diff --git a/CHANGELOG b/CHANGELOG
index 78678e8a57f3d3ac835b7ee1db5b13313db117a6..619737659da8ef4cd3c21a798cbbf784ec44b50d 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -2,6 +2,7 @@ minerva (19.0.0~alpha.0) stable; urgency=medium
* Backward incompatible: copying annotations into complex children moved
to a dedicated annotator (#2216)
* Backward incompatible: caching should be done in the background (#1656)
+ * Backward incompatible: annotations are performed asynchronously (#1657)
* Backward incompatible: MiRNA search has been removed (#2102)
* Backward incompatible: degraded does not have a name (#2116)
* Backward incompatible: custom annotation validation on project upload
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
index 0861b2a4170de7ef671a11d5dbca878372226d7e..a00cad55195a4d25b71f710aa45f4e32acf0c084 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
@@ -4,15 +4,21 @@ import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
import lcsb.mapviewer.annotation.services.annotators.ElementAnnotator;
import lcsb.mapviewer.annotation.services.annotators.IElementAnnotator;
import lcsb.mapviewer.common.IProgressUpdater;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.user.UserAnnotationSchema;
import lcsb.mapviewer.model.user.UserClassAnnotators;
import lcsb.mapviewer.model.user.annotator.AnnotatorData;
import lcsb.mapviewer.modelutils.map.ClassTreeNode;
import lcsb.mapviewer.modelutils.map.ElementUtils;
+import lcsb.mapviewer.persist.DbUtils;
+import lcsb.mapviewer.persist.dao.map.ReactionDao;
+import lcsb.mapviewer.persist.dao.map.ReactionProperty;
+import lcsb.mapviewer.persist.dao.map.species.ElementDao;
+import lcsb.mapviewer.persist.dao.map.species.ElementProperty;
import lcsb.mapviewer.persist.dao.user.UserAnnotationSchemaDao;
import org.apache.commons.collections4.ListUtils;
import org.apache.logging.log4j.LogManager;
@@ -21,9 +27,9 @@ import org.springframework.aop.framework.Advised;
import org.springframework.aop.support.AopUtils;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
-import org.springframework.transaction.annotation.Transactional;
import java.util.ArrayList;
+import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedList;
@@ -31,19 +37,11 @@ import java.util.List;
import java.util.Map;
import java.util.Queue;
import java.util.Set;
+import java.util.stream.Collectors;
-/**
- * This class annotates all elements in the model.
- *
- * @author Piotr Gawron
- */
@Service
-@Transactional
public class ModelAnnotator {
- /**
- * Default class logger.
- */
private static final Logger logger = LogManager.getLogger();
/**
@@ -51,37 +49,22 @@ public class ModelAnnotator {
*/
private final List<IElementAnnotator> availableAnnotators;
- /**
- * List of all available {@link ElementAnnotator} objects.
- */
- private final List<IElementAnnotator> defaultAnnotators;
-
private final UserAnnotationSchemaDao userAnnotationSchemaDao;
+ private final ElementDao elementDao;
+ private final ReactionDao reactionDao;
+ private final DbUtils dbUtils;
- /**
- * Constructor
- */
@Autowired
public ModelAnnotator(final List<IElementAnnotator> availableAnnotators,
- final UserAnnotationSchemaDao userAnnotationSchemaDao) {
+ final UserAnnotationSchemaDao userAnnotationSchemaDao,
+ final ElementDao elementDao,
+ final ReactionDao reactionDao,
+ final DbUtils dbUtils) {
this.availableAnnotators = availableAnnotators;
this.userAnnotationSchemaDao = userAnnotationSchemaDao;
- defaultAnnotators = new ArrayList<>();
- for (final IElementAnnotator annotator : availableAnnotators) {
- if (annotator.isDefault()) {
- defaultAnnotators.add(annotator);
- }
- }
- }
-
- /**
- * Performs all possible and automatic annotations on the model.
- *
- * @param model model to update
- * @param progressUpdater callback function used for updating progress of the function
- */
- public void performAnnotations(final Model model, final IProgressUpdater progressUpdater) {
- performAnnotations(model, progressUpdater, new UserAnnotationSchema());
+ this.dbUtils = dbUtils;
+ this.elementDao = elementDao;
+ this.reactionDao = reactionDao;
}
/**
@@ -89,39 +72,69 @@ public class ModelAnnotator {
*
* @param inputAnnotationSchema information about {@link ElementAnnotator} objects that should be
* used for a given classes
- * @param model model to update
+ * @param project project to update
* @param progressUpdater callback function used for updating progress of the function
*/
- public void performAnnotations(final Model model, final IProgressUpdater progressUpdater, final UserAnnotationSchema inputAnnotationSchema) {
-
+ public void performAnnotations(final Project project, final IProgressUpdater progressUpdater, final UserAnnotationSchema inputAnnotationSchema) {
UserAnnotationSchema annotationSchema = inputAnnotationSchema;
if (annotationSchema != null && annotationSchema.getId() > 0) {
annotationSchema = userAnnotationSchemaDao.getById(annotationSchema.getId());
}
+ if (annotationSchema == null) {
+ logger.error("Annotation Schema does not exist");
+ annotationSchema = new UserAnnotationSchema();
+ }
+ ElementUtils elementUtils = new ElementUtils();
progressUpdater.setProgress(0);
- List<Model> models = new ArrayList<>();
- models.add(model);
- models.addAll(model.getSubmodels());
- final double size = models.size();
+
double counter = 0;
- for (final Model m : models) {
- final double ratio = counter / size;
+ Map<ElementProperty, Object> elementFilter = new HashMap<>();
+ elementFilter.put(ElementProperty.PROJECT_ID, Collections.singletonList(project.getProjectId()));
- annotateModel(m, progress -> progressUpdater.setProgress(ratio * IProgressUpdater.MAX_PROGRESS / size), annotationSchema);
- counter++;
- }
- }
+ List<Integer> elementIds = dbUtils.callInTransactionWithResult(() -> elementDao.getAll(elementFilter))
+ .stream()
+ .map(Element::getId)
+ .collect(Collectors.toList());
- protected void annotateModel(final Model model, final IProgressUpdater progressUpdater, final UserAnnotationSchema annotationSchema) {
- progressUpdater.setProgress(0);
- ElementUtils elementUtils = new ElementUtils();
+ Map<ReactionProperty, Object> reactionFilter = new HashMap<>();
+ reactionFilter.put(ReactionProperty.PROJECT_ID, Collections.singletonList(project.getProjectId()));
- double counter = 0;
- double amount = model.getElements().size() + model.getReactions().size();
+ List<Integer> reactionIds = dbUtils.callInTransactionWithResult(() -> reactionDao.getAll(reactionFilter))
+ .stream()
+ .map(Reaction::getId)
+ .collect(Collectors.toList());
+
+ double amount = elementIds.size() + reactionIds.size();
// annotate all elements
- for (final BioEntity element : model.getBioEntities()) {
+ for (final Integer reactionId : reactionIds) {
+ Reaction reaction = dbUtils.callInTransactionWithResult(() -> reactionDao.getById(reactionId));
+
+ List<AnnotatorData> list = annotationSchema.getAnnotatorsForClass(reaction.getClass());
+ if (list == null) {
+ list = getDefaultAnnotators(reaction.getClass());
+ }
+ for (final AnnotatorData annotatorData : list) {
+ IElementAnnotator elementAnnotator = null;
+ try {
+ elementAnnotator = getAnnotator(annotatorData);
+ elementAnnotator.annotateElement(reaction, annotatorData);
+ dbUtils.callInTransaction(() -> {
+ reactionDao.update(reaction);
+ return null;
+ });
+ } catch (final AnnotatorException e) {
+ logger.warn("{} annotation problem.", elementUtils.getElementTag(reaction, elementAnnotator), e);
+ }
+ }
+ counter++;
+ progressUpdater.setProgress(IProgressUpdater.MAX_PROGRESS * counter / amount);
+ }
+
+ for (final Integer elementId : elementIds) {
+ Element element = dbUtils.callInTransactionWithResult(() -> elementDao.getById(elementId));
+
List<AnnotatorData> list = annotationSchema.getAnnotatorsForClass(element.getClass());
if (list == null) {
list = getDefaultAnnotators(element.getClass());
@@ -131,35 +144,30 @@ public class ModelAnnotator {
try {
elementAnnotator = getAnnotator(annotatorData);
elementAnnotator.annotateElement(element, annotatorData);
+ dbUtils.callInTransaction(() -> {
+ elementDao.update(element);
+ return null;
+ });
} catch (final AnnotatorException e) {
- logger.warn(elementUtils.getElementTag(element, elementAnnotator) + " annotation problem.", e);
+ logger.warn("{} annotation problem.", elementUtils.getElementTag(element, elementAnnotator), e);
}
}
counter++;
progressUpdater.setProgress(IProgressUpdater.MAX_PROGRESS * counter / amount);
}
+
}
private IElementAnnotator getAnnotator(final AnnotatorData annotatorData) throws AnnotatorException {
for (final IElementAnnotator proxiedElementAnnotator : availableAnnotators) {
IElementAnnotator elementAnnotator = (IElementAnnotator) unwrapProxy(proxiedElementAnnotator);
if (annotatorData.getAnnotatorClassName().isAssignableFrom(elementAnnotator.getClass())) {
- return elementAnnotator;
+ return proxiedElementAnnotator;
}
}
throw new AnnotatorException("Annotator not supported: " + annotatorData.getAnnotatorClassName());
}
- /**
- * Returns list of default annotators ({@link ElementAnnotator} with
- * {@link ElementAnnotator#isDefault()} flag).
- *
- * @return list of default annotators
- */
- List<IElementAnnotator> getDefaultAnnotators() {
- return defaultAnnotators;
- }
-
/**
* Returns list of default {@link ElementAnnotator} names that are available
* for class given in the parameter.
@@ -215,30 +223,6 @@ public class ModelAnnotator {
return result;
}
- /**
- * Converts list of strings into list of {@link ElementAnnotator}. Strings
- * must be valid {@link ElementAnnotator} common names.
- *
- * @param list list of {@link ElementAnnotator#getCommonName()}.
- * @return list of {@link ElementAnnotator annotators}
- */
- public List<IElementAnnotator> getAnnotatorsFromCommonNames(final List<AnnotatorData> list) {
- List<IElementAnnotator> result = new ArrayList<>();
- for (final AnnotatorData annotatorData : list) {
- boolean added = false;
- for (final IElementAnnotator annotator : availableAnnotators) {
- if (annotatorData.getAnnotatorClassName().isAssignableFrom(unwrapProxy(annotator).getClass())) {
- added = true;
- result.add(annotator);
- }
- }
- if (!added) {
- throw new InvalidArgumentException("Unknown annotator name: " + annotatorData.getAnnotatorClassName());
- }
- }
- return result;
- }
-
/**
* Returns map with information about default valid {@link MiriamType miriam
* types } for {@link BioEntity} class type.
@@ -247,15 +231,15 @@ public class ModelAnnotator {
*/
@SuppressWarnings("unchecked")
public Map<Class<? extends BioEntity>, Set<MiriamType>> getDefaultValidClasses() {
- Map<Class<? extends BioEntity>, Set<MiriamType>> result = new HashMap<Class<? extends BioEntity>, Set<MiriamType>>();
+ Map<Class<? extends BioEntity>, Set<MiriamType>> result = new HashMap<>();
ElementUtils eu = new ElementUtils();
ClassTreeNode tree = eu.getAnnotatedElementClassTree();
- Queue<ClassTreeNode> nodes = new LinkedList<ClassTreeNode>();
+ Queue<ClassTreeNode> nodes = new LinkedList<>();
nodes.add(tree);
while (!nodes.isEmpty()) {
ClassTreeNode node = nodes.poll();
- Set<MiriamType> set = new HashSet<MiriamType>();
+ Set<MiriamType> set = new HashSet<>();
Class<? extends BioEntity> clazz = (Class<? extends BioEntity>) node.getClazz();
for (final MiriamType mt : MiriamType.values()) {
for (final Class<?> clazz2 : mt.getValidClass()) {
@@ -265,9 +249,7 @@ public class ModelAnnotator {
}
}
result.put(clazz, set);
- for (final ClassTreeNode child : node.getChildren()) {
- nodes.add(child);
- }
+ nodes.addAll(node.getChildren());
}
return result;
}
@@ -302,9 +284,7 @@ public class ModelAnnotator {
}
}
result.put(clazz, set);
- for (final ClassTreeNode child : node.getChildren()) {
- nodes.add(child);
- }
+ nodes.addAll(node.getChildren());
}
return result;
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/CopyMissingCellDesignerMiriamDataAnnotatorImpl.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/CopyMissingCellDesignerMiriamDataAnnotatorImpl.java
index d6557cb24d6c272abcab765e5952211b35789a89..92589a43d4667ef868c136169c9d53929e4cfae6 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/CopyMissingCellDesignerMiriamDataAnnotatorImpl.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/CopyMissingCellDesignerMiriamDataAnnotatorImpl.java
@@ -14,6 +14,7 @@ import lcsb.mapviewer.persist.dao.map.species.ElementProperty;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.Pageable;
import org.springframework.stereotype.Service;
+import org.springframework.transaction.annotation.Transactional;
import java.util.ArrayList;
import java.util.Collections;
@@ -22,6 +23,7 @@ import java.util.List;
import java.util.Map;
@Service
+@Transactional
public class CopyMissingCellDesignerMiriamDataAnnotatorImpl extends ElementAnnotator implements CopyMissingCellDesignerMiriamDataAnnotator {
private final ElementDao elementDao;
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java
index f20fbaed811e371cf0fd3deaf862546e8cbb4048..c9725246dd9fd85d4ce8e429ac83a1ca629f898b 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java
@@ -6,7 +6,6 @@ import lcsb.mapviewer.common.comparator.SetComparator;
import lcsb.mapviewer.common.comparator.StringComparator;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerChemical;
import lcsb.mapviewer.model.LogMarker;
import lcsb.mapviewer.model.ProjectLogEntryType;
import lcsb.mapviewer.model.map.BioEntity;
@@ -101,7 +100,7 @@ public abstract class ElementAnnotator extends CachableInterface implements IEle
*
* @param bioEntity object to be annotated
* @param parameters list of parameters passed to the annotator which is expected to be
- * in the same order as its {@link this#parameterDefs}
+ * in the same order as its {@link this#paramsDefs}
* @throws AnnotatorException thrown when there is a problem with annotating not related to data
*/
@Override
@@ -109,10 +108,10 @@ public abstract class ElementAnnotator extends CachableInterface implements IEle
if (isAnnotatable(bioEntity)) {
final BioEntityProxy proxy = new BioEntityProxy(bioEntity, parameters);
List<AnnotatorInputParameter> inputParameters = parameters.getInputParameters();
- if (inputParameters.size() == 0) {
+ if (inputParameters.isEmpty()) {
inputParameters = getAvailableInputParameters();
}
- if (parameters.getOutputParameters().size() == 0) {
+ if (parameters.getOutputParameters().isEmpty()) {
parameters.addAnnotatorParameters(this.getAvailableOuputProperties());
}
final List<Set<Object>> inputs = getInputsParameters(bioEntity, inputParameters);
@@ -164,8 +163,7 @@ public abstract class ElementAnnotator extends CachableInterface implements IEle
* the parameter.
*
* @param object object to be tested if can be annotated
- * @return <code>true</code> if object can be annotated by this annotator,
- * <code>false</code> otherwise
+ * @return <code>true</code> if object can be annotated by this annotator, <code>false</code> otherwise
*/
@Override
public boolean isAnnotatable(final BioEntity object) {
@@ -183,8 +181,7 @@ public abstract class ElementAnnotator extends CachableInterface implements IEle
* class type.
*
* @param clazz class to be tested if can be annotated
- * @return <code>true</code> if class can be annotated by this annotator,
- * <code>false</code> otherwise
+ * @return <code>true</code> if class can be annotated by this annotator, <code>false</code> otherwise
*/
@Override
public boolean isAnnotatable(final Class<?> clazz) {
@@ -327,8 +324,6 @@ public abstract class ElementAnnotator extends CachableInterface implements IEle
/**
* Creates default {@link AnnotatorData} for this {@link ElementAnnotator}.
- *
- * @return
*/
@Override
public AnnotatorData createAnnotatorData() {
@@ -456,9 +451,9 @@ public abstract class ElementAnnotator extends CachableInterface implements IEle
if (!parameters.hasOutputField(field)) {
return false;
}
- if (oldCollection == null || oldCollection.size() == 0) {
+ if (oldCollection == null || oldCollection.isEmpty()) {
return true;
- } else if (newCollection == null || newCollection.size() == 0) {
+ } else if (newCollection == null || newCollection.isEmpty()) {
return false;
} else {
final SetComparator<String> stringSetComparator = new SetComparator<>(new StringComparator());
@@ -526,13 +521,13 @@ public abstract class ElementAnnotator extends CachableInterface implements IEle
public void setFormerSymbols(final Collection<String> formerSymbols) {
if (originalBioEntity instanceof Element) {
final Element element = (Element) originalBioEntity;
- if (canAssignStringSet(formerSymbols, element.getFormerSymbols(), BioEntityField.SYMBOL)) {
+ if (canAssignStringSet(formerSymbols, element.getFormerSymbols(), BioEntityField.PREVIOUS_SYMBOLS)) {
final List<String> sorted = new ArrayList<>(formerSymbols);
Collections.sort(sorted);
element.setFormerSymbols(sorted);
}
} else {
- logger.warn("Cannot assign " + BioEntityField.SYMBOL.getCommonName() + " to "
+ logger.warn("Cannot assign " + BioEntityField.PREVIOUS_SYMBOLS.getCommonName() + " to "
+ originalBioEntity.getClass().getSimpleName());
}
}
@@ -571,7 +566,7 @@ public abstract class ElementAnnotator extends CachableInterface implements IEle
}
/**
- * Sets {@link CellDesignerChemical#smiles}.
+ * Sets {@link Chemical#getSmiles()}.
*
* @param smile value to set
*/
@@ -588,7 +583,7 @@ public abstract class ElementAnnotator extends CachableInterface implements IEle
}
/**
- * Sets {@link Species#charge}.
+ * Sets {@link Species#getCharge()}.
*
* @param charge value to set
*/
@@ -605,7 +600,7 @@ public abstract class ElementAnnotator extends CachableInterface implements IEle
}
/**
- * Sets {@link Reaction#subsystem}.
+ * Sets {@link Reaction#getSubsystem()}.
