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#266 - Change validation information #271

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merged 6 commits into from
Mar 22, 2024
Merged

#266 - Change validation information #271

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9368876
#266 - Change validation information
michael-82 Mar 20, 2024
1ab2fd0
#266 - Change validation information
michael-82 Mar 21, 2024
6c01c8f
#266 - Change validation information
michael-82 Mar 21, 2024
2ca7f48
#266 - Change validation information
michael-82 Mar 21, 2024
04952d4
#266 - Change validation information
michael-82 Mar 22, 2024
3783b08
#266 - Change validation information
michael-82 Mar 22, 2024
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15 changes: 13 additions & 2 deletions src/main/java/de/numcodex/feasibility_gui_backend/common/api/Criterion.java
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Expand Up @@ -6,6 +6,7 @@
import de.numcodex.feasibility_gui_backend.query.api.AttributeFilter;
import de.numcodex.feasibility_gui_backend.query.api.TimeRestriction;
import de.numcodex.feasibility_gui_backend.query.api.ValueFilter;
import de.numcodex.feasibility_gui_backend.query.api.status.ValidationIssue;
import lombok.Builder;

import java.util.List;
Expand All @@ -17,7 +18,17 @@ public record Criterion (
@JsonProperty("termCodes") List<TermCode> termCodes,
@JsonProperty("attributeFilters") List<AttributeFilter> attributeFilters,
@JsonProperty("valueFilter") ValueFilter valueFilter,
@JsonProperty("timeRestriction") TimeRestriction timeRestriction
@JsonProperty("timeRestriction") TimeRestriction timeRestriction,
@JsonProperty("issues") List<ValidationIssue> validationIssues
) {

public static Criterion createImmutableCriterion(MutableCriterion mutableCriterion) {
return Criterion.builder()
.termCodes(mutableCriterion.termCodes)
.context(mutableCriterion.context)
.attributeFilters(mutableCriterion.attributeFilters)
.valueFilter(mutableCriterion.valueFilter)
.timeRestriction(mutableCriterion.timeRestriction)
.validationIssues(mutableCriterion.validationIssues)
.build();
}
}
36 changes: 36 additions & 0 deletions src/main/java/de/numcodex/feasibility_gui_backend/common/api/MutableCriterion.java
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@@ -0,0 +1,36 @@
package de.numcodex.feasibility_gui_backend.common.api;

import com.fasterxml.jackson.annotation.JsonInclude;
import com.fasterxml.jackson.annotation.JsonInclude.Include;
import com.fasterxml.jackson.annotation.JsonProperty;
import de.numcodex.feasibility_gui_backend.query.api.AttributeFilter;
import de.numcodex.feasibility_gui_backend.query.api.TimeRestriction;
import de.numcodex.feasibility_gui_backend.query.api.ValueFilter;
import de.numcodex.feasibility_gui_backend.query.api.status.ValidationIssue;
import lombok.Builder;
import lombok.Data;

import java.util.List;

@JsonInclude(Include.NON_NULL)
@Builder
@Data
public class MutableCriterion {
@JsonProperty("context") TermCode context;
@JsonProperty("termCodes") List<TermCode> termCodes;
@JsonProperty("attributeFilters") List<AttributeFilter> attributeFilters;
@JsonProperty("valueFilter") ValueFilter valueFilter;
@JsonProperty("timeRestriction") TimeRestriction timeRestriction;
@JsonProperty("issues") List<ValidationIssue> validationIssues;

public static MutableCriterion createMutableCriterion (Criterion criterion) {
return MutableCriterion.builder()
.termCodes(criterion.termCodes())
.context(criterion.context())
.attributeFilters(criterion.attributeFilters())
.valueFilter(criterion.valueFilter())
.timeRestriction(criterion.timeRestriction())
.validationIssues(criterion.validationIssues())
.build();
}
}
72 changes: 44 additions & 28 deletions src/main/java/de/numcodex/feasibility_gui_backend/query/QueryHandlerService.java
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Expand Up @@ -2,7 +2,6 @@

import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import de.numcodex.feasibility_gui_backend.common.api.Criterion;
import de.numcodex.feasibility_gui_backend.query.api.Query;
import de.numcodex.feasibility_gui_backend.query.api.QueryTemplate;
import de.numcodex.feasibility_gui_backend.query.api.SavedQuery;
Expand All @@ -15,7 +14,7 @@
import de.numcodex.feasibility_gui_backend.query.result.ResultService;
import de.numcodex.feasibility_gui_backend.query.templates.QueryTemplateException;
import de.numcodex.feasibility_gui_backend.query.templates.QueryTemplateHandler;
import de.numcodex.feasibility_gui_backend.terminology.validation.TermCodeValidation;
import de.numcodex.feasibility_gui_backend.terminology.validation.StructuredQueryValidation;
import lombok.NonNull;
import lombok.RequiredArgsConstructor;
import org.springframework.dao.DataIntegrityViolationException;
Expand Down Expand Up @@ -61,7 +60,7 @@ public enum ResultDetail {
private final SavedQueryRepository savedQueryRepository;

