ -0,0 +1,173 @@
+package fr.inrae.toulouse.metexplore.met4j_toolbox.reconstruction;
+
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.*;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.multinetwork.CommunityNetworkBuilder;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.multinetwork.PrefixedMetaEntityFactory;
+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.jsbml.writer.JsbmlWriter;
+import fr.inrae.toulouse.metexplore.met4j_io.jsbml.writer.Met4jSbmlWriterException;
+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.EnumParameterTypes;
+import fr.inrae.toulouse.metexplore.met4j_toolbox.generic.annotations.Format;
+import fr.inrae.toulouse.metexplore.met4j_toolbox.generic.annotations.ParameterType;
+import org.kohsuke.args4j.Option;
+
+import java.util.HashMap;
+import java.util.NoSuchElementException;
+import java.util.Objects;
+import java.util.UUID;
+import java.util.function.Function;
+
+import static fr.inrae.toulouse.metexplore.met4j_toolbox.generic.annotations.EnumFormats.Sbml;
+import static fr.inrae.toulouse.metexplore.met4j_toolbox.generic.annotations.EnumParameterTypes.InputFile;
+import static fr.inrae.toulouse.metexplore.met4j_toolbox.reconstruction.CreateMetaNetwork.strategy.*;
+
+public class CreateMetaNetwork extends AbstractMet4jApplication {
+
+ //arguments
+ @Format(name = Sbml)
+ @ParameterType(name = InputFile)
+ @Option(name = "-n1", aliases = {"--network1"}, usage = "input SBML file: path to first network, in sbml format.", required = true)
+ public String sbml1FilePath;
+ @Option(name = "-n2", aliases = {"--network2"}, usage = "input SBML file: path to second network, in sbml format.", required = true)
+ public String sbml2FilePath;
+
+ @Option(name = "-n1ex", aliases = {"--external1"}, usage = "external compartment identifier in first network.", required = true)
+ public String external1;
+ @Option(name = "-n2ex", aliases = {"--external2"}, usage = "external compartment identifier in second network.", required = true)
+ public String external2;
+
+ @Option(name = "-n1px", aliases = {"--n1prefix"}, usage = "prefix that will be added to first network's entities identifiers", required = false)
+ public String n1prefix = "Net1_";
+ @Option(name = "-n2px", aliases = {"--n2prefix"}, usage = "prefix that will be added to second network's entities identifiers", required = false)
+ public String n2prefix = "Net2_";
+
+ @Option(name = "-k", aliases = {"--keepCompartment"}, usage = "keep the original external compartments in the meta-network, otherwise, they will be fused into the new shared external compartment", required = false)
+ public boolean keepCompartment = false;
+
+ enum strategy {by_metanetx, by_name, by_id}
+ @Option(name = "-mc", aliases = {"--mergingCriterion"}, usage = "field used to identify the same metabolites across the two different networks. " +
+ "\"by_name\"/\"by_id\" can be used if names/identifiers are consistent and unambiguous across source models, \"by_metanetx\" can be used if models contains MetaNetX identifiers in annotation field using standard miriam format.")
+ public CreateMetaNetwork.strategy mergingCriterion = by_name;
+
+ @ParameterType(name = EnumParameterTypes.OutputFile)
+ @Format(name = EnumFormats.Sbml)
+ @Option(name = "-o", usage = "output meta-network SBML file", required = true)
+ public String outputPath = null;
+
+ public static void main(String[] args) throws Met4jSbmlWriterException {
+ CreateMetaNetwork app = new CreateMetaNetwork();
+ app.parseArguments(args);
+ app.run();
+ }
+
+ public void run() throws Met4jSbmlWriterException {
+
+ if(Objects.equals(this.n1prefix, this.n2prefix)){
+ System.err.println("Error: prefixes must be different");
+ System.exit(1);
+ }
+
+ //import networks
+ System.out.print("Importing network 1...");
+ JsbmlReader reader = new JsbmlReader(this.sbml1FilePath);
+ BioNetwork network1 = null;
+ try {
+ network1 = reader.read();
+ } catch (Met4jSbmlReaderException e) {
+ System.err.println("Error while reading the first SBML file");
+ System.err.println(e.getMessage());
+ System.exit(1);
+ }
+ BioCompartment co1ex = network1.getCompartment(external1);
+ if(co1ex==null){
+ System.err.println("Error: external compartment " + external1 + " not found in network 1");
+ System.exit(1);
+ }
+ System.out.println(" Done.");
+
+
+ System.out.print("Importing network 2...");
+ reader = new JsbmlReader(this.sbml2FilePath);
+ BioNetwork network2 = null;
+ try {
+ network2 = reader.read();
+ } catch (Met4jSbmlReaderException e) {
+ System.err.println("Error while reading the second SBML file");
+ System.err.println(e.getMessage());
+ System.exit(1);
+ }
+ BioCompartment co2ex = network2.getCompartment(external2);
+ if(co2ex==null){
+ System.err.println("Error: external compartment " + external2 + " not found in network 2");
+ System.exit(1);
+ }
+ System.out.println(" Done.");
+
+ System.out.print("Creating meta-network...");
+ //setup
+ BioCompartment medium=new BioCompartment("medium"); medium.setName("medium");
+ HashMap<BioNetwork,String> alias = new HashMap<>();
+ alias.put(network1,n1prefix);alias.put(network2,n2prefix);
+ CommunityNetworkBuilder builder = new CommunityNetworkBuilder(medium);
+ builder.setEntityFactory(new PrefixedMetaEntityFactory(alias,"pool"));
+ Function<BioMetabolite, String> getSharedIdFunction;
+ switch (mergingCriterion) {
+ case by_metanetx:
+ getSharedIdFunction = x -> {
+ try {
+ BioRef r = x.getRefs("metanetx.chemical").iterator().next();
+ return r.getId();
+ } catch (NoSuchElementException|java.lang.NullPointerException e) {
+ return "unknown_"+UUID.randomUUID();
+ }
+ };
+ break;
+ case by_id:
+ getSharedIdFunction = BioEntity::getId;
+ break;
+ case by_name:
+ getSharedIdFunction = BioEntity::getName;
+ break;
+ default:
+ throw new IllegalArgumentException("Invalid merging criterion: " + mergingCriterion);
+ }
+ builder.setGetSharedIdFunction(getSharedIdFunction);
+ builder.add(network1);
+ builder.add(network2);
+
+ //build meta-network
+ if(!keepCompartment){
+ builder.fuseCompartmentIntoSharedCompartment(network1,co1ex,medium);
+ builder.fuseCompartmentIntoSharedCompartment(network2,co2ex,medium);
+ }else{
