search_type.py

# -*- coding: utf-8 -*-
"""search_type.ipynb

Automatically generated by Colaboratory.

Original file is located at
    https://colab.research.google.com/drive/1GjBNkarjfwIzmCChUyTEUAX498pnzri9

Import the libraries so that they can be used within the notebook

* **requests** is used to make HTTP calls
* **json** is used to encode and decode strings into JSON
* **string** is used to perform text manipulation and checking
"""

import requests
import json
import string

"""The **remove_non_printable** function ensures that the returned text does not contain any unprintable characters"""

def remove_non_printable(text):
    return ''.join(i for i in text if i in string.printable)

"""The **base_url** holds the URL to the SEEK instance that will be used in the notebook

**headers** holds the HTTP headers that will be sent with every HTTP call

* **Content-type: application/vnd.api+json** - indicates that any data sent will be in JSON API format
* **Accept: application/vnd.api+json** - indicates that the notebook expects any data returned to be in JSON API format
* **Accept-Charset: ISO-8859-1** - indicates that the notebook expects any text returned to be in ISO-8859-1 character set
"""

base_url = 'http://www.fairdomhub.org/'

headers = {"Content-type": "application/vnd.api+json",
           "Accept": "application/vnd.api+json",
           "Accept-Charset": "ISO-8859-1"}

"""**term** holds the search term entered by the user"""

term = input("Enter the search term: ")

"""**type_choices** lists the types of SEEK resources that can be searched for.

**response** holds the user's choice of type
"""

type_choices = ["assays",
        "content_blobs",
        "data_files",
        "documents",
        "events",
        "models",
        "organisms",
        "people",
        "presentations",
        "programmes",
        "projects",
        "publications",
        "sample_types",
        "sops",
        "studies"]

print ("Enter the type of object:")
response = None
while response not in type_choices:
    response = input("Please enter one of: " + ', '.join(type_choices))

print (response)

"""The **payload** indicates that the parameters to the HTTP call will be **q=** *term* and **search_type=** *response*

The notebook then makes a HTTP GET using the search using the **headers** and the **payload** parameters

The result of the **GET** is within **r**.

If the request failed then raise an error
"""

payload = {'q' : term, 'search_type' : response}

r = requests.get(base_url + 'search', headers=headers, params=payload)

r.raise_for_status()

"""For every entry in the returned JSON, print its **type** and **title**."""

for entry in r.json()['data'] :
    title = entry['attributes']['title']
    entry_type = entry['type']
    print ("Type: {0}   Title: {1}".format(remove_non_printable(entry_type),
                                            remove_non_printable(title)))