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Refactor dao classes to extract param build, row insert (#1001)
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@dexamundsen
dexamundsen committed Sep 17, 2024
1 parent eb38866 commit d5bd468
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Showing 17 changed files with 374 additions and 232 deletions.
1 change: 1 addition & 0 deletions gradle/config/checkstyle/suppressions.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,7 @@
<suppress checks="JavadocStyle"/>
<suppress checks="JavadocType"/>
<suppress checks="JavaNCSS"/>
<suppress checks="ParameterNumber"/>
<!-- Spotless is canonical for line length. -->
<suppress checks="LineLength"/>
<suppress checks="MethodLength"/>
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60 changes: 30 additions & 30 deletions service/src/main/java/bio/terra/tanagra/app/controller/CohortsApiController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -195,36 +195,36 @@ public ResponseEntity<ApiInstanceCountList> queryCohortCounts(

private static CohortRevision.CriteriaGroupSection fromApiObject(ApiCriteriaGroupSection apiObj) {
BooleanAndOrFilter.LogicalOperator operator;
JoinOperator joinOperator =
switch (apiObj.getOperator()) {
case OR -> {
operator = BooleanAndOrFilter.LogicalOperator.OR;
yield null;
}
case AND -> {
operator = BooleanAndOrFilter.LogicalOperator.AND;
yield null;
}
case DURING_SAME_ENCOUNTER -> {
operator = BooleanAndOrFilter.LogicalOperator.OR;
yield JoinOperator.DURING_SAME_ENCOUNTER;
}
case WITHIN_NUM_DAYS -> {
operator = BooleanAndOrFilter.LogicalOperator.OR;
yield JoinOperator.WITHIN_NUM_DAYS;
}
case NUM_DAYS_BEFORE -> {
operator = BooleanAndOrFilter.LogicalOperator.OR;
yield JoinOperator.NUM_DAYS_BEFORE;
}
case NUM_DAYS_AFTER -> {
operator = BooleanAndOrFilter.LogicalOperator.OR;
yield JoinOperator.NUM_DAYS_AFTER;
}
default ->
throw new IllegalArgumentException(
"Unknown criteria group section operator: " + apiObj.getOperator());
};
JoinOperator joinOperator;
switch (apiObj.getOperator()) {
case OR:
operator = BooleanAndOrFilter.LogicalOperator.OR;
joinOperator = null;
break;
case AND:
operator = BooleanAndOrFilter.LogicalOperator.AND;
joinOperator = null;
break;
case DURING_SAME_ENCOUNTER:
operator = BooleanAndOrFilter.LogicalOperator.OR;
joinOperator = JoinOperator.DURING_SAME_ENCOUNTER;
break;
case WITHIN_NUM_DAYS:
operator = BooleanAndOrFilter.LogicalOperator.OR;
joinOperator = JoinOperator.WITHIN_NUM_DAYS;
break;
case NUM_DAYS_BEFORE:
operator = BooleanAndOrFilter.LogicalOperator.OR;
joinOperator = JoinOperator.NUM_DAYS_BEFORE;
break;
case NUM_DAYS_AFTER:
operator = BooleanAndOrFilter.LogicalOperator.OR;
joinOperator = JoinOperator.NUM_DAYS_AFTER;
break;
default:
throw new IllegalArgumentException(
"Unknown criteria group section operator: " + apiObj.getOperator());
}

return CohortRevision.CriteriaGroupSection.builder()
.id(apiObj.getId())
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177 changes: 112 additions & 65 deletions service/src/main/java/bio/terra/tanagra/db/AnnotationDao.java
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@
import bio.terra.tanagra.service.artifact.model.AnnotationKey;
import bio.terra.tanagra.service.artifact.model.AnnotationValue;
import jakarta.annotation.Nullable;
import java.sql.Date;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
Expand Down Expand Up @@ -78,37 +79,21 @@ public AnnotationDao(NamedParameterJdbcTemplate jdbcTemplate) {