+ builder.bumpCompartmentIntoSharedCompartment(network1,co1ex,medium);
+ builder.bumpCompartmentIntoSharedCompartment(network2,co2ex,medium);
+ }
+ BioNetwork metaNetwork = builder.build();
+ System.out.println(" Done.");
+
+ //export the meta-network
+ System.out.print("Exporting MetaNetwork...");
+ new JsbmlWriter(outputPath,metaNetwork).write();
+ System.out.println(" Done.");
+
+ }
+
+ @Override
+ public String getLabel() {return this.getClass().getSimpleName();}
+
+ @Override
+ public String getLongDescription() {
+ return "Create a Meta-Network from two sub-networks in SBML format.";
+ }
+
+ @Override
+ public String getShortDescription() {
+ return "Create a Meta-Network from two sub-networks in SBML format. A meta-network is a single model which contains several sub-networks that remains individualized within" +
+ "the meta-network (as opposed to models fusion), but which can share some of their components with " +
+ "other sub-networks through a shared \"medium\" compartment.";
+ }
+}
--
GitLab
From 7ba7f81adb038d8b10ce1ecdc271765740fd38a1 Mon Sep 17 00:00:00 2001
From: cfrainay <clement.frainay@inrae.fr>
Date: Fri, 20 Sep 2024 17:20:30 +0200
Subject: [PATCH 04/17] refactoring, isolate builder init
---
.../reconstruction/CreateMetaNetwork.java | 45 ++++++++++---------
1 file changed, 25 insertions(+), 20 deletions(-)
diff --git a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/reconstruction/CreateMetaNetwork.java b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/reconstruction/CreateMetaNetwork.java
index d5767c203..fa81d37d7 100644
--- a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/reconstruction/CreateMetaNetwork.java
+++ b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/reconstruction/CreateMetaNetwork.java
@@ -111,6 +111,29 @@ public class CreateMetaNetwork extends AbstractMet4jApplication {
BioCompartment medium=new BioCompartment("medium"); medium.setName("medium");
HashMap<BioNetwork,String> alias = new HashMap<>();
alias.put(network1,n1prefix);alias.put(network2,n2prefix);
+ CommunityNetworkBuilder builder = initMetaNetworkBuilder(medium, alias);
+ builder.add(network1);
+ builder.add(network2);
+
+ //build meta-network
+ if(!keepCompartment){
+ builder.fuseCompartmentIntoSharedCompartment(network1,co1ex,medium);
+ builder.fuseCompartmentIntoSharedCompartment(network2,co2ex,medium);
+ }else{
+ builder.bumpCompartmentIntoSharedCompartment(network1,co1ex,medium);
+ builder.bumpCompartmentIntoSharedCompartment(network2,co2ex,medium);
+ }
+ BioNetwork metaNetwork = builder.build();
+ System.out.println(" Done.");
+
+ //export the meta-network
+ System.out.print("Exporting MetaNetwork...");
+ new JsbmlWriter(outputPath,metaNetwork).write();
+ System.out.println(" Done.");
+
+ }
+
+ private CommunityNetworkBuilder initMetaNetworkBuilder(BioCompartment medium, HashMap<BioNetwork, String> alias) {
CommunityNetworkBuilder builder = new CommunityNetworkBuilder(medium);
builder.setEntityFactory(new PrefixedMetaEntityFactory(alias,"pool"));
Function<BioMetabolite, String> getSharedIdFunction;
@@ -120,7 +143,7 @@ public class CreateMetaNetwork extends AbstractMet4jApplication {
try {
BioRef r = x.getRefs("metanetx.chemical").iterator().next();
return r.getId();
- } catch (NoSuchElementException|java.lang.NullPointerException e) {
+ } catch (NoSuchElementException | NullPointerException e) {
return "unknown_"+UUID.randomUUID();
}
};
@@ -135,25 +158,7 @@ public class CreateMetaNetwork extends AbstractMet4jApplication {
throw new IllegalArgumentException("Invalid merging criterion: " + mergingCriterion);
}
builder.setGetSharedIdFunction(getSharedIdFunction);
- builder.add(network1);
- builder.add(network2);
-
- //build meta-network
- if(!keepCompartment){
- builder.fuseCompartmentIntoSharedCompartment(network1,co1ex,medium);
- builder.fuseCompartmentIntoSharedCompartment(network2,co2ex,medium);
- }else{
- builder.bumpCompartmentIntoSharedCompartment(network1,co1ex,medium);
- builder.bumpCompartmentIntoSharedCompartment(network2,co2ex,medium);
- }
- BioNetwork metaNetwork = builder.build();
- System.out.println(" Done.");
-
- //export the meta-network
- System.out.print("Exporting MetaNetwork...");
- new JsbmlWriter(outputPath,metaNetwork).write();
- System.out.println(" Done.");
-
+ return builder;
}
@Override
--
GitLab
From e565319c889beaebe59aa9df503a9c5e7b238387 Mon Sep 17 00:00:00 2001
From: cfrainay <clement.frainay@inrae.fr>
Date: Tue, 24 Sep 2024 18:10:54 +0200
Subject: [PATCH 05/17] enable iterative metanetwork building
---
.../reconstruction/CreateMetaNetwork.java | 17 ++++++++++++++++-
1 file changed, 16 insertions(+), 1 deletion(-)
diff --git a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/reconstruction/CreateMetaNetwork.java b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/reconstruction/CreateMetaNetwork.java
index fa81d37d7..7815cf68f 100644
--- a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/reconstruction/CreateMetaNetwork.java
+++ b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/reconstruction/CreateMetaNetwork.java
@@ -47,6 +47,9 @@ public class CreateMetaNetwork extends AbstractMet4jApplication {
@Option(name = "-k", aliases = {"--keepCompartment"}, usage = "keep the original external compartments in the meta-network, otherwise, they will be fused into the new shared external compartment", required = false)
public boolean keepCompartment = false;
+ @Option(name = "-n1meta", aliases = {"--firstAsMeta"}, usage = "Treat first network as meta-network, allowing more than two sub-models with iterative fusions. This will overwrite shared compartment and pool compounds (which must follow the \"pool_\" prefix convention) and will ignore --n1prefix argument", required = false)
+ public boolean firstIsMeta = false;
+
enum strategy {by_metanetx, by_name, by_id}
@Option(name = "-mc", aliases = {"--mergingCriterion"}, usage = "field used to identify the same metabolites across the two different networks. " +
"\"by_name\"/\"by_id\" can be used if names/identifiers are consistent and unambiguous across source models, \"by_metanetx\" can be used if models contains MetaNetX identifiers in annotation field using standard miriam format.")
