Examples with PublicationIdsQuery org.edamontology.edammap.core.query.PublicationIdsQuery used on opensource projects

Example 1 with PublicationIdsQuery

use of org.edamontology.edammap.core.query.PublicationIdsQuery in project edammap by edamontology.

the class Report method writeArticle.

private static void writeArticle(CoreArgs args, QueryType type, Writer writer, Map<EdamUri, Concept> concepts, Query query, int queriesSize, List<Publication> publications, List<Webpage> webpages, List<Webpage> docs, MappingTest mapping, int page, int nr, int nrMin, int nrMax) throws IOException {
    FetcherArgs fetcherArgs = args.getFetcherArgs();
    writer.write("<article>\n");
    writer.write("\t<h2 id=\"" + nr + "\"><span>");
    if (queriesSize > 1) {
        writer.write("<span class=\"rank\">" + nr + ". </span>");
    }
    writer.write("<span>" + (query.getName() != null ? FetcherCommon.escapeHtml(query.getName()) : "") + "</span>");
    if (query.getId() != null) {
        if (type == QueryType.biotools) {
            writer.write("<a href=\"" + FetcherCommon.escapeHtmlAttribute(QueryLoader.BIOTOOLS + query.getId()) + "\" class=\"biotools-link\"></a>");
        } else {
            writer.write("<span> (" + FetcherCommon.escapeHtml(query.getId()) + ")</span>");
        }
    }
    writer.write("</span><span>");
    String next = "";
    if (nr == nrMax && nr < queriesSize) {
        next = "index" + (page + 1) + ".html#" + (nr + 1);
    } else if (nr < nrMax) {
        next = "#" + (nr + 1);
    }
    if (next.isEmpty()) {
        writer.write("<span class=\"next\"></span>");
    } else {
        writer.write("<a href=\"" + next + "\" class=\"next\"></a>");
    }
    String previous = "";
    if (nr == nrMin && nr > 1) {
        previous = "index" + (page - 1 == 1 ? "" : page - 1) + ".html#" + (nr - 1);
    } else if (nr > nrMin) {
        previous = "#" + (nr - 1);
    }
    if (previous.isEmpty()) {
        writer.write("<span class=\"previous\"></span>");
    } else {
        writer.write("<a href=\"" + previous + "\" class=\"previous\"></a>");
    }
    writer.write("<a href=\"#" + nr + "\" class=\"current\"></a>");
    writer.write("</span></h2>\n");
    boolean webpagesPresent = false;
    if (query.getWebpageUrls() != null) {
        for (Link link : query.getWebpageUrls()) {
            if (link != null && link.getUrl() != null && !link.getUrl().isEmpty()) {
                webpagesPresent = true;
                break;
            }
        }
    }
    boolean docsPresent = false;
    if (query.getDocUrls() != null) {
        for (Link link : query.getDocUrls()) {
            if (link != null && link.getUrl() != null && !link.getUrl().isEmpty()) {
                docsPresent = true;
                break;
            }
        }
    }
    boolean miscPresent = (query.getKeywords() != null && !query.getKeywords().isEmpty()) || (query.getDescription() != null && !query.getDescription().isEmpty()) || webpagesPresent || docsPresent;
    boolean publicationsPresent = false;
    if (query.getPublicationIds() != null) {
        for (PublicationIdsQuery publicationIds : query.getPublicationIds()) {
            if (publicationIds != null && !publicationIds.isEmpty()) {
                publicationsPresent = true;
