Examples with AnnotationValueObject ubic.gemma.model.common.description.AnnotationValueObject used on opensource projects

Example 1 with AnnotationValueObject

use of ubic.gemma.model.common.description.AnnotationValueObject in project Gemma by PavlidisLab.

the class CharacteristicBrowserController method browse.

public JsonReaderResponse<AnnotationValueObject> browse(ListBatchCommand batch) {
    Integer count = characteristicService.countAll();
    List<AnnotationValueObject> results = new ArrayList<>();
    Collection<Characteristic> records;
    if (StringUtils.isNotBlank(batch.getSort())) {
        String o = batch.getSort();
        String orderBy;
        switch(o) {
            case "className":
                orderBy = "category";
                break;
            case "termName":
                orderBy = "value";
                break;
            case "evidenceCode":
                orderBy = "evidenceCode";
                break;
            default:
                throw new IllegalArgumentException("Unknown sort field: " + o);
        }
        boolean descending = batch.getDir() != null && batch.getDir().equalsIgnoreCase("DESC");
        records = characteristicService.browse(batch.getStart(), batch.getLimit(), orderBy, descending);
    } else {
        records = characteristicService.browse(batch.getStart(), batch.getLimit());
    }
    Map<Characteristic, Object> charToParent = characteristicService.getParents(records);
    for (Object o : records) {
        Characteristic c = (Characteristic) o;
        Object parent = charToParent.get(c);
        AnnotationValueObject avo = new AnnotationValueObject();
        avo.setId(c.getId());
        avo.setClassName(c.getCategory());
        avo.setTermName(c.getValue());
        if (c.getEvidenceCode() != null)
            avo.setEvidenceCode(c.getEvidenceCode().toString());
        populateClassValues(c, avo);
        if (parent != null) {
            populateParentInformation(avo, parent);
        }
        results.add(avo);
    }
    return new JsonReaderResponse<>(results, count);
}

Example 2 with AnnotationValueObject

use of ubic.gemma.model.common.description.AnnotationValueObject in project Gemma by PavlidisLab.

the class CharacteristicUpdateTaskImpl method convertToFactorValuesWithCharacteristics.

/**
 * This is used to handle the special case of FactorValues that are being updated to have a characteristic.
 *
 * @return for each given AnnotationValueObject, the corresponding FactorValue with an associated persistent
 * Characteristic.
 * @throws IllegalStateException if the corresponding FactorValue already has at least one Characteristic. This
 *                               method is just intended for filling that in if it's empty.
 */
private Collection<FactorValue> convertToFactorValuesWithCharacteristics(Collection<AnnotationValueObject> avos) {
    Collection<FactorValue> result = new HashSet<>();
    for (AnnotationValueObject avo : avos) {
        if (avo.getObjectClass() == null || !avo.getObjectClass().equals(FactorValue.class.getSimpleName()))
            continue;
        if (avo.getId() == null) {
            log.warn("No id");
            continue;
        }
        /*
             * load the factor value, and create a characteristic
             */
        FactorValue fv = factorValueService.load(avo.getId());
        if (fv == null)
            continue;
        if (!fv.getCharacteristics().isEmpty()) {
            throw new IllegalStateException("Don't use the annotator to update factor values that already have characteristics");
        }
        VocabCharacteristic vc = convertAvo2Characteristic(avo);
        vc.setId(null);
        if (vc.getEvidenceCode() == null) {
            vc.setEvidenceCode(GOEvidenceCode.IC);
        }
        vc = (VocabCharacteristic) characteristicService.create(vc);
        fv.setValue(vc.getValue());
        fv.getCharacteristics().add(vc);
        result.add(fv);
    }
    return result;
}

Example 3 with AnnotationValueObject

use of ubic.gemma.model.common.description.AnnotationValueObject in project Gemma by PavlidisLab.

the class CharacteristicUpdateTaskImpl method doUpdate.

