OHDSI · anton-abushkevich · Aug 13, 2021 · Apr 26, 2021 · Apr 27, 2021 · Apr 27, 2021
diff --git a/pom.xml b/pom.xml
@@ -254,6 +254,12 @@
     <!-- I18n -->
     <i18n.enabled>true</i18n.enabled>
     <i18n.defaultLocale>en</i18n.defaultLocale>
+
+    <!-- Tags -->
+    <tag.enabled>true</tag.enabled>
+    <!-- Period between refreshes of materialized view with statistics -->
+    <!-- 10 minutes by default -->
+    <tag.refreshStat.period>600000</tag.refreshStat.period>
   </properties>
   <build>
     <finalName>WebAPI</finalName>

diff --git a/.../ohdsi/webapi/analysis/converter/AnalysisCohortDefinitionToCohortDefinitionConverter.java b/.../ohdsi/webapi/analysis/converter/AnalysisCohortDefinitionToCohortDefinitionConverter.java
@@ -5,7 +5,9 @@
 import org.ohdsi.webapi.cohortdefinition.CohortDefinition;
 import org.ohdsi.webapi.cohortdefinition.CohortDefinitionDetails;
 import org.ohdsi.webapi.converter.BaseConversionServiceAwareConverter;
+import org.springframework.stereotype.Component;
 
+@Component
 public class AnalysisCohortDefinitionToCohortDefinitionConverter<T extends AnalysisCohortDefinition> extends BaseConversionServiceAwareConverter<T, CohortDefinition> {
 
     @Override

diff --git a/src/main/java/org/ohdsi/webapi/check/builder/tag/MandatoryTagValidatorBuilder.java b/src/main/java/org/ohdsi/webapi/check/builder/tag/MandatoryTagValidatorBuilder.java
@@ -0,0 +1,22 @@
+package org.ohdsi.webapi.check.builder.tag;
+
+import org.ohdsi.webapi.check.builder.ValidatorBuilder;
+import org.ohdsi.webapi.check.validator.Validator;
+import org.ohdsi.webapi.check.validator.tag.MandatoryTagValidator;
+import org.ohdsi.webapi.tag.TagService;
+import org.ohdsi.webapi.tag.dto.TagDTO;
+
+import java.util.Collection;
+
+public class MandatoryTagValidatorBuilder<T extends Collection<? extends TagDTO>> extends ValidatorBuilder<T> {
+    private final TagService tagService;
+
+    public MandatoryTagValidatorBuilder(TagService tagService) {
+        this.tagService = tagService;
+    }
+
+    @Override
+    public Validator<T> build() {
+        return new MandatoryTagValidator<>(createChildPath(), severity, errorMessage, this.tagService);
+    }
+}
diff --git a/src/main/java/org/ohdsi/webapi/check/checker/characterization/CharacterizationChecker.java b/src/main/java/org/ohdsi/webapi/check/checker/characterization/CharacterizationChecker.java
@@ -2,7 +2,10 @@
 
 import org.ohdsi.webapi.check.builder.ValidatorGroupBuilder;
 import org.ohdsi.webapi.check.checker.BaseChecker;
+import org.ohdsi.webapi.check.checker.tag.helper.TagHelper;
 import org.ohdsi.webapi.cohortcharacterization.dto.CohortCharacterizationDTO;
+import org.ohdsi.webapi.cohortdefinition.dto.CohortDTO;
+import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Component;
 
 import javax.annotation.PostConstruct;
@@ -15,6 +18,11 @@
 
 @Component
 public class CharacterizationChecker extends BaseChecker<CohortCharacterizationDTO> {
+    private final TagHelper<CohortCharacterizationDTO> tagHelper;
+
+    public CharacterizationChecker(TagHelper<CohortCharacterizationDTO> tagHelper) {
+        this.tagHelper = tagHelper;
+    }
 
