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Merge pull request #528 from wcmc-its/development
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Fix for #527
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@paulalbert1
paulalbert1 authored Apr 4, 2024
2 parents 095905c + acb75d6 commit dd525c3
Showing 1 changed file with 127 additions and 99 deletions.
226 changes: 127 additions & 99 deletions src/main/java/reciter/controller/ReCiterController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -30,6 +30,7 @@
import java.util.Map;
import java.util.Set;
import java.util.stream.Collectors;
import java.util.Arrays;

import org.apache.commons.lang3.StringUtils;
import org.slf4j.Logger;
Expand Down Expand Up @@ -490,113 +491,140 @@ public ResponseEntity runFeatureGenerator(@RequestParam(value = "uid") String ui
analysis != null
&&
(useGoldStandard == UseGoldStandard.AS_EVIDENCE || useGoldStandard == null)) {//This was added to ensure to use analysis results only in evidence mode
List<Long> finalArticles = analysis.getReCiterFeature().getReCiterArticleFeatures().stream().map(article -> article.getPmid()).collect(Collectors.toList());
GoldStandard goldStandard = dynamoDbGoldStandardService.findByUid(uid);
List<Long> finalArticles =null;
if(analysis.getReCiterFeature()!=null && analysis.getReCiterFeature().getReCiterArticleFeatures()!=null)
{
finalArticles = analysis.getReCiterFeature().getReCiterArticleFeatures().stream().map(article -> article.getPmid()).collect(Collectors.toList());
}
else
{
finalArticles = new ArrayList<Long>(Arrays.asList(0L));;
}
GoldStandard goldStandard = dynamoDbGoldStandardService.findByUid(uid);
List<Long> knownPmids = null;
if (goldStandard == null) {
knownPmids = new ArrayList<>();
} else {
knownPmids = goldStandard.getKnownPmids();
}
//Count pending pubs
analysis.getReCiterFeature().setCountPendingArticles(analysis.getReCiterFeature().getReCiterArticleFeatures().stream()
.filter(reCiterArticleFeature -> (reCiterArticleFeature.getTotalArticleScoreStandardized() >= totalScore
&&
reCiterArticleFeature.getUserAssertion() == PublicationFeedback.NULL))
.count());
if(analysis.getReCiterFeature()!=null && analysis.getReCiterFeature().getReCiterArticleFeatures()!=null)
{
analysis.getReCiterFeature().setCountPendingArticles(analysis.getReCiterFeature().getReCiterArticleFeatures().stream()
.filter(reCiterArticleFeature -> (reCiterArticleFeature.getTotalArticleScoreStandardized() >= totalScore
&&
reCiterArticleFeature.getUserAssertion() == PublicationFeedback.NULL))
.count());
}
else if(analysis.getReCiterFeature()!=null)
{
analysis.getReCiterFeature().setCountPendingArticles(0);
}
//All the results are filtered based on filterByFeedback
if(filterByFeedback == FilterFeedbackType.ALL || filterByFeedback == null) {
analysis.getReCiterFeature().setReCiterArticleFeatures(analysis.getReCiterFeature().getReCiterArticleFeatures().stream()
.filter(reCiterArticleFeature -> (reCiterArticleFeature.getTotalArticleScoreStandardized() >= totalScore
&&
reCiterArticleFeature.getUserAssertion() == PublicationFeedback.NULL)
||
reCiterArticleFeature.getUserAssertion() == PublicationFeedback.ACCEPTED
||
reCiterArticleFeature.getUserAssertion() == PublicationFeedback.REJECTED
)
.collect(Collectors.toList()));
List<Long> selectedArticles = analysis.getReCiterFeature().getReCiterArticleFeatures().stream().map(article -> article.getPmid()).collect(Collectors.toList());
Analysis featureAnalysis = Analysis.performAnalysis(finalArticles, selectedArticles, knownPmids);
