Examples with AbstractSnomedDsvExportItem com.b2international.snowowl.snomed.datastore.internal.rf2.AbstractSnomedDsvExportItem used on opensource projects

Example 1 with AbstractSnomedDsvExportItem

use of com.b2international.snowowl.snomed.datastore.internal.rf2.AbstractSnomedDsvExportItem in project snow-owl by b2ihealthcare.

the class SnomedRefSetDSVExportTest method transformToExportItems.

private List<AbstractSnomedDsvExportItem> transformToExportItems() /*final Iterable<SnomedConstraint> constraints*/
{
    // XXX: Migrate to new MRCM model
    List<AbstractSnomedDsvExportItem> results = Lists.newArrayList();
    // for (final SnomedConstraint constraint : constraints) {
    // SnomedPredicate predicate = constraint.getPredicate();
    // 
    // // Inspect the predicate within the cardinality predicate
    // if (predicate instanceof SnomedCardinalityPredicate) {
    // predicate = ((SnomedCardinalityPredicate) predicate).getPredicate();
    // }
    // 
    // if (predicate instanceof SnomedDescriptionPredicate) {
    // final String descriptionTypeId = ((SnomedDescriptionPredicate) predicate).getTypeId();
    // final ComponentIdSnomedDsvExportItem descriptionExportItem = new ComponentIdSnomedDsvExportItem(SnomedDsvExportItemType.DESCRIPTION, descriptionTypeId, descriptionTypeId);
    // results.add(descriptionExportItem);
    // } else if (predicate instanceof SnomedRelationshipPredicate) {
    // final String typeId = ((SnomedRelationshipPredicate) predicate).getAttributeExpression(); // XXX: only single-SCTID expressions are accepted
    // final ComponentIdSnomedDsvExportItem relationshipExportItem = new ComponentIdSnomedDsvExportItem(SnomedDsvExportItemType.RELATIONSHIP, typeId, typeId);
    // results.add(relationshipExportItem);
    // } else if (predicate instanceof SnomedConcreteDomainPredicate) {
    // final String attributeId = ((SnomedConcreteDomainPredicate) predicate).getAttributeExpression(); // XXX: only single-SCTID expressions are accepted
    // final DataType dataType = ((SnomedConcreteDomainPredicate) predicate).getRange();
    // final boolean dataTypeBoolean = DataType.BOOLEAN.equals(dataType);
    // final DatatypeSnomedDsvExportItem datatypeExportItem = new DatatypeSnomedDsvExportItem(SnomedDsvExportItemType.DATAYPE, attributeId, attributeId, dataTypeBoolean);
    // results.add(datatypeExportItem);
    // }
    // }
    results.add(new SimpleSnomedDsvExportItem(SnomedDsvExportItemType.PREFERRED_TERM));
    results.add(new SimpleSnomedDsvExportItem(SnomedDsvExportItemType.MODULE));
    results.add(new SimpleSnomedDsvExportItem(SnomedDsvExportItemType.EFFECTIVE_TIME));
    results.add(new SimpleSnomedDsvExportItem(SnomedDsvExportItemType.STATUS_LABEL));
    results.add(new SimpleSnomedDsvExportItem(SnomedDsvExportItemType.DEFINITION_STATUS));
    return results;
}

Example 2 with AbstractSnomedDsvExportItem

use of com.b2international.snowowl.snomed.datastore.internal.rf2.AbstractSnomedDsvExportItem in project snow-owl by b2ihealthcare.

the class SnomedSimpleTypeRefSetDSVExporter method writeValues.

