@Before
public void setUp() throws Exception {
taxonGroup = new TaxonGroup();
taxonGroup.setName("Birds");
taxonGroup = taxaDAO.save(taxonGroup);
speciesA = new IndicatorSpecies();
speciesA.setCommonName("Indicator Species A");
speciesA.setScientificName("Indicator Species A");
speciesA.setTaxonGroup(taxonGroup);
speciesA = taxaDAO.save(speciesA);
speciesB = new IndicatorSpecies();
speciesB.setCommonName("Indicator Species B");
speciesB.setScientificName("Indicator Species B");
speciesB.setTaxonGroup(taxonGroup);
speciesB = taxaDAO.save(speciesB);
List<Attribute> attributeList = new ArrayList<Attribute>();
Attribute attr;
for (AttributeType attrType : AttributeType.values()) {
for (AttributeScope scope :
new AttributeScope[] {AttributeScope.RECORD, AttributeScope.SURVEY, null}) {
attr = new Attribute();
attr.setRequired(true);
attr.setName(attrType.toString());
attr.setTypeCode(attrType.getCode());
attr.setScope(scope);
attr.setTag(false);
if (AttributeType.STRING_WITH_VALID_VALUES.equals(attrType)) {
List<AttributeOption> optionList = new ArrayList<AttributeOption>();
for (int i = 0; i < 4; i++) {
AttributeOption opt = new AttributeOption();
opt.setValue(String.format("Option %d", i));
opt = taxaDAO.save(opt);
optionList.add(opt);
}
attr.setOptions(optionList);
}
attr = taxaDAO.save(attr);
attributeList.add(attr);
}
}
survey = new Survey();
survey.setName("SingleSiteMultiTaxaSurvey 1234");
survey.setActive(true);
survey.setStartDate(new Date());
survey.setDescription("Single Site Multi Taxa Survey Description");
Metadata md = survey.setFormRendererType(SurveyFormRendererType.SINGLE_SITE_MULTI_TAXA);
metadataDAO.save(md);
survey.setAttributes(attributeList);
survey = surveyDAO.save(survey);
}
@RolesAllowed({Role.USER, Role.POWERUSER, Role.SUPERVISOR, Role.ADMIN})
@RequestMapping(value = "/bdrs/user/atlas.htm", method = RequestMethod.GET)
public ModelAndView addRecord(
HttpServletRequest request,
HttpServletResponse response,
@RequestParam(value = "surveyId", required = true) int surveyId,
@RequestParam(value = "taxonSearch", required = false) String taxonSearch,
@RequestParam(value = "recordId", required = false, defaultValue = "0") int recordId,
@RequestParam(value = "guid", required = false) String guid) {
Survey survey = surveyDAO.getSurvey(surveyId);
Record record = recordDAO.getRecord(recordId);
record = record == null ? new Record() : record;
IndicatorSpecies species = null;
if (guid != null && !guid.isEmpty()) {
species = taxaDAO.getIndicatorSpeciesByGuid(guid);
}
if (species == null && taxonSearch != null && !taxonSearch.isEmpty()) {
List<IndicatorSpecies> speciesList =
surveyDAO.getSpeciesForSurveySearch(surveyId, taxonSearch);
if (speciesList.isEmpty()) {
species = null;
} else if (speciesList.size() == 1) {
species = speciesList.get(0);
} else {
log.warn(
"Multiple species found for survey "
+ surveyId
+ " and taxon search \""
+ taxonSearch
+ "\". Using the first.");
species = speciesList.get(0);
}
}
if (species == null && record.getSpecies() != null) {
species = record.getSpecies();
}
ModelAndView mv;
if (species == null) {
InputStreamReader reader = null;
try {
Preference p = preferenceDAO.getPreferenceByKey("ala.species.short.url");
URL url;
if (p != null) {
url = new URL(p.getValue() + "/" + guid + ".json");
} else {
url =
new URL(
"http://bie.ala.org.au/species/shortProfile/"
+ guid
+ ".json"); // fallback to the BIE
}
URLConnection conn = url.openConnection();
reader = new InputStreamReader(conn.getInputStream());
StringBuffer buff = new StringBuffer();
int c;
while ((c = reader.read()) != -1) {
buff.append((char) c);
}
JSONObject ob = JSONObject.fromObject(buff.toString());
IndicatorSpecies taxon = new IndicatorSpecies();
log.debug("Found species information from the atlas : ");
log.debug(buff.toString());
// Scientific Name
taxon.setScientificName(ob.getString("scientificName"));
taxon.setAuthor(ob.getString("author"));
taxon.setScientificNameAndAuthor(
ob.getString("scientificName") + " " + ob.getString("scientificNameAuthorship"));
taxon.setYear(ob.getString("year"));
Metadata md = new Metadata();
md.setKey(Metadata.SCIENTIFIC_NAME_SOURCE_DATA_ID);
md.setValue(guid);
metadataDAO.save(md);
taxon.getMetadata().add(md);
// Rank
TaxonRank rank = TaxonRank.findByIdentifier(ob.getString("rank"));
taxon.setTaxonRank(rank);
// Common Name
taxon.setCommonName(ob.getString("commonName"));
md = new Metadata();
md.setKey(Metadata.COMMON_NAME_SOURCE_DATA_ID);
md.setValue(ob.getString("commonNameGUID"));
metadataDAO.save(md);
taxon.getMetadata().add(md);
// Group
String family = ob.getString("family");
if (family != null) {
TaxonGroup g = taxaDAO.getTaxonGroup(family);
if (g == null) {
g = taxaDAO.createTaxonGroup(family, false, false, false, false, false, true);
}
taxon.setTaxonGroup(g);
} else {
TaxonGroup g = taxaDAO.createTaxonGroup("Other", false, false, false, false, false, true);
taxon.setTaxonGroup(g);
}
// Images.