analysis.getReCiterFeature().setCountSuggestedArticles(analysis.getReCiterFeature().getReCiterArticleFeatures().size());
analysis.getReCiterFeature().setPrecision(featureAnalysis.getPrecision());
analysis.getReCiterFeature().setRecall(featureAnalysis.getRecall());
analysis.getReCiterFeature().setOverallAccuracy(featureAnalysis.getAccuracy());
} else if(filterByFeedback == FilterFeedbackType.ACCEPTED_ONLY) {
analysis.getReCiterFeature().setReCiterArticleFeatures(analysis.getReCiterFeature().getReCiterArticleFeatures().stream()
.filter(reCiterArticleFeature -> reCiterArticleFeature.getUserAssertion() == PublicationFeedback.ACCEPTED)
.collect(Collectors.toList()));
List<Long> selectedArticles = analysis.getReCiterFeature().getReCiterArticleFeatures().stream().map(article -> article.getPmid()).collect(Collectors.toList());
Analysis featureAnalysis = Analysis.performAnalysis(finalArticles, selectedArticles, knownPmids);
analysis.getReCiterFeature().setCountSuggestedArticles(analysis.getReCiterFeature().getReCiterArticleFeatures().size());
analysis.getReCiterFeature().setPrecision(featureAnalysis.getPrecision());
analysis.getReCiterFeature().setRecall(featureAnalysis.getRecall());
analysis.getReCiterFeature().setOverallAccuracy(featureAnalysis.getAccuracy());
} else if(filterByFeedback == FilterFeedbackType.REJECTED_ONLY) {
analysis.getReCiterFeature().setReCiterArticleFeatures(analysis.getReCiterFeature().getReCiterArticleFeatures().stream()
.filter(reCiterArticleFeature -> reCiterArticleFeature.getUserAssertion() == PublicationFeedback.REJECTED)
.collect(Collectors.toList()));
List<Long> selectedArticles = analysis.getReCiterFeature().getReCiterArticleFeatures().stream().map(article -> article.getPmid()).collect(Collectors.toList());
Analysis featureAnalysis = Analysis.performAnalysis(finalArticles, selectedArticles, knownPmids);
analysis.getReCiterFeature().setCountSuggestedArticles(analysis.getReCiterFeature().getReCiterArticleFeatures().size());
analysis.getReCiterFeature().setPrecision(featureAnalysis.getPrecision());
analysis.getReCiterFeature().setRecall(featureAnalysis.getRecall());
analysis.getReCiterFeature().setOverallAccuracy(featureAnalysis.getAccuracy());
} else if(filterByFeedback == FilterFeedbackType.ACCEPTED_AND_NULL) {
analysis.getReCiterFeature().setReCiterArticleFeatures(analysis.getReCiterFeature().getReCiterArticleFeatures().stream()
.filter(reCiterArticleFeature -> (reCiterArticleFeature.getTotalArticleScoreStandardized() >= totalScore
&&
reCiterArticleFeature.getUserAssertion() == PublicationFeedback.NULL)
||
reCiterArticleFeature.getUserAssertion() == PublicationFeedback.ACCEPTED
)
.collect(Collectors.toList()));
List<Long> selectedArticles = analysis.getReCiterFeature().getReCiterArticleFeatures().stream().map(article -> article.getPmid()).collect(Collectors.toList());
Analysis featureAnalysis = Analysis.performAnalysis(finalArticles, selectedArticles, knownPmids);
analysis.getReCiterFeature().setCountSuggestedArticles(analysis.getReCiterFeature().getReCiterArticleFeatures().size());
analysis.getReCiterFeature().setPrecision(featureAnalysis.getPrecision());
analysis.getReCiterFeature().setRecall(featureAnalysis.getRecall());
analysis.getReCiterFeature().setOverallAccuracy(featureAnalysis.getAccuracy());
} else if(filterByFeedback == FilterFeedbackType.REJECTED_AND_NULL) {
analysis.getReCiterFeature().setReCiterArticleFeatures(analysis.getReCiterFeature().getReCiterArticleFeatures().stream()
.filter(reCiterArticleFeature -> (reCiterArticleFeature.getTotalArticleScoreStandardized() >= totalScore
&&
