Reading in ISA-Tab or ISA JSON

Using the ISA API you can validate ISA-Tab and ISA JSON files.


Reading ISA-Tab from disk

  • To validate ISA-Tab files in a given directory ./tabdir/ against the default reference ISA xml configuration (isaconfig-default_v2015-07-02), do something like the following, with for instance a folder called BII-S-3:

from isatools import isatab
my_json_report = isatab.validate(open(os.path.join('./BII-S-3/', 'i_investigation.txt'))

Tip

The validator will then read the location of your study and assay table files from the investigation file in order to validate those.

Tip

If no path to XML configurations is provided, the ISA API will automatically select and use the isaconfig-default_v2015-07-02 configurations.

  • To validate ISA-Tab files in a given directory ./tabdir/ against a different, custoom made ISA xml configuration found in a directory ./my_custom_covid_study_isaconfig_v2021/, do something like the following, making sure to point to the investigation file of your ISA-Tab, and providing the XML configurations. :

from isatools import isatab
my_json_report = isatab.validate(open(os.path.join('./tabdir/', 'i_investigation.txt')),
								 './my_custom_covid_study_isaconfig_v2021/')

This ISA-Tab validator has been tested against the sample data sets:

All of which that are found in the isatools package.

Warning

the ISA sample datasets used to test the ISA tools also contains studies which harbour errors. BII-S-4 and BII-S-5 will fail validation owing to an error in the investigation file (Publication list instead of Publication List)


Reading ISA JSON from disk

To read an ISA JSON file against the ISA JSON version 1.0 specification you can use do so by doing this by doing something like:

from isatools import isajson
my_json_report = isajson.validate(open('isa.json'))

The rules we check for in the new validators are documented in this working document in Google spreadsheets. Please be aware as this is a working document, some of these rules may be amended as we get more feedback and evolve the ISA API code.

This ISA JSON validator has been tested against a range of dummy test data found in ISAdatasets GitHub repository.

The validator will return a JSON-formatted report of warnings and errors.