@NonNull
private final TermCodeValidation termCodeValidation;
private final StructuredQueryValidation structuredQueryValidation;

@NonNull
private ObjectMapper jsonUtil;
Expand Down Expand Up @@ -242,35 +241,52 @@ public String getAuthorId(Long queryId) throws QueryNotFoundException {

public QueryListEntry convertQueryToQueryListEntry(de.numcodex.feasibility_gui_backend.query.persistence.Query query,
boolean skipValidation) {
List<Criterion> invalidCriteria;
if (skipValidation) {
invalidCriteria = List.of();
} else {
try {
var sq = jsonUtil.readValue(query.getQueryContent().getQueryContent(), StructuredQuery.class);
invalidCriteria = termCodeValidation.getInvalidCriteria(sq);
} catch (JsonProcessingException e) {
invalidCriteria = List.of();
}
boolean isValid = true;
if (!skipValidation) {
try {
var sq = jsonUtil.readValue(query.getQueryContent().getQueryContent(), StructuredQuery.class);
isValid = structuredQueryValidation.isValid(sq);
} catch (JsonProcessingException e) {
isValid = false;
}
}

if (query.getSavedQuery() != null) {
return
QueryListEntry.builder()
.id(query.getId())
.label(query.getSavedQuery().getLabel())
.comment(query.getSavedQuery().getComment())
.totalNumberOfPatients(query.getSavedQuery().getResultSize())
.createdAt(query.getCreatedAt())
.invalidCriteria(invalidCriteria)
.build();
if (skipValidation) {
return
QueryListEntry.builder()
.id(query.getId())
.label(query.getSavedQuery().getLabel())
.comment(query.getSavedQuery().getComment())
.totalNumberOfPatients(query.getSavedQuery().getResultSize())
.createdAt(query.getCreatedAt())
.build();
} else {
return
QueryListEntry.builder()
.id(query.getId())
.label(query.getSavedQuery().getLabel())
.comment(query.getSavedQuery().getComment())
.totalNumberOfPatients(query.getSavedQuery().getResultSize())
.createdAt(query.getCreatedAt())
.isValid(isValid)
.build();
}
} else {
return
QueryListEntry.builder()
.id(query.getId())
.createdAt(query.getCreatedAt())
.invalidCriteria(invalidCriteria)
.build();
if (skipValidation) {
return
QueryListEntry.builder()
.id(query.getId())
.createdAt(query.getCreatedAt())
.build();
} else {
return
QueryListEntry.builder()
.id(query.getId())
.createdAt(query.getCreatedAt())
.isValid(isValid)
.build();
}
}
}

Expand Down
54 changes: 54 additions & 0 deletions src/main/java/de/numcodex/feasibility_gui_backend/query/api/MutableStructuredQuery.java
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@@ -0,0 +1,54 @@
package de.numcodex.feasibility_gui_backend.query.api;

import com.fasterxml.jackson.annotation.JsonInclude;
import com.fasterxml.jackson.annotation.JsonInclude.Include;
import com.fasterxml.jackson.annotation.JsonProperty;
import de.numcodex.feasibility_gui_backend.common.api.Criterion;
import de.numcodex.feasibility_gui_backend.common.api.MutableCriterion;
import de.numcodex.feasibility_gui_backend.query.api.validation.StructuredQueryValidation;
import lombok.Builder;
import lombok.Data;

import java.net.URI;
import java.util.ArrayList;
import java.util.List;

@JsonInclude(Include.NON_EMPTY)
@Builder
@Data
public class MutableStructuredQuery {
@JsonProperty URI version;
@JsonProperty("inclusionCriteria") List<List<MutableCriterion>> inclusionCriteria;
@JsonProperty("exclusionCriteria") List<List<MutableCriterion>> exclusionCriteria;
@JsonProperty("display") String display;

public static MutableStructuredQuery createMutableStructuredQuery(StructuredQuery structuredQuery) {
List<List<MutableCriterion>> mutableInclusionCriteria = new ArrayList<>();
if (structuredQuery.inclusionCriteria() != null) {
for (List<Criterion> outerList : structuredQuery.inclusionCriteria()) {
List<MutableCriterion> innerList = new ArrayList<>();
for (Criterion criterion : outerList) {
innerList.add(MutableCriterion.createMutableCriterion(criterion));
}
mutableInclusionCriteria.add(innerList);
}
}

List<List<MutableCriterion>> mutableExclusionCriteria = new ArrayList<>();
if (structuredQuery.exclusionCriteria() != null) {
for (List<Criterion> outerList : structuredQuery.exclusionCriteria()) {
List<MutableCriterion> innerList = new ArrayList<>();
for (Criterion criterion : outerList) {
innerList.add(MutableCriterion.createMutableCriterion(criterion));
}
mutableExclusionCriteria.add(innerList);
}
}
return MutableStructuredQuery.builder()
.version(structuredQuery.version())
.inclusionCriteria(mutableInclusionCriteria)
.exclusionCriteria(mutableExclusionCriteria)
.display(structuredQuery.display())
.build();
}
}
6 changes: 1 addition & 5 deletions src/main/java/de/numcodex/feasibility_gui_backend/query/api/Query.java
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Expand Up @@ -3,19 +3,15 @@
import com.fasterxml.jackson.annotation.JsonInclude;
import com.fasterxml.jackson.annotation.JsonInclude.Include;
import com.fasterxml.jackson.annotation.JsonProperty;
import de.numcodex.feasibility_gui_backend.common.api.Criterion;
import lombok.Builder;

import java.util.List;