@@ -86,6 +89,14 @@ public class CreateMetaNetwork extends AbstractMet4jApplication {
System.err.println("Error: external compartment " + external1 + " not found in network 1");
System.exit(1);
}
+ if(firstIsMeta){
+ n1prefix = "";
+ network1.removeOnCascade(network1
+ .getCompartment(external1)
+ .getComponentsView().stream()
+ .filter(e -> e instanceof BioMetabolite)
+ .filter(m -> m.getId().startsWith("pool_")).toArray(BioEntity[]::new));
+ }
System.out.println(" Done.");
@@ -120,7 +131,11 @@ public class CreateMetaNetwork extends AbstractMet4jApplication {
builder.fuseCompartmentIntoSharedCompartment(network1,co1ex,medium);
builder.fuseCompartmentIntoSharedCompartment(network2,co2ex,medium);
}else{
- builder.bumpCompartmentIntoSharedCompartment(network1,co1ex,medium);
+ if(firstIsMeta) {
+ builder.fuseCompartmentIntoSharedCompartment(network1, co1ex, medium);
+ }else{
+ builder.bumpCompartmentIntoSharedCompartment(network1, co1ex, medium);
+ }
builder.bumpCompartmentIntoSharedCompartment(network2,co2ex,medium);
}
BioNetwork metaNetwork = builder.build();
--
GitLab
From c4c0d01452c2891adfc44398de8fee94acc0ccce Mon Sep 17 00:00:00 2001
From: cfrainay <clement.frainay@inrae.fr>
Date: Fri, 4 Oct 2024 14:46:57 +0200
Subject: [PATCH 06/17] create exchange reaction, suffix separator as parameter
---
.../multinetwork/MetaNetworkBuilder.java | 18 ++++++++++++++++++
.../PrefixedMetaEntityFactory.java | 11 ++++++-----
.../reconstruction/CreateMetaNetwork.java | 16 +++++++++++-----
3 files changed, 35 insertions(+), 10 deletions(-)
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaNetworkBuilder.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaNetworkBuilder.java
index b5b5b2958..7d4da1b58 100644
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaNetworkBuilder.java
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaNetworkBuilder.java
@@ -34,11 +34,21 @@ public class MetaNetworkBuilder implements MultiNetworkBuilder{
@Setter
private String sharedTransportPrefix = "transport_";
@Setter
+ private String exchangeReactionPrefix = "exchange_";
+ @Setter
protected BiFunction<BioMetabolite, BioMetabolite, BioReaction> createLinkWithSharedPool = (m, pool) -> {
BioReaction r=new BioReaction(poolReactionPrefix+ m.getId());
r.setReversible(true);
return r;
};
+
+ @Setter
+ protected Function<BioMetabolite, BioReaction> createPoolExchangeReaction = (pool) -> {
+ BioReaction r=new BioReaction(exchangeReactionPrefix+pool.getId());
+ r.setReversible(true);
+ return r;
+ };
+
@Setter
protected BiFunction<BioMetabolite, BioCompartment, BioReaction> createTransportWithSharedComp = (m, comp) -> {
BioReaction r=new BioReaction(sharedTransportPrefix+ m.getId()+"_to_"+comp.getId());
@@ -50,6 +60,8 @@ public class MetaNetworkBuilder implements MultiNetworkBuilder{
protected MetaEntityFactory entityFactory;
protected HashMap<BioCompartment,BioCompartment> fuseMap= new HashMap<>();
protected Boolean keepGPR = false;
+ @Setter
+ public Boolean addExchangeReaction = true;
/**
* enable a compartment to be shared between multiple organisms
@@ -310,6 +322,12 @@ public class MetaNetworkBuilder implements MultiNetworkBuilder{
meta.affectRight(r,1.0, sharedComp,e);
meta.affectLeft(r,1.0, sharedComp,pool);
}
+ //if option selected, add exchange reaction to the pool for flux modeling
+ if(addExchangeReaction){
+ BioReaction r = this.createPoolExchangeReaction.apply(pool);
+ meta.add(r);
+ meta.affectLeft(r,1.0, sharedComp,pool);
+ }
}
}
}
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/PrefixedMetaEntityFactory.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/PrefixedMetaEntityFactory.java
index 3137021eb..2b26d4964 100644
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/PrefixedMetaEntityFactory.java
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/PrefixedMetaEntityFactory.java
@@ -18,6 +18,7 @@ public class PrefixedMetaEntityFactory implements MetaEntityFactory {
Map<BioNetwork,String> sourcePrefixMap;
String poolPrefix;
+ String sep = "";
public PrefixedMetaEntityFactory(Map<BioNetwork,String> sourcePrefixMap, String poolPrefix){
this.sourcePrefixMap=sourcePrefixMap;
@@ -27,13 +28,13 @@ public class PrefixedMetaEntityFactory implements MetaEntityFactory {
/**
* create prefix-id from network alias
*/
- public BiFunction<String, BioNetwork, String> addSourcePrefix = (id, bn) -> sourcePrefixMap.get(bn)+"_"+id;
+ public BiFunction<String, BioNetwork, String> addSourcePrefix = (id, bn) -> sourcePrefixMap.get(bn)+sep+id;
/**
* create sharedCompartment-suffix id
*/
- public BiFunction<String, BioCompartment, String> addCompSuffix = (id, comp) -> id+"_"+comp.getId();
- public BiFunction<String, BioCompartment, String> addCompPreffix = (id, comp) -> comp.getId()+"_"+id;
+ public BiFunction<String, BioCompartment, String> addCompSuffix = (id, comp) -> id+sep+comp.getId();
+ public BiFunction<String, BioCompartment, String> addCompPreffix = (id, comp) -> comp.getId()+sep+id;
/**
@@ -41,7 +42,7 @@ public class PrefixedMetaEntityFactory implements MetaEntityFactory {
*/
public Function<String, String> removeSourceSuffix = id -> {
for(String s : sourcePrefixMap.values()) {
- id = id.replaceAll("^" + s + "_","");
+ id = id.replaceAll("^" + s + sep,"");
};
return id;
};
@@ -49,7 +50,7 @@ public class PrefixedMetaEntityFactory implements MetaEntityFactory {
/**
* create pool-prefix id
*/
- public Function<String, String> addPoolFlag = (id) -> poolPrefix+"_"+id;
+ public Function<String, String> addPoolFlag = (id) -> poolPrefix+sep+id;
@SneakyThrows
diff --git a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/reconstruction/CreateMetaNetwork.java b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/reconstruction/CreateMetaNetwork.java
index 7815cf68f..50204fe75 100644
--- a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/reconstruction/CreateMetaNetwork.java
