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BI-2489 - Could Not Prepare Statment Error #48

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BI-2489 - Could Not Prepare Statment Error #48

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55 changes: 50 additions & 5 deletions src/main/java/org/brapi/test/BrAPITestServer/controller/germ/GermplasmApiController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,11 @@
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
import org.springframework.jdbc.core.namedparam.MapSqlParameterSource;
import org.springframework.jdbc.core.namedparam.NamedParameterJdbcTemplate;
import org.springframework.jdbc.core.namedparam.SqlParameterSource;
import org.springframework.stereotype.Controller;
import org.springframework.web.bind.annotation.CrossOrigin;
import org.springframework.web.bind.annotation.PathVariable;
Expand All @@ -48,15 +52,20 @@ public class GermplasmApiController extends BrAPIController implements Germplasm
private final PedigreeService pedigreeService;
private final SearchService searchService;
private final HttpServletRequest request;
private final NamedParameterJdbcTemplate jdbcTemplate;

@Autowired
public GermplasmApiController(GermplasmService germplasmService, PedigreeService pedigreeService,
SearchService searchService, HttpServletRequest request) {
public GermplasmApiController(GermplasmService germplasmService,
PedigreeService pedigreeService,
SearchService searchService,
HttpServletRequest request,
NamedParameterJdbcTemplate jdbcTemplate) {
this.germplasmService = germplasmService;
this.pedigreeService = pedigreeService;
this.searchService = searchService;
this.request = request;
}
this.jdbcTemplate = jdbcTemplate;
}

@CrossOrigin
@Override
Expand Down Expand Up @@ -182,12 +191,48 @@ public ResponseEntity<GermplasmListResponse> germplasmPost(@RequestBody List<Ger
return responseOK(new GermplasmListResponse(), new GermplasmListResponseResult(), data);
}

private String[] toArrayOrNull(List<String> list) {
if (list == null || list.isEmpty())
{
return null;
}
return list.toArray(new String[list.size()]);
}

@CrossOrigin
@Override
public ResponseEntity<? extends BrAPIResponse> searchGermplasmPost(@RequestBody GermplasmSearchRequest body,
@RequestHeader(value = "Authorization", required = false) String authorization)
throws BrAPIServerException {

// Prepare parameters.
SqlParameterSource namedParameters = new MapSqlParameterSource()
.addValue("accessionNumbers", toArrayOrNull(body.getAccessionNumbers()))
.addValue("binomialNames", toArrayOrNull(body.getBinomialNames()))
.addValue("collections", toArrayOrNull(body.getCollections()))
.addValue("commonCropNames", toArrayOrNull(body.getCommonCropNames()))
.addValue("externalReferenceIds", toArrayOrNull(body.getExternalReferenceIDs()))
.addValue("externalReferenceSources", toArrayOrNull(body.getExternalReferenceSources()))
.addValue("familyCodes", toArrayOrNull(body.getFamilyCodes()))
.addValue("genus_list", toArrayOrNull(body.getGenus()))
.addValue("germplasmDbIds", toArrayOrNull(body.getGermplasmDbIds()))
.addValue("germplasmNames", toArrayOrNull(body.getGermplasmNames()))
.addValue("germplasmPUIs", toArrayOrNull(body.getGermplasmPUIs()))
.addValue("instituteCodes", toArrayOrNull(body.getInstituteCodes()))
.addValue("parentDbIds", toArrayOrNull(body.getParentDbIds()))
.addValue("progenyDbIds", toArrayOrNull(body.getProgenyDbIds()))
.addValue("programDbIds", toArrayOrNull(body.getProgramDbIds()))
.addValue("programNames", toArrayOrNull(body.getProgramNames()))
.addValue("species_list", toArrayOrNull(body.getSpecies()))
.addValue("studyDbIds", toArrayOrNull(body.getStudyDbIds()))
.addValue("studyNames", toArrayOrNull(body.getStudyNames()))
.addValue("synonyms", toArrayOrNull(body.getSynonyms()))
.addValue("trialDbIds", toArrayOrNull(body.getTrialDbIds()))
.addValue("trialNames", toArrayOrNull(body.getTrialNames()));

