From 7ec9cde5c06bbed09bde5ed8da7fe4ab4378ef48 Mon Sep 17 00:00:00 2001
From: lcottret <ludovic.cottret@inrae.fr>
Date: Tue, 15 Nov 2022 07:35:02 +0100
Subject: [PATCH 01/21] create new class to handle entity type exception
---
.../attributes/EntityTypeException.java | 43 +++++++++++++++++++
1 file changed, 43 insertions(+)
create mode 100644 met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/EntityTypeException.java
diff --git a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/EntityTypeException.java b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/EntityTypeException.java
new file mode 100644
index 000000000..47f9544df
--- /dev/null
+++ b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/EntityTypeException.java
@@ -0,0 +1,43 @@
+/*
+ * Copyright INRAE (2022)
+ *
+ * contact-metexplore@inrae.fr
+ *
+ * This software is a computer program whose purpose is to [describe
+ * functionalities and technical features of your software].
+ *
+ * This software is governed by the CeCILL license under French law and
+ * abiding by the rules of distribution of free software. You can use,
+ * modify and/ or redistribute the software under the terms of the CeCILL
+ * license as circulated by CEA, CNRS and INRIA at the following URL
+ * "https://cecill.info/licences/Licence_CeCILL_V2.1-en.html".
+ *
+ * As a counterpart to the access to the source code and rights to copy,
+ * modify and redistribute granted by the license, users are provided only
+ * with a limited warranty and the software's author, the holder of the
+ * economic rights, and the successive licensors have only limited
+ * liability.
+ *
+ * In this respect, the user's attention is drawn to the risks associated
+ * with loading, using, modifying and/or developing or reproducing the
+ * software by the user in light of its specific status of free software,
+ * that may mean that it is complicated to manipulate, and that also
+ * therefore means that it is reserved for developers and experienced
+ * professionals having in-depth computer knowledge. Users are therefore
+ * encouraged to load and test the software's suitability as regards their
+ * requirements in conditions enabling the security of their systems and/or
+ * data to be ensured and, more generally, to use and operate it in the
+ * same conditions as regards security.
+ *
+ * The fact that you are presently reading this means that you have had
+ * knowledge of the CeCILL license and that you accept its terms.
+ *
+ */
+package fr.inrae.toulouse.metexplore.met4j_io.tabulated.attributes;
+
+public class EntityTypeException extends RuntimeException {
+
+ public EntityTypeException(String errorMessage) {
+ super(errorMessage);
+ }
+}
--
GitLab
From cdf68a1ea1096c6ba811397065781bbeb8ad8113 Mon Sep 17 00:00:00 2001
From: lcottret <ludovic.cottret@inrae.fr>
Date: Tue, 15 Nov 2022 07:37:02 +0100
Subject: [PATCH 02/21] add new entity type : Compartment
---
.../metexplore/met4j_io/tabulated/attributes/EntityType.java | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/EntityType.java b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/EntityType.java
index 8b2ee8d96..ea6f95d1a 100644
--- a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/EntityType.java
+++ b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/EntityType.java
@@ -36,5 +36,5 @@
package fr.inrae.toulouse.metexplore.met4j_io.tabulated.attributes;
public enum EntityType {
- REACTION, METABOLITE, GENE, PROTEIN, PATHWAY
+ REACTION, METABOLITE, GENE, PROTEIN, PATHWAY, COMPARTMENT
}
--
GitLab
From 5a6d8506ce6e74d9d938c62e02d8f7dd1fd5d397 Mon Sep 17 00:00:00 2001
From: lcottret <ludovic.cottret@inrae.fr>
Date: Tue, 15 Nov 2022 07:37:33 +0100
Subject: [PATCH 03/21] add entity Compartment and EntityTypeException
---
.../AbstractSetAttributesFromFile.java | 54 +++++++++++--------
1 file changed, 32 insertions(+), 22 deletions(-)
diff --git a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/AbstractSetAttributesFromFile.java b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/AbstractSetAttributesFromFile.java
index b390b6192..a91f0307a 100644
--- a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/AbstractSetAttributesFromFile.java
+++ b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/AbstractSetAttributesFromFile.java
@@ -80,13 +80,13 @@ public abstract class AbstractSetAttributesFromFile {
*
* @param colId a int.
* @param colAttr : number of the attribute column
- * @param bn : BioNetwork
+ * @param bn : {@link BioNetwork}
* @param fileIn : tabulated file containing the ids and the attributes
* @param c : comment character
- * @param nSkip a int.
+ * @param nSkip a int. Number of lines to skip
* @param entityType a {@link EntityType}
- * @param p a {@link Boolean} object.
- * @param s a {@link Boolean} object.
+ * @param p a {@link Boolean} object : To match the objects in the sbml file, adds the prefix R_ to reactions and M_ to metabolites
+ * @param s a {@link Boolean} object : To match the objects in the sbml file, adds the suffix _comparmentID to metabolite
*/
public AbstractSetAttributesFromFile(int colId, int colAttr, BioNetwork bn, String fileIn, String c, int nSkip, EntityType entityType,
Boolean p, Boolean s) {
@@ -104,24 +104,34 @@ public abstract class AbstractSetAttributesFromFile {
this.entityType = entityType;
- if (this.entityType.equals(EntityType.REACTION)) {
- this.objectIds = bn.getReactionsView().getIds();
- }
-
- if (this.entityType.equals(EntityType.METABOLITE)) {
- this.objectIds = bn.getMetabolitesView().getIds();
- }
-
- if (this.entityType.equals(EntityType.PROTEIN)) {
- this.objectIds = bn.getProteinsView().getIds();
- }
-
- if (this.entityType.equals(EntityType.GENE)) {
- this.objectIds = bn.getGenesView().getIds();
- }
-
- if (this.entityType.equals(EntityType.PATHWAY)) {
- this.objectIds = bn.getPathwaysView().getIds();
+ switch (entityType) {
+ case REACTION: {
+ this.objectIds = bn.getReactionsView().getIds();
+ break;
+ }
+ case METABOLITE: {
+ this.objectIds = bn.getMetabolitesView().getIds();
+ break;
+ }
+ case PROTEIN: {
+ this.objectIds = bn.getProteinsView().getIds();
+ break;
+ }
+ case GENE: {
+ this.objectIds = bn.getGenesView().getIds();
+ break;
+ }
+ case COMPARTMENT: {
+ this.objectIds = bn.getCompartmentsView().getIds();
+ break;
+ }
+ case PATHWAY: {
+ this.objectIds = bn.getPathwaysView().getIds();
+ break;
+ }
+ default: {
+ throw new EntityTypeException("Entity "+entityType+" not recognized");
+ }
}
if (this.colId < 0) {
--
GitLab
From 086ae53adfea9583aa1585b9ec6bf5bfbe6d475c Mon Sep 17 00:00:00 2001
From: lcottret <ludovic.cottret@inrae.fr>
Date: Tue, 15 Nov 2022 07:39:13 +0100
Subject: [PATCH 04/21] add constructor by copy with new id
---
.../met4j_core/biodata/BioCompartment.java | 13 +++++++++++++
1 file changed, 13 insertions(+)
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioCompartment.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioCompartment.java
index 555573328..dd83ee581 100644
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioCompartment.java
