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issue #121 test #20
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@Schmoho
Schmoho committed Jul 26, 2024
1 parent 580418e commit 1538292
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53 changes: 41 additions & 12 deletions src/main/java/edu/ucsd/sbrg/bigg/annotation/ReactionAnnotation.java
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@
import edu.ucsd.sbrg.bigg.polishing.PolishingUtils;
import edu.ucsd.sbrg.db.BiGGDB;
import edu.ucsd.sbrg.db.QueryOnce;
import edu.ucsd.sbrg.miriam.Registry;
import edu.ucsd.sbrg.util.GPRParser;
import edu.ucsd.sbrg.util.SBMLUtils;
import org.sbml.jsbml.CVTerm.Qualifier;
Expand All @@ -20,9 +21,6 @@
import java.util.logging.Logger;
import java.util.stream.Collectors;

import static edu.ucsd.sbrg.bigg.annotation.BiGGAnnotation.getBiGGIdFromResources;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.TYPE_REACTION;

public class ReactionAnnotation extends CVTermAnnotation {

/**
Expand Down Expand Up @@ -64,7 +62,6 @@ public void annotate() {
});
}


/**
* Checks if {@link Species#getId()} returns a correct {@link BiGGId} and tries to retrieve a corresponding
* {@link BiGGId} based on annotations present.
Expand All @@ -77,20 +74,52 @@ public Optional<BiGGId> checkId() {
String id = reaction.getId();
// extracting BiGGId if not present for species
boolean isBiGGid = id.matches("^(R_)?([a-zA-Z][a-zA-Z0-9_]+)(?:_([a-z][a-z0-9]?))?(?:_([A-Z][A-Z0-9]?))?$")
&& QueryOnce.isReaction(id);
&& QueryOnce.isReaction(id);
if (!isBiGGid) {
// Flatten all resources for all CVTerms into a list
List<String> resources =
reaction.getAnnotation().getListOfCVTerms().stream().filter(cvTerm -> cvTerm.getQualifier() == Qualifier.BQB_IS)
.flatMap(term -> term.getResources().stream()).collect(Collectors.toList());
if (!resources.isEmpty()) {
// update id if we found something
id = getBiGGIdFromResources(resources, TYPE_REACTION).orElse(id);
}
Set<String> ids = reaction.getAnnotation().getListOfCVTerms()
.stream()
.filter(cvTerm -> cvTerm.getQualifier() == Qualifier.BQB_IS)
.flatMap(term -> term.getResources().stream())
.map(Registry::checkResourceUrl)
.flatMap(Optional::stream)
.map(Registry::getPartsFromIdentifiersURI)
.map(parts -> {
String prefix = parts.get(0);
String synonymId = parts.get(1);
return BiGGDB.getBiggIdsForReactionForeignId(prefix, synonymId);
})
.flatMap(Collection::stream)
.filter(this::matchingCompartments)
.map(fr -> fr.reactionId)
.collect(Collectors.toSet());
id = ids.stream()
.findFirst()
.orElse(id);
}
return BiGGId.createReactionId(id);
}

private boolean matchingCompartments(BiGGDB.ForeignReaction foreignReaction) {
if (!reaction.isSetCompartment()
&& null == foreignReaction.compartmentId
&& null == foreignReaction.compartmentName) {
return true;
} else if (!reaction.isSetCompartment()
&& (null != foreignReaction.compartmentId
|| null != foreignReaction.compartmentName)) {
return false;
} else if (reaction.isSetCompartment()) {
return reaction.getCompartment()
.equals(foreignReaction.compartmentId);
} else if (reaction.isSetCompartmentInstance()
&& reaction.getCompartmentInstance().isSetName()) {
return reaction.getCompartmentInstance().getName()
.equals(foreignReaction.compartmentName);
} else
return false;
}