*
* @param subsystem value to set
*/
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotatorImpl.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotatorImpl.java
index f361ea9493f22e1a7eaf1eb2a84d6627762b8c74..a50a6452f080558ad6d76d563cf7f69d46d99959 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotatorImpl.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotatorImpl.java
@@ -66,7 +66,7 @@ public class HgncAnnotatorImpl extends ElementAnnotator implements HgncAnnotator
proteinAlias.addMiriamData(getExampleValidAnnotation());
annotateElement(proteinAlias);
- if (proteinAlias.getFullName() == null || proteinAlias.getFullName().equals("")) {
+ if (proteinAlias.getFullName() == null || proteinAlias.getFullName().isEmpty()) {
status.setStatus(ExternalServiceStatusType.CHANGED);
} else {
status.setStatus(ExternalServiceStatusType.OK);
@@ -98,7 +98,7 @@ public class HgncAnnotatorImpl extends ElementAnnotator implements HgncAnnotator
Node response = XmlParser.getNode("response", xml.getChildNodes());
Node result = XmlParser.getNode("result", response.getChildNodes());
String count = XmlParser.getNodeAttr("numFound", result);
- if (count == null || count.equals("") || count.equals("0")) {
+ if (count == null || count.isEmpty() || count.equals("0")) {
// print warn info when we have only hgnc identifiers (or no
// identifiers at all)
logger.warn(element.getLogMarker(ProjectLogEntryType.CANNOT_FIND_INFORMATION),
@@ -124,7 +124,7 @@ public class HgncAnnotatorImpl extends ElementAnnotator implements HgncAnnotator
element.addMiriamData(MiriamType.ENTREZ, XmlParser.getNodeValue(node));
} else if (type.equals("symbol")) {
if (!identifier.getDataType().equals(MiriamType.HGNC_SYMBOL) || !element.contains(identifier)) {
- // add hgnc symbol annnotation only when there was no
+ // add hgnc symbol annotation only when there was no
// hgnc_symbol in the element
element.addMiriamData(MiriamType.HGNC_SYMBOL, XmlParser.getNodeValue(node));
}
@@ -214,6 +214,7 @@ public class HgncAnnotatorImpl extends ElementAnnotator implements HgncAnnotator
new AnnotatorOutputParameter(MiriamType.REFSEQ),
new AnnotatorOutputParameter(MiriamType.UNIPROT),
new AnnotatorOutputParameter(BioEntityField.SYMBOL),
+ new AnnotatorOutputParameter(BioEntityField.PREVIOUS_SYMBOLS),
new AnnotatorOutputParameter(BioEntityField.SYNONYMS),
new AnnotatorOutputParameter(BioEntityField.NAME),
new AnnotatorOutputParameter(BioEntityField.FULL_NAME));
@@ -273,7 +274,7 @@ public class HgncAnnotatorImpl extends ElementAnnotator implements HgncAnnotator
Node response = XmlParser.getNode("response", xml.getChildNodes());
Node resultNode = XmlParser.getNode("result", response.getChildNodes());
String count = XmlParser.getNodeAttr("numFound", resultNode);
- if (count == null || count.equals("") || count.equals("0")) {
+ if (count == null || count.isEmpty() || count.equals("0")) {
return result;
} else {
Node entry = XmlParser.getNode("doc", resultNode.getChildNodes());
@@ -332,7 +333,7 @@ public class HgncAnnotatorImpl extends ElementAnnotator implements HgncAnnotator
Node response = XmlParser.getNode("response", xml.getChildNodes());
Node resultNode = XmlParser.getNode("result", response.getChildNodes());
String count = XmlParser.getNodeAttr("numFound", resultNode);
- if (count == null || count.equals("") || count.equals("0")) {
+ if (count == null || count.isEmpty() || count.equals("0")) {
return null;
} else {
Node entry = XmlParser.getNode("doc", resultNode.getChildNodes());
@@ -400,7 +401,7 @@ public class HgncAnnotatorImpl extends ElementAnnotator implements HgncAnnotator
Node response = XmlParser.getNode("response", xml.getChildNodes());
Node result = XmlParser.getNode("result", response.getChildNodes());
String count = XmlParser.getNodeAttr("numFound", result);
- if (count == null || count.equals("") || count.equals("0")) {
+ if (count == null || count.isEmpty() || count.equals("0")) {
return null;
} else {
Node entry = XmlParser.getNode("doc", result.getChildNodes());
@@ -420,9 +421,7 @@ public class HgncAnnotatorImpl extends ElementAnnotator implements HgncAnnotator
}
}
return null;
- } catch (final IOException e) {
- throw new AnnotatorException(e);
- } catch (final InvalidXmlSchemaException e) {
+ } catch (final IOException | InvalidXmlSchemaException e) {
throw new AnnotatorException(e);
}
}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/AnnotationNoTransactionTestFunctions.java b/annotation/src/test/java/lcsb/mapviewer/annotation/AnnotationNoTransactionTestFunctions.java
new file mode 100644
index 0000000000000000000000000000000000000000..43ecc94b43f82eccf880b0b854fd3b8a17afb516
--- /dev/null
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/AnnotationNoTransactionTestFunctions.java
@@ -0,0 +1,123 @@
+package lcsb.mapviewer.annotation;
+
+import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.common.tests.TestUtils;
+import lcsb.mapviewer.common.tests.UnitTestFailedWatcher;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.graphics.HorizontalAlign;
+import lcsb.mapviewer.model.graphics.LineType;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.graphics.VerticalAlign;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Ion;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.persist.dao.cache.CacheTypeDao;
+import org.junit.Rule;
+import org.junit.runner.RunWith;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.test.context.ContextConfiguration;
+import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
+
+import java.util.HashMap;
+import java.util.Map;
+
+@ContextConfiguration(classes = SpringAnnotationTestConfig.class)
+@RunWith(SpringJUnit4ClassRunner.class)
+public abstract class AnnotationNoTransactionTestFunctions extends TestUtils {
+
+ private static final Map<String, Model> models = new HashMap<>();
+
+ @Rule
+ public UnitTestFailedWatcher unitTestFailedWatcher = new UnitTestFailedWatcher();
+
+ @Autowired
+ protected GeneralCacheInterface cache;
+
+ @Autowired
+ protected CacheTypeDao cacheTypeDao;
+
+ private static int idCounter = 0;
+
+ protected Model getModelForFile(final String fileName, final boolean fromCache) throws Exception {
+ if (!fromCache) {
+ logger.debug("File without cache: {}", fileName);
+ return new CellDesignerXmlParser().createModel(new ConverterParams().filename(fileName));
+ }
+ Model result = AnnotationNoTransactionTestFunctions.models.get(fileName);
+ if (result == null) {
+ logger.debug("File to cache: {}", fileName);
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ result = parser.createModel(new ConverterParams().filename(fileName).sizeAutoAdjust(false));
+ AnnotationNoTransactionTestFunctions.models.put(fileName, result);
+ }
+ return result;
+ }
+
+ public GenericProtein createProtein() {
+ GenericProtein result = new GenericProtein("s" + (idCounter++));
+ populateRandomData(result);
+
+ return result;
+ }
+
+ private static void populateRandomData(final Species result) {
+ result.setNameX(faker.number().numberBetween(10, 100));
+ result.setNameY(faker.number().numberBetween(10, 100));
+ result.setZ(faker.number().numberBetween(10, 100));
+ result.setNameWidth(faker.number().numberBetween(10, 100));
+ result.setNameHeight(faker.number().numberBetween(10, 100));
+ result.setHomodimer(faker.number().numberBetween(1, 10));
+ result.setNameHorizontalAlign(faker.options().option(HorizontalAlign.class));
+ result.setNameVerticalAlign(faker.options().option(VerticalAlign.class));
+ result.setHypothetical(faker.bool().bool());
+ result.setName(faker.name().fullName());
+ }
+
+ public Ion createIon() {
+ Ion result = new Ion("s" + (idCounter++));
+ populateRandomData(result);
+
+ return result;
+ }
+
+ public ModelData createModelData() {
+ ModelData model = new ModelData();
+ model.setWidth(faker.number().numberBetween(1, 1000));
+ model.setHeight(faker.number().numberBetween(1, 1000));
+
+ return model;
+ }
+
+ public Project createProject() {
+ User admin = new User();
+ admin.setId(BUILT_IN_TEST_ADMIN_ID);
+
+ Project project = new Project();
+ project.setProjectId(faker.numerify("T######"));
+ project.setOwner(admin);
+
+ return project;
+ }
+
+ protected Reaction createEmptyReaction() {
+ Reaction reaction = new Reaction(faker.numerify("re######"));
+ reaction.setLine(createLine());
+ reaction.setZ(faker.number().numberBetween(1, 10));
+
+ return reaction;
+ }
+
+ private PolylineData createLine() {
+ PolylineData line = new PolylineData();
+ line.setType(faker.options().option(LineType.class));
+ return line;
+ }
+
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/AnnotationTestFunctions.java b/annotation/src/test/java/lcsb/mapviewer/annotation/AnnotationTestFunctions.java
index 773ea51aca3896bd6bfa673b7273b961d0b6e4a7..1b385167c0db6ac5b6614c20a45e7401c9133534 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/AnnotationTestFunctions.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/AnnotationTestFunctions.java
@@ -1,95 +1,13 @@
package lcsb.mapviewer.annotation;
-import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
-import lcsb.mapviewer.common.tests.TestUtils;
-import lcsb.mapviewer.common.tests.UnitTestFailedWatcher;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.graphics.HorizontalAlign;
-import lcsb.mapviewer.model.graphics.VerticalAlign;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelData;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Ion;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.persist.dao.cache.CacheTypeDao;
-import org.junit.Rule;
import org.junit.runner.RunWith;
-import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.test.context.ContextConfiguration;
import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
import org.springframework.transaction.annotation.Transactional;
-import java.util.HashMap;
-import java.util.Map;
-
@Transactional
@ContextConfiguration(classes = SpringAnnotationTestConfig.class)
@RunWith(SpringJUnit4ClassRunner.class)
-public abstract class AnnotationTestFunctions extends TestUtils {
-
- private static final Map<String, Model> models = new HashMap<>();
-
- @Rule
- public UnitTestFailedWatcher unitTestFailedWatcher = new UnitTestFailedWatcher();
-
- @Autowired
- protected GeneralCacheInterface cache;
-
- @Autowired
- protected CacheTypeDao cacheTypeDao;
-
- private static int idCounter = 0;
-
- protected Model getModelForFile(final String fileName, final boolean fromCache) throws Exception {
- if (!fromCache) {
- logger.debug("File without cache: {}", fileName);
- return new CellDesignerXmlParser().createModel(new ConverterParams().filename(fileName));
- }
- Model result = AnnotationTestFunctions.models.get(fileName);
- if (result == null) {
- logger.debug("File to cache: {}", fileName);
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- result = parser.createModel(new ConverterParams().filename(fileName).sizeAutoAdjust(false));
- AnnotationTestFunctions.models.put(fileName, result);
- }
- return result;
- }
-
- public GenericProtein createProtein() {
- GenericProtein result = new GenericProtein("s" + (idCounter++));
- populateRandomData(result);
-
- return result;
- }
-
- private static void populateRandomData(final Species result) {
- result.setNameX(faker.number().numberBetween(10, 100));
- result.setNameY(faker.number().numberBetween(10, 100));
- result.setZ(faker.number().numberBetween(10, 100));
- result.setNameWidth(faker.number().numberBetween(10, 100));
- result.setNameHeight(faker.number().numberBetween(10, 100));
- result.setHomodimer(faker.number().numberBetween(1, 10));
- result.setNameHorizontalAlign(faker.options().option(HorizontalAlign.class));
- result.setNameVerticalAlign(faker.options().option(VerticalAlign.class));
- result.setHypothetical(faker.bool().bool());
- result.setName(faker.name().fullName());
- }
-
- public Ion createIon() {
- Ion result = new Ion("s" + (idCounter++));
- populateRandomData(result);
-
- return result;
- }
-
- public ModelData createModelData() {
- ModelData model = new ModelData();
- model.setWidth(faker.number().numberBetween(1, 1000));
- model.setHeight(faker.number().numberBetween(1, 1000));
-
- return model;
- }
+public abstract class AnnotationTestFunctions extends AnnotationNoTransactionTestFunctions {
}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java
index 4c0b8d8d3b740145734cf83af26ac7ec29461195..ee55829d8da801de411ff11c1b4c98622c79bc04 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java
@@ -1,16 +1,17 @@
package lcsb.mapviewer.annotation.services;
-import lcsb.mapviewer.annotation.AnnotationTestFunctions;
+import lcsb.mapviewer.annotation.AnnotationNoTransactionTestFunctions;
import lcsb.mapviewer.annotation.services.annotators.IElementAnnotator;
import lcsb.mapviewer.common.IProgressUpdater;
+import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
import lcsb.mapviewer.model.map.model.SubmodelType;
-import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Ion;
@@ -18,6 +19,8 @@ import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.user.UserAnnotationSchema;
import lcsb.mapviewer.model.user.UserClassAnnotators;
+import lcsb.mapviewer.persist.DbUtils;
+import lcsb.mapviewer.persist.dao.ProjectDao;
import lcsb.mapviewer.persist.dao.map.ModelDao;
import org.apache.commons.lang3.mutable.MutableDouble;
import org.junit.After;
@@ -38,11 +41,8 @@ import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertTrue;
-public class ModelAnnotatorTest extends AnnotationTestFunctions {
- private final IProgressUpdater updater = new IProgressUpdater() {
- @Override
- public void setProgress(final double progress) {
- }
+public class ModelAnnotatorTest extends AnnotationNoTransactionTestFunctions {
+ private final IProgressUpdater updater = progress -> {
};
@Autowired
@@ -51,50 +51,72 @@ public class ModelAnnotatorTest extends AnnotationTestFunctions {
@Autowired
private ModelDao modelDao;
+ @Autowired
+ private ProjectDao projectDao;
+
+ @Autowired
+ private DbUtils dbUtils;
+
+ private List<Project> projects = new ArrayList<>();
+
@Before
public void setUp() throws Exception {
+ projects = new ArrayList<>();
}
@After
public void tearDown() throws Exception {
+ for (Project project : projects) {
+ dbUtils.callInTransaction(() -> {
+ projectDao.delete(projectDao.getById(project.getId()));
+ return null;
+ });
+ }
}
@Test
public void testAnnotateModel() {
- Model model = new ModelFullIndexed(null);
-
- model.addReaction(new Reaction("re"));
+ ModelData modelData = createModelData();
+ modelData.addReaction(createEmptyReaction());
- Species protein1 = new GenericProtein("a1");
+ Species protein1 = createProtein();
protein1.setName("SNCA");
- Species protein2 = new GenericProtein("a2");
+ Species protein2 = createProtein();
protein2.setName("PDK1");
protein2.addMiriamData(new MiriamData(MiriamType.CAS, "c"));
- model.addElement(protein1);
- model.addElement(protein2);
+ modelData.addElement(protein1);
+ modelData.addElement(protein2);
+ Project project = createProject();
+ project.addModel(modelData);
+ this.persistProject(project);
- modelAnnotator.annotateModel(model, updater, modelAnnotator.createDefaultAnnotatorSchema());
+ modelAnnotator.performAnnotations(project, updater, modelAnnotator.createDefaultAnnotatorSchema());
- assertTrue(model.getElementByElementId("a1").getMiriamData().size() > 0);
- assertTrue(model.getElementByElementId("a2").getMiriamData().size() >= 1);
+ dbUtils.callInTransaction(() -> {
+ Model model = new ModelFullIndexed(modelDao.getById(modelData.getId()));
+ assertFalse(model.getElementByElementId(protein1.getElementId()).getMiriamData().isEmpty());
+ assertFalse(model.getElementByElementId(protein2.getElementId()).getMiriamData().isEmpty());
- modelAnnotator.annotateModel(model, updater, modelAnnotator.createDefaultAnnotatorSchema());
+ return null;
+ });
+ modelAnnotator.performAnnotations(project, updater, modelAnnotator.createDefaultAnnotatorSchema());
}
+
@Test
- public void testAnnotateModelWithGivenAnnotators() throws Exception {
- Model model = new ModelFullIndexed(null);
- GenericProtein species = new GenericProtein("id1");
+ public void testAnnotateModelWithGivenAnnotators() {
+ ModelData modelData = createModelData();
+ GenericProtein species = createProtein();
species.setName("SNCA");
- model.addElement(species);
+ modelData.addElement(species);
- Ion species2 = new Ion("id2");
+ Ion species2 = createIon();
species2.setName("h2o");
species2.addMiriamData(new MiriamData(MiriamType.CHEBI, "12345"));
- model.addElement(species2);
- model.addReaction(new Reaction("re"));
+ modelData.addElement(species2);
+ modelData.addReaction(createEmptyReaction());
UserAnnotationSchema annotationSchema = new UserAnnotationSchema();
@@ -106,140 +128,196 @@ public class ModelAnnotatorTest extends AnnotationTestFunctions {
ionAnnotators.setAnnotators(modelAnnotator.getDefaultAnnotators(Ion.class));
annotationSchema.addClassAnnotator(ionAnnotators);
- modelAnnotator.annotateModel(model, updater, annotationSchema);
+ Project project = createProject();
+ project.addModel(modelData);
+ this.persistProject(project);
- // we didn't annotate protein
- assertEquals(0, species.getMiriamData().size());
- // but we should annotate ion
- assertFalse(species2.getFullName().isEmpty());
+ modelAnnotator.performAnnotations(project, updater, annotationSchema);
+
+ dbUtils.callInTransaction(() -> {
+ Model model = new ModelFullIndexed(modelDao.getById(modelData.getId()));
+
+ Element protein = model.getElementByElementId(species.getElementId());
+ Element ion = model.getElementByElementId(species2.getElementId());
+ // we didn't annotate protein
+ assertEquals(0, protein.getMiriamData().size());
+ // but we should annotate ion
+ assertFalse(ion.getFullName().isEmpty());
+
+ return null;
+ });
}
@Test
public void testDuplicateAnnotations() throws Exception {
- int counter = 0;
- Model model = getModelForFile("testFiles/annotation/duplicate.xml", false);
+ ModelData modelData = getModelForFile("testFiles/annotation/duplicate.xml", false).getModelData();
- Set<String> knowAnnotations = new HashSet<String>();
+ Project project = createProject();
+ project.addModel(modelData);
+ this.persistProject(project);
- modelAnnotator.annotateModel(model, updater, modelAnnotator.createDefaultAnnotatorSchema());
- for (final MiriamData md : model.getElementByElementId("sa1").getMiriamData()) {
- knowAnnotations.add(md.getDataType() + ":" + md.getRelationType() + ":" + md.getResource());
- }
- counter = 0;
- for (final String string : knowAnnotations) {
- if (string.contains("29108")) {
- counter++;
+ modelAnnotator.performAnnotations(project, updater, modelAnnotator.createDefaultAnnotatorSchema());
+
+ dbUtils.callInTransaction(() -> {
+ Model model = new ModelFullIndexed(modelDao.getById(project.getTopModel().getId()));
+ Set<String> knowAnnotations = new HashSet<>();
+ for (final MiriamData md : model.getElementByElementId("sa1").getMiriamData()) {
+ knowAnnotations.add(md.getDataType() + ":" + md.getRelationType() + ":" + md.getResource());
}
- }
- assertEquals(1, counter);
+ int counter = 0;
+ for (final String string : knowAnnotations) {
+ if (string.contains("29108")) {
+ counter++;
+ }
+ }
+ assertEquals(1, counter);
+ return null;
+ });
- modelAnnotator.annotateModel(model, updater, modelAnnotator.createDefaultAnnotatorSchema());
+ modelAnnotator.performAnnotations(project, updater, modelAnnotator.createDefaultAnnotatorSchema());
- knowAnnotations.clear();
- for (final MiriamData md : model.getElementByElementId("sa1").getMiriamData()) {
- knowAnnotations.add(md.getDataType() + ":" + md.getRelationType() + ":" + md.getResource());
- }
- counter = 0;
- for (final String string : knowAnnotations) {
- if (string.contains("29108")) {
- counter++;
+ dbUtils.callInTransaction(() -> {
+ Model model = new ModelFullIndexed(modelDao.getById(project.getTopModel().getId()));
+ Set<String> knowAnnotations = new HashSet<>();
+ for (final MiriamData md : model.getElementByElementId("sa1").getMiriamData()) {
+ knowAnnotations.add(md.getDataType() + ":" + md.getRelationType() + ":" + md.getResource());
}
- }
- assertEquals(1, counter);
+ int counter = 0;
+ for (final String string : knowAnnotations) {
+ if (string.contains("29108")) {
+ counter++;
+ }
+ }
+ assertEquals(1, counter);
+ return null;
+ });
}
@Test
public void testGetAnnotationsForSYN() throws Exception {
- Model model = getModelForFile("testFiles/annotation/emptyAnnotationsSyn1.xml", true);