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioCompartment.java
@@ -82,6 +82,19 @@ public class BioCompartment extends BioPhysicalEntity {
components = new BioCollection<>();
}
+ /**
+ * Copy of a compartment with a new id
+ * Do not copy the list of components
+ *
+ * @param compartment the original compartment
+ * @param id the new id
+ */
+ public BioCompartment(BioCompartment compartment, String id) {
+ super(compartment, id);
+
+ components = new BioCollection<>();
+ }
+
/**
* <p>getComponentsView.</p>
*
--
GitLab
From 35bca210fa8ab2e59daeb359c068750c0bea06ac Mon Sep 17 00:00:00 2001
From: lcottret <ludovic.cottret@inrae.fr>
Date: Tue, 15 Nov 2022 07:39:26 +0100
Subject: [PATCH 05/21] add constructor by copy with new id
---
.../met4j_core/biodata/BioEntity.java | 18 ++++++++++++++++--
1 file changed, 16 insertions(+), 2 deletions(-)
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioEntity.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioEntity.java
index 82248804b..973a7b428 100755
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioEntity.java
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioEntity.java
@@ -109,8 +109,22 @@ public abstract class BioEntity {
* @param e the original bioentity
*/
public BioEntity(@NonNull BioEntity e) {
- this.id = e.getId();
- this.name = e.getName();
+ this(e.getId(), e.getName());
+ this.setSynonyms(new ArrayList<>(e.getSynonyms()));
+ this.setComment(e.getComment());
+ this.setRefs(new HashMap<>(e.getRefs()));
+ this.setAttributes(new HashMap<>(e.getAttributes()));
+ }
+
+ /**
+ * Deep copy with a new id
+ * <p>
+ * The refs and attributes are not deeply copied
+ *
+ * @param e the original bioentity
+ */
+ public BioEntity(@NonNull BioEntity e, String newId) {
+ this(newId, e.getName());
this.setSynonyms(new ArrayList<>(e.getSynonyms()));
this.setComment(e.getComment());
this.setRefs(new HashMap<>(e.getRefs()));
--
GitLab
From 81ecf10652923e719e6ff87dcab32b0d48484f29 Mon Sep 17 00:00:00 2001
From: lcottret <ludovic.cottret@inrae.fr>
Date: Tue, 15 Nov 2022 07:39:38 +0100
Subject: [PATCH 06/21] add constructor by copy with new id
---
.../met4j_core/biodata/BioPhysicalEntity.java | 11 +++++++++++
1 file changed, 11 insertions(+)
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioPhysicalEntity.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioPhysicalEntity.java
index 8ccb703ef..ff1ffc5af 100755
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioPhysicalEntity.java
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioPhysicalEntity.java
@@ -73,4 +73,15 @@ public abstract class BioPhysicalEntity extends BioEntity {
super(p);
}
+ /**
+ * Deep copy with a new Id
+ *
+ * @param p the original {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioPhysicalEntity}
+ * @param id the new id
+ */
+ public BioPhysicalEntity(BioPhysicalEntity p, String id)
+ {
+ super(p, id);
+ }
+
}
--
GitLab
From 0493f773586f7ea80c5b34388fab5b4133f89eb6 Mon Sep 17 00:00:00 2001
From: lcottret <ludovic.cottret@inrae.fr>
Date: Tue, 15 Nov 2022 07:39:50 +0100
Subject: [PATCH 07/21] add constructor by copy with new id
---
.../toulouse/metexplore/met4j_core/biodata/BioGene.java | 9 +++++++++
1 file changed, 9 insertions(+)
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioGene.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioGene.java
index 834bc8558..32dadae13 100755
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioGene.java
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioGene.java
@@ -71,4 +71,13 @@ public class BioGene extends BioEntity {
super(gene);
}
+ /**
+ * Copy of a gene with a new Id
+ *
+ * @param gene the original gene
+ */
+ public BioGene(BioGene gene, String id) {
+ super(gene, id);
+ }
+
}
--
GitLab
From 8b389a7580ab6b12eb59224d916079d898ced5d1 Mon Sep 17 00:00:00 2001
From: lcottret <ludovic.cottret@inrae.fr>
Date: Tue, 15 Nov 2022 07:39:56 +0100
Subject: [PATCH 08/21] add constructor by copy with new id
---
.../metexplore/met4j_core/biodata/BioMetabolite.java | 10 ++++++++++
1 file changed, 10 insertions(+)
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioMetabolite.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioMetabolite.java
index 52ecb43b9..a761696cf 100644
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioMetabolite.java
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioMetabolite.java
@@ -98,4 +98,14 @@ public class BioMetabolite extends BioPhysicalEntity {
this.setChemicalFormula(metabolite.getChemicalFormula());
}
+
+ public BioMetabolite(@NonNull BioMetabolite metabolite, String newId) {
+ super(metabolite, newId);
+
+ this.setInchi(metabolite.getInchi());
+ this.setSmiles(metabolite.getSmiles());
+ this.setCharge(metabolite.getCharge());
+ this.setMolecularWeight(metabolite.getMolecularWeight());
+ this.setChemicalFormula(metabolite.getChemicalFormula());
+ }
}
--
GitLab
From 8a06da91802dfe6780a0147692e79f19c4c3fc71 Mon Sep 17 00:00:00 2001
From: lcottret <ludovic.cottret@inrae.fr>
Date: Tue, 15 Nov 2022 07:40:00 +0100
Subject: [PATCH 09/21] add constructor by copy with new id
---
.../metexplore/met4j_core/biodata/BioPathway.java | 11 +++++++++++
1 file changed, 11 insertions(+)
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioPathway.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioPathway.java
index 3de598b16..ca3f1bea8 100755
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioPathway.java
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioPathway.java
@@ -82,6 +82,17 @@ public class BioPathway extends BioEntity {
reactions = new BioCollection<>();
}
+ /**
+ * Copy pathway attributes but not the reactions
+ * Set new id
+ *
+ * @param pathway the original pathway
+ */
+ public BioPathway(@NonNull BioPathway pathway, String id) {
+ super(pathway, id);
+ reactions = new BioCollection<>();
+ }
+
/**
* Get reactions involved in the pathway
*
--
GitLab
From 4dacc1fbd612b74b466daf719a559fbf6d6947f1 Mon Sep 17 00:00:00 2001
From: lcottret <ludovic.cottret@inrae.fr>
Date: Tue, 15 Nov 2022 07:40:04 +0100
Subject: [PATCH 10/21] add constructor by copy with new id
---
.../met4j_core/biodata/BioReaction.java | 18 +++++++++++++++++-
1 file changed, 17 insertions(+), 1 deletion(-)
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioReaction.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioReaction.java
index 618587de7..80ce4f583 100755
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioReaction.java
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioReaction.java
@@ -106,7 +106,7 @@ public class BioReaction extends BioEntity {
}
/**
- * <p>Constructor for BioReaction.</p>
+ * <p>Copy of a BioReaction (only atomic attributes, not left nor right).</p>
*
* @param reaction a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioReaction} object.
*/
@@ -120,6 +120,22 @@ public class BioReaction extends BioEntity {
this.reversible = reaction.reversible;
}
+ /**
+ * <p>Copy of a BioReaction (only atomic attributes, not left nor right) with new id</p>
+ *
+ * @param reaction a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioReaction} object.
