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Lint things
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Luke Sikina committed Oct 11, 2024
1 parent e749611 commit de8397f
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Showing 40 changed files with 664 additions and 851 deletions.
6 changes: 3 additions & 3 deletions src/main/java/edu/harvard/dbmi/avillach/dictionary/DictionaryApplication.java
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Original file line number Diff line number Diff line change
Expand Up @@ -6,8 +6,8 @@
@SpringBootApplication
public class DictionaryApplication {

public static void main(String[] args) {
SpringApplication.run(DictionaryApplication.class, args);
}
public static void main(String[] args) {
SpringApplication.run(DictionaryApplication.class, args);
}

}
33 changes: 9 additions & 24 deletions src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -22,25 +22,19 @@ public class ConceptController {
private Integer MAX_DEPTH;


public ConceptController(
@Autowired ConceptService conceptService
) {
public ConceptController(@Autowired ConceptService conceptService) {
this.conceptService = conceptService;
}


@PostMapping(path = "/concepts")
public ResponseEntity<Page<Concept>> listConcepts(
@RequestBody Filter filter,
@RequestParam(name = "page_number", defaultValue = "0", required = false) int page,
@RequestBody Filter filter, @RequestParam(name = "page_number", defaultValue = "0", required = false) int page,
@RequestParam(name = "page_size", defaultValue = "10", required = false) int size
) {
PageRequest pagination = PageRequest.of(page, size);
PageImpl<Concept> pageResp = new PageImpl<>(
conceptService.listConcepts(filter, pagination),
pagination,
conceptService.countConcepts(filter)
);
PageImpl<Concept> pageResp =
new PageImpl<>(conceptService.listConcepts(filter, pagination), pagination, conceptService.countConcepts(filter));

return ResponseEntity.ok(pageResp);
}
Expand All @@ -52,35 +46,26 @@ public ResponseEntity<Page<Concept>> dumpConcepts(
) {
PageRequest pagination = PageRequest.of(page, size);
PageImpl<Concept> pageResp = new PageImpl<>(
conceptService.listDetailedConcepts(new Filter(List.of(), "", List.of()), pagination),
pagination,
conceptService.listDetailedConcepts(new Filter(List.of(), "", List.of()), pagination), pagination,
conceptService.countConcepts(new Filter(List.of(), "", List.of()))
);

return ResponseEntity.ok(pageResp);
}

@PostMapping(path = "/concepts/detail/{dataset}")
public ResponseEntity<Concept> conceptDetail(
@PathVariable(name = "dataset") String dataset,
@RequestBody() String conceptPath
) {
return conceptService.conceptDetail(dataset, conceptPath)
.map(ResponseEntity::ok)
.orElse(ResponseEntity.notFound().build());
public ResponseEntity<Concept> conceptDetail(@PathVariable(name = "dataset") String dataset, @RequestBody() String conceptPath) {
return conceptService.conceptDetail(dataset, conceptPath).map(ResponseEntity::ok).orElse(ResponseEntity.notFound().build());
}

@PostMapping(path = "/concepts/tree/{dataset}")
public ResponseEntity<Concept> conceptTree(
@PathVariable(name = "dataset") String dataset,
@RequestBody() String conceptPath,
@PathVariable(name = "dataset") String dataset, @RequestBody() String conceptPath,
@RequestParam(name = "depth", required = false, defaultValue = "2") Integer depth
) {
if (depth < 0 || depth > MAX_DEPTH) {
return ResponseEntity.badRequest().build();
}
return conceptService.conceptTree(dataset, conceptPath, depth)
.map(ResponseEntity::ok)
.orElse(ResponseEntity.notFound().build());
return conceptService.conceptTree(dataset, conceptPath, depth).map(ResponseEntity::ok).orElse(ResponseEntity.notFound().build());
}
}
89 changes: 41 additions & 48 deletions src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptFilterQueryGenerator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -34,40 +34,35 @@ AND concept_node_meta.KEY IN (:disallowed_meta_keys)
""";

private static final String CONSENT_QUERY = """
dataset.dataset_id IN (
SELECT
consent.dataset_id
FROM consent
LEFT JOIN dataset ON dataset.dataset_id = consent.dataset_id
WHERE
concat(dataset.ref, '.', consent.consent_code) IN (:consents) OR
(dataset.ref IN (:consents) AND consent.consent_code = '')
UNION
SELECT
dataset_harmonization.harmonized_dataset_id
FROM consent
JOIN dataset_harmonization ON dataset_harmonization.source_dataset_id = consent.dataset_id
LEFT JOIN dataset ON dataset.dataset_id = dataset_harmonization.source_dataset_id
WHERE
concat(dataset.ref, '.', consent.consent_code) IN (:consents) OR
(dataset.ref IN (:consents) AND consent.consent_code = '')
) AND
""";
dataset.dataset_id IN (
SELECT
consent.dataset_id
FROM consent
LEFT JOIN dataset ON dataset.dataset_id = consent.dataset_id
WHERE
concat(dataset.ref, '.', consent.consent_code) IN (:consents) OR
(dataset.ref IN (:consents) AND consent.consent_code = '')
UNION
SELECT
dataset_harmonization.harmonized_dataset_id
FROM consent
JOIN dataset_harmonization ON dataset_harmonization.source_dataset_id = consent.dataset_id
LEFT JOIN dataset ON dataset.dataset_id = dataset_harmonization.source_dataset_id
WHERE
concat(dataset.ref, '.', consent.consent_code) IN (:consents) OR
(dataset.ref IN (:consents) AND consent.consent_code = '')
) AND
""";