// Thumbnail
if (ob.containsKey("thumbnail")) {
SpeciesProfile sp = new SpeciesProfile();
sp.setType(
SpeciesProfile
.SPECIES_PROFILE_THUMBNAIL); // this is a 100x100 image, might resize for the
// other ones.
sp.setHeader("Thumbnail");
sp.setDescription("Thumbnail for " + taxon.getScientificName());
String filename = ob.getString("thumbnail");
String ext = getExtension(filename);
ManagedFile mf = new ManagedFile();
mf.setContentType("");
mf.setCredit("");
mf.setLicense("");
mf.setDescription(taxon.getScientificName() + " - " + taxon.getCommonName());
mf.setFilename(mf.getUuid() + ext);
mf = managedFileDAO.save(mf);
fileService.createFile(
mf.getClass(), mf.getId(), mf.getFilename(), downloadFile(new URL(filename)));
mf.setContentType(fileService.getFile(mf, mf.getFilename()).getContentType());
managedFileDAO.save(mf);
sp.setContent(mf.getUuid());
speciesProfileDAO.save(sp);
taxon.getInfoItems().add(sp);
// Now thumbnail the thumbnail...
BufferedImage fortyXforty =
imageService.resizeImage(
fileService.getFile(mf, mf.getFilename()).getInputStream(), 40, 40);
ByteArrayOutputStream baos = new ByteArrayOutputStream();
ImageIO.write(fortyXforty, "png", baos);
baos.flush();
byte[] data = baos.toByteArray();
baos.close();
sp = new SpeciesProfile();
sp.setType(
SpeciesProfile
.SPECIES_PROFILE_IMAGE_40x40); // this is a 100x100 image, might resize for the
// other ones.
sp.setHeader("40x40 Thumbnail");
sp.setDescription("40x40 Thumbnail for " + taxon.getScientificName());
mf = new ManagedFile();
mf.setContentType("");
mf.setCredit("");
mf.setLicense("");
mf.setDescription(taxon.getScientificName() + " - " + taxon.getCommonName());
mf.setFilename(mf.getUuid() + ".png");
mf = managedFileDAO.save(mf);
fileService.createFile(mf.getClass(), mf.getId(), mf.getFilename(), data);
mf.setContentType(fileService.getFile(mf, mf.getFilename()).getContentType());
managedFileDAO.save(mf);
sp.setContent(mf.getUuid());
speciesProfileDAO.save(sp);
taxon.getInfoItems().add(sp);
}
// Main Image
if (ob.containsKey("imageURL")) {
SpeciesProfile sp = new SpeciesProfile();
sp.setType(SpeciesProfile.SPECIES_PROFILE_IMAGE);
sp.setHeader("Image");
sp.setDescription("Image for " + taxon.getScientificName());
String filename = ob.getString("imageURL");
String ext = getExtension(filename);
ManagedFile mf = new ManagedFile();
mf.setContentType("");
mf.setCredit("");
mf.setLicense("");
mf.setDescription(taxon.getScientificName() + " - " + taxon.getCommonName());
mf.setFilename(mf.getUuid() + ext);
mf = managedFileDAO.save(mf);
fileService.createFile(
mf.getClass(), mf.getId(), mf.getFilename(), downloadFile(new URL(filename)));
mf.setContentType(fileService.getFile(mf, mf.getFilename()).getContentType());
managedFileDAO.save(mf);
sp.setContent(mf.getUuid());
speciesProfileDAO.save(sp);
taxon.getInfoItems().add(sp);
}
// Save the Taxon
species = taxaDAO.save(taxon);
} catch (IOException ioe) {
log.error("Could not retrieve species profile from the Atlas", ioe);
species = null;
} finally {
if (reader != null) {
try {
reader.close();
} catch (IOException ioe) {
log.error("Error closing stream from Atlas webservice, possible network error", ioe);
}
}
}
}
if (species == null) {
log.debug("Could not determine species, reverting to tracker form");
// The atlas form relies upon a preconfigured species.
