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1
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from datetime import datetime
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2
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3
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rels = dict(issupplementto="IsSupplementTo", issupplementedby="IsSupplementedBy", references="References",
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4
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isreferencedby="IsReferencedBy")
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5
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6
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pid_resolver = {
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7
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"pdb": "http://www.rcsb.org/pdb/explore/explore.do?structureId=%s",
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8
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"ncbi-n": "http://www.ncbi.nlm.nih.gov/gquery/?term=%s",
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9
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"pmid": "http://www.ncbi.nlm.nih.gov/pubmed/%s",
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10
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"pmcid": "http://www.ncbi.nlm.nih.gov/pmc/articles/%s",
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11
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"pubmedid": "http://www.ncbi.nlm.nih.gov/pubmed/%s",
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12
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"doi": "http://dx.doi.org/%s",
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13
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"genbank": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",
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14
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"nuccore": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",
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15
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"swiss-prot": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",
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16
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"arrayexpress": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",
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17
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"biomodels": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",
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18
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"bmrb": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",
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19
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"ena": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",
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20
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"geo": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",
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21
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"ensembl": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",
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22
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"mgi": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",
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23
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"bind": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",
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24
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"pride": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",
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25
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"ddbj": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",
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26
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"bioproject": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",
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27
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"embl": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",
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28
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"sra": "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank",
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29
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}
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30
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31
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32
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def resolveIdentifier(pid, pid_type):
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33
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if pid_type != None:
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34
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if pid_type.lower() in pid_resolver:
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35
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return pid_resolver[pid_type.lower()] % pid
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36
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else:
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37
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return "http://identifiers.org/%s:%s" % (pid_type, pid)
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38
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39
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40
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def get_scholix_resource(item):
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41
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title = ''
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42
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if 'title' in item:
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43
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title = item.title
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44
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if len(title):
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45
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if title[0] == '"' and title[-1] == '"':
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46
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title = title[1:-1]
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47
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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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48
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item.identifier]
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49
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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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50
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creator = []
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51
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if 'creator' in item:
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52
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creator = [dict(Name=x.name) for x in item.creator]
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53
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publicationDate = None
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54
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if 'publicationDate' in item:
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55
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publicationDate = item.publicationDate
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56
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publisher = []
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57
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if 'publisher' in item:
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58
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publisher = [dict(name= x.name) for x in item.publisher]
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59
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c_type = item.objectType
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60
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if item.objectType == 'publication':
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61
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c_type = 'literature'
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62
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63
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resource = dict(Title=title, Identifier=identifier, Creator=creator, PublicationDate= publicationDate, Publisher = publisher, Type= c_type)
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64
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65
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return resource
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66
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67
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68
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def create_response(response, current_page):
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69
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result = {'totalLinks': response.hits.total, 'currentPage': current_page,
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70
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'totalPages': 1 + response.hits.total / 100, 'result': []}
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71
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now = datetime.now()
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72
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for item in response.hits:
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73
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current_item = {'LinkPublicationDate': now.strftime("%Y-%m-%d"), 'HarvestedDate': now.strftime("%Y-%m-%d"),
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74
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"LinkProvider": []}
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75
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for linkProvider in item.linkprovider:
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76
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current_item['LinkProvider'].append(dict(name=linkProvider.name,
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77
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identifier=[dict(ID=x.identifier, IDScheme=x.schema) for x in
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78
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linkProvider.identifiers]))
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79
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80
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rel_sub_type = rels.get(item.relationship.name.lower(), "IsRelatedTo")
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81
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current_item['RelationshipType'] = dict(Name=rel_sub_type, SubType=item.relationship.name,
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82
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SubTypeSchema=item.relationship.schema)
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83
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84
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current_item['source'] = get_scholix_resource(item.source)
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85
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current_item['target'] = get_scholix_resource(item.target)
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86
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87
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result['result'].append(current_item)
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88
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89
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return result
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