D-Net

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'], res])

                .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'],

                              res[2],

                              res[1]['oaf:result']['country'],

                ])

                .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();

    this.publicationInfo.record = data[14];

    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[0]['bestaccessright'] && data[0]['bestaccessright'].hasOwnProperty("classid")) {

      this.publicationInfo.accessMode = data[0]['bestaccessright'].classid;

    }

    if(data[1] != null) {

      if(Array.isArray(data[1])) {

        this.publicationInfo.title = data[1][0].content;

      } else {

        this.publicationInfo.title = 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*/, this.publicationInfo.accessMode);

            }

            /**********************************************************/

          }

        }

      }

      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[15] != null) {

      this.publicationInfo.countries = this.parsingFunctions.parseCountries(data[15]);

    }

    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);

      });

    }

    if(this.publicationInfo.relatedResearchResults) {

      let self = this;

      this.publicationInfo.relatedResearchResults.forEach(function (value, key, map) {

        self.publicationInfo.relatedResearchResults.set(key, self.parsingFunctions.sortByPercentage(value));

      });

    }

    this.publicationInfo.similarResearchResults = this.parsingFunctions.sortByPercentage(this.publicationInfo.similarResearchResults);

    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;

  }

}