/**
* @param biggId
Expand Down
137 changes: 67 additions & 70 deletions src/main/java/edu/ucsd/sbrg/db/BiGGDB.java
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Original file line number Diff line number Diff line change
Expand Up @@ -14,81 +14,23 @@
*/
package edu.ucsd.sbrg.db;

import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.TYPE_GENE_PRODUCT;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.TYPE_REACTION;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.TYPE_SPECIES;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Column.ACCESSION_VALUE;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Column.BIGG_ID;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Column.CHARGE;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Column.COMPARTMENTALIZED_COMPONENT_ID;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Column.COMPARTMENT_ID;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Column.COMPONENT_ID;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Column.DATA_SOURCE_ID;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Column.DATE_TIME;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Column.FORMULA;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Column.GENE_REACTION_RULE;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Column.GENOME_ID;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Column.ID;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Column.LOCUS_TAG;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Column.MODEL_ID;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Column.NAME;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Column.OME_ID;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Column.ORGANISM;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Column.PSEUDOREACTION;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Column.PUBLICATION_ID;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Column.REACTION_ID;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Column.REFERENCE_ID;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Column.REFERENCE_TYPE;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Column.SUBSYSTEM;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Column.SYNONYM_COL;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Column.TAXON_ID;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Column.TYPE;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Table.COMPARTMENT;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Table.COMPARTMENTALIZED_COMPONENT;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Table.COMPONENT;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Table.DATABASE_VERSION;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Table.DATA_SOURCE;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Table.GENE;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Table.GENOME;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Table.GENOME_REGION;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Table.MCC;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Table.MODEL;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Table.MODEL_REACTION;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Table.OLD_BIGG_ID;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Table.PUBLICATION;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Table.PUBLICATION_MODEL;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Table.REACTION;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Table.REFSEQ_NAME;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Table.REFSEQ_PATTERN;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Table.SYNONYM;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Table.URL;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Table.URL_PREFIX;
import static java.text.MessageFormat.format;
import static org.sbml.jsbml.util.Pair.pairOf;
import de.zbit.util.ResourceManager;
import de.zbit.util.Utils;
import edu.ucsd.sbrg.bigg.BiGGId;
import edu.ucsd.sbrg.miriam.Registry;
import org.sbml.jsbml.util.Pair;

import java.sql.Connection;
import java.sql.Date;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.LinkedHashSet;
import java.util.LinkedList;
import java.util.List;
import java.util.Optional;
import java.util.ResourceBundle;
import java.util.Set;
import java.util.TreeSet;
import java.sql.*;
import java.util.*;
import java.util.logging.Logger;
import java.util.stream.Collectors;

import org.sbml.jsbml.util.Pair;

import de.zbit.util.ResourceManager;
import de.zbit.util.Utils;
import edu.ucsd.sbrg.bigg.BiGGId;
import edu.ucsd.sbrg.miriam.Registry;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Column.*;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.*;
import static edu.ucsd.sbrg.db.BiGGDBContract.Constants.Table.*;
import static java.text.MessageFormat.format;
import static org.sbml.jsbml.util.Pair.pairOf;

/**
* @author Andreas Dr&auml;ger
Expand Down Expand Up @@ -757,4 +699,59 @@ public static Optional<String> getBiggIdFromSynonym(String dataSourceId, String
return Optional.empty();
}
}


public static class ForeignReaction {
public final String reactionId;
public final String compartmentId;
public final String compartmentName;

public ForeignReaction(String reactionId, String compartmentId, String compartmentName) {
this.reactionId = reactionId;
this.compartmentId = compartmentId;
this.compartmentName = compartmentName;
}
}

/**
* @param synonym
* @param dataSourceId
* @return String
*/
public static Collection<ForeignReaction> getBiggIdsForReactionForeignId(String dataSourceId,
String synonym) {
Set<ForeignReaction> results = new HashSet<>();

var query = "SELECT R.BIGG_ID AS REACTION_BIGG_ID, "
+ "C.BIGG_ID AS COMPARTMENT_BIGG_ID, "
+ "C.NAME AS COMPARTMENT_NAME "
+ "FROM REACTION R "
+ "left join REACTION_MATRIX RM "
+ "on RM.REACTION_ID = R.ID "
+ "left join COMPARTMENTALIZED_COMPONENT CC "
+ "on RM.COMPARTMENTALIZED_COMPONENT_ID = CC.ID "
+ "left join COMPARTMENT C "
+ "on CC.COMPARTMENT_ID = C.ID "
+ "join synonym s "
+ "on synonym = ? and r.id = s.ome_id "
+ "join data_source d "
+ "on s.data_source_id = d.id and d.bigg_id = ?";