String sql = "SELECT * FROM search_germplasm(:accessionNumbers, :binomialNames, :collections, :commonCropNames, :externalReferenceIds, :externalReferenceSources, :familyCodes, :genus_list, :germplasmDbIds, :germplasmNames, :germplasmPUIs, :instituteCodes, :parentDbIds, :progenyDbIds, :programDbIds, :programNames, :species_list, :studyDbIds, :studyNames, :synonyms, :trialDbIds, :trialNames);";
String result = jdbcTemplate.queryForObject(sql, namedParameters, String.class);

log.debug("Request: " + request.getRequestURI());
validateSecurityContext(request, "ROLE_ANONYMOUS", "ROLE_USER");
validateAcceptHeader(request);
Expand All @@ -197,8 +242,8 @@ public ResponseEntity<? extends BrAPIResponse> searchGermplasmPost(@RequestBody
if (searchReqDbId != null) {
return responseAccepted(searchReqDbId);
} else {
List<Germplasm> data = germplasmService.findGermplasm(body, metadata);
return responseOK(new GermplasmListResponse(), new GermplasmListResponseResult(), data, metadata);
//germplasmService.findGermplasm(body, metadata);
return new ResponseEntity(result, HttpStatus.OK);
}
}

Expand Down
226 changes: 226 additions & 0 deletions src/main/resources/db/migration/V002.014__search_germplasm_plpgsql.sql
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Original file line number Diff line number Diff line change
@@ -0,0 +1,226 @@

CREATE OR REPLACE FUNCTION search_germplasm(
accessionNumbers text[],
binomialNames text[],
collections text[],
commonCropNames text[],
externalReferenceIds text[],
externalReferenceSources text[],
familyCodes text[],
genus_list text[], -- TODO: make "genus" but handle name ambiguity.
germplasmDbIds text[],
germplasmNames text[],
germplasmPUIs text[],
instituteCodes text[],
parentDbIds text[],
progenyDbIds text[],
programDbIds text[],
programNames text[],
species_list text[], -- TODO: make "species" but handle name ambiguity.
studyDbIds text[],
studyNames text[],
synonyms text[],
trialDbIds text[],
trialNames text[]
)
RETURNS json AS $$
DECLARE
BEGIN
RETURN (
SELECT
json_build_object(
'@context', '[]'::json,
'metadata', '{}'::json, -- TODO: pagination, count, status, etc.
'result', json_build_object(
'data',
COALESCE(
json_agg(
json_build_object(
'germplasmDbId', g.id,
'germplasmName', g.germplasm_name,
'externalReferences', COALESCE((SELECT json_agg(
json_build_object('referenceID',
xr.external_reference_id,
'referenceId',
xr.external_reference_id,
'referenceSource',
xr.external_reference_source))
FROM germplasm_external_references gxr
LEFT JOIN external_reference xr ON gxr.external_references_id = xr.id
WHERE gxr.germplasm_entity_id = g.id), '[]'::json),
'additionalInfo', g.additional_info,
'accessionNumber', g.accession_number,
'acquisitionDate', TO_CHAR(g.acquisition_date, 'YYYY-MM-DD'),
'biologicalStatusOfAccessionCode', g.biological_status_of_accession_code,
'biologicalStatusOfAccessionDescription',
'TODO', -- TODO: store actual text value in database, currently only a java enum.
'breedingMethodDbId', g.breeding_method_id,
'breedingMethodName', bm.name,
'collection', g.collection,
'commonCropName', c.crop_name,
'countryOfOriginCode', g.country_of_origin_code,
'defaultDisplayName', g.default_display_name,
'documentationURL', g.documentationurl,
'donors', COALESCE((SELECT json_agg(
json_build_object('donorAccessionNumber',
donor.donor_accession_number,
'donorInstituteCode',
donor.donor_institute_code,
'germplasmPUI',
donor.germplasmpui)
)
FROM germplasm_donor donor
WHERE donor.germplasm_id = g.id), '[]'::json),
'genus', g.genus,
'germplasmOrigin',
COALESCE(
(SELECT json_agg(
json_build_object(
'coordinateUncertainty', go.coordinate_uncertainty,
'coordinates', json_build_object(
'geometry', json_build_object(
'coordinates',
json_build_array(crd.latitude, crd.longitude, crd.altitude),
'type', geo.type
),
'type',
'Feature' -- TODO: is this dynamic, or hard coded?
)
)
)
FROM germplasm_origin go
LEFT JOIN geojson geo ON go.coordinates_id = geo.id
LEFT JOIN coordinate crd on geo.id = crd.geojson_id
WHERE go.germplasm_id = g.id),
'[]'::json
),
'germplasmPUI', g.germplasmpui,
'germplasmPreprocessing', g.germplasm_preprocessing,
'instituteCode', gi.institute_code,
'instituteName', gi.institute_name,
'pedigree', COALESCE(this_node.pedigree_string, ''), -- TODO: is this the best way?
'seedSource', g.seed_source,
'seedSourceDescription', g.seed_source_description,
'species', g.species,
'speciesAuthority', g.species_authority,
-- TODO: store actual text values for storageTypes in