@WriteTransaction
public void createAnnotationKey(String cohortId, AnnotationKey annotationKey) {
String sql =
"INSERT INTO annotation_key (cohort_id, id, display_name, description, data_type) "
+ "VALUES (:cohort_id, :id, :display_name, :description, :data_type)";
LOGGER.debug("CREATE annotation key: {}", sql);
MapSqlParameterSource params =
new MapSqlParameterSource()
.addValue("cohort_id", cohortId)
.addValue("id", annotationKey.getId())
.addValue("display_name", annotationKey.getDisplayName())
.addValue("description", annotationKey.getDescription())
.addValue("data_type", annotationKey.getDataType().name());
int rowsAffected = jdbcTemplate.update(sql, params);
LOGGER.debug("CREATE annotation key rowsAffected = {}", rowsAffected);
MapSqlParameterSource keyParamSets =
buildKeyParam(
cohortId,
annotationKey.getId(),
annotationKey.getDisplayName(),
annotationKey.getDescription(),
annotationKey.getDataType().name());
insertKeyRows(List.of(keyParamSets));

if (!annotationKey.getEnumVals().isEmpty()) {
sql =
"INSERT INTO annotation_key_enum_value (cohort_id, annotation_key_id, enum) "
+ "VALUES (:cohort_id, :annotation_key_id, :enum)";
LOGGER.debug("CREATE annotation key enum value: {}", sql);
MapSqlParameterSource[] enumParamSets =
List<MapSqlParameterSource> enumValueParamSets =
annotationKey.getEnumVals().stream()
.map(
ev ->
new MapSqlParameterSource()
.addValue("cohort_id", cohortId)
.addValue("annotation_key_id", annotationKey.getId())
.addValue("enum", ev))
.toList()
.toArray(new MapSqlParameterSource[0]);
rowsAffected = Arrays.stream(jdbcTemplate.batchUpdate(sql, enumParamSets)).sum();
LOGGER.debug("CREATE annotation key enum value rowsAffected = {}", rowsAffected);
.map(val -> buildEnumValueParam(cohortId, annotationKey.getId(), val))
.toList();
insertEnumValueRows(enumValueParamSets);
}
}

Expand Down Expand Up @@ -189,36 +174,29 @@ private List<AnnotationKey> getAnnotationKeysHelper(
return Collections.emptyList();
}

// Fetch enum vals. (annotation key id -> enum)
String sql =
ANNOTATION_KEY_ENUM_VALUE_SELECT_SQL + " WHERE annotation_key_id IN (:annotation_key_ids)";
MapSqlParameterSource params =
new MapSqlParameterSource()
.addValue(
"annotation_key_ids",
annotationKeys.stream()
.map(AnnotationKey.Builder::getId)
.collect(Collectors.toSet()));
List<Pair<String, String>> enumVals =
jdbcTemplate.query(sql, params, ANNOTATION_KEY_ENUM_VALUE_ROW_MAPPER);

// Put enum vals into their respective annotation keys.
Map<String, AnnotationKey.Builder> annotationKeysMap =
annotationKeys.stream()
.collect(Collectors.toMap(AnnotationKey.Builder::getId, Function.identity()));
enumVals.forEach(
pair -> {
String annotationKeyId = pair.getKey();
String enumVal = pair.getValue();
annotationKeysMap.get(annotationKeyId).addEnumVal(enumVal);
});

// Fetch enum vals. (annotation key id -> enum)
List<Pair<String, String>> enumVals = getEnumValuesMatchingList(annotationKeysMap.keySet());
enumVals.forEach(pair -> annotationKeysMap.get(pair.getKey()).addEnumVal(pair.getValue()));

// Preserve the order returned by the original query.
return annotationKeys.stream()
.map(a -> annotationKeysMap.get(a.getId()).build())
.collect(Collectors.toList());
}

public List<Pair<String, String>> getEnumValuesMatchingList(Set<String> keyIds) {
String sql =
ANNOTATION_KEY_ENUM_VALUE_SELECT_SQL + " WHERE annotation_key_id IN (:annotation_key_ids)";
MapSqlParameterSource params =
new MapSqlParameterSource().addValue("annotation_key_ids", keyIds);
return jdbcTemplate.query(sql, params, ANNOTATION_KEY_ENUM_VALUE_ROW_MAPPER);
}

@WriteTransaction
@SuppressWarnings("PMD.UseObjectForClearerAPI")
public void updateAnnotationKey(
Expand Down Expand Up @@ -268,27 +246,21 @@ public void updateAnnotationValues(
LOGGER.debug("DELETE annotation values rowsAffected = {}", rowsAffected);