                break;
            }
        }
    }
    if (miscPresent || publicationsPresent) {
        if (publicationsPresent) {
            writer.write("\t<section class=\"query\">\n");
        } else {
            writer.write("\t<section class=\"query query-no-publications\">\n");
        }
        if (miscPresent) {
            writer.write("\t\t<section class=\"misc\">\n");
            if (query.getKeywords() != null && !query.getKeywords().isEmpty()) {
                Map<String, List<Keyword>> keywords = new LinkedHashMap<>();
                for (Keyword keyword : query.getKeywords()) {
                    if (keywords.get(keyword.getType()) == null) {
                        keywords.put(keyword.getType(), new ArrayList<>());
                    }
                    keywords.get(keyword.getType()).add(keyword);
                }
                for (Map.Entry<String, List<Keyword>> entry : keywords.entrySet()) {
                    writer.write("\t\t\t<div class=\"generic\">\n");
                    writer.write("\t\t\t\t<h3>" + FetcherCommon.escapeHtml(entry.getKey()) + "</h3><br>\n");
                    writer.write("\t\t\t\t<div>");
                    writer.write(entry.getValue().stream().map(k -> FetcherCommon.getLinkHtml(k.getUrl(), k.getValue())).collect(Collectors.joining("; ")));
                    writer.write("</div>\n");
                    writer.write("\t\t\t</div>\n");
                }
            }
            if (query.getDescription() != null && !query.getDescription().isEmpty()) {
                writer.write("\t\t\t<div class=\"generic\">\n");
                writer.write("\t\t\t\t<h3>Description</h3><br>\n");
                writer.write("\t\t\t\t<div>" + FetcherCommon.getParagraphsHtml(query.getDescription()) + "</div>\n");
                writer.write("\t\t\t</div>\n");
            }
            if (webpagesPresent) {
                writer.write("\t\t\t<div class=\"links\">\n");
                writer.write("\t\t\t\t<h3>Links</h3><br>\n");
                writer.write("\t\t\t\t<div>\n");
                writeLinks(fetcherArgs, writer, query.getWebpageUrls(), webpages);
                writer.write("\t\t\t\t</div>\n");
                writer.write("\t\t\t</div>\n");
            }
            if (docsPresent) {
                writer.write("\t\t\t<div class=\"links\">\n");
                writer.write("\t\t\t\t<h3>Documentation</h3><br>\n");
                writer.write("\t\t\t\t<div>\n");
                writeLinks(fetcherArgs, writer, query.getDocUrls(), docs);
                writer.write("\t\t\t\t</div>\n");
                writer.write("\t\t\t</div>\n");
            }
            writer.write("\t\t</section>\n");
        }
        if (publicationsPresent) {
            writer.write("\t\t<section class=\"publications\">\n");
            writePublications(fetcherArgs, writer, query.getPublicationIds(), publications);
            writer.write("\t\t</section>\n");
        }
        writer.write("\t</section>\n");
    }
    writer.write("\t<section class=\"mapping\">\n");
    writeMatches(args.getMapperArgs().getScoreArgs(), writer, concepts, query, publications, mapping);
    writer.write("\t</section>\n");
    writer.write("</article>\n\n");
}

