Validation and Conversion
The filled out template can be validated against the FAANG rules, using the on-line tool. It will provide a report highlighting problems for review. This is under development, so please query FAANG DCC if you have any concerns about the validation result.
To start validation please follow these steps:
- Click on 'Choose file'' button to choose filled out template file
- Click on 'Upload a File' button to upload template to validation service
- Check 'Status' badge for updates. It might have three different values:
- If status has 'Success' value you can start validation. For this click on 'Start validation' button
- Check 'Status' badge in '3. Validation results:' section for updates.
It might have three different values:
- Review all 'Errors' and 'Warnings'. For this click on the cell that contains any issues, pop-up window will have detailed information about 'Errors' and 'Warnings'
'Errors' are problems that have to be dealt with. You will not be able to convert the FAANG sample spreadsheet to the BioSamples JSON format if the spreadsheet contains errors. 'Warnings' are items for you to review. They might be fine, but you need to decide. Any warnings left in a submission are likely to be reviewed by the FAANG DCC. You may be asked to update the sample record later if the metadata group agrees a certain value should be improved.
For descriptions and explanations of the different error messages that the validation tool can provide please see FAANG validation error message explanations.
Metadata fields are organized into biologically-meaningful type schemas, for example a 'specimen from organism' or 'cell specimen'. Each type schema inherits a core schema, containing the minimal fields necessary for that type (standard rule group in samples ruleset). Also template could have custom fields (defined by user).
For each of these types of schemas 'Errors' and 'Warnings' information will be provided in '3. Validation results' section, for example 'Core errors' or 'Type warnings'.
Having run the validation tool on your spreadsheet, you will need to update it to deal with the errors shown. Review the warnings and consider making changes to deal with these. Re-validate your spreadsheet, and repeat the process until there are no errors left and you are comfortable with everything that has triggered a warning. If there are some things that you cannot resolve, contact FAANG DCC for help. Eventually, you will have a set of metadata that passes the validation checks and is ready for conversion.
To start conversion you need to fix all 'Errors' in template. When data is ready follow these steps to get converted data in JSON format:
- Click on 'Get submission data' button (it will start conversion process)
- Check 'Status' badge in '4. Get data for submission:' section for updates.
- Click on 'Dowload data' button to get JSON file that is suitable for BioSamples submission.