private void writeValues(BufferedWriter writer, SnomedConcepts chunk) throws IOException {
    List<String> dataRow = newArrayList();
    for (SnomedConcept concept : chunk) {
        dataRow.clear();
        for (AbstractSnomedDsvExportItem exportItem : exportItems) {
            switch(exportItem.getType()) {
                case DESCRIPTION:
                    {
                        final ComponentIdSnomedDsvExportItem descriptionItem = (ComponentIdSnomedDsvExportItem) exportItem;
                        final String typeId = descriptionItem.getComponentId();
                        int occurrences = descriptionCount.get(typeId);
                        final Map<String, String> termsById = concept.getDescriptions().stream().filter(d -> typeId.equals(d.getTypeId())).collect(Collectors.toMap(SnomedDescription::getId, SnomedDescription::getTerm));
                        addCells(dataRow, occurrences, includeDescriptionId, termsById);
                        break;
                    }
                case RELATIONSHIP:
                    {
                        final ComponentIdSnomedDsvExportItem relationshipItem = (ComponentIdSnomedDsvExportItem) exportItem;
                        for (Integer propertyGroup : propertyCountByGroup.keySet()) {
                            final String typeId = relationshipItem.getComponentId();
                            final Map<String, Integer> groupOccurrences = propertyCountByGroup.getOrDefault(propertyGroup, NO_OCCURRENCES);
                            final int occurrences = groupOccurrences.getOrDefault(typeId, 0);
                            concept.getRelationships().stream().filter(r -> typeId.equals(r.getTypeId()) && Objects.equals(r.getRelationshipGroup(), propertyGroup) && (Concepts.INFERRED_RELATIONSHIP.equals(r.getCharacteristicTypeId()) || Concepts.ADDITIONAL_RELATIONSHIP.equals(r.getCharacteristicTypeId()))).forEach(relationship -> {
                                if (relationship.hasValue()) {
                                    addCells(dataRow, occurrences, includeRelationshipId, ImmutableMap.of(relationship.getValue(), ""));
                                } else {
                                    addCells(dataRow, occurrences, includeRelationshipId, ImmutableMap.of(relationship.getDestinationId(), getPreferredTerm(relationship.getDestination())));
                                }
                            });
                        }
                        break;
                    }
                case DATAYPE:
                    {
                        final DatatypeSnomedDsvExportItem datatypeItem = (DatatypeSnomedDsvExportItem) exportItem;
                        for (Integer propertyGroup : propertyCountByGroup.keySet()) {
                            Map<String, Integer> groupedOccurrences = propertyCountByGroup.getOrDefault(propertyGroup, NO_OCCURRENCES);
                            final String typeId = datatypeItem.getComponentId();
                            int occurrences = groupedOccurrences.getOrDefault(typeId, 0);
                            if (occurrences < 1) {
                                break;
                            }
                            final List<String> properties = concept.getMembers().stream().filter(m -> SnomedRefSetType.CONCRETE_DATA_TYPE.equals(m.type()) && m.isActive() && typeId.equals(m.getProperties().get(SnomedRf2Headers.FIELD_TYPE_ID)) && Objects.equals(m.getProperties().get(SnomedRf2Headers.FIELD_RELATIONSHIP_GROUP), propertyGroup) && (Concepts.INFERRED_RELATIONSHIP.equals(m.getProperties().get(SnomedRf2Headers.FIELD_CHARACTERISTIC_TYPE_ID)) || Concepts.ADDITIONAL_RELATIONSHIP.equals(m.getProperties().get(SnomedRf2Headers.FIELD_CHARACTERISTIC_TYPE_ID)))).map(m -> m.getProperties().get(SnomedRf2Headers.FIELD_VALUE)).map(p -> {
                                if (datatypeItem.isBooleanDatatype()) {
                                    return "1".equals(p) ? "Yes" : "No";
                                } else {
                                    return p.toString();
                                }
                            }).sorted().collect(Collectors.toList());
                            for (String value : properties) {
                                dataRow.add(value);
                                occurrences--;
                            }
                            while (occurrences > 0) {
                                dataRow.add("");
                                occurrences--;
                            }
                        }
                        break;
                    }
                case PREFERRED_TERM:
                    if (includeDescriptionId) {
                        dataRow.add(getPreferredTermId(concept));
                        dataRow.add(getPreferredTerm(concept));
                    } else {
                        dataRow.add(getPreferredTerm(concept));
                    }
                    break;
                case CONCEPT_ID:
                    dataRow.add(concept.getId());
                    break;
                case MODULE:
                    dataRow.add(concept.getModuleId());
                    break;
                case EFFECTIVE_TIME:
                    dataRow.add(EffectiveTimes.format(concept.getEffectiveTime()));
                    break;
                case STATUS_LABEL:
                    dataRow.add(concept.isActive() ? "Active" : "Inactive");
                    break;
                case DEFINITION_STATUS:
                    dataRow.add(concept.getDefinitionStatusId());
                    break;
                default:
                    break;
            }
        }
        writer.write(joiner.join(dataRow));
        writer.write(lineSeparator);
    }
}

Example 3 with AbstractSnomedDsvExportItem

use of com.b2international.snowowl.snomed.datastore.internal.rf2.AbstractSnomedDsvExportItem in project snow-owl by b2ihealthcare.

the class SnomedSimpleTypeRefSetDSVExporter method computeHeader.