- Element sa1 = model.getElementByElementId("sa1");
- Element sa2 = model.getElementByElementId("sa2");
-
- assertFalse(sa1.getNotes().contains("Symbol"));
- assertFalse(sa2.getNotes().contains("Symbol"));
- modelAnnotator.annotateModel(model, updater, modelAnnotator.createDefaultAnnotatorSchema());
- assertFalse(sa2.getNotes().contains("Symbol"));
- assertNotNull(sa1.getSymbol());
- assertNotEquals("", sa1.getSymbol());
- // modelAnnotator.removeIncorrectAnnotations(model, updater);
- assertNotNull(sa1.getSymbol());
- assertNotEquals("", sa1.getSymbol());
- assertFalse(sa1.getNotes().contains("Symbol"));
- assertFalse(sa2.getNotes().contains("Symbol"));
- assertNull(sa2.getSymbol());
-
- for (final Species el : model.getSpeciesList()) {
- if (el.getNotes() != null) {
- assertFalse("Invalid notes: " + el.getNotes(), el.getNotes().contains("Symbol"));
- assertFalse("Invalid notes: " + el.getNotes(), el.getNotes().contains("HGNC"));
+ ModelData modelData = getModelForFile("testFiles/annotation/emptyAnnotationsSyn1.xml", true).getModelData();
+
+ Project project = createProject();
+ project.addModel(modelData);
+ this.persistProject(project);
+ modelAnnotator.performAnnotations(project, updater, modelAnnotator.createDefaultAnnotatorSchema());
+
+ dbUtils.callInTransaction(() -> {
+ Project p = projectDao.getProjectByProjectId(project.getProjectId());
+ Model model = new ModelFullIndexed(modelDao.getById(p.getTopModel().getId()));
+
+ Element sa1 = model.getElementByElementId("sa1");
+ Element sa2 = model.getElementByElementId("sa2");
+
+ assertFalse(sa2.getNotes().contains("Symbol"));
+ assertNotNull(sa1.getSymbol());
+ assertNotEquals("", sa1.getSymbol());
+ // modelAnnotator.removeIncorrectAnnotations(model, updater);
+ assertNotNull(sa1.getSymbol());
+ assertNotEquals("", sa1.getSymbol());
+ assertFalse(sa1.getNotes().contains("Symbol"));
+ assertFalse(sa2.getNotes().contains("Symbol"));
+ assertNull(sa2.getSymbol());
+
+ for (final Species el : model.getSpeciesList()) {
+ if (el.getNotes() != null) {
+ assertFalse("Invalid notes: " + el.getNotes(), el.getNotes().contains("Symbol"));
+ assertFalse("Invalid notes: " + el.getNotes(), el.getNotes().contains("HGNC"));
+ }
}
- }
+ return null;
+ });
+
}
@Test
public void testAnnotateModelWithDrugMolecule() throws Exception {
- Model model = super.getModelForFile("testFiles/annotation/problematic.xml", false);
+ ModelData modelData = super.getModelForFile("testFiles/annotation/problematic.xml", false).getModelData();
+
+ Project project = createProject();
+ project.addModel(modelData);
+ this.persistProject(project);
- modelAnnotator.annotateModel(model, updater, modelAnnotator.createDefaultAnnotatorSchema());
- modelDao.add(model);
+ modelAnnotator.performAnnotations(project, updater, modelAnnotator.createDefaultAnnotatorSchema());
- modelDao.delete(model);
}
+
@Test
- public void testGetDefaultRequired() throws Exception {
+ public void testGetDefaultRequired() {
Map<Class<? extends BioEntity>, Set<MiriamType>> map1 = modelAnnotator.getDefaultRequiredClasses();
assertNotNull(map1);
}
@Test
- public void testGetDefaultValid() throws Exception {
+ public void testGetDefaultValid() {
Map<Class<? extends BioEntity>, Set<MiriamType>> map2 = modelAnnotator.getDefaultValidClasses();
assertNotNull(map2);
}
@Test
- public void testPerformAnnotationAndCheckProgress() throws Exception {
- Model model = new ModelFullIndexed(null);
- Model submodel = new ModelFullIndexed(null);
- Model submodel2 = new ModelFullIndexed(null);
+ public void testPerformAnnotationAndCheckProgress() {
+ dbUtils.callInTransaction(() -> {
+ Project project = createProject();
+ Model model = new ModelFullIndexed(null);
+ Model submodel = new ModelFullIndexed(null);
+ Model submodel2 = new ModelFullIndexed(null);
- GenericProtein protein = new GenericProtein("el");
+ GenericProtein protein = createProtein();
- model.addSubmodelConnection(new ModelSubmodelConnection(submodel, SubmodelType.UNKNOWN));
- model.addSubmodelConnection(new ModelSubmodelConnection(submodel2, SubmodelType.UNKNOWN));
+ model.addSubmodelConnection(new ModelSubmodelConnection(submodel, SubmodelType.UNKNOWN));
+ model.addSubmodelConnection(new ModelSubmodelConnection(submodel2, SubmodelType.UNKNOWN));
- model.addElement(protein);
- submodel.addElement(protein);
- submodel2.addElement(protein);
+ model.addElement(protein);
+ submodel.addElement(protein);
+ submodel2.addElement(protein);
- final MutableDouble maxProgress = new MutableDouble(0.0);
+ final MutableDouble maxProgress = new MutableDouble(0.0);
- modelAnnotator.performAnnotations(model, new IProgressUpdater() {
- @Override
- public void setProgress(final double progress) {
- maxProgress.setValue(Math.max(progress, maxProgress.getValue()));
- }
- });
- assertTrue(maxProgress.getValue() <= IProgressUpdater.MAX_PROGRESS);
+ project.addModel(model);
+ project.addModel(submodel);
+ project.addModel(submodel2);
+ projectDao.add(project);
+
+
+ modelAnnotator.performAnnotations(project,
+ progress -> maxProgress.setValue(Math.max(progress, maxProgress.getValue())), new UserAnnotationSchema());
+ assertTrue(maxProgress.getValue() <= IProgressUpdater.MAX_PROGRESS);
+ projectDao.delete(project);
+
+ return null;
+ });
}
@Test
public void testGetAvailableAnnotators() {
List<IElementAnnotator> list = modelAnnotator.getAvailableAnnotators(Protein.class);
- assertTrue(list.size() > 0);
+ assertFalse(list.isEmpty());
}
@Test
public void testGetAvailableAnnotators2() {
List<IElementAnnotator> list = modelAnnotator.getAvailableAnnotators();
- assertTrue(list.size() > 0);
+ assertFalse(list.isEmpty());
}
@Test
public void testGetAvailableDefaultAnnotators() {
List<IElementAnnotator> list = modelAnnotator.getAvailableDefaultAnnotators(Protein.class);
- assertTrue(list.size() > 0);
+ assertFalse(list.isEmpty());
+ }
+
+ protected Project persistProject(final Project project) {
+ Project projectData = dbUtils.callInTransactionWithResult(() -> {
+ try {
+ return projectDao.add(project);
+ } catch (Exception e) {
+ throw new RuntimeException(e);
+ }
+ });
+ projects.add(projectData);
+ return projectData;
}
}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotatorTest.java
index d0b2c8083a06fe301aa485c9dda95ff0cf7a4c97..513373614491627c0adec42d51e30c57d0a48dcb 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotatorTest.java
@@ -1,24 +1,5 @@
package lcsb.mapviewer.annotation.services.annotators;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import static org.mockito.ArgumentMatchers.anyString;
-import static org.mockito.ArgumentMatchers.nullable;
-import static org.mockito.Mockito.when;
-
-import java.io.IOException;
-import java.util.List;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.test.util.ReflectionTestUtils;
-
import lcsb.mapviewer.annotation.AnnotationTestFunctions;
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
import lcsb.mapviewer.annotation.cache.WebPageDownloader;
@@ -28,6 +9,24 @@ import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Species;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.test.util.ReflectionTestUtils;
+
+import java.io.IOException;
+import java.util.List;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import static org.mockito.ArgumentMatchers.anyString;
+import static org.mockito.ArgumentMatchers.nullable;
+import static org.mockito.Mockito.when;
public class HgncAnnotatorTest extends AnnotationTestFunctions {
@@ -37,7 +36,7 @@ public class HgncAnnotatorTest extends AnnotationTestFunctions {
@Autowired
private GeneralCacheInterface cache;
- private WebPageDownloader webPageDownloader = new WebPageDownloader();
+ private final WebPageDownloader webPageDownloader = new WebPageDownloader();
@Before
public void setUp() {
@@ -112,10 +111,10 @@ public class HgncAnnotatorTest extends AnnotationTestFunctions {
proteinAlias.addMiriamData(nsmf);
hgncAnnotator.annotateElement(proteinAlias);
assertNotNull(proteinAlias.getSymbol());
- assertTrue(proteinAlias.getFormerSymbols().size() > 0);
+ assertFalse(proteinAlias.getFormerSymbols().isEmpty());
assertNotNull(proteinAlias.getFullName());
assertTrue(proteinAlias.getMiriamData().size() > 1);
- assertTrue(proteinAlias.getSynonyms().size() > 0);
+ assertFalse(proteinAlias.getSynonyms().isEmpty());
boolean ensemble = false;
boolean hgncId = false;
@@ -314,13 +313,13 @@ public class HgncAnnotatorTest extends AnnotationTestFunctions {
MiriamData data1 = new MiriamData(MiriamType.HGNC_SYMBOL, "PTGS1");
MiriamData entrez = hgncAnnotator.hgncToEntrez(data1);
assertNotNull(entrez);
- assertTrue(new MiriamData(MiriamType.ENTREZ, "5742").equals(entrez));
+ assertEquals(new MiriamData(MiriamType.ENTREZ, "5742"), entrez);
// check by id
data1 = new MiriamData(MiriamType.HGNC, "11138");
entrez = hgncAnnotator.hgncToEntrez(data1);
assertNotNull(entrez);
- assertTrue(new MiriamData(MiriamType.ENTREZ, "6622").equals(entrez));
+ assertEquals(new MiriamData(MiriamType.ENTREZ, "6622"), entrez);
}
@Test
diff --git a/commons/src/main/java/lcsb/mapviewer/common/tests/TestUtils.java b/commons/src/main/java/lcsb/mapviewer/common/tests/TestUtils.java
index 13abad157870eb17f7a4e97a1b2e252b7c15f469..9b7ee6fecb51e8095505a0712b77d5aa6d8a9af4 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/tests/TestUtils.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/tests/TestUtils.java
@@ -61,6 +61,8 @@ public class TestUtils {
protected static final String BUILT_IN_TEST_ADMIN_PASSWORD = "admin";
protected static final String BUILT_IN_TEST_ADMIN_LOGIN = "admin";
+ protected static final int BUILT_IN_TEST_ADMIN_ID = 1;
+
protected static final String BUILT_IN_PROJECT = "empty";
protected static final int BUILT_IN_MAP_ID = 3;
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/MapGenerator.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/MapGenerator.java
index 6a153c0cdd3fc754a1f0c164583df9d66217427a..eb8e9b4f61bfbd83213b3026e80f23c8c5532f5b 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/MapGenerator.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/MapGenerator.java
@@ -1,25 +1,24 @@
package lcsb.mapviewer.converter.graphics;
-import java.io.File;
-import java.io.IOException;
-
-import org.apache.commons.io.FileUtils;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.IProgressUpdater;
import lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params;
import lcsb.mapviewer.model.map.layout.ProjectBackground;
import lcsb.mapviewer.model.map.layout.ProjectBackgroundImageLayer;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelData;
+import org.apache.commons.io.FileUtils;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+import java.io.File;
+import java.io.IOException;
/**
* This class allows to generate set of images that could be later on used by
* Google Maps API.
- *
+ *
* @author Piotr Gawron
- *
*/
public class MapGenerator {
@@ -42,17 +41,14 @@ public class MapGenerator {
/**
* Default class logger.
*/
- private static Logger logger = LogManager.getLogger();
+ private static final Logger logger = LogManager.getLogger();
/**
* This method generates PNG images used by GoogleMaps API.
*
- * @param params
- * {@link MapGeneratorParams params} used for generating images
- * @throws IOException
- * exception thrown when there are some problems with creating images
- * @throws DrawingException
- * thrown when there was a problem with drawing a map
+ * @param params {@link MapGeneratorParams params} used for generating images
+ * @throws IOException exception thrown when there are some problems with creating images
+ * @throws DrawingException thrown when there was a problem with drawing a map
*/
public void generateMapImages(final MapGeneratorParams params) throws IOException, DrawingException {
@@ -137,32 +133,28 @@ public class MapGenerator {
/**
* Computes how many zoom levels should exists for the map model.
*
- * @param model
- * map model
+ * @param model map model
* @return zoom levels for the model
*/
- public int computeZoomLevels(final Model model) {
+ public int computeZoomLevels(final ModelData model) {
return (int) Math.ceil(Math.log(computeZoomFactor(model)) / Math.log(2));
}
/**
* Computes the scale that should be used on the top zoom level.
*
- * @param model
- * model for which computation is done
+ * @param model model for which computation is done
* @return scale on the top zoom level
*/
- public double computeZoomFactor(final Model model) {
+ public double computeZoomFactor(final ModelData model) {
return Math.max(model.getHeight(), model.getWidth()) / (TILE_SIZE);
}
/**
* Removes files that were generated for the layout.
*
- * @param background
- * layout object for which images will be removed
- * @throws IOException
- * thrown when there are some problems with removing files
+ * @param background layout object for which images will be removed
+ * @throws IOException thrown when there are some problems with removing files
*/
public void removeProjectBackground(final ProjectBackground background) throws IOException {
removeProjectBackground(background, null);
@@ -171,12 +163,9 @@ public class MapGenerator {
/**
* Removes files that were generated for the layout.
*
- * @param background
- * background for which images will be removed
- * @param homeDir
- * determines the directory where images are stored (it's optional)
- * @throws IOException
- * thrown when there are some problems with removing files
+ * @param background background for which images will be removed
+ * @param homeDir determines the directory where images are stored (it's optional)
+ * @throws IOException thrown when there are some problems with removing files
*/
public void removeProjectBackground(final ProjectBackground background, final String homeDir) throws IOException {
for (final ProjectBackgroundImageLayer imageLayer : background.getProjectBackgroundImageLayer()) {
@@ -205,36 +194,29 @@ public class MapGenerator {
* <li>{@link #levels}</li>.
* </ul>
*
- *
* @author Piotr Gawron
- *
*/
public class MapGeneratorParams {
/**
* Information about map to be generated.
- *
*/
private Model model;
/**
* Where we want to put the files. The structure of the directory will be as
* follows: directory/subDirA/subDirB/file.PNG. subDirA is a level of zooming.
* subDirB is x coordinate of the image. file is y coordinate of the image.
- *
*/
private String directory;
/**
* Do we want to generate images in hierarchical view or normal.
- *
*/
private boolean nested = false;
/**
* Should we remove empty elements in nested view.
- *
*/
private boolean removeEmpty = false;
/**
* Callback function that update progress information.
- *
*/
private IProgressUpdater updater = new IProgressUpdater() {
@Override
@@ -258,27 +240,25 @@ public class MapGenerator {
private boolean sbgn;
/**
- * @param model
- * the model to set
- * @see #model
+ * @param model the model to set
* @return full {@link MapGeneratorParams} object
+ * @see #model
*/
public MapGeneratorParams model(final Model model) {
this.model = model;
if (zoomFactor == null) {
- zoomFactor = computeZoomFactor(model);
+ zoomFactor = computeZoomFactor(model.getModelData());
}
if (levels == null) {
- levels = computeZoomLevels(model);
+ levels = computeZoomLevels(model.getModelData());
}
return this;
}
/**
- * @param directory
- * the directory to set
- * @see #directory
+ * @param directory the directory to set
* @return full {@link MapGeneratorParams} object
+ * @see #directory
*/
public MapGeneratorParams directory(final String directory) {
this.directory = directory;
@@ -294,10 +274,9 @@ public class MapGenerator {
}
/**
- * @param nested
- * the nested to set
- * @see #nested
+ * @param nested the nested to set
* @return full {@link MapGeneratorParams} object
+ * @see #nested
*/
public MapGeneratorParams nested(final boolean nested) {
this.nested = nested;
@@ -313,10 +292,9 @@ public class MapGenerator {
}
/**
- * @param removeEmpty
- * the removeEmpty to set
- * @see #removeEmpty
+ * @param removeEmpty the removeEmpty to set
* @return full {@link MapGeneratorParams} object
+ * @see #removeEmpty
*/
public MapGeneratorParams removeEmpty(final boolean removeEmpty) {
this.removeEmpty = removeEmpty;
@@ -332,10 +310,9 @@ public class MapGenerator {
}
/**
- * @param updater
- * the updater to set
- * @see #updater
+ * @param updater the updater to set
* @return full {@link MapGeneratorParams} object
+ * @see #updater
*/
public MapGeneratorParams updater(final IProgressUpdater updater) {
this.updater = updater;
@@ -351,10 +328,9 @@ public class MapGenerator {
}
/**
- * @param zoomFactor
- * the zoomFactor to set
- * @see #zoomFactor
+ * @param zoomFactor the zoomFactor to set
* @return full {@link MapGeneratorParams} object
+ * @see #zoomFactor
*/
public MapGeneratorParams zoomFactor(final Double zoomFactor) {
this.zoomFactor = zoomFactor;
@@ -370,10 +346,9 @@ public class MapGenerator {
}
/**
- * @param levels
- * the levels to set
- * @see #levels
+ * @param levels the levels to set
* @return full {@link MapGeneratorParams} object
+ * @see #levels
*/
public MapGeneratorParams levels(final Integer levels) {
this.levels = levels;
@@ -389,10 +364,9 @@ public class MapGenerator {
}
/**
- * @param sbgn
- * the sbgn to set
- * @see #sbgn
+ * @param sbgn the sbgn to set
* @return object with all parameters
+ * @see #sbgn
*/
public MapGeneratorParams sbgn(final boolean sbgn) {
this.sbgn = sbgn;
diff --git a/frontend-js/src/main/js/ServerConnector.js b/frontend-js/src/main/js/ServerConnector.js
index 9e6b35a1bd898e7935c56b20e785814eda2c2749..8965fe3a575b33146f5be0df4bea5ae4b33aa85b 100644
--- a/frontend-js/src/main/js/ServerConnector.js
+++ b/frontend-js/src/main/js/ServerConnector.js
@@ -474,6 +474,20 @@ ServerConnector.getApiUrl = function (paramObj) {
return result;
};
+ServerConnector.getNewApiUrl = function (paramObj) {
+ var type = paramObj.type;
+ var params = this.createGetParams(paramObj.params);
+
+ var result = paramObj.url;
+ if (result === undefined) {
+ result = this.getNewApiBaseUrl() + type;
+ }
+ if (params !== "") {
+ result += "?" + params;
+ }
+ return result;
+};
+
/**
*
* @param [queryParams]
@@ -487,6 +501,19 @@ ServerConnector.getProjectsUrl = function (queryParams, filterParams) {
});
};
+/**
+ *
+ * @param [queryParams]
+ * @param [filterParams]
+ * @return {string}
+ */
+ServerConnector.getNewApiProjectsUrl = function (queryParams, filterParams) {
+ return this.getNewApiUrl({
+ type: "projects/",
+ params: filterParams
+ });
+};
+
ServerConnector.getPluginsUrl = function (queryParams, filterParams) {
return this.getApiUrl({
type: "plugins/",
@@ -538,6 +565,14 @@ ServerConnector.getProjectUrl = function (queryParams, filterParams) {
});
};
+ServerConnector.getNewApiProjectUrl = function (queryParams, filterParams) {
+ var id = this.getIdOrAsterisk(queryParams.projectId);
+ return this.getNewApiUrl({
+ url: this.getNewApiProjectsUrl(queryParams) + id + "/",
+ params: filterParams
+ });
+};
+
ServerConnector.getMoveProjectUrl = function (queryParams, filterParams) {
var id = this.getIdOrAsterisk(queryParams.projectId);
return this.getNewApiBaseUrl() + 'projects/' + id + ':move';
@@ -620,6 +655,17 @@ ServerConnector.getProjectLogsUrl = function (queryParams, filterParams) {
params: filterParams
});
};
+
+ServerConnector.getProjectJobsUrl = function (queryParams, filterParams) {
+ filterParams.page = filterParams.page || 0;
+ filterParams.size = filterParams.size || 10;
+
+ return this.getNewApiUrl({
+ url: this.getNewApiProjectUrl(queryParams) + "job/",
+ params: filterParams
+ });
+};
+
ServerConnector.getMeshUrl = function (queryParams, filterParams) {
return this.getApiUrl({
type: "mesh/" + queryParams.id,
@@ -3301,6 +3347,33 @@ ServerConnector.getProjectLogs = function (params) {
return JSON.parse(content);
});
};
+/**
+ *
+ * @param {Object} [params]
+ * @param {number} [params.start]
+ * @param {number} [params.length]
+ * @param {string} [params.projectId]
+ * @return {Promise}
+ */
+ServerConnector.getProjectJobs = function (params) {
+ var self = this;
+ if (params === undefined) {
+ params = {};
+ }
+
+ var queryParams = {};
+ var filterParams = {
+ page: params.start,
+ size: params.length
+ };
+ return self.getProjectId(params.projectId).then(function (result) {
+ queryParams.projectId = result;
+ return self.sendGetRequest(self.getProjectJobsUrl(queryParams, filterParams));
