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Improve (slightly) stability & helpfulness of error messages
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@GenieTim
GenieTim committed Oct 23, 2019
1 parent d1cd163 commit b2317d4
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Showing 5 changed files with 154 additions and 192 deletions.
157 changes: 70 additions & 87 deletions src/main/java/edu/harvard/mcz/imagecapture/CandidateImageFile.java
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Original file line number Diff line number Diff line change
Expand Up @@ -40,6 +40,7 @@

import com.adobe.internal.xmp.XMPException;
import com.adobe.internal.xmp.XMPMeta;
import com.google.zxing.*;
import edu.harvard.mcz.imagecapture.jobs.JobSingleBarcodeScan;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.CommandLineParser;
Expand All @@ -62,12 +63,6 @@
import com.drew.metadata.exif.ExifSubIFDDirectory;
import com.drew.metadata.jpeg.JpegDirectory;
import com.drew.metadata.xmp.XmpDirectory;
import com.google.zxing.BinaryBitmap;
import com.google.zxing.DecodeHintType;
import com.google.zxing.LuminanceSource;
import com.google.zxing.NotFoundException;
import com.google.zxing.ReaderException;
import com.google.zxing.Result;
import com.google.zxing.client.j2se.BufferedImageLuminanceSource;
import com.google.zxing.common.HybridBinarizer;
import com.google.zxing.qrcode.QRCodeReader;
Expand Down Expand Up @@ -152,8 +147,7 @@ public CandidateImageFile(File aFile) throws UnreadableFileException {

try {
template = new PositionTemplate(templateName);
log.info("template ID is.........." + template.getTemplateId());
//log.info("templateName is......." + templateName);
log.info("template ID is " + template.getTemplateId());
} catch (NoSuchTemplateException e) {
log.error("Position template detector returned an unknown template name: " + templateName + ".", e);
}
Expand All @@ -170,8 +164,36 @@ public CandidateImageFile(File aFile) throws UnreadableFileException {
log.error("Unable to OCR file: " + candidateFile.getName() + " " + e.getMessage());
}
}
templateUsed = template;

templateUsed = template;
}

/**
* Constructor
*
* @param aFile the image file that may contain a barcode or text.
* @param aTemplate the PositionTemplate to use to identify where a barcode or OCR text may occur
* in the image provided by aFile.
*
* @throws UnreadableFileException if aFile cannot be read.
* @throws OCRReadException
*/
public CandidateImageFile(File aFile, PositionTemplate aTemplate) throws UnreadableFileException {
setFile(aFile, aTemplate);
if (!aFile.canRead()) {
try {
throw new UnreadableFileException("Can't read file " + aFile.getCanonicalPath());
} catch (IOException e) {
throw new UnreadableFileException("IOException on trying to get filename.");
}
}
}

/**
* Constructor with no parameters to use to access convenience static methods.
* Must follow with setFile() to use for processing images.
* @see this.setFile(...);
*/
public CandidateImageFile() {
}

/**
Expand Down Expand Up @@ -272,9 +294,7 @@ public static void debugCheckHeightWidth(File aFile) {
} catch (MetadataException e) {
log.debug("Error reading EXIF orientation metadata." + e.getMessage() );
}
} catch (NullPointerException e1) {
log.debug("Error processing EXIF data." + e1.getMessage());
} catch (ImageProcessingException e1) {
} catch (NullPointerException | ImageProcessingException e1) {
log.debug("Error processing EXIF data." + e1.getMessage());
} catch (IOException e1) {
log.error("Error reading file. " + e1.getMessage());
Expand Down Expand Up @@ -376,35 +396,6 @@ protected static BulkMedia parseOneFileToBulkMedia(String filename) {
}
log.debug(result.toString());
return result;
}

