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chen-regenanthonysena
chen-regen
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anthonysena
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Cohort reporting additions (#230)
Cohort reporting additions #223
1 parent a064b5b commit 5e67ca7

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7 files changed

+1113
-2
lines changed

7 files changed

+1113
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lines changed

‎src/main/java/org/ohdsi/webapi/cohortresults/DataCompletenessAttr.java

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package org.ohdsi.webapi.cohortresults;
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/**
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*
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*/
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public class DataCompletenessAttr {
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private String covariance;
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private float genderP;
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private float raceP;
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private float ethP;
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/**
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* @return the covariance
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*/
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public String getCovariance() {
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return covariance;
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}
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/**
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* @param covariance the covariance to set
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*/
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public void setCovariance(String covariance) {
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this.covariance = covariance;
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}
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/**
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* @return the genderP
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*/
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public float getGenderP() {
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return genderP;
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}
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/**
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* @param genderP the genderP to set
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*/
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public void setGenderP(float genderP) {
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this.genderP = genderP;
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}
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/**
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* @return the raceP
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*/
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public float getRaceP() {
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return raceP;
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}
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/**
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* @param raceP the raceP to set
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*/
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public void setRaceP(float raceP) {
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this.raceP = raceP;
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}
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/**
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* @return the ethP
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*/
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public float getEthP() {
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return ethP;
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}
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/**
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* @param ethP the ethP to set
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*/
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public void setEthP(float ethP) {
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this.ethP = ethP;
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}
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}

‎src/main/java/org/ohdsi/webapi/cohortresults/EntropyAttr.java

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package org.ohdsi.webapi.cohortresults;
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/**
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*
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*/
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public class EntropyAttr {
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private String date;
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private float entropy;
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private String insitution;
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/**
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* @return the date
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*/
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public String getDate() {
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return date;
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}
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/**
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* @param date the date to set
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*/
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public void setDate(String date) {
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this.date = date;
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}
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/**
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* @return the entropy
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*/
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public float getEntropy() {
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return entropy;
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}
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/**
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* @param entropy the entropy to set
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*/
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public void setEntropy(float entropy) {
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this.entropy = entropy;
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}
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/**
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* @return the insitution
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*/
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public String getInsitution() {
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return insitution;
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}
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/**
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* @param insitution the insitution to set
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*/
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public void setInsitution(String insitution) {
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this.insitution = insitution;
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}
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}

‎src/main/java/org/ohdsi/webapi/cohortresults/mapper/AnalysisResultsMapper.java

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package org.ohdsi.webapi.cohortresults.mapper;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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import org.ohdsi.webapi.model.results.AnalysisResults;
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import org.springframework.jdbc.core.RowMapper;
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/**
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*
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*/
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public class AnalysisResultsMapper implements RowMapper<AnalysisResults> {
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/**
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* @see org.springframework.jdbc.core.RowMapper#mapRow(java.sql.ResultSet, int)
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*/
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@Override
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public AnalysisResults mapRow(ResultSet rs, int rowNum) throws SQLException {
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AnalysisResults ar = new AnalysisResults();
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ar.setAnalysisId(rs.getInt("ANALYSIS_ID"));
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ar.setCohortDefinitionId(rs.getInt("COHORT_DEFINITION_ID"));
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ar.setStratum1(rs.getString("STRATUM_1"));
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ar.setStratum2(rs.getString("STRATUM_2"));
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ar.setStratum3(rs.getString("STRATUM_3"));
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ar.setStratum4(rs.getString("STRATUM_4"));
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ar.setStratum5(rs.getString("STRATUM_5"));
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ar.setCountValue(rs.getInt("count_value"));
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return ar;
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}
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}

