Opened 4 years ago

Closed 18 months ago

#819 closed defect (fixed)

GlycanArray - cannot read a certain version of a GenePix file

Reported by: sena Owned by: yukie
Priority: high Milestone: Module - Glycan array analysis
Component: Glycan Array management Version: GRITS 1.1.x
Severity: critical Keywords:
Cc:

Description

The current GenePix parser handles three different GenePix file formats based on the version number and type of the file. However, the attached file, although it has the same version number and the type of the handled formats, does not have the same columns as the other files in this version. It causes the GenePix parser to fail since it cannot find the values in the expected columns.

In addition, the error is not reported properly in the dialog (see attached screenshot)

Here is the exception:

[ERROR] 2017-02-01 16:55:48,505 [uk.ac.imperial.glycosciences.glycanarray.parser.GenePixParser parse 188] - Value should have been a number
java.lang.NumberFormatException: For input string: "0.000"

at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
at java.lang.Integer.parseInt(Integer.java:580)
at java.lang.Integer.parseInt(Integer.java:615)
at uk.ac.imperial.glycosciences.glycanarray.parser.GenePixParser.parse(GenePixParser.java:145)
at uk.ac.imperial.glycosciences.glycanarray.util.FileUtils.processGenePixFile(Unknown Source)
at uk.ac.imperial.glycosciences.glycanarray.wizards.WizardPageFour.processFile(WizardPageFour.java:336)
at uk.ac.imperial.glycosciences.glycanarray.wizards.WizardPageFour.doProcessing(WizardPageFour.java:296)
at uk.ac.imperial.glycosciences.glycanarray.wizards.WizardPageFour.access$1(WizardPageFour.java:291)
at uk.ac.imperial.glycosciences.glycanarray.wizards.WizardPageFour$8$1.run(WizardPageFour.java:255)
at org.eclipse.jface.operation.ModalContext$ModalContextThread.run(ModalContext.java:119)

[ERROR] 2017-02-01 16:55:48,510 [uk.ac.imperial.glycosciences.glycanarray.wizards.WizardPageFour$8$1 run 257] - Cannot process the data file
java.io.IOException: Value should have been a number: For input string: "0.000"

at uk.ac.imperial.glycosciences.glycanarray.parser.GenePixParser.parse(GenePixParser.java:190)
at uk.ac.imperial.glycosciences.glycanarray.util.FileUtils.processGenePixFile(Unknown Source)
at uk.ac.imperial.glycosciences.glycanarray.wizards.WizardPageFour.processFile(WizardPageFour.java:336)
at uk.ac.imperial.glycosciences.glycanarray.wizards.WizardPageFour.doProcessing(WizardPageFour.java:296)
at uk.ac.imperial.glycosciences.glycanarray.wizards.WizardPageFour.access$1(WizardPageFour.java:291)
at uk.ac.imperial.glycosciences.glycanarray.wizards.WizardPageFour$8$1.run(WizardPageFour.java:255)
at org.eclipse.jface.operation.ModalContext$ModalContextThread.run(ModalContext.java:119)

[ERROR] 2017-02-01 16:55:48,547 [uk.ac.imperial.glycosciences.glycanarray.wizards.WizardPageFour$8 widgetSelected 273] - Error uploading files:
org.eclipse.swt.SWTException: Invalid thread access

at org.eclipse.swt.SWT.error(SWT.java:4533)
at org.eclipse.swt.SWT.error(SWT.java:4448)
at org.eclipse.swt.SWT.error(SWT.java:4419)
at org.eclipse.swt.widgets.Widget.error(Widget.java:799)
at org.eclipse.swt.widgets.Widget.checkWidget(Widget.java:589)
at org.eclipse.swt.widgets.Text.getText(Text.java:1184)
at org.eclipse.jface.dialogs.TitleAreaDialog.updateMessage(TitleAreaDialog.java:624)
at org.eclipse.jface.dialogs.TitleAreaDialog.showMessage(TitleAreaDialog.java:610)
at org.eclipse.jface.dialogs.TitleAreaDialog.setMessage(TitleAreaDialog.java:584)
at org.eclipse.jface.wizard.WizardDialog.updateMessage(WizardDialog.java:1347)
at org.eclipse.jface.wizard.WizardPage.setMessage(WizardPage.java:275)
at org.eclipse.jface.dialogs.DialogPage.setMessage(DialogPage.java:413)
at uk.ac.imperial.glycosciences.glycanarray.wizards.WizardPageFour$8$1.run(WizardPageFour.java:258)
at org.eclipse.jface.operation.ModalContext$ModalContextThread.run(ModalContext.java:119)

Attachments (2)

Screen Shot 2017-02-01 at 4.56.03 PM.png (54.2 KB) - added by sena 4 years ago.
genepix_trial_cy3_analysis_19_06_13.gpr.zip (206.5 KB) - added by sena 4 years ago.

Download all attachments as: .zip

Change History (6)

Changed 4 years ago by sena

comment:1 Changed 4 years ago by yukie

Priority: highlowest

27/Feb/2017

comment:2 Changed 4 years ago by yukie

Priority: lowesthigh

<Plugin/Package>
uk.ac.imperial.glycosciences.glycanarray.parser.GenePixParser.parse(GenePixParser.java:190)
util.FileUtils

<Comments>
I have to check about the parser / whether I need to create a new parser or modify it ??

  • I have to find the reason for this bug.
  • getConfigFor
  • FileUtils gives/recognizes the "Type" and "version" of the GenePix files. However, for this input data, the File Type and File Version are matched BUT the contents were NOT match.


<Estimate>
3 weeks

comment:3 Changed 2 years ago by yukie

Resolution: fixed
Status: newreview

comment:4 Changed 18 months ago by Rene Ranzinger

Status: reviewclosed
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