/**
* Constructor
*
* @param aFile the image file that may contain a barcode or text.
* @param aTemplate the PositionTemplate to use to identify where a barcode or OCR text may occur
* in the image provided by aFile.
*
* @throws UnreadableFileException if aFile cannot be read.
* @throws OCRReadException
*/
public CandidateImageFile(File aFile, PositionTemplate aTemplate) throws UnreadableFileException {
setFile(aFile, aTemplate);
if (!aFile.canRead()) {
try {
throw new UnreadableFileException("Can't read file " + aFile.getCanonicalPath());
} catch (IOException e) {
throw new UnreadableFileException("IOException on trying to get filename.");
}
}
}

/**
* Constructor with no parameters to use to access convenience static methods.
* Must follow with setFile() to use for processing images.
* @see this.setFile(...);
*/
public CandidateImageFile() {
}


Expand Down Expand Up @@ -824,9 +815,6 @@ public String getExifUserCommentText() {
} catch (IOException e) {
log.error("Error reading file for exif metadata.");
log.error(e.getMessage());
} catch (ImageProcessingException e) {
log.error("Error processing file for metadata.");
log.error(e.getMessage());
}
if (exifComment==null || exifComment.trim().length()==0) {
// Try to see if there is an xmp dc:description block
Expand Down Expand Up @@ -947,7 +935,8 @@ public static String getBarcodeTextFromImage(BufferedImage image, PositionTempla
}
}
return returnValue;
}
}

/**
* Convenience method to check an image for a barcode. Does not set any instance variables of CandidateImageFile,
* and does not behave precisely as the getBarcodeText() methods. Result state is not available from getBarcodeStatus()
Expand All @@ -970,12 +959,7 @@ public static String getBarcodeUnitTrayTextFromImage(BufferedImage image, Positi
Result result;
BinaryBitmap bitmap = new BinaryBitmap(new HybridBinarizer(source));
try {
QRCodeReader reader = new QRCodeReader();
Hashtable<DecodeHintType, Object> hints = null;
hints = new Hashtable<DecodeHintType, Object>(3);
hints.put(DecodeHintType.TRY_HARDER, Boolean.TRUE);
result = reader.decode(bitmap,hints);
returnValue= result.getText();
returnValue = getQRCodeText(bitmap);
} catch (ReaderException e) {
returnValue = "";
}
Expand All @@ -997,7 +981,19 @@ public static String getBarcodeUnitTrayTextFromImage(BufferedImage image, Positi
}
}
return returnValue;
}
}

private static String getQRCodeText(BinaryBitmap bitmap) throws NotFoundException, ChecksumException, FormatException {
Result result;
String returnValue;
QRCodeReader reader = new QRCodeReader();
Hashtable<DecodeHintType, Object> hints = null;
hints = new Hashtable<DecodeHintType, Object>(3);
hints.put(DecodeHintType.TRY_HARDER, Boolean.TRUE);
result = reader.decode(bitmap,hints);
returnValue= result.getText();
return returnValue;
}

public String getBarcodeTextAtFoundTemplate() {
return getBarcodeText(this.templateUsed);
Expand All @@ -1021,7 +1017,7 @@ public String getBarcodeText(PositionTemplate positionTemplate) {
return catalogNumberBarcodeText;
}

String returnValue = "";
String returnValue = null;
if (positionTemplate.getTemplateId().equals(PositionTemplate.TEMPLATE_NO_COMPONENT_PARTS)) {
// Check the entire image for a barcode and return.
returnValue = getBarcodeText();
Expand All @@ -1033,12 +1029,11 @@ public String getBarcodeText(PositionTemplate positionTemplate) {
try {
image = ImageIO.read(candidateFile);
} catch (IOException e) {
error = e.toString() + " " + e.getMessage();
returnValue = error;
log.error(e);
}
if (image == null) {
returnValue = "Could not decode image. " + error;
barcodeStatus = RESULT_ERROR;
log.error("Image null. Could not decode...");
} else {
if (image.getWidth() > positionTemplate.getBarcodeULPosition().width && image.getWidth() == Math.round(positionTemplate.getImageSize().getWidth())) {
// image might plausibly match template
Expand Down Expand Up @@ -1072,47 +1067,36 @@ public String getBarcodeText(PositionTemplate positionTemplate) {
return returnValue;
}

