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import os
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from fastapi import FastAPI, Form
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import logging
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from starlette.staticfiles import StaticFiles
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from starlette.responses import FileResponse
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from eu.dnetlib.es_connector import DLIESConnector
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import sys
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from eu.dnetlib.metrics_utils import metrics
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from eu.dnetlib.metricsMiddleware import PrometheusMiddleware
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_CURDIR = os.path.dirname(os.path.abspath(__file__))
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app = FastAPI()
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app.mount('/static', StaticFiles(directory=os.path.join(_CURDIR, 'static' )))
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base_dnet_url = "http://aggregator-dli.openaire.eu/dli/"
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pid_resolver = {
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"pdb": "http://www.rcsb.org/pdb/explore/explore.do?structureId=%s",
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"ncbi-n": "http://www.ncbi.nlm.nih.gov/gquery/?term=%s",
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"pmid": "http://www.ncbi.nlm.nih.gov/pubmed/%s",
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"pmcid": "http://www.ncbi.nlm.nih.gov/pmc/articles/%s",
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"pubmedid": "http://www.ncbi.nlm.nih.gov/pubmed/%s",
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"doi": "http://dx.doi.org/%s",
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"genbank": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",
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"nuccore": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",
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"swiss-prot": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",
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"arrayexpress": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",
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"biomodels": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",
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"bmrb": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",
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"ena": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",
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"geo": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",
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"ensembl": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",
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"mgi": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",
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"bind": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",
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"pride": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",
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"ddbj": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",
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"bioproject": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",
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"embl": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",
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"sra": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",
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}
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log = logging.getLogger("scholexplorer-portal")
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log.setLevel(logging.INFO)
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fh = logging.StreamHandler(sys.stdout)
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fh.setLevel(logging.INFO)
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formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')
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fh.setFormatter(formatter)
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log.addHandler(fh)
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log.info("Scholexplorer Portal Restarted")
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app.add_middleware(PrometheusMiddleware)
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app.add_route("/metrics/", metrics)
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@app.get('/')
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def root():
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return FileResponse(os.path.join(os.path.join(_CURDIR, 'static' ),'index.html'))
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@app.get("/favicon.ico")
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def favicon():
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return FileResponse(os.path.join(os.path.join(_CURDIR, 'static' ),'favicon.ico'))
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@app.get("/api/main_page_stats")
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def main_page_stats():
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connector= DLIESConnector()
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return dict(result=connector.get_main_page_stats())
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@app.post('/api/queryPid/')
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def query_pid(*, pid:str= Form(...)):
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print (pid)
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connector = DLIESConnector()
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return dict(result=connector.query_by_id(pid))
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@app.post('/api/post/')
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def query_post(*, start:int= Form(default=0), action:str=Form(default="query"), query:str=Form(...),filter:str=Form(default=None)):
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filter_key = None
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result = {}
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if filter:
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filter_key = filter
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if action == 'query' and query is not None:
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print(query)
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connector = DLIESConnector()
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try:
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result = connector.simple_query(query, start=start, user_filter=filter_key)
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except Exception as e:
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log.error(e)
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return dict(result=result)
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else:
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return dict(error={'error_code': 'an error occur during query on server'})
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@app.get('/api/item/{identifier}')
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@app.post('/api/item/{identifier}')
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def get_item(identifier:str, object_type:str=Form(default=None), start:int=Form(default=0)):
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if identifier:
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connector = DLIESConnector()
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return dict(result=connector.item_by_id(identifier, object_type, start))
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else:
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return None
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