+ }).then(function (content) {
+ return JSON.parse(content);
+ });
+};
+
/**
*
diff --git a/frontend-js/src/main/js/gui/admin/JobListDialog.js b/frontend-js/src/main/js/gui/admin/JobListDialog.js
new file mode 100644
index 0000000000000000000000000000000000000000..77716074b01af11f18a8ca844206efa8463b7d99
--- /dev/null
+++ b/frontend-js/src/main/js/gui/admin/JobListDialog.js
@@ -0,0 +1,216 @@
+"use strict";
+
+var Promise = require("bluebird");
+var $ = require('jquery');
+
+/* exported logger */
+
+var AbstractGuiElement = require('../AbstractGuiElement');
+
+var Functions = require('../../Functions');
+var GuiConnector = require('../../GuiConnector');
+
+
+/**
+ *
+ * @param {Object} params
+ * @param {HTMLElement} params.element
+ * @param {CustomMap} [params.customMap]
+ * @param {Configuration} params.configuration
+ * @param {Project} [params.project]
+ * @param {string} params.projectId
+ * @param {ServerConnector} params.serverConnector
+ *
+ * @constructor
+ * @extends AbstractGuiElement
+ */
+function JobListDialog(params) {
+ AbstractGuiElement.call(this, params);
+ var self = this;
+ self.createJobListDialogGui();
+
+ /**
+ * @type {string}
+ * @private
+ */
+ self._projectId = params.projectId;
+}
+
+JobListDialog.prototype = Object.create(AbstractGuiElement.prototype);
+JobListDialog.prototype.constructor = JobListDialog;
+
+/**
+ *
+ */
+JobListDialog.prototype.createJobListDialogGui = function () {
+ var self = this;
+ var head = Functions.createElement({
+ type: "thead",
+ content: "<tr>" +
+ "<th>ID</th>" +
+ "<th>Type</th>" +
+ "<th>Status</th>" +
+ "<th>Progress</th>" +
+ "<th>Created at</th>" +
+ "<th>Finished at</th>" +
+ "<th>Priority</th>" +
+ "</tr>"
+ });
+ var body = Functions.createElement({
+ type: "tbody"
+ });
+ var tableElement = Functions.createElement({
+ type: "table",
+ className: "minerva-logs-table",
+ style: "width: 100%"
+ });
+
+ tableElement.appendChild(head);
+ tableElement.appendChild(body);
+
+ self.tableElement = tableElement;
+ self.getElement().appendChild(tableElement);
+
+ var menuRow = Functions.createElement({
+ type: "div",
+ className: "minerva-menu-row",
+ style: "display:table-row; margin:10px"
+ });
+ self.getElement().appendChild(menuRow);
+
+};
+
+function removeNull(object) {
+ if (object === null || object === undefined) {
+ return "";
+ }
+ return object;
+}
+
+function entryToRow(entry) {
+ var row = [];
+ row[0] = removeNull(entry.id);
+ row[1] = removeNull(entry.jobType);
+ row[2] = removeNull(entry.jobStatus);
+ row[3] = removeNull(entry.progress);
+ row[4] = removeNull(entry.jobStarted);
+ row[5] = removeNull(entry.jobFinished);
+ row[6] = removeNull(entry.priority);
+ return row;
+}
+
+/**
+ *
+ * @param {Object} data
+ * @param {number} data.start
+ * @param {number} data.length
+ * @param {Object} data.search
+ * @param {Object} data.draw
+ * @param {Array} data.order
+ * @param {function} callback
+ * @returns {Promise}
+ * @private
+ */
+JobListDialog.prototype._dataTableAjaxCall = function (data, callback) {
+ var self = this;
+ return self.getServerConnector().getProjectJobs({
+ start: data.start / data.length,
+ length: data.length,
+ projectId: self._projectId
+ }).then(function (jobEntries) {
+ var out = [];
+
+ for (var i = 0; i < jobEntries.content.length; i++) {
+ var entry = jobEntries.content[i];
+
+ var row = entryToRow(entry);
+ out.push(row);
+ }
+ callback({
+ draw: data.draw,
+ recordsTotal: jobEntries.totalElements,
+ recordsFiltered: jobEntries.totalElements,
+ data: out
+ });
+ });
+};
+
+JobListDialog.prototype.open = function () {
+ var self = this;
+ if (!$(self.getElement()).hasClass("ui-dialog-content")) {
+ $(self.getElement()).dialog({
+ dialogClass: 'minerva-logs-dialog',
+ title: "Job list",
+ autoOpen: false,
+ resizable: false,
+ width: Math.max(window.innerWidth / 2, window.innerWidth - 100),
+ height: Math.max(window.innerHeight / 2, window.innerHeight - 100)
+ });
+ }
+
+ $(self.getElement()).dialog("open");
+
+ if (!$.fn.DataTable.isDataTable(self.tableElement)) {
+ return new Promise(function (resolve) {
+ $(self.tableElement).dataTable({
+ serverSide: true,
+ ordering: false,
+ searching: false,
+ ajax: function (data, callback) {
+ resolve(self._dataTableAjaxCall(data, callback));
+ },
+ columns: self.getColumnsDefinition()
+ });
+ });
+ } else {
+ $(self.tableElement).dataTable().api(true).draw();
+ return Promise.resolve();
+ }
+
+};
+
+/**
+ *
+ * @returns {Array}
+ */
+JobListDialog.prototype.getColumnsDefinition = function () {
+ return [{
+ name: "id"
+ }, {
+ name: "jobType"
+ }, {
+ name: "jobStatus"
+ }, {
+ name: "progress"
+ }, {
+ name: "jobStarted"
+ }, {
+ name: "jobFinished"
+ }, {
+ name: "priority"
+ }];
+};
+
+/**
+ *
+ * @returns {Promise}
+ */
+JobListDialog.prototype.init = function () {
+ return Promise.resolve();
+};
+
+/**
+ *
+ */
+JobListDialog.prototype.destroy = function () {
+ var self = this;
+ var div = self.getElement();
+ if ($(div).hasClass("ui-dialog-content")) {
+ $(div).dialog("destroy");
+ }
+ if ($.fn.DataTable.isDataTable(self.tableElement)) {
+ $(self.tableElement).DataTable().destroy();
+ }
+};
+
+module.exports = JobListDialog;
diff --git a/frontend-js/src/main/js/gui/admin/MapsAdminPanel.js b/frontend-js/src/main/js/gui/admin/MapsAdminPanel.js
index 5179db7a0a50eb3726b5e4bec6a112ff21f9b65e..aa8a38d6adb45a1cdbbbda81f118bfb3caab449d 100644
--- a/frontend-js/src/main/js/gui/admin/MapsAdminPanel.js
+++ b/frontend-js/src/main/js/gui/admin/MapsAdminPanel.js
@@ -7,6 +7,7 @@ var AbstractAdminPanel = require('./AbstractAdminPanel');
var AddProjectDialog = require('./AddProjectDialog');
var EditProjectDialog = require('./EditProjectDialog');
var LogListDialog = require('./LogListDialog');
+var JobListDialog = require('./JobListDialog');
var PrivilegeType = require('../../map/data/PrivilegeType');
var ConfigurationType = require('../../ConfigurationType');
var NetworkError = require('../../NetworkError');
@@ -242,6 +243,11 @@ MapsAdminPanel.prototype._createProjectTableRow = function () {
return self.showLogs($(button).attr("data")).catch(GuiConnector.alert);
});
+ $(projectsTable).on("click", "[name='showJobs']", function () {
+ var button = this;
+ return self.showJobs($(button).attr("data")).catch(GuiConnector.alert);
+ });
+
$(projectsTable).on("click", "[name='minerva-shared']", function () {
var field = this;
var projectId = $(field).attr('data');
@@ -448,6 +454,14 @@ MapsAdminPanel.prototype.projectToTableRow = function (project, row, user) {
}
}
+ if (isAdmin) {
+ icon = "<i class='fa fa-info' style='font-size:18px; padding-right:10px;color:#337ab7'></i>";
+ status += " <a name='showJobs' href='#' data='" + project.getProjectId() + "'>" + icon + "</a>";
+ } else {
+ status += icon;
+ }
+
+
row[0] = formattedProjectId;
var date = project.getCreationDate();
if (date === undefined) {
@@ -768,6 +782,36 @@ MapsAdminPanel.prototype.getLogDialog = function (projectId) {
}
};
+/**
+ *
+ * @param {string} projectId
+ * @returns {Promise<JobListDialog>}
+ */
+MapsAdminPanel.prototype.getJobDialog = function (projectId) {
+ var self = this;
+ if (self._jobDialogs === undefined) {
+ self._jobDialogs = [];
+ }
+ var dialog = self._jobDialogs[projectId];
+ if (dialog === undefined) {
+ dialog = new JobListDialog({
+ element: Functions.createElement({
+ type: "div"
+ }),
+ configuration: self.getConfiguration(),
+ projectId: projectId,
+ serverConnector: self.getServerConnector(),
+ customMap: null
+ });
+ self._jobDialogs[projectId] = dialog;
+ return dialog.init().then(function () {
+ return dialog;
+ });
+ } else {
+ return Promise.resolve(dialog);
+ }
+};
+
/**
*
* @param {string} id projectId
@@ -804,6 +848,21 @@ MapsAdminPanel.prototype.showLogs = function (id) {
});
};
+/**
+ *
+ * @param {string} id projectId
+ * @returns {Promise<JobListDialog>}
+ */
+MapsAdminPanel.prototype.showJobs = function (id) {
+ var self = this;
+ GuiConnector.showProcessing();
+ return self.getJobDialog(id).then(function (dialog) {
+ return dialog.open();
+ }).finally(function () {
+ GuiConnector.hideProcessing();
+ });
+};
+
/**
*
* @param {string} id projectId
diff --git a/frontend-js/src/test/js/ServerConnector-mock.js b/frontend-js/src/test/js/ServerConnector-mock.js
index 1a1a1f8e86ec676c98c60fadb7e4b31855dc76b2..dd895873a048190ef7d75968c74d7a6a29b4c588 100644
--- a/frontend-js/src/test/js/ServerConnector-mock.js
+++ b/frontend-js/src/test/js/ServerConnector-mock.js
@@ -97,16 +97,39 @@ ServerConnectorMock._sendRequest = function (params) {
});
};
-ServerConnectorMock.getApiBaseUrl = function () {
- return "./testFiles/apiCalls/";
-};
+ServerConnectorMock.Original = {
+ getApiBaseUrl: ServerConnectorMock.getApiBaseUrl,
+ getNewApiBaseUrl: ServerConnectorMock.getNewApiBaseUrl,
+ getApiUrl: ServerConnectorMock.getApiUrl
+}
-var originalGetApiUrl = OriginalServerConnector.getApiUrl;
+ServerConnectorMock.Mock = {
+ getApiBaseUrl: function () {
+ return "./testFiles/apiCalls/";
+ },
+ getNewApiBaseUrl: function () {
+ return "./testFiles/apiCallsNew/";
+ },
+ getApiUrl: function (paramObj) {
+ // replace '?' (or '/?') with '/'
+ // the call is done on ServerConnectorObject (so 'this' is set properly)
+ return ServerConnectorMock.Original.getApiUrl.call(this, paramObj).replace(/\/?\?/g, '/');
+ }
+}
-ServerConnectorMock.getApiUrl = function (paramObj) {
- // replace '?' (or '/?') with '/'
- // the call is done on ServerConnectorObject (so 'this' is set properly)
- return originalGetApiUrl.call(this, paramObj).replace(/\/?\?/g, '/');
-};
+ServerConnectorMock.useMock = function () {
+ ServerConnectorMock.getApiBaseUrl = ServerConnectorMock.Mock.getApiBaseUrl;
+ ServerConnectorMock.getApiUrl = ServerConnectorMock.Mock.getApiUrl;
+ ServerConnectorMock.getNewApiBaseUrl = ServerConnectorMock.Mock.getNewApiBaseUrl;
+
+}
+
+ServerConnectorMock.useOriginal = function () {
+ ServerConnectorMock.getApiBaseUrl = ServerConnectorMock.Original.getApiBaseUrl;
+ ServerConnectorMock.getApiUrl = ServerConnectorMock.Original.getApiUrl;
+ ServerConnectorMock.getNewApiBaseUrl = ServerConnectorMock.Original.getNewApiBaseUrl;
+}
+
+ServerConnectorMock.useMock();
module.exports = ServerConnectorMock;
diff --git a/frontend-js/src/test/js/ServerConnector-test.js b/frontend-js/src/test/js/ServerConnector-test.js
index e677b8bf178c0e389b66290bb5186e551fa29fbd..628c01c574a057bb3a3cf9e6b9e98fa3f42881f7 100644
--- a/frontend-js/src/test/js/ServerConnector-test.js
+++ b/frontend-js/src/test/js/ServerConnector-test.js
@@ -467,5 +467,14 @@ describe('ServerConnector', function () {
});
});
+ it('getProjectJobsUrl', function () {
+ try {
+ ServerConnector.useOriginal();
+ var url = ServerConnector.getProjectJobsUrl("test", {});
+ assert.isTrue(url.includes('new_api'), url);
+ } finally {
+ ServerConnector.useMock();
+ }
+ });
});
diff --git a/model/src/main/java/lcsb/mapviewer/model/LogMarker.java b/model/src/main/java/lcsb/mapviewer/model/LogMarker.java
index 57c34da00a960c61d7d244207aead11fc34f1e56..c6f57a9d0a427c7f9ee377d8739a651f7aefea76 100644
--- a/model/src/main/java/lcsb/mapviewer/model/LogMarker.java
+++ b/model/src/main/java/lcsb/mapviewer/model/LogMarker.java
@@ -1,25 +1,25 @@
package lcsb.mapviewer.model;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.Marker;
-
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.layout.graphics.LayerText;
import lcsb.mapviewer.model.map.reaction.ReactionNode;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.Marker;
+import org.hibernate.proxy.HibernateProxy;
public class LogMarker implements Marker {
private static final Logger logger = LogManager.getLogger(LogMarker.class);
/**
- *
+ *
*/
private static final long serialVersionUID = 1L;
public static final Marker IGNORE = new IgnoredLogMarker();
- private ProjectLogEntry entry;
+ private final ProjectLogEntry entry;
public LogMarker(final ProjectLogEntryType type, final BioEntity bioEntity) {
entry = new ProjectLogEntry();
@@ -27,8 +27,8 @@ public class LogMarker implements Marker {
if (bioEntity != null) {
entry.setObjectIdentifier(bioEntity.getElementId());
entry.setObjectClass(bioEntity.getClass().getSimpleName());
- if (bioEntity.getModel() != null) {
- entry.setMapName(bioEntity.getModel().getName());
+ if (bioEntity.getModelData() != null && !(bioEntity.getModelData() instanceof HibernateProxy)) {
+ entry.setMapName(bioEntity.getModelData().getName());
}
}
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/Project.java b/model/src/main/java/lcsb/mapviewer/model/Project.java
index 81e8d53a14feed3a516e0d9d922d9ddd1a38c672..300e8294fa1357153f178ea4831633e146ba96d2 100644
--- a/model/src/main/java/lcsb/mapviewer/model/Project.java
+++ b/model/src/main/java/lcsb/mapviewer/model/Project.java
@@ -375,7 +375,7 @@ public class Project implements Serializable, MinervaEntity {
}
- public void addLogEntries(final Set<ProjectLogEntry> createLogEntries) {
+ public void addLogEntries(final Collection<ProjectLogEntry> createLogEntries) {
for (final ProjectLogEntry projectLogEntry : createLogEntries) {
addLogEntry(projectLogEntry);
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/ProjectStatus.java b/model/src/main/java/lcsb/mapviewer/model/ProjectStatus.java
index b2a0c9a1eb29d46154eb1108c29a6b7afc38eacc..36e6d8858c6f94049498980f5202c56820fc3dcd 100644
--- a/model/src/main/java/lcsb/mapviewer/model/ProjectStatus.java
+++ b/model/src/main/java/lcsb/mapviewer/model/ProjectStatus.java
@@ -17,11 +17,6 @@ public enum ProjectStatus {
*/
PARSING_DATA("Parsing data"),
- /**
- * Model is annotated by the annotation tool.
- */
- ANNOTATING("Annotating"),
-
/**
* Model is being uploaded to the database.
*/
diff --git a/model/src/main/java/lcsb/mapviewer/model/job/MinervaJob.java b/model/src/main/java/lcsb/mapviewer/model/job/MinervaJob.java
index 835cd5dd426f0cbeffe1d5b2bdb1070cf3fc3535..d878ed679186da961660f27e67c7167c4003e1f0 100644
--- a/model/src/main/java/lcsb/mapviewer/model/job/MinervaJob.java
+++ b/model/src/main/java/lcsb/mapviewer/model/job/MinervaJob.java
@@ -49,6 +49,12 @@ public class MinervaJob implements MinervaEntity {
private Calendar jobFinished;
+ private Double progress;
+
+ private Class<?> externalObjectClass;
+
+ private Integer externalObjectId;
+
@JsonIgnore
private String logs;
@@ -128,4 +134,35 @@ public class MinervaJob implements MinervaEntity {
public EntityType getEntityType() {
throw new NotImplementedException();
}
+
+ public Double getProgress() {
+ return progress;
+ }
+
+ public void setProgress(final Double progress) {
+ this.progress = progress;
+ }
+
+ public Class<?> getExternalObjectClass() {
+ return externalObjectClass;
+ }
+
+ public void setExternalObjectClass(final Class<?> externalObjectClass) {
+ this.externalObjectClass = externalObjectClass;
+ }
+
+ public Integer getExternalObjectId() {
+ return externalObjectId;
+ }
+
+ public void setExternalObjectId(final Integer externalObjectId) {
+ this.externalObjectId = externalObjectId;
+ }
+
+ public void setExternalObject(final MinervaEntity entity) {
+ if (entity != null) {
+ this.externalObjectClass = entity.getClass();
+ this.externalObjectId = entity.getId();
+ }
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/job/MinervaJobType.java b/model/src/main/java/lcsb/mapviewer/model/job/MinervaJobType.java
index 58050aaa7d03229d12da7fc44da1f1e231076974..95fb89e72483a69dac5a359d25480465e411b784 100644
--- a/model/src/main/java/lcsb/mapviewer/model/job/MinervaJobType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/job/MinervaJobType.java
@@ -17,7 +17,10 @@ public enum MinervaJobType {
CREATE_PROJECT_FAILURE,
DELETE_BACKGROUND,
- REVIVE_BACKGROUNDS;
+ REVIVE_BACKGROUNDS,
+
+ ANNOTATE_PROJECT,
+ ;
private final boolean allowDuplicates;
diff --git a/model/src/test/java/lcsb/mapviewer/model/ProjectTest.java b/model/src/test/java/lcsb/mapviewer/model/ProjectTest.java
index 6d49dcb99ca85ada289b1d37091d118099872187..8750df2c3639733f121143a1d64c555c58e8c185 100644
--- a/model/src/test/java/lcsb/mapviewer/model/ProjectTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/ProjectTest.java
@@ -1,17 +1,5 @@
package lcsb.mapviewer.model;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-
-import java.util.Calendar;
-import java.util.HashSet;
-import java.util.Set;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
import lcsb.mapviewer.ModelTestFunctions;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.model.cache.UploadedFileEntry;
@@ -19,6 +7,17 @@ import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import java.util.Calendar;
+import java.util.HashSet;
+import java.util.Set;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
public class ProjectTest extends ModelTestFunctions {
@@ -60,13 +59,13 @@ public class ProjectTest extends ModelTestFunctions {
@Test
public void testGetters() {
MiriamData organism = new MiriamData();
- int id = 5;
- String projectId = "str";
- ProjectStatus status = ProjectStatus.ANNOTATING;
- double progress = 4.5;
+ int id = faker.number().numberBetween(1, Integer.MAX_VALUE);
+ String projectId = faker.numerify("P####");
+ ProjectStatus status = faker.options().option(ProjectStatus.class);
+ double progress = faker.number().randomDouble(2, 1, 100);
Set<ModelData> models = new HashSet<>();
- String directory = "dir";
- String name = "name3";
+ String directory = faker.numerify("dir-####");
+ String name = faker.name().fullName();
MiriamData disease = new MiriamData();
Project project = new Project("str");
boolean sbgn = true;
@@ -107,7 +106,7 @@ public class ProjectTest extends ModelTestFunctions {
}
@Test
- public void testsetCreationDate() {
+ public void testSetCreationDate() {
Project project = new Project();
Calendar creationDate = Calendar.getInstance();
project.setCreationDate(creationDate);
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/DbUtils.java b/persist/src/main/java/lcsb/mapviewer/persist/DbUtils.java
index 8d3e13e38f43574315cdaea02021b9cc2d337abe..5863891af7caa866ccb58f11cf46f19ad3fca532 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/DbUtils.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/DbUtils.java
@@ -1,11 +1,5 @@
package lcsb.mapviewer.persist;
-import java.sql.Connection;
-import java.sql.SQLException;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.Observable;
-
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.hibernate.SessionFactory;
@@ -15,6 +9,14 @@ import org.hibernate.internal.SessionFactoryImpl;
import org.hibernate.jdbc.Work;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
+import org.springframework.transaction.annotation.Transactional;
+
+import java.sql.Connection;
+import java.sql.SQLException;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Observable;
+import java.util.function.Supplier;
/**
* This class contains a set of methods that allow to manage hibernate sessions
@@ -26,9 +28,8 @@ import org.springframework.stereotype.Service;
* </ul>
* Class extends {@link Observable}. Whenever session is created or closed
* observers are notified.
- *
+ *
* @author Piotr Gawron
- *
*/
@SuppressWarnings("deprecation")
@Service
@@ -37,7 +38,7 @@ public class DbUtils extends Observable {
/**
* Default class logger.
*/
- private static Logger logger = LogManager.getLogger();
+ private static final Logger logger = LogManager.getLogger();
/**
* This determines if every add/update/delete operation should be flushed (for
@@ -49,7 +50,7 @@ public class DbUtils extends Observable {
* might be some problems with long transactions.</li>
* </ol>
*/
- private static Map<Long, Boolean> autoFlushForThread = new HashMap<>();
+ private static final Map<Long, Boolean> autoFlushForThread = new HashMap<>();
/**
* Hibernate session factory.
@@ -70,8 +71,7 @@ public class DbUtils extends Observable {
}
/**
- * @param sessionFactory
- * the sessionFactory to set
+ * @param sessionFactory the sessionFactory to set
* @see #sessionFactory
*/
public void setSessionFactory(final SessionFactory sessionFactory) {
@@ -81,9 +81,9 @@ public class DbUtils extends Observable {
/**
* Returns info if the flush is automatically done or not in current
* {@link Thread}.
- *
+ *
* @return <code>true</code> if flush is automatically done,
- * <code>false</code> otherwise
+ * <code>false</code> otherwise
* @see #autoFlushForThread
*/
public boolean isAutoFlush() {
@@ -104,9 +104,8 @@ public class DbUtils extends Observable {
/**
* Set autoFlush for current {@link Thread}.
