def send_heart_beat(automat_host):
"""Send heartbeat."""
heart_rate = config.get('heart_rate', 30)
logger.debug(f'contacting {automat_host}')
automat_heart_beat_url = f'{automat_host}/heartbeat'
plater_address = config.get('PLATER_SERVICE_ADDRESS')
if not plater_address:
logger.error(
'PLATER_SERVICE_ADDRESS environment variable not set. Please set '
'this variable to the address of the host PLATER is running on.'
)
raise ValueError(
'PLATER_SERVICE_ADDRESS cannot be None when joining automat '
'cluster.'
)
payload = {
'host': plater_address,
'tag': PLATER_TITLE,
'port': config.get('WEB_PORT', 8080)
}
while True:
try:
resp = httpx.post(
automat_heart_beat_url,
json=payload,
timeout=0.5,
)
logger.debug(
'heartbeat to %s returned %d',
automat_host,
resp.status_code,
)
except Exception as err:
logger.error(f'[X] Error contacting automat server {err}')
time.sleep(heart_rate)
def construct_open_api_schema(app, trapi_version, prefix=""):
plater_title = config.get('PLATER_TITLE', 'Plater API')
plater_version = os.environ.get('PLATER_VERSION', '1.0.0')
if app.openapi_schema:
return app.openapi_schema
open_api_schema = get_openapi(
title=plater_title,
version=plater_version,
description='',
routes=app.routes,
)
open_api_extended_file_path = config.get_resource_path(
f'../openapi-config.yaml')
with open(open_api_extended_file_path) as open_api_file:
open_api_extended_spec = yaml.load(open_api_file,
Loader=yaml.SafeLoader)
x_translator_extension = open_api_extended_spec.get("x-translator")
contact_config = open_api_extended_spec.get("contact")
terms_of_service = open_api_extended_spec.get("termsOfService")
servers_conf = open_api_extended_spec.get("servers")
tags = open_api_extended_spec.get("tags")
title_override = (open_api_extended_spec.get("title")
or plater_title) + f' (trapi v-{trapi_version})'
description = open_api_extended_spec.get("description")
if tags:
open_api_schema['tags'] = tags
if x_translator_extension:
# if x_translator_team is defined amends schema with x_translator extension
open_api_schema["info"]["x-translator"] = x_translator_extension
open_api_schema["info"]["x-translator"][
"biolink-version"] = config.get("BL_VERSION", "1.5.0")
if contact_config:
open_api_schema["info"]["contact"] = contact_config
if terms_of_service:
open_api_schema["info"]["termsOfService"] = terms_of_service
if description:
open_api_schema["info"]["description"] = description
if title_override:
open_api_schema["info"]["title"] = title_override
if servers_conf:
for cnf in servers_conf:
if prefix and 'url' in cnf:
cnf['url'] = cnf['url'] + prefix
open_api_schema["servers"] = servers_conf
open_api_schema["info"]["x-trapi"] = {"version": trapi_version}
return open_api_schema
def __init__(self, host, port, auth):
self.driver = Neo4jHTTPDriver(host=host, port=port, auth=auth)
self.schema = None
self.summary = None
self.meta_kg = None
self.bl_version = config.get('BL_VERSION', '1.5.0')
self.bl_url = f'https://raw.githubusercontent.com/biolink/biolink-model/{self.bl_version}/biolink-model.yaml'
self.toolkit = Toolkit(self.bl_url)
def __init__(self, bl_url=config.get('bl_url')):
self.bl_url = bl_url
def get_bl_helper():
"""Get Biolink helper."""
return BLHelper(config.get('BL_HOST', 'https://bl-lookup-sri.renci.org'))
def get_graph_interface():
"""Get graph interface."""
return GraphInterface(
config.get('NEO4J_HOST'), config.get('NEO4J_HTTP_PORT'),
(config.get('NEO4J_USERNAME'), config.get('NEO4J_PASSWORD')))
"""Plater heartbeat."""
