route_login_platform = 'https://<hostname>.emedgene.com/api/auth/v2/api_login/'
payload = {"username": user_name, "password": password}
response = requests.post(route_login_platform, json=payload)
access_token = response.json().get('access_token')
token_type = response.json().get('token_type')
print(f'{token_type.capitalize()} {access_token}')

route_login_platform = 'https://<hostname>.emg.illumina.com/api/auth/v2/api_login/'
payload = {"username": user_name, "password": password}
response = requests.post(route_login_platform, json=payload)
access_token = response.json().get('access_token')
token_type = response.json().get('token_type')
bearer_token = f'{token_type.capitalize()} {access_token}'
print(bearer_token)

import base64

api_key = 'my-api-key'
route_token_platform = 'https://<hostname>.login.illumina.com/platform-services-manager/Token'

# Prepare the API Key
client_id_apikey = f'emedgene:{api_key}'
client_id_apikey_bytes = client_id_apikey.encode("ascii")
client_id_apikey_base64_bytes_encoded = base64.b64encode(client_id_apikey_bytes)
client_id_decoded = client_id_apikey_base64_bytes_encoded.decode("ascii")

# Use the API Key
headers = {
    'Authorization': f'Basic {client_id_decoded}'
}
params = {
    "audience": "emedgene", 
    "grant_type": "api_key"
}
response = requests.post(route_token_platform, params=params, headers=headers)

access_token = response.json().get('access_token')
token_type = response.json().get('token_type')
bearer_token = f'{token_type.capitalize()} {access_token}'
print(bearer_token)

curl -X 'POST' 'https://<hostname>.emg.illumina.com/api/some/command/path/' 
   -H 'Authorization': 'Bearer your-auth-token'  
   -d '{"DataName": "DataValue", ...}' 

import requests
url = 'https://<hostname>.emg.illumina.com/api/some/command/path'
headers = {
    'Authorization': 'Bearer your-auth-token',
}
data = {
    'DataName': 'DataValue',
}
response = requests.post(url=url, headers=headers, json=data)

import requests
url = 'https://<hostname>.emg.illumina.com/api/some/command/path'
headers = {
    'Authorization': 'Bearer your-auth-token',
}
response = requests.get(url=url, headers=headers)

import requests

headers = {
    'Authorization': 'Bearer your-auth-token',
}

# Store the API response in a response variable
response = requests.get('https://<hostname>.emg.illumina.com/api/test', headers=headers)

# Display the response status code
print(f"Response status code: {response.status_code}")

# Display the data from the request
print(response.json().get("hits"))

import json

# Print JSON data in readable format with indentation and sorting.
print(json.dumps(response.json().get("hits"), indent=3, sort_keys=True))

import requests

params = {
    'from': 5,    # get the 6th case
    'size': 10    # get 10 cases
}

headers = {
    'Authorization': 'Bearer your-auth-token',
}

# Store the API response in a response variable
response = requests.get('https://<hostname>.emg.illumina.com/api/test', params=params, headers=headers)

url = 'https://<hostname>.emg.illumina.com/api/storage'
headers = {
    'Authorization': 'Bearer your-auth-token',
}
response = requests.get(url, headers=headers)
print(response.json().get("hits"))

url = 'https://<hostname>.emedgene.com/api/cases/v2/cases'
headers = {
    'Authorization': 'Bearer your-auth-token' 
}
data = {...}
response = requests.post(url, json=data, headers=headers)

case_name = response.json().get("name")

url = f'https://<hostname>.emg.illumina.com/api/test/{case_name}?test_fields=status'
headers = {
    'Authorization': 'Bearer your-auth-token' 
}
response = requests.get(url, headers=headers)
print(response.json())

url = f'https://<hostname>.emg.illumina.com/api/test/{case_name}'
headers = {
    'Authorization': 'Bearer your-auth-token' 
}
response = requests.get(url, headers=headers)
print(response.json())

url = f'https://<hostname>.emg.illumina.com/api/test/{case_name}?test_fields=status&test_fields=participants&test_fields=patients'
headers = {
    'Authorization': 'Bearer your-auth-token' 
}
response = requests.get(url, headers=headers)
print(response.json())

url = f'https://<hostname>.emg.illumina.com/api/candidates/{case_name}'
headers = {
    'Authorization': 'Bearer your-auth-token' 
}
response = requests.get(url, headers=headers)
print(response.json().get("hits"))

url = f'https://<hostname>.emg.illumina.com/api/test/{case_name}/export'
headers = {
    'Authorization': 'Bearer your-auth-token' 
}
response = requests.get(url, headers=headers)
print(response.json().get("hits"))