@JsonInclude(Include.NON_NULL)
@Builder
public record Query(
@JsonProperty long id,
@JsonProperty StructuredQuery content,
@JsonProperty String label,
@JsonProperty String comment,
@JsonProperty List<Criterion> invalidCriteria
@JsonProperty String comment
) {

}
4 changes: 1 addition & 3 deletions src/main/java/de/numcodex/feasibility_gui_backend/query/api/QueryListEntry.java
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Expand Up @@ -3,11 +3,9 @@
import com.fasterxml.jackson.annotation.JsonInclude;
import com.fasterxml.jackson.annotation.JsonInclude.Include;
import com.fasterxml.jackson.annotation.JsonProperty;
import de.numcodex.feasibility_gui_backend.common.api.Criterion;
import lombok.Builder;

import java.sql.Timestamp;
import java.util.List;

@JsonInclude(Include.NON_NULL)
@Builder
Expand All @@ -17,7 +15,7 @@ public record QueryListEntry(
@JsonProperty String comment,
@JsonProperty Timestamp createdAt,
@JsonProperty Long totalNumberOfPatients,
@JsonProperty List<Criterion> invalidCriteria
@JsonProperty Boolean isValid
) {

}
4 changes: 0 additions & 4 deletions src/main/java/de/numcodex/feasibility_gui_backend/query/api/QueryTemplate.java
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Expand Up @@ -3,12 +3,9 @@
import com.fasterxml.jackson.annotation.JsonInclude;
import com.fasterxml.jackson.annotation.JsonInclude.Include;
import com.fasterxml.jackson.annotation.JsonProperty;
import de.numcodex.feasibility_gui_backend.common.api.Criterion;
import de.numcodex.feasibility_gui_backend.query.api.validation.QueryTemplateValidation;
import lombok.Builder;

import java.util.List;

@JsonInclude(Include.NON_NULL)
@QueryTemplateValidation
@Builder
Expand All @@ -19,7 +16,6 @@ public record QueryTemplate(
@JsonProperty String comment,
@JsonProperty String lastModified,
@JsonProperty String createdBy,
@JsonProperty List<Criterion> invalidCriteria,
@JsonProperty Boolean isValid
) {

Expand Down
28 changes: 27 additions & 1 deletion src/main/java/de/numcodex/feasibility_gui_backend/query/api/StructuredQuery.java
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Expand Up @@ -4,11 +4,12 @@
import com.fasterxml.jackson.annotation.JsonInclude.Include;
import com.fasterxml.jackson.annotation.JsonProperty;
import de.numcodex.feasibility_gui_backend.common.api.Criterion;
import de.numcodex.feasibility_gui_backend.common.api.TermCode;
import de.numcodex.feasibility_gui_backend.common.api.MutableCriterion;
import de.numcodex.feasibility_gui_backend.query.api.validation.StructuredQueryValidation;
import lombok.Builder;

import java.net.URI;
import java.util.ArrayList;
import java.util.List;

@JsonInclude(Include.NON_EMPTY)
Expand All @@ -20,5 +21,30 @@ public record StructuredQuery(
@JsonProperty("exclusionCriteria") List<List<Criterion>> exclusionCriteria,
@JsonProperty("display") String display
) {
public static StructuredQuery createImmutableStructuredQuery(MutableStructuredQuery mutableStructuredQuery) {
List<List<Criterion>> inclusionCriteria = new ArrayList<>();
for (List<MutableCriterion> outerList : mutableStructuredQuery.getInclusionCriteria()) {
List<Criterion> innerList = new ArrayList<>();
for (MutableCriterion criterion : outerList) {
innerList.add(Criterion.createImmutableCriterion(criterion));
}
inclusionCriteria.add(innerList);
}

List<List<Criterion>> exclusionCriteria = new ArrayList<>();
for (List<MutableCriterion> outerList : mutableStructuredQuery.getExclusionCriteria()) {
List<Criterion> innerList = new ArrayList<>();
for (MutableCriterion criterion : outerList) {
innerList.add(Criterion.createImmutableCriterion(criterion));
}
exclusionCriteria.add(innerList);
}

return StructuredQuery.builder()
.version(mutableStructuredQuery.getVersion())
.display(mutableStructuredQuery.getDisplay())
.inclusionCriteria(inclusionCriteria)
.exclusionCriteria(exclusionCriteria)
.build();
}
}
15 changes: 0 additions & 15 deletions src/main/java/de/numcodex/feasibility_gui_backend/query/api/ValidatedStructuredQuery.java
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