Plugin examples#
OpenVariant offers a plugin system, where the user will be able to build their own plugins and make a customized data transformation. First of all, you will need to create a plugin; hence, check Command-line interface (CLI) section and Command-line interface (CLI) examples to understand how a plugin template can be generated. Also, it is important to know how plugins works and how they are composed in order to understand the following examples that we introduce.
We are going to introduce you two little plugins that we will use them in the example. The two plugins are described and built as:
Add date plugin#
It will generate a new field and it will add the today’s date. run function will be executed for each line of the input file, adding this new field. We can see on the following block the different codes that we add to obtain this.
On the annotation file we described the field that we want to add on the output file.
- type: plugin
plugin: add_date
field: DATE
In addition, after generating the plugin template with the command-line, we overwrite the Add_dateContext class and Add_datePlugin class, in order to add the today’s date on one field of the output.
from datetime import date
from openvariant.plugins.context import Context
from openvariant.plugins.plugin import Plugin
# Context subclass
class Add_dateContext(Context):
def __init__(self, row: dict, field_name: str, file_path: str) -> None:
super().__init__(row, field_name, file_path)
# Plugin subclass
class Add_datePlugin(Plugin):
def run(self, context: Add_dateContext) -> dict:
context.row[context.field_name] = str(date.today())
return context.row[context.field_name]
Get length plugin#
On this second plugin, we will get the length between two different numbers that are annotated as fields. For each row of the input file, run function will be executed. It will get on the START field and END field and then it will get the length between these two values (the difference).
In the annotation file we find the following fields described as:
- type: plugin
plugin: get_length
field: LENGTH
- type: internal
field: START
fieldSource:
- 'loc.start'
- type: internal
field: END
fieldSource:
- 'loc.end'
Also, like in the previous plugin, we generated the plugin templated with command-line and then we overwrite them to extract the length between the two fields.
from openvariant.plugins.context import Context
from openvariant.plugins.plugin import Plugin
# Context subclass
class Get_lengthContext(Context):
def __init__(self, row: dict, field_name: str, file_path: str) -> None:
super().__init__(row, field_name, file_path)
# Plugin subclass
class Get_lengthPlugin(Plugin):
def run(self, context: Get_lengthContext) -> dict:
context.row[context.field_name] = str(int(context.row['END']) - int(context.row['START']))
return context.row[context.field_name]
These two plugins are used in the following example:
We can find all the examples on the repository: OpenVariant examples.