+++ b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/reconstruction/CreateMetaNetwork.java
@@ -22,7 +22,7 @@ import java.util.function.Function;
import static fr.inrae.toulouse.metexplore.met4j_toolbox.generic.annotations.EnumFormats.Sbml;
import static fr.inrae.toulouse.metexplore.met4j_toolbox.generic.annotations.EnumParameterTypes.InputFile;
-import static fr.inrae.toulouse.metexplore.met4j_toolbox.reconstruction.CreateMetaNetwork.strategy.*;
+import static fr.inrae.toulouse.metexplore.met4j_toolbox.reconstruction.CreateMetaNetwork.strategy.by_name;
public class CreateMetaNetwork extends AbstractMet4jApplication {
@@ -91,11 +91,15 @@ public class CreateMetaNetwork extends AbstractMet4jApplication {
}
if(firstIsMeta){
n1prefix = "";
- network1.removeOnCascade(network1
- .getCompartment(external1)
+ BioMetabolite[] pool1 = network1.getCompartment(external1)
.getComponentsView().stream()
.filter(e -> e instanceof BioMetabolite)
- .filter(m -> m.getId().startsWith("pool_")).toArray(BioEntity[]::new));
+ .filter(m -> m.getId().startsWith("pool_"))
+ .toArray(BioMetabolite[]::new);
+ for(BioMetabolite pool : pool1){
+ network1.removeOnCascade(network1.getReactionsFromMetabolite(pool));
+ }
+ network1.removeOnCascade(pool1);
}
System.out.println(" Done.");
@@ -150,7 +154,9 @@ public class CreateMetaNetwork extends AbstractMet4jApplication {
private CommunityNetworkBuilder initMetaNetworkBuilder(BioCompartment medium, HashMap<BioNetwork, String> alias) {
CommunityNetworkBuilder builder = new CommunityNetworkBuilder(medium);
- builder.setEntityFactory(new PrefixedMetaEntityFactory(alias,"pool"));
+ PrefixedMetaEntityFactory factory = new PrefixedMetaEntityFactory(alias,"pool_");
+ factory.addCompSuffix = (id, comp) -> id+"_"+comp.getId();
+ builder.setEntityFactory(factory);
Function<BioMetabolite, String> getSharedIdFunction;
switch (mergingCriterion) {
case by_metanetx:
--
GitLab
From 762840f67bf6451a953915f6aadb5b881f509175 Mon Sep 17 00:00:00 2001
From: cfrainay <clement.frainay@inrae.fr>
Date: Tue, 8 Oct 2024 17:34:38 +0200
Subject: [PATCH 07/17] add test + better handling of prefixed pool compounds
---
.../multinetwork/MetaNetworkBuilder.java | 2 +-
.../PrefixedMetaEntityFactory.java | 11 +-
.../multinetwork/TestMetaNetworkBuilder.java | 108 +++++++++++++++++-
3 files changed, 114 insertions(+), 7 deletions(-)
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaNetworkBuilder.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaNetworkBuilder.java
index 7d4da1b58..9c214f4b0 100644
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaNetworkBuilder.java
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaNetworkBuilder.java
@@ -61,7 +61,7 @@ public class MetaNetworkBuilder implements MultiNetworkBuilder{
protected HashMap<BioCompartment,BioCompartment> fuseMap= new HashMap<>();
protected Boolean keepGPR = false;
@Setter
- public Boolean addExchangeReaction = true;
+ protected Boolean addExchangeReaction = true;
/**
* enable a compartment to be shared between multiple organisms
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/PrefixedMetaEntityFactory.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/PrefixedMetaEntityFactory.java
index 2b26d4964..7cb874ebb 100644
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/PrefixedMetaEntityFactory.java
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/PrefixedMetaEntityFactory.java
@@ -4,6 +4,7 @@ import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioCompartment;
import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEntity;
import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioMetabolite;
import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
+import lombok.Setter;
import lombok.SneakyThrows;
import java.lang.reflect.InvocationTargetException;
@@ -14,11 +15,15 @@ import java.util.Map;
import java.util.function.BiFunction;
import java.util.function.Function;
+import static fr.inrae.toulouse.metexplore.met4j_core.utils.StringUtils.isVoid;
+
public class PrefixedMetaEntityFactory implements MetaEntityFactory {
Map<BioNetwork,String> sourcePrefixMap;
- String poolPrefix;
- String sep = "";
+ @Setter
+ protected String poolPrefix;
+ @Setter
+ protected String sep = "_";
public PrefixedMetaEntityFactory(Map<BioNetwork,String> sourcePrefixMap, String poolPrefix){
this.sourcePrefixMap=sourcePrefixMap;
@@ -28,7 +33,7 @@ public class PrefixedMetaEntityFactory implements MetaEntityFactory {
/**
* create prefix-id from network alias
*/
- public BiFunction<String, BioNetwork, String> addSourcePrefix = (id, bn) -> sourcePrefixMap.get(bn)+sep+id;
+ public BiFunction<String, BioNetwork, String> addSourcePrefix = (id, bn) -> isVoid(sourcePrefixMap.get(bn)) ? id : sourcePrefixMap.get(bn)+sep+id;
/**
* create sharedCompartment-suffix id
diff --git a/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/TestMetaNetworkBuilder.java b/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/TestMetaNetworkBuilder.java
index 75a02f9fb..31d2bbd88 100644
--- a/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/TestMetaNetworkBuilder.java
+++ b/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/TestMetaNetworkBuilder.java
@@ -1,10 +1,16 @@
package fr.inrae.toulouse.metexplore.met4j_core.biodata.multinetwork;
-import fr.inrae.toulouse.metexplore.met4j_core.biodata.*;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioCompartment;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioMetabolite;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioReaction;
import org.junit.BeforeClass;
import org.junit.Test;
+import java.util.Arrays;
import java.util.HashMap;
+import java.util.Set;
+import java.util.stream.Collectors;
import static org.junit.Assert.*;
@@ -27,7 +33,10 @@ public class TestMetaNetworkBuilder {
medium2=new BioCompartment("medium2");
