POST experiment

create an experiment in MaveDB via the API

To begin, import the modeules below.

import os
from mavetools.client.client import Client
from mavetools.models.experiment import NewExperiment

Here your base_url is set to localhost, http://127.0.0.1:8000/api/. This default funcionality is what you would want to use when working with a local instance of MaveDB (e.g., a development branch). If working with production mavedb you would set base url to https://www.mavedb.org/api/.

In the cell below, comment out the base_url you will not be using.

base_url = 'http://127.0.0.1:8000/api/'
#base_url = 'https://www.mavedb.org/api/'

Next, you will need an auth_token to make POST requests to MaveDB. If you have one, substitute it in the example provided below. If you need one, please follow these instructions:

1. go to https://www.mavedb.org
2. login using your ORCID ID
3. go to settings
4. generate new auth token
5. copy auth token and pase it in the auth_token field below

# Generate a new auth_token in your profile and post it here
auth_token = 'R2skRbpBD3Rsf5dNHoQxDZevdEE74T5lCKMFyBhBwwPFH4ZfTrxDz7TZ0kbFLtEZ'

Here you instantiate the Client object. The Client object is the object by which the POST request is performed. The client object is instantiated with the value of base_url provided earlier, so make sure that is up-to-date. If base_url does not exist, base_url is defaulted to localhost, http://127.0.0.1:8000/api/.

client = Client(base_url, auth_token=auth_token) if base_url else Client(auth_token=auth_token)

test_file_dir is the path to the directory in which the files needed for making a scoreset POST resquest exist. The required files are as follows:

  1. abstract.md

  2. method.md

For the abstrct.md and method.md files, simply paste your content into these files.

We have an example directory in mavetools that holds the files of interest. Though this directory can exist anywhere on your computer, you must put the correct path to that directory as the value to test_file_dir.

# here is an example if your copy of mavetools exists within Pycharm
test_file_dir = '~/PycharmProjects/mavetools/tests/test_upload_scoreset/test_files'

Here, we will want to validate the data that will be POSTed. Run the validation code.

#validate

Create a NewExperiment object and populate the required attributes. You will need to substitute the values of the attributes for your own.

#with open(f"{test_file_dir}/abstract.md") as handle:
#    test_abstract_text = handle.read()
#with open(f"{test_file_dir}/method.md") as handle:
#    test_method_text = handle.read()

# substitute the each attribute for your experiment attributes
new_experiment = NewExperiment(
    # experimentset=experimentset_urn,
    title='exp_test_title',
    short_description='exp_test_short_description',
    #abstract_text=test_abstract_text,
    #method_text=test_method_text,
    abstract_text="abstract",
    method_text="method",

    sra_ids=['SRP109119'],
    pubmed_ids=['23035249'],
    doi_ids=['10.1038/s41467-019-11526-w'],
)

POST the model instance by passing the NewExperiment object as an argument to the post_model_istance funtion that operates on the Client object. This will POST the model instance to the approprate API endpoint.

client.post_model_instance(new_experiment)