reCiterArticleFeature.getUserAssertion() == PublicationFeedback.NULL)
||
reCiterArticleFeature.getUserAssertion() == PublicationFeedback.REJECTED
)
.collect(Collectors.toList()));
List<Long> selectedArticles = analysis.getReCiterFeature().getReCiterArticleFeatures().stream().map(article -> article.getPmid()).collect(Collectors.toList());
Analysis featureAnalysis = Analysis.performAnalysis(finalArticles, selectedArticles, knownPmids);
analysis.getReCiterFeature().setCountSuggestedArticles(analysis.getReCiterFeature().getReCiterArticleFeatures().size());
analysis.getReCiterFeature().setPrecision(featureAnalysis.getPrecision());
analysis.getReCiterFeature().setRecall(featureAnalysis.getRecall());
analysis.getReCiterFeature().setOverallAccuracy(featureAnalysis.getAccuracy());
} else if(filterByFeedback == FilterFeedbackType.ACCEPTED_AND_REJECTED) {
analysis.getReCiterFeature().setReCiterArticleFeatures(analysis.getReCiterFeature().getReCiterArticleFeatures().stream()
.filter(reCiterArticleFeature -> reCiterArticleFeature.getUserAssertion() == PublicationFeedback.ACCEPTED
||
reCiterArticleFeature.getUserAssertion() == PublicationFeedback.REJECTED)
.collect(Collectors.toList()));
List<Long> selectedArticles = analysis.getReCiterFeature().getReCiterArticleFeatures().stream().map(article -> article.getPmid()).collect(Collectors.toList());
Analysis featureAnalysis = Analysis.performAnalysis(finalArticles, selectedArticles, knownPmids);
analysis.getReCiterFeature().setCountSuggestedArticles(analysis.getReCiterFeature().getReCiterArticleFeatures().size());
analysis.getReCiterFeature().setPrecision(featureAnalysis.getPrecision());
analysis.getReCiterFeature().setRecall(featureAnalysis.getRecall());
analysis.getReCiterFeature().setOverallAccuracy(featureAnalysis.getAccuracy());
} else if(filterByFeedback == FilterFeedbackType.NULL) {
analysis.getReCiterFeature().setReCiterArticleFeatures(analysis.getReCiterFeature().getReCiterArticleFeatures().stream()
.filter(reCiterArticleFeature -> reCiterArticleFeature.getTotalArticleScoreStandardized() >= totalScore
&&
reCiterArticleFeature.getUserAssertion() == PublicationFeedback.NULL)
.collect(Collectors.toList()));
List<Long> selectedArticles = analysis.getReCiterFeature().getReCiterArticleFeatures().stream().map(article -> article.getPmid()).collect(Collectors.toList());
Analysis featureAnalysis = Analysis.performAnalysis(finalArticles, selectedArticles, knownPmids);
analysis.getReCiterFeature().setCountSuggestedArticles(analysis.getReCiterFeature().getReCiterArticleFeatures().size());
analysis.getReCiterFeature().setPrecision(featureAnalysis.getPrecision());
analysis.getReCiterFeature().setRecall(featureAnalysis.getRecall());
analysis.getReCiterFeature().setOverallAccuracy(featureAnalysis.getAccuracy());
}
if(analysis.getReCiterFeature()!=null && analysis.getReCiterFeature().getReCiterArticleFeatures()!=null)
{

if(filterByFeedback == FilterFeedbackType.ALL || filterByFeedback == null) {
analysis.getReCiterFeature().setReCiterArticleFeatures(analysis.getReCiterFeature().getReCiterArticleFeatures().stream()
.filter(reCiterArticleFeature -> (reCiterArticleFeature.getTotalArticleScoreStandardized() >= totalScore
&&
reCiterArticleFeature.getUserAssertion() == PublicationFeedback.NULL)
||
reCiterArticleFeature.getUserAssertion() == PublicationFeedback.ACCEPTED
||
reCiterArticleFeature.getUserAssertion() == PublicationFeedback.REJECTED
)
.collect(Collectors.toList()));
List<Long> selectedArticles = analysis.getReCiterFeature().getReCiterArticleFeatures().stream().map(article -> article.getPmid()).collect(Collectors.toList());