‎src/main/java/org/ohdsi/webapi/service/CohortResultsService.java

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@@ -4,6 +4,7 @@
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import java.sql.SQLException;
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import java.util.ArrayList;
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import java.util.Collection;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Map;
@@ -44,12 +45,16 @@
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import org.ohdsi.webapi.cohortresults.CohortSpecificSummary;
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import org.ohdsi.webapi.cohortresults.CohortSpecificTreemap;
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import org.ohdsi.webapi.cohortresults.CohortVisitsDrilldown;
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import org.ohdsi.webapi.cohortresults.DataCompletenessAttr;
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import org.ohdsi.webapi.cohortresults.EntropyAttr;
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import org.ohdsi.webapi.cohortresults.HierarchicalConceptRecord;
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import org.ohdsi.webapi.cohortresults.ScatterplotRecord;
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import org.ohdsi.webapi.cohortresults.VisualizationData;
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import org.ohdsi.webapi.cohortresults.VisualizationDataRepository;
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import org.ohdsi.webapi.cohortresults.mapper.AnalysisResultsMapper;
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import org.ohdsi.webapi.helper.ResourceHelper;
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import org.ohdsi.webapi.model.results.Analysis;
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import org.ohdsi.webapi.model.results.AnalysisResults;
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import org.ohdsi.webapi.source.Source;
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import org.ohdsi.webapi.source.SourceDaimon;
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import org.ohdsi.webapi.util.SessionUtils;
@@ -1595,7 +1600,130 @@ public List<CohortAttribute> getHeraclesHeel(@PathParam("id") final int id,
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return attrs;
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}
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public List<AnalysisResults> getCohortAnalysesForDataCompleteness(@PathParam("id") final int id,
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@PathParam("sourceKey") String sourceKey) {
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String sql = null;
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sql = ResourceHelper.GetResourceAsString("/resources/cohortresults/sql/datacompleteness/getCohortDataCompleteness.sql");
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Source source = getSourceRepository().findBySourceKey(sourceKey);
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String resultsTableQualifier = source.getTableQualifier(SourceDaimon.DaimonType.Results);
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sql = SqlRender.renderSql(sql, new String[]{"tableQualifier", "cohortDefinitionId"},
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new String[]{resultsTableQualifier, String.valueOf(id)});
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sql = SqlTranslate.translateSql(sql, getSourceDialect(), source.getSourceDialect());
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AnalysisResultsMapper arm = new AnalysisResultsMapper();
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return getSourceJdbcTemplate(source).query(sql, arm);
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}
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@GET
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@Path("{sourceKey}/{id}/datacompleteness")
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@Produces(MediaType.APPLICATION_JSON)
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public List<DataCompletenessAttr> getDataCompleteness(@PathParam("id") final int id,
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@PathParam("sourceKey") String sourceKey) {
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List<AnalysisResults> arl = this.getCohortAnalysesForDataCompleteness(id, sourceKey);
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List<DataCompletenessAttr> dcal = new ArrayList<DataCompletenessAttr>();
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Map<Integer, AnalysisResults> resultMap = new HashMap<Integer, AnalysisResults>();
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for(AnalysisResults ar : arl){
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resultMap.put(ar.getAnalysisId(), ar);
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}
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DataCompletenessAttr aca = new DataCompletenessAttr();
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aca.setCovariance("0~10");
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aca.setGenderP(Float.parseFloat(resultMap.get(2001).getStratum1()));
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aca.setRaceP(Float.parseFloat(resultMap.get(2011).getStratum1()));
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aca.setEthP(Float.parseFloat(resultMap.get(2021).getStratum1()));
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dcal.add(aca);
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aca = new DataCompletenessAttr();
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aca.setCovariance("10~20");
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aca.setGenderP(Float.parseFloat(resultMap.get(2002).getStratum1()));
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aca.setRaceP(Float.parseFloat(resultMap.get(2012).getStratum1()));
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aca.setEthP(Float.parseFloat(resultMap.get(2022).getStratum1()));
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dcal.add(aca);
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aca = new DataCompletenessAttr();
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aca.setCovariance("20~30");
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aca.setGenderP(Float.parseFloat(resultMap.get(2003).getStratum1()));
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aca.setRaceP(Float.parseFloat(resultMap.get(2013).getStratum1()));
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aca.setEthP(Float.parseFloat(resultMap.get(2023).getStratum1()));
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dcal.add(aca);
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aca = new DataCompletenessAttr();
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aca.setCovariance("30~40");
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aca.setGenderP(Float.parseFloat(resultMap.get(2004).getStratum1()));
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aca.setRaceP(Float.parseFloat(resultMap.get(2014).getStratum1()));
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aca.setEthP(Float.parseFloat(resultMap.get(2024).getStratum1()));
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dcal.add(aca);
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aca = new DataCompletenessAttr();
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aca.setCovariance("40~50");
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aca.setGenderP(Float.parseFloat(resultMap.get(2005).getStratum1()));
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aca.setRaceP(Float.parseFloat(resultMap.get(2015).getStratum1()));
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aca.setEthP(Float.parseFloat(resultMap.get(2025).getStratum1()));
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dcal.add(aca);
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aca = new DataCompletenessAttr();
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aca.setCovariance("50~60");
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aca.setGenderP(Float.parseFloat(resultMap.get(2006).getStratum1()));
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aca.setRaceP(Float.parseFloat(resultMap.get(2016).getStratum1()));
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aca.setEthP(Float.parseFloat(resultMap.get(2026).getStratum1()));
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dcal.add(aca);
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aca = new DataCompletenessAttr();
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aca.setCovariance("60+");
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aca.setGenderP(Float.parseFloat(resultMap.get(2007).getStratum1()));
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aca.setRaceP(Float.parseFloat(resultMap.get(2017).getStratum1()));
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aca.setEthP(Float.parseFloat(resultMap.get(2027).getStratum1()));
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dcal.add(aca);
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return dcal;
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}
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public List<AnalysisResults> getCohortAnalysesEntropy(final int id, String sourceKey) {
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String sql = null;
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sql = ResourceHelper
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.GetResourceAsString("/resources/cohortresults/sql/entropy/getEntropy.sql");
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Source source = getSourceRepository().findBySourceKey(sourceKey);
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String resultsTableQualifier = source.getTableQualifier(SourceDaimon.DaimonType.Results);
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sql = SqlRender.renderSql(sql, new String[] { "tableQualifier", "cohortDefinitionId" },
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new String[] { resultsTableQualifier, String.valueOf(id) });
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sql = SqlTranslate.translateSql(sql, getSourceDialect(), source.getSourceDialect());
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AnalysisResultsMapper arm = new AnalysisResultsMapper();
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return getSourceJdbcTemplate(source).query(sql, arm);
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}
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@GET
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@Path("{sourceKey}/{id}/entropy")
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@Produces(MediaType.APPLICATION_JSON)
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public List<EntropyAttr> getEntropy(@PathParam("id") final int id,
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@PathParam("sourceKey") String sourceKey) {
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List<AnalysisResults> arl = this.getCohortAnalysesEntropy(id, sourceKey);
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List<EntropyAttr> el = new ArrayList<EntropyAttr>();
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for(AnalysisResults ar : arl){
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EntropyAttr ea = new EntropyAttr();
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ea.setDate(ar.getStratum1());
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ea.setEntropy(Float.parseFloat(ar.getStratum2()));
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el.add(ea);
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}
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return el;
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}
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private String JoinArray(final String[] array) {
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String result = "";
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