private TaskResult doUpdate() {
    Collection<AnnotationValueObject> avos = taskCommand.getAnnotationValueObjects();
    if (avos.size() == 0)
        return new TaskResult(taskCommand, false);
    log.info("Updating " + avos.size() + " characteristics or uncharacterized factor values...");
    StopWatch timer = new StopWatch();
    timer.start();
    Collection<Characteristic> asChars = convertToCharacteristic(avos);
    Collection<FactorValue> factorValues = convertToFactorValuesWithCharacteristics(avos);
    if (asChars.size() == 0 && factorValues.size() == 0) {
        log.info("Nothing to update");
        return new TaskResult(taskCommand, false);
    }
    for (FactorValue factorValue : factorValues) {
        factorValueService.update(factorValue);
    }
    if (asChars.size() == 0)
        return new TaskResult(taskCommand, true);
    Map<Characteristic, Object> charToParent = characteristicService.getParents(asChars);
    for (Characteristic cFromClient : asChars) {
        Long characteristicId = cFromClient.getId();
        if (characteristicId == null) {
            continue;
        }
        Characteristic cFromDatabase = characteristicService.load(characteristicId);
        if (cFromDatabase == null) {
            log.warn("No such characteristic with id=" + characteristicId);
            continue;
        }
        VocabCharacteristic vcFromClient = (cFromClient instanceof VocabCharacteristic) ? (VocabCharacteristic) cFromClient : null;
        VocabCharacteristic vcFromDatabase = (cFromDatabase instanceof VocabCharacteristic) ? (VocabCharacteristic) cFromDatabase : null;
        /*
             * if one of the characteristics is a VocabCharacteristic and the other is not, we have to change the
             * characteristic in the database so that it matches the one from the client; since we can't change the
             * class of the object, we have to remove the old characteristic and make a new one of the appropriate
             * class.
             */
        Object parent = charToParent.get(cFromDatabase);
        /*
             * Check needed because Characteristics are not securable.
             */
        if (parent != null && Securable.class.isAssignableFrom(parent.getClass()) && !securityService.isEditable((Securable) parent)) {
            throw new AccessDeniedException("Access is denied");
        }
        if (vcFromClient != null && vcFromDatabase == null) {
            VocabCharacteristic vc = VocabCharacteristic.Factory.newInstance();
            vc.setValue(StringUtils.strip(cFromDatabase.getValue()));
            vc.setEvidenceCode(cFromDatabase.getEvidenceCode());
            vc.setDescription(cFromDatabase.getDescription());
            vc.setCategory(cFromDatabase.getCategory());
            vc.setName(cFromDatabase.getName());
            vcFromDatabase = (VocabCharacteristic) characteristicService.create(vc);
            removeFromParent(cFromDatabase, parent);
            characteristicService.remove(cFromDatabase);
            addToParent(vcFromDatabase, parent);
            cFromDatabase = vcFromDatabase;
        } else if (vcFromClient == null && vcFromDatabase != null) {
            // don't copy AuditTrail or Status to avoid cascade error... vcFromDatabase.getAuditTrail()
            cFromDatabase = characteristicService.create(Characteristic.Factory.newInstance(vcFromDatabase.getName(), vcFromDatabase.getDescription(), null, StringUtils.strip(vcFromDatabase.getValue()), vcFromDatabase.getCategory(), vcFromDatabase.getCategoryUri(), vcFromDatabase.getEvidenceCode()));
            removeFromParent(vcFromDatabase, parent);
            characteristicService.remove(vcFromDatabase);
            addToParent(cFromDatabase, parent);
        }
        /*
             * at this point, cFromDatabase points to the class-corrected characteristic in the database that must be
             * updated with the information coming from the client.
             */
        assert cFromDatabase != null;
        cFromDatabase.setValue(cFromClient.getValue());
        cFromDatabase.setCategory(cFromClient.getCategory());
        if (cFromDatabase instanceof VocabCharacteristic) {
            vcFromDatabase = (VocabCharacteristic) cFromDatabase;
            if (vcFromClient != null) {
                if (vcFromDatabase.getValueUri() == null || vcFromDatabase.getValueUri() == null || !vcFromDatabase.getValueUri().equals(vcFromClient.getValueUri())) {
                    log.info("Characteristic value update: " + vcFromDatabase + " " + vcFromDatabase.getValueUri() + " -> " + vcFromClient.getValueUri() + " associated with " + parent);
                    vcFromDatabase.setValueUri(vcFromClient.getValueUri());
                }
                if (vcFromDatabase.getCategory() == null || vcFromDatabase.getCategoryUri() == null || !vcFromDatabase.getCategoryUri().equals(vcFromClient.getCategoryUri())) {
                    log.info("Characteristic category update: " + vcFromDatabase + " " + vcFromDatabase.getCategoryUri() + " -> " + vcFromClient.getCategoryUri() + " associated with " + parent);
                    vcFromDatabase.setCategoryUri(vcFromClient.getCategoryUri());
                }
            }
        }
        if (cFromClient.getEvidenceCode() == null) {
            // characteristic has been manually updated
            cFromDatabase.setEvidenceCode(GOEvidenceCode.IC);
        } else {
            if (!cFromDatabase.getEvidenceCode().equals(cFromClient.getEvidenceCode())) {
                log.info("Characteristic evidence code update: " + cFromDatabase + " " + cFromDatabase.getEvidenceCode() + " -> " + cFromClient.getEvidenceCode());
            }
            // let them change it.
            cFromDatabase.setEvidenceCode(cFromClient.getEvidenceCode());
        }
        characteristicService.update(cFromDatabase);
    }
    timer.stop();
    if (timer.getTime() > 1000) {
        log.info("Update took: " + timer.getTime());
    }
    return new TaskResult(taskCommand, true);
}