// If we do not have one, fall back to the tracker form.
mv = new ModelAndView(new RedirectView("tracker.htm"));
mv.addAllObjects(request.getParameterMap());
mv.addObject("surveyId", surveyId);
return mv;
} else {
// Add all attribute form fields
Map<String, FormField> formFieldMap = new HashMap<String, FormField>();
// Add all property form fields
for (String propertyName : RECORD_PROPERTY_NAMES) {
formFieldMap.put(
propertyName,
formFieldFactory.createRecordFormField(
survey, record, propertyName, species, Taxonomic.TAXONOMIC));
}
// Determine the file attribute to use for the form (if there is one)
// Sort the list of survey attributes by weight so that we can
// correctly select the first file attribute.
List<Attribute> attributeList = survey.getAttributes();
Collections.sort(attributeList, new ComparePersistentImplByWeight());
// Retrieve the first file attribute and if present, the associated
// record attribute.
Attribute fileAttr = null;
AttributeValue fileRecAttr = null;
for (Attribute attr : attributeList) {
if (fileAttr == null && AttributeType.FILE.equals(attr.getType())) {
// Attribute found.
fileAttr = attr;
// Try to locate matching record attribute
for (AttributeValue recAttr : record.getAttributes()) {
if (fileRecAttr == null && fileAttr.equals(recAttr.getAttribute())) {
fileRecAttr = recAttr;
}
}
}
}
// Map all the existing file attributes to record attributes.
Map<Attribute, AttributeValue> fileAttrToRecAttrMap =
new HashMap<Attribute, AttributeValue>();
FormField fileFormField =
formFieldFactory.createRecordFormField(survey, record, fileAttr, fileRecAttr);
Map<String, String> errorMap =
(Map<String, String>) getRequestContext().getSessionAttribute("errorMap");
getRequestContext().removeSessionAttribute("errorMap");
Map<String, String> valueMap =
(Map<String, String>) getRequestContext().getSessionAttribute("valueMap");
getRequestContext().removeSessionAttribute("valueMap");
Metadata predefinedLocationsMD = survey.getMetadataByKey(Metadata.PREDEFINED_LOCATIONS_ONLY);
boolean predefinedLocationsOnly =
predefinedLocationsMD != null && Boolean.parseBoolean(predefinedLocationsMD.getValue());
Set<Location> locations = new TreeSet<Location>(new LocationNameComparator());
locations.addAll(survey.getLocations());
if (!predefinedLocationsOnly) {
locations.addAll(locationDAO.getUserLocations(getRequestContext().getUser()));
}
Metadata defaultLocId =
getRequestContext().getUser().getMetadataObj(Metadata.DEFAULT_LOCATION_ID);
Location defaultLocation;
if (defaultLocId == null) {
defaultLocation = null;
} else {
int defaultLocPk = Integer.parseInt(defaultLocId.getValue());
defaultLocation = locationDAO.getLocation(defaultLocPk);
}
mv = new ModelAndView("atlas");
mv.addObject("record", record);
mv.addObject("taxon", species);
mv.addObject("survey", survey);
mv.addObject("locations", locations);
mv.addObject("formFieldMap", formFieldMap);
mv.addObject("fileFormField", fileFormField);
mv.addObject("preview", request.getParameter("preview") != null);
mv.addObject("defaultLocation", defaultLocation);
mv.addObject("errorMap", errorMap);
mv.addObject("valueMap", valueMap);
}
return mv;
}
protected void parseAttributeValue(
String paramKey,
String fileKey,
Attribute attribute,
Map<String, String[]> parameterMap,
Map<String, MultipartFile> fileMap,
TypedAttributeValue attributeValue)
throws ParseException {
AttributeType attrType = attribute.getType();
if (attrType == AttributeType.TIME) {
// parse out the time attribute if required...