+ */
+ public BioReaction(@NonNull BioReaction reaction, String id) {
+ super(reaction, id);
+ left = new BioCollection<>();
+ right = new BioCollection<>();
+ enzymes = new BioCollection<>();
+ this.spontaneous = reaction.spontaneous;
+ this.ecNumber = reaction.ecNumber;
+ this.reversible = reaction.reversible;
+ }
+
+
/**
* <p>Getter for the field <code>ecNumber</code>.</p>
*
--
GitLab
From 96463bb02eee67ce335590dd3bd9c65fe5c295a4 Mon Sep 17 00:00:00 2001
From: lcottret <ludovic.cottret@inrae.fr>
Date: Tue, 15 Nov 2022 07:40:17 +0100
Subject: [PATCH 11/21] add constructor by copy with new id
---
.../met4j_core/biodata/classesForTests/BioEntityFake.java | 4 ++++
1 file changed, 4 insertions(+)
diff --git a/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/classesForTests/BioEntityFake.java b/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/classesForTests/BioEntityFake.java
index ce64b6073..9a7701991 100644
--- a/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/classesForTests/BioEntityFake.java
+++ b/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/classesForTests/BioEntityFake.java
@@ -49,4 +49,8 @@ public class BioEntityFake extends BioEntity {
super(id);
}
+ public BioEntityFake(BioEntityFake e, String id) {
+ super(e, id);
+ }
+
}
--
GitLab
From 672887d12524e657f41a26ff378b8b3cf7eb4f31 Mon Sep 17 00:00:00 2001
From: lcottret <ludovic.cottret@inrae.fr>
Date: Tue, 15 Nov 2022 07:40:30 +0100
Subject: [PATCH 12/21] add test of copy with new id
---
.../metexplore/met4j_core/biodata/BioEntityTest.java | 10 +++++++++-
1 file changed, 9 insertions(+), 1 deletion(-)
diff --git a/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioEntityTest.java b/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioEntityTest.java
index f681a39c9..6d5db6a07 100644
--- a/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioEntityTest.java
+++ b/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioEntityTest.java
@@ -59,7 +59,7 @@ import org.junit.Test;
public class BioEntityTest {
public static BioRef ref;
- public static BioEntity bioEntityTest;
+ public static BioEntityFake bioEntityTest;
public static void init() {
ref = new BioRef("origin", "dbName", "dbId", 1);
@@ -234,4 +234,12 @@ public class BioEntityTest {
assertEquals("value", bioEntityTest.getAttribute("test"));
}
+
+ @Test
+ public void copyWithNewId() {
+ BioEntityFake newEntity = new BioEntityFake(bioEntityTest, "newId");
+
+ assertEquals("newId", newEntity.getId());
+
+ }
}
--
GitLab
From f4b07d55a46a54965e5bcff509601a62367b6c30 Mon Sep 17 00:00:00 2001
From: lcottret <ludovic.cottret@inrae.fr>
Date: Tue, 15 Nov 2022 07:40:55 +0100
Subject: [PATCH 13/21] add removeFromCompartment method
---
.../metexplore/met4j_core/biodata/BioNetwork.java | 11 +++++++++++
1 file changed, 11 insertions(+)
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioNetwork.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioNetwork.java
index 688ef9c8c..270396600 100755
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioNetwork.java
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioNetwork.java
@@ -1276,6 +1276,17 @@ public class BioNetwork extends BioEntity {
}
}
+ /**
+ * Remove a component from a compartment
+ * @param compartment
+ * @param entities
+ */
+ public void removeFromCompartment(@NonNull BioCompartment compartment, @NonNull BioEntity... entities) {
+ for(BioEntity ent : entities) {
+ compartment.getComponents().remove(ent);
+ }
+ }
+
/**
* Return true if the entity is in the list of metabolites, reactions, genes,
* pathways, proteins, etc...
--
GitLab
From 599c17b089eef6e648ec1135c28fa3d7b4af6c20 Mon Sep 17 00:00:00 2001
From: lcottret <ludovic.cottret@inrae.fr>
Date: Tue, 15 Nov 2022 07:41:13 +0100
Subject: [PATCH 14/21] add test for removeFromCompartment
---
.../met4j_core/biodata/BioNetworkTest.java | 15 +++++++++++++++
1 file changed, 15 insertions(+)
diff --git a/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioNetworkTest.java b/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioNetworkTest.java
index a7769a488..86efe6605 100644
--- a/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioNetworkTest.java
+++ b/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioNetworkTest.java
@@ -2338,4 +2338,19 @@ public class BioNetworkTest {
public void TestContainsBadEntityWithSameId() {
this.network.containsEntityWithSameId(this.network);
}
+
+ @Test
+ public void removeFromCompartment() {
+
+ this.addTestReactionToNetwork();
+
+ this.network.removeFromCompartment(cpt, s1, p1);
+
+ assertEquals(2, this.network.getCompartment("cpt").getComponents().size());
+
+ assertNull(this.network.getCompartment("cpt").getComponents().get("s1"));
+ assertNull(this.network.getCompartment("cpt").getComponents().get("p1"));
+
+ }
+
}
--
GitLab
From 0fe3e88775ff14fe87071aabf4892ac9b93d89d7 Mon Sep 17 00:00:00 2001
From: lcottret <ludovic.cottret@inrae.fr>
Date: Tue, 15 Nov 2022 07:41:48 +0100
Subject: [PATCH 15/21] add compartment entity case
---
.../attributes/SetNamesFromFile.java | 44 +++++++++++++------
1 file changed, 30 insertions(+), 14 deletions(-)
diff --git a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetNamesFromFile.java b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetNamesFromFile.java
index 6cad2f176..e0dde0f5a 100644
--- a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetNamesFromFile.java
+++ b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetNamesFromFile.java
@@ -107,20 +107,36 @@ public class SetNamesFromFile extends AbstractSetAttributesFromFile {
String name = this.getIdAttributeMap().get(id);
- if(this.entityType.equals(EntityType.METABOLITE)) {
- object = this.bn.getMetabolite(id);
- }
- else if(this.entityType.equals(EntityType.GENE)) {
- object = this.bn.getGene(id);
- }
- else if(this.entityType.equals(EntityType.PROTEIN)) {
- object = this.bn.getProtein(id);
- }
- else if(this.entityType.equals(EntityType.PATHWAY)) {
- object = this.bn.getPathway(id);
- }
- else {
- object = this.bn.getReaction(id);
+ switch (this.entityType) {
+ case METABOLITE:
+ {
+ object = this.bn.getMetabolite(id);
+ break;
+ }
+ case GENE: {
+ object = this.bn.getGene(id);
+ break;
+ }
+ case PROTEIN: {
+ object = this.bn.getProtein(id);
+ break;
+ }
+ case PATHWAY: {
+ object = this.bn.getPathway(id);
+ break;
+ }
+ case REACTION: {
+ object = this.bn.getReaction(id);
+ break;
+ }
+ case COMPARTMENT: {
+ object = this.bn.getCompartment(id);
+ break;
+ }
+ default: {
+ throw new EntityTypeException("Entity type "+this.entityType+" is not recognized");
+ }
+
}
object.setName(name);
--
GitLab
From c9d72c1cff63c4aaef0c2d2364c4f2b866155347 Mon Sep 17 00:00:00 2001
