Examples with FieldDTO edu.harvard.iq.dataverse.api.dto.FieldDTO used on opensource projects

Example 1 with FieldDTO

use of edu.harvard.iq.dataverse.api.dto.FieldDTO in project dataverse by IQSS.

the class ImportGenericServiceBean method processXMLElement.

private void processXMLElement(XMLStreamReader xmlr, String currentPath, String openingTag, ForeignMetadataFormatMapping foreignFormatMapping, DatasetDTO datasetDTO) throws XMLStreamException {
    logger.fine("entering processXMLElement; (" + currentPath + ")");
    for (int event = xmlr.next(); event != XMLStreamConstants.END_DOCUMENT; event = xmlr.next()) {
        if (event == XMLStreamConstants.START_ELEMENT) {
            String currentElement = xmlr.getLocalName();
            ForeignMetadataFieldMapping mappingDefined = datasetfieldService.findFieldMapping(foreignFormatMapping.getName(), currentPath + currentElement);
            if (mappingDefined != null) {
                DatasetFieldType mappingDefinedFieldType = datasetfieldService.findByNameOpt(mappingDefined.getDatasetfieldName());
                boolean compound = mappingDefinedFieldType.isCompound();
                DatasetFieldCompoundValue cachedCompoundValue = null;
                String dataverseFieldName = mappingDefined.getDatasetfieldName();
                // Process attributes, if any are defined in the mapping:
                if (mappingDefinedFieldType.isCompound()) {
                    List<HashSet<FieldDTO>> compoundField = new ArrayList<>();
                    HashSet<FieldDTO> set = new HashSet<>();
                    for (ForeignMetadataFieldMapping childMapping : mappingDefined.getChildFieldMappings()) {
                        if (childMapping.isAttribute()) {
                            String attributeName = childMapping.getForeignFieldXPath();
                            String attributeValue = xmlr.getAttributeValue(null, attributeName);
                            if (attributeValue != null) {
                                String mappedFieldName = childMapping.getDatasetfieldName();
                                logger.fine("looking up dataset field " + mappedFieldName);
                                DatasetFieldType mappedFieldType = datasetfieldService.findByNameOpt(mappedFieldName);
                                if (mappedFieldType != null) {
                                    try {
                                        addToSet(set, attributeName, attributeValue);
                                    // FieldDTO value = FieldDTO.createPrimitiveFieldDTO(attributeName, attributeValue);
                                    // FieldDTO attribute = FieldDTO.createCompoundFieldDTO(attributeName, value);
                                    // MetadataBlockDTO citationBlock = datasetDTO.getDatasetVersion().getMetadataBlocks().get("citation");
                                    // citationBlock.getFields().add(value);
                                    // TO DO replace database output with Json                                        cachedCompoundValue = createDatasetFieldValue(mappedFieldType, cachedCompoundValue, attributeValue, datasetVersion);
                                    } catch (Exception ex) {
                                        logger.warning("Caught unknown exception when processing attribute " + currentPath + currentElement + "{" + attributeName + "} (skipping);");
                                    }
                                } else {
                                    throw new EJBException("Bad foreign metadata field mapping: no such DatasetField " + mappedFieldName + "!");
                                }
                            }
                        }
                    }
                    if (!set.isEmpty()) {
                        compoundField.add(set);
                        MetadataBlockDTO citationBlock = datasetDTO.getDatasetVersion().getMetadataBlocks().get(mappingDefinedFieldType.getMetadataBlock().getName());
                        citationBlock.addField(FieldDTO.createMultipleCompoundFieldDTO(mappingDefined.getDatasetfieldName(), compoundField));
                    } else {
                        FieldDTO value = null;
                        if (mappingDefinedFieldType.isAllowMultiples()) {
                            List<String> values = new ArrayList<>();
                            values.add(parseText(xmlr));
                            value = FieldDTO.createMultiplePrimitiveFieldDTO(dataverseFieldName, values);
                        } else {
                            value = FieldDTO.createPrimitiveFieldDTO(dataverseFieldName, parseText(xmlr));
                        }
                        value = makeDTO(mappingDefinedFieldType, value, dataverseFieldName);
                        MetadataBlockDTO citationBlock = datasetDTO.getDatasetVersion().getMetadataBlocks().get(mappingDefinedFieldType.getMetadataBlock().getName());
                        citationBlock.addField(value);
                    }
                } else // xxString dataverseFieldName = mappingDefined.getDatasetfieldName();
                if (dataverseFieldName != null && !dataverseFieldName.isEmpty()) {
                    DatasetFieldType dataverseFieldType = datasetfieldService.findByNameOpt(dataverseFieldName);
                    FieldDTO value;
                    if (dataverseFieldType != null) {
                        if (dataverseFieldType.isControlledVocabulary()) {
                            value = FieldDTO.createVocabFieldDTO(dataverseFieldName, parseText(xmlr));
                        } else {
                            value = FieldDTO.createPrimitiveFieldDTO(dataverseFieldName, parseText(xmlr));
                        }
                        value = makeDTO(dataverseFieldType, value, dataverseFieldName);
                        // value = FieldDTO.createPrimitiveFieldDTO(dataverseFieldName, parseText(xmlr));
                        // FieldDTO dataverseField = FieldDTO.createCompoundFieldDTO(dataverseFieldName, value);
                        MetadataBlockDTO citationBlock = datasetDTO.getDatasetVersion().getMetadataBlocks().get(mappingDefinedFieldType.getMetadataBlock().getName());
                        citationBlock.addField(value);
                    // TO DO replace database output with Json                             createDatasetFieldValue(dataverseFieldType, cachedCompoundValue, elementTextPayload, datasetVersion);
                    } else {
                        throw new EJBException("Bad foreign metadata field mapping: no such DatasetField " + dataverseFieldName + "!");
                    }
                }
            } else {
                // recursively, process the xml stream further down:
                processXMLElement(xmlr, currentPath + currentElement + ":", currentElement, foreignFormatMapping, datasetDTO);
            }
        } else if (event == XMLStreamConstants.END_ELEMENT) {
            if (xmlr.getLocalName().equals(openingTag))
                return;
        }
    }
}