CommunityNetworkBuilder builder = new CommunityNetworkBuilder(medium);
builder.addNewSharedCompartment(medium2);
- builder.setEntityFactory(new PrefixedMetaEntityFactory(alias,"pool"));
+ PrefixedMetaEntityFactory factory = new PrefixedMetaEntityFactory(alias,"pool");
+ factory.setSep("_");
+ builder.setEntityFactory(factory);
+ builder.setAddExchangeReaction(false);
builder.add(bn1);
builder.add(bn2);
builder.add(bn3);
@@ -50,7 +59,10 @@ public class TestMetaNetworkBuilder {
medium2=new BioCompartment("medium2");
CommunityNetworkBuilder builder = new CommunityNetworkBuilder(medium);
builder.addNewSharedCompartment(medium2);
- builder.setEntityFactory(new PrefixedMetaEntityFactory(alias,"pool"));
+ PrefixedMetaEntityFactory factory = new PrefixedMetaEntityFactory(alias,"pool");
+ factory.setSep("_");
+ builder.setEntityFactory(factory);
+ builder.setAddExchangeReaction(false);
builder.add(bn1,co1ex);
builder.add(bn2,co2ex);
builder.add(bn3,co3ex);
@@ -59,6 +71,65 @@ public class TestMetaNetworkBuilder {
return builder.build();
}
+ public static BioNetwork initFuseIncremental() {
+ HashMap<BioNetwork,String> alias = new HashMap<>();
+ alias.put(bn1,"model1");
+ alias.put(bn2,"model2");
+
+ BioCompartment medium0=new BioCompartment("medium");
+ CommunityNetworkBuilder builder = new CommunityNetworkBuilder(medium0);
+ PrefixedMetaEntityFactory factory = new PrefixedMetaEntityFactory(alias,"pool");
+ factory.setSep("_");
+ builder.setEntityFactory(factory);
+ builder.setAddExchangeReaction(false);
+ builder.add(bn1,co1ex);
+ builder.add(bn2,co2ex);
+ BioNetwork firstIter = builder.build();
+
+ System.out.println(Arrays.toString(bn1.getMetabolitesView().stream().map(x -> x.getId()).toArray()));
+ System.out.println(Arrays.toString(bn1.getReactionsView().stream().map(x -> x.getId()).toArray()));
+ System.out.println("+");
+ System.out.println(Arrays.toString(bn2.getMetabolitesView().stream().map(x -> x.getId()).toArray()));
+ System.out.println(Arrays.toString(bn2.getReactionsView().stream().map(x -> x.getId()).toArray()));
+ System.out.println("=");
+ System.out.println(Arrays.toString(firstIter.getMetabolitesView().stream().map(x -> x.getId()).toArray()));
+ System.out.println(Arrays.toString(firstIter.getReactionsView().stream().map(x -> x.getId()).toArray()));
+
+ BioMetabolite[] pool1 = firstIter.getCompartment("medium")
+ .getComponentsView().stream()
+ .filter(e -> e instanceof BioMetabolite)
+ .filter(m -> m.getId().startsWith("pool_"))
+ .toArray(BioMetabolite[]::new);
+ for(BioMetabolite pool : pool1){
+ firstIter.removeOnCascade(firstIter.getReactionsFromMetabolite(pool));
+ }
+ firstIter.removeOnCascade(pool1);
+
+ System.out.println("->");
+ System.out.println(Arrays.toString(firstIter.getMetabolitesView().stream().map(x -> x.getId()).toArray()));
+ System.out.println(Arrays.toString(firstIter.getReactionsView().stream().map(x -> x.getId()).toArray()));
+
+ medium=new BioCompartment("medium");
+ medium2=new BioCompartment("medium2");
+ builder = new CommunityNetworkBuilder(medium);
+ builder.addNewSharedCompartment(medium2);
+ alias = new HashMap<>();
+ alias.put(firstIter,"");
+ alias.put(bn3,"model3");
+ alias.put(bn4,"model4");
+ builder.setEntityFactory(new PrefixedMetaEntityFactory(alias,"pool"));
+ builder.setAddExchangeReaction(false);
+ builder.add(firstIter,medium0);
+ builder.add(bn3,co3ex);
+ builder.add(bn4);
+ builder.fuseCompartmentIntoSharedCompartment(bn4,co4ex,medium2);
+
+ BioNetwork output = builder.build();
+ System.out.println(Arrays.toString(output.getMetabolitesView().stream().map(x -> x.getId()).toArray()));
+ System.out.println(Arrays.toString(output.getReactionsView().stream().map(x -> x.getId()).toArray()));
+ return output;
+ }
+
@BeforeClass
public static void beforeClass() {
bn1 = new BioNetwork("bn1");
@@ -147,6 +218,37 @@ public class TestMetaNetworkBuilder {
assertEquals(6,meta.getCompartmentsView().size());
}
+ @Test
+ public void testCompoundsFuseIncremental(){
+ BioNetwork meta = initFuseIncremental();
+ assertEquals(14,meta.getMetabolitesView().size());
+ assertNotNull(meta.getMetabolite("model1_a_in"));
+ assertNotNull(meta.getMetabolite("model1_c_in"));
+ assertNotNull(meta.getMetabolite("model1_c_ex"));
+ assertNotNull(meta.getMetabolite("model2_c_ex"));
+ assertNotNull(meta.getMetabolite("model2_c_in"));
+
+ Set<String> metabolites = meta.getMetabolitesView().stream().map(x -> x.getId()).collect(Collectors.toSet());
+ assertTrue(metabolites.contains("pool_medium_model1_c_ex")||metabolites.contains("pool_medium_model2_c_ex"));
+ assertNotNull(meta.getMetabolite("pool_medium_d_ex"));
+ assertNotNull(meta.getMetabolite("pool_medium2_d_ex"));
+ }
+
+ @Test
+ public void testReactionsFuseIncremental() {
+ BioNetwork meta = initFuseIncremental();
+ assertEquals(10, meta.getReactionsView().size());
+ assertNotNull(meta.getReaction("poolReaction_model2_c_ex"));
+ assertNotNull(meta.getReaction("poolReaction_model1_c_ex"));
+ assertNotNull(meta.getReaction("poolReaction_model3_d_ex"));
+ }
+
+ @Test
+ public void testCompartmentFuseIncremental(){
+ BioNetwork meta = initFuseIncremental();
+ assertEquals(6,meta.getCompartmentsView().size());
+ }
+
@Test
public void testCompoundsBump(){
--
GitLab
From c6c40d9f56b3bd464de80c207b405ad86d89e3c6 Mon Sep 17 00:00:00 2001
From: cfrainay <clement.frainay@inrae.fr>
Date: Thu, 10 Oct 2024 15:57:55 +0200
Subject: [PATCH 08/17] fix sbml annotation handling and export issue
---
.../reconstruction/CreateMetaNetwork.java | 16 ++++++++++------
1 file changed, 10 insertions(+), 6 deletions(-)
diff --git a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/reconstruction/CreateMetaNetwork.java b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/reconstruction/CreateMetaNetwork.java
index 50204fe75..925b914a0 100644