- *
- * @param autoFlush
- * the new autoflush value
+ *
+ * @param autoFlush the new autoflush value
* @see #autoFlushForThread
*/
public void setAutoFlush(final boolean autoFlush) {
@@ -143,4 +142,15 @@ public class DbUtils extends Observable {
public void dumpDbToFile(final String filename) {
sessionFactory.getCurrentSession().createNativeQuery("SCRIPT '" + filename + "'").executeUpdate();
}
+
+ @Transactional
+ public void callInTransaction(final Supplier<Void> function) {
+ function.get();
+ }
+
+ @Transactional
+ public <T> T callInTransactionWithResult(final Supplier<T> function) {
+ return function.get();
+ }
+
}
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/BaseDao.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/BaseDao.java
index b27d5bafdc5cb28290ae9fc44ea88a6a81ae5430..ac96b749dde60d3b5d6e1d0eef1bbe8ef79da870 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/BaseDao.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/BaseDao.java
@@ -360,6 +360,11 @@ public abstract class BaseDao<T extends MinervaEntity, S extends MinervaEntityPr
return new PageImpl<>(sublist, pageable, count);
}
+ public List<T> getAll(final Map<S, Object> filterOptions) {
+ return getAll(filterOptions, Pageable.unpaged()).getContent();
+ }
+
+
protected List<Order> getOrder(final Sort sort, final CriteriaBuilder criteriaBuilder, final Root<T> root) {
for (Iterator<Sort.Order> iterator = sort.iterator(); iterator.hasNext(); ) {
Sort.Order order = iterator.next();
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/MinervaJobDao.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/MinervaJobDao.java
index 18f50b8e8d87d91d534922787254be6812794357..c9fd86bb635549ffa93bffbf012f5abf9372eb4d 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/MinervaJobDao.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/MinervaJobDao.java
@@ -1,5 +1,6 @@
package lcsb.mapviewer.persist.dao;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.job.MinervaJob;
import lcsb.mapviewer.model.job.MinervaJobStatus;
import lcsb.mapviewer.model.job.MinervaJobType;
@@ -7,14 +8,17 @@ import org.springframework.stereotype.Repository;
import javax.persistence.criteria.CriteriaBuilder;
import javax.persistence.criteria.CriteriaQuery;
+import javax.persistence.criteria.Predicate;
import javax.persistence.criteria.Root;
+import java.util.ArrayList;
import java.util.Arrays;
import java.util.Calendar;
+import java.util.Collection;
import java.util.List;
import java.util.Map;
@Repository
-public class MinervaJobDao extends BaseDao<MinervaJob, MinervaEntityProperty<MinervaJob>> {
+public class MinervaJobDao extends BaseDao<MinervaJob, MinervaJobProperty> {
public MinervaJobDao() {
super(MinervaJob.class);
@@ -88,4 +92,35 @@ public class MinervaJobDao extends BaseDao<MinervaJob, MinervaEntityProperty<Min
.setParameter("job_type", jobType)
.list();
}
+
+ @Override
+ protected Predicate createPredicate(final Map<MinervaJobProperty, Object> filterOptions, final Root<MinervaJob> root) {
+ CriteriaBuilder builder = getSession().getCriteriaBuilder();
+ List<Predicate> predicates = new ArrayList<>();
+
+ for (MinervaJobProperty key : filterOptions.keySet()) {
+ if (key.equals(MinervaJobProperty.EXTERNAL_OBJECT_CLASS)) {
+ Collection<Class<?>> values = (Collection<Class<?>>) filterOptions.get(key);
+
+ final CriteriaBuilder.In<Class<?>> predicate = builder.in(root.get("externalObjectClass"));
+ for (final Class<?> object : values) {
+ predicate.value(object);
+ }
+ predicates.add(predicate);
+ } else if (key.equals(MinervaJobProperty.EXTERNAL_OBJECT_ID)) {
+ Collection<Integer> values = (Collection<Integer>) filterOptions.get(key);
+
+ final CriteriaBuilder.In<Integer> predicate = builder.in(root.get("externalObjectId"));
+ for (final Integer object : values) {
+ predicate.value(object);
+ }
+ predicates.add(predicate);
+ } else {
+ throw new InvalidArgumentException("Unknown property: " + key);
+ }
+ }
+ Predicate predicate = builder.and(predicates.toArray(new Predicate[0]));
+ return predicate;
+
+ }
}
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/MinervaJobProperty.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/MinervaJobProperty.java
new file mode 100644
index 0000000000000000000000000000000000000000..4f7bbff5f593cc50b46e74145b95b293c2e75688
--- /dev/null
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/MinervaJobProperty.java
@@ -0,0 +1,8 @@
+package lcsb.mapviewer.persist.dao;
+
+import lcsb.mapviewer.model.job.MinervaJob;
+
+public enum MinervaJobProperty implements MinervaEntityProperty<MinervaJob> {
+ EXTERNAL_OBJECT_CLASS,
+ EXTERNAL_OBJECT_ID,
+}
diff --git a/persist/src/main/resources/db/migration/hsql/19.0.0~alpha.0/V19.0.0.20250227.2__add_progress_to_minerva_job.sql b/persist/src/main/resources/db/migration/hsql/19.0.0~alpha.0/V19.0.0.20250227.2__add_progress_to_minerva_job.sql
new file mode 100644
index 0000000000000000000000000000000000000000..eb923d432a7c6c918ea92789ec1f3bd6848bdb3a
--- /dev/null
+++ b/persist/src/main/resources/db/migration/hsql/19.0.0~alpha.0/V19.0.0.20250227.2__add_progress_to_minerva_job.sql
@@ -0,0 +1,2 @@
+alter table minerva_job_table
+ add column progress double precision;
\ No newline at end of file
diff --git a/persist/src/main/resources/db/migration/hsql/19.0.0~alpha.0/V19.0.0.20250227.3__add_object_connection_to_minerva_job.sql b/persist/src/main/resources/db/migration/hsql/19.0.0~alpha.0/V19.0.0.20250227.3__add_object_connection_to_minerva_job.sql
new file mode 100644
index 0000000000000000000000000000000000000000..4a735d4e773c6732a663c02cbe20ba56fcd20c80
--- /dev/null
+++ b/persist/src/main/resources/db/migration/hsql/19.0.0~alpha.0/V19.0.0.20250227.3__add_object_connection_to_minerva_job.sql
@@ -0,0 +1,5 @@
+alter table minerva_job_table
+ add column external_object_id integer;
+
+alter table minerva_job_table
+ add column external_object_class character varying(512);
diff --git a/persist/src/main/resources/db/migration/hsql/19.0.0~alpha.0/V19.0.0.20250227__remove_annotating_project_status.sql b/persist/src/main/resources/db/migration/hsql/19.0.0~alpha.0/V19.0.0.20250227__remove_annotating_project_status.sql
new file mode 100644
index 0000000000000000000000000000000000000000..e6de86f9f4de92fc8656ddcc9996aa6d227503b8
--- /dev/null
+++ b/persist/src/main/resources/db/migration/hsql/19.0.0~alpha.0/V19.0.0.20250227__remove_annotating_project_status.sql
@@ -0,0 +1,3 @@
+update project_table
+set status ='UNKNOWN'
+where status in ('ANNOTATING');
\ No newline at end of file
diff --git a/persist/src/main/resources/db/migration/postgres/19.0.0~alpha.0/V19.0.0.20250227.2__add_progress_to_minerva_job.sql b/persist/src/main/resources/db/migration/postgres/19.0.0~alpha.0/V19.0.0.20250227.2__add_progress_to_minerva_job.sql
new file mode 100644
index 0000000000000000000000000000000000000000..eb923d432a7c6c918ea92789ec1f3bd6848bdb3a
--- /dev/null
+++ b/persist/src/main/resources/db/migration/postgres/19.0.0~alpha.0/V19.0.0.20250227.2__add_progress_to_minerva_job.sql
@@ -0,0 +1,2 @@
+alter table minerva_job_table
+ add column progress double precision;
\ No newline at end of file
diff --git a/persist/src/main/resources/db/migration/postgres/19.0.0~alpha.0/V19.0.0.20250227.3__add_object_connection_to_minerva_job.sql b/persist/src/main/resources/db/migration/postgres/19.0.0~alpha.0/V19.0.0.20250227.3__add_object_connection_to_minerva_job.sql
new file mode 100644
index 0000000000000000000000000000000000000000..4a735d4e773c6732a663c02cbe20ba56fcd20c80
--- /dev/null
+++ b/persist/src/main/resources/db/migration/postgres/19.0.0~alpha.0/V19.0.0.20250227.3__add_object_connection_to_minerva_job.sql
@@ -0,0 +1,5 @@
+alter table minerva_job_table
+ add column external_object_id integer;
+
+alter table minerva_job_table
+ add column external_object_class character varying(512);
diff --git a/persist/src/main/resources/db/migration/postgres/19.0.0~alpha.0/V19.0.0.20250227__remove_annotating_project_status.sql b/persist/src/main/resources/db/migration/postgres/19.0.0~alpha.0/V19.0.0.20250227__remove_annotating_project_status.sql
new file mode 100644
index 0000000000000000000000000000000000000000..e6de86f9f4de92fc8656ddcc9996aa6d227503b8
--- /dev/null
+++ b/persist/src/main/resources/db/migration/postgres/19.0.0~alpha.0/V19.0.0.20250227__remove_annotating_project_status.sql
@@ -0,0 +1,3 @@
+update project_table
+set status ='UNKNOWN'
+where status in ('ANNOTATING');
\ No newline at end of file
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/utils/TransactionalElementDao.java b/persist/src/test/java/lcsb/mapviewer/persist/utils/TransactionalElementDao.java
index d173897f9c4c4387e0eea6dcf58305a9aabcf1a8..ca5a1a88f05f6c2b0302ba1926f1a58a05783fd0 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/utils/TransactionalElementDao.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/utils/TransactionalElementDao.java
@@ -1,16 +1,15 @@
package lcsb.mapviewer.persist.utils;
-import java.util.Map;
-
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.persist.dao.map.species.ElementDao;
+import lcsb.mapviewer.persist.dao.map.species.ElementProperty;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.Page;
import org.springframework.data.domain.PageRequest;
import org.springframework.stereotype.Component;
import org.springframework.transaction.annotation.Transactional;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.persist.dao.map.species.ElementDao;
-import lcsb.mapviewer.persist.dao.map.species.ElementProperty;
+import java.util.Map;
@Component
@Transactional
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java b/rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java
index 08d1652c7ce7ff605273ff079e4c22f38757bccf..7cbaf4f9eb6436467c4f75d3eef07b29fb771562 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java
@@ -21,8 +21,8 @@ import lcsb.mapviewer.modelutils.serializer.model.security.PrivilegeKeyDeseriali
import lcsb.mapviewer.services.InvalidTokenException;
import lcsb.mapviewer.services.ObjectExistsException;
import lcsb.mapviewer.services.ObjectNotFoundException;
+import lcsb.mapviewer.services.interfaces.IAnnotationService;
import lcsb.mapviewer.services.interfaces.IConfigurationService;
-import lcsb.mapviewer.services.interfaces.IProjectService;
import lcsb.mapviewer.services.interfaces.IUserService;
import lcsb.mapviewer.services.utils.EmailException;
import lcsb.mapviewer.services.utils.EmailSender;
@@ -82,7 +82,7 @@ import java.util.stream.Collectors;
public class UserController extends BaseController {
private final IUserService userService;
- private final IProjectService projectService;
+ private final IAnnotationService annotationService;
private final IConfigurationService configurationService;
private final PasswordEncoder passwordEncoder;
private final EmailSender emailSender;
@@ -94,14 +94,14 @@ public class UserController extends BaseController {
final PasswordEncoder passwordEncoder,
final EmailSender emailSender,
final IConfigurationService configurationService,
- final IProjectService projectService,
+ final IAnnotationService annotationService,
final SessionRegistry sessionRegistry) {
this.userService = userService;
this.passwordEncoder = passwordEncoder;
this.emailSender = emailSender;
- this.projectService = projectService;
this.configurationService = configurationService;
this.sessionRegistry = sessionRegistry;
+ this.annotationService = annotationService;
}
/**
@@ -129,7 +129,7 @@ public class UserController extends BaseController {
throw new ObjectNotFoundException("User doesn't exist");
}
if (user.getAnnotationSchema() == null) {
- user.setAnnotationSchema(projectService.prepareUserAnnotationSchema(user, true));
+ user.setAnnotationSchema(annotationService.prepareUserAnnotationSchema(user, true));
}
Boolean ldapAvailable = false;
if (columnSet.contains("ldapAccountAvailable")) {
@@ -221,7 +221,7 @@ public class UserController extends BaseController {
throw new ObjectNotFoundException("User doesn't exist");
}
- final UserAnnotationSchema schema = projectService.prepareUserAnnotationSchema(modifiedUser, true);
+ final UserAnnotationSchema schema = annotationService.prepareUserAnnotationSchema(modifiedUser, true);
if (body.getPreferences().getValidateMiriamTypes() != null) {
schema.setValidateMiriamTypes(body.getPreferences().getValidateMiriamTypes());
@@ -305,7 +305,7 @@ public class UserController extends BaseController {
data.add(new UserDTO(user, ldapAvailability.get(user.getLogin()), getLastActive(user)));
}
data = data.stream()
- .sorted(Comparator.comparing(user -> user.getLogin(), Comparator.reverseOrder()))
+ .sorted(Comparator.comparing(User::getLogin, Comparator.reverseOrder()))
.collect(Collectors.toList());
return createResponseWithColumns(columns, data);
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/AnnotationService.java b/service/src/main/java/lcsb/mapviewer/services/impl/AnnotationService.java
new file mode 100644
index 0000000000000000000000000000000000000000..31c6bdc94320c7f3b48ddeaab8e119ac62f31fbb
--- /dev/null
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/AnnotationService.java
@@ -0,0 +1,132 @@
+package lcsb.mapviewer.services.impl;
+
+import lcsb.mapviewer.annotation.services.ModelAnnotator;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.job.MinervaJob;
+import lcsb.mapviewer.model.job.MinervaJobType;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.model.user.UserAnnotationSchema;
+import lcsb.mapviewer.model.user.UserClassAnnotators;
+import lcsb.mapviewer.modelutils.map.ClassTreeNode;
+import lcsb.mapviewer.modelutils.map.ElementUtils;
+import lcsb.mapviewer.services.interfaces.IAnnotationService;
+import lcsb.mapviewer.services.interfaces.IMinervaJobService;
+import lcsb.mapviewer.services.interfaces.IProjectService;
+import lcsb.mapviewer.services.interfaces.IUserService;
+import lcsb.mapviewer.services.jobs.AnnotateProjectMinervaJob;
+import lcsb.mapviewer.services.search.drug.IDrugService;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+
+import javax.annotation.PostConstruct;
+import java.util.LinkedList;
+import java.util.Queue;
+import java.util.function.Consumer;
+
+@Service
+public class AnnotationService implements IAnnotationService {
+
+ private final Logger logger = LogManager.getLogger();
+
+ private final ModelAnnotator modelAnnotator;
+
+ private final IUserService userService;
+
+ private final IMinervaJobService minervaJobService;
+
+ @Autowired
+ private IAnnotationService self;
+
+ private final IProjectService projectService;
+ private final IDrugService drugService;
+
+ @Autowired
+ public AnnotationService(final IMinervaJobService minervaJobService,
+ final ModelAnnotator modelAnnotator,
+ final IUserService userService,
+ final IProjectService projectService,
+ final IDrugService drugService) {
+ this.minervaJobService = minervaJobService;
+ this.modelAnnotator = modelAnnotator;
+ this.userService = userService;
+ this.projectService = projectService;
+ this.drugService = drugService;
+ }
+
+ @PostConstruct
+ public void init() {
+ minervaJobService.registerExecutor(MinervaJobType.ANNOTATE_PROJECT, self);
+ }
+
+
+ @Override
+ public void execute(final MinervaJob job) throws Exception {
+ if (job.getJobType() == MinervaJobType.ANNOTATE_PROJECT) {
+ AnnotateProjectMinervaJob parameters = new AnnotateProjectMinervaJob(job.getJobParameters());
+ self.handleAnnotateProjectJob(parameters, (final Double progress) -> minervaJobService.updateJobProgress(job, progress));
+
+ Project project = projectService.getProjectByProjectId(parameters.getProjectId());
+
+ projectService.submitRefreshChemicalInfoJobs(parameters.getProjectId());
+ drugService.submitRefreshChemblSuggestedQueryList(project.getOrganism(), project);
+ drugService.submitRefreshDrugBankSuggestedQueryList(project.getOrganism(), project);
+
+ } else {
+ throw new NotImplementedException(job.getJobType() + " not implemented");
+ }
+ }
+
+
+ /**
+ * Retrieves (or creates) annotation schema for a given user.
+ *
+ * @return {@link UserAnnotationSchema} for {@link User}
+ */
+ @Override
+ public UserAnnotationSchema prepareUserAnnotationSchema(final User user, final boolean initializeLazy) {
+ UserAnnotationSchema annotationSchema = null;
+ if (user != null) {
+ annotationSchema = userService.getById(user.getId()).getAnnotationSchema();
+ if (annotationSchema != null && annotationSchema.getClassAnnotators().isEmpty()) {
+ for (final UserClassAnnotators uca : modelAnnotator.createDefaultAnnotatorSchema().getClassAnnotators()) {
+ annotationSchema.addClassAnnotator(uca);
+ }
+ }
+ }
+ if (annotationSchema == null) {
+ annotationSchema = modelAnnotator.createDefaultAnnotatorSchema();
+
+ final ElementUtils elementUtils = new ElementUtils();
+
+ final ClassTreeNode top = elementUtils.getAnnotatedElementClassTree();
+
+ final Queue<ClassTreeNode> nodes = new LinkedList<>();
+ nodes.add(top);
+
+ while (!nodes.isEmpty()) {
+ final ClassTreeNode element = nodes.poll();
+ annotationSchema.addClassAnnotator(new UserClassAnnotators(element.getClazz(),
+ modelAnnotator.getDefaultAnnotators(element.getClazz())));
+ nodes.addAll(element.getChildren());
+ }
+ if (user != null) {
+ final User dbUser = userService.getById(user.getId());
+ dbUser.setAnnotationSchema(annotationSchema);
+ userService.update(dbUser);
+ }
+ }
+ if (user != null) {
+ return userService.getUserByLogin(user.getLogin(), initializeLazy).getAnnotationSchema();
+ }
+ return annotationSchema;
+ }
+
+ @Override
+ public void handleAnnotateProjectJob(final AnnotateProjectMinervaJob parameters, final Consumer<Double> updateProgress) {
+ Project project = projectService.getProjectByProjectId(parameters.getProjectId());
+ modelAnnotator.performAnnotations(project, updateProgress::accept, parameters.getSchema());
+ }
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/MinervaJobService.java b/service/src/main/java/lcsb/mapviewer/services/impl/MinervaJobService.java
index 21ea237cb907f290a1f32544047eddbf7cef2677..f70ac17dbd094d0d531901469ddb489543503b9a 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/MinervaJobService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/MinervaJobService.java
@@ -3,6 +3,7 @@ package lcsb.mapviewer.services.impl;
import lcsb.mapviewer.annotation.cache.CacheQueryMinervaJob;
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
import lcsb.mapviewer.common.MinervaConfigurationHolder;
+import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.cache.CacheQuery;
import lcsb.mapviewer.model.cache.CacheType;
import lcsb.mapviewer.model.job.MinervaJob;
@@ -12,6 +13,7 @@ import lcsb.mapviewer.model.job.MinervaJobStatus;
import lcsb.mapviewer.model.job.MinervaJobType;
import lcsb.mapviewer.persist.CustomDatabasePopulator;
import lcsb.mapviewer.persist.dao.MinervaJobDao;
+import lcsb.mapviewer.persist.dao.MinervaJobProperty;
import lcsb.mapviewer.persist.dao.cache.CacheTypeDao;
import lcsb.mapviewer.services.interfaces.IMinervaJobService;
import org.apache.commons.lang3.exception.ExceptionUtils;
@@ -22,6 +24,8 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.boot.SpringApplication;
import org.springframework.context.ApplicationContext;
import org.springframework.context.ApplicationContextAware;
+import org.springframework.data.domain.Page;
+import org.springframework.data.domain.Pageable;
import org.springframework.jdbc.datasource.init.ScriptException;
import org.springframework.stereotype.Service;
import org.springframework.transaction.annotation.Transactional;
@@ -135,7 +139,7 @@ public class MinervaJobService implements IMinervaJobService, ApplicationContext
logger.error("QUEUE interrupted", e);
break;
}
- logger.info("Recovering attempt: " + errorIssues);
+ logger.info("Recovering attempt: {}", errorIssues);
}
}
if (MinervaJobService.shutdownOnFailure) {
@@ -164,7 +168,6 @@ public class MinervaJobService implements IMinervaJobService, ApplicationContext
@Override
public void setApplicationContext(final ApplicationContext context) throws BeansException {
this.context = context;
-
}
@Override
@@ -248,6 +251,12 @@ public class MinervaJobService implements IMinervaJobService, ApplicationContext
return minervaJobDao.getCount(status);
}
+ @Override
+ public long getCount(final Map<MinervaJobProperty, Object> filterOptions) {
+ return minervaJobDao.getCount(filterOptions);
+ }
+
+
@Override
public void registerExecutor(final MinervaJobType jobType, final MinervaJobExecutor executor) {
executors.put(jobType, executor);
@@ -303,6 +312,17 @@ public class MinervaJobService implements IMinervaJobService, ApplicationContext
MinervaJobService.queueEnabled = false;
}
+ @Override
+ public void updateJobProgress(final MinervaJob job, final Double progress) {
+ MinervaJob dbJob = self.getJobById(job.getId());
+ if (dbJob != null) {
+ dbJob.setProgress(progress);
+ minervaJobDao.update(dbJob);
+ } else {
+ logger.warn("Job not found: {}", job.getId());
+ }
+ }
+
private Callable<Object> createJobExecutionWrapper(final MinervaJob job) {
return new Callable<Object>() {
@Override
@@ -312,10 +332,12 @@ public class MinervaJobService implements IMinervaJobService, ApplicationContext
MinervaJobExecutor executor = getExecutor(job.getJobType());
if (executor == null) {
- logger.error("Cannot find executor for job: " + job.getJobType() + " (job id: " + job.getId() + ")");
- job.setJobStatus(MinervaJobStatus.FAILED);
- job.setLogs("Cannot find executor for job: " + job.getJobType() + " (job id: " + job.getId() + ")");
- return self.updateJob(job);
+ logger.error("Cannot find executor for job: {} (job id: {})", job.getJobType(), job.getId());
+
+ MinervaJob dbJob = self.getJobById(job.getId());
+ dbJob.setJobStatus(MinervaJobStatus.FAILED);
+ dbJob.setLogs("Cannot find executor for job: " + dbJob.getJobType() + " (job id: " + dbJob.getId() + ")");
+ return self.updateJob(dbJob);
}
executor.execute(job);
@@ -356,22 +378,49 @@ public class MinervaJobService implements IMinervaJobService, ApplicationContext
}
private void startJob(final MinervaJob job) {
- logger.debug("Starting job: " + job.getId() + ", " + job.getJobType() + ", priority: " + job.getPriority() + ", " + job.getJobParameters());
- job.setJobStatus(MinervaJobStatus.RUNNING);
- self.updateJob(job);
+ logger.debug("Starting job: {}, {}, priority: {}, {}", job.getId(), job.getJobType(), job.getPriority(), job.getJobParameters());
+ MinervaJob dbJob = self.getJobById(job.getId());
+ dbJob.setJobStatus(MinervaJobStatus.RUNNING);
+ self.updateJob(dbJob);
}
private MinervaJob finishJob(final MinervaJob job) {
- logger.debug("Job finished: " + job.getId());
- job.setJobStatus(MinervaJobStatus.DONE);
- return self.updateJob(job);
+ logger.debug("Job finished: {}", job.getId());
+ MinervaJob dbJob = self.getJobById(job.getId());
+ dbJob.setJobStatus(MinervaJobStatus.DONE);
+ return self.updateJob(dbJob);
}
private MinervaJob finishJobWithProblems(final MinervaJob job, final Throwable e) {
- logger.error("Problem with executing job: " + job.getJobType() + " (job id: " + job.getId() + ")", e);
- job.setJobStatus(MinervaJobStatus.FAILED);
- job.setLogs(ExceptionUtils.getStackTrace(e));
- return self.updateJob(job);
+ logger.error("Problem with executing job: {} (job id: {})", job.getJobType(), job.getId(), e);
+ MinervaJob dbJob = self.getJobById(job.getId());
+ dbJob.setJobStatus(MinervaJobStatus.FAILED);
+ dbJob.setLogs(ExceptionUtils.getStackTrace(e));
+ return self.updateJob(dbJob);
+ }
+
+ @Override
+ public Page<MinervaJob> getAll(final Map<MinervaJobProperty, Object> filter, final Pageable pageable) {
+ return minervaJobDao.getAll(filter, pageable);
}
+ @Override
+ public MinervaJob getById(final int id) {
+ return minervaJobDao.getById(id);
+ }
+
+ @Override
+ public void update(final MinervaJob object) {
+ self.updateJob(object);
+ }
+
+ @Override
+ public void remove(final MinervaJob object) {
+ throw new NotImplementedException();
+ }
+
+ @Override
+ public void add(final MinervaJob object) {
+ self.addJob(object);
+ }
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
index 813e4f2b662119c657f78dc43ae494c8470bd26a..11e01fb110b161a1daef817dfa9260062bbddf80 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
@@ -1,7 +1,6 @@
package lcsb.mapviewer.services.impl;
import lcsb.mapviewer.annotation.services.MeSHParser;
-import lcsb.mapviewer.annotation.services.ModelAnnotator;
import lcsb.mapviewer.annotation.services.TaxonomyBackend;
import lcsb.mapviewer.annotation.services.TaxonomySearchException;
import lcsb.mapviewer.commands.ClearColorModelCommand;
@@ -12,7 +11,6 @@ import lcsb.mapviewer.common.IProgressUpdater;
import lcsb.mapviewer.common.MinervaConfigurationHolder;
import lcsb.mapviewer.common.MinervaLoggerAppender;
import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.ColorSchemaReader;
import lcsb.mapviewer.converter.ComplexZipConverter;
@@ -54,25 +52,25 @@ import lcsb.mapviewer.model.overlay.InvalidDataOverlayException;
import lcsb.mapviewer.model.user.ConfigurationElementType;
import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.model.user.UserAnnotationSchema;
-import lcsb.mapviewer.model.user.UserClassAnnotators;
-import lcsb.mapviewer.modelutils.map.ClassTreeNode;
-import lcsb.mapviewer.modelutils.map.ElementUtils;
import lcsb.mapviewer.persist.DbUtils;
import lcsb.mapviewer.persist.ObjectValidator;
import lcsb.mapviewer.persist.dao.ProjectDao;
import lcsb.mapviewer.persist.dao.ProjectLogEntryDao;
import lcsb.mapviewer.persist.dao.ProjectLogEntryProperty;
import lcsb.mapviewer.persist.dao.ProjectProperty;
+import lcsb.mapviewer.persist.dao.graphics.LayerProperty;
import lcsb.mapviewer.persist.dao.map.ModelProperty;
-import lcsb.mapviewer.persist.dao.user.UserDao;
+import lcsb.mapviewer.persist.dao.user.UserAnnotationSchemaDao;
import lcsb.mapviewer.services.interfaces.ICommentService;
import lcsb.mapviewer.services.interfaces.IConfigurationService;
import lcsb.mapviewer.services.interfaces.IFileService;
+import lcsb.mapviewer.services.interfaces.ILayerService;
import lcsb.mapviewer.services.interfaces.IMinervaJobService;
import lcsb.mapviewer.services.interfaces.IModelService;
import lcsb.mapviewer.services.interfaces.IProjectBackgroundService;
import lcsb.mapviewer.services.interfaces.IProjectService;
import lcsb.mapviewer.services.interfaces.IUserService;
+import lcsb.mapviewer.services.jobs.AnnotateProjectMinervaJob;
import lcsb.mapviewer.services.jobs.CreateProjectFailureMinervaJob;
import lcsb.mapviewer.services.jobs.CreateProjectMinervaJob;
import lcsb.mapviewer.services.jobs.DeleteBackgroundMinervaJob;
@@ -82,8 +80,6 @@ import lcsb.mapviewer.services.jobs.RefreshChemicalSuggestedQueryListMinervaJob;
import lcsb.mapviewer.services.jobs.RefreshDrugInfoMinervaJob;
import lcsb.mapviewer.services.jobs.RefreshMiriamInfoMinervaJob;
import lcsb.mapviewer.services.jobs.ReviveBackgroundsMinervaJob;
-import lcsb.mapviewer.services.search.chemical.IChemicalService;
-import lcsb.mapviewer.services.search.drug.IDrugService;
import lcsb.mapviewer.services.utils.CreateProjectParams;
import lcsb.mapviewer.services.utils.EmailException;
import lcsb.mapviewer.services.utils.EmailSender;
@@ -99,7 +95,6 @@ import org.springframework.data.domain.Pageable;
import org.springframework.stereotype.Service;
import javax.annotation.PostConstruct;
-import javax.mail.MessagingException;
import javax.persistence.PersistenceException;
import java.io.ByteArrayInputStream;
import java.io.File;
@@ -109,11 +104,9 @@ import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
-import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.Objects;
-import java.util.Queue;
import java.util.Set;
/**
@@ -140,23 +133,17 @@ public class ProjectService implements IProjectService {
/**
* Data access object for projects.