Analysis featureAnalysis = Analysis.performAnalysis(finalArticles, selectedArticles, knownPmids);
analysis.getReCiterFeature().setCountSuggestedArticles(analysis.getReCiterFeature().getReCiterArticleFeatures().size());
analysis.getReCiterFeature().setPrecision(featureAnalysis.getPrecision());
analysis.getReCiterFeature().setRecall(featureAnalysis.getRecall());
analysis.getReCiterFeature().setOverallAccuracy(featureAnalysis.getAccuracy());
} else if(filterByFeedback == FilterFeedbackType.ACCEPTED_ONLY) {
analysis.getReCiterFeature().setReCiterArticleFeatures(analysis.getReCiterFeature().getReCiterArticleFeatures().stream()
.filter(reCiterArticleFeature -> reCiterArticleFeature.getUserAssertion() == PublicationFeedback.ACCEPTED)
.collect(Collectors.toList()));
List<Long> selectedArticles = analysis.getReCiterFeature().getReCiterArticleFeatures().stream().map(article -> article.getPmid()).collect(Collectors.toList());
Analysis featureAnalysis = Analysis.performAnalysis(finalArticles, selectedArticles, knownPmids);
analysis.getReCiterFeature().setCountSuggestedArticles(analysis.getReCiterFeature().getReCiterArticleFeatures().size());
analysis.getReCiterFeature().setPrecision(featureAnalysis.getPrecision());
analysis.getReCiterFeature().setRecall(featureAnalysis.getRecall());
analysis.getReCiterFeature().setOverallAccuracy(featureAnalysis.getAccuracy());
} else if(filterByFeedback == FilterFeedbackType.REJECTED_ONLY) {
analysis.getReCiterFeature().setReCiterArticleFeatures(analysis.getReCiterFeature().getReCiterArticleFeatures().stream()
.filter(reCiterArticleFeature -> reCiterArticleFeature.getUserAssertion() == PublicationFeedback.REJECTED)
.collect(Collectors.toList()));
List<Long> selectedArticles = analysis.getReCiterFeature().getReCiterArticleFeatures().stream().map(article -> article.getPmid()).collect(Collectors.toList());
Analysis featureAnalysis = Analysis.performAnalysis(finalArticles, selectedArticles, knownPmids);
analysis.getReCiterFeature().setCountSuggestedArticles(analysis.getReCiterFeature().getReCiterArticleFeatures().size());
analysis.getReCiterFeature().setPrecision(featureAnalysis.getPrecision());
analysis.getReCiterFeature().setRecall(featureAnalysis.getRecall());
analysis.getReCiterFeature().setOverallAccuracy(featureAnalysis.getAccuracy());
} else if(filterByFeedback == FilterFeedbackType.ACCEPTED_AND_NULL) {
analysis.getReCiterFeature().setReCiterArticleFeatures(analysis.getReCiterFeature().getReCiterArticleFeatures().stream()
.filter(reCiterArticleFeature -> (reCiterArticleFeature.getTotalArticleScoreStandardized() >= totalScore
&&
reCiterArticleFeature.getUserAssertion() == PublicationFeedback.NULL)
||
reCiterArticleFeature.getUserAssertion() == PublicationFeedback.ACCEPTED
)
.collect(Collectors.toList()));
List<Long> selectedArticles = analysis.getReCiterFeature().getReCiterArticleFeatures().stream().map(article -> article.getPmid()).collect(Collectors.toList());
Analysis featureAnalysis = Analysis.performAnalysis(finalArticles, selectedArticles, knownPmids);
analysis.getReCiterFeature().setCountSuggestedArticles(analysis.getReCiterFeature().getReCiterArticleFeatures().size());
analysis.getReCiterFeature().setPrecision(featureAnalysis.getPrecision());
analysis.getReCiterFeature().setRecall(featureAnalysis.getRecall());
analysis.getReCiterFeature().setOverallAccuracy(featureAnalysis.getAccuracy());
} else if(filterByFeedback == FilterFeedbackType.REJECTED_AND_NULL) {
analysis.getReCiterFeature().setReCiterArticleFeatures(analysis.getReCiterFeature().getReCiterArticleFeatures().stream()