/** Scan the entire image for any QR Code barcode (could find a taxon barcode or a catalog number barcode).
/**
* Scan the entire image for any QR Code barcode (could find a taxon barcode or a catalog number barcode).
* Check for error states with a call to getBarcodeStatus(). Does not store or set the state with any read
* barcode value.
*
* @return a string representing the text of the barcode, if any.
*/
public String getBarcodeText() {
String returnValue = "";
String returnValue;
BufferedImage image = null;
String error = "";
barcodeStatus = RESULT_ERROR;
try {
image = ImageIO.read(candidateFile);
} catch (IOException e) {
error = e.toString() + " " + e.getMessage();
returnValue = error;
log.error(e);
}
if (image == null) {
returnValue = "Could not decode image. " + error;
returnValue = null;
log.error("Image could not be decoded: is null");
barcodeStatus = RESULT_ERROR;
} else {
LuminanceSource source = new BufferedImageLuminanceSource(image);
Result result;
try {
BinaryBitmap bitmap = new BinaryBitmap(new HybridBinarizer(source));
QRCodeReader reader = new QRCodeReader();
Hashtable<DecodeHintType, Object> hints = null;
hints = new Hashtable<DecodeHintType, Object>(3);
hints.put(DecodeHintType.TRY_HARDER, Boolean.TRUE);
result = reader.decode(bitmap,hints);
returnValue= result.getText();
returnValue = getQRCodeText(bitmap);
barcodeStatus = RESULT_BARCODE_SCANNED;
} catch (ReaderException | IllegalArgumentException e) {
returnValue = e.toString() + " " + e.getMessage();
} catch (Exception e) {
returnValue = null;
log.error(e);
barcodeStatus = RESULT_ERROR;
} // seen in MCZ-ENT00051680
catch (Exception e2) {
// Just in case reader.decode throws some other error,
// we should trap it rather than failing.
returnValue = "Unexpected error from ZXing decoder: " + e2.getMessage();
barcodeStatus = RESULT_ERROR;
}
}
return returnValue;
Expand Down Expand Up @@ -1168,6 +1152,7 @@ public void setTemplateUsed(PositionTemplate templateUsed) {
* @param height in pixels of the area to decode
*
* @return string content of barcode found, or an empty string
* TODO: refactor this abdomen
*/
public static String readBarcodeFromLocation(BufferedImage image, int left, int top, int width, int height, boolean quickCheck) {
String returnValue = "";
Expand All @@ -1191,7 +1176,7 @@ public static String readBarcodeFromLocation(BufferedImage image, int left, int

