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from pydantic import BaseModel, Schema
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from typing import Dict, List
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from datetime import datetime
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from fastapi import HTTPException
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import logging
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from time import time
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rels = dict(issupplementto="IsSupplementTo", issupplementedby="IsSupplementedBy", references="References",
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isreferencedby="IsReferencedBy")
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10
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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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"ncbi": "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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def resolveIdentifier(pid, pid_type):
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if pid_type != None:
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if pid_type.lower() in pid_resolver:
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return pid_resolver[pid_type.lower()] % pid
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else:
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return "http://identifiers.org/%s:%s" % (pid_type, pid)
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class LinkProvider(BaseModel):
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name:str = Schema(None, title= "The name of the Provider that provides the links", max_length= 300)
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totalRelationships:int=Schema(None, title= "The number of links that It provides")
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class LinkPublisher(BaseModel):
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name:str = Schema(None, title= "The name of the Publisher that provides the links", max_length= 300)
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totalRelationships:int=Schema(None, title= "The number of links that It provides")
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class IdentifierType(BaseModel):
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ID: str = None
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IDScheme:str = None
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IDURL:str= None
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class ScholixProviderType(BaseModel):
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name:str = None
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identifier:List[IdentifierType] = []
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class RelationshipType(BaseModel):
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Name:str
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SubType:str = None
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SubTypeSchema:str = None
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class CreatorType(BaseModel):
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Name: str
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Identifier:List[IdentifierType] = []
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class ScholixItemType(BaseModel):
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Identifier:List[IdentifierType] = []
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Title:str = None
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Type:str
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Creator:List[CreatorType] = []
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PublicationDate:str = None
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Publisher:List[ScholixProviderType] =[]
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class ScholixType(BaseModel):
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HarvestDate:str=None
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LicenseURL:str=None
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LinkProvider:List[ScholixProviderType] =[]
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LinkPublicationDate: str = None
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RelationshipType:RelationshipType
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source:ScholixItemType
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target:ScholixItemType
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class PageResultType(BaseModel):
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currentPage:int
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totalLinks:int
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totalPages:int
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result:List[ScholixType] = []
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def get_scholix_resource(item):
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title = ''
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if 'title' in item:
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title = item.title
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if title is not None and len(title):
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if title[0] == '"' and title[-1] == '"':
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title = title[1:-1]
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identifier = [dict(ID=x.identifier, IDScheme=x.schema, IDURL=resolveIdentifier(x.identifier, x.schema)) for x in
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item.identifier]
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identifier.append(dict(ID=item.dnetIdentifier, IDScheme='D-Net Identifier', IDURL='http://scholexplorer.openaire.eu/index.html#/detail/%s'%item.dnetIdentifier))
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creator = []
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if 'creator' in item and item.creator is not None:
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creator = [dict(Name=x.name) for x in item.creator]
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publicationDate = None
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if 'publicationDate' in item:
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publicationDate = item.publicationDate
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publisher = []
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if 'publisher' in item and item.publisher is not None:
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publisher = [dict(name= x.name) for x in item.publisher if x.name is not None]
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c_type = item.objectType
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if item.objectType == 'publication':
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c_type = 'literature'
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resource = dict(Title=title, Identifier=identifier, Creator=creator, PublicationDate= publicationDate, Publisher = publisher, Type= c_type)
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return resource
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def convert_response(response):
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now = datetime.now()
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log = logging.getLogger("scholexplorer")
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start = time()
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for item in response.hits:
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current_item = {'LinkPublicationDate': now.strftime("%Y-%m-%d"), 'HarvestDate': now.strftime("%Y-%m-%d"),
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"LinkProvider": []}
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for linkProvider in item.linkprovider:
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current_item['LinkProvider'].append(ScholixProviderType(name=linkProvider.name,
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identifier=[IdentifierType(ID=x.identifier, IDScheme=x.schema) for x in
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linkProvider.identifiers]))
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rel_sub_type = rels.get(item.relationship.name.lower(), "IsRelatedTo")
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current_item['RelationshipType'] = dict(Name=rel_sub_type, SubType=item.relationship.name,
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SubTypeSchema=item.relationship.schema)
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current_item['source'] = get_scholix_resource(item.source)
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current_item['target'] = get_scholix_resource(item.target)
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yield current_item
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end = time()
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log.debug("response converted in {} ms".format(end-start))
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def create_response(response, current_page):
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log = logging.getLogger("scholexplorer")
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if current_page > 9999:
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raise HTTPException(status_code=400,detail="MAX NUMBER OF PAGE REACHED")
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start = time()
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result = {'totalLinks': response.hits.total.value, 'currentPage': current_page /100,
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'totalPages': 1 + response.hits.total.value / 100, 'result': []}
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result['result'] = convert_response(response)
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end = time()
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log.debug("response created in {} ms".format(end-start))
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return result
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