From: lcottret <ludovic.cottret@inrae.fr>
Date: Tue, 15 Nov 2022 07:41:57 +0100
Subject: [PATCH 16/21] add compartment entity case
---
.../tabulated/attributes/SetRefsFromFile.java | 42 ++++++++++++-------
1 file changed, 28 insertions(+), 14 deletions(-)
diff --git a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetRefsFromFile.java b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetRefsFromFile.java
index b692e5bf8..6f6bd05bf 100644
--- a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetRefsFromFile.java
+++ b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetRefsFromFile.java
@@ -111,20 +111,34 @@ public class SetRefsFromFile extends AbstractSetAttributesFromFile {
BioEntity object;
n++;
- if(this.entityType.equals(EntityType.METABOLITE)) {
- object = this.bn.getMetabolite(id);
- }
- else if(this.entityType.equals(EntityType.GENE)) {
- object = this.bn.getGene(id);
- }
- else if(this.entityType.equals(EntityType.PROTEIN)) {
- object = this.bn.getProtein(id);
- }
- else if(this.entityType.equals(EntityType.PATHWAY)) {
- object = this.bn.getPathway(id);
- }
- else {
- object = this.bn.getReaction(id);
+ switch (this.entityType) {
+ case METABOLITE: {
+ object = this.bn.getMetabolite(id);
+ break;
+ }
+ case GENE: {
+ object = this.bn.getGene(id);
+ break;
+ }
+ case PROTEIN: {
+ object = this.bn.getProtein(id);
+ break;
+ }
+ case PATHWAY: {
+ object = this.bn.getPathway(id);
+ break;
+ }
+ case REACTION: {
+ object = this.bn.getReaction(id);
+ break;
+ }
+ case COMPARTMENT: {
+ object = this.bn.getCompartment(id);
+ break;
+ }
+ default: {
+ throw new EntityTypeException("Entity type " + this.entityType + " is not recognized");
+ }
}
object.addRef(new BioRef("attributesTable", this.ref, this.getIdAttributeMap().get(id), 1));
--
GitLab
From 74ad5606c9a001d8b5376220b50f72167af1b5c7 Mon Sep 17 00:00:00 2001
From: lcottret <ludovic.cottret@inrae.fr>
Date: Tue, 15 Nov 2022 07:46:42 +0100
Subject: [PATCH 17/21] add test for compartments
---
.../attributes/SetNamesFromFileTest.java | 23 ++++++++++++++++++-
1 file changed, 22 insertions(+), 1 deletion(-)
diff --git a/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetNamesFromFileTest.java b/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetNamesFromFileTest.java
index 2dbb97acb..f5843f828 100644
--- a/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetNamesFromFileTest.java
+++ b/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetNamesFromFileTest.java
@@ -54,6 +54,8 @@ public class SetNamesFromFileTest {
private BioGene gene;
private BioPathway pathway;
+ private BioCompartment compartment;
+
@Before
public void init() {
network = new BioNetwork();
@@ -62,8 +64,9 @@ public class SetNamesFromFileTest {
protein = new BioProtein("p");
gene = new BioGene("g");
pathway = new BioPathway("pathway");
+ compartment = new BioCompartment("cpt");
- network.add(reaction, metabolite, protein, gene, pathway);
+ network.add(reaction, metabolite, protein, gene, pathway, compartment);
}
@@ -166,6 +169,24 @@ public class SetNamesFromFileTest {
}
+ @Test
+ public void setAttributesCompartment() throws IOException {
+
+ SetNamesFromFile setNamesFromFile = Mockito.spy(new SetNamesFromFile(0, 1, network, "", "", 0, false, false, EntityType.COMPARTMENT));
+ Mockito.doReturn(true).when(setNamesFromFile).parseAttributeFile();
+
+ String line = "cpt\tcompartment\n";
+
+ Boolean flag = setNamesFromFile.parseLine(line, 1);
+
+ assertTrue(flag);
+
+ setNamesFromFile.setAttributes();
+
+ assertEquals("compartment", compartment.getName());
+
+ }
+
}
\ No newline at end of file
--
GitLab
From 0d9980f68f004010cbd5e698a5c9f9943672b3f7 Mon Sep 17 00:00:00 2001
From: lcottret <ludovic.cottret@inrae.fr>
Date: Tue, 15 Nov 2022 07:48:32 +0100
Subject: [PATCH 18/21] add test for compartments
---
.../attributes/SetRefsFromFileTest.java | 20 ++++++++++++++++++-
1 file changed, 19 insertions(+), 1 deletion(-)
diff --git a/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetRefsFromFileTest.java b/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetRefsFromFileTest.java
index 179d33846..6ffbbc186 100644
--- a/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetRefsFromFileTest.java
+++ b/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetRefsFromFileTest.java
@@ -54,6 +54,7 @@ public class SetRefsFromFileTest {
private BioProtein protein;
private BioPathway pathway;
private BioGene gene;
+ private BioCompartment compartment;
@Before
public void init() {
@@ -63,8 +64,9 @@ public class SetRefsFromFileTest {
protein = new BioProtein("p");
pathway = new BioPathway("pathway");
gene = new BioGene("g");
+ compartment = new BioCompartment("cpt");
- network.add(reaction, metabolite, protein, pathway, gene);
+ network.add(reaction, metabolite, protein, pathway, gene, compartment);
}
@Test
@@ -156,4 +158,20 @@ public class SetRefsFromFileTest {
assertTrue(pathway.getRefs().get("refTest").contains(refRef));
}
+ @Test
+ public void setAttributesCompartment() throws IOException {
+ SetRefsFromFile setRefsFromFile = Mockito.spy(new SetRefsFromFile(0, 1, network, "", "", 0, false, false, "refTest", EntityType.COMPARTMENT));
+ Mockito.doReturn(true).when(setRefsFromFile).parseAttributeFile();
+
+ String line = "cpt\trefValue";
+ Boolean flag = setRefsFromFile.parseLine(line, 1);
+
+ assertTrue(flag);
+
+ setRefsFromFile.setAttributes();
+ assertTrue(compartment.getRefs().containsKey("refTest"));
+ BioRef refRef = new BioRef("attributeTable", "refTest", "refValue", 1);
+ assertTrue(compartment.getRefs().get("refTest").contains(refRef));
+ }
+
}
\ No newline at end of file
--
GitLab
From 2e5822955b93a6a13ef9012b0fa0828b2db9326c Mon Sep 17 00:00:00 2001
From: lcottret <ludovic.cottret@inrae.fr>
Date: Tue, 15 Nov 2022 09:58:41 +0100
Subject: [PATCH 19/21] met4j-io : add class SetIdsFromFile
---
.../tabulated/attributes/SetIdsFromFile.java | 286 ++++++++++++++++++
.../attributes/SetIdsFromFileTest.java | 260 ++++++++++++++++
2 files changed, 546 insertions(+)
create mode 100644 met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetIdsFromFile.java
create mode 100644 met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetIdsFromFileTest.java
diff --git a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetIdsFromFile.java b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetIdsFromFile.java
new file mode 100644
index 000000000..f32a689cb
--- /dev/null
+++ b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetIdsFromFile.java
@@ -0,0 +1,286 @@
+/*
+ * Copyright INRAE (2022)
+ *
+ * contact-metexplore@inrae.fr
+ *
+ * This software is a computer program whose purpose is to [describe
+ * functionalities and technical features of your software].