private void computeHeader(SnomedConcepts chunk) {
    for (SnomedConcept concept : chunk) {
        for (AbstractSnomedDsvExportItem exportItem : exportItems) {
            switch(exportItem.getType()) {
                case DESCRIPTION:
                    ComponentIdSnomedDsvExportItem descriptionItem = (ComponentIdSnomedDsvExportItem) exportItem;
                    String descriptionTypeId = descriptionItem.getComponentId();
                    Integer matchingDescriptions = concept.getDescriptions().stream().filter(d -> descriptionTypeId.equals(d.getTypeId())).collect(Collectors.reducing(0, description -> 1, Integer::sum));
                    descriptionCount.merge(descriptionTypeId, matchingDescriptions, Math::max);
                    break;
                case RELATIONSHIP:
                    ComponentIdSnomedDsvExportItem relationshipItem = (ComponentIdSnomedDsvExportItem) exportItem;
                    String relationshipTypeId = relationshipItem.getComponentId();
                    Map<Integer, Integer> matchingRelationships = concept.getRelationships().stream().filter(r -> relationshipTypeId.equals(r.getTypeId()) && (Concepts.INFERRED_RELATIONSHIP.equals(r.getCharacteristicTypeId()) || Concepts.ADDITIONAL_RELATIONSHIP.equals(r.getCharacteristicTypeId()))).collect(Collectors.groupingBy(SnomedRelationship::getRelationshipGroup, Collectors.reducing(0, relationship -> 1, Integer::sum)));
                    matchingRelationships.entrySet().stream().forEach(entry -> {
                        propertyCountByGroup.compute(entry.getKey(), (key, oldValue) -> {
                            Map<String, Integer> propertyCountForGroup = ofNullable(oldValue).orElseGet(HashMap::new);
                            propertyCountForGroup.merge(relationshipTypeId, entry.getValue(), Math::max);
                            return propertyCountForGroup;
                        });
                    });
                    break;
                case DATAYPE:
                    ComponentIdSnomedDsvExportItem dataTypeItem = (ComponentIdSnomedDsvExportItem) exportItem;
                    String dataTypeId = dataTypeItem.getComponentId();
                    Map<Integer, Integer> matchingMembers = concept.getMembers().stream().filter(m -> SnomedRefSetType.CONCRETE_DATA_TYPE.equals(m.type()) && m.isActive() && dataTypeId.equals(m.getProperties().get(SnomedRf2Headers.FIELD_TYPE_ID)) && (Concepts.INFERRED_RELATIONSHIP.equals(m.getProperties().get(SnomedRf2Headers.FIELD_CHARACTERISTIC_TYPE_ID)) || Concepts.ADDITIONAL_RELATIONSHIP.equals(m.getProperties().get(SnomedRf2Headers.FIELD_CHARACTERISTIC_TYPE_ID)))).collect(Collectors.groupingBy(m -> (Integer) m.getProperties().get(SnomedRf2Headers.FIELD_RELATIONSHIP_GROUP), Collectors.reducing(0, relationship -> 1, Integer::sum)));
                    matchingMembers.entrySet().stream().forEach(entry -> {
                        propertyCountByGroup.compute(entry.getKey(), (key, oldValue) -> {
                            Map<String, Integer> propertyCountForGroup = ofNullable(oldValue).orElseGet(HashMap::new);
                            propertyCountForGroup.merge(dataTypeId, entry.getValue(), Math::max);
                            return propertyCountForGroup;
                        });
                    });
                    break;
                default:
                    // Single-use fields don't need to be counted in advance
                    break;
            }
        }
    }
}

Example 4 with AbstractSnomedDsvExportItem

use of com.b2international.snowowl.snomed.datastore.internal.rf2.AbstractSnomedDsvExportItem in project snow-owl by b2ihealthcare.

the class SnomedSimpleTypeRefSetDSVExporter method writeHeader.

