Merge pull request #124 from draeger-lab/draeger-lab/ModelPolisher/#121…

…-polishing-unit-tests

Draeger lab/model polisher/#121 polishing unit tests

build.gradle

@@ -1,3 +1,6 @@
+import org.gradle.api.tasks.testing.logging.TestExceptionFormat
+import org.gradle.api.tasks.testing.logging.TestLogEvent
+
 plugins {
     id "java"
     id "application"
@@ -49,6 +52,17 @@ test {
     }
 }
 
+tasks.withType(Test) {
+    testLogging {
+        events TestLogEvent.FAILED
+        exceptionFormat TestExceptionFormat.FULL
+        showCauses true
+        showExceptions true
+        showStackTraces true
+        showStandardStreams false
+    }
+}
+
 repositories {
     mavenCentral()
     maven { url "https://oss.sonatype.org/content/repositories/snapshots" }
@@ -73,6 +87,8 @@ dependencies {
     implementation "de.uni-rostock.sbi:CombineArchive:1.4.1"
     implementation "com.zaxxer:HikariCP:5.0.1"
     testImplementation "org.junit.jupiter:junit-jupiter-api:${jupiterVersion}"
+    testImplementation "org.testcontainers:testcontainers:1.17.3"
+    testImplementation "org.testcontainers:junit-jupiter:1.17.3"
     testRuntimeOnly "org.junit.jupiter:junit-jupiter-engine:${jupiterVersion}"
 }
 

docker/preloaded_bigg_docker/Dockerfile

@@ -0,0 +1,22 @@
+FROM bigg_db_current:latest AS dumper
+# NOTE: this image is curently not available anywhere, but it is nothing more than postgres:14
+# with the current DB dump + restore script from mephenors image
+
+RUN ["sed", "-i", "s/exec \"$@\"/echo \"skipping...\"/", "/usr/local/bin/docker-entrypoint.sh"]
+
+RUN mkdir -p /var/lib/postgresql-static/data
+ENV PGDATA=/var/lib/postgresql-static/data
+ENV POSTGRES_USER=postgres
+ENV POSTGRES_PASSWORD=postgres
+
+RUN ["/usr/local/bin/docker-entrypoint.sh", "postgres"]
+
+FROM postgres:14
+
+COPY --from=dumper /var/lib/postgresql-static/data $PGDATA
+
+# ENTRYPOINT ["/usr/bin/env"]
+
+# USER postgres
+
+# CMD ["postgres"]

src/main/java/edu/ucsd/sbrg/bigg/annotation/ReactionAnnotation.java

@@ -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;
@@ -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 {
 
   /**
@@ -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.
@@ -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

src/main/java/edu/ucsd/sbrg/bigg/annotation/SpeciesAnnotation.java

@@ -71,7 +71,6 @@ public void annotate() {
    */
   @Override
   public Optional<BiGGId> checkId() {
-    // TODO: compartments are not handled correctly -- is this at all possible to get right?
     Optional<BiGGId> metaboliteId = BiGGId.createMetaboliteId(species.getId());
     Optional<String> id = metaboliteId.flatMap(biggId -> {
       // extracting BiGGId if not present for species

src/main/java/edu/ucsd/sbrg/bigg/polishing/ModelPolishing.java

@@ -17,9 +17,11 @@
 import org.sbml.jsbml.ext.fbc.GeneProduct;
 import org.sbml.jsbml.ext.fbc.Objective;
 
+import java.util.Collection;
 import java.util.ResourceBundle;
 import java.util.function.Predicate;
 import java.util.logging.Logger;
+import java.util.stream.Collectors;
 
 import static java.text.MessageFormat.format;
 
@@ -91,13 +93,18 @@ public void polishListOfObjectives(FBCModelPlugin modelPlug) {
           strict &= SBMLFix.fixObjective(model.getId(), model.getListOfReactions(), modelPlug,
             Parameters.get().fluxCoefficients(), Parameters.get().fluxObjectives());
         }
-        if (objective.isSetListOfFluxObjectives()) {
+        if (objective.isSetListOfFluxObjectives() || objective.getListOfFluxObjectives().size() == 0) {
           polishListOfFluxObjectives(objective);
         }
       }
       // removed unused objectives, i.e. those without flux objectives
-      modelPlug.getListOfObjectives().stream().filter(Predicate.not(Objective::isSetListOfFluxObjectives))
-               .forEach(modelPlug::removeObjective);
+      // modelPlug.getListOfObjectives().remove
+      Collection<Objective> removals = modelPlug.getListOfObjectives()
+              .stream()
+              .filter(Predicate.not(Objective::isSetListOfFluxObjectives)
+              .or(o -> o.getListOfFluxObjectives().size() == 0))
+              .collect(Collectors.toList());
+      modelPlug.getListOfObjectives().removeAll(removals);
     }
   }