openaire-library/landingPages/publication/publication.service.ts

import {Injectable} from '@angular/core';
import {Http, Response} from '@angular/http';
import {Observable}     from 'rxjs/Observable';
import {PublicationInfo} from '../../utils/entities/publicationInfo';
import 'rxjs/add/observable/of';
import 'rxjs/add/operator/do';
import 'rxjs/add/operator/share';
import 'rxjs/add/operator/map';
import{EnvProperties} from '../../utils/properties/env-properties';


import { ParsingFunctions } from '../landing-utils/parsingFunctions.class';

@Injectable()
export class PublicationService {

  constructor(private http: Http ) {
    this.parsingFunctions = new ParsingFunctions();
  }

  public parsingFunctions: ParsingFunctions;
  publicationInfo: PublicationInfo;

  getPublicationInfo (id: string, properties:EnvProperties):any {
    console.info("getPublicationInfo in service");
    let url = properties.searchAPIURLLAst + 'publications/' +id+"?format=json";
    let key = url;

    return this.http.get((properties.useCache)? (properties.cacheUrl+encodeURIComponent(url)): url)
                .map(res => <any> res.json())
                .map(res => [res['result']['header']['dri:status'], res['result']['metadata']['oaf:entity']])
                .map(res => [ res[1]['oaf:result'],
                              res[1]['oaf:result']['title'],
                              res[1]['oaf:result']['rels']['rel'],
                              res[1]['oaf:result']['children'],
                              res[1]['oaf:result']['pid'],
                              res[1]['oaf:result']['journal'],
                              res[1]['oaf:result']['language'],
                              res[1]['oaf:result']['subject'],
                              res[1]['oaf:result']['bestaccessright'],
                              res[1]['oaf:result']['collectedfrom'],
                              (res[1]['extraInfo']!= undefined && res[1]['extraInfo']['citations']!= undefined)? res[1]['extraInfo']['citations']['citation']:null,
                              res[1]['oaf:result']['context'],
                              res[0],
                              res[1]['oaf:result']['creator']
                ])
                .map(res => this.parsePublicationInfo(res));
  }

  private handleError (error: Response) {
  // in a real world app, we may send the error to some remote logging infrastructure
  // instead of just logging it to the console
    console.log(error);
    return Observable.throw(error  || 'Server error');
  }

  parsePublicationInfo (data: any):any {
    this.publicationInfo = new PublicationInfo();

    if(data[0] != null) {
      var date:string = (data[0].dateofacceptance)+""; // transform to string in case it is an integer
      this.publicationInfo.date  = (date && (date).indexOf('-') !== -1)?date.split('-')[0]:date;
      this.publicationInfo.dateofacceptance = data[0].dateofacceptance;
      this.publicationInfo.publisher = data[0].publisher;
      if(!Array.isArray(data[0].description)) {
          this.publicationInfo.description = data[0].description;
      } else {
          this.publicationInfo.description = data[0].description[0];
      }
      this.publicationInfo.embargoEndDate = data[0].embargoenddate;
    }

    this.publicationInfo.title = {"name": "", "url": "", "accessMode": ""};
    if(data[0]['bestaccessright'] && data[0]['bestaccessright'].hasOwnProperty("classid")) {
      this.publicationInfo.title.accessMode = data[0]['bestaccessright'].classid;
    }

    if(data[1] != null) {
      if(Array.isArray(data[1])) {
        this.publicationInfo.title['name'] = data[1][0].content;
      } else {
        this.publicationInfo.title['name'] = data[1].content;
      }
    }

    if(data[2] != null) {
      let relation;
      let length = Array.isArray(data[2]) ? data[2].length : 1;

      for(let i=0; i<length; i++) {
        relation = Array.isArray(data[2]) ? data[2][i] : data[2];
        if(relation.hasOwnProperty("to")) {
          if(relation['to'].class == "isProducedBy") {
            this.publicationInfo.fundedByProjects = this.parsingFunctions.parseFundingByProjects(this.publicationInfo.fundedByProjects, relation, this.publicationInfo.projectsProvenanceVocabulary);
          } else if(relation['to'].class == "isRelatedTo") {
            let provenanceAction: string;
            if(relation.provenanceaction in this.publicationInfo.researchResultsProvenanceVocabulary) {
              provenanceAction = this.publicationInfo.researchResultsProvenanceVocabulary[relation.provenanceaction];
            } else {
              provenanceAction = "Other";
            }

