A standardized spreadsheet editor and validator that can be run offline and locally, and which includes templates for SARS-CoV-2 sampling data.

Watch Rhiannon Cameron and Damion Dooley describe this application on YouTube at the Canadian Research Software Conference (CRSC2021).

Download the zipped source code from the latest release at: https://github.com/Public-Health-Bioinformatics/DataHarmonizer/releases

Extract the zipped file.

To run the application, navigate to the extracted folder and open main.html.

The default template loaded is the "CanCOGeN Covid-19" template. To change the spreadsheet template, select the white text box to the right of Template, it always contains the name of template currently active, or navigated to File followed by Change Template. An in-app window will appear that allows you to select from the available templates in the drop-down menu. After selecting the desired template, click Open to activate the template.

A second way to access templates directly, rather than by the hard-coded menu system, is to specify the DataHarmonizer template subfolder via a "template" URL parameter. This enables development and use of customized templates, or new ones, that DH doesn't have programmed in menu.

For example, http://genepio.org/DataHarmonizer/main.html?template=gisaid accesses the /template/gsiaid/ subfolder's template directly.

See more on the Wiki DataHarmonizer templates page.

You can edit the cells manually, or upload xlsx, xls, tsv and csv files via File > Open. You can also save the spreadsheet's contents to your local hard-drive in the aforementioned formats, or File > Export your data as an .xls document formatted for submission a specified portal, database, or repository.

Click the Validate button to validate your spreadsheet's values against a standardized vocabulary. You can then browse through the errors using the Next Error button. Missing value are indicated in dark red, while incorrect values are light red.

Double click any column headers for information on the template's vocabulary.

You can quickly navigate to a column by selecting Settings > Jump to.... An in-app window will appear, select the desired column header from the drop-down list or begin typing it's name to narrow down the list options. Selecting the column header from the drop down list will immediately relocate you to that column on the spreadsheet.

You can also automatically fill a column with a specified value, but only in rows with corresponding values in the first sample ID column. To use this feature select Settings > Fill column.... Select the desired column header from the drop-down list or begin typing it's name to narrow down the list options, then specify the value to fill with and click Ok to apply.

For more information on available application features, select the Help button followed by Getting Started from within the DataHarmonizer application.

Templates with example data testing functionalities can be found within the following folder structure when available:

. TOP LEVEL DIRECTORY
├── images
├── libraries
├── script
└── template
│   ├── templateOfInterest
│   │   └── exampleInput
│   └── ...

Alternatively, you can find links to all available test data below:

• canada_covid19 CanCOGeN Covid-19

For more information about the DataHarmonizer, it's templates, and how to use them, check out the DataHarmonizer Wiki.

If you have any ideas for improving the application, or have encountered any problems running the application, please open an issue for discussion.

This project is currently in the beta phase, with new features being added occasionally.

Versioning of templates, features, and functionality is modeled on semantic versioning (i.e. versions are expressed as “DataHarmonizer X.Y.Z”). Changes to vocabulary in template pick lists are updated by incremental increases to the third position in the version (i.e. “Z” position). Changes to fields and features are updated by incremental increases to the second position in the version (i.e. “Y” position). Changes to basic infrastructure or major changes to functionality are updated by incremental increases to the first position in the version (i.e. “X” position).

Descriptions of updates are provided in release notes for every new version.

Discussions contributing to updates may be tracked on the DataHarmonizer GitHub Issuetracker.

• Handsontable was used to build the grid. DataHarmonizer is configured to reference the "non-commercial-and-evaluation" handsontable license "for purposes not intended toward monetary compensation such as, but not limited to, teaching, academic research, evaluation, testing and experimentation"; if this application is used for commercial purposes, this should be revised as per https://handsontable.com/docs/license-key/
• SheetJS was used to open and save local files. The community edition was used under the Apache 2.0 license.

DataHarmonizer javascript, python and other code not mentioned in the Acknowledgement above is covered by the MIT license.