#!/usr/bin/env python
# coding: utf-8

# # Using POST
# 
# POST allows you to run a query with multiple inputs at once. The output will be a dictionary of dictionaries.

# In[ ]:


import requests, sys
from pprint import pprint

server = "http://rest.ensembl.org"
ext = "/lookup/id"
headers={ "Content-Type" : "application/json", "Accept" : "application/json"}
r = requests.post(server+ext, headers=headers, data='{ "ids" : ["ENSG00000157764", "ENSG00000248378" ] }')

# error checking removed for space
 
decoded = r.json()
pprint (decoded)


# There is a helper function in POST. You can specify both helper functions in your script and use whichever one you need.

# In[ ]:


def fetch_endpoint_POST(server, request, data, content_type='application/json'):

    r = requests.post(server+request,
                      headers={ "Accept" : content_type},
                      data=data )

    if not r.ok:
        r.raise_for_status()
        sys.exit()

    if content_type == 'application/json':
        return r.json()
    else:
        return r.text


# ### Optional parameters
# 
# In order to add optional parameters to your POST query, you can just add them onto the extention with a slash. For example if you wanted to mask UTRs when running the [sequence_id_post](http://rest.ensembl.org/documentation/info/sequence_id_post) endpoint, you could specify your extension as:
# 
#         `ext = "sequence/id/mask_feature=1"`
# 
# 
# ### Input
# 
# Your input list for POST queries need to be a JSON list. You can create this from a list in Python using the [JSON module](https://docs.python.org/3/library/json.html):
# 
#         `data = json.dumps({ "ids" : my_list })`
# 
# ### Output
# 
# The Output from POST queries will be a dictionary of dictionaries. To access items, you could use your input list as your keys, or you could move through the dictionary with:
# 
# 		`for key, value in post_query.items():`
# 
# ## Example
# 
# The following scripts inputs a list of variants in HGVS format into the VEP and gets out the IDs of known colocated variants, including failed variants (an optional parameter):

# In[ ]:


import requests, sys, json
from pprint import pprint

def fetch_endpoint(server, request, content_type):

    r = requests.get(server+request, headers={ "Accept" : content_type})

    if not r.ok:
        r.raise_for_status()
        sys.exit()

    if content_type == 'application/json':
        return r.json()
    else:
        return r.text

def fetch_endpoint_POST(server, request, data, content_type):

    r = requests.post(server+request,
                      headers={ "Accept" : content_type},
                      data=data )

    if not r.ok:
        r.raise_for_status()
        sys.exit()

    if content_type == 'application/json':
        return r.json()
    else:
        return r.text

# define the server, extension and content type
server = "http://rest.ensembl.org/"
con = "application/json"
vep_ext = "vep/homo_sapiens/hgvs/failed=1"

# create the list of HGVS annotations
hgvs = ["ENST00000366667.4:c.803T>C", "ENST00000335295.4:c.20A>T", "ENST00000415952.1:c.-149-34206G>T"]

# convert the list into json format
hgvs_json = json.dumps({ "hgvs_notations" : hgvs })

# run the query
post_vep = fetch_endpoint_POST(server, vep_ext, hgvs_json, con)

# move through the results
for variant in post_vep:
    
    # get the data
    input = variant['input']
    colocated_list = []
    for colocated in variant['colocated_variants']:
        colocated_list.append(colocated['id'])  
    print (input + ": " + (', '.join(colocated_list)))


# # Exercises 6
# 
# 1\. Fetch the all the transcripts of *ESPN* using the lookup endpoint. Fetch the cDNA sequences of all transcripts using a single POST request, and print in FASTA format.

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# Exercise 6.1


# 2\. You have the following list of variants:
# ```rs1415919662, rs957333053, rs762944488, rs1372123943, rs553810871, rs1451237599, rs751376931```
# Get the variant class, evidence attributes, source and the most_severe_consequence for all variants using the variation POST endpoint.

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# Exercise 6.2


# [Next page: Exercises 6 – answers](6_Using_POST_answers.ipynb)