// First, try the source crop directly.
CandidateImageFile temp = new CandidateImageFile();
TextStatus checkResult = temp.checkSourceForBarcode(source, true);
TextStatus checkResult = temp.checkSourceForBarcode(source, log.isDebugEnabled());
if (checkResult.getStatus()!=CandidateImageFile.RESULT_ERROR) {
returnValue = checkResult.getText();
}
Expand Down Expand Up @@ -1236,22 +1221,22 @@ public static String readBarcodeFromLocation(BufferedImage image, int left, int
boolean sharpen = false;
boolean brighter = false;
boolean dimmer = false;
// assert (!(widthToTry.contains("sharpen") && widthToTry.contains("brighter") && widthToTry.contains("dimmer")));
if (widthToTry.contains("sharpen")) {
sharpen = true;
widthToTry = widthToTry.replace("sharpen", "");
}
if (widthToTry.contains("brighter")) {
} else if (widthToTry.contains("brighter")) {
brighter = true;
dimmer = false;
widthToTry = widthToTry.replace("brighter", "");
}
if (widthToTry.contains("dimmer")) {
} else if (widthToTry.contains("dimmer")) {
brighter = false;
dimmer = true;
widthToTry = widthToTry.replace("dimmer", "");
}
// strip out any remaining non-numeric characters (sharpen'ed')
widthToTry = widthToTry.replaceAll("[^0-9.]", "");
log.debug("WidthToTry: " + widthToTry.toString());
// Try rescaling to a configured scaling width value.
Double scalingWidth = 0d;
try {
Expand Down Expand Up @@ -1351,10 +1336,9 @@ public static String readBarcodeFromLocation(BufferedImage image, int left, int
}
if (returnValue == null) {
// Try again with some small displacements of window
boolean doneLoop = false;
doubleLoop:
for (int shiftLeft=left-3; shiftLeft<=left+3; shiftLeft=shiftLeft+6) {
for (int shiftTop = top - 3; shiftTop <= top + 3; shiftTop = shiftTop + 6) {
if (!doneLoop) {
inBounds = false;
try {
log.debug("Trying displacement of crop: " + shiftLeft + "," + shiftTop);
Expand All @@ -1367,10 +1351,9 @@ public static String readBarcodeFromLocation(BufferedImage image, int left, int
checkResult = temp.checkSourceForBarcode(source, true);
if (checkResult.getStatus() != CandidateImageFile.RESULT_ERROR) {
returnValue = checkResult.getText();
doneLoop = true;
break doubleLoop;
}
}
}
}
}

Expand Down
24 changes: 15 additions & 9 deletions src/main/java/edu/harvard/mcz/imagecapture/data/SpecimenLifeCycle.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -18,8 +18,10 @@
import org.hibernate.criterion.Example;
import org.hibernate.criterion.Projections;
import org.hibernate.criterion.Restrictions;
import org.hibernate.exception.ConstraintViolationException;
import org.hibernate.query.Query;

import javax.persistence.PersistenceException;
import java.math.BigDecimal;
import java.util.ArrayList;
import java.util.Iterator;
Expand Down Expand Up @@ -78,8 +80,12 @@ public void persist(Specimen transientInstance) throws SaveFailedException, Spec
session.getTransaction().commit();
log.debug("persist successful");
track(transientInstance);
} catch (HibernateException e) {
} catch (PersistenceException e) {
session.getTransaction().rollback();
try {
session.close();
} catch (SessionException se) {
}
String message = e.getMessage();
String pmessage = "";
try {
Expand All @@ -89,19 +95,19 @@ public void persist(Specimen transientInstance) throws SaveFailedException, Spec
}
log.error("persist failed", e);
String existsPattern = "^Duplicate entry '.*' for key 'Barcode'$";
if (message.matches(existsPattern) || pmessage.matches(existsPattern) ) {
if (message.matches(existsPattern) || pmessage.matches(existsPattern) || e instanceof ConstraintViolationException) {
log.debug("specimen exists");
throw new SpecimenExistsException("Specimen record exists for " + transientInstance.getBarcode());
} else {
} else {
log.debug("specimen save failed");
throw new SaveFailedException("Unable to save specimen " + transientInstance.getBarcode());
}
}
try { session.close(); } catch (SessionException e) { }
} catch (SpecimenExistsException see) {
} catch (SpecimenExistsException | SaveFailedException see) {
// Pass on upwards unchanged
log.error("persist failed see", see);
throw see;
} catch (SaveFailedException sfe) {
// Pass on upwards unchanged
throw sfe;
} catch (RuntimeException re) {
// Catch, log, and pass on any other exception.
log.error("persist failed", re);
Expand Down Expand Up @@ -294,8 +300,8 @@ public List<Specimen> findByBarcode(String barcode) {
session.beginTransaction();
List<Specimen> results = null;
try {
Query query = session.createQuery("From Specimen as s where s.barcode = ?");
query.setParameter(0, barcode);
Query query = session.createQuery("From Specimen as s where s.barcode = ?1");
query.setParameter(1, barcode);
results = (List<Specimen>) query.list();
log.debug("find query successful, result size: " + results.size());
session.getTransaction().commit();
Expand Down
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