            this.publicationInfo.relatedResearchResults = this.parsingFunctions.parseRelatedResearchResults(this.publicationInfo.relatedResearchResults, relation, provenanceAction);
          } else if(relation['to'].class == "hasAmongTopNSimilarDocuments") {
            this.publicationInfo.similarResearchResults = this.parsingFunctions.parseSimilarResearchResults(this.publicationInfo.similarResearchResults, relation);
          } else if(relation['to'].class == "hasAuthorInstitution") {
            this.publicationInfo.organizations = this.parseRelatedOrganizations(this.publicationInfo.organizations, relation);
          }
        }
      }
    }

    if(data[3] != null) {
      if(data[3].hasOwnProperty("instance")) {
        //this.publicationInfo.collectedFrom = new Array<{"name": string, "id": string}>();
        //this.publicationInfo.downloadFrom = new Map<string, {"url": string[], "accessMode": string[], "bestAccessMode": string}>();
        //this.publicationInfo.publishedIn = new Map<string, {"url": string[], "accessMode": string[], "bestAccessMode": string}>();


        this.publicationInfo.hostedBy_collectedFrom = new Array<{"downloadName": string, "downloadUrl": string[], "collectedName": string, "collectedId": string, "accessMode": string[], "bestAccessMode": string, "type": string, "year":string}>();


        this.publicationInfo.types = new Array<string>();
        let types = new Set<string>();

        let counter = 0;
        let instance;

        let length = Array.isArray(data[3]['instance']) ? data[3]['instance'].length : 1;

        for(let i=0; i<length; i++) {
          instance = Array.isArray(data[3]['instance']) ? data[3]['instance'][i] : data[3]['instance'];

          this.parsingFunctions.parseTypes(this.publicationInfo.types, types, instance);

          if(instance.hasOwnProperty("webresource")) {
            let url;
            if(!Array.isArray(instance['webresource'])) {
              url = instance['webresource'].url;
            } else{
              url = instance['webresource'][0].url;
            }

            /**********************************************************/
            if(instance.hasOwnProperty("hostedby")) {
              counter = this.parsingFunctions.parseHostedBy_collectedFrom(this.publicationInfo.hostedBy_collectedFrom, instance, data[0], url, counter, this.publicationInfo.title);
            }
            /**********************************************************/
          }
        }
      }

      if(data[3].hasOwnProperty("externalreference")) {
        let externalResults: [Map<string, Map<string, string>>, { "name": string, "url": string}[]] = this.parseBioentitiesAndSoftware(data[3]);
        this.publicationInfo.bioentities = externalResults[0];
        this.publicationInfo.software = externalResults[1];
      }
    }

    if(data[4] != null) {
      this.publicationInfo.identifiers = this.parsingFunctions.parseIdentifiers(data[4]);
    }

    if(data[5] != null) {
      this.publicationInfo.journal = {"journal": "", "issn": "", "lissn": "", "volume": "", "start_page": "", "end_page": ""}

      this.publicationInfo.journal['journal'] = data[5].content;
      this.publicationInfo.journal['issn'] = data[5].issn;
      this.publicationInfo.journal['lissn'] = data[5].lissn;
      this.publicationInfo.journal['volume'] = data[5].vol;
      this.publicationInfo.journal['start_page'] = data[5].sp;
      this.publicationInfo.journal['end_page'] = data[5].ep;
    }

    if(data[6] != null) {
      this.publicationInfo.languages = this.parsingFunctions.parseLanguages(data[6]);
    }

    if(data[7] != null) {
      let subjectResults: [string[], Map<string, string[]>, Map<string, string[]>] = this.parsingFunctions.parseAllSubjects(data[7]);
      this.publicationInfo.subjects = subjectResults[0];
      this.publicationInfo.otherSubjects = subjectResults[1];
      this.publicationInfo.classifiedSubjects = subjectResults[2];
    }

    // if(data[8] != null) {
    //     this.publicationInfo.bestaccessright = data[8].classid;
    // }