// Write the annotation values.
sql =
"INSERT INTO annotation_value (cohort_id, annotation_key_id, review_id, primary_entity_instance_id, bool_val, int64_val, string_val, date_val) "
+ "VALUES (:cohort_id, :annotation_key_id, :review_id, :primary_entity_instance_id, :bool_val, :int64_val, :string_val, :date_val)";
LOGGER.debug("CREATE annotation values: {}", sql);
MapSqlParameterSource[] valueParamSets =
List<MapSqlParameterSource> valueParamSets =
annotationValues.stream()
.map(
av ->
new MapSqlParameterSource()
.addValue("cohort_id", cohortId)
.addValue("annotation_key_id", annotationKeyId)
.addValue("review_id", reviewId)
.addValue("primary_entity_instance_id", instanceId)
.addValue("bool_val", av.getBooleanVal())
.addValue("int64_val", av.getInt64Val())
.addValue("string_val", av.getStringVal())
.addValue("date_val", av.getDateVal()))
.toList()
.toArray(new MapSqlParameterSource[0]);
rowsAffected = Arrays.stream(jdbcTemplate.batchUpdate(sql, valueParamSets)).sum();
LOGGER.debug("CREATE annotation values rowsAffected = {}", rowsAffected);
buildValueParam(
cohortId,
annotationKeyId,
reviewId,
instanceId,
av.getBooleanVal(),
av.getInt64Val(),
av.getStringVal(),
av.getDateVal()))
.toList();
insertValueRows(valueParamSets);
}

@ReadTransaction
Expand All @@ -298,4 +270,79 @@ public List<AnnotationValue.Builder> getAllAnnotationValues(String cohortId) {
MapSqlParameterSource params = new MapSqlParameterSource().addValue("cohort_id", cohortId);
return jdbcTemplate.query(sql, params, ANNOTATION_VALUE_ROW_MAPPER);
}

void insertKeyRows(List<MapSqlParameterSource> keyParamSets) {
String sql =
"INSERT INTO annotation_key (cohort_id, id, display_name, description, data_type) "
+ "VALUES (:cohort_id, :id, :display_name, :description, :data_type)";
LOGGER.debug("CREATE annotation key: {}", sql);
int rowsAffected =
Arrays.stream(
jdbcTemplate.batchUpdate(sql, keyParamSets.toArray(new MapSqlParameterSource[0])))
.sum();
LOGGER.debug("CREATE annotation key rowsAffected = {}", rowsAffected);
}

void insertEnumValueRows(List<MapSqlParameterSource> enumValueParamSets) {
String sql =
"INSERT INTO annotation_key_enum_value (cohort_id, annotation_key_id, enum) "
+ "VALUES (:cohort_id, :annotation_key_id, :enum)";
LOGGER.debug("CREATE annotation key enum value: {}", sql);
int rowsAffected =
Arrays.stream(
jdbcTemplate.batchUpdate(
sql, enumValueParamSets.toArray(new MapSqlParameterSource[0])))
.sum();
LOGGER.debug("CREATE annotation key enum value rowsAffected = {}", rowsAffected);
}

void insertValueRows(List<MapSqlParameterSource> valueParamSets) {
// Write the annotation values.
String sql =
"INSERT INTO annotation_value (cohort_id, annotation_key_id, review_id, primary_entity_instance_id, bool_val, int64_val, string_val, date_val) "
+ "VALUES (:cohort_id, :annotation_key_id, :review_id, :primary_entity_instance_id, :bool_val, :int64_val, :string_val, :date_val)";
LOGGER.debug("CREATE annotation values: {}", sql);
int rowsAffected =
Arrays.stream(
jdbcTemplate.batchUpdate(sql, valueParamSets.toArray(new MapSqlParameterSource[0])))
.sum();
LOGGER.debug("CREATE annotation values rowsAffected = {}", rowsAffected);
}

MapSqlParameterSource buildKeyParam(
String cohortId, String id, String displayName, String description, String dataTypeName) {
return new MapSqlParameterSource()
.addValue("cohort_id", cohortId)
.addValue("id", id)
.addValue("display_name", displayName)
.addValue("description", description)
.addValue("data_type", dataTypeName);
}

MapSqlParameterSource buildEnumValueParam(String cohortId, String keyId, String enumValue) {
return new MapSqlParameterSource()
.addValue("cohort_id", cohortId)
.addValue("annotation_key_id", keyId)
.addValue("enum", enumValue);
}

MapSqlParameterSource buildValueParam(
String cohortId,
String keyId,
String reviewId,
String instanceId,
Boolean booelanVal,
Long int64Val,
String stringVal,
Date dateVal) {
return new MapSqlParameterSource()
.addValue("cohort_id", cohortId)
.addValue("annotation_key_id", keyId)
.addValue("review_id", reviewId)
.addValue("primary_entity_instance_id", instanceId)
.addValue("bool_val", booelanVal)
.addValue("int64_val", int64Val)
.addValue("string_val", stringVal)
.addValue("date_val", dateVal);
}
}
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