Examples with Publication uk.ac.ebi.spot.goci.model.Publication used on opensource projects

Example 1 with Publication

use of uk.ac.ebi.spot.goci.model.Publication in project goci by EBISPOT.

the class FilteringTest method testFilter.

@Test
public void testFilter() {
    SingleNucleotidePolymorphism template = template(SingleNucleotidePolymorphism.class);
    Filter<SingleNucleotidePolymorphism, String> filter = refine(template).on(template.getRsId()).hasValue("rs123456");
    assertEquals("Filter type does not match expected", SingleNucleotidePolymorphism.class, filter.getFilteredType());
    assertEquals("Filtered method does not match expected", "getRsId", filter.getFilteredMethod().getName());
    assertEquals("Filtered value does not match expected", "rs123456", filter.getFilteredValues().get(0));
    Association template2 = template(Association.class);
    Filter<Association, Float> filter2 = refine(template2).on(template2.getPvalueMantissa()).hasValue(Float.valueOf("10"));
    assertEquals("Filter type does not match expected", Association.class, filter2.getFilteredType());
    assertEquals("Filtered method does not match expected", "getPvalueMantissa", filter2.getFilteredMethod().getName());
    assertEquals(Float.valueOf("10"), filter2.getFilteredValues().get(0), 0.0d);
    DateFormat df1 = new SimpleDateFormat("yyyy-MM-dd");
    DateFormat df2 = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss.S");
    Date from = null;
    Date to = null;
    try {
        from = df1.parse("2005-01-01");
        to = df1.parse("2010-01-01");
    } catch (ParseException e) {
        e.printStackTrace();
    }
    String fromValue = df2.format(from).toString();
    String toValue = df2.format(to).toString();
    System.out.println(fromValue);
    System.out.println(toValue);
    Publication publication = template(Publication.class);
    Filter dateFilter = refine(publication).on(publication.getPublicationDate()).hasRange(fromValue, toValue);
    Filter dateFilter2 = refine(publication).on(publication.getPublicationDate()).hasRange(fromValue, toValue);
    assertEquals("Filter type does not match expected", Publication.class, dateFilter.getFilteredType());
    assertEquals("Filtered method does not match expected", "getPublicationDate", dateFilter.getFilteredMethod().getName());
    assertEquals("Filtered value does not match expected", "2010-01-01T00:00:00.0", dateFilter.getFilteredRange().to());
    assertEquals("Hashcodes of the two date filters differ", dateFilter.hashCode(), dateFilter2.hashCode());
}

Example 2 with Publication

use of uk.ac.ebi.spot.goci.model.Publication in project goci by EBISPOT.

the class EuropePMCDeserializer method getPublicatonInfo.

public Publication getPublicatonInfo(JsonNode info) {
    Publication publication = new Publication();
    JsonNode root = info.get("resultList").get("result").get(0);
    System.out.println("Publication");
    publication.setPubmedId(root.get("pmid").asText());
    // publication.setPublicationDate(root.get("firstPublicationDate").asText());
    publication.setPublication(root.get("journalInfo").get("journal").get("medlineAbbreviation").asText());
    publication.setTitle(root.get("title").asText());
    SimpleDateFormat format = new SimpleDateFormat("yyyy-MM-dd");
    /**
     * Priority to eletronicDate. *
     */
    String datePublication = "";
    if (root.has("electronicPublicationDate")) {
        datePublication = root.get("electronicPublicationDate").asText();
    } else {
        if (root.get("journalInfo").has("printPublicationDate")) {
            datePublication = root.get("journalInfo").get("printPublicationDate").asText();
        }
    }
    if (datePublication.contains("/")) {
        datePublication = datePublication.replace("/", "-");
    }
    java.util.Date studyDate = null;
    try {
        studyDate = format.parse(datePublication);
    } catch (ParseException e1) {
        e1.printStackTrace();
    }
    publication.setPublicationDate(new Date(studyDate.getTime()));
    return publication;
}

Example 3 with Publication

use of uk.ac.ebi.spot.goci.model.Publication in project goci by EBISPOT.

the class PussycatGOCIController method setDateFilter.

private Filter setDateFilter(String dateMin, String dateMax) {
    Filter dateFilter;
    DateFormat df_input = new SimpleDateFormat("yyyy-MM-dd");
    Date to, from;
    try {
        if (dateMax != null) {
            int endYearVar = Integer.parseInt(dateMax.split("-")[0]);
            int endMonthVar = Integer.parseInt(dateMax.split("-")[1]);
            String end_month, end_year;
            // API call provides date for "up to and including the end of" - must increment month for query
            if (endMonthVar == 12) {
                end_month = "01";
                endYearVar++;
                end_year = Integer.toString(endYearVar);
            } else {
                endMonthVar++;
                if (endMonthVar > 9) {
                    end_month = Integer.toString(endMonthVar);
                } else {
                    end_month = "0".concat(Integer.toString(endMonthVar));
                }
                end_year = Integer.toString(endYearVar);
            }
            to = df_input.parse(end_year + "-" + end_month + "-01");
        } else {
            // change to use today's date
            to = df_input.parse(df_input.format(new Date()));
        }
        if (dateMin != null) {
            from = df_input.parse(dateMin + "-01");
        } else {
            from = df_input.parse("2005-01-01");
        }
        Calendar fromValue = Calendar.getInstance();
        fromValue.setTime(from);
        Calendar toValue = Calendar.getInstance();
        toValue.setTime(to);
        // Study study = template(Study.class);
        // dateFilter = refine(study).on(study.getPublicationId().getPublicationDate()).hasRange(fromValue, toValue);
        Publication publication = template(Publication.class);
        dateFilter = refine(publication).on(publication.getPublicationDate()).hasRange(fromValue, toValue);
    } catch (ParseException e) {
        getLog().error("Bad date in URL for date range '" + dateMin + "' to '" + dateMax, e);
        throw new RuntimeException("Bad date in URL for date range '" + dateMin + "' to '" + dateMax, e);
    }
    return dateFilter;
}