--- a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/reconstruction/CreateMetaNetwork.java
+++ b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/reconstruction/CreateMetaNetwork.java
@@ -3,8 +3,11 @@ package fr.inrae.toulouse.metexplore.met4j_toolbox.reconstruction;
import fr.inrae.toulouse.metexplore.met4j_core.biodata.*;
import fr.inrae.toulouse.metexplore.met4j_core.biodata.multinetwork.CommunityNetworkBuilder;
import fr.inrae.toulouse.metexplore.met4j_core.biodata.multinetwork.PrefixedMetaEntityFactory;
+import fr.inrae.toulouse.metexplore.met4j_io.annotations.network.NetworkAttributes;
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.jsbml.reader.plugin.*;
+import fr.inrae.toulouse.metexplore.met4j_io.jsbml.units.BioUnitDefinition;
import fr.inrae.toulouse.metexplore.met4j_io.jsbml.writer.JsbmlWriter;
import fr.inrae.toulouse.metexplore.met4j_io.jsbml.writer.Met4jSbmlWriterException;
import fr.inrae.toulouse.metexplore.met4j_toolbox.generic.AbstractMet4jApplication;
@@ -14,10 +17,7 @@ import fr.inrae.toulouse.metexplore.met4j_toolbox.generic.annotations.Format;
import fr.inrae.toulouse.metexplore.met4j_toolbox.generic.annotations.ParameterType;
import org.kohsuke.args4j.Option;
-import java.util.HashMap;
-import java.util.NoSuchElementException;
-import java.util.Objects;
-import java.util.UUID;
+import java.util.*;
import java.util.function.Function;
import static fr.inrae.toulouse.metexplore.met4j_toolbox.generic.annotations.EnumFormats.Sbml;
@@ -76,9 +76,12 @@ public class CreateMetaNetwork extends AbstractMet4jApplication {
//import networks
System.out.print("Importing network 1...");
JsbmlReader reader = new JsbmlReader(this.sbml1FilePath);
+ ArrayList<PackageParser> pkgs = new ArrayList<>(Arrays.asList(
+ new NotesParser(false), new AnnotationParser(true), new FBCParser(), new GroupPathwayParser()));
+
BioNetwork network1 = null;
try {
- network1 = reader.read();
+ network1 = reader.read(pkgs);
} catch (Met4jSbmlReaderException e) {
System.err.println("Error while reading the first SBML file");
System.err.println(e.getMessage());
@@ -108,7 +111,7 @@ public class CreateMetaNetwork extends AbstractMet4jApplication {
reader = new JsbmlReader(this.sbml2FilePath);
BioNetwork network2 = null;
try {
- network2 = reader.read();
+ network2 = reader.read(pkgs);
} catch (Met4jSbmlReaderException e) {
System.err.println("Error while reading the second SBML file");
System.err.println(e.getMessage());
@@ -147,6 +150,7 @@ public class CreateMetaNetwork extends AbstractMet4jApplication {
//export the meta-network
System.out.print("Exporting MetaNetwork...");
+ NetworkAttributes.addUnitDefinition(metaNetwork, new BioUnitDefinition());
new JsbmlWriter(outputPath,metaNetwork).write();
System.out.println(" Done.");
--
GitLab
From 280df1461eb5173e0d7cbbc97a82692ff2e6fdef Mon Sep 17 00:00:00 2001
From: Clement Frainay <clement.frainay@inra.fr>
Date: Tue, 29 Oct 2024 17:00:05 +0100
Subject: [PATCH 09/17] fix typo
---
.../met4j_core/biodata/multinetwork/MetaNetworkBuilder.java | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaNetworkBuilder.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaNetworkBuilder.java
index 9c214f4b0..da8edbbc2 100644
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaNetworkBuilder.java
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaNetworkBuilder.java
@@ -11,7 +11,7 @@ import java.util.function.Function;
import java.util.stream.Collectors;
/**
- * A class that creates a meta-networks from multiple sub-networks. A meta-network is a single model which contains several
+ * A class that creates a meta-network from multiple sub-networks. A meta-network is a single model which contains several
* sub-networks that remains individualized within the meta-network (as opposed to models fusion), but which can share
* some of their components with other sub-networks through shared compartments.
*/
--
GitLab
From 79a9ec4f7dd974c50420c87e7736c5653c4703a2 Mon Sep 17 00:00:00 2001
From: Clement Frainay <clement.frainay@inra.fr>
Date: Tue, 29 Oct 2024 17:00:21 +0100
Subject: [PATCH 10/17] fix typo
---
.../met4j_core/biodata/multinetwork/MetaNetworkBuilder.java | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaNetworkBuilder.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaNetworkBuilder.java
index da8edbbc2..571630093 100644
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaNetworkBuilder.java
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaNetworkBuilder.java
@@ -12,7 +12,7 @@ import java.util.stream.Collectors;
/**
* A class that creates a meta-network from multiple sub-networks. A meta-network is a single model which contains several
- * sub-networks that remains individualized within the meta-network (as opposed to models fusion), but which can share
+ * sub-networks that remain individualized within the meta-network (as opposed to models fusion), but which can share
* some of their components with other sub-networks through shared compartments.
*/
public class MetaNetworkBuilder implements MultiNetworkBuilder{
--
GitLab
From 1efe74591ae056f88aa740a0c4e7ff8e23140b38 Mon Sep 17 00:00:00 2001
From: Clement Frainay <clement.frainay@inra.fr>
Date: Tue, 29 Oct 2024 17:00:31 +0100
Subject: [PATCH 11/17] fix typo
---
.../met4j_core/biodata/multinetwork/MetaNetworkBuilder.java | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaNetworkBuilder.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaNetworkBuilder.java
index 571630093..9ddd7f131 100644
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaNetworkBuilder.java
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaNetworkBuilder.java
@@ -73,7 +73,7 @@ public class MetaNetworkBuilder implements MultiNetworkBuilder{
/**
* Fuse a sub-network's compartment into a meta-network's shared compartment. The former will be replaced by the latter during build.
