Examples with Source org.orcid.jaxb.model.common_v2.Source used on opensource projects

Example 46 with Source

use of org.orcid.jaxb.model.common_v2.Source in project h2o-2 by h2oai.

the class GLMTest2 method testProximal.

@Test
public void testProximal() {
    //    glmnet's result:
    //    res2 <- glmnet(x=M,y=D$CAPSULE,lower.limits=-.5,upper.limits=.5,family='binomial')
    //    res2$beta[,58]
    //    AGE        RACE          DPROS       PSA         VOL         GLEASON
    //    -0.00616326 -0.50000000  0.50000000  0.03628192 -0.01249324  0.50000000 //    res2$a0[100]
    //    res2$a0[58]
    //    s57
    //    -4.155864
    //    lambda = 0.001108, null dev =  512.2888, res dev = 379.7597
    Key parsed = Key.make("prostate_parsed");
    Key modelKey = Key.make("prostate_model");
    GLMModel model = null;
    Frame fr = getFrameForFile(parsed, "smalldata/logreg/prostate.csv", new String[] { "ID" }, "CAPSULE");
    Key k = Key.make("rebalanced");
    H2O.submitTask(new RebalanceDataSet(fr, k, 64)).join();
    fr.delete();
    fr = DKV.get(k).get();
    fr.remove("ID");
    Key betaConsKey = Key.make("beta_constraints");
    //String[] cfs1 = new String[]{"RACE", "AGE", "DPROS", "DCAPS", "PSA", "VOL", "GLEASON","Intercept"};
    //double[] vals = new double[]{0, 0, 0.54788332,0.53816534, 0.02380097, 0, 0.98115670,-8.945984};
    // [AGE, RACE, DPROS, DCAPS, PSA, VOL, GLEASON, Intercept]
    FVecTest.makeByteVec(betaConsKey, "names, beta_given, rho\n AGE, 0.1, 1\nRACE, -0.1, 1 \n DPROS, 10, 1 \n DCAPS, -10, 1 \n PSA, 0, 1\n VOL, 0, 1\nGLEASON, 0, 1\n Intercept, 0, 0 \n");
    Frame betaConstraints = ParseDataset2.parse(parsed, new Key[] { betaConsKey });
    try {
        // H2O differs on intercept and race, same residual deviance though
        GLM2.Source src = new GLM2.Source((Frame) fr.clone(), fr.vec("CAPSULE"), false, true);
        //.setHighAccuracy().doInit().fork().get();
        new GLM2("GLM offset test on prostate.", Key.make(), modelKey, src, Family.binomial).setNonNegative(false).setRegularization(new double[] { 0 }, new double[] { 0.000 }).setBetaConstraints(betaConstraints).setHighAccuracy().doInit().fork().get();
        model = DKV.get(modelKey).get();
        fr.add("CAPSULE", fr.remove("CAPSULE"));
        DataInfo dinfo = new DataInfo(fr, 1, true, false, TransformType.NONE, DataInfo.TransformType.NONE);
        GLMIterationTask glmt = new GLMTask.GLMIterationTask(0, null, dinfo, new GLMParams(Family.binomial), false, true, true, model.beta(), 0, 1.0 / 380, ModelUtils.DEFAULT_THRESHOLDS, null).doAll(dinfo._adaptedFrame);
        double[] beta = model.beta();
        double[] grad = glmt.gradient(0, 0);
        for (int i = 0; i < beta.length; ++i) Assert.assertEquals(0, grad[i] + betaConstraints.vec("rho").at(i) * (beta[i] - betaConstraints.vec("beta_given").at(i)), 1e-8);
        // now standardized
        src = new GLM2.Source((Frame) fr.clone(), fr.vec("CAPSULE"), true, true);
        //.setHighAccuracy().doInit().fork().get();
        new GLM2("GLM offset test on prostate.", Key.make(), modelKey, src, Family.binomial).setNonNegative(false).setRegularization(new double[] { 0 }, new double[] { 0.000 }).setBetaConstraints(betaConstraints).setHighAccuracy().doInit().fork().get();
        model = DKV.get(modelKey).get();
        fr.add("CAPSULE", fr.remove("CAPSULE"));
        dinfo = new DataInfo(fr, 1, true, false, TransformType.STANDARDIZE, DataInfo.TransformType.NONE);
        glmt = new GLMTask.GLMIterationTask(0, null, dinfo, new GLMParams(Family.binomial), false, true, true, model.norm_beta(0), 0, 1.0 / 380, ModelUtils.DEFAULT_THRESHOLDS, null).doAll(dinfo._adaptedFrame);
        double[] beta2 = model.norm_beta(0);
        double[] grad2 = glmt.gradient(0, 0);
        for (int i = 0; i < beta.length - 1; ++i) Assert.assertEquals("grad[" + i + "] != 0", 0, grad2[i] + betaConstraints.vec("rho").at(i) * (beta2[i] - betaConstraints.vec("beta_given").at(i) * dinfo._adaptedFrame.vec(i).sigma()), 1e-8);
        Assert.assertEquals("grad[intercept] != 0", 0, grad2[grad2.length - 1], 1e-8);
    } finally {
        fr.delete();
        if (model != null)
            model.delete();
    }
}

