GUDMAP1/GUDMAP2/nGUDMAP: Automated checking protocols - Spreadsheet 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 spreadsheet in GUDMAP1, GUDMAP2 and nGUDMAP.

Procedure

Running the Spreadsheet 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”.

1. Open up the ‘input.properties’ files. The parameters in this file must match the type of Excel spreadsheet the submitter is using.

For a high resolution spreadsheet, ensure you have set the following parameters:

• stage=hires
• format=hires

For a TS23 low resolution spreadsheet, ensure you have set the following parameters:

• stage=23
• format=23

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

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

jar -xf submitparser.jar

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

java -cp .:/Users/Chris/Documents/dbData/mysql_3.1.12.jar hgu.submitparser.bin.Submit_Parser -f ./input.properties

1. By pressing Enter, you will run the spreadsheet 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:dbData eo$ 

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

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

Consortium

GenitoUrinary Development Molecular Anatomy Project (GUDMAP) Consortium