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

Example 26 with Association

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

the class PussycatGOCIController method renderTrait.

@RequestMapping(value = "/traits/{efoURI}")
@ResponseBody
public String renderTrait(@PathVariable String efoURI, HttpSession session) throws PussycatSessionNotReadyException, NoRenderableDataException {
    Association ta = template(Association.class);
    Filter filter = refine(ta).on(ta.getEfoTraits()).hasValue(URI.create(efoURI));
    return getPussycatSession(session).performRendering(getRenderletNexus(session), filter);
}

Example 27 with Association

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

the class TestFiltering 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);
    Study study = template(Study.class);
    Filter dateFilter = refine(study).on(study.getPublicationDate()).hasRange(fromValue, toValue);
    Filter dateFilter2 = refine(study).on(study.getPublicationDate()).hasRange(fromValue, toValue);
    assertEquals("Filter type does not match expected", Study.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 28 with Association

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

the class MappingDetailsService method createMappingSummary.

/**
     * An additional date should be added to the "Curator information" tab called "Last automated mapping date". This
     * should record the last date all SNPs were mapped using the automated mapping pipeline i.e. when there has been an
     * Ensembl release. This should be left blank for studies where SNPs have different mapping dates or were mapped by
     * a curator, indicating that the curator should check the "SNP associations page" for last mapping info.
     *
     * @param study Study with mapping details
     */
public MappingDetails createMappingSummary(Study study) {
    MappingDetails mappingSummary = new MappingDetails();
    Collection<Association> studyAssociations = associationRepository.findByStudyId(study.getId());
    if (studyAssociations != null && !studyAssociations.isEmpty()) {
        // Determine if we have more than one performer
        Set<String> allAssociationMappingPerformers = new HashSet<String>();
        for (Association association : studyAssociations) {
            allAssociationMappingPerformers.add(association.getLastMappingPerformedBy());
        }
        Map<String, String> mappingDateToPerformerMap = new HashMap<>();
        SimpleDateFormat dt = new SimpleDateFormat("yyyy-MM-dd");
        // If only one performer we need to check dates to see mapping didn't happen at different times
        if (allAssociationMappingPerformers.size() == 1) {
            String performer = allAssociationMappingPerformers.iterator().next();
            // Only care about automated mapping
            if (performer != null) {
                if (performer.equals("automatic_mapping_process")) {
                    // Go through all associations and store mapping performer and date
                    for (Association association : studyAssociations) {
                        String date = dt.format(association.getLastMappingDate());
                        mappingDateToPerformerMap.put(date, performer);
                    }
                }
            }
        }
        // If its only been mapped by an automated process, all with same date
        if (mappingDateToPerformerMap.size() == 1) {
            for (String date : mappingDateToPerformerMap.keySet()) {
                Date newDate = null;
                try {
                    newDate = dt.parse(date);
                } catch (ParseException e) {
                    e.printStackTrace();
                }
                mappingSummary.setMappingDate(newDate);
                mappingSummary.setPerformer(mappingDateToPerformerMap.get(date));
            }
        }
    }
    return mappingSummary;
}

Example 29 with Association

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

the class SingleSnpMultiSnpAssociationService method createAssociation.

