Create a simple ISA descriptor¶

# If executing the notebooks on `Google Colab`,uncomment the following command 
# and run it to install the required python libraries. Also, make the test datasets available.

# !pip install -r requirements.txt

from isatools.model import (
    Investigation,
    Study,
    OntologyAnnotation,
    Sample,
    Source,
    Protocol,
    ProtocolParameter,
    Process
)
import datetime

investigation = Investigation()
study = Study(filename="s_study.txt")
study.identifier = "S1"
study.title = "My Simple ISA Study"
study.description = "We could alternatively use the class constructor's parameters to set some default " \
          "values at the time of creation, however we want to demonstrate how to use the " \
          "object's instance variables to set values."
study.submission_date = str(datetime.datetime.today())
study.public_release_date = str(datetime.datetime.today())
study.sources = [Source(name="source1")]
study.samples = [Sample(name="sample1")]
study.protocols = [
    Protocol(name="sample collection"),
    Protocol(
        name="data analysis with Galaxy",
        uri="https://doi.org/10.5464/workflow.cwl",
        protocol_type=OntologyAnnotation(term="data transformation"),
        parameters=[
            ProtocolParameter(parameter_name=OntologyAnnotation(term="genome assembly")),
            ProtocolParameter(parameter_name=OntologyAnnotation(term="cut-off value"))
        ]
    ),
    Protocol(
        name="data visualization with Intermine",
        uri="https://intermine.org/10.5464/network.svg",
        protocol_type=OntologyAnnotation(term="data visualization"),
    )
]
study.process_sequence = [
    Process(
        executes_protocol=study.protocols[-1],
        inputs=[study.sources[-1]],
        outputs=[study.samples[-1]]
    )
]
investigation.studies = [study]

# Let's see the object :
investigation

from isatools.isatab import dumps
print(dumps(investigation))

import json
from isatools.isajson import ISAJSONEncoder
print(json.dumps(investigation, cls=ISAJSONEncoder, sort_keys=True, indent=4, separators=(',', ': ')))