Example 47 with Source

use of org.orcid.jaxb.model.common_v2.Source in project h2o-2 by h2oai.

the class GLMTest2 method testPoissonRegression.

/**
  * Test Poisson regression on simple and small synthetic dataset.
  * Equation is: y = exp(x+1);
  */
@Test
public void testPoissonRegression() throws InterruptedException, ExecutionException {
    Key raw = Key.make("poisson_test_data_raw");
    Key parsed = Key.make("poisson_test_data_parsed");
    Key modelKey = Key.make("poisson_test");
    GLMModel model = null;
    Frame fr = null;
    try {
        // make data so that the expected coefficients is icept = col[0] = 1.0
        FVecTest.makeByteVec(raw, "x,y\n0,2\n1,4\n2,8\n3,16\n4,32\n5,64\n6,128\n7,256");
        fr = ParseDataset2.parse(parsed, new Key[] { raw });
        new GLM2("GLM test of poisson regression.", Key.make(), modelKey, new Source(fr, fr.lastVec(), false), Family.poisson).setRegularization(new double[] { 0 }, new double[] { 0 }).doInit().fork().get();
        model = DKV.get(modelKey).get();
        for (double c : model.beta()) assertEquals(Math.log(2), c, 1e-4);
        // Test 2, example from http://www.biostat.umn.edu/~dipankar/bmtry711.11/lecture_13.pdf
        //new byte []{1,2,3,4,5,6,7,8, 9, 10,11,12,13,14},
        //     new byte []{0,1,2,3,1,4,9,18,23,31,20,25,37,45});
        model.delete();
        fr.delete();
        FVecTest.makeByteVec(raw, "x,y\n1,0\n2,1\n3,2\n4,3\n5,1\n6,4\n7,9\n8,18\n9,23\n10,31\n11,20\n12,25\n13,37\n14,45\n");
        fr = ParseDataset2.parse(parsed, new Key[] { raw });
        new GLM2("GLM test of poisson regression(2).", Key.make(), modelKey, new Source(fr, fr.lastVec(), false), Family.poisson).setRegularization(new double[] { 0 }, new double[] { 0 }).doInit().fork().get();
        model = DKV.get(modelKey).get();
        testHTML(model);
        assertEquals(0.3396, model.beta()[1], 5e-3);
        assertEquals(0.2565, model.beta()[0], 5e-3);
    } finally {
        if (fr != null)
            fr.delete();
        if (model != null)
            model.delete();
    }
}

Example 48 with Source

use of org.orcid.jaxb.model.common_v2.Source in project ORCID-Source by ORCID.

the class ProfileKeywordManagerImpl method updateKeyword.

@Override
@Transactional
public Keyword updateKeyword(String orcid, Long putCode, Keyword keyword, boolean isApiRequest) {
    SourceEntity sourceEntity = sourceManager.retrieveSourceEntity();
    ProfileKeywordEntity updatedEntity = profileKeywordDao.getProfileKeyword(orcid, putCode);
    Visibility originalVisibility = Visibility.fromValue(updatedEntity.getVisibility().value());
    //Save the original source
    String existingSourceId = updatedEntity.getSourceId();
    String existingClientSourceId = updatedEntity.getClientSourceId();
    // Validate the keyword
    PersonValidator.validateKeyword(keyword, sourceEntity, false, isApiRequest, originalVisibility);
    // Validate it is not duplicated
    List<ProfileKeywordEntity> existingKeywords = profileKeywordDao.getProfileKeywors(orcid, getLastModified(orcid));
    for (ProfileKeywordEntity existing : existingKeywords) {
        if (isDuplicated(existing, keyword, sourceEntity)) {
            Map<String, String> params = new HashMap<String, String>();
            params.put("type", "keyword");
            params.put("value", keyword.getContent());
            throw new OrcidDuplicatedElementException(params);
        }
    }
    orcidSecurityManager.checkSource(updatedEntity);
    adapter.toProfileKeywordEntity(keyword, updatedEntity);
    updatedEntity.setLastModified(new Date());
    //Be sure it doesn't overwrite the source
    updatedEntity.setSourceId(existingSourceId);
    updatedEntity.setClientSourceId(existingClientSourceId);
    profileKeywordDao.merge(updatedEntity);
    return adapter.toKeyword(updatedEntity);
}