.filter(reCiterArticleFeature -> (reCiterArticleFeature.getTotalArticleScoreStandardized() >= totalScore
&&
reCiterArticleFeature.getUserAssertion() == PublicationFeedback.NULL)
||
reCiterArticleFeature.getUserAssertion() == PublicationFeedback.REJECTED
)
.collect(Collectors.toList()));
List<Long> selectedArticles = analysis.getReCiterFeature().getReCiterArticleFeatures().stream().map(article -> article.getPmid()).collect(Collectors.toList());
Analysis featureAnalysis = Analysis.performAnalysis(finalArticles, selectedArticles, knownPmids);
analysis.getReCiterFeature().setCountSuggestedArticles(analysis.getReCiterFeature().getReCiterArticleFeatures().size());
analysis.getReCiterFeature().setPrecision(featureAnalysis.getPrecision());
analysis.getReCiterFeature().setRecall(featureAnalysis.getRecall());
analysis.getReCiterFeature().setOverallAccuracy(featureAnalysis.getAccuracy());
} else if(filterByFeedback == FilterFeedbackType.ACCEPTED_AND_REJECTED) {
analysis.getReCiterFeature().setReCiterArticleFeatures(analysis.getReCiterFeature().getReCiterArticleFeatures().stream()
.filter(reCiterArticleFeature -> reCiterArticleFeature.getUserAssertion() == PublicationFeedback.ACCEPTED
||
reCiterArticleFeature.getUserAssertion() == PublicationFeedback.REJECTED)
.collect(Collectors.toList()));
List<Long> selectedArticles = analysis.getReCiterFeature().getReCiterArticleFeatures().stream().map(article -> article.getPmid()).collect(Collectors.toList());
Analysis featureAnalysis = Analysis.performAnalysis(finalArticles, selectedArticles, knownPmids);
analysis.getReCiterFeature().setCountSuggestedArticles(analysis.getReCiterFeature().getReCiterArticleFeatures().size());
analysis.getReCiterFeature().setPrecision(featureAnalysis.getPrecision());
analysis.getReCiterFeature().setRecall(featureAnalysis.getRecall());
analysis.getReCiterFeature().setOverallAccuracy(featureAnalysis.getAccuracy());
} else if(filterByFeedback == FilterFeedbackType.NULL) {
analysis.getReCiterFeature().setReCiterArticleFeatures(analysis.getReCiterFeature().getReCiterArticleFeatures().stream()
.filter(reCiterArticleFeature -> reCiterArticleFeature.getTotalArticleScoreStandardized() >= totalScore
&&
reCiterArticleFeature.getUserAssertion() == PublicationFeedback.NULL)
.collect(Collectors.toList()));
List<Long> selectedArticles = analysis.getReCiterFeature().getReCiterArticleFeatures().stream().map(article -> article.getPmid()).collect(Collectors.toList());
Analysis featureAnalysis = Analysis.performAnalysis(finalArticles, selectedArticles, knownPmids);
analysis.getReCiterFeature().setCountSuggestedArticles(analysis.getReCiterFeature().getReCiterArticleFeatures().size());
analysis.getReCiterFeature().setPrecision(featureAnalysis.getPrecision());
analysis.getReCiterFeature().setRecall(featureAnalysis.getRecall());
analysis.getReCiterFeature().setOverallAccuracy(featureAnalysis.getAccuracy());
}
}
else if(analysis.getReCiterFeature()!=null)
{
analysis.getReCiterFeature().setReCiterArticleFeatures(new ArrayList<reciter.engine.analysis.ReCiterArticleFeature>());
analysis.getReCiterFeature().setCountSuggestedArticles(0);
analysis.getReCiterFeature().setPrecision(0.0);
analysis.getReCiterFeature().setRecall(0.0);
analysis.getReCiterFeature().setOverallAccuracy(null);
}
stopWatch.stop();
log.info(stopWatch.getId() + " took " + stopWatch.getTotalTimeSeconds() + "s");
return new ResponseEntity<>(analysis.getReCiterFeature(), HttpStatus.OK);
Expand Down

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