private void writeHeader(BufferedWriter writer) throws IOException {
    Map<String, String> descriptionTypeIdMap = createTypeIdMap(Concepts.DESCRIPTION_TYPE_ROOT_CONCEPT);
    // includes object and data attributes
    Map<String, String> propertyTypeIdMap = createTypeIdMap(Concepts.CONCEPT_MODEL_ATTRIBUTE);
    List<String> propertyHeader = newArrayList();
    List<String> detailHeader = newArrayList();
    for (AbstractSnomedDsvExportItem exportItem : exportItems) {
        switch(exportItem.getType()) {
            case DESCRIPTION:
                {
                    ComponentIdSnomedDsvExportItem descriptionItem = (ComponentIdSnomedDsvExportItem) exportItem;
                    String typeId = descriptionItem.getComponentId();
                    String displayName = descriptionTypeIdMap.getOrDefault(typeId, descriptionItem.getDisplayName());
                    int occurrences = descriptionCount.get(typeId);
                    if (occurrences < 2) {
                        if (includeDescriptionId) {
                            propertyHeader.add(displayName);
                            propertyHeader.add(displayName);
                            detailHeader.add("ID");
                            detailHeader.add("Term");
                        } else {
                            propertyHeader.add(displayName);
                            detailHeader.add("");
                        }
                    } else {
                        for (int j = 1; j <= occurrences; j++) {
                            String numberedDisplayName = String.format("%s (%s)", displayName, j);
                            if (includeDescriptionId) {
                                propertyHeader.add(numberedDisplayName);
                                propertyHeader.add(numberedDisplayName);
                                detailHeader.add("ID");
                                detailHeader.add("Term");
                            } else {
                                propertyHeader.add(numberedDisplayName);
                                detailHeader.add("");
                            }
                        }
                    }
                    break;
                }
            case RELATIONSHIP:
                {
                    ComponentIdSnomedDsvExportItem relationshipItem = (ComponentIdSnomedDsvExportItem) exportItem;
                    String typeId = relationshipItem.getComponentId();
                    String displayName = propertyTypeIdMap.getOrDefault(typeId, relationshipItem.getDisplayName());
                    for (Integer group : propertyCountByGroup.keySet()) {
                        Map<String, Integer> occurrencesByType = propertyCountByGroup.getOrDefault(group, NO_OCCURRENCES);
                        int occurrences = occurrencesByType.getOrDefault(typeId, 0);
                        if (occurrences < 1) {
                            continue;
                        }
                        String groupTag = group == 0 ? "" : String.format(" (AG%s)", group);
                        if (occurrences < 2) {
                            if (includeRelationshipId) {
                                String groupedDisplayName = displayName + groupTag;
                                propertyHeader.add(groupedDisplayName);
                                propertyHeader.add(groupedDisplayName);
                                detailHeader.add("ID");
                                detailHeader.add("Destination");
                            } else {
                                propertyHeader.add(displayName);
                                detailHeader.add("");
                            }
                        } else {
                            for (int j = 1; j <= occurrences; j++) {
                                String numberedDisplayName = String.format("%s (%s)%s", displayName, j, groupTag);
                                if (includeRelationshipId) {
                                    propertyHeader.add(numberedDisplayName);
                                    propertyHeader.add(numberedDisplayName);
                                    detailHeader.add("ID");
                                    detailHeader.add("Destination");
                                } else {
                                    propertyHeader.add(numberedDisplayName);
                                    detailHeader.add("");
                                }
                            }
                        }
                    }
                    break;
                }
            case DATAYPE:
                {
                    ComponentIdSnomedDsvExportItem dataTypeItem = (ComponentIdSnomedDsvExportItem) exportItem;
                    String typeId = dataTypeItem.getComponentId();
                    String displayName = propertyTypeIdMap.getOrDefault(typeId, dataTypeItem.getDisplayName());
                    for (Integer groupId : propertyCountByGroup.keySet()) {
                        Map<String, Integer> occurrencesByType = propertyCountByGroup.getOrDefault(groupId, NO_OCCURRENCES);
                        int occurrences = occurrencesByType.getOrDefault(typeId, 0);
                        if (occurrences < 1) {
                            continue;
                        }
                        String groupTag = groupId == 0 ? "" : String.format(" (AG%s)", groupId);
                        if (occurrences < 2) {
                            String groupedDisplayName = displayName + groupTag;
                            propertyHeader.add(groupedDisplayName);
                            detailHeader.add("");
                        } else {
                            for (int j = 1; j <= occurrences; j++) {
                                String numberedDisplayName = String.format("%s (%s)%s", displayName, j, groupTag);
                                propertyHeader.add(numberedDisplayName);
                                detailHeader.add("");
                            }
                        }
                    }
                    break;
                }
            case PREFERRED_TERM:
                if (includeDescriptionId) {
                    propertyHeader.add(exportItem.getDisplayName());
                    propertyHeader.add(exportItem.getDisplayName());
                    detailHeader.add("ID");
                    detailHeader.add("Term");
                } else {
                    propertyHeader.add(exportItem.getDisplayName());
                    detailHeader.add("");
                }
                break;
            default:
                propertyHeader.add(exportItem.getDisplayName());
                detailHeader.add("");
                break;
        }
    }
    // write the header to the file
    writer.write(joiner.join(propertyHeader));
    writer.write(lineSeparator);
    if (includeDescriptionId || includeRelationshipId) {
        writer.write(joiner.join(detailHeader));
        writer.write(lineSeparator);
    }
}