@Autowired
public ConceptFilterQueryGenerator(
@Value("${filtering.unfilterable_concepts}") List<String> disallowedMetaFields
) {
public ConceptFilterQueryGenerator(@Value("${filtering.unfilterable_concepts}") List<String> disallowedMetaFields) {
this.disallowedMetaFields = disallowedMetaFields;
}

/**
* This generates a query that will return a list of concept_node IDs for the given filter.
* <p>
* A filter object has a list of facets, each belonging to a category. Within a category,
* facets are ORed together. Between categories, facets are ANDed together.
* In SQL, this is represented as N clauses for N facets, all INTERSECTed together. Search
* also acts as its own special facet here.
* This generates a query that will return a list of concept_node IDs for the given filter. <p> A filter object has a list of facets,
* each belonging to a category. Within a category, facets are ORed together. Between categories, facets are ANDed together. In SQL,
* this is represented as N clauses for N facets, all INTERSECTed together. Search also acts as its own special facet here.
*
* @param filter universal filter object for the page
* @param pageable pagination, if applicable
Expand Down Expand Up @@ -113,8 +108,7 @@ ORDER BY max((1 + rank) * coalesce(rank_adjustment, 1)) DESC, q.concept_node_id
LIMIT :limit
OFFSET :offset
""";
params.addValue("limit", pageable.getPageSize())
.addValue("offset", pageable.getOffset());
params.addValue("limit", pageable.getPageSize()).addValue("offset", pageable.getOffset());
}

superQuery = " concepts_filtered_sorted AS (\n" + superQuery + "\n)";
Expand Down Expand Up @@ -150,26 +144,26 @@ private String createValuelessNodeFilter(String search, List<String> consents) {
continuous_max.value <> '' OR
categorical_values.value <> ''
)
""".formatted(rankQuery, rankWhere, consentWhere);
"""
.formatted(rankQuery, rankWhere, consentWhere);
}

private List<String> createFacetFilter(Filter filter, MapSqlParameterSource params) {
String consentWhere = CollectionUtils.isEmpty(filter.consents()) ? "" : CONSENT_QUERY;
return filter.facets().stream()
.collect(Collectors.groupingBy(Facet::category))
.entrySet().stream()
.map(facetsForCategory -> {
params
// The templating here is to namespace the params for each facet category in the query
.addValue("facets_for_category_%s".formatted(facetsForCategory.getKey()), facetsForCategory.getValue().stream().map(Facet::name).toList())
.addValue("category_%s".formatted(facetsForCategory.getKey()), facetsForCategory.getKey());
String rankQuery = "0";
String rankWhere = "";
if (StringUtils.hasLength(filter.search())) {
rankQuery = "ts_rank(searchable_fields, (phraseto_tsquery(:search)::text || ':*')::tsquery)";
rankWhere = "concept_node.searchable_fields @@ (phraseto_tsquery(:search)::text || ':*')::tsquery AND";
}
return """
return filter.facets().stream().collect(Collectors.groupingBy(Facet::category)).entrySet().stream().map(facetsForCategory -> {
params
// The templating here is to namespace the params for each facet category in the query
.addValue(
"facets_for_category_%s".formatted(facetsForCategory.getKey()),
facetsForCategory.getValue().stream().map(Facet::name).toList()
).addValue("category_%s".formatted(facetsForCategory.getKey()), facetsForCategory.getKey());
String rankQuery = "0";
String rankWhere = "";
if (StringUtils.hasLength(filter.search())) {
rankQuery = "ts_rank(searchable_fields, (phraseto_tsquery(:search)::text || ':*')::tsquery)";
rankWhere = "concept_node.searchable_fields @@ (phraseto_tsquery(:search)::text || ':*')::tsquery AND";
}
return """
(
SELECT
facet__concept_node.concept_node_id AS concept_node_id,
Expand All @@ -187,8 +181,7 @@ facet.name IN (:facets_for_category_%s ) AND facet_category.name = :category_%s
facet__concept_node.concept_node_id
)
""".formatted(rankQuery, rankWhere, consentWhere, facetsForCategory.getKey(), facetsForCategory.getKey());
})
.toList();
}).toList();
}

}
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