    // if(data[9] != null) {
    //   this.publicationInfo.collectedFrom = this.parsingFunctions.parseCollectedFrom(data[9]);
    // }

    this.publicationInfo.hostedBy_collectedFrom = this.parsingFunctions.addPublisherToHostedBy_collectedFrom(
                this.publicationInfo.hostedBy_collectedFrom, this.publicationInfo.publisher,
                this.publicationInfo.journal, this.publicationInfo.identifiers,
                this.publicationInfo.title);

    if(data[10] != null) {
      this.publicationInfo.references = this.parseReferences(data[10]);
    }

    if(data[11] != null) {
      this.publicationInfo.contexts = this.parsingFunctions.parseContexts(data[11]);
    }

    if(data[12] != null && data[12] == "under curation") {
      this.publicationInfo.underCurationMessage = true;
    } else {
      this.publicationInfo.underCurationMessage = false;
    }

    if(data[13] != null) {
      if(this.publicationInfo.authors == undefined) {
        this.publicationInfo.authors = new Array<string>();
      }

      let authors = data[13];
      let length = Array.isArray(authors) ? authors.length : 1;

      for(let i=0; i<length; i++) {
        let author = Array.isArray(authors) ? authors[i] : authors;
        this.publicationInfo.authors[author.rank-1] = author.content;
      }
      this.publicationInfo.authors = this.publicationInfo.authors.filter(function (item) {
        return (item != undefined);
      });
    }

    return this.publicationInfo;
  }

  parseRelatedOrganizations(organizations: {"name": string, "shortname":string, "id": string, "websiteUrl": string, "country": string, "trust": number}[], relation: any):
                  {"name": string, "shortname":string, "id": string, "websiteUrl": string, "country": string, "trust": number}[] {
    if(organizations == undefined) {
      organizations = new Array<{
                  "name": string, "shortname": string,
                  "id": string, "websiteUrl": string,
                  "country": string, "trust": number}>();
    }

    let organization: { "name": string, "shortname": string,
                        "id": string, "websiteUrl": string,
                        "country": string, "trust": number
                      } = {
                        "name": "", "shortname": "",
                        "id": "", "websiteUrl": "",
                        "country": "", "trust": null
                      };

    organization.id = relation['to'].content;
    organization.name = relation.legalname;
    organization.shortname = relation.legalshortname;
    organization.websiteUrl = relation.websiteurl;
    if(relation.country) {
      organization.country = relation.country.classname;
    }
    if(relation.trust) {
      organization.trust = Math.round(relation.trust*100);
    }

    organizations.push(organization);
    return organizations;
  }

  parseBioentitiesAndSoftware(children: any) : [Map<string, Map<string, string>>, { "name": string, "url": string}[]] {
    let bioentities: Map<string, Map<string, string>>;
    let software: {"name": string, "url": string}[];

    let length = Array.isArray(children['externalreference']) ? children['externalreference'].length : 1;

    let externalreference;
    for(let i=0; i<length; i++) {
      externalreference = Array.isArray(children['externalreference']) ? children['externalreference'][i] : children['externalreference'];

      if(externalreference.hasOwnProperty("qualifier")) {
        if(externalreference['qualifier'].classid == "accessionNumber") {

          if(bioentities == undefined) {
            bioentities = new Map<string, Map<string, string>>();
          }

          if(!bioentities.has(externalreference.sitename)) {
            bioentities.set(externalreference.sitename, new Map<string, string>());
          }
          bioentities.get(externalreference.sitename).set(externalreference.refidentifier, externalreference.url);

        } else if(externalreference['qualifier'].classid == "software") {

          if(software == undefined) {
            software = new Array<{"name": string, "url": string}>();
          }

          software.push({"name": externalreference.sitename, "url": externalreference.url});
        }
      }
    }

    return [bioentities, software];
  }

  parseReferences(citations: any): {"name": string, "url": string}[] {
    let references = new Array<{"name": string, "url": string}>();

    let citation;
    let length = Array.isArray(citations) ? citations.length : 1;
    for(let i=0; i<length; i++) {
      citation = Array.isArray(citations) ? citations[i] : citations;

      let url;
      if(citation.hasOwnProperty("id")) {
        let citationId;
        let length1 = Array.isArray(citation['id']) ? citation['id'].length : 1;
        for(let j=0; j<length1; j++) {
          citationId = Array.isArray(citation['id']) ? citation['id'][j] : citation['id'];

          if(citationId.type == "pmid") {
            url = "http://www.ncbi.nlm.nih.gov/pubmed/"+citationId.value;
          }
        }
      }

      references[citation.position-1] = { "name": "", "url": ""};
      references[citation.position-1]['name'] = citation.rawText;
      references[citation.position-1]['url'] = url;
    }
    return references;
  }
}