*/
- private ProjectDao projectDao;
+ private final ProjectDao projectDao;
/**
* Data access object for models.
*/
private final ProjectLogEntryDao projectLogEntryDao;
- /**
- * Data access object for users.
- */
- private final UserDao userDao;
-
- /**
- * Service that allows to access and manage models.
- */
private final IModelService modelService;
+ private final ILayerService layerService;
+
/**
* Service that allows to access and manage comments.
*/
@@ -172,24 +159,9 @@ public class ProjectService implements IProjectService {
*/
private final IUserService userService;
- /**
- * Services that access data about chemicals.
- */
- private final IChemicalService chemicalService;
-
- /**
- * Services that access data about drugs.
- */
- private final IDrugService drugService;
-
@Autowired
private IFileService fileService;
- /**
- * Module that allows to annotate maps.
- */
- private final ModelAnnotator modelAnnotator;
-
private final IProjectBackgroundService projectBackgroundService;
private final IMinervaJobService minervaJobService;
@@ -217,8 +189,10 @@ public class ProjectService implements IProjectService {
private final MinervaConfigurationHolder minervaConfigurationHolder;
+ private final UserAnnotationSchemaDao userAnnotationSchemaDao;
+
/**
- * Class that helps to generate images for google maps API.
+ * Class that helps to generate images for frontend.
*/
private final MapGenerator generator = new MapGenerator();
@@ -226,35 +200,31 @@ public class ProjectService implements IProjectService {
public ProjectService(final MinervaConfigurationHolder minervaConfigurationHolder,
final ProjectDao projectDao,
final ProjectLogEntryDao projectLogEntryDao,
- final UserDao userDao,
final IModelService modelService,
+ final ILayerService layerService,
final ICommentService commentService,
final IConfigurationService configurationService,
final IUserService userService,
- final IChemicalService chemicalService,
- final IDrugService drugService,
- final ModelAnnotator modelAnnotator,
final DbUtils dbUtils,
final MeSHParser meshParser,
final TaxonomyBackend taxonomyBackend,
final IProjectBackgroundService projectBackgroundService,
- final IMinervaJobService minervaJobService) {
+ final IMinervaJobService minervaJobService,
+ final UserAnnotationSchemaDao userAnnotationSchemaDao) {
this.minervaConfigurationHolder = minervaConfigurationHolder;
this.projectDao = projectDao;
this.projectLogEntryDao = projectLogEntryDao;
- this.userDao = userDao;
this.modelService = modelService;
+ this.layerService = layerService;
this.commentService = commentService;
this.configurationService = configurationService;
this.userService = userService;
- this.chemicalService = chemicalService;
- this.drugService = drugService;
- this.modelAnnotator = modelAnnotator;
this.dbUtils = dbUtils;
this.meshParser = meshParser;
this.taxonomyBackend = taxonomyBackend;
this.projectBackgroundService = projectBackgroundService;
this.minervaJobService = minervaJobService;
+ this.userAnnotationSchemaDao = userAnnotationSchemaDao;
}
@PostConstruct
@@ -278,7 +248,7 @@ public class ProjectService implements IProjectService {
@Override
public Project getProjectByProjectId(final String projectId, final boolean initializeLazy) {
- final Project result = getProjectByProjectId(projectId);
+ final Project result = self.getProjectByProjectId(projectId);
if (result != null && initializeLazy) {
initLazy(result);
}
@@ -287,7 +257,7 @@ public class ProjectService implements IProjectService {
@Override
public boolean projectExists(final String projectName) {
- if (projectName == null || projectName.equals("")) {
+ if (projectName == null || projectName.isEmpty()) {
return false;
}
return projectDao.isProjectExistsByName(projectName);
@@ -297,14 +267,14 @@ public class ProjectService implements IProjectService {
public List<Project> getAllProjects() {
final List<Project> projects = projectDao.getAll();
for (final Project project : projects) {
- project.getLogEntries().size();
+ Hibernate.initialize(project.getLogEntries());
}
return projects;
}
@Override
public List<Project> getAllProjects(final boolean initializeLazy) {
- final List<Project> result = getAllProjects();
+ final List<Project> result = self.getAllProjects();
if (initializeLazy) {
for (final Project project : result) {
initLazy(project);
@@ -319,6 +289,7 @@ public class ProjectService implements IProjectService {
final DeleteProjectMinervaJob jobParameters = new DeleteProjectMinervaJob(project.getProjectId(), homeDir);
final MinervaJob job = new MinervaJob(MinervaJobType.DELETE_PROJECT, MinervaJobPriority.MEDIUM, jobParameters);
+ job.setExternalObject(project);
minervaJobService.addJob(job);
return job;
}
@@ -378,7 +349,7 @@ public class ProjectService implements IProjectService {
}
} catch (final Exception e) {
- self.projectFailure(project.getProjectId(), ProjectLogEntryType.OTHER,
+ self.projectFailure(projectId, ProjectLogEntryType.OTHER,
"Severe problem with removing object. Underlying error:\n" + e.getMessage()
+ "\nMore information can be found in log file.",
e);
@@ -414,7 +385,7 @@ public class ProjectService implements IProjectService {
self.addLogEntries(params.getProjectId(), createLogEntries(appender));
createRefreshDrugInfoJobs(params.getProjectId());
- createRefreshChemicalInfoJobs(params.getProjectId());
+ submitRefreshChemicalInfoJobs(params.getProjectId());
createRefreshMiriamInfoJobs(params.getProjectId());
self.updateProjectStatus(params.getProjectId(), ProjectStatus.DONE, IProgressUpdater.MAX_PROGRESS);
@@ -435,10 +406,11 @@ public class ProjectService implements IProjectService {
+ "You might violated some unhandled constraints or you run out of memory. Underlying error:\n"
+ e.getMessage() + "\nMore information can be found in log file.",
e);
- } catch (final OutOfMemoryError oome) {
+ } catch (final OutOfMemoryError outOfMemoryError) {
// release some memory
outOfMemoryBuffer = null;
- self.projectFailure(params.getProjectId(), ProjectLogEntryType.OUT_OF_MEMORY, "Out of memory: " + oome.getMessage(), oome);
+ self.projectFailure(params.getProjectId(), ProjectLogEntryType.OUT_OF_MEMORY,
+ "Out of memory: " + outOfMemoryError.getMessage(), outOfMemoryError);
} catch (final Throwable e) {
outOfMemoryBuffer = null;
self.projectFailure(params.getProjectId(), ProjectLogEntryType.OTHER,
@@ -465,6 +437,7 @@ public class ProjectService implements IProjectService {
final CreateProjectMinervaJob jobParameters = new CreateProjectMinervaJob(params);
final MinervaJob job = new MinervaJob(MinervaJobType.CREATE_PROJECT, MinervaJobPriority.HIGH, jobParameters);
+ job.setExternalObject(project);
minervaJobService.addJob(job);
return job;
@@ -483,7 +456,7 @@ public class ProjectService implements IProjectService {
}
}
- public void createRefreshChemicalInfoJobs(final String projectId) {
+ public void submitRefreshChemicalInfoJobs(final String projectId) {
Project project = self.getProjectByProjectId(projectId, true);
MiriamData disease = project.getDisease();
if (disease != null) {
@@ -491,7 +464,9 @@ public class ProjectService implements IProjectService {
minervaJobService.addJob(createRefreshChemicalInfoJob(miriamData, disease));
}
RefreshChemicalSuggestedQueryListMinervaJob parameters = new RefreshChemicalSuggestedQueryListMinervaJob(disease, project.getId());
- minervaJobService.addJob(new MinervaJob(MinervaJobType.REFRESH_CHEMICAL_SUGGESTED_QUERY_LIST, MinervaJobPriority.LOWEST, parameters));
+ MinervaJob job = new MinervaJob(MinervaJobType.REFRESH_CHEMICAL_SUGGESTED_QUERY_LIST, MinervaJobPriority.LOWEST, parameters);
+ job.setExternalObject(project);
+ minervaJobService.addJob(job);
}
}
@@ -536,9 +511,9 @@ public class ProjectService implements IProjectService {
@Override
public void update(final Project project) {
projectDao.update(project);
- for (final ProjectBackground background : getBackgrounds(project.getProjectId(), false)) {
+ for (final ProjectBackground background : self.getBackgrounds(project.getProjectId(), false)) {
background.setCreator(project.getOwner());
- updateBackground(background);
+ self.updateBackground(background);
}
if (project.getOrganism() != null) {
minervaJobService.addJob(createRefreshMiriamInfoJob(project.getOrganism()));
@@ -548,53 +523,6 @@ public class ProjectService implements IProjectService {
}
}
- /**
- * Retrieves (or creates) annotation schema for a given user.
- *
- * @return {@link UserAnnotationSchema} for {@link User}
- */
- @Override
- public UserAnnotationSchema prepareUserAnnotationSchema(final User user, final boolean initializeLazy) {
- UserAnnotationSchema annotationSchema = null;
- if (user != null) {
- annotationSchema = userDao.getById(user.getId()).getAnnotationSchema();
- if (annotationSchema != null && annotationSchema.getClassAnnotators().size() == 0) {
- for (final UserClassAnnotators uca : modelAnnotator.createDefaultAnnotatorSchema().getClassAnnotators()) {
- annotationSchema.addClassAnnotator(uca);
- }
- }
- }
- if (annotationSchema == null) {
- annotationSchema = modelAnnotator.createDefaultAnnotatorSchema();
-
- final ElementUtils elementUtils = new ElementUtils();
-
- final ClassTreeNode top = elementUtils.getAnnotatedElementClassTree();
-
- final Map<Class<? extends BioEntity>, Set<MiriamType>> validMiriam = modelAnnotator.getDefaultValidClasses();
- final Map<Class<? extends BioEntity>, Set<MiriamType>> requiredMiriam = modelAnnotator.getDefaultRequiredClasses();
-
- final Queue<ClassTreeNode> nodes = new LinkedList<ClassTreeNode>();
- nodes.add(top);
-
- while (!nodes.isEmpty()) {
- final ClassTreeNode element = nodes.poll();
- annotationSchema.addClassAnnotator(new UserClassAnnotators(element.getClazz(),
- modelAnnotator.getDefaultAnnotators(element.getClazz())));
- nodes.addAll(element.getChildren());
- }
- if (user != null) {
- final User dbUser = userDao.getById(user.getId());
- dbUser.setAnnotationSchema(annotationSchema);
- userDao.update(dbUser);
- }
- }
- if (user != null) {
- return userService.getUserByLogin(user.getLogin(), initializeLazy).getAnnotationSchema();
- }
- return annotationSchema;
- }
-
/**
* This method creates set of images for the model backgrounds.
*
@@ -609,9 +537,9 @@ public class ProjectService implements IProjectService {
if (!params.isImages()) {
return;
}
- final Project project = getProjectByProjectId(params.getProjectId());
+ final Project project = self.getProjectByProjectId(params.getProjectId());
project.getTopModel();
- updateProjectStatus(params.getProjectId(), ProjectStatus.GENERATING_IMAGES, 0);
+ self.updateProjectStatus(params.getProjectId(), ProjectStatus.GENERATING_IMAGES, 0);
final int projectSize = project.getProjectBackgrounds().size();
int counter = 0;
@@ -619,13 +547,11 @@ public class ProjectService implements IProjectService {
final ProjectBackground background = project.getProjectBackgrounds().get(i);
final double imgCounter = counter;
final double finalSize = projectSize;
- final IProgressUpdater updater = new IProgressUpdater() {
- @Override
- public void setProgress(final double progress) {
- updateProjectStatus(params.getProjectId(), ProjectStatus.GENERATING_IMAGES,
- IProgressUpdater.MAX_PROGRESS * imgCounter / finalSize + progress / finalSize);
- }
- };
+ final IProgressUpdater updater = progress -> self.updateProjectStatus(
+ params.getProjectId(),
+ ProjectStatus.GENERATING_IMAGES,
+ IProgressUpdater.MAX_PROGRESS * imgCounter / finalSize + progress / finalSize
+ );
generateImagesForBuiltInBackground(background, updater);
counter++;
}
@@ -663,97 +589,54 @@ public class ProjectService implements IProjectService {
@Override
public Project createModel(final CreateProjectParams params)
- throws InvalidInputDataExecption, ConverterException, IOException, InvalidDataOverlayException, InstantiationException, IllegalAccessException,
- CommandExecutionException {
- final Project project = getProjectByProjectId(params.getProjectId());
+ throws InvalidInputDataExecption, ConverterException, IOException, InvalidDataOverlayException, CommandExecutionException {
final User dbUser = userService.getUserByLogin(params.getUserLogin());
UserAnnotationSchema userAnnotationSchema = dbUser.getAnnotationSchema();
if (userAnnotationSchema == null) {
userAnnotationSchema = new UserAnnotationSchema();
}
- final UploadedFileEntry file = fileService.getById(params.getProjectFileId());
if (params.isComplex()) {
- try {
- Class<? extends Converter> clazz = CellDesignerXmlParser.class;
- if (params.getParser() != null) {
- clazz = params.getParser();
- }
- final ComplexZipConverter parser = new ComplexZipConverter(clazz);
- final ComplexZipConverterParams complexParams;
- complexParams = new ComplexZipConverterParams().zipFile(file);
- complexParams.visualizationDir(params.getProjectDir());
- for (final ZipEntryFile entry : params.getZipEntries()) {
- complexParams.entry(entry);
- }
- final ProjectFactory projectFactory = new ProjectFactory(parser);
- projectFactory.create(complexParams, project);
- for (final DataOverlay overlay : project.getDataOverlays()) {
- overlay.setCreator(dbUser);
- }
- } catch (final IOException e) {
- throw new InvalidInputDataExecption("Problem with processing input file", e);
- }
+ self.createComplexProject(params);
} else {
- final Converter parser = params.getParser().newInstance();
- if (parser == null) {
- throw new InvalidArgumentException("Parser is undefined");
- }
- final InputStream input = new ByteArrayInputStream(file.getFileContent());
- final Model model = parser
- .createModel(new ConverterParams().inputStream(input, file.getOriginalFileName())
- .sizeAutoAdjust(params.isAutoResize()).sbgnFormat(project.isSbgnFormat()));
- project.addModel(model);
+ self.createSimpleProject(params);
}
- final Model topModel = project.getTopModel();
- final Set<Model> models = new HashSet<>();
- models.add(topModel);
- for (final ModelSubmodelConnection connection : topModel.getSubmodelConnections()) {
- models.add(connection.getSubmodel().getModel());
- }
- for (final Model m : models) {
- for (final Layer l : m.getLayers()) {
- if (!l.getName().equals(CreateHierarchyCommand.TEXT_LAYER_NAME)) {
- l.setVisible(false);
- }
+ Map<LayerProperty, Object> layerFilter = new HashMap<>();
+ layerFilter.put(LayerProperty.PROJECT_ID, params.getProjectId());
+ List<Layer> layers = layerService.getAll(layerFilter, Pageable.unpaged()).getContent();
+ for (final Layer layer : layers) {
+ if (!layer.getName().equals(CreateHierarchyCommand.TEXT_LAYER_NAME)) {
+ layer.setVisible(false);
+ layerService.update(layer);
}
}
- fixProjectIssues(project);
- assignZoomLevelDataToModel(topModel);
+ self.updateProjectStatus(params.getProjectId(), ProjectStatus.UPLOADING_TO_DB, 0.0);
- updateProjectStatus(params.getProjectId(), ProjectStatus.UPLOADING_TO_DB, 0.0);
+ self.addBuiltInBackgrounds(params);
- addBuiltInBackgrounds(params, project, dbUser);
- self.update(project);
- validateDataOverlays(project);
- if (params.isUpdateAnnotations()) {
- logger.debug("Updating annotations");
- modelAnnotator.performAnnotations(topModel, new IProgressUpdater() {
+ self.validateDataOverlays(params.getProjectId());
- @Override
- public void setProgress(final double progress) {
- updateProjectStatus(params.getProjectId(), ProjectStatus.ANNOTATING, progress);
- }
- }, userAnnotationSchema);
- logger.debug("Annotations updated");
- }
- logger.debug("Model created");
- final Model originalModel = project.getTopModel();
- new CreateHierarchyCommand(originalModel, generator.computeZoomLevels(originalModel),
- generator.computeZoomFactor(originalModel)).execute();
- for (final Model model : originalModel.getSubmodels()) {
- new CreateHierarchyCommand(model, generator.computeZoomLevels(model), generator.computeZoomFactor(model))
- .execute();
+ self.createHierarchicalView(params.getProjectId());
+
+ self.updateProjectStatus(params.getProjectId(), ProjectStatus.UPLOADING_TO_DB, 100.0);
+
+ logger.trace("Model {} created", params.getProjectId());
+
+ if (params.isUpdateAnnotations()) {
+ self.submitAnnotateProjectJob(params.getProjectId(), userAnnotationSchema);
}
- logger.debug("Hierarchy view added");
- return project;
+
+ return self.getProjectByProjectId(params.getProjectId());
}
- private void addBuiltInBackgrounds(final CreateProjectParams params, final Project project, final User dbUser)
+ @Override
+ public void addBuiltInBackgrounds(final CreateProjectParams params)
throws InvalidInputDataExecption {
+ User dbUser = userService.getUserByLogin(params.getUserLogin());
+ Project project = self.getProjectByProjectId(params.getProjectId());
final List<BuildInBackgrounds> buildInBackgrounds = new ArrayList<>();
if (params.isNetworkBackgroundAsDefault()) {
buildInBackgrounds.add(BuildInBackgrounds.NORMAL);
@@ -786,7 +669,7 @@ public class ProjectService implements IProjectService {
final String directory = params.getProjectDir() + "/" + buildInBackground.getDirectorySuffix() + submodelId + "/";
background.addProjectBackgroundImageLayer(new ProjectBackgroundImageLayer(connection.getSubmodel(), directory));
- assignZoomLevelDataToModel(connection.getSubmodel().getModel());
+ assignZoomLevelDataToModel(connection.getSubmodel().getModel().getModelData());
submodelId++;
}
}
@@ -796,7 +679,9 @@ public class ProjectService implements IProjectService {
}
}
- private void validateDataOverlays(final Project project) throws IOException, InvalidDataOverlayException {
+ @Override
+ public void validateDataOverlays(final String projectId) throws IOException, InvalidDataOverlayException {
+ Project project = self.getProjectByProjectId(projectId);
for (final DataOverlay l : project.getDataOverlays()) {
if (l.getInputData() != null) {
final ColorSchemaReader reader = new ColorSchemaReader();
@@ -811,11 +696,79 @@ public class ProjectService implements IProjectService {
}
}
- private void assignZoomLevelDataToModel(final Model topModel) throws InvalidInputDataExecption {
- final Integer maxZoomLevels = Integer
+ @Override
+ public void createHierarchicalView(final String projectId) throws CommandExecutionException {
+ Project project = self.getProjectByProjectId(projectId);
+ final Model originalModel = project.getTopModel();
+ new CreateHierarchyCommand(originalModel, generator.computeZoomLevels(originalModel.getModelData()),
+ generator.computeZoomFactor(originalModel.getModelData())).execute();
+ for (final Model model : originalModel.getSubmodels()) {
+ new CreateHierarchyCommand(model, generator.computeZoomLevels(model.getModelData()), generator.computeZoomFactor(model.getModelData()))
+ .execute();
+ }
+ self.update(project);
+ logger.debug("Hierarchy view added");
+ }
+
+ @Override
+ public void createComplexProject(final CreateProjectParams params) throws InvalidInputDataExecption {
+ try {
+ final UploadedFileEntry file = fileService.getById(params.getProjectFileId());
+ Project project = self.getProjectByProjectId(params.getProjectId());
+ User dbUser = userService.getUserByLogin(params.getUserLogin());
+
+ Class<? extends Converter> clazz = CellDesignerXmlParser.class;
+ if (params.getParser() != null) {
+ clazz = params.getParser();
+ }
+ final ComplexZipConverter parser = new ComplexZipConverter(clazz);
+ final ComplexZipConverterParams complexParams;
+ complexParams = new ComplexZipConverterParams().zipFile(file);
+ complexParams.visualizationDir(params.getProjectDir());
+ for (final ZipEntryFile entry : params.getZipEntries()) {
+ complexParams.entry(entry);
+ }
+ final ProjectFactory projectFactory = new ProjectFactory(parser);
+ projectFactory.create(complexParams, project);
+ for (final DataOverlay overlay : project.getDataOverlays()) {
+ overlay.setCreator(dbUser);
+ }
+ for (ModelData modelData : project.getModels()) {
+ project.addLogEntries(fixModelIssues(modelData));
+ }
+ self.update(project);
+ } catch (final IOException | ConverterException e) {
+ throw new InvalidInputDataExecption("Problem with processing input file", e);
+ }
+ }
+
+ @Override
+ public void createSimpleProject(final CreateProjectParams params) throws ConverterException {
+ try {
+ final UploadedFileEntry file = fileService.getById(params.getProjectFileId());
+ Project project = self.getProjectByProjectId(params.getProjectId());
+
+ final Converter parser = params.getParser().newInstance();
+ final InputStream input = new ByteArrayInputStream(file.getFileContent());
+ final Model model = parser.createModel(new ConverterParams()
+ .inputStream(input, file.getOriginalFileName())
+ .sizeAutoAdjust(params.isAutoResize())
+ .sbgnFormat(project.isSbgnFormat()));
+ project.addLogEntries(fixModelIssues(model.getModelData()));
+ assignZoomLevelDataToModel(model.getModelData());
+ modelService.add(model.getModelData());
+ project.setTopModel(model);
+ self.update(project);
+ } catch (InvalidInputDataExecption | InstantiationException | IllegalAccessException e) {
+ throw new ConverterException(e);
+ }
+ }
+
+ private void assignZoomLevelDataToModel(final ModelData topModel) throws InvalidInputDataExecption {
+ final int maxZoomLevels = Integer
.parseInt(configurationService.getValue(ConfigurationElementType.MAX_NUMBER_OF_MAP_LEVELS).getValue());
- final Integer zoomLevels = generator.computeZoomLevels(topModel);
+ final int zoomLevels = generator.computeZoomLevels(topModel);
if (zoomLevels > maxZoomLevels) {
throw new InvalidInputDataExecption(
"Map " + topModel.getName() + " too big. You can change the max number of map zoom levels in configuration.");
@@ -834,42 +787,25 @@ public class ProjectService implements IProjectService {
*/
@Override
public void updateProjectStatus(final String projectId, final ProjectStatus status, final double progress) {
- final Project project = getProjectByProjectId(projectId);
+ final Project project = self.getProjectByProjectId(projectId);
if (project != null) {
if (!status.equals(project.getStatus())
|| (Math.abs(progress - project.getProgress()) > IProgressUpdater.PROGRESS_BAR_UPDATE_RESOLUTION)) {
project.setStatus(status);
project.setProgress(progress);
- fixProjectIssues(project);
self.update(project);
}
} else {
- logger.debug("status: " + status + ", " + progress);
+ logger.trace("Update project status: {}, {}", status, progress);
}
}
- /**
- * @return the projectDao
- * @see #projectDao
- */
- public ProjectDao getProjectDao() {
- return projectDao;
- }
-
- /**
- * @param projectDao the projectDao to set
- * @see #projectDao
- */
- public void setProjectDao(final ProjectDao projectDao) {
- this.projectDao = projectDao;
- }
-
/**
* Sends notification email that map was removed.