Example 49 with Source

use of org.orcid.jaxb.model.common_v2.Source in project ORCID-Source by ORCID.

the class OrcidSecurityManagerImpl method checkAndFilter.

/**
     * Check the permissions of a request over an element. Private
     * implementation that will also include a parameter that indicates if we
     * should check the token or, if it was already checked previously
     * 
     * @param orcid
     *            The user owner of the element
     * @param element
     *            The element to check
     * @param requiredScope
     *            The required scope to access this element
     * @param tokenAlreadyChecked
     *            Indicates if the token was already checked previously, so, we
     *            don't expend time checking it again
     * @throws OrcidUnauthorizedException
     *             In case the token used was not issued for the owner of the
     *             element
     * @throws OrcidAccessControlException
     *             In case the request doesn't have the required scopes
     * @throws OrcidVisibilityException
     *             In case the element is not visible due the visibility
     */
private void checkAndFilter(String orcid, VisibilityType element, ScopePathType requiredScope, boolean tokenAlreadyChecked) {
    if (element == null) {
        return;
    }
    // Check the token was issued for this user
    if (!tokenAlreadyChecked) {
        isMyToken(orcid);
    }
    // Check if the client is the source of the element
    if (element instanceof Filterable) {
        Filterable filterable = (Filterable) element;
        OAuth2Authentication oAuth2Authentication = getOAuth2Authentication();
        if (oAuth2Authentication != null) {
            OAuth2Request authorizationRequest = oAuth2Authentication.getOAuth2Request();
            String clientId = authorizationRequest.getClientId();
            if (clientId.equals(filterable.retrieveSourcePath())) {
                // The client doing the request is the source of the element
                return;
            }
        }
    }
    // /read-public scope
    if (Visibility.PUBLIC.equals(element.getVisibility())) {
        try {
            checkScopes(ScopePathType.READ_PUBLIC);
            // can return it
            return;
        } catch (OrcidAccessControlException e) {
        // Just continue filtering
        }
    }
    // Filter
    filter(element, requiredScope);
}

Example 50 with Source

use of org.orcid.jaxb.model.common_v2.Source in project ORCID-Source by ORCID.

the class FundingForm method valueOf.