Example 2 with PublicationIdsQuery

use of org.edamontology.edammap.core.query.PublicationIdsQuery in project edammap by edamontology.

the class Report method writePublications.

private static void writePublications(FetcherArgs fetcherArgs, Writer writer, List<PublicationIdsQuery> publicationIds, List<Publication> publications) throws IOException {
    for (int i = 0; i < publicationIds.size(); ++i) {
        PublicationIdsQuery publicationId = publicationIds.get(i);
        Publication publication = publications.get(i);
        if (publicationId == null || publicationId.isEmpty())
            continue;
        String status = "";
        String statusIcon = "pub-info";
        if (publication == null) {
            status = "missing";
            statusIcon = "pub-warning";
        } else if (publication.isEmpty()) {
            status = "empty";
            statusIcon = "pub-warning";
        } else if (!publication.isUsable(fetcherArgs)) {
            status = "non-usable";
            statusIcon = "pub-warning";
        } else if (!publication.isFinal(fetcherArgs)) {
            status = "non-final";
            statusIcon = "pub-info-warning";
        }
        writer.write("\t\t\t<div class=\"publication\">\n");
        writer.write("\t\t\t\t<div class=\"pub-head");
        if (!status.isEmpty()) {
            writer.write(" pub-" + status);
        }
        writer.write("\">");
        if (publication != null || !publicationId.isEmpty()) {
            writer.write("<div class=\"" + statusIcon + "\" tabindex=\"0\"><div class=\"" + (statusIcon.equals("pub-info-warning") ? "pub-info" : statusIcon) + "-box\" tabindex=\"0\">\n");
            if (!publicationId.isEmpty()) {
                writePublicationId(writer, "pmid", publicationId.getPmid(), FetcherCommon.getPmidLinkHtml(publicationId.getPmid()), publicationId.getPmidUrl());
                writePublicationId(writer, "pmcid", publicationId.getPmcid(), FetcherCommon.getPmcidLinkHtml(publicationId.getPmcid()), publicationId.getPmcidUrl());
                writePublicationId(writer, "doi", publicationId.getDoi(), FetcherCommon.getDoiLinkHtml(publicationId.getDoi()), publicationId.getDoiUrl());
                if (publication != null) {
                    writer.write("\t\t\t\t\t<hr>\n");
                }
            }
            if (publication != null) {
                writer.write(publication.toStringMetaHtml("\t\t\t\t\t"));
                writer.write("\n");
            }
            writer.write("\t\t\t\t</div></div>");
        }
        if (!status.isEmpty()) {
            writer.write("<span>" + status.toUpperCase(Locale.ROOT) + "</span> ");
        }
        writer.write("Publication");
        if (publicationId.getType() != null && !publicationId.getType().isEmpty()) {
            writer.write(" (" + FetcherCommon.escapeHtml(publicationId.getType()) + ")");
        }
        if (publication != null) {
            writer.write("&nbsp; <span class=\"" + (publication.isOA() ? "oa" : "not-oa") + "\">" + (publication.isOA() ? "" : "Not ") + "Open Access</span>");
        }
        writer.write("</div>\n");
        writer.write("\t\t\t\t<div class=\"pub-body\">\n");
        if (publication != null && (publication.getIdCount() > 0 || !publication.isEmpty())) {
            if (!publication.getPmid().isEmpty()) {
                writePublicationPartMeta(fetcherArgs, writer, publication, PublicationPartName.pmid);
                writer.write("<span class=\"dt\">pmid:</span> " + FetcherCommon.getPmidLinkHtml(publication.getPmid().getContent()) + "</div>\n");
            }
            if (!publication.getPmcid().isEmpty()) {
                writePublicationPartMeta(fetcherArgs, writer, publication, PublicationPartName.pmcid);
                writer.write("<span class=\"dt\">pmcid:</span> " + FetcherCommon.getPmcidLinkHtml(publication.getPmcid().getContent()) + "</div>\n");
            }
            if (!publication.getDoi().isEmpty()) {
                writePublicationPartMeta(fetcherArgs, writer, publication, PublicationPartName.doi);
                writer.write("<span class=\"dt\">doi:</span> " + FetcherCommon.getDoiLinkHtml(publication.getDoi().getContent()) + "</div>\n");
            }
            if (publication.getIdCount() > 0 && !publication.isEmpty()) {
                writer.write("\t\t\t\t\t<hr>\n");
            }
            if (!publication.getTitle().isEmpty()) {
                writePublicationPartMeta(fetcherArgs, writer, publication, PublicationPartName.title);
                writer.write("<span class=\"dt\">Title:</span> " + publication.getTitle().toStringPlainHtml() + "</div>\n");
            }
            if (!publication.getKeywords().isEmpty()) {
                writePublicationPartMeta(fetcherArgs, writer, publication, PublicationPartName.keywords);
                writer.write("<span class=\"dt\">Keywords:</span> " + publication.getKeywords().toStringPlainHtml() + "</div>\n");
            }
            if (!publication.getMeshTerms().isEmpty()) {
                writePublicationPartMeta(fetcherArgs, writer, publication, PublicationPartName.mesh);
                writer.write("<span class=\"dt\">MeSH terms:</span> " + publication.getMeshTerms().toStringPlainHtml() + "</div>\n");
            }
            if (!publication.getEfoTerms().isEmpty()) {
                writePublicationPartMeta(fetcherArgs, writer, publication, PublicationPartName.efo);
                writer.write("<span class=\"dt\">EFO terms:</span> " + publication.getEfoTerms().toStringPlainHtml() + "</div>\n");
            }
            if (!publication.getGoTerms().isEmpty()) {
                writePublicationPartMeta(fetcherArgs, writer, publication, PublicationPartName.go);
                writer.write("<span class=\"dt\">GO terms:</span> " + publication.getGoTerms().toStringPlainHtml() + "</div>\n");
            }
            if (!publication.getAbstract().isEmpty()) {
                writePublicationPartMeta(fetcherArgs, writer, publication, PublicationPartName.theAbstract);
                writer.write("<span class=\"dt\">Abstract:</span> " + publication.getAbstract().toStringPlainHtml() + "</div>\n");
            }
            if (!publication.getFulltext().isEmpty()) {
                writePublicationPartMeta(fetcherArgs, writer, publication, PublicationPartName.fulltext);
                writer.write("<span class=\"dt\">Full text present:</span> [" + publication.getFulltext().getSize() + " characters]</div>\n");
            }
        }
        writer.write("\t\t\t\t</div>\n");
        writer.write("\t\t\t</div>\n");
    }
}

