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Merge pull request #331 from qbicsoftware/development
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@KochTobi
KochTobi authored Jul 25, 2023
2 parents b0e9f16 + 2e0d672 commit 27bc600
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Showing 70 changed files with 2,064 additions and 1,526 deletions.
170 changes: 91 additions & 79 deletions commons/src/main/java/life/qbic/application/commons/ApplicationException.java
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Original file line number Diff line number Diff line change
Expand Up @@ -16,87 +16,19 @@
*/
public class ApplicationException extends RuntimeException {

/**
* The error code of an ApplicationException. This code can be used to determine what kind of
* error occurred. This allows for the message of the ApplicationException to hold debug
* information and avoids string matching to search for the error message.
*/
public enum ErrorCode {
GENERAL,
INVALID_EXPERIMENTAL_DESIGN,
INVALID_PROJECT_OBJECTIVE,
INVALID_PROJECT_TITLE,
INVALID_PROJECT_CODE,
DUPLICATE_PROJECT_CODE,
UNDEFINED_VARIABLE_LEVEL,
NO_SPECIES_DEFINED,
NO_SPECIMEN_DEFINED,
NO_ANALYTE_DEFINED,
;

@Override
public String toString() {
return this.getClass().getSimpleName() + "." + this.name();
}

}

/**
* Error parameters to be used in error messages.
*
* @param value an ordered array of parameters
*/
public record ErrorParameters(Object[] value) {

public static ErrorParameters create() {
return new ErrorParameters(new Object[]{});
}

public static ErrorParameters of(Object... parameters) {
return new ErrorParameters(parameters);
}

@Override
public boolean equals(Object o) {
if (this == o) {
return true;
}
if (o == null || getClass() != o.getClass()) {
return false;
}

ErrorParameters that = (ErrorParameters) o;

return Arrays.equals(value, that.value);
}

@Override
public int hashCode() {
return Arrays.hashCode(value);
}

@Override
public String toString() {
return new StringJoiner(", ", ErrorParameters.class.getSimpleName() + "[", "]")
.add("value=" + Arrays.toString(value))
.toString();
}
}

private final ErrorCode errorCode;

private final ErrorParameters errorParameters;

public ApplicationException() {
this(ErrorCode.GENERAL, ErrorParameters.create());
this(ErrorCode.GENERAL, ErrorParameters.empty());
}

public ApplicationException(String message) {
this(message, ErrorCode.GENERAL, ErrorParameters.create());
this(message, ErrorCode.GENERAL, ErrorParameters.empty());
}

public ApplicationException(String message, Throwable cause) {
this(message, cause, ErrorCode.GENERAL, ErrorParameters.create());
this(message, cause, ErrorCode.GENERAL, ErrorParameters.empty());
}

public ApplicationException(ErrorCode errorCode, ErrorParameters errorParameters) {
Expand Down Expand Up @@ -132,14 +64,6 @@ public ApplicationException(String message, Throwable cause, boolean enableSuppr
this.errorParameters = errorParameters;
}

public ErrorCode errorCode() {
return errorCode;
}

public ErrorParameters errorParameters() {
return errorParameters;
}

/**
* Wraps the provided throwable into an ApplicationException and sets the provided error message.
* <p>
Expand Down Expand Up @@ -185,6 +109,14 @@ public static ApplicationException wrapping(Throwable e) {
}
}

public ErrorCode errorCode() {
return errorCode;
}

public ErrorParameters errorParameters() {
return errorParameters;
}

@Override
public String toString() {
return new StringJoiner(", ", ApplicationException.class.getSimpleName() + "[", "]")
Expand All @@ -193,4 +125,84 @@ public String toString() {
.add("errorParameters=" + errorParameters)
.toString();
}

/**
* The error code of an ApplicationException. This code can be used to determine what kind of
* error occurred. This allows for the message of the ApplicationException to hold debug
* information and avoids string matching to search for the error message.
*/
public enum ErrorCode {
GENERAL,
INVALID_EXPERIMENTAL_DESIGN,
INVALID_PROJECT_OBJECTIVE,
INVALID_PROJECT_TITLE,
INVALID_PROJECT_CODE,
DUPLICATE_PROJECT_CODE,
UNDEFINED_VARIABLE_LEVEL,
NO_SPECIES_DEFINED,
NO_SPECIMEN_DEFINED,
NO_ANALYTE_DEFINED,
;

@Override
public String toString() {
return this.getClass().getSimpleName() + "." + this.name();
}

}

/**
* Error parameters to be used in error messages.
*
* @param value an ordered array of parameters
*/
public record ErrorParameters(Object[] value) {