+ *
+ * This software is governed by the CeCILL license under French law and
+ * abiding by the rules of distribution of free software. You can use,
+ * modify and/ or redistribute the software under the terms of the CeCILL
+ * license as circulated by CEA, CNRS and INRIA at the following URL
+ * "https://cecill.info/licences/Licence_CeCILL_V2.1-en.html".
+ *
+ * As a counterpart to the access to the source code and rights to copy,
+ * modify and redistribute granted by the license, users are provided only
+ * with a limited warranty and the software's author, the holder of the
+ * economic rights, and the successive licensors have only limited
+ * liability.
+ *
+ * In this respect, the user's attention is drawn to the risks associated
+ * with loading, using, modifying and/or developing or reproducing the
+ * software by the user in light of its specific status of free software,
+ * that may mean that it is complicated to manipulate, and that also
+ * therefore means that it is reserved for developers and experienced
+ * professionals having in-depth computer knowledge. Users are therefore
+ * encouraged to load and test the software's suitability as regards their
+ * requirements in conditions enabling the security of their systems and/or
+ * data to be ensured and, more generally, to use and operate it in the
+ * same conditions as regards security.
+ *
+ * The fact that you are presently reading this means that you have had
+ * knowledge of the CeCILL license and that you accept its terms.
+ *
+ */
+package fr.inrae.toulouse.metexplore.met4j_io.tabulated.attributes;
+
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.*;
+import fr.inrae.toulouse.metexplore.met4j_core.utils.StringUtils;
+
+import java.io.IOException;
+
+public class SetIdsFromFile extends AbstractSetAttributesFromFile {
+
+
+ /**
+ * <p>Constructor for AbstractSetAttributesFromFile.</p>
+ *
+ * @param colId a int.
+ * @param colAttr : number of the attribute column
+ * @param bn : {@link BioNetwork}
+ * @param fileIn : tabulated file containing the ids and the attributes
+ * @param c : comment character
+ * @param nSkip a int. Number of lines to skip
+ * @param entityType a {@link EntityType}
+ * @param p a {@link Boolean} object : To match the objects in the sbml file, adds the prefix R_ to reactions and M_ to metabolites
+ * @param s a {@link Boolean} object : To match the objects in the sbml file, adds the suffix _comparmentID to metabolite
+ */
+ public SetIdsFromFile(int colId, int colAttr, BioNetwork bn, String fileIn, String c, int nSkip, EntityType entityType, Boolean p, Boolean s) {
+ super(colId, colAttr, bn, fileIn, c, nSkip, entityType, p, s);
+ }
+
+ @Override
+ public Boolean testAttribute(String attribute) {
+ return !StringUtils.isVoid(attribute);
+ }
+
+ @Override
+ public Boolean setAttributes() throws IOException {
+ Boolean flag;
+
+ try {
+ flag = this.parseAttributeFile();
+ } catch (IOException e) {
+ return false;
+ }
+
+ if (!flag) {
+ return false;
+ }
+
+ int n = 0;
+
+ for (String id : this.getIdAttributeMap().keySet()) {
+
+ String newId = this.getIdAttributeMap().get(id);
+
+ if (!id.equals(newId)) {
+
+ n++;
+
+ switch (entityType) {
+ case GENE: {
+ this.setGeneId(id, newId);
+ break;
+ }
+ case PATHWAY: {
+ this.setPathwayId(id, newId);
+ break;
+ }
+ case METABOLITE: {
+ this.setMetaboliteId(id, newId);
+ break;
+ }
+ case REACTION: {
+ this.setReactionId(id, newId);
+ break;
+ }
+ case COMPARTMENT: {
+ this.setCompartmentId(id, newId);
+ break;
+ }
+ default: {
+ throw new EntityTypeException("Entity type "+this.entityType+" not recognized");
+ }
+ }
+ }
+ }
+
+ System.err.println(n + " entities processed");
+
+ return flag;
+ }
+
+ /**
+ * Replace a compartment with the same compartment with another id
+ *
+ * @param id : the original id
+ * @param newId : the new id
+ */
+ private void setCompartmentId(String id, String newId) {
+ BioCompartment compartment = this.bn.getCompartment(id);
+
+ if (compartment != null) {
+ BioCompartment newCompartment = new BioCompartment(compartment, newId);
+ this.bn.add(newCompartment);
+
+ // Add metabolites
+ this.bn.affectToCompartment(newCompartment, compartment.getComponentsView());
+
+ // Change compartment in each left reactant
+ this.bn.getReactionsView().forEach(r -> {
+ r.getLeftReactantsView().forEach(reactant -> {
+ if (reactant.getLocation().equals(compartment)) {
+ BioMetabolite metabolite = reactant.getMetabolite();
+ Double sto = reactant.getQuantity();
+ this.bn.affectLeft(r, sto, newCompartment, metabolite);
+ this.bn.removeLeft(metabolite, compartment, r);
+ }
+ });
+ });
+
+ // Change compartment in each right reactant
+ this.bn.getReactionsView().forEach(r -> {
+ r.getRightReactantsView().forEach(reactant -> {
+ if (reactant.getLocation().equals(compartment)) {
+ BioMetabolite metabolite = reactant.getMetabolite();
+ Double sto = reactant.getQuantity();
+ this.bn.affectRight(r, sto, newCompartment, metabolite);
+ this.bn.removeRight(metabolite, compartment, r);
+ }
+ });
+ });
+
+ this.bn.removeOnCascade(compartment);
+
+ }
+ }
+
+ /**
+ * Replace a reaction with the same reaction with another id
+ *
+ * @param id : the original id
+ * @param newId : the new id
+ */
+ private void setReactionId(String id, String newId) {
+ BioReaction reaction = this.bn.getReaction(id);
+
+ if (reaction != null) {
+ BioReaction newReaction = new BioReaction(reaction, newId);
+ this.bn.add(newReaction);
+
+ // Add enzymes
+ this.bn.affectEnzyme(newReaction, reaction.getEnzymesView());
+
+ // Change reaction in the pathways
+ this.bn.getPathwaysFromReaction(reaction).forEach(p -> {
+ this.bn.affectToPathway(p, newReaction);
+ });
+
+ // Add lefts and rights
+ this.bn.affectLeft(newReaction, reaction.getLeftReactantsView());
+ this.bn.affectRight(newReaction, reaction.getRightReactantsView());
+
+ this.bn.removeOnCascade(reaction);
+ }
+ }
+
+ /**
+ * Replace a metabolite with the same metabolite with another id
+ *
+ * @param id : the original id
+ * @param newId : the new id
+ */
+ private void setMetaboliteId(String id, String newId) {
+ BioMetabolite metabolite = this.bn.getMetabolite(id);
+
+ if (metabolite != null) {
+ BioMetabolite newMetabolite = new BioMetabolite(metabolite, newId);
+ this.bn.add(newMetabolite);
+
+ // Change the metabolite in the compartments
+ this.bn.getCompartmentsView().stream().filter(c -> c.getComponentsView().contains(metabolite)).forEach(c -> {
+ this.bn.removeFromCompartment(c, metabolite);
+ this.bn.affectToCompartment(c, newMetabolite);
+ });
+
+ // Change the metabolite in the left reactants
+ this.bn.getReactionsView().forEach(r -> {
+ r.getLeftReactantsView().stream().filter(reactant -> reactant.getMetabolite().equals(metabolite))
+ .forEach(reactant -> {
+ Double sto = reactant.getQuantity();
+ BioCompartment cpt = reactant.getLocation();
+ this.bn.affectLeft(r, sto, cpt, newMetabolite);
+ });
+ });
+
+ // Change the metabolite in the right reactants
+ this.bn.getReactionsView().forEach(r ->
+ r.getRightReactantsView()
+ .stream().filter(reactant -> reactant.getMetabolite().equals(metabolite))
+ .forEach(reactant -> {
+ Double sto = reactant.getQuantity();
+ BioCompartment cpt = reactant.getLocation();
+ this.bn.affectRight(r, sto, cpt, newMetabolite);
+ }));
+
+ // Change the metabolite in the enzymes
+ this.bn.getEnzymesView().