Example 2 with FieldDTO

use of edu.harvard.iq.dataverse.api.dto.FieldDTO in project dataverse by IQSS.

the class ImportDDIServiceBean method handleChildField.

private void handleChildField(MetadataBlockDTO customBlock, DatasetFieldType dsfType, String fieldValue) throws ImportException {
    DatasetFieldType parent = dsfType.getParentDatasetFieldType();
    // Create child Field
    FieldDTO child = null;
    if (dsfType.isAllowControlledVocabulary()) {
        child = FieldDTO.createVocabFieldDTO(dsfType.getName(), fieldValue);
    } else if (dsfType.isPrimitive()) {
        child = FieldDTO.createPrimitiveFieldDTO(dsfType.getName(), fieldValue);
    } else {
        throw new ImportException("Unsupported custom child field type: " + dsfType);
    }
    // Create compound field with this child as its only element
    FieldDTO compound = null;
    if (parent.isAllowMultiples()) {
        compound = FieldDTO.createMultipleCompoundFieldDTO(parent.getName(), child);
    } else {
        compound = FieldDTO.createCompoundFieldDTO(parent.getName(), child);
    }
    customBlock.addField(compound);
}

Example 3 with FieldDTO

use of edu.harvard.iq.dataverse.api.dto.FieldDTO in project dataverse by IQSS.

the class ImportDDIServiceBean method processTargetSampleSize.

private void processTargetSampleSize(XMLStreamReader xmlr, MetadataBlockDTO socialScience) throws XMLStreamException {
    FieldDTO sampleSize = null;
    FieldDTO sampleSizeFormula = null;
    for (int event = xmlr.next(); event != XMLStreamConstants.END_DOCUMENT; event = xmlr.next()) {
        if (event == XMLStreamConstants.START_ELEMENT) {
            if (xmlr.getLocalName().equals("sampleSize")) {
                sampleSize = FieldDTO.createPrimitiveFieldDTO("targetSampleActualSize", parseText(xmlr, "sampleSize"));
            } else if (xmlr.getLocalName().equals("sampleSizeFormula")) {
                sampleSizeFormula = FieldDTO.createPrimitiveFieldDTO("targetSampleSizeFormula", parseText(xmlr, "sampleSizeFormula"));
            }
        } else if (event == XMLStreamConstants.END_ELEMENT) {
            if (xmlr.getLocalName().equals("targetSampleSize")) {
                if (sampleSize != null || sampleSizeFormula != null) {
                    socialScience.getFields().add(FieldDTO.createCompoundFieldDTO("targetSampleSize", sampleSize, sampleSizeFormula));
                }
                return;
            }
        }
    }
}

Example 4 with FieldDTO

use of edu.harvard.iq.dataverse.api.dto.FieldDTO in project dataverse by IQSS.

the class DatasetVersionDTOTest method testReadDataSet.