public Association createAssociation(SnpAssociationStandardMultiForm form) {
    // Set common string, boolean and float association attributes
    Association association = setCommonAssociationElements(form);
    association.setSnpInteraction(false);
    // Add loci to association, for multi-snp and standard snps we assume their is only one locus
    Collection<Locus> loci = new ArrayList<>();
    Locus locus = new Locus();
    // Set locus description and haplotype count
    // Set this number to the number of rows entered by curator
    Integer numberOfRows = form.getSnpFormRows().size();
    if (numberOfRows > 1) {
        locus.setHaplotypeSnpCount(numberOfRows);
        association.setMultiSnpHaplotype(true);
    }
    if (form.getMultiSnpHaplotypeDescr() != null && !form.getMultiSnpHaplotypeDescr().isEmpty()) {
        locus.setDescription(form.getMultiSnpHaplotypeDescr());
    } else {
        if (numberOfRows > 1) {
            locus.setDescription(numberOfRows + "-SNP haplotype");
        } else {
            locus.setDescription("Single variant");
        }
    }
    // Create gene from each string entered, may sure to check pre-existence
    Collection<String> authorReportedGenes = form.getAuthorReportedGenes();
    Collection<Gene> locusGenes = lociAttributesService.createGene(authorReportedGenes);
    // Set locus genes
    locus.setAuthorReportedGenes(locusGenes);
    // Handle rows entered for haplotype by curator
    Collection<SnpFormRow> rows = form.getSnpFormRows();
    Collection<RiskAllele> locusRiskAlleles = new ArrayList<>();
    for (SnpFormRow row : rows) {
        // Create snps from row information
        String curatorEnteredSNP = row.getSnp();
        SingleNucleotidePolymorphism snp = lociAttributesService.createSnp(curatorEnteredSNP);
        // Get the curator entered risk allele
        String curatorEnteredRiskAllele = row.getStrongestRiskAllele();
        // Create a new risk allele and assign newly created snp
        RiskAllele riskAllele = lociAttributesService.createRiskAllele(curatorEnteredRiskAllele, snp);
        // If association is not a multi-snp haplotype save frequency to risk allele
        if (!form.getMultiSnpHaplotype()) {
            riskAllele.setRiskFrequency(form.getRiskFrequency());
        }
        // Check for proxies and if we have one create a proxy snps
        if (row.getProxySnps() != null && !row.getProxySnps().isEmpty()) {
            Collection<SingleNucleotidePolymorphism> riskAlleleProxySnps = new ArrayList<>();
            for (String curatorEnteredProxySnp : row.getProxySnps()) {
                SingleNucleotidePolymorphism proxySnp = lociAttributesService.createSnp(curatorEnteredProxySnp);
                riskAlleleProxySnps.add(proxySnp);
            }
            riskAllele.setProxySnps(riskAlleleProxySnps);
        }
        locusRiskAlleles.add(riskAllele);
    }
    // Assign all created risk alleles to locus
    locus.setStrongestRiskAlleles(locusRiskAlleles);
    // Add locus to collection and link to our association
    loci.add(locus);
    association.setLoci(loci);
    return association;
}

Example 30 with Association

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

the class SnpAssociationFormService method setCommonAssociationElements.

/**
     * Set common association attributes
     *
     * @return Form, contains details of association to create
     */
default default Association setCommonAssociationElements(SnpAssociationForm form) {
    Association association = new Association();
    // Set common string, boolean and float association attributes
    association.setSnpType(form.getSnpType());
    association.setSnpApproved(form.getSnpApproved());
    association.setStandardError(form.getStandardError());
    // Add collection of EFO traits
    association.setEfoTraits(form.getEfoTraits());
    // Set mantissa and exponent
    association.setPvalueMantissa(form.getPvalueMantissa());
    association.setPvalueExponent(form.getPvalueExponent());
    // Set OR/Beta values
    association.setOrPerCopyNum(form.getOrPerCopyNum());
    association.setOrPerCopyRecip(form.getOrPerCopyRecip());
    association.setBetaNum(form.getBetaNum());
    association.setBetaDirection(form.getBetaDirection());
    // Tidy up common string values
    if (form.getPvalueDescription() != null) {
        association.setPvalueDescription(form.getPvalueDescription().trim());
    }
    if (form.getRange() != null) {
        association.setRange(form.getRange().trim());
    }
    if (form.getDescription() != null) {
        association.setDescription(form.getDescription().trim());
    }
    if (form.getRiskFrequency() != null) {
        association.setRiskFrequency(form.getRiskFrequency().trim());
    }
    if (form.getOrPerCopyRecipRange() != null) {
        association.setOrPerCopyRecipRange(form.getOrPerCopyRecipRange().trim());
    }
    if (form.getBetaUnit() != null) {
        association.setBetaUnit(form.getBetaUnit().trim());
    }
    return association;
}