+ forEach(e -> e.getParticipantsView()
+ .stream().filter(p -> p.getPhysicalEntity().equals(metabolite))
+ .forEach(partcipant -> {
+ Double sto = partcipant.getQuantity();
+ this.bn.affectSubUnit(e, sto, newMetabolite);
+ }));
+
+ this.bn.removeOnCascade(metabolite);
+ }
+ }
+
+ /**
+ * Replace a pathway with the same pathway with another id
+ *
+ * @param id : the original id
+ * @param newId : the new id
+ */
+ private void setPathwayId(String id, String newId) {
+ BioPathway originalPathway = this.bn.getPathway(id);
+
+ if (originalPathway != null) {
+ BioPathway newPathway = new BioPathway(originalPathway, newId);
+ this.bn.add(newPathway);
+ this.bn.affectToPathway(newPathway, this.bn.getReactionsFromPathways(originalPathway));
+ this.bn.removeOnCascade(originalPathway);
+ }
+ }
+
+ /**
+ * Replace a gene with the same gene with another id
+ *
+ * @param id : the origina id
+ * @param newId : the new id
+ */
+ private void setGeneId(String id, String newId) {
+ BioGene originalGene = this.bn.getGene(id);
+
+ if (originalGene != null) {
+ BioGene newGene = new BioGene(originalGene, newId);
+ this.bn.add(newGene);
+ this.bn.getProteinsView().stream().filter(p -> p.getGene().equals(originalGene)).forEach(p -> {
+ this.bn.affectGeneProduct(p, newGene);
+ });
+ this.bn.removeOnCascade(originalGene);
+ }
+ }
+}
diff --git a/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetIdsFromFileTest.java b/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetIdsFromFileTest.java
new file mode 100644
index 000000000..579b835b8
--- /dev/null
+++ b/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetIdsFromFileTest.java
@@ -0,0 +1,260 @@
+/*
+ * Copyright INRAE (2022)
+ *
+ * contact-metexplore@inrae.fr
+ *
+ * This software is a computer program whose purpose is to [describe
+ * functionalities and technical features of your software].
+ *
+ * This software is governed by the CeCILL license under French law and
+ * abiding by the rules of distribution of free software. You can use,
+ * modify and/ or redistribute the software under the terms of the CeCILL
+ * license as circulated by CEA, CNRS and INRIA at the following URL
+ * "https://cecill.info/licences/Licence_CeCILL_V2.1-en.html".
+ *
+ * As a counterpart to the access to the source code and rights to copy,
+ * modify and redistribute granted by the license, users are provided only
+ * with a limited warranty and the software's author, the holder of the
+ * economic rights, and the successive licensors have only limited
+ * liability.
+ *
+ * In this respect, the user's attention is drawn to the risks associated
+ * with loading, using, modifying and/or developing or reproducing the
+ * software by the user in light of its specific status of free software,
+ * that may mean that it is complicated to manipulate, and that also
+ * therefore means that it is reserved for developers and experienced
+ * professionals having in-depth computer knowledge. Users are therefore
+ * encouraged to load and test the software's suitability as regards their
+ * requirements in conditions enabling the security of their systems and/or
+ * data to be ensured and, more generally, to use and operate it in the
+ * same conditions as regards security.
+ *
+ * The fact that you are presently reading this means that you have had
+ * knowledge of the CeCILL license and that you accept its terms.
+ *
+ */
+
+package fr.inrae.toulouse.metexplore.met4j_io.tabulated.attributes;
+
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.*;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import java.io.IOException;
+
+import static org.junit.Assert.*;
+
+public class SetIdsFromFileTest {
+
+
+ private BioNetwork network;
+
+ private SetIdsFromFile setIdsFromFile;
+
+ @Before
+ public void init() {
+ network = new BioNetwork();
+ }
+
+ @Test
+ public void setGeneIds() throws IOException {
+ BioGene gene = new BioGene("g1");
+ BioProtein protein = new BioProtein("p1");
+
+ network.add(gene, protein);
+
+ network.affectGeneProduct(protein, gene);
+
+ setIdsFromFile = Mockito.spy(new SetIdsFromFile(0, 1, network, "", "", 0, EntityType.GENE,false, false));
+
+ Mockito.doReturn(true).when(setIdsFromFile).parseAttributeFile();
+
+ String line = "g1\tgene1\n";
+
+ Boolean flag = setIdsFromFile.parseLine(line, 1);
+
+ assertTrue(flag);
+
+ setIdsFromFile.setAttributes();
+
+ assertEquals(1, network.getGenesView().size());
+ assertNotNull(network.getGene("gene1"));
+
+ assertEquals(1, network.getProteinsView().size());
+
+ }
+
+ @Test
+ public void setMetaboliteIds() throws IOException {
+ BioMetabolite metabolite = new BioMetabolite("m1");
+ BioCompartment cpt = new BioCompartment("cpt");
+ BioReaction r1 = new BioReaction("r1");
+ BioReaction r2 = new BioReaction("r2");
+ BioEnzyme e = new BioEnzyme("e");
+
+ network.add(metabolite, cpt, r1, r2, e);
+
+ network.affectToCompartment(cpt, metabolite);
+ network.affectLeft(r1, 1.0, cpt, metabolite);
+ network.affectRight(r2, 1.0, cpt, metabolite);
+ network.affectSubUnit(e, 1.0, metabolite);
+
+ setIdsFromFile = Mockito.spy(new SetIdsFromFile(0, 1, network, "", "", 0, EntityType.METABOLITE,false, false));
+
+ Mockito.doReturn(true).when(setIdsFromFile).parseAttributeFile();
+
+ String line = "m1\tmetabolite1\n";
+
+ Boolean flag = setIdsFromFile.parseLine(line, 1);
+
+ assertTrue(flag);
+
+ setIdsFromFile.setAttributes();
+
+ assertEquals(1, network.getMetabolitesView().size());
+
+ BioMetabolite newMetabolite = network.getMetabolite("metabolite1");
+
+ assertNotNull(newMetabolite);
+
+ BioCompartment newCpt = network.getCompartment("cpt");
+
+ assertNotNull(newCpt);
+
+ assertNotNull(newCpt.getComponentsView().get("metabolite1"));
+
+ assertEquals(2, network.getReactionsView().size());
+
+ assertEquals(1, r1.getLeftsView().size());
+ assertTrue(r1.getLeftsView().contains(newMetabolite));
+
+ assertEquals(1, r2.getRightsView().size());
+ assertTrue(r2.getRightsView().contains(newMetabolite));
+
+ assertEquals(1, network.getEnzymesView().size());
+ assertTrue(e.getParticipantsView().stream().anyMatch(p -> p.getPhysicalEntity().equals(newMetabolite)));
+ assertFalse(e.getParticipantsView().stream().anyMatch(p -> p.getPhysicalEntity().equals(metabolite)));