*
* @param projectId identifier of the project
* @param email notification email
- * @throws MessagingException thrown when there is a problem with sending email
+ * @throws EmailException thrown when there is a problem with sending email
*/
protected void sendSuccesfullRemoveEmail(final String projectId, final String email) throws EmailException {
final EmailSender emailSender = new EmailSender(configurationService);
@@ -964,6 +900,23 @@ public class ProjectService implements IProjectService {
return result;
}
+ private ProjectLogEntry createLogEntry(final Pair<Object, String> pair) {
+ final ProjectLogEntry entry = new ProjectLogEntry();
+ entry.setContent(pair.getRight());
+ final Object left = pair.getLeft();
+ if (left instanceof BioEntity) {
+ final BioEntity bioEntity = (BioEntity) left;
+ entry.setMapName(bioEntity.getModelData().getName());
+ entry.setObjectClass(bioEntity.getClass().getSimpleName());
+ entry.setObjectIdentifier(bioEntity.getElementId());
+ } else if (left instanceof ModelData) {
+ entry.setMapName(((ModelData) left).getName());
+ }
+ entry.setSeverity("WARNING");
+ entry.setType(ProjectLogEntryType.DATABASE_PROBLEM);
+ return entry;
+ }
+
private ProjectLogEntry createLogEntry(final String severity, final LogEvent event) {
if (event.getMarker() instanceof IgnoredLogMarker) {
return null;
@@ -983,30 +936,31 @@ public class ProjectService implements IProjectService {
return entry;
}
+ List<ProjectLogEntry> fixModelIssues(final ModelData model) {
+ List<ProjectLogEntry> result = new ArrayList<>();
+ final ObjectValidator validator = new ObjectValidator();
+ final List<Pair<Object, String>> issues = validator.getValidationIssues(model);
+ if (!issues.isEmpty()) {
+ for (final Pair<Object, String> pair : issues) {
+ result.add(createLogEntry(pair));
+ }
+ }
+ validator.fixValidationIssues(model);
+ return result;
+ }
+
void fixProjectIssues(final Project project) {
final ObjectValidator validator = new ObjectValidator();
final List<Pair<Object, String>> issues = validator.getValidationIssues(project);
- if (issues.size() > 0) {
+ if (!issues.isEmpty()) {
for (final Pair<Object, String> pair : issues) {
- final ProjectLogEntry entry = new ProjectLogEntry();
- entry.setContent(pair.getRight());
- final Object left = pair.getLeft();
- if (left instanceof BioEntity) {
- final BioEntity bioEntity = (BioEntity) left;
- entry.setMapName(bioEntity.getModelData().getName());
- entry.setObjectClass(bioEntity.getClass().getSimpleName());
- entry.setObjectIdentifier(bioEntity.getElementId());
- } else if (left instanceof ModelData) {
- entry.setMapName(((ModelData) left).getName());
- }
- entry.setSeverity("WARNING");
- entry.setType(ProjectLogEntryType.DATABASE_PROBLEM);
- project.addLogEntry(entry);
+ project.addLogEntry(createLogEntry(pair));
}
}
validator.fixValidationIssues(project);
}
+
@Override
public void removeBackground(final ProjectBackground projectBackground) {
projectBackgroundService.delete(projectBackground);
@@ -1053,7 +1007,7 @@ public class ProjectService implements IProjectService {
@Override
public UploadedFileEntry getFileByProjectId(final String projectId) {
- final Project project = getProjectByProjectId(projectId);
+ final Project project = self.getProjectByProjectId(projectId);
if (project == null) {
return null;
}
@@ -1063,7 +1017,7 @@ public class ProjectService implements IProjectService {
@Override
public List<ProjectBackground> getBackgrounds(final String projectId, final boolean initializeLazy) {
- final Project project = getProjectByProjectId(projectId);
+ final Project project = self.getProjectByProjectId(projectId);
if (project != null) {
for (final ProjectBackground projectBackground : project.getProjectBackgrounds()) {
if (initializeLazy) {
@@ -1109,7 +1063,7 @@ public class ProjectService implements IProjectService {
public void execute(final MinervaJob job) throws Exception {
if (job.getJobType() == MinervaJobType.DELETE_PROJECT) {
final DeleteProjectMinervaJob parameters = new DeleteProjectMinervaJob(job.getJobParameters());
- removeProject(parameters.getProjectId(), parameters.getDirectory());
+ self.removeProject(parameters.getProjectId(), parameters.getDirectory());
} else if (job.getJobType() == MinervaJobType.CREATE_PROJECT) {
final CreateProjectMinervaJob parameters = new CreateProjectMinervaJob(job.getJobParameters());
createProject(parameters.getParameters());
@@ -1146,12 +1100,12 @@ public class ProjectService implements IProjectService {
public void addLogEntries(final String projectId, final Set<ProjectLogEntry> createLogEntries) {
final Project project = self.getProjectByProjectId(projectId);
project.addLogEntries(createLogEntries);
- update(project);
+ self.update(project);
}
@Override
public void submitArchiveProjectJob(final String projectId) {
- final Project project = getProjectByProjectId(projectId);
+ final Project project = self.getProjectByProjectId(projectId);
final String homeDir = getProjectHomeDir(project);
project.setStatus(ProjectStatus.ARCHIVED);
@@ -1159,10 +1113,24 @@ public class ProjectService implements IProjectService {
for (final ProjectBackground background : project.getProjectBackgrounds()) {
final DeleteBackgroundMinervaJob jobParameters = new DeleteBackgroundMinervaJob(background.getId(), homeDir);
final MinervaJob job = new MinervaJob(MinervaJobType.DELETE_BACKGROUND, MinervaJobPriority.LOW, jobParameters);
+ job.setExternalObject(project);
minervaJobService.addJob(job);
}
}
+ @Override
+ public void submitAnnotateProjectJob(final String projectId, final UserAnnotationSchema schema) {
+ UserAnnotationSchema userAnnotationSchema = schema;
+ if (schema != null && schema.getId() != 0) {
+ userAnnotationSchema = userAnnotationSchemaDao.getById(schema.getId());
+ }
+ Project project = self.getProjectByProjectId(projectId);
+ final AnnotateProjectMinervaJob jobParameters = new AnnotateProjectMinervaJob(projectId, userAnnotationSchema);
+ final MinervaJob job = new MinervaJob(MinervaJobType.ANNOTATE_PROJECT, MinervaJobPriority.MEDIUM, jobParameters);
+ job.setExternalObject(project);
+ minervaJobService.addJob(job);
+ }
+
@Override
public String getProjectHomeDir(final Project project) {
final String homeDir;
@@ -1177,26 +1145,28 @@ public class ProjectService implements IProjectService {
@Override
public void submitReviveProjectJob(final String projectId) {
- final Project project = getProjectByProjectId(projectId);
+ final Project project = self.getProjectByProjectId(projectId);
project.setStatus(ProjectStatus.GENERATING_IMAGES);
final ReviveBackgroundsMinervaJob jobParameters = new ReviveBackgroundsMinervaJob(projectId);
final MinervaJob job = new MinervaJob(MinervaJobType.REVIVE_BACKGROUNDS, MinervaJobPriority.MEDIUM, jobParameters);
+ job.setExternalObject(project);
minervaJobService.addJob(job);
}
@Override
public void reviveBackgrounds(final String projectId) {
try {
- final Project project = getProjectByProjectId(projectId);
+ final Project project = self.getProjectByProjectId(projectId);
final CreateProjectParams params = new CreateProjectParams()
.projectId(projectId)
+ .setUser(project.getOwner())
.projectDir(getProjectHomeDir(project))
.images(true);
- addBuiltInBackgrounds(params, project, project.getOwner());
- createImages(params);
+ self.addBuiltInBackgrounds(params);
+ self.createImages(params);
project.setStatus(ProjectStatus.DONE);
} catch (final Exception e) {
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/IAnnotationService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/IAnnotationService.java
new file mode 100644
index 0000000000000000000000000000000000000000..467bb0f88e79b7e7ecdd76021618e2d55932486c
--- /dev/null
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/IAnnotationService.java
@@ -0,0 +1,18 @@
+package lcsb.mapviewer.services.interfaces;
+
+import lcsb.mapviewer.model.job.MinervaJobExecutor;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.model.user.UserAnnotationSchema;
+import lcsb.mapviewer.services.jobs.AnnotateProjectMinervaJob;
+import org.springframework.transaction.annotation.Transactional;
+
+import java.util.function.Consumer;
+
+public interface IAnnotationService extends MinervaJobExecutor {
+
+ @Transactional
+ UserAnnotationSchema prepareUserAnnotationSchema(final User user, final boolean initializeLazy);
+
+ void handleAnnotateProjectJob(final AnnotateProjectMinervaJob parameters, Consumer<Double> updateProgress);
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/IMinervaJobService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/IMinervaJobService.java
index a6da66f3c85933d1f9763ffd165333a8d09a15d8..cf81e304f49afd17b7ed3203020cc430cdb8bd8a 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/IMinervaJobService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/IMinervaJobService.java
@@ -5,12 +5,13 @@ import lcsb.mapviewer.model.job.MinervaJob;
import lcsb.mapviewer.model.job.MinervaJobExecutor;
import lcsb.mapviewer.model.job.MinervaJobStatus;
import lcsb.mapviewer.model.job.MinervaJobType;
+import lcsb.mapviewer.persist.dao.MinervaJobProperty;
import org.springframework.transaction.annotation.Transactional;
import java.util.Calendar;
import java.util.List;
-public interface IMinervaJobService {
+public interface IMinervaJobService extends CrudService<MinervaJob, MinervaJobProperty> {
boolean addJob(MinervaJob job);
@@ -51,4 +52,7 @@ public interface IMinervaJobService {
void enableQueue(boolean shutdownOnFailure);
void disableQueue();
+
+ @Transactional
+ void updateJobProgress(MinervaJob job, Double progress);
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/IProjectService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/IProjectService.java
index fc153a2c3724f8c0b80af947b7c0509d53537673..0f73a7bcca41dc17fcdac39724d66f7593159904 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/IProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/IProjectService.java
@@ -14,7 +14,6 @@ import lcsb.mapviewer.model.job.MinervaJobExecutor;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.layout.ProjectBackground;
import lcsb.mapviewer.model.overlay.InvalidDataOverlayException;
-import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.model.user.UserAnnotationSchema;
import lcsb.mapviewer.persist.dao.ProjectLogEntryProperty;
import lcsb.mapviewer.persist.dao.ProjectProperty;
@@ -74,12 +73,8 @@ public interface IProjectService extends MinervaJobExecutor, CrudService<Project
@Transactional
MinervaJob submitCreateProjectJob(final CreateProjectParams params) throws SecurityException;
- @Transactional
Project createProject(final CreateProjectParams params) throws SecurityException;
- @Transactional
- UserAnnotationSchema prepareUserAnnotationSchema(final User user, final boolean initializeLazy);
-
@Transactional
void removeBackground(final ProjectBackground projectBackground);
@@ -110,7 +105,6 @@ public interface IProjectService extends MinervaJobExecutor, CrudService<Project
@Transactional
void removeProject(String projectId, String directory);
- @Transactional
Project createModel(CreateProjectParams params)
throws InvalidInputDataExecption, ConverterException, IOException, InvalidDataOverlayException, InstantiationException, IllegalAccessException,
CommandExecutionException;
@@ -168,4 +162,24 @@ public interface IProjectService extends MinervaJobExecutor, CrudService<Project
@Transactional
Page<ProjectLogEntry> getLogEntries(Map<ProjectLogEntryProperty, Object> searchFilter, Pageable pageable);
+
+ @Transactional
+ void addBuiltInBackgrounds(final CreateProjectParams params) throws InvalidInputDataExecption;
+
+ @Transactional
+ void validateDataOverlays(final String projectId) throws IOException, InvalidDataOverlayException;
+
+ @Transactional
+ void createHierarchicalView(final String projectId) throws CommandExecutionException;
+
+ @Transactional
+ void createComplexProject(CreateProjectParams params) throws InvalidInputDataExecption;
+
+ @Transactional
+ void createSimpleProject(CreateProjectParams params) throws ConverterException;
+
+ @Transactional
+ void submitAnnotateProjectJob(final String projectId, final UserAnnotationSchema schema);
+
+ void submitRefreshChemicalInfoJobs(final String projectId);
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/jobs/AnnotateProjectMinervaJob.java b/service/src/main/java/lcsb/mapviewer/services/jobs/AnnotateProjectMinervaJob.java
new file mode 100644
index 0000000000000000000000000000000000000000..46dcc914bee8426680d810112a6f22217c794931
--- /dev/null
+++ b/service/src/main/java/lcsb/mapviewer/services/jobs/AnnotateProjectMinervaJob.java
@@ -0,0 +1,73 @@
+package lcsb.mapviewer.services.jobs;
+
+import com.fasterxml.jackson.core.type.TypeReference;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import lcsb.mapviewer.model.job.InvalidMinervaJobParameters;
+import lcsb.mapviewer.model.job.MinervaJobParameters;
+import lcsb.mapviewer.model.user.UserAnnotationSchema;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+import java.util.HashMap;
+import java.util.Map;
+
+public class AnnotateProjectMinervaJob extends MinervaJobParameters {
+
+ private static final Logger logger = LogManager.getLogger();
+
+ private String projectId;
+
+ private UserAnnotationSchema schema;
+
+ public AnnotateProjectMinervaJob(final String projectId, final UserAnnotationSchema schema) {
+ this.projectId = projectId;
+ this.schema = schema;
+ }
+
+ public AnnotateProjectMinervaJob(final Map<String, Object> jobParameters) throws InvalidMinervaJobParameters {
+ super(jobParameters);
+ }
+
+ @Override
+ protected void assignData(final Map<String, Object> jobParameters) {
+ ObjectMapper mapper = new ObjectMapper();
+
+ this.projectId = (String) jobParameters.get("projectId");
+ Object schemaData = jobParameters.get("schema");
+ if (schemaData != null) {
+ try {
+ String serializedSchema = mapper.writeValueAsString(schemaData);
+ this.schema = mapper.readValue(serializedSchema, new TypeReference<UserAnnotationSchema>() {
+ });
+ } catch (Exception e) {
+ logger.error("Problem with deserializing task", e);
+ this.schema = null;
+ }
+ }
+ }
+
+ @Override
+ protected Map<String, Object> getJobParameters() {
+ ObjectMapper mapper = new ObjectMapper();
+ Map<String, Object> jobParameters = new HashMap<>();
+ jobParameters.put("projectId", projectId);
+ try {
+ String serializedSchema = mapper.writeValueAsString(schema);
+ jobParameters.put("schema", mapper.readValue(serializedSchema, new TypeReference<Map<String, Object>>() {
+ }));
+ } catch (Exception e) {
+ logger.error("Problem with serializing task", e);
+ this.schema = null;
+ }
+
+ return jobParameters;
+ }
+
+ public String getProjectId() {
+ return projectId;
+ }
+
+ public UserAnnotationSchema getSchema() {
+ return schema;
+ }
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/chemical/ChemicalService.java b/service/src/main/java/lcsb/mapviewer/services/search/chemical/ChemicalService.java
index df9615befa8998026fcd0c95ace310c790ba966f..14983096fe746a592c12b8331fa0ea4e64b89198 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/chemical/ChemicalService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/chemical/ChemicalService.java
@@ -171,7 +171,9 @@ public class ChemicalService extends DbSearchService implements IChemicalService
if (result == null) {
chemicalParser.setChemicalSuggestedQueryList(project.getId(), disease, Collections.singletonList(" "));
RefreshChemicalSuggestedQueryListMinervaJob parameters = new RefreshChemicalSuggestedQueryListMinervaJob(disease, project.getId());
- minervaJobService.addJob(new MinervaJob(MinervaJobType.REFRESH_CHEMICAL_SUGGESTED_QUERY_LIST, MinervaJobPriority.LOWEST, parameters));
+ MinervaJob job = new MinervaJob(MinervaJobType.REFRESH_CHEMICAL_SUGGESTED_QUERY_LIST, MinervaJobPriority.LOWEST, parameters);
+ job.setExternalObject(project);
+ minervaJobService.addJob(job);
result = new ArrayList<>();
}
return result;
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/drug/DrugService.java b/service/src/main/java/lcsb/mapviewer/services/search/drug/DrugService.java
index 4ca81e45d23318d13df8a401fd01b664de235e92..9be0ef00d02263a522649146a8bf9e090287f041 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/drug/DrugService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/drug/DrugService.java
@@ -181,7 +181,7 @@ public class DrugService extends DbSearchService implements IDrugService {
@Override
public Drug getByName(final String name, final DbSearchCriteria searchCriteria) {
- if (name.trim().equals("")) {
+ if (name.trim().isEmpty()) {
return null;
}
DrugAnnotation secondParser = chEMBLParser;
@@ -253,7 +253,7 @@ public class DrugService extends DbSearchService implements IDrugService {
addProjectTargets(searchCriteria.getProject(), drug);
}
- Collections.sort(drugList, new Drug.NameComparator());
+ drugList.sort(new Drug.NameComparator());
return drugList;
}
@@ -285,8 +285,7 @@ public class DrugService extends DbSearchService implements IDrugService {
List<String> chemblList = chEMBLParser.getSuggestedQueryList(project, organism);
if (drugBankList == null) {
drugBankParser.setDrugSuggestedQueryList(project.getId(), organism, Collections.singletonList(" "));
- RefreshDrugSuggestedQueryListMinervaJob parameters = new RefreshDrugSuggestedQueryListMinervaJob(organism, project.getId());
- minervaJobService.addJob(new MinervaJob(MinervaJobType.REFRESH_DRUG_BANK_SUGGESTED_QUERY_LIST, MinervaJobPriority.LOWEST, parameters));
+ submitRefreshDrugBankSuggestedQueryList(organism, project);
} else {
for (final String string : drugBankList) {
resultSet.add(string.toLowerCase());
@@ -295,8 +294,7 @@ public class DrugService extends DbSearchService implements IDrugService {
if (chemblList == null) {
chEMBLParser.setDrugSuggestedQueryList(project.getId(), organism, Collections.singletonList(" "));
- RefreshDrugSuggestedQueryListMinervaJob parameters = new RefreshDrugSuggestedQueryListMinervaJob(organism, project.getId());
- minervaJobService.addJob(new MinervaJob(MinervaJobType.REFRESH_CHEMBL_SUGGESTED_QUERY_LIST, MinervaJobPriority.LOWEST, parameters));
+ submitRefreshChemblSuggestedQueryList(organism, project);
} else {
for (final String string : chemblList) {
resultSet.add(string.toLowerCase());
@@ -308,6 +306,22 @@ public class DrugService extends DbSearchService implements IDrugService {
return result;
}
+ @Override
+ public void submitRefreshChemblSuggestedQueryList(final MiriamData organism, final Project project) {
+ RefreshDrugSuggestedQueryListMinervaJob parameters = new RefreshDrugSuggestedQueryListMinervaJob(organism, project.getId());
+ MinervaJob job = new MinervaJob(MinervaJobType.REFRESH_CHEMBL_SUGGESTED_QUERY_LIST, MinervaJobPriority.LOWEST, parameters);
+ job.setExternalObject(project);
+ minervaJobService.addJob(job);
+ }
+
+ @Override
+ public void submitRefreshDrugBankSuggestedQueryList(final MiriamData organism, final Project project) {
+ RefreshDrugSuggestedQueryListMinervaJob parameters = new RefreshDrugSuggestedQueryListMinervaJob(organism, project.getId());
+ MinervaJob job = new MinervaJob(MinervaJobType.REFRESH_DRUG_BANK_SUGGESTED_QUERY_LIST, MinervaJobPriority.LOWEST, parameters);
+ job.setExternalObject(project);
+ minervaJobService.addJob(job);
+ }
+
@Override
public void execute(final MinervaJob job) throws Exception {
if (job.getJobType() == MinervaJobType.REFRESH_DRUG_INFO) {
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/drug/IDrugService.java b/service/src/main/java/lcsb/mapviewer/services/search/drug/IDrugService.java
index 99e3407ece37b96115dab339b6b36aea0ec439b0..6cfe842af73ace439828f5f344f1f7ed55fb5d35 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/drug/IDrugService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/drug/IDrugService.java
@@ -1,7 +1,5 @@
package lcsb.mapviewer.services.search.drug;
-import java.util.List;
-
import lcsb.mapviewer.annotation.data.Drug;
import lcsb.mapviewer.annotation.services.DrugSearchException;
import lcsb.mapviewer.model.Project;
@@ -9,14 +7,18 @@ import lcsb.mapviewer.model.job.MinervaJobExecutor;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.services.search.IDbSearchService;
+import java.util.List;
+
/**
* Service for accessing information about drugs.