try (var connection = connector.getConnection()) {
var pStatement = connection.prepareStatement(query);
pStatement.setString(1, synonym);
pStatement.setString(2, dataSourceId);
var resultSet = pStatement.executeQuery();
while (resultSet.next()) {
var reactionBiggId = resultSet.getString(1);
var compartmentBiggId = resultSet.getString(2);
var compartmentName = resultSet.getString(3);
var r = new ForeignReaction(reactionBiggId, compartmentBiggId, compartmentName);
results.add(r);
}
} catch (SQLException exc) {
logger.warning(Utils.getMessage(exc));
}
return results;
}
}
22 changes: 15 additions & 7 deletions src/test/java/edu/ucsd/sbrg/bigg/annotation/ReactionAnnotationTest.java
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
package edu.ucsd.sbrg.bigg.annotation;

import edu.ucsd.sbrg.bigg.ModelPolisherOptions;
import org.junit.jupiter.api.Test;
import org.sbml.jsbml.CVTerm;
import org.sbml.jsbml.Model;
Expand All @@ -10,6 +11,7 @@
import org.sbml.jsbml.ext.groups.GroupsModelPlugin;
import org.sbml.jsbml.ext.groups.Member;

import java.util.Map;
import java.util.Set;
import java.util.stream.Collectors;

Expand All @@ -20,22 +22,26 @@ public class ReactionAnnotationTest extends BiGGDBTest {

@Test
public void getBiGGIdFromResourcesTest() {
initParameters();
initParameters(Map.of(ModelPolisherOptions.INCLUDE_ANY_URI.getOptionName(),
"true"));
var m = new Model("iJO1366", 3, 2);
var r1 = m.createReaction("some_name");
var r2 = m.createReaction("some_other_name");
var r3 = m.createReaction("some_third_name");

r1.setCompartment("m");
r1.addCVTerm(new CVTerm(
CVTerm.Type.BIOLOGICAL_QUALIFIER,
CVTerm.Qualifier.BQB_IS,
"http://identifiers.org/biocyc/META:ACETATEKIN-RXN"));

r2.setCompartment("e");
r2.addCVTerm(new CVTerm(
CVTerm.Type.BIOLOGICAL_QUALIFIER,
CVTerm.Qualifier.BQB_IS,
"http://identifiers.org/metanetx.reaction/MNXR103371"));

r3.setCompartment("c");
r3.addCVTerm(new CVTerm(
CVTerm.Type.BIOLOGICAL_QUALIFIER,
CVTerm.Qualifier.BQB_IS,
Expand All @@ -44,27 +50,29 @@ public void getBiGGIdFromResourcesTest() {
var gPlugin = (GroupsModelPlugin) m.getPlugin(GroupsConstants.shortLabel);
assertEquals(0, gPlugin.getGroupCount());

new ReactionAnnotation(r1).annotate();
new ReactionAnnotation(r1).annotate();
new ReactionAnnotation(r2).annotate();
new ReactionAnnotation(r3).annotate();

var r1FbcPlugin = (FBCReactionPlugin) r1.getPlugin(FBCConstants.shortLabel);
var gpa1 = r1FbcPlugin.getGeneProductAssociation();
assertNull(gpa1);
assertEquals(false, r1.isSetCompartment());
assertEquals("", r1.getName());
assertEquals("Acetate kinase, mitochondrial", r1.getName());
assertEquals(1, r1.getCVTermCount());
assertEquals(1, r1.getCVTerm(0).getNumResources());
assertEquals(11, r1.getCVTerm(0).getNumResources());

var r2FbcPlugin = (FBCReactionPlugin) r2.getPlugin(FBCConstants.shortLabel);
var gpa2 = r2FbcPlugin.getGeneProductAssociation();
assertNull(gpa2);
assertEquals("", r2.getName());
assertEquals(1, r2.getCVTermCount());
assertEquals(1, r2.getCVTerm(0).getNumResources());

var r3FbcPlugin = (FBCReactionPlugin) r3.getPlugin(FBCConstants.shortLabel);
var gpa3 = r3FbcPlugin.getGeneProductAssociation();
assertNotNull(gpa3);
assertEquals("G_b2388", ((GeneProductRef) gpa3.getAssociation()).getGeneProduct());
assertEquals(false, r1.isSetCompartment());
assertEquals("", r1.getName());
assertEquals("Hexokinase (D-glucose:ATP)", r3.getName());
assertEquals(1, r3.getCVTermCount());
assertEquals(11, r3.getCVTerm(0).getNumResources());

Expand Down

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