+
+ }
+
+ @Test
+ public void setPathwayIds() throws IOException {
+ BioPathway pathway = new BioPathway("p1");
+ BioReaction r1 = new BioReaction("r1");
+ BioReaction r2 = new BioReaction("r2");
+
+ network.add(pathway, r1, r2);
+ network.affectToPathway(pathway, r1, r2);
+
+ setIdsFromFile = Mockito.spy(new SetIdsFromFile(0, 1, network, "", "", 0, EntityType.PATHWAY,false, false));
+
+ Mockito.doReturn(true).when(setIdsFromFile).parseAttributeFile();
+
+ String line = "p1\tpathway1\n";
+
+ Boolean flag = setIdsFromFile.parseLine(line, 1);
+
+ assertTrue(flag);
+
+ setIdsFromFile.setAttributes();
+
+ assertEquals(1, network.getPathwaysView().size());
+
+ BioPathway newPathway = network.getPathway("pathway1");
+ assertNotNull(newPathway);
+ assertEquals(2, network.getReactionsFromPathways(newPathway).size());
+
+ }
+
+ @Test
+ public void setReactionIds() throws IOException {
+ BioPathway pathway = new BioPathway("p1");
+ BioReaction r1 = new BioReaction("r1");
+ BioMetabolite metabolite = new BioMetabolite("m1");
+ BioMetabolite metabolite2 = new BioMetabolite("m2");
+ BioCompartment cpt = new BioCompartment("cpt");
+ BioEnzyme e = new BioEnzyme("e");
+
+ this.network.add(pathway, r1, metabolite, metabolite2, cpt, e);
+
+ this.network.affectToPathway(pathway, r1);
+ this.network.affectToCompartment(cpt, metabolite2, metabolite);
+ this.network.affectLeft(r1, 1.0, cpt, metabolite);
+ this.network.affectRight(r1, 1.0, cpt, metabolite2);
+ this.network.affectEnzyme(r1, e);
+
+ setIdsFromFile = Mockito.spy(new SetIdsFromFile(0, 1, network, "", "", 0, EntityType.REACTION,false, false));
+
+ Mockito.doReturn(true).when(setIdsFromFile).parseAttributeFile();
+
+ String line = "r1\treaction1\n";
+
+ Boolean flag = setIdsFromFile.parseLine(line, 1);
+
+ assertTrue(flag);
+
+ setIdsFromFile.setAttributes();
+
+ assertEquals(1, network.getReactionsView().size());
+
+ BioReaction newReaction = network.getReaction("reaction1");
+
+ assertNotNull(newReaction);
+
+ assertEquals(1, network.getPathwaysView().size());
+
+ assertEquals(1, network.getReactionsFromPathways(pathway).size());
+
+ assertTrue(network.getReactionsFromPathways(pathway).contains(newReaction));
+
+ assertTrue(r1.getEnzymesView().contains(e));
+
+ assertEquals(1, newReaction.getLeftsView().size());
+ assertEquals(1, newReaction.getRightsView().size());
+ }
+
+ @Test
+ public void setCompartmentIds() throws IOException {
+
+ BioReaction r1 = new BioReaction("r1");
+ BioMetabolite metabolite = new BioMetabolite("m1");
+ BioMetabolite metabolite2 = new BioMetabolite("m2");
+ BioCompartment cpt = new BioCompartment("cpt");
+
+ this.network.add(r1, metabolite, metabolite2, cpt);
+
+ this.network.affectToCompartment(cpt, metabolite2, metabolite);
+ this.network.affectLeft(r1, 1.0, cpt, metabolite);
+ this.network.affectRight(r1, 1.0, cpt, metabolite2);
+
+ setIdsFromFile = Mockito.spy(new SetIdsFromFile(0, 1, network, "", "", 0, EntityType.COMPARTMENT,false, false));
+
+ Mockito.doReturn(true).when(setIdsFromFile).parseAttributeFile();
+
+ String line = "cpt\tcompartment\n";
+
+ Boolean flag = setIdsFromFile.parseLine(line, 1);
+
+ assertTrue(flag);
+
+ setIdsFromFile.setAttributes();
+
+ assertEquals(1, this.network.getCompartmentsView().size());
+
+ BioCompartment newCpt = this.network.getCompartment("compartment");
+
+ assertNotNull(newCpt);
+
+ assertEquals(2, newCpt.getComponentsView().size());
+
+ assertEquals(1, this.network.getReactionsView().size());
+
+ assertEquals(1, r1.getLeftsView().size());
+ assertEquals(1, r1.getRightsView().size());
+
+ assertTrue(r1.getLeftReactantsView().stream().allMatch(reactant -> reactant.getLocation().equals(newCpt)));
+ assertTrue(r1.getRightReactantsView().stream().allMatch(reactant -> reactant.getLocation().equals(newCpt)));
+
+ }
+}
\ No newline at end of file
--
GitLab
From ff5428be183f86df7f4f4b8b53b25ca96d9eb9f0 Mon Sep 17 00:00:00 2001
From: lcottret <ludovic.cottret@inrae.fr>
Date: Tue, 15 Nov 2022 10:50:13 +0100
Subject: [PATCH 20/21] met4j-toolbox: add SbmlSetIdsFromFile
---
.../attributes/SbmlSetIdsFromFile.java | 112 ++++++++++++++++++
1 file changed, 112 insertions(+)
create mode 100644 met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/attributes/SbmlSetIdsFromFile.java
diff --git a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/attributes/SbmlSetIdsFromFile.java b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/attributes/SbmlSetIdsFromFile.java
new file mode 100644
index 000000000..12def855d
--- /dev/null
+++ b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/attributes/SbmlSetIdsFromFile.java
@@ -0,0 +1,112 @@
+/*
+ * Copyright INRAE (2022)
+ *
+ * contact-metexplore@inrae.fr
+ *
+ * This software is a computer program whose purpose is to [describe
+ * functionalities and technical features of your software].
+ *
+ * This software is governed by the CeCILL license under French law and
+ * abiding by the rules of distribution of free software. You can use,
+ * modify and/ or redistribute the software under the terms of the CeCILL
+ * license as circulated by CEA, CNRS and INRIA at the following URL
+ * "https://cecill.info/licences/Licence_CeCILL_V2.1-en.html".
+ *
+ * As a counterpart to the access to the source code and rights to copy,
+ * modify and redistribute granted by the license, users are provided only
+ * with a limited warranty and the software's author, the holder of the
+ * economic rights, and the successive licensors have only limited
+ * liability.
+ *
+ * In this respect, the user's attention is drawn to the risks associated
+ * with loading, using, modifying and/or developing or reproducing the
+ * software by the user in light of its specific status of free software,
+ * that may mean that it is complicated to manipulate, and that also
+ * therefore means that it is reserved for developers and experienced
+ * professionals having in-depth computer knowledge. Users are therefore
+ * encouraged to load and test the software's suitability as regards their
+ * requirements in conditions enabling the security of their systems and/or
+ * data to be ensured and, more generally, to use and operate it in the
+ * same conditions as regards security.