     @PostConstruct
     public void init() {
@@ -25,6 +33,7 @@ public void init() {
     protected List<ValidatorGroupBuilder<CohortCharacterizationDTO, ?>> getGroupBuilder() {
 
         return Arrays.asList(
+                tagHelper.prepareTagBuilder(),
                 prepareCohortBuilder(),
                 prepareFeatureAnalysesBuilder(),
                 prepareStratifyRuleBuilder()

diff --git a/...n/java/org/ohdsi/webapi/check/checker/characterization/helper/CharacterizationHelper.java b/...n/java/org/ohdsi/webapi/check/checker/characterization/helper/CharacterizationHelper.java
@@ -7,6 +7,7 @@
 import org.ohdsi.webapi.cohortcharacterization.dto.CcStrataDTO;
 import org.ohdsi.webapi.cohortcharacterization.dto.CohortCharacterizationDTO;
 import org.ohdsi.webapi.cohortdefinition.dto.CohortMetadataDTO;
+import org.ohdsi.webapi.cohortdefinition.dto.CohortMetadataImplDTO;
 import org.ohdsi.webapi.feanalysis.dto.FeAnalysisShortDTO;
 
 import java.util.Collection;
@@ -22,9 +23,9 @@ public static ValidatorGroupBuilder<CohortCharacterizationDTO, Collection<FeAnal
         return builder;
     }
 
-    public static ValidatorGroupBuilder<CohortCharacterizationDTO, Collection<CohortMetadataDTO>> prepareCohortBuilder() {
+    public static ValidatorGroupBuilder<CohortCharacterizationDTO, Collection<CohortMetadataImplDTO>> prepareCohortBuilder() {
 
-        ValidatorGroupBuilder<CohortCharacterizationDTO, Collection<CohortMetadataDTO>> builder = new ValidatorGroupBuilder<CohortCharacterizationDTO, Collection<CohortMetadataDTO>>()
+        ValidatorGroupBuilder<CohortCharacterizationDTO, Collection<CohortMetadataImplDTO>> builder = new ValidatorGroupBuilder<CohortCharacterizationDTO, Collection<CohortMetadataImplDTO>>()
                 .attrName("cohorts")
                 .valueGetter(BaseCcDTO::getCohorts)
                 .validators(new NotNullNotEmptyValidatorBuilder<>());