duckPunchTimeParameter("", attribute, parameterMap);
}
String attrValue = getParameter(parameterMap, paramKey);
attrFile = fileMap.get(fileKey);
if (AttributeType.MULTI_CHECKBOX.equals(attrType)
|| AttributeType.MULTI_SELECT.equals(attrType)
|| AttributeType.SINGLE_CHECKBOX.equals(attrType)) {
// These types may have a null attrValue and still be valid.
addOrUpdateAttribute = true;
switch (attrType) {
case MULTI_CHECKBOX:
addOrUpdateAttribute = true;
attributeValue.setMultiCheckboxValue(parameterMap.get(paramKey));
break;
case MULTI_SELECT:
addOrUpdateAttribute = true;
attributeValue.setMultiSelectValue(parameterMap.get(paramKey));
break;
case SINGLE_CHECKBOX:
// Just clean up the input into "true" or "false"
attributeValue.setBooleanValue(Boolean.valueOf(attrValue).toString());
break;
default:
// Absolutely cannot get here.
log.warn("Unknown Attribute Type: " + attribute.getType());
break;
}
} else if (attrValue != null || attrFile != null) {
addOrUpdateAttribute = true;
attributeValue.setStringValue(attrValue);
switch (attrType) {
case TIME:
case STRING:
case STRING_AUTOCOMPLETE:
case TEXT:
case BARCODE:
case REGEX:
case HTML:
case HTML_RAW:
case HTML_NO_VALIDATION:
case HTML_COMMENT:
case HTML_HORIZONTAL_RULE:
break;
case STRING_WITH_VALID_VALUES:
addOrUpdateAttribute = !attrValue.isEmpty();
break;
case INTEGER:
case INTEGER_WITH_RANGE:
case DECIMAL:
addOrUpdateAttribute = !attrValue.isEmpty();
if (addOrUpdateAttribute) {
attributeValue.setNumericValue(new BigDecimal(attrValue));
}
break;
case DATE:
addOrUpdateAttribute = !attrValue.isEmpty();
if (addOrUpdateAttribute) {
attributeValue.setDateValue(dateFormat.parse(attrValue));
}
break;
case IMAGE:
case AUDIO:
case VIDEO:
case FILE:
// attrValue is empty when a file is cleared or the client
// does not have javascript enabled when uploading a file.
// Without javascript, it is not possible to clear a file.
// attrFile will always have size zero unless a file
// is uploaded.
// If there is already a file, but the
// record is updated, without changing the file input,
// addAttribute will be true but attrFile will
// have size zero.
addOrUpdateAttribute =
(attrValue != null && !attrValue.isEmpty())
|| (attrFile != null && attrFile.getSize() > 0);
if (addOrUpdateAttribute && attrFile != null && attrFile.getSize() > 0) {
attributeValue.setStringValue(attrFile.getOriginalFilename());
} else {
// Simplifies the need for users of this class to know about
// zero sized files.
attrFile = null;
}
break;
case SPECIES:
addOrUpdateAttribute = !attrValue.isEmpty();
if (addOrUpdateAttribute) {
// Regardless, attrValue should contain the verbatim name.
String[] values = parameterMap.get(paramKey);
if (values.length > 1 && values[1] != null && StringUtils.hasLength(values[1].trim())) {
// use the id to retrieve a species.
attributeValue.setStringValue(attrValue);
IndicatorSpecies species = null;
try {
Integer speciesId = Integer.valueOf(values[1]);
species = taxaDAO.getIndicatorSpecies(speciesId);
} catch (NumberFormatException e) {
log.warn("Could not parse string to int for species id", e);
}
attributeValue.setSpecies(species);
} else {
// use the name string to search.
List<IndicatorSpecies> taxaList =
taxaDAO.getIndicatorSpeciesByNameSearchExact(attrValue);
// validation has already been done by now so we can just grab the 0th index if it
// exists.
IndicatorSpecies species = null;
if (!taxaList.isEmpty()) {
species = taxaList.get(0);
}
attributeValue.setStringValue(attrValue);
attributeValue.setSpecies(species);
}
}
break;
case CENSUS_METHOD_ROW:
case CENSUS_METHOD_COL:
// census method types do not have a string value, but should be added or updated
addOrUpdateAttribute = true;
attributeValue.setStringValue("");
break;
default:
log.warn("Unknown Attribute Type: " + attrType);
break;
}
} else if (AttributeType.isCensusMethodType(attrType)) {
// census method types do not have a string value, but should be added or updated
addOrUpdateAttribute = true;
} else {
addOrUpdateAttribute = false;
}
}