@Test
public void testReadDataSet() {
    try {
        File file = new File("src/test/java/edu/harvard/iq/dataverse/util/json/JsonDatasetVersion.txt");
        String text = new Scanner(file).useDelimiter("\\Z").next();
        Gson gson = new Gson();
        DatasetVersionDTO dto = gson.fromJson(text, DatasetVersionDTO.class);
        HashSet<FieldDTO> author1Fields = new HashSet<>();
        author1Fields.add(FieldDTO.createPrimitiveFieldDTO("authorAffiliation", "Top"));
        author1Fields.add(FieldDTO.createPrimitiveFieldDTO("authorIdentifier", "ellenid"));
        author1Fields.add(FieldDTO.createVocabFieldDTO("authorIdentifierScheme", "ORCID"));
        author1Fields.add(FieldDTO.createPrimitiveFieldDTO("authorName", "Privileged, Pete"));
        HashSet<FieldDTO> author2Fields = new HashSet<>();
        author2Fields.add(FieldDTO.createPrimitiveFieldDTO("authorAffiliation", "Bottom"));
        author2Fields.add(FieldDTO.createPrimitiveFieldDTO("authorIdentifier", "audreyId"));
        author2Fields.add(FieldDTO.createVocabFieldDTO("authorIdentifierScheme", "DAISY"));
        author2Fields.add(FieldDTO.createPrimitiveFieldDTO("authorName", "Awesome, Audrey"));
        List<HashSet<FieldDTO>> authorList = new ArrayList<>();
        authorList.add(author1Fields);
        authorList.add(author2Fields);
        FieldDTO expectedDTO = new FieldDTO();
        expectedDTO.setTypeName("author");
        expectedDTO.setMultipleCompound(authorList);
        FieldDTO authorDTO = dto.getMetadataBlocks().get("citation").getFields().get(1);
        // write both dto's to json to compare them with gson parser
        JsonElement expected = gson.toJsonTree(expectedDTO, FieldDTO.class);
        JsonElement result = gson.toJsonTree(authorDTO);
        Assert.assertEquals(expected, result);
    } catch (IOException e) {
        e.printStackTrace();
    }
}

Example 5 with FieldDTO

use of edu.harvard.iq.dataverse.api.dto.FieldDTO in project dataverse by IQSS.

the class JsonParser method remapGeographicCoverage.

/**
 * Special processing for GeographicCoverage compound field:
 * Handle parsing exceptions caused by invalid controlled vocabulary in the "country" field by
 * putting the invalid data in "otherGeographicCoverage" in a new compound value.
 *
 * @param ex - contains the invalid values to be processed
 * @return a compound DatasetField that contains the newly created values, in addition to
 * the original valid values.
 * @throws JsonParseException
 */
private DatasetField remapGeographicCoverage(CompoundVocabularyException ex) throws JsonParseException {
    List<HashSet<FieldDTO>> geoCoverageList = new ArrayList<>();
    // For each exception, create HashSet of otherGeographic Coverage and add to list
    for (ControlledVocabularyException vocabEx : ex.getExList()) {
        HashSet<FieldDTO> set = new HashSet<>();
        set.add(FieldDTO.createPrimitiveFieldDTO(DatasetFieldConstant.otherGeographicCoverage, vocabEx.getStrValue()));
        geoCoverageList.add(set);
    }
    FieldDTO geoCoverageDTO = FieldDTO.createMultipleCompoundFieldDTO(DatasetFieldConstant.geographicCoverage, geoCoverageList);
    // convert DTO to datasetField so we can back valid values.
    Gson gson = new Gson();
    String jsonString = gson.toJson(geoCoverageDTO);
    JsonReader jsonReader = Json.createReader(new StringReader(jsonString));
    JsonObject obj = jsonReader.readObject();
    DatasetField geoCoverageField = parseField(obj);
    // add back valid values
    for (DatasetFieldCompoundValue dsfcv : ex.getValidValues()) {
        if (!dsfcv.getChildDatasetFields().isEmpty()) {
            dsfcv.setParentDatasetField(geoCoverageField);
            geoCoverageField.getDatasetFieldCompoundValues().add(dsfcv);
        }
    }
    return geoCoverageField;
}