diff --git a/src/main/java/org/ohdsi/webapi/check/checker/cohort/CohortChecker.java b/src/main/java/org/ohdsi/webapi/check/checker/cohort/CohortChecker.java
@@ -0,0 +1,48 @@
+package org.ohdsi.webapi.check.checker.cohort;
+
+import org.ohdsi.analysis.estimation.comparativecohortanalysis.design.CohortMethodAnalysis;
+import org.ohdsi.analysis.estimation.comparativecohortanalysis.design.ComparativeCohortAnalysis;
+import org.ohdsi.webapi.check.builder.DuplicateValidatorBuilder;
+import org.ohdsi.webapi.check.builder.IterableForEachValidatorBuilder;
+import org.ohdsi.webapi.check.builder.NotNullNotEmptyValidatorBuilder;
+import org.ohdsi.webapi.check.builder.ValidatorGroupBuilder;
+import org.ohdsi.webapi.check.checker.BaseChecker;
+import org.ohdsi.webapi.check.checker.tag.helper.TagHelper;
+import org.ohdsi.webapi.cohortcharacterization.dto.BaseCcDTO;
+import org.ohdsi.webapi.cohortcharacterization.dto.CohortCharacterizationDTO;
+import org.ohdsi.webapi.cohortdefinition.dto.CohortDTO;
+import org.ohdsi.webapi.feanalysis.dto.FeAnalysisShortDTO;
+import org.ohdsi.webapi.service.dto.CommonEntityExtDTO;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Component;
+
+import javax.annotation.PostConstruct;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.List;
+
+import static org.ohdsi.webapi.check.checker.characterization.helper.CharacterizationHelper.prepareCohortBuilder;
+import static org.ohdsi.webapi.check.checker.characterization.helper.CharacterizationHelper.prepareFeatureAnalysesBuilder;
+import static org.ohdsi.webapi.check.checker.characterization.helper.CharacterizationHelper.prepareStratifyRuleBuilder;
+
+@Component
+public class CohortChecker extends BaseChecker<CohortDTO> {
+    private final TagHelper<CohortDTO> tagHelper;
+
+    public CohortChecker(TagHelper<CohortDTO> tagHelper) {
+        this.tagHelper = tagHelper;
+    }
+
+    @PostConstruct
+    public void init() {
+        createValidator();
+    }
+
+    @Override
+    protected List<ValidatorGroupBuilder<CohortDTO, ?>> getGroupBuilder() {
+
+        return Arrays.asList(
+                tagHelper.prepareTagBuilder()
+        );
+    }
+}
diff --git a/src/main/java/org/ohdsi/webapi/check/checker/conceptset/ConceptSetChecker.java b/src/main/java/org/ohdsi/webapi/check/checker/conceptset/ConceptSetChecker.java
@@ -0,0 +1,35 @@
+package org.ohdsi.webapi.check.checker.conceptset;
+
+import org.ohdsi.webapi.check.builder.ValidatorGroupBuilder;
+import org.ohdsi.webapi.check.checker.BaseChecker;
+import org.ohdsi.webapi.check.checker.tag.helper.TagHelper;
+import org.ohdsi.webapi.cohortdefinition.dto.CohortDTO;
+import org.ohdsi.webapi.service.dto.ConceptSetDTO;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Component;
+
+import javax.annotation.PostConstruct;
+import java.util.Arrays;
+import java.util.List;
+
+@Component
+public class ConceptSetChecker extends BaseChecker<ConceptSetDTO> {
+    private final TagHelper<ConceptSetDTO> tagHelper;
+
+    public ConceptSetChecker(TagHelper<ConceptSetDTO> tagHelper) {
+        this.tagHelper = tagHelper;
+    }
+
+    @PostConstruct
+    public void init() {
+        createValidator();
+    }
+
+    @Override
+    protected List<ValidatorGroupBuilder<ConceptSetDTO, ?>> getGroupBuilder() {
+
+        return Arrays.asList(
+                tagHelper.prepareTagBuilder()
+        );
+    }
+}
diff --git a/src/main/java/org/ohdsi/webapi/check/checker/ir/IRChecker.java b/src/main/java/org/ohdsi/webapi/check/checker/ir/IRChecker.java
@@ -6,11 +6,19 @@
 import org.ohdsi.webapi.check.builder.ValidatorGroupBuilder;
 import org.ohdsi.webapi.check.checker.BaseChecker;
 import org.ohdsi.webapi.check.checker.ir.helper.IRHelper;
+import org.ohdsi.webapi.check.checker.tag.helper.TagHelper;
+import org.ohdsi.webapi.cohortcharacterization.dto.CohortCharacterizationDTO;
 import org.ohdsi.webapi.service.dto.IRAnalysisDTO;
+import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Component;
 
 @Component
 public class IRChecker extends BaseChecker<IRAnalysisDTO> {
+    private final TagHelper<IRAnalysisDTO> tagHelper;
+
+    public IRChecker(TagHelper<IRAnalysisDTO> tagHelper) {
+        this.tagHelper = tagHelper;
+    }
 
     @PostConstruct
     public void init() {
@@ -21,6 +29,7 @@ public void init() {
     protected List<ValidatorGroupBuilder<IRAnalysisDTO, ?>> getGroupBuilder() {
 
         return Arrays.asList(
+                tagHelper.prepareTagBuilder(),
                 IRHelper.prepareAnalysisExpressionBuilder()
         );
     }

diff --git a/src/main/java/org/ohdsi/webapi/check/checker/pathway/PathwayChecker.java b/src/main/java/org/ohdsi/webapi/check/checker/pathway/PathwayChecker.java
@@ -6,11 +6,19 @@
 import org.ohdsi.webapi.check.builder.ValidatorGroupBuilder;
 import org.ohdsi.webapi.check.checker.BaseChecker;
 import org.ohdsi.webapi.check.checker.pathway.helper.PathwayHelper;
+import org.ohdsi.webapi.check.checker.tag.helper.TagHelper;
 import org.ohdsi.webapi.pathway.dto.PathwayAnalysisDTO;
+import org.ohdsi.webapi.service.dto.IRAnalysisDTO;
+import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Component;
 