- * All compartment's component will be added to the shared compartment
+ * All compartment's components will be added to the shared compartment
* @param n
* @param c
* @param sc
--
GitLab
From c9312b649fb0f17f44d3d5884f41c120e6584d56 Mon Sep 17 00:00:00 2001
From: Clement Frainay <clement.frainay@inra.fr>
Date: Tue, 29 Oct 2024 17:02:09 +0100
Subject: [PATCH 12/17] fix description method
---
.../met4j_toolbox/reconstruction/CreateMetaNetwork.java | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/reconstruction/CreateMetaNetwork.java b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/reconstruction/CreateMetaNetwork.java
index 925b914a0..d41bf6285 100644
--- a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/reconstruction/CreateMetaNetwork.java
+++ b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/reconstruction/CreateMetaNetwork.java
@@ -190,7 +190,7 @@ public class CreateMetaNetwork extends AbstractMet4jApplication {
public String getLabel() {return this.getClass().getSimpleName();}
@Override
- public String getLongDescription() {
+ public String getShortDescription() {
return "Create a Meta-Network from two sub-networks in SBML format.";
}
--
GitLab
From 87303bd748126410d6491e4a810e6ee48ca80aee Mon Sep 17 00:00:00 2001
From: cfrainay <clement.frainay@inrae.fr>
Date: Tue, 29 Oct 2024 17:02:59 +0100
Subject: [PATCH 13/17] fix description method
---
.../met4j_toolbox/reconstruction/CreateMetaNetwork.java | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/reconstruction/CreateMetaNetwork.java b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/reconstruction/CreateMetaNetwork.java
index d41bf6285..574000ec2 100644
--- a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/reconstruction/CreateMetaNetwork.java
+++ b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/reconstruction/CreateMetaNetwork.java
@@ -195,7 +195,7 @@ public class CreateMetaNetwork extends AbstractMet4jApplication {
}
@Override
- public String getShortDescription() {
+ public String getLongDescription() {
return "Create a Meta-Network from two sub-networks in SBML format. A meta-network is a single model which contains several sub-networks that remains individualized within" +
"the meta-network (as opposed to models fusion), but which can share some of their components with " +
"other sub-networks through a shared \"medium\" compartment.";
--
GitLab
From aecf043504a613000b649d41262a309419e9f9c2 Mon Sep 17 00:00:00 2001
From: cfrainay <clement.frainay@inrae.fr>
Date: Tue, 29 Oct 2024 17:17:36 +0100
Subject: [PATCH 14/17] fix javadoc
---
.../multinetwork/MetaNetworkBuilder.java | 28 ++++++++++++-------
1 file changed, 18 insertions(+), 10 deletions(-)
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaNetworkBuilder.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaNetworkBuilder.java
index 9ddd7f131..36cd946d2 100644
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaNetworkBuilder.java
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaNetworkBuilder.java
@@ -65,7 +65,7 @@ public class MetaNetworkBuilder implements MultiNetworkBuilder{
/**
* enable a compartment to be shared between multiple organisms
- * @param sc
+ * @param sc a compartment that will be shared between multiple bionetworks
*/
public void addNewSharedCompartment(BioCompartment sc) {
metaCompComposition.put(sc,new HashSet<>());
@@ -74,9 +74,9 @@ public class MetaNetworkBuilder implements MultiNetworkBuilder{
/**
* Fuse a sub-network's compartment into a meta-network's shared compartment. The former will be replaced by the latter during build.
* All compartment's components will be added to the shared compartment
- * @param n
- * @param c
- * @param sc
+ * @param n the sub-network
+ * @param c the sub-network's compartment to be fused
+ * @param sc the shared meta-compartment that will receive the compartment's components
*/
public void fuseCompartmentIntoSharedCompartment(BioNetwork n, BioCompartment c, BioCompartment sc) {
if(!metaCompComposition.containsKey(sc)) throw new IllegalArgumentException("Shared meta-compartment "+sc.getId()+" not found in network");
@@ -86,9 +86,9 @@ public class MetaNetworkBuilder implements MultiNetworkBuilder{
/**
* Bump a sub-network's compartment into a meta-network's shared compartment. For each compartment's component,
* a copy is created within the shared compartment
- * @param n
- * @param c
- * @param sc
+ * @param n the sub-network
+ * @param c the sub-network's compartment to be bumped
+ * @param sc the shared meta-compartment that will receive the compartment's components
*/
public void bumpCompartmentIntoSharedCompartment(BioNetwork n, BioCompartment c, BioCompartment sc) {
BioCollection<BioMetabolite> toShare = n.getMetabolitesView().stream()
@@ -98,7 +98,7 @@ public class MetaNetworkBuilder implements MultiNetworkBuilder{
}
/**
- *
+ * Exchange a compound from a sub-network's compartment to a meta-network's shared compartment. A copy of the compound will be created
* @param sourceNetwork the original subnetwork of the compound
* @param sourceCompartment the original compartment of the compound in the subnetwork
* @param metabolite the compound
@@ -110,7 +110,7 @@ public class MetaNetworkBuilder implements MultiNetworkBuilder{
}
/**
- *
+ * Exchange compounds from a sub-network's compartment to a meta-network's shared compartment. A copy of each exchanged compound will be created
* @param sourceNetwork the original subnetwork of the compounds
* @param sourceCompartment the original compartment of the compounds in the subnetwork
* @param metabolites the compounds
@@ -254,6 +254,14 @@ public class MetaNetworkBuilder implements MultiNetworkBuilder{
}
}
+ /**
+ * Set the alias prefixes for the entities of the sub-networks. This allows to distinguish entities from different sub-networks
+ * that have the same name. The prefixes are added to the entity names in the meta-network.
+ * @param aliases a map of sub-networks and their respective prefixes
+ * (e.g. {subNetwork1: "prefix1", subNetwork2: "prefix2"})
+ * The prefixes are added to the entity names in the meta-network.
+ * If a sub-network is not in the map, or is in the map but has a null or empty prefix, its entities will not be prefixed.
+ **/
public void setAliasPrefixes(Map<BioNetwork,String> aliases, String poolPrefix){
this.setEntityFactory(new PrefixedMetaEntityFactory(aliases, poolPrefix));
}
@@ -296,7 +304,7 @@ public class MetaNetworkBuilder implements MultiNetworkBuilder{
/**
* Links the source-specific metabolites representing the same compounds in the shared compartments, by creating a shared "pool" entity
* alongside their interconversion reactions.
- * @param meta
+ * @param meta the meta-network
*/
protected void linkCompoundsInSharedComp(BioNetwork meta) {
//loop over each shared compartment
--
GitLab
From e0af67341446ae825c49b94158ab785b3a7ec2b9 Mon Sep 17 00:00:00 2001
From: cfrainay <clement.frainay@inrae.fr>
Date: Fri, 8 Nov 2024 17:17:57 +0100
Subject: [PATCH 15/17] add doc
---
.../multinetwork/MetaEntityFactory.java | 24 +++++++++++++++++++
.../PrefixedMetaEntityFactory.java | 16 +++++++++----
2 files changed, 36 insertions(+), 4 deletions(-)
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaEntityFactory.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaEntityFactory.java
index c7254a7cf..9b709b4ab 100644
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaEntityFactory.java
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaEntityFactory.java
@@ -7,10 +7,34 @@ import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
import java.util.Collection;
+/**
+* Factory to create new instances of BioEntity and avoid id conflicts between subnetworks in a meta-graph.
+**/
public interface MetaEntityFactory {
+ /**
+ * Create a copy of a subnetwork's BioEntity for its MetaGraph, while guaranteeing no id conflicts if the same
+ * original id was used in another subnetworks. This may be done by referencing in the new id the source network
+ * passed as parameter.
+ * @param originalEntity the original entity
+ * @param source the source network
+ **/
<E extends BioEntity> E createMetaEntity(E originalEntity, BioNetwork source);
+
+ /**
+ * Create a copy of a subnetwork's BioMetabolite in a shared compartment.