import requests

route_case_creation_url = 'https://<hostname>.emg.illumina.com/api/cases/v2/cases/'
payload = {
    "sharing_level": 0,
    "should_upload": False,
    "test_data": {
        "analysis_type": None,
        "boostGenes": False,
        "consanguinity": False,
        "disease_penetrance": 100,
        "disease_severity": "",
        "diseases": [],
        "gene_list": {
            "id": 1,
            "type": "all",
            "visible": False
        },
        "incidental_findings": None,
        "inheritance_modes": [],
        "labels": [],
        "notes": "",
        "patients": {
            "other": [],
            "proband": {
                "dead": False,
                "detailed_ethnicity": {
                    "maternal": [],
                    "paternal": []
                },
                "fastq_sample": "<proband sample name>",
                "gender": "<proband gender>",
                "healthy": False,
                "id": "proband",
                "ignore": False,
                "notes": "",
                "phenotypes": [
                    {
                        "id": "phenotypes/<EMG_PHENOTYPE_0011856>",
                        "name": "Pica"
                    },
                    {
                        "id": "phenotypes/<EMG_PHENOTYPE_0000969>",
                        "name": "Edema"
                    }
                ],
                "quality": "",
                "relationship": "Test Subject",
                "zygosity": ""
            }
        },
        "sample_type": "<fastq or vcf>",
        "samples": [
            {
                "directoryPath": "",
                "fastq": "<proband sample name>",
                "sampleFiles": [
                    {
                        "filename": "<proband file 1>.fastq.gz",
                        "path": "<full path/proband file 1>.fastq.gz",
                        "size": <file size>,
                        "status": "uploaded",
                        "storage_id": <storage provider id>
                    },
                    {
                        "filename": "<proband file 2>.fastq.gz",
                        "path": "<full path/proband file 2>.fastq.gz",
                        "size": <file size>,
                        "status": "uploaded",
                        "storage_id": <storage provider id>
                    }
                ],
                "sampleType": "<fastq or vcf>",
                "status": "uploaded",
                "storage_id": <storage provider id>
            }
        ],
        "selected_preset_set": None,
        "sequence_info": {
            "intersect_bed_id": None,
            "kit": "<kit name>",
            "kit_id": <kit id>
        },
        "type": "<case type>"
    }
}

headers = {'Authorization': 'Bearer <your-auth-token>'}
response = requests.post(route_case_creation_url, json=payload, headers=headers)

# Check response status:
status = response.json().get("Status")

# Get the case name:
case_name = response.json().get("name")

import requests

# Define the email addresses you want to search for
emails_to_search = ["[email protected]", "[email protected]"]

participant_ids = []
user_url = 'https://<hostname>.emg.illumina.com/api/user/org_users/'
response = requests.get(user_url, headers=headers)
if response.status_code == 200:
    users = response.json().get("hits", [])
    for user in users:
        if user.get("email") in emails_to_search:
            participant_ids.append(user.get("id"))

assign_url = f'https://<hostname>.emg.illumina.com/api/participant/{case_name}'

payload = {"action": "assign", "ids": participant_ids}

response = requests.post(url=assign_url, json=payload, headers=headers)

if response.status_code == 200:
    print(f"Participants {participant_ids} assigned to case {case_name}.")
else:
    print(f"Failed to assign participants to case {case_name}. Response: {response.json()}")

import requests

url = 'https://<hostname>.emg.illumina.com/api/test/{case_name}/info'
headers = {
    'Authorization': 'Bearer <your-auth-token>'
}

response = requests.get(url=url, headers=headers)

# Output the case information
print(response.json())

import requests

url = 'https://<hostname>.emg.illumina.com/api/candidates/{case_name}'
headers = {
    'Authorization': 'Bearer <your-auth-token>'
}

response = requests.get(url=url, headers=headers)

# Output the variants with tags and their information
print(response.json())

case_name = case.get("name")
update_url = f'https://<hostname>.emg.illumina.com/api/test/{case_name}'

payload = {"status": "custom_status_1"}

response = requests.put(url=update_url, json=payload, headers=headers)

if response.status_code == 200:
    print(f"Case {case_name} updated to 'custom_status_1'.")
else:
    print(f"Failed to update case {case_name}. Response: {response.json()}")

from datetime import datetime, timedelta

# Calculate the date 24 hours ago
from_status_change_date = (datetime.now() - timedelta(days=1)).isoformat()

url = f'https://<hostname>.emg.illumina.com/api/test?from_status_change_date={from_status_change_date}&status=finalized'

response = requests.get(url=url, headers=headers)

finalized_cases = response.json()

url = 'https://<hostname>.emg.illumina.com/api/test/{case_name}/reports/English/null/?candidates=true&full_export=true&incidental=true'
headers = {
    'Authorization': 'Bearer <your-auth-token>'
}
response = requests.get(url=url, headers=headers)
print(response.json())

import requests

case_name = "EMG123456789"
url = f'https://<hostname>.emg.illumina.com/api/test/<case_name>/preset_group'

headers = {'Authorization': 'Bearer <your-api-key>'}

# Define the gene lists to be added on top of the existing preset group
first_gene_list_name = "my gene list"
first_gene_list_id = 1
second_gene_list_name = "my gene list 2"
second_gene_list_id = 2

data = {
    "name": "<name-of-new-custom-preset-group>",
    "filter": {
        "search": [
            {
                "id": first_gene_list_id,
                "name": first_gene_list_name,
                "type": "gene list",
                "value": first_gene_list_name
            },
            {
                "id": second_gene_list_id,
                "name": second_gene_list_name,
                "type": "gene list",
                "value": second_gene_list_name
            }
        ]
    }
}

response = requests.post(url, json=data, headers=headers)

if response.status_code == 201:
    print("Custom preset group created successfully.")
else:
    print(f"Failed to create custom preset group. Status code: {response.status_code}")