 @Component
 public class PathwayChecker extends BaseChecker<PathwayAnalysisDTO> {
+    private final TagHelper<PathwayAnalysisDTO> tagHelper;
+
+    public PathwayChecker(TagHelper<PathwayAnalysisDTO> tagHelper) {
+        this.tagHelper = tagHelper;
+    }
 
     @PostConstruct
     public void init() {
@@ -20,6 +28,7 @@ public void init() {
     @Override
     protected List<ValidatorGroupBuilder<PathwayAnalysisDTO, ?>> getGroupBuilder() {
         return Arrays.asList(
+                tagHelper.prepareTagBuilder(),
                 PathwayHelper.prepareTargetCohortsBuilder(),
                 PathwayHelper.prepareEventCohortsBuilder(),
                 PathwayHelper.prepareCombinationWindowBuilder(),

diff --git a/src/main/java/org/ohdsi/webapi/check/checker/tag/helper/TagHelper.java b/src/main/java/org/ohdsi/webapi/check/checker/tag/helper/TagHelper.java
@@ -0,0 +1,39 @@
+package org.ohdsi.webapi.check.checker.tag.helper;
+
+import org.ohdsi.webapi.check.builder.ValidatorGroupBuilder;
+import org.ohdsi.webapi.check.builder.tag.MandatoryTagValidatorBuilder;
+import org.ohdsi.webapi.check.warning.WarningSeverity;
+import org.ohdsi.webapi.service.dto.CommonEntityExtDTO;
+import org.ohdsi.webapi.tag.TagService;
+import org.ohdsi.webapi.tag.dto.TagDTO;
+import org.ohdsi.webapi.tag.repository.TagRepository;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.stereotype.Component;
+
+import java.util.Collection;
+
+@Component
+public class TagHelper<T extends CommonEntityExtDTO> {
+    private final TagService tagService;
+
+    @Value("${tag.enabled}")
+    private boolean enabled;
+
+    public TagHelper(TagService tagService) {
+        this.tagService = tagService;
+    }
+
+    public ValidatorGroupBuilder<T, Collection<? extends TagDTO>> prepareTagBuilder() {
+        ValidatorGroupBuilder<T, Collection<? extends TagDTO>> builder =
+                new ValidatorGroupBuilder<T, Collection<? extends TagDTO>>()
+                        .attrName("Tags")
+                        .conditionGetter(t -> enabled)
+                        .severity(WarningSeverity.WARNING)
+                        .valueGetter(T::getTags)
+                        .validators(
+                                new MandatoryTagValidatorBuilder<>(tagService)
+                        );
+        return builder;
+    }
+}
diff --git a/src/main/java/org/ohdsi/webapi/check/validator/Validator.java b/src/main/java/org/ohdsi/webapi/check/validator/Validator.java
@@ -28,14 +28,18 @@ public Validator(Path path, WarningSeverity severity, String errorMessage, Funct
 
     public abstract boolean validate(T value, Context context);
 
-    protected String getErrorMessage(T value) {
+    protected String getErrorMessage(T value, Object... params) {
         StringBuilder sb = new StringBuilder();
         if (this.attrNameValueGetter != null) {
             sb.append("(")
                     .append(this.attrNameValueGetter.apply(value))
                     .append(") - ");
         }
-        sb.append(this.errorMessage != null ? this.errorMessage : getDefaultErrorMessage());
+        String msg = this.errorMessage != null ? this.errorMessage : getDefaultErrorMessage();
+        if (params.length > 0) {
+            msg = String.format(msg, params);
+        }
+        sb.append(msg);
         return sb.toString();
     }
 