import argparse
import time
import httpx
from PLATER.services.config import config
from PLATER.services.util.logutil import LoggingUtil
logger = LoggingUtil.init_logging(
__name__,
config.get('logging_level'),
config.get('logging_format'),
)
PLATER_TITLE = config.get("PLATER_TITLE", "Plater API")
def send_heart_beat(automat_host):
"""Send heartbeat."""
heart_rate = config.get('heart_rate', 30)
logger.debug(f'contacting {automat_host}')
automat_heart_beat_url = f'{automat_host}/heartbeat'
plater_address = config.get('PLATER_SERVICE_ADDRESS')
if not plater_address:
logger.error(
'PLATER_SERVICE_ADDRESS environment variable not set. Please set '
'this variable to the address of the host PLATER is running on.'
)
raise ValueError(
'PLATER_SERVICE_ADDRESS cannot be None when joining automat '
import base64
import traceback
import httpx
from PLATER.services.config import config
from PLATER.services.util.logutil import LoggingUtil
from bmt import Toolkit
logger = LoggingUtil.init_logging(__name__, config.get('logging_level'),
config.get('logging_format'))
class Neo4jHTTPDriver:
def __init__(self,
host: str,
port: int,
auth: tuple,
scheme: str = 'http'):
self._host = host
self._neo4j_transaction_endpoint = "/db/data/transaction/commit"
self._scheme = scheme
self._full_transaction_path = f"{self._scheme}://{self._host}:{port}{self._neo4j_transaction_endpoint}"
self._port = port
self._supports_apoc = None
self._header = {
'Accept':
'application/json; charset=UTF-8',
'Content-Type':
'application/json',
'Authorization':
"""FastAPI app."""
import os
from fastapi import FastAPI
from fastapi.openapi.utils import get_openapi
from starlette.middleware.cors import CORSMiddleware
from PLATER.services.config import config
from PLATER.services.util.logutil import LoggingUtil
from PLATER.services.app_trapi_1_0 import APP_TRAPI_1_0
from PLATER.services.app_trapi_1_1 import APP_TRAPI_1_1
from PLATER.services.util.api_utils import construct_open_api_schema
TITLE = config.get('PLATER_TITLE', 'Plater API')
VERSION = os.environ.get('PLATER_VERSION', '1.0.1')
logger = LoggingUtil.init_logging(
__name__,
config.get('logging_level'),
config.get('logging_format'),
)
APP = FastAPI()
# Mount 1.1 app at /1.1
APP.mount('/1.1', APP_TRAPI_1_1, 'Trapi 1.1')
# Mount default 1.0 app at /
APP.mount('/', APP_TRAPI_1_0, 'Trapi 1.0')
# Add all routes of each app for open api generation at /openapi.json
# This will create an aggregate openapi spec.
APP.include_router(APP_TRAPI_1_1.router, prefix='/1.1')
APP.include_router(APP_TRAPI_1_0.router)
import base64
import traceback
import httpx
from PLATER.services.config import config
from PLATER.services.util.logutil import LoggingUtil
from bmt import Toolkit
from PLATER.services.util.attribute_mapping import get_attribute_bl_info
logger = LoggingUtil.init_logging(__name__,
config.get('logging_level'),
config.get('logging_format')
)
class Neo4jHTTPDriver:
def __init__(self, host: str, port: int, auth: tuple, scheme: str = 'http'):
self._host = host
self._neo4j_transaction_endpoint = "/db/data/transaction/commit"
self._scheme = scheme
self._full_transaction_path = f"{self._scheme}://{self._host}:{port}{self._neo4j_transaction_endpoint}"
self._port = port
self._supports_apoc = None
self._header = {
'Accept': 'application/json; charset=UTF-8',
'Content-Type': 'application/json',
'Authorization': 'Basic %s' % base64.b64encode(f"{auth[0]}:{auth[1]}".encode('utf-8')).decode('utf-8')
}
# ping and raise error if neo4j doesn't respond.
logger.debug('PINGING NEO4J')