public static FundingForm valueOf(Funding funding) {
    FundingForm result = new FundingForm();
    result.setDateSortString(PojoUtil.createDateSortString(funding.getStartDate(), funding.getEndDate()));
    if (funding.getPutCode() != null)
        result.setPutCode(Text.valueOf(funding.getPutCode()));
    if (funding.getAmount() != null) {
        if (StringUtils.isNotEmpty(funding.getAmount().getContent())) {
            String cleanNumber = funding.getAmount().getContent().trim();
            result.setAmount(Text.valueOf(cleanNumber));
        }
        if (funding.getAmount().getCurrencyCode() != null)
            result.setCurrencyCode(Text.valueOf(funding.getAmount().getCurrencyCode()));
        else
            result.setCurrencyCode(new Text());
    } else {
        result.setAmount(new Text());
        result.setCurrencyCode(new Text());
    }
    if (StringUtils.isNotEmpty(funding.getDescription()))
        result.setDescription(Text.valueOf(funding.getDescription()));
    else
        result.setDescription(new Text());
    if (funding.getStartDate() != null)
        result.setStartDate(Date.valueOf(funding.getStartDate()));
    if (funding.getEndDate() != null)
        result.setEndDate(Date.valueOf(funding.getEndDate()));
    if (funding.getType() != null)
        result.setFundingType(Text.valueOf(funding.getType().value()));
    else
        result.setFundingType(new Text());
    if (funding.getOrganizationDefinedType() != null) {
        OrgDefinedFundingSubType OrgDefinedFundingSubType = new OrgDefinedFundingSubType();
        OrgDefinedFundingSubType.setSubtype(Text.valueOf(funding.getOrganizationDefinedType().getContent()));
        OrgDefinedFundingSubType.setAlreadyIndexed(false);
        result.setOrganizationDefinedFundingSubType(OrgDefinedFundingSubType);
    }
    Source source = funding.getSource();
    if (source != null) {
        result.setSource(source.retrieveSourcePath());
        if (source.getSourceName() != null) {
            result.setSourceName(source.getSourceName().getContent());
        }
    }
    if (funding.getTitle() != null) {
        FundingTitleForm fundingTitle = new FundingTitleForm();
        if (funding.getTitle().getTitle() != null)
            fundingTitle.setTitle(Text.valueOf(funding.getTitle().getTitle().getContent()));
        else
            fundingTitle.setTitle(new Text());
        if (funding.getTitle().getTranslatedTitle() != null) {
            TranslatedTitleForm translatedTitle = new TranslatedTitleForm();
            translatedTitle.setContent(funding.getTitle().getTranslatedTitle().getContent());
            translatedTitle.setLanguageCode(funding.getTitle().getTranslatedTitle().getLanguageCode());
            fundingTitle.setTranslatedTitle(translatedTitle);
        }
        result.setFundingTitle(fundingTitle);
    } else {
        FundingTitleForm fundingTitle = new FundingTitleForm();
        fundingTitle.setTitle(new Text());
        result.setFundingTitle(fundingTitle);
    }
    if (funding.getUrl() != null)
        result.setUrl(Text.valueOf(funding.getUrl().getValue()));
    else
        result.setUrl(new Text());
    if (funding.getVisibility() != null)
        result.setVisibility(Visibility.valueOf(funding.getVisibility()));
    // Set the disambiguated organization
    Organization organization = funding.getOrganization();
    result.setFundingName(Text.valueOf(organization.getName()));
    DisambiguatedOrganization disambiguatedOrganization = organization.getDisambiguatedOrganization();
    if (disambiguatedOrganization != null) {
        if (StringUtils.isNotEmpty(disambiguatedOrganization.getDisambiguatedOrganizationIdentifier())) {
            result.setDisambiguatedFundingSourceId(Text.valueOf(disambiguatedOrganization.getDisambiguatedOrganizationIdentifier()));
            result.setDisambiguationSource(Text.valueOf(disambiguatedOrganization.getDisambiguationSource()));
        }
    }
    OrganizationAddress organizationAddress = organization.getAddress();
    if (organizationAddress != null) {
        if (!PojoUtil.isEmpty(organizationAddress.getCity()))
            result.setCity(Text.valueOf(organizationAddress.getCity()));
        else
            result.setCity(new Text());
        if (!PojoUtil.isEmpty(organizationAddress.getRegion()))
            result.setRegion(Text.valueOf(organizationAddress.getRegion()));
        else
            result.setRegion(new Text());
        if (organizationAddress.getCountry() != null)
            result.setCountry(Text.valueOf(organizationAddress.getCountry().value()));
        else
            result.setCountry(new Text());
    } else {
        result.setCountry(new Text());
        result.setCity(new Text());
        result.setRegion(new Text());
    }
    // Set contributors
    if (funding.getContributors() != null) {
        List<Contributor> contributors = new ArrayList<Contributor>();
        for (FundingContributor fContributor : funding.getContributors().getContributor()) {
            Contributor contributor = Contributor.valueOf(fContributor);
            contributors.add(contributor);
        }
        result.setContributors(contributors);
    }
    List<FundingExternalIdentifierForm> externalIdentifiersList = new ArrayList<FundingExternalIdentifierForm>();
    // Set external identifiers 
    if (funding.getExternalIdentifiers() != null) {
        for (ExternalID fExternalIdentifier : funding.getExternalIdentifiers().getExternalIdentifier()) {
            FundingExternalIdentifierForm fundingExternalIdentifierForm = FundingExternalIdentifierForm.valueOf(fExternalIdentifier);
            externalIdentifiersList.add(fundingExternalIdentifierForm);
        }
    }
    result.setExternalIdentifiers(externalIdentifiersList);
    result.setCreatedDate(Date.valueOf(funding.getCreatedDate()));
    result.setLastModified(Date.valueOf(funding.getLastModifiedDate()));
    return result;
}