diff --git a/src/main/java/org/ohdsi/webapi/check/validator/tag/MandatoryTagValidator.java b/src/main/java/org/ohdsi/webapi/check/validator/tag/MandatoryTagValidator.java
@@ -0,0 +1,63 @@
+package org.ohdsi.webapi.check.validator.tag;
+
+import org.ohdsi.webapi.check.validator.Context;
+import org.ohdsi.webapi.check.validator.Path;
+import org.ohdsi.webapi.check.validator.Validator;
+import org.ohdsi.webapi.check.warning.WarningSeverity;
+import org.ohdsi.webapi.tag.TagService;
+import org.ohdsi.webapi.tag.domain.Tag;
+import org.ohdsi.webapi.tag.dto.TagDTO;
+import org.ohdsi.webapi.tag.repository.TagRepository;
+
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Objects;
+import java.util.Set;
+import java.util.stream.Collectors;
+
+public class MandatoryTagValidator<T extends Collection<? extends TagDTO>> extends Validator<T> {
+    private static final String INVALID = "no assigned tags from mandatory groups %s";
+
+    private final TagService tagService;
+
+    public MandatoryTagValidator(Path path, WarningSeverity severity, String errorMessage,
+                                 TagService tagService) {
+        super(path, severity, errorMessage);
+        this.tagService = tagService;
+    }
+
+    @Override
+    public boolean validate(T value, Context context) {
+        boolean isValid = true;
+        if (Objects.nonNull(value)) {
+            Set<Integer> groupIds = new HashSet<>();
+            value.forEach(tagDTO -> {
+                Set<Integer> ids = tagService.getAllGroupsForTag(tagDTO.getId());
+                groupIds.addAll(ids);
+            });
+            List<Tag> mandatoryTags = tagService.findMandatoryTags();
+            List<Tag> absentTags = mandatoryTags.stream()
+                    .filter(t -> !groupIds.contains(t.getId()))
+                    .collect(Collectors.toList());
+
+            isValid = absentTags.size() == 0;
+            if (!isValid) {
+                String absentTagNames = absentTags.stream()
+                        .map(Tag::getName)
+                        .collect(Collectors.joining("], [", "[", "]"));
+                context.addWarning(getSeverity(), getErrorMessage(value, absentTagNames), path);
+            }
+        } else {
+            isValid = tagService.findMandatoryTags().size() == 0;
+        }
+        return isValid;
+    }
+
+    @Override
+    protected String getDefaultErrorMessage() {
+        return INVALID;
+    }
+}
diff --git a/src/main/java/org/ohdsi/webapi/check/warning/WarningUtils.java b/src/main/java/org/ohdsi/webapi/check/warning/WarningUtils.java
@@ -0,0 +1,31 @@
+package org.ohdsi.webapi.check.warning;
+
+public class WarningUtils {
+    public static Warning convertCirceWarning(org.ohdsi.circe.check.Warning circeWarning) {
+        WarningSeverity severity = convertCirceWarningSeverity(
+                ((org.ohdsi.circe.check.warnings.BaseWarning) circeWarning).getSeverity());
+        Warning warning;
+        if (circeWarning instanceof org.ohdsi.circe.check.warnings.ConceptSetWarning) {
+            warning = new ConceptSetWarning(severity, circeWarning.toMessage(), ((org.ohdsi.circe.check.warnings.ConceptSetWarning) circeWarning).getConceptSet());
+        } else {
+            warning = new DefaultWarning(severity, circeWarning.toMessage());
+        }
+        return warning;
+    }
+
+    private static WarningSeverity convertCirceWarningSeverity(
+            org.ohdsi.circe.check.WarningSeverity circeWarningSeverity) {
+        WarningSeverity severity = WarningSeverity.WARNING;
+        switch (circeWarningSeverity) {
+            case CRITICAL: {
+                severity = WarningSeverity.CRITICAL;
+                break;
+            }
+            case INFO: {
+                severity = WarningSeverity.INFO;
+                break;
+            }
+        }
+        return severity;
+    }
+}