isabella232 / ingest-fastq-validator

HCA FASTQ Validation Service

Scripts for metadata validation

CLI application

Validation service

This script listens for messages from ingest API messaging queue and validates each metadata created in the ingest service

python validation-app.py

Metadata JSON documents are validated against specified schemas. A list of the current applicable schemas are located here. Documents must specify the schema against which they are to be validated. The URL of the schema must be located at the JSON path core.schema_url within the JSON document. After validation has completed, a validation report will be attached to the metadata document living in the ingestion-infrastructure database at api.ingest.dev.data.humancellatlas.org

Development Notes

Python's virtualenv

To easily facilitate development, it is recommended to set up a Python virtual environment tool, particularly the virtualenv to manage packages and dependencies necessary to develop, test, and run the code. The documentation for setting up virtualenv can be found on Python 3's official documentation.

virtualenv Best Practices

There are 2 general approaches to managing virtual environments on the local machine. One is to set up a common repository for all virtual environments such as $HOME/.venvs (there's no widely accepted naming convention on this). Another approach is to set up one locally in the specific root directory of the project. Further instructions on how exactly to create and manage virtual environments through virtualenv can be found on the documentation specified above.

In this repository, the venv directory has been set up to be ignored by version control. It can be used to contain virtual environments for the local development machine.

Dependencies

Setting Up Dependencies

To install required modules needed to develop and run this codebase, the following command is used:

pip install -r requirements.txt

Keeping Dependencies Up to Date

The requirements.txt file specifies a list of modules that are needed to be installed to successfully run the code. When new modules are added through pip, it is advised to keep the list up to date by using freeze:

pip freeze > requirements.txt

This command will overwrite the text file with all the modules needed including the last ones installed along with the versions used for the local environment.

Unit Testing

Test driven development is observed for this project and unit tests are required for any fairly complex part of the system. Unit tests are written using Python's unittest module, and can be run using the built-in testing system. However, for finer grain control on testing, nosetests can also be used. For one, nosetests can run a single test from any given test module. For example, to run test_addition test method in test_arithmetic_operations module, the following can be used:

nosetests tests.test_arithmentic_operations:TestArithmeticOperations.test_addtion

In the sample above, TestArithmeticOperations is the name of the test case (i.e. the Python class that extends unittest.TestCase). More options can be found at the official nose test documentation Web site.

Debugging with IDE

Being able to run a single test from any given test case means it's possible to debug a specific block of code using any IDE's debugging tool. JetBrains' PyCharm in particular support single test call through a few selected tools one of which is nosetest. To set nosetest as the default test runner in PyCharm, set the Default test runner option in Tools > Python Integrated Tools pane of the IDE preferences.