+ * @param originalEntity the original entity
+ * @param sharedComp the target shared compartment
+ * @return
+ */
BioMetabolite createSharedCompound(BioMetabolite originalEntity, BioCompartment sharedComp);
+
+ /**
+ * Create a new BioMetabolite in a shared compartment, that represent a pool of compounds from different subnetworks.
+ * @param entities the matching entities in different subnetworks
+ * @param sharedComp the target shared compartment
+ * @return
+ */
BioMetabolite createPoolCompound (Collection<BioMetabolite> entities, BioCompartment sharedComp);
}
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/PrefixedMetaEntityFactory.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/PrefixedMetaEntityFactory.java
index 7cb874ebb..29437aa06 100644
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/PrefixedMetaEntityFactory.java
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/PrefixedMetaEntityFactory.java
@@ -17,6 +17,10 @@ import java.util.function.Function;
import static fr.inrae.toulouse.metexplore.met4j_core.utils.StringUtils.isVoid;
+/**
+ * Factory to create new instances of BioEntity using prefixed ids from user-defined alias, in order to avoid id conflicts between subnetworks
+ * in a meta-graph.
+ **/
public class PrefixedMetaEntityFactory implements MetaEntityFactory {
Map<BioNetwork,String> sourcePrefixMap;
@@ -31,7 +35,8 @@ public class PrefixedMetaEntityFactory implements MetaEntityFactory {
}
/**
- * create prefix-id from network alias
+ * create prefixed id. This function will be called to create a new id for a BioEntity, using the
+ * alias of the network it comes from (if it exists) and its original id.
*/
public BiFunction<String, BioNetwork, String> addSourcePrefix = (id, bn) -> isVoid(sourcePrefixMap.get(bn)) ? id : sourcePrefixMap.get(bn)+sep+id;
@@ -39,7 +44,10 @@ public class PrefixedMetaEntityFactory implements MetaEntityFactory {
* create sharedCompartment-suffix id
*/
public BiFunction<String, BioCompartment, String> addCompSuffix = (id, comp) -> id+sep+comp.getId();
- public BiFunction<String, BioCompartment, String> addCompPreffix = (id, comp) -> comp.getId()+sep+id;
+ /**
+ * create sharedCompartment-prefix id
+ */
+ public BiFunction<String, BioCompartment, String> addCompPrefix = (id, comp) -> comp.getId()+sep+id;
/**
@@ -53,7 +61,7 @@ public class PrefixedMetaEntityFactory implements MetaEntityFactory {
};
/**
- * create pool-prefix id
+ * create a pool-prefix id. This is used to identify a pool of compounds originating from different subnetworks.
*/
public Function<String, String> addPoolFlag = (id) -> poolPrefix+sep+id;
@@ -75,7 +83,7 @@ public class PrefixedMetaEntityFactory implements MetaEntityFactory {
public BioMetabolite createPoolCompound(Collection<BioMetabolite> entities, BioCompartment sharedCompartment) {
BioMetabolite entity = entities.iterator().next();
return newEntityInstance(entity, removeSourceSuffix
- .andThen(s -> addCompPreffix.apply(s,sharedCompartment))
+ .andThen(s -> addCompPrefix.apply(s,sharedCompartment))
.andThen(addPoolFlag)
.apply(entity.getId()));
}
--
GitLab
From 503bea1a2861ab083dc8dad64cf4949398b22f31 Mon Sep 17 00:00:00 2001
From: Clement Frainay <clement.frainay@inra.fr>
Date: Tue, 3 Dec 2024 14:08:54 +0100
Subject: [PATCH 16/17] add javadoc
---
.../biodata/multinetwork/MetaNetworkBuilder.java | 9 +++++++++
1 file changed, 9 insertions(+)
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaNetworkBuilder.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaNetworkBuilder.java
index 36cd946d2..6180d7b80 100644
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaNetworkBuilder.java
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/multinetwork/MetaNetworkBuilder.java
@@ -129,6 +129,11 @@ public class MetaNetworkBuilder implements MultiNetworkBuilder{
networks.add(bn);
}
+ /**
+ * creates all maps for conversion (original bioentity, new meta-entity)
+ * instantiate meta-network as new bionetwork
+ * @return an empty meta-network
+ */
protected BioNetwork initMetaNetwork(){
this.metaboliteConversion = new HashMap<>();
this.compartmentConversion = new HashMap<>();
@@ -139,6 +144,10 @@ public class MetaNetworkBuilder implements MultiNetworkBuilder{
return new BioNetwork();
}
+ /**
+ * add all copied bioentity to the newly built meta-network
+ * @param meta the (usually empty) meta-network
+ */
protected void populateMetaNetwork(BioNetwork meta){
for(BioNetwork sub : networks){
--
GitLab
From 6433a6d76363c9e5489c43365630511155f2e831 Mon Sep 17 00:00:00 2001
From: lcottret <ludovic.cottret@inrae.fr>
Date: Fri, 27 Dec 2024 16:36:01 +0100
Subject: [PATCH 17/17] add missing decorator InputFile
---
.../toulouse/metexplore/met4j_toolbox/GenerateGalaxyFiles.java | 1 -
.../met4j_toolbox/reconstruction/CreateMetaNetwork.java | 1 +
2 files changed, 1 insertion(+), 1 deletion(-)
diff --git a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/GenerateGalaxyFiles.java b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/GenerateGalaxyFiles.java
index ecd9317c2..1d26274c5 100644
--- a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/GenerateGalaxyFiles.java
+++ b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/GenerateGalaxyFiles.java
@@ -57,7 +57,6 @@ import java.lang.reflect.Method;
import java.net.URL;
import java.util.Comparator;
import java.util.List;
-import java.util.Set;
import java.util.stream.Collectors;
public class GenerateGalaxyFiles extends AbstractMet4jApplication {
diff --git a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/reconstruction/CreateMetaNetwork.java b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/reconstruction/CreateMetaNetwork.java
index 574000ec2..a0ef3029a 100644
--- a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/reconstruction/CreateMetaNetwork.java
+++ b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/reconstruction/CreateMetaNetwork.java
@@ -31,6 +31,7 @@ public class CreateMetaNetwork extends AbstractMet4jApplication {
@ParameterType(name = InputFile)
@Option(name = "-n1", aliases = {"--network1"}, usage = "input SBML file: path to first network, in sbml format.", required = true)
public String sbml1FilePath;
+ @ParameterType(name = InputFile)
@Option(name = "-n2", aliases = {"--network2"}, usage = "input SBML file: path to second network, in sbml format.", required = true)
public String sbml2FilePath;
--
GitLab