- *
+ *
* @author Piotr Gawron
- *
*/
public interface IDrugService extends IDbSearchService<Drug>, MinervaJobExecutor {
List<String> getSuggestedQueryList(final Project project, final MiriamData disease) throws DrugSearchException;
+ void submitRefreshChemblSuggestedQueryList(final MiriamData organism, final Project project);
+
+ void submitRefreshDrugBankSuggestedQueryList(final MiriamData organism, final Project project);
}
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/MinervaJobServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/MinervaJobServiceTest.java
index 88d63c13fb13efe4d3074307bb55bbdcec8b6441..cad28d28e52529d650a9ae280191d7e30393e04e 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/MinervaJobServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/MinervaJobServiceTest.java
@@ -5,6 +5,7 @@ import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
import lcsb.mapviewer.common.tests.TestUtils;
import lcsb.mapviewer.common.tests.UnitTestFailedWatcher;
+import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.cache.CacheQuery;
import lcsb.mapviewer.model.cache.CacheType;
import lcsb.mapviewer.model.job.MinervaJob;
@@ -14,6 +15,7 @@ import lcsb.mapviewer.model.job.MinervaJobStatus;
import lcsb.mapviewer.model.job.MinervaJobType;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.services.SpringServiceTestConfig;
import lcsb.mapviewer.services.interfaces.IMinervaJobService;
import lcsb.mapviewer.services.interfaces.IMiriamService;
@@ -205,4 +207,67 @@ public class MinervaJobServiceTest extends TestUtils {
}
}
+ @Test
+ public void testUpdateProgress() {
+ minervaJobService.disableQueue();
+ try {
+ RefreshMiriamInfoMinervaJob params = new RefreshMiriamInfoMinervaJob(-1);
+ MinervaJob job = new MinervaJob(MinervaJobType.REFRESH_MIRIAM_INFO, MinervaJobPriority.MEDIUM, params);
+ minervaJobService.addJob(job);
+
+ minervaJobService.updateJobProgress(job, 50.0);
+
+ job = minervaJobService.getJobById(job.getId());
+ assertEquals(50.0, job.getProgress(), EPSILON);
+ } finally {
+ minervaJobService.enableQueue(false);
+ }
+ }
+
+ @Test
+ public void testUpdateProgressInvalidJob() {
+ minervaJobService.disableQueue();
+ try {
+ RefreshMiriamInfoMinervaJob params = new RefreshMiriamInfoMinervaJob(-1);
+ MinervaJob job = new MinervaJob(MinervaJobType.REFRESH_MIRIAM_INFO, MinervaJobPriority.MEDIUM, params);
+
+ minervaJobService.updateJobProgress(job, 50.0);
+
+ assertNull(minervaJobService.getJobById(job.getId()));
+ } finally {
+ minervaJobService.enableQueue(false);
+ }
+ }
+
+ @Test
+ public void testAddJobWithExternalObject() {
+ Project project = createProject();
+ minervaJobService.disableQueue();
+ try {
+ RefreshMiriamInfoMinervaJob params = new RefreshMiriamInfoMinervaJob(-1);
+ MinervaJob job = new MinervaJob(MinervaJobType.REFRESH_MIRIAM_INFO, MinervaJobPriority.MEDIUM, params);
+ job.setExternalObject(project);
+
+ minervaJobService.addJob(job);
+
+ job = minervaJobService.getJobById(job.getId());
+
+ assertNotNull(job.getExternalObjectClass());
+ assertNotNull(job.getExternalObjectId());
+ } finally {
+ minervaJobService.enableQueue(false);
+ }
+ }
+
+ public Project createProject() {
+ User admin = new User();
+ admin.setId(BUILT_IN_TEST_ADMIN_ID);
+
+ Project project = new Project();
+ project.setProjectId(faker.numerify("T######"));
+ project.setOwner(admin);
+
+ return project;
+ }
+
}
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceNoTransactionTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceNoTransactionTest.java
index 7a697ee84b6038ec66ea40af8758eb9e5acff678..000a7709de727c9ec0257db9e571669131b4dacb 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceNoTransactionTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceNoTransactionTest.java
@@ -538,7 +538,7 @@ public class ProjectServiceNoTransactionTest extends TestUtils {
ProjectService projectService = new ProjectService(null, mockProjectDao,
Mockito.mock(ProjectLogEntryDao.class),
- null, null, null, null, null, null, null, null, null, null, null, Mockito.mock(ProjectBackgroundService.class), null);
+ null, null, null, null, null, null, null, null, Mockito.mock(ProjectBackgroundService.class), null, null);
ReflectionTestUtils.setField(projectService, "self", projectService);
projectService.createImages(params);
@@ -637,8 +637,8 @@ public class ProjectServiceNoTransactionTest extends TestUtils {
GenericProtein protein = new GenericProtein("1");
project.addModel(model);
model.addElement(protein);
- service.fixProjectIssues(project);
- assertFalse(project.getLogEntries().isEmpty());
+ List<ProjectLogEntry> entries = service.fixModelIssues(model);
+ assertFalse(entries.isEmpty());
}
diff --git a/service/src/test/java/lcsb/mapviewer/services/jobs/AnnotateProjectMinervaJobTest.java b/service/src/test/java/lcsb/mapviewer/services/jobs/AnnotateProjectMinervaJobTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..0eaeba78fe6c8a441c1f1a68ae96e872a3f15c4a
--- /dev/null
+++ b/service/src/test/java/lcsb/mapviewer/services/jobs/AnnotateProjectMinervaJobTest.java
@@ -0,0 +1,40 @@
+package lcsb.mapviewer.services.jobs;
+
+import lcsb.mapviewer.annotation.services.ModelAnnotator;
+import lcsb.mapviewer.model.user.UserAnnotationSchema;
+import lcsb.mapviewer.services.ServiceTestFunctions;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import static org.junit.Assert.assertEquals;
+
+public class AnnotateProjectMinervaJobTest extends ServiceTestFunctions {
+
+ @Autowired
+ private ModelAnnotator modelAnnotator;
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testJobSerialization() {
+ UserAnnotationSchema schema = modelAnnotator.createDefaultAnnotatorSchema();
+ AnnotateProjectMinervaJob job = new AnnotateProjectMinervaJob("test", schema);
+
+ AnnotateProjectMinervaJob job2 = new AnnotateProjectMinervaJob("test", new UserAnnotationSchema());
+
+ job2.assignData(job.getJobParameters());
+
+ UserAnnotationSchema serializedSchema = job2.getSchema();
+
+ assertEquals(schema.getClassAnnotators().size(), serializedSchema.getClassAnnotators().size());
+ assertEquals(job.getJobParameters(), job2.getJobParameters());
+ }
+}
diff --git a/web/src/main/java/lcsb/mapviewer/web/api/project/NewProjectJobController.java b/web/src/main/java/lcsb/mapviewer/web/api/project/NewProjectJobController.java
new file mode 100644
index 0000000000000000000000000000000000000000..bf9087eb7775120c9e138337818b5f5b895f74cb
--- /dev/null
+++ b/web/src/main/java/lcsb/mapviewer/web/api/project/NewProjectJobController.java
@@ -0,0 +1,73 @@
+package lcsb.mapviewer.web.api.project;
+
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.job.MinervaJob;
+import lcsb.mapviewer.persist.dao.MinervaJobProperty;
+import lcsb.mapviewer.services.FailedDependencyException;
+import lcsb.mapviewer.services.ObjectNotFoundException;
+import lcsb.mapviewer.services.interfaces.IMinervaJobService;
+import lcsb.mapviewer.services.interfaces.IProjectService;
+import lcsb.mapviewer.web.api.NewApiResponseSerializer;
+import org.hibernate.validator.constraints.NotBlank;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.data.domain.Page;
+import org.springframework.data.domain.Pageable;
+import org.springframework.http.MediaType;
+import org.springframework.http.ResponseEntity;
+import org.springframework.security.access.prepost.PreAuthorize;
+import org.springframework.validation.annotation.Validated;
+import org.springframework.web.bind.annotation.GetMapping;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RestController;
+
+import java.io.IOException;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Map;
+
+@RestController
+@Validated
+@RequestMapping(
+ value = {
+ "/minerva/new_api/projects/{projectId:.+}/job",
+ },
+ produces = MediaType.APPLICATION_JSON_VALUE)
+public class NewProjectJobController {
+
+ private final IProjectService projectService;
+ private final IMinervaJobService minervaJobService;
+ private final NewApiResponseSerializer serializer;
+
+ @Autowired
+ public NewProjectJobController(
+ final IProjectService projectService,
+ final NewApiResponseSerializer serializer,
+ final IMinervaJobService minervaJobService
+ ) {
+ this.projectService = projectService;
+ this.serializer = serializer;
+ this.minervaJobService = minervaJobService;
+ }
+
+ @PreAuthorize("hasAuthority('IS_ADMIN')"
+ + " or hasAuthority('IS_CURATOR') and hasAuthority('READ_PROJECT:' + #projectId)")
+ @GetMapping
+ public ResponseEntity<?> getLogEntries(
+ final @NotBlank @PathVariable(value = "projectId") String projectId,
+ final Pageable pageable)
+ throws ObjectNotFoundException, FailedDependencyException, IOException {
+ Project project = projectService.getProjectByProjectId(projectId);
+ if (project == null) {
+ throw new ObjectNotFoundException();
+ }
+ Map<MinervaJobProperty, Object> searchFilter = new HashMap<>();
+ searchFilter.put(MinervaJobProperty.EXTERNAL_OBJECT_CLASS, Collections.singleton(Project.class));
+ searchFilter.put(MinervaJobProperty.EXTERNAL_OBJECT_ID, Collections.singleton(project.getId()));
+
+ Page<MinervaJob> page = minervaJobService.getAll(searchFilter, pageable);
+
+ return serializer.prepareResponse(page);
+
+ }
+}
\ No newline at end of file
diff --git a/web/src/main/java/lcsb/mapviewer/web/api/user/NewUserController.java b/web/src/main/java/lcsb/mapviewer/web/api/user/NewUserController.java
index f6555a3e5ee7b18488dc0a78bc7740b56b223d70..abefda97ed55655b347da82eae753d350abf9d23 100644
--- a/web/src/main/java/lcsb/mapviewer/web/api/user/NewUserController.java
+++ b/web/src/main/java/lcsb/mapviewer/web/api/user/NewUserController.java
@@ -18,9 +18,9 @@ import lcsb.mapviewer.persist.dao.user.UserProperty;
import lcsb.mapviewer.services.InvalidTokenException;
import lcsb.mapviewer.services.ObjectExistsException;
import lcsb.mapviewer.services.ObjectNotFoundException;
+import lcsb.mapviewer.services.interfaces.IAnnotationService;
import lcsb.mapviewer.services.interfaces.IConfigurationService;
import lcsb.mapviewer.services.interfaces.ILdapService;
-import lcsb.mapviewer.services.interfaces.IProjectService;
import lcsb.mapviewer.services.interfaces.IUserService;
import lcsb.mapviewer.services.utils.EmailException;
import lcsb.mapviewer.services.utils.EmailSender;
@@ -71,7 +71,7 @@ public class NewUserController extends BaseController {
private final IUserService userService;
private final ILdapService ldapService;
- private final IProjectService projectService;
+ private final IAnnotationService annotationService;
private final IConfigurationService configurationService;
private final PasswordEncoder passwordEncoder;
private final EmailSender emailSender;
@@ -86,16 +86,16 @@ public class NewUserController extends BaseController {
final EmailSender emailSender,
final IConfigurationService configurationService,
final ILdapService ldapService,
- final IProjectService projectService,
+ final IAnnotationService annotationService,
final SessionRegistry sessionRegistry,
final NewApiResponseSerializer serializer) {
this.userService = userService;
this.passwordEncoder = passwordEncoder;
this.emailSender = emailSender;
- this.projectService = projectService;
this.configurationService = configurationService;
this.serializer = serializer;
this.ldapService = ldapService;
+ this.annotationService = annotationService;
this.userResponseDecorator = new NewUserResponseDecorator(ldapUsernames, sessionRegistry);
this.refreshLdapUsernames();
}
@@ -128,7 +128,7 @@ public class NewUserController extends BaseController {
throw new ObjectNotFoundException("User doesn't exist");
}
if (user.getAnnotationSchema() == null) {
- user.setAnnotationSchema(projectService.prepareUserAnnotationSchema(user, true));
+ user.setAnnotationSchema(annotationService.prepareUserAnnotationSchema(user, true));
}
return serializer.prepareResponse(user, this.userResponseDecorator);
}
diff --git a/web/src/test/java/lcsb/mapviewer/web/ControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/ControllerIntegrationTest.java
index 4443155aeb282b3024f0ed6e1fb87fffb15b9778..19c48cc114adc7c47e18a2d6a480ac71e8ee9ca5 100644
--- a/web/src/test/java/lcsb/mapviewer/web/ControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/ControllerIntegrationTest.java
@@ -2,6 +2,7 @@ package lcsb.mapviewer.web;
import com.fasterxml.jackson.core.type.TypeReference;
import com.fasterxml.jackson.databind.ObjectMapper;
+import lcsb.mapviewer.annotation.cache.CacheQueryMinervaJob;
import lcsb.mapviewer.annotation.data.serializer.ChemicalSerializer;
import lcsb.mapviewer.annotation.services.PubmedSearchException;
import lcsb.mapviewer.common.TextFileUtils;
@@ -20,6 +21,9 @@ import lcsb.mapviewer.model.graphics.HorizontalAlign;
import lcsb.mapviewer.model.graphics.LineType;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.graphics.VerticalAlign;
+import lcsb.mapviewer.model.job.MinervaJob;
+import lcsb.mapviewer.model.job.MinervaJobPriority;
+import lcsb.mapviewer.model.job.MinervaJobType;
import lcsb.mapviewer.model.map.Comment;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
@@ -1035,4 +1039,11 @@ public abstract class ControllerIntegrationTest extends TestUtils {
return result;
}
+ protected MinervaJob createMinervaJob() {
+ return new MinervaJob(
+ MinervaJobType.REFRESH_CACHE,
+ MinervaJobPriority.LOWEST,
+ new CacheQueryMinervaJob("https://google.lu", -1));
+ }
+
}
diff --git a/web/src/test/java/lcsb/mapviewer/web/ProjectControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/ProjectControllerIntegrationTest.java
index 41176a4ddac27fe0c0ff93e6cadfe4ff21b7e42c..29819fe5e649b8e86f2b6fb61ca03bc723b7571b 100644
--- a/web/src/test/java/lcsb/mapviewer/web/ProjectControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/ProjectControllerIntegrationTest.java
@@ -1403,6 +1403,8 @@ public class ProjectControllerIntegrationTest extends ControllerIntegrationTest
project.removeProjectBackground(project.getProjectBackgrounds().get(0));
projectService.update(project);
+ minervaJobService.waitForTasksToFinish();
+
final String projectHomeDir = projectService.getProjectHomeDir(project);
new File(projectHomeDir).mkdirs();
diff --git a/web/src/test/java/lcsb/mapviewer/web/api/project/NewProjectDiseaseControllerTest.java b/web/src/test/java/lcsb/mapviewer/web/api/project/NewProjectDiseaseControllerTest.java
index 82115c106f112e87700899bbf5da8d6cf73e8fbd..5883cab8a302b5fc485e0465d6b1e2e812c33026 100644
--- a/web/src/test/java/lcsb/mapviewer/web/api/project/NewProjectDiseaseControllerTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/api/project/NewProjectDiseaseControllerTest.java
@@ -93,6 +93,8 @@ public class NewProjectDiseaseControllerTest extends ControllerIntegrationTest {
project.setDisease(null);
projectService.update(project);
+ minervaJobService.waitForTasksToFinish();
+
NewMiriamDataDTO data = createMiriamDataDTO(MiriamType.MESH_2012, "D010300");
RequestBuilder request = post("/minerva/new_api/projects/{projectId}/disease", TEST_PROJECT)
diff --git a/web/src/test/java/lcsb/mapviewer/web/api/project/NewProjectJobControllerTest.java b/web/src/test/java/lcsb/mapviewer/web/api/project/NewProjectJobControllerTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..bb4cf8a6f5a77993c0d19fd09b614de0c4ec9f6d
--- /dev/null
+++ b/web/src/test/java/lcsb/mapviewer/web/api/project/NewProjectJobControllerTest.java
@@ -0,0 +1,70 @@
+package lcsb.mapviewer.web.api.project;
+
+import com.fasterxml.jackson.core.type.TypeReference;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.job.MinervaJob;
+import lcsb.mapviewer.services.interfaces.IMinervaJobService;
+import lcsb.mapviewer.web.ControllerIntegrationTest;
+import lcsb.mapviewer.web.api.NewApiResponseSerializer;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.data.domain.Page;
+import org.springframework.mock.web.MockHttpSession;
+import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
+import org.springframework.test.web.servlet.RequestBuilder;
+
+import static org.junit.Assert.assertEquals;
+import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuilders.get;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
+
+@RunWith(SpringJUnit4ClassRunner.class)
+public class NewProjectJobControllerTest extends ControllerIntegrationTest {
+
+ @Autowired
+ private IMinervaJobService minervaJobService;
+
+ @Autowired
+ private NewApiResponseSerializer newApiResponseSerializer;
+
+ private ObjectMapper objectMapper;
+
+ @Before
+ public void setUp() throws Exception {
+ objectMapper = newApiResponseSerializer.getObjectMapper();
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ minervaJobService.waitForTasksToFinish();
+ removeProject(TEST_PROJECT);
+ }
+
+ @Test
+ public void testGetJobsForProject() throws Exception {
+ Project project = createAndPersistProject(TEST_PROJECT);
+
+ MinervaJob job = createMinervaJob();
+ job.setExternalObject(project);
+ minervaJobService.add(job);
+
+ MinervaJob job2 = createMinervaJob();
+ minervaJobService.add(job2);
+
+ MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
+
+ RequestBuilder request = get(
+ "/minerva/new_api/projects/{projectId}/job/",
+ TEST_PROJECT).session(session);
+
+ String response = mockMvc.perform(request)
+ .andExpect(status().is2xxSuccessful())
+ .andReturn().getResponse().getContentAsString();
+ Page<Object> result = objectMapper.readValue(response, new TypeReference<Page<Object>>() {
+ });
+ assertEquals(1, result.getTotalElements());
+ }
+}