@Override public String getAnnotationSource() { return this.relocationService.getRelocation(ANNOTATION_SOURCE); }
@Override public String getAnnotationSource() { return this.relocationService.getRelocation(ANNOTATION_SOURCE); }
@Override public String getAnnotationSource() { return this.relocationService.getRelocation(ANNOTATION_SOURCE); }
@Override public String getSourceLocation() { return this.relocationService.getRelocation(this.getDefaultSourceLocation()); }
private void loadGeneReviews() { try (BufferedReader in = new BufferedReader( new InputStreamReader(new URL(this.relocationService.getRelocation(GENEREVIEWS_MAPPING_URL)) .openConnection().getInputStream(), ENCODING))) { for (CSVRecord row : CSVFormat.TDF.withHeader().parse(in)) { SolrInputDocument term = this.data.get(row.get(2)); if (term != null) { term.setField("gene_reviews_link", "https://www.ncbi.nlm.nih.gov/books/" + row.get(0)); } } } catch (IOException ex) { this.logger.error("Failed to load OMIM-GeneReviews links: {}", ex.getMessage(), ex); } }
private void loadGenes() { try (BufferedReader in = new BufferedReader( new InputStreamReader(new URL(this.relocationService.getRelocation(GENE_ANNOTATIONS_URL)) .openConnection().getInputStream(), ENCODING))) { for (CSVRecord row : CSVFormat.TDF.withCommentMarker('#').parse(in)) { SolrInputDocument term = this.data.get(row.get(0).trim()); if (term != null) { String gs = row.get(3).trim(); if (StringUtils.isNotBlank(gs)) { term.addField(GENE_FIELD, gs); } String eidLine = row.get(4).trim(); if (StringUtils.isNotBlank(eidLine)) { String[] eids = StringUtils.split(eidLine, ","); for (String eid : eids) { term.addField(GENE_FIELD, eid.trim()); } } } } } catch (IOException ex) { this.logger.error("Failed to load OMIM-Gene links: {}", ex.getMessage(), ex); } }