Example 4 with Publication

use of uk.ac.ebi.spot.goci.model.Publication in project goci by EBISPOT.

the class PublicationOperationsService method addPublication.

@Transactional
public Publication addPublication(String pubmedId, EuropePMCData europePMCResult, Boolean newImport) throws Exception {
    Publication publication = publicationService.createOrFindByPumedId(pubmedId);
    publication.setPubmedId(pubmedId);
    publication.setPublication(europePMCResult.getPublication().getPublication());
    publication.setTitle(europePMCResult.getPublication().getTitle());
    // The date was already curated. So we don't want to import again this data
    if (newImport) {
        publication.setPublicationDate(europePMCResult.getPublication().getPublicationDate());
    }
    publicationService.save(publication);
    authorOperationsService.addAuthorsToPublication(publication, europePMCResult);
    addFirstAuthorToPublication(publication, europePMCResult);
    return publication;
}

Example 5 with Publication

use of uk.ac.ebi.spot.goci.model.Publication in project goci by EBISPOT.

the class PublicationOperationsService method importNewPublications.

// Import the a list of pubmedid
public ArrayList<HashMap<String, String>> importNewPublications(String pubmedIdList, SecureUser currentUser) {
    getLog().info("Importing publications: {}", pubmedIdList);
    ArrayList<HashMap<String, String>> listPublications = new ArrayList<>();
    String regex = "[0-9, /,]+";
    // Remove whitespace
    String pubmedIdListTrim = pubmedIdList.trim();
    if (!pubmedIdListTrim.matches(regex)) {
        getLog().error("Error found when parsing publication list: Pubmed list must be number follow by comma");
        HashMap<String, String> error = new HashMap<String, String>();
        error.put("pubmedId", "general");
        error.put("error", "Pubmed List must be number follow by comma");
        listPublications.add(error);
        return listPublications;
    }
    List<String> pubmedIds = Arrays.asList(pubmedIdListTrim.split("\\s*,\\s*"));
    for (String pubmedId : pubmedIds) {
        HashMap<String, String> pubmedResult = new HashMap<String, String>();
        pubmedId = pubmedId.trim();
        if (pubmedId == "") {
            getLog().error("Error found when processing pubmed entry: Found empty Pubmed ID");
            pubmedResult.put("pubmedId", "general");
            pubmedResult.put("error", "Empty pubmed id - The pubmedId is mandatory");
            listPublications.add(pubmedResult);
        }
        // Check if there is an existing study with the same pubmed id
        Collection<Study> existingStudies = publicationService.findStudiesByPubmedId(pubmedId);
        if (existingStudies != null) {
            pubmedResult.put("pubmedId", "general");
            pubmedResult.put("error", "Pubmed " + pubmedId + " already exists.");
            listPublications.add(pubmedResult);
        } else {
            // Study importedStudy = defaultPubMedSearchService.findPublicationSummary(pubmedId);
            try {
                getLog().debug("Publication ");
                getLog().debug(pubmedId);
                Publication publication = importSinglePublication(pubmedId, true);
                Study importedStudy = new Study();
                importedStudy.setPublicationId(publication);
                Study savedStudy = studyOperationsService.createStudy(importedStudy, currentUser);
                pubmedResult.put("pubmedId", pubmedId);
                pubmedResult.put("author", savedStudy.getPublicationId().getFirstAuthor().getFullname());
                pubmedResult.put("title", savedStudy.getPublicationId().getTitle());
                pubmedResult.put("study_id", "studies/" + savedStudy.getId().toString());
                listPublications.add(pubmedResult);
                // Create directory to store associated files
                studyFileService.createStudyDir(savedStudy.getId());
            } catch (NoStudyDirectoryException e) {
                getLog().error("No study directory exception");
                pubmedResult.put("pubmedId", "general");
                pubmedResult.put("error", "No study directory exception for pubmed: " + pubmedId);
                listPublications.add(pubmedResult);
            } catch (PubmedLookupException ple) {
                getLog().error("Encountered Pubmed lookup exception: {}", ple.getMessage(), ple);
                pubmedResult.put("pubmedId", "general");
                pubmedResult.put("error", "Pubmed " + pubmedId + " lookup exception: " + ple.getMessage());
                listPublications.add(pubmedResult);
            } catch (Exception e) {
                getLog().error("Encountered error: {}", e.getMessage(), e);
                pubmedResult.put("pubmedId", "general");
                pubmedResult.put("error", "Pubmed " + pubmedId + " encountered error: " + e.getMessage());
                listPublications.add(pubmedResult);
            }
        }
    }
    return listPublications;
}