GET experiment
==============

get an experiment from MaveDB via the API
-----------------------------------------

To begin, import the modeules below.

.. code:: ipython3

    import attr, os
    from pprint import PrettyPrinter
    from mavetools.client.client import Client
    from mavetools.models.experiment import Experiment

Pretty printer is used to format the output nicely.

.. code:: ipython3

    pp = PrettyPrinter(indent=2)  # displayes results in readable format

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.

.. code:: ipython3

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

Set experiment_urn to match the experiment you want to get.

.. code:: ipython3

    experiment_urn = 'urn:mavedb:00000001-a'

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

.. code:: ipython3

    # 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/.

.. code:: ipython3

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

GET the model instance by passing the model type (Experiment, in this
instance) and the experiment_urn as arguments to the get_model_istance
funtion that operates on the Client object. This will GET the model
instance (resource) from the server via the approprate API endpoint.

.. code:: ipython3

    experiment = client.get_model_instance(Experiment, experiment_urn)

Now, display the results!

.. code:: ipython3

    pp.pprint(attr.asdict(experiment))


.. parsed-literal::

    { 'abstract_text': 'Although we now routinely sequence human genomes, we can '
                       'confidently identify only a fraction of the sequence '
                       'variants that have a functional impact. Here, we developed '
                       'a deep mutational scanning framework that produces '
                       'exhaustive maps for human missense variants by combining '
                       'random codon mutagenesis and multiplexed functional '
                       'variation assays with computational imputation and '
                       'refinement. We applied this framework to four proteins '
                       'corresponding to six human genes: UBE2I (encoding SUMO E2 '
                       'conjugase), SUMO1 (small ubiquitin-like modifier), TPK1 '
                       '(thiamin pyrophosphokinase), and CALM1/2/3 (three genes '
                       'encoding the protein calmodulin). The resulting maps '
                       'recapitulate known protein features and confidently '
                       'identify pathogenic variation. Assays potentially amenable '
                       'to deep mutational scanning are already available for 57% '
                       'of human disease genes, suggesting that DMS could '
                       'ultimately map functional variation for all human disease '
                       'genes.',
      'approved': None,
      'contributors': ['0000-0003-1628-9390'],
      'created_by': '0000-0003-1628-9390',
      'creation_date': '2018-06-26',
      'doi_ids': [],
      'experimentset': 'urn:mavedb:00000001',
      'extra_metadata': {},
      'keywords': [ {'text': 'E2'},
                    {'text': 'sumoylation'},
                    {'text': 'imputation'},
                    {'text': 'complementation'}],
      'last_child_value': None,
      'method_text': 'A Deep Mutational Scan of UBE2I using functional '
                     'complementation in yeast was performed using two different '
                     'methods: DMS-BarSeq and DMS-TileSeq, both datasets were '
                     'combined and a machine-learning method was used to impute '
                     'the effects of missing variants and refine measurements of '
                     'lower confidence. See [**Weile *et al.* '
                     '2017**](http://msb.embopress.org/content/13/12/957) for '
                     'details.',
      'modification_date': '2019-08-08',
      'modified_by': '0000-0003-1628-9390',
      'private': None,
      'publish_date': '2018-06-26',
      'pubmed_ids': [ { 'dbname': 'PubMed',
                        'dbversion': None,
                        'identifier': '29269382',
                        'url': 'http://www.ncbi.nlm.nih.gov/pubmed/29269382'}],
      'scoresets': [ 'urn:mavedb:00000001-a-2',
                     'urn:mavedb:00000001-a-3',
                     'urn:mavedb:00000001-a-4',
                     'urn:mavedb:00000001-a-1'],
      'short_description': 'A Deep Mutational Scan of the human SUMO E2 conjugase '
                           'UBE2I using functional complementation in yeast.',
      'sra_ids': [ { 'dbname': 'SRA',
                     'dbversion': None,
                     'identifier': 'SRP109101',
                     'url': 'http://www.ebi.ac.uk/ena/data/view/SRP109101'},
                   { 'dbname': 'SRA',
                     'dbversion': None,
                     'identifier': 'SRP109119',
                     'url': 'http://www.ebi.ac.uk/ena/data/view/SRP109119'}],
      'title': 'UBE2I yeast complementation',
      'urn': 'urn:mavedb:00000001-a'}