GUDMAP1/GUDMAP2/nGUDMAP: Automated checking protocols - Image Checker (Version 1.0)

Version

1.0

Notice

This page is the corresponding protocol tomestone page generated as part of the ATLAS-D2K shutdown in July 2025. Many links on this page may be broken.

Authors

Richard Baldock

Release Date

2017-09-19

Abstract

This protocol describes methods used by the Editorial Office in the University of Edinburgh for checking data entries for images in GUDMAP1, GUDMAP2 and nGUDMAP.

Procedure

Running the Image Checker

1. Copy a tab-delimited text version of the excel spreadsheet to be checked into the “parser_input” folder.

Rename this file “input.txt”.

Also, copy the “listings.txt” file into this folder.

1. Open up a terminal shell (on toolbar). Navigate to the folder “Documents/parser_image_check/” and press Enter.

1. Type the following on the command line and press Enter.

java -jar checkimages.jar -f /Users/eo/Documents/parser_image_check/input.properties

1. By pressing Enter, you will run the image checker program.

You will see something like the following:

DO YOU WISH TO PROCEED? Y/N

1. Press ‘y’.

You will see a list of filenames, which will end with something like this.

********* FINISHED ********** 
Number of Rows transformed: 8 
sbms07689:parser_image_check eo$

Ensure that the number of rows transformed is equivalent to the number of submissions in the spreadsheet.

An error report entitled “image_error_report.txt” will have been generated in the “parser_error_report” folder.

Consortium

GenitoUrinary Development Molecular Anatomy Project (GUDMAP) Consortium