/**
* This example shows how to obtain a color.
*
* @param g
* @param monitor
* @throws RenderException
*/
public void render(Graphics2D g, IProgressMonitor monitor) throws RenderException {
if (monitor == null) monitor = new NullProgressMonitor();
CsvReader reader = null;
try {
ILayer layer = getContext().getLayer();
IGeoResource resource = layer.findGeoResource(CSV.class);
if (resource == null) return;
ReferencedEnvelope bounds = getRenderBounds();
monitor.subTask("connecting");
CSV csv = resource.resolve(CSV.class, null);
// LOOK UP STYLE
IStyleBlackboard style = layer.getStyleBlackboard();
Color color = (Color) style.get(ColorStyle.ID);
// DATA TO WORLD
CoordinateReferenceSystem dataCRS = layer.getCRS();
CoordinateReferenceSystem worldCRS = context.getCRS();
MathTransform dataToWorld = CRS.findMathTransform(dataCRS, worldCRS, false);
// DRAW FILE
monitor.beginTask("csv render", csv.getSize());
reader = csv.reader();
reader.readHeaders();
int nameIndex = reader.getIndex("name");
Coordinate worldLocation = new Coordinate();
while (reader.readRecord()) {
Point point = CSV.getPoint(reader);
Coordinate dataLocation = point.getCoordinate();
try {
JTS.transform(dataLocation, worldLocation, dataToWorld);
} catch (TransformException e) {
continue;
}
if (bounds != null && !bounds.contains(worldLocation)) {
continue; // optimize!
}
java.awt.Point p = getContext().worldToPixel(worldLocation);
g.setColor(color);
g.fillRect(p.x - 2, p.y - 2, 6, 6);
g.setColor(Color.BLACK);
String name = reader.get(nameIndex);
g.drawString(name, p.x + 15, p.y + 15);
monitor.worked(1);
if (monitor.isCanceled()) break;
}
} catch (IOException e) {
throw new RenderException(e); // rethrow any exceptions encountered
} catch (FactoryException e) {
throw new RenderException(e); // rethrow any exceptions encountered
} finally {
if (reader != null) reader.close();
monitor.done();
}
}
public StringBuffer uploadAndReportCustomDataFile(
InputStream inputStream,
long size,
String fileFormat,
char delimChar,
List<String> listOfUIDsToUpdate,
CustomFieldGroup customFieldGroup,
PhenoCollection phenoCollection,
boolean overwriteExisting)
throws FileFormatException, ArkSystemException {
List<PhenoCollection> phenoCollectionsWithTheirDataToInsert = new ArrayList<PhenoCollection>();
delimiterCharacter = delimChar;
uploadReport = new StringBuffer();
InputStream convertedInputStream;
if (fileFormat.equalsIgnoreCase(Constants.FileFormat.XLS.toString())) {
XLStoCSV xlsToCSV = new XLStoCSV(delimiterCharacter);
convertedInputStream = xlsToCSV.convertXlsInputStreamToCsv(inputStream);
} else {
convertedInputStream = inputStream;
}
InputStreamReader inputStreamReader = null;
CsvReader csvReader = null;
DecimalFormat decimalFormat = new DecimalFormat("0.00");
int subjectCount = 0;
long updateFieldsCount = 0L;
long insertFieldsCount = 0L;
long emptyDataCount = 0L;
try {
inputStreamReader = new InputStreamReader(convertedInputStream);
csvReader = new CsvReader(inputStreamReader, delimiterCharacter);
String[] stringLineArray;
List<LinkSubjectStudy> allSubjectWhichWillBeUpdated = null;
if (listOfUIDsToUpdate.size() > 0) {
allSubjectWhichWillBeUpdated =
iArkCommonService.getUniqueSubjectsWithTheseUIDs(study, listOfUIDsToUpdate);
} else {
allSubjectWhichWillBeUpdated = new ArrayList<LinkSubjectStudy>();
}
if (size <= 0) {
uploadReport.append(
"ERROR: The input size was not greater than 0. Actual length reported: ");
uploadReport.append(size);
uploadReport.append("\n");
throw new FileFormatException(
"The input size was not greater than 0. Actual length reported: " + size);
}
csvReader.readHeaders();
List<String> fieldNameCollection = Arrays.asList(csvReader.getHeaders());
ArkFunction phenoCustomFieldArkFunction =
iArkCommonService.getArkFunctionByName(
Constants.FUNCTION_KEY_VALUE_PHENO_COLLECTION); // ");
List<CustomFieldDisplay> cfdsThatWeNeed =
iArkCommonService.getCustomFieldDisplaysIn(
fieldNameCollection, study, phenoCustomFieldArkFunction, customFieldGroup);
// Paul has requested - in pheno we only insert List<PhenoData> dataThatWeHave =
// iArkCommonService.getCustomFieldDataFor(cfdsThatWeNeed, allSubjectWhichWillBeUpdated);
// read one line which contains potentially many custom fields
QuestionnaireStatus uploadingStatus =
iPhenotypicService.getPhenoCollectionStatusByName(
Constants.PHENO_COLLECTION_STATUS_UPLOADED);
while (csvReader.readRecord()) {
List<PhenoData> phenoDataToInsertForThisPhenoCollection = new ArrayList<PhenoData>();
log.info("reading record " + subjectCount);
stringLineArray = csvReader.getValues();
String subjectUID = stringLineArray[0];
String recordDate = stringLineArray[1];
Date recordDate_asDate =
