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https://github.com/bluebrain/data-validation-framework
Simple framework to create data validation workflows.
https://github.com/bluebrain/data-validation-framework
data data-analysis python validation validation-tool
Last synced: about 4 hours ago
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Simple framework to create data validation workflows.
- Host: GitHub
- URL: https://github.com/bluebrain/data-validation-framework
- Owner: BlueBrain
- License: apache-2.0
- Created: 2021-12-10T13:52:43.000Z (almost 3 years ago)
- Default Branch: main
- Last Pushed: 2024-11-18T11:41:48.000Z (about 18 hours ago)
- Last Synced: 2024-11-18T12:52:31.768Z (about 17 hours ago)
- Topics: data, data-analysis, python, validation, validation-tool
- Language: Python
- Homepage: https://data-validation-framework.readthedocs.io
- Size: 501 KB
- Stars: 7
- Watchers: 5
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: CONTRIBUTING.md
- License: LICENSE.txt
- Authors: AUTHORS.md
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# Data Validation Framework
This project provides simple tools to create data validation workflows.
The workflows are based on the [luigi](https://luigi.readthedocs.io/en/stable) library.
The main objective of this framework is to gather in a same place both the specifications that the
data must follow and the code that actually tests the data. This avoids having multiple documents
to store the specifications and a repository to store the code.
## Installation
This package should be installed using pip:
```bash
pip install data-validation-framework
```
## Usage
### Building a workflow
Building a new workflow is simple, as you can see in the following example:
```python
import luigi
import data_validation_framework as dvf
class ValidationTask1(dvf.task.ElementValidationTask):
"""Use the class docstring to describe the specifications of the ValidationTask1."""
output_columns = {"col_name": None}
@staticmethod
def validation_function(row, output_path, *args, **kwargs):
# Return the validation result for one row of the dataset
if row["col_name"] <= 10:
return dvf.result.ValidationResult(is_valid=True)
else:
return dvf.result.ValidationResult(
is_valid=False,
ret_code=1,
comment="The value should always be <= 10"
)
def external_validation_function(df, output_path, *args, **kwargs):
# Update the dataset inplace here by setting values to the 'is_valid' column.
# The 'ret_code' and 'comment' values are optional, they will be added to the report
# in order to help the user to understand why the dataset did not pass the validation.
# We can use the value from kwargs["param_value"] here.
if int(kwargs["param_value"]) <= 10:
df["is_valid"] = True
else:
df["is_valid"] = False
df["ret_code"] = 1
df["comment"] = "The value should always be <= 10"
class ValidationTask2(dvf.task.SetValidationTask):
"""In some cases you might want to keep the docstring to describe what a developer
needs to know, not the end-user. In this case, you can use the ``__specifications__``
attribute to store the specifications."""
a_parameter = luigi.Parameter()
__specifications__ = """Use the __specifications__ to describe the specifications of the
ValidationTask2."""
def inputs(self):
return {ValidationTask1: {"col_name": "new_col_name_in_current_task"}}
def kwargs(self):
return {"param_value": self.a_parameter}
validation_function = staticmethod(external_validation_function)
class ValidationWorkflow(dvf.task.ValidationWorkflow):
"""Use the global workflow specifications to give general context to the end-user."""
def inputs(self):
return {
ValidationTask1: {},
ValidationTask2: {},
}
```
Where the `ValidationWorkflow` class only defines the sub-tasks that should be called for the
validation. The sub-tasks can be either a `dvf.task.ElementValidationTask` or a
`dvf.task.SetValidationTask`. In both cases, you can define relations between these sub-tasks
since one could need the result of another one to run properly. This is defined in two steps:
1. in the required task, a `output_columns` attribute should be defined so that the next tasks
can know what data is available, as shown in the previous example for the `ValidationTask1`.
2. in the task that requires another task, a `inputs` method should be defined, as shown in the
previous example for the `ValidationTask2`.
The sub-classes of `dvf.task.ElementValidationTask` should return a
`dvf.result.ValidationResult` object. The sub-classes of `dvf.task.SetValidationTask` should
return a `Pandas.DataFrame` object with at least the following columns
`["is_valid", "ret_code", "comment", "exception"]` and with the same index as the input dataset.
## Generate the specifications of a workflow
The specifications that the data should follow can be generated with the following luigi command:
```bash
luigi --module test_validation ValidationWorkflow --log-level INFO --local-scheduler --result-path out --ValidationTask2-a-parameter 15 --specifications-only
```
## Running a workflow
The workflow can be run with the following luigi command (note that the module `test_validation`
must be available in your `sys.path`):
```bash
luigi --module test_validation ValidationWorkflow --log-level INFO --local-scheduler --dataset-df dataset.csv --result-path out --ValidationTask2-a-parameter 15
```
This workflow will generate the following files:
* `out/report_ValidationWorkflow.pdf`: the PDF validation report.
* `out/ValidationTask1/report.csv`: The CSV containing the validity values of the task
`ValidationTask1`.
* `out/ValidationTask2/report.csv`: The CSV containing the validity values of the task
`ValidationTask2`.
* `out/ValidationWorkflow/report.csv`: The CSV containing the validity values of the complete
workflow.
.. note::
As any `luigi `_ workflow, the values can be stored
into a `luigi.cfg` file instead of being passed to the CLI.
## Advanced features
### Require a regular Luigi task
In some cases, one want to execute a regular Luigi task in a validation workflow. In this case, it
is possible to use the `extra_requires()` method to pass these extra requirements. In the
validation task it is then possible to get the targets of these extra requirements using the
`extra_input()` method.
```python
class TestTaskA(luigi.Task):
def run(self):
# Do something and write the 'target.file'
def output(self):
return target.OutputLocalTarget("target.file")
class TestTaskB(task.SetValidationTask):
output_columns = {"extra_target_path": None}
def kwargs(self):
return {"extra_task_target_path": self.extra_input().path}
def extra_requires(self):
return TestTaskA()
@staticmethod
def validation_function(df, output_path, *args, **kwargs):
df["is_valid"] = True
df["extra_target_path"] = kwargs["extra_task_target_path"]
```
## Funding & Acknowledgment
The development of this software was supported by funding to the Blue Brain Project, a research
center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government’s ETH
Board of the Swiss Federal Institutes of Technology.
For license and authors, see `LICENSE.txt` and `AUTHORS.md` respectively.
Copyright © 2022-2023 Blue Brain Project/EPFL