+ *
+ * The fact that you are presently reading this means that you have had
+ * knowledge of the CeCILL license and that you accept its terms.
+ *
+ */
+package fr.inrae.toulouse.metexplore.met4j_toolbox.attributes;
+
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
+import fr.inrae.toulouse.metexplore.met4j_io.tabulated.attributes.SetIdsFromFile;
+import fr.inrae.toulouse.metexplore.met4j_io.tabulated.attributes.SetNamesFromFile;
+import fr.inrae.toulouse.metexplore.met4j_toolbox.generic.annotations.EnumParameterTypes;
+import fr.inrae.toulouse.metexplore.met4j_toolbox.generic.annotations.ParameterType;
+import org.kohsuke.args4j.Option;
+
+public class SbmlSetIdsFromFile extends AbstractSbmlSetAny {
+
+ @ParameterType(name= EnumParameterTypes.Integer)
+ @Option(name="-cnew", usage="[2] number of the column where are the new ids")
+ public int colname=2;
+
+ /** {@inheritDoc} */
+ @Override
+ public String getLabel() {
+ return this.getClass().getSimpleName();
+ }
+
+ /** {@inheritDoc} */
+ @Override
+ public String getLongDescription() {
+ return this.getShortDescription()+"\n" +
+ this.setDescription+"\n";
+ }
+
+ /** {@inheritDoc} */
+ @Override
+ public String getShortDescription() {
+ return "Set new ids to network objects from a tabulated file containing the old ids and the new ids";
+ }
+
+ /**
+ * <p>main.</p>
+ *
+ * @param args an array of {@link java.lang.String} objects.
+ */
+ public static void main(String[] args) {
+
+ SbmlSetIdsFromFile app = new SbmlSetIdsFromFile();
+
+ app.parseArguments(args);
+
+ app.run();
+
+ }
+
+ private void run() {
+
+ BioNetwork bn = this.readSbml();
+
+ SetIdsFromFile setter = new SetIdsFromFile(this.colid-1, this.colname-1,
+ bn, this.tab, this.c, this.nSkip, this.o, this.p, this.s);
+
+ Boolean flag = true;
+
+ try {
+ flag = setter.setAttributes();
+ } catch (Exception e) {
+ flag=false;
+ }
+
+ if(!flag) {
+ System.err.println("Error in "+this.getLabel());
+ System.exit(1);
+ }
+
+ this.writeSbml(bn);
+
+ System.exit(0);
+
+
+ }
+
+}
--
GitLab
From 86837cfe0e9ebbe979ba7a0959d13b2435e8262c Mon Sep 17 00:00:00 2001
From: lcottret <ludovic.cottret@inrae.fr>
Date: Tue, 15 Nov 2022 12:36:30 +0100
Subject: [PATCH 21/21] replace / by _ in the name of the branches
Otherwise, the name of the branch is understood as a path in the singularity or docker registry
---
.gitlab-ci.yml | 11 +++++++----
1 file changed, 7 insertions(+), 4 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 826bb9d63..b7eed923f 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -19,8 +19,8 @@ stages:
# version in lower case
- if [ "$CI_COMMIT_BRANCH" = "develop" -o "$CI_COMMIT_BRANCH" = "master" -a "$VERSION" != "$LOWER_CASE_VERSION" ]; then docker build -t "$DOCKER_IMAGE:$LOWER_CASE_VERSION" .; fi
- if [ "$CI_COMMIT_BRANCH" = "develop" -o "$CI_COMMIT_BRANCH" = "master" -a "$VERSION" != "$LOWER_CASE_VERSION" ]; then docker push "$DOCKER_IMAGE:$LOWER_CASE_VERSION"; fi
- - docker build -t "$DOCKER_IMAGE:$CI_COMMIT_BRANCH" .
- - docker push "$DOCKER_IMAGE:$CI_COMMIT_BRANCH"
+ - docker build -t "$DOCKER_IMAGE:$FORMATTED_COMMIT_BRANCH" .
+ - docker push "$DOCKER_IMAGE:$FORMATTED_COMMIT_BRANCH"
# branch in lower case
- docker build -t "$DOCKER_IMAGE:$LOWER_CASE_COMMIT_BRANCH" .
- docker push "$DOCKER_IMAGE:$LOWER_CASE_COMMIT_BRANCH"
@@ -56,9 +56,12 @@ build:
- VERSION=$TRUEVERSION
- if [ "$CI_COMMIT_BRANCH" = "master" ]; then VERSION=${VERSION%"-SNAPSHOT"}; fi
- LOWER_CASE_VERSION=${VERSION,,}
- - LOWER_CASE_COMMIT_BRANCH=${CI_COMMIT_BRANCH,,}
+ # Replace / by _ in the name of the commit
+ - FORMATTED_COMMIT_BRANCH=${CI_COMMIT_BRANCH//\//_}
+ - LOWER_CASE_COMMIT_BRANCH=${FORMATTED_COMMIT_BRANCH,,}
- echo "VERSION=$VERSION" >> build.env
- echo "TRUEVERSION=$TRUEVERSION" >> build.env
+ - echo "FORMATTED_COMMIT_BRANCH=$FORMATTED_COMMIT_BRANCH" >> build.env
- echo "LOWER_CASE_VERSION=$LOWER_CASE_VERSION" >> build.env
- echo "LOWER_CASE_COMMIT_BRANCH=$LOWER_CASE_COMMIT_BRANCH" >> build.env
artifacts:
@@ -162,7 +165,7 @@ buildSingularity:
- if [ "$CI_COMMIT_BRANCH" = "develop" -o "$CI_COMMIT_BRANCH" = "master" ]; then singularity push --docker-username "${CI_REGISTRY_USER}" --docker-password "${CI_REGISTRY_PASSWORD}" met4j-toolbox.sif oras://"$CI_REGISTRY_IMAGE"/met4j-singularity:"$VERSION"; fi
# version in lower case
- if [ "$CI_COMMIT_BRANCH" = "develop" -o "$CI_COMMIT_BRANCH" = "master" -a "$VERSION" != "$LOWER_CASE_VERSION"]; then singularity push --docker-username "${CI_REGISTRY_USER}" --docker-password "${CI_REGISTRY_PASSWORD}" met4j-toolbox.sif oras://"$CI_REGISTRY_IMAGE"/met4j-singularity:"$LOWER_CASE_VERSION"; fi
- - singularity push --docker-username "${CI_REGISTRY_USER}" --docker-password "${CI_REGISTRY_PASSWORD}" met4j-toolbox.sif oras://"$CI_REGISTRY_IMAGE"/met4j-singularity:"$CI_COMMIT_BRANCH"
+ - singularity push --docker-username "${CI_REGISTRY_USER}" --docker-password "${CI_REGISTRY_PASSWORD}" met4j-toolbox.sif oras://"$CI_REGISTRY_IMAGE"/met4j-singularity:"$FORMATTED_COMMIT_BRANCH"
# branch in lower case
- singularity push --docker-username "${CI_REGISTRY_USER}" --docker-password "${CI_REGISTRY_PASSWORD}" met4j-toolbox.sif oras://"$CI_REGISTRY_IMAGE"/met4j-singularity:"$LOWER_CASE_COMMIT_BRANCH"
rules:
--
GitLab