(recordDate.isEmpty() ? new Date() : simpleDateFormat.parse(recordDate));
LinkSubjectStudy subject =
getSubjectByUIDFromExistList(allSubjectWhichWillBeUpdated, subjectUID);
// log.info("get subject from list");
CustomField customField = null;
List<PhenoCollection> subjectExistingMatchingPhenoCollections =
iPhenotypicService.getSubjectMatchingPhenoCollections(
subject, customFieldGroup, recordDate_asDate);
PhenoCollection phenoCollectionIntoDB = new PhenoCollection();
if (subjectExistingMatchingPhenoCollections.size() == 0 || !overwriteExisting) {
phenoCollectionIntoDB.setDescription(phenoCollection.getDescription());
phenoCollectionIntoDB.setLinkSubjectStudy(subject);
// phenoCollectionIntoDB.setName(phenoCollection.getName());
phenoCollectionIntoDB.setQuestionnaire(customFieldGroup);
if (recordDate.isEmpty()) {
phenoCollectionIntoDB.setRecordDate(new Date());
} else {
phenoCollectionIntoDB.setRecordDate(recordDate_asDate);
}
phenoCollectionIntoDB.setStatus(
uploadingStatus); // TODO for this to be UPLOADED TYPE STATUS
} else {
if (subjectExistingMatchingPhenoCollections.size() == 1) {
recordDate_asDate =
(recordDate.isEmpty() ? new Date() : simpleDateFormat.parse(recordDate));
phenoCollectionIntoDB = subjectExistingMatchingPhenoCollections.get(0);
} else {
subjectCount++;
continue;
}
}
for (CustomFieldDisplay cfd : cfdsThatWeNeed) {
String theDataAsString = null;
customField = cfd.getCustomField();
if (csvReader.getIndex(cfd.getCustomField().getName()) < 0) {
for (String nameAsSeenInFile : fieldNameCollection) {
if (nameAsSeenInFile.equalsIgnoreCase(cfd.getCustomField().getName())) {
theDataAsString = csvReader.get(nameAsSeenInFile);
}
}
} else {
theDataAsString = csvReader.get(cfd.getCustomField().getName());
}
if (theDataAsString != null && !theDataAsString.isEmpty()) {
PhenoData dataToInsert = new PhenoData();
dataToInsert.setCustomFieldDisplay(cfd);
// as much as i disagree...pheno data isn't tied to subject....pheno collection is
// dataToInsert.setLinkSubjectStudy(subject);
setValue(customField, cfd, dataToInsert, theDataAsString);
boolean flag = true;
for (PhenoData phenoData : phenoCollectionIntoDB.getPhenoData()) {
if (phenoData.getCustomFieldDisplay().getId() == cfd.getId()) {
phenoData.setDateDataValue(dataToInsert.getDateDataValue());
phenoData.setErrorDataValue(dataToInsert.getErrorDataValue());
phenoData.setNumberDataValue(dataToInsert.getNumberDataValue());
phenoData.setTextDataValue(dataToInsert.getTextDataValue());
flag = false;
break;
}
}
if (flag) {
phenoDataToInsertForThisPhenoCollection.add(dataToInsert);
}
insertFieldsCount++;
} else {
emptyDataCount++;
}
}
phenoCollectionIntoDB.getPhenoData().addAll(phenoDataToInsertForThisPhenoCollection);
log.info(phenoCollectionIntoDB.toString());
phenoCollectionsWithTheirDataToInsert.add(phenoCollectionIntoDB);
subjectCount++;
}
log.info(
"finished message for "
+ subjectCount
+ "\n DATA inserts = "
+ insertFieldsCount
+ " phenocollections = "
+ phenoCollectionsWithTheirDataToInsert.size()
+ " amount of empty scells ="
+ emptyDataCount);
} catch (IOException ioe) {
uploadReport.append(
"SYSTEM ERROR: Unexpected I/O exception whilst reading the subject data file\n");
log.error("processMatrixSubjectFile IOException stacktrace:", ioe);
throw new ArkSystemException("Unexpected I/O exception whilst reading the subject data file");
} catch (Exception ex) {
uploadReport.append(
"SYSTEM ERROR: Unexpected exception whilst reading the subject data file\n");
log.error("processMatrixSubjectFile Exception stacktrace:", ex);
throw new ArkSystemException(
"Unexpected exception occurred when trying to process subject data file");
} finally {
uploadReport.append("Total file size: ");
uploadReport.append(decimalFormat.format(size / 1024.0 / 1024.0));
uploadReport.append(" MB");
uploadReport.append("\n");
if (csvReader != null) {
try {
csvReader.close();
} catch (Exception ex) {
log.error("Cleanup operation failed: csvRdr.close()", ex);
}
}
if (inputStreamReader != null) {
try {
inputStreamReader.close();
} catch (Exception ex) {
log.error("Cleanup operation failed: isr.close()", ex);
}
}
}
uploadReport.append("Processed ");
uploadReport.append(subjectCount);
uploadReport.append(" rows.");
uploadReport.append("\n");
uploadReport.append("Inserted ");
uploadReport.append(insertFieldsCount);
uploadReport.append(" rows of data.");
uploadReport.append("\n");
uploadReport.append("Updated ");
uploadReport.append(updateFieldsCount);
uploadReport.append(" rows of data.");
uploadReport.append("\n");
// TODO better exceptionhandling
iPhenotypicService.processPhenoCollectionsWithTheirDataToInsertBatch(
phenoCollectionsWithTheirDataToInsert, study);
return uploadReport;
}