Example 3 with PublicationIdsQuery

use of org.edamontology.edammap.core.query.PublicationIdsQuery in project edammap by edamontology.

the class Processor method getProcessedQuery.

public QueryProcessed getProcessedQuery(Query query, QueryType type, PreProcessor pp, Idf queryIdf, FetcherArgs fetcherArgs) {
    QueryProcessed queryProcessed = new QueryProcessed();
    boolean removeBroken = (type == QueryType.Bioconductor);
    if (query.getName() != null) {
        List<String> nameTokens = pp.process(query.getName());
        if (!nameTokens.isEmpty()) {
            queryProcessed.setNameTokens(nameTokens);
            if (queryIdf != null) {
                queryProcessed.setNameIdfs(queryIdf.getIdf(nameTokens));
            }
        }
    }
    if (query.getKeywords() != null) {
        for (Keyword keyword : query.getKeywords()) {
            String keywordValue = keyword.getValue();
            List<String> keywordTokens = null;
            List<Double> keywordIdfs = null;
            if (keywordValue != null) {
                keywordTokens = pp.process(keywordValue);
                if (keywordTokens.isEmpty()) {
                    keywordTokens = null;
                } else if (queryIdf != null) {
                    keywordIdfs = queryIdf.getIdf(keywordTokens);
                }
            }
            queryProcessed.addKeywordTokens(keywordTokens);
            queryProcessed.addKeywordIdfs(keywordIdfs);
        }
    }
    if (query.getDescription() != null) {
        List<String> descriptionTokens = pp.process(query.getDescription());
        if (!descriptionTokens.isEmpty()) {
            queryProcessed.setDescriptionTokens(descriptionTokens);
            if (queryIdf != null) {
                queryProcessed.setDescriptionIdfs(queryIdf.getIdf(descriptionTokens));
            }
        }
    }
    if (query.getWebpageUrls() != null) {
        for (Iterator<Link> it = query.getWebpageUrls().iterator(); it.hasNext(); ) {
            String webpageUrl = it.next().getUrl();
            Webpage webpage = FetcherCommon.getWebpage(webpageUrl, database, fetcher, fetcherArgs);
            List<String> webpageTokens = null;
            List<Double> webpageIdfs = null;
            if (webpage != null && webpage.isUsable(fetcherArgs)) {
                webpageTokens = pp.process(webpage.getTitle() + " " + webpage.getContent());
                if (webpageTokens.isEmpty()) {
                    webpageTokens = null;
                } else if (queryIdf != null) {
                    webpageIdfs = queryIdf.getIdf(webpageTokens);
                }
            }
            if (webpageTokens == null && removeBroken) {
                it.remove();
            } else {
                queryProcessed.addWebpage(webpage);
                queryProcessed.addWebpageTokens(webpageTokens);
                queryProcessed.addWebpageIdfs(webpageIdfs);
            }
        }
    }
    if (query.getDocUrls() != null) {
        for (Iterator<Link> it = query.getDocUrls().iterator(); it.hasNext(); ) {
            String docUrl = it.next().getUrl();
            Webpage doc = FetcherCommon.getDoc(docUrl, database, fetcher, fetcherArgs);
            List<String> docTokens = null;
            List<Double> docIdfs = null;
            if (doc != null && doc.isUsable(fetcherArgs)) {
                docTokens = pp.process(doc.getTitle() + " " + doc.getContent());
                if (docTokens.isEmpty()) {
                    docTokens = null;
                } else if (queryIdf != null) {
                    docIdfs = queryIdf.getIdf(docTokens);
                }
            }
            if (docTokens == null && removeBroken) {
                it.remove();
            } else {
                queryProcessed.addDoc(doc);
                queryProcessed.addDocTokens(docTokens);
                queryProcessed.addDocIdfs(docIdfs);
            }
        }
    }
    if (query.getPublicationIds() != null) {
        for (PublicationIdsQuery publicationIds : query.getPublicationIds()) {
            Publication publication = FetcherCommon.getPublication(publicationIds, database, fetcher, null, fetcherArgs);
            if (publication != null) {
                queryProcessed.addPublication(publication);
                queryProcessed.addProcessedPublication(processPublication(publication, pp, queryIdf, fetcherArgs));
            } else {
                queryProcessed.addPublication(null);
                queryProcessed.addProcessedPublication(null);
            }
        }
    }
    return queryProcessed;
}