Example 4 with AnnotationValueObject

use of ubic.gemma.model.common.description.AnnotationValueObject in project Gemma by PavlidisLab.

the class CharacteristicUpdateTaskImpl method convertToCharacteristic.

/**
 * Convert incoming AVOs into Characteristics (if the AVO objectClass is not FactorValue)
 */
private Collection<Characteristic> convertToCharacteristic(Collection<AnnotationValueObject> avos) {
    Collection<Characteristic> result = new HashSet<>();
    for (AnnotationValueObject avo : avos) {
        if (avo.getObjectClass() != null && avo.getObjectClass().equals(FactorValue.class.getSimpleName()))
            continue;
        VocabCharacteristic vc = convertAvo2Characteristic(avo);
        result.add(vc);
    }
    return result;
}

Example 5 with AnnotationValueObject

use of ubic.gemma.model.common.description.AnnotationValueObject in project Gemma by PavlidisLab.

the class BioMaterialController method getAnnotation.

public Collection<AnnotationValueObject> getAnnotation(EntityDelegator bm) {
    if (bm == null || bm.getId() == null)
        return null;
    BioMaterial bioM = bioMaterialService.load(bm.getId());
    Collection<AnnotationValueObject> annotation = new ArrayList<>();
    for (Characteristic c : bioM.getCharacteristics()) {
        AnnotationValueObject annotationValue = new AnnotationValueObject();
        annotationValue.setId(c.getId());
        annotationValue.setClassName(c.getCategory());
        annotationValue.setTermName(c.getValue());
        annotationValue.setObjectClass(BioMaterial.class.getSimpleName());
        if (c.getEvidenceCode() != null) {
            annotationValue.setEvidenceCode(c.getEvidenceCode().toString());
        }
        if (c instanceof VocabCharacteristic) {
            VocabCharacteristic vc = (VocabCharacteristic) c;
            annotationValue.setClassUri(vc.getCategoryUri());
            String className = getLabelFromUri(vc.getCategoryUri());
            if (className != null)
                annotationValue.setClassName(className);
            annotationValue.setTermUri(vc.getValueUri());
            String termName = getLabelFromUri(vc.getValueUri());
            if (termName != null)
                annotationValue.setTermName(termName);
        }
        annotation.add(annotationValue);
    }
    return annotation;
}