/**
* Creates a new instance of an empty error parameter array
*
* @return
* @since 1.0.0
*/
public static ErrorParameters empty() {
return new ErrorParameters(new Object[]{});
}

/**
* Creates a new instance with the provided error parameters
*
* @param parameters the error parameters
* @return
* @since 1.0.0
*/
public static ErrorParameters of(Object... parameters) {
return new ErrorParameters(parameters);
}

@Override
public boolean equals(Object o) {
if (this == o) {
return true;
}
if (o == null || getClass() != o.getClass()) {
return false;
}

ErrorParameters that = (ErrorParameters) o;

return Arrays.equals(value, that.value);
}

@Override
public int hashCode() {
return Arrays.hashCode(value);
}

@Override
public String toString() {
return new StringJoiner(", ", ErrorParameters.class.getSimpleName() + "[", "]")
.add("value=" + Arrays.toString(value))
.toString();
}
}
}
2 changes: 1 addition & 1 deletion ...src/main/java/life/qbic/projectmanagement/experiment/persistence/SampleJpaRepository.java
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Original file line number Diff line number Diff line change
Expand Up @@ -70,7 +70,7 @@ public Result<Collection<Sample>, SampleInformationService.ResponseCode> findSam
} catch (Exception e) {
log.error(
"Retrieving Samples for experiment with id " + experimentId.value() + " failed: " + e);
return Result.fromError(SampleInformationService.ResponseCode.SAMPLES_NOT_FOUND);
return Result.fromError(SampleInformationService.ResponseCode.QUERY_FAILED);
}
return Result.fromValue(samples);
}
Expand Down
133 changes: 129 additions & 4 deletions ...n/java/life/qbic/projectmanagement/experiment/persistence/SamplePreviewJpaRepository.java
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Original file line number Diff line number Diff line change
@@ -1,15 +1,20 @@
package life.qbic.projectmanagement.experiment.persistence;

import jakarta.persistence.criteria.Expression;
import jakarta.persistence.criteria.Join;
import jakarta.persistence.criteria.Predicate;
import java.util.List;
import java.util.Objects;
import life.qbic.persistence.OffsetBasedRequest;
import life.qbic.projectmanagement.application.SortOrder;
import life.qbic.projectmanagement.application.sample.SamplePreview;
import life.qbic.projectmanagement.application.sample.SamplePreviewLookup;
import life.qbic.projectmanagement.domain.project.experiment.ExperimentId;
import org.eclipse.jetty.util.StringUtil;
import org.springframework.context.annotation.Scope;
import org.springframework.data.domain.Sort;
import org.springframework.data.domain.Sort.Order;
import org.springframework.data.jpa.domain.Specification;
import org.springframework.stereotype.Component;

/**
Expand All @@ -30,7 +35,7 @@ public SamplePreviewJpaRepository(SamplePreviewRepository samplePreviewRepositor

@Override
public List<SamplePreview> queryByExperimentId(ExperimentId experimentId, int offset, int limit,
List<SortOrder> sortOrders) {
List<SortOrder> sortOrders, String filter) {
List<Order> orders = sortOrders.stream().map(it -> {
Order order;
if (it.isDescending()) {
Expand All @@ -40,13 +45,133 @@ public List<SamplePreview> queryByExperimentId(ExperimentId experimentId, int of
}
return order;
}).toList();
return samplePreviewRepository.findSamplePreviewByExperimentId(experimentId,

Specification<SamplePreview> filterSpecification = generateExperimentIdandFilterSpecification(
experimentId, filter);
return samplePreviewRepository.findAll(filterSpecification,
new OffsetBasedRequest(offset, limit, Sort.by(orders))).getContent();
}

@Override
public int queryCountByExperimentId(ExperimentId experimentId) {
return samplePreviewRepository.countSamplePreviewsByExperimentId(experimentId);
public int queryCountByExperimentId(ExperimentId experimentId, String filter) {
Specification<SamplePreview> filterSpecification = generateExperimentIdandFilterSpecification(
experimentId, filter);
return (int) samplePreviewRepository.count(filterSpecification);
}

private Specification<SamplePreview> generateExperimentIdandFilterSpecification(
ExperimentId experimentId, String filter) {
Specification<SamplePreview> isBlankSpec = SamplePreviewSpecs.isBlank(filter);
Specification<SamplePreview> experimentIdSpec = SamplePreviewSpecs.experimentIdEquals(
experimentId);
Specification<SamplePreview> sampleCodeSpec = SamplePreviewSpecs.sampleCodeContains(filter);
Specification<SamplePreview> sampleLabelSpec = SamplePreviewSpecs.sampleLabelContains(filter);
Specification<SamplePreview> batchLabelSpec = SamplePreviewSpecs.batchLabelContains(filter);
Specification<SamplePreview> bioReplicateLabelSpec = SamplePreviewSpecs.bioReplicateLabelContains(
filter);
Specification<SamplePreview> conditionSpec = SamplePreviewSpecs.conditionContains(filter);
Specification<SamplePreview> speciesSpec = SamplePreviewSpecs.speciesContains(filter);
Specification<SamplePreview> specimenSpec = SamplePreviewSpecs.specimenContains(filter);
Specification<SamplePreview> analyteSpec = SamplePreviewSpecs.analyteContains(filter);
Specification<SamplePreview> analysisTypeSpec = SamplePreviewSpecs.analysisTypeContains(filter);
Specification<SamplePreview> commentSpec = SamplePreviewSpecs.commentContains(filter);
Specification<SamplePreview> containsFilterSpec = Specification.anyOf(sampleCodeSpec,
sampleLabelSpec, batchLabelSpec, bioReplicateLabelSpec, conditionSpec, speciesSpec,
specimenSpec, analyteSpec, analysisTypeSpec, commentSpec);
Specification<SamplePreview> isDistinctSpec = SamplePreviewSpecs.isDistinct();
return Specification.where(experimentIdSpec).and(isBlankSpec)
.and(containsFilterSpec)
.and(isDistinctSpec);
}

private static class SamplePreviewSpecs {

//We need to ensure that we only count and retrieve unique samplePreviews
public static Specification<SamplePreview> isDistinct() {
return (root, query, builder) -> {
query.distinct(true);
return null;
};
}

//If no filter was provided return all SamplePreviews
public static Specification<SamplePreview> isBlank(String filter) {
return (root, query, builder) -> {
if (StringUtil.isBlank(filter)) {
return builder.conjunction();
}
return null;
};
}

public static Specification<SamplePreview> experimentIdEquals(ExperimentId experimentId) {
return (root, query, builder) ->
StringUtil.isBlank(experimentId.value()) ?
builder.conjunction() :
builder.equal(root.get("experimentId"), experimentId);
}

public static Specification<SamplePreview> sampleCodeContains(String filter) {
return (root, query, builder) ->
builder.like(root.get("sampleCode"), "%" + filter + "%");
}


public static Specification<SamplePreview> batchLabelContains(String filter) {
return (root, query, builder) ->
builder.like(root.get("batchLabel"), "%" + filter + "%");
}

public static Specification<SamplePreview> bioReplicateLabelContains(String filter) {
return (root, query, builder) ->
builder.like(root.get("bioReplicateLabel"), "%" + filter + "%");
}

public static Specification<SamplePreview> sampleLabelContains(String filter) {
return (root, query, builder) ->
builder.like(root.get("sampleLabel"), "%" + filter + "%");
}

public static Specification<SamplePreview> conditionContains(String filter) {
return (root, query, builder) -> {
Join<?, ?> expVariablesJoin = root.join("experimentalGroup").join("condition")
.join("variableLevels");
Expression<String> varNameExp = expVariablesJoin.get("variableName").as(String.class);
Expression<String> varValueValueExp = expVariablesJoin.get("experimentalValue").get("value")
.as(String.class);
Expression<String> varUnitExp = expVariablesJoin.get("experimentalValue").get("unit")
.as(String.class);
Predicate varValuePred = builder.like(varValueValueExp, "%" + filter + "%");
Predicate varUnitPred = builder.like(varUnitExp, "%" + filter + "%");
Predicate varNamePred = builder.like(varNameExp, "%" + filter + "%");
return builder.or(varNamePred, varValuePred, varUnitPred);
};
}

public static Specification<SamplePreview> speciesContains(String filter) {
return (root, query, builder) ->
builder.like(root.get("species"), "%" + filter + "%");
}

public static Specification<SamplePreview> specimenContains(String filter) {
return (root, query, builder) ->
builder.like(root.get("specimen"), "%" + filter + "%");
}

public static Specification<SamplePreview> analyteContains(String filter) {
return (root, query, builder) ->
builder.like(root.get("analyte"), "%" + filter + "%");
}

public static Specification<SamplePreview> analysisTypeContains(String filter) {
return (root, query, builder) ->
builder.like(root.get("analysisType"), "%" + filter + "%");
}

public static Specification<SamplePreview> commentContains(String filter) {
return (root, query, builder) ->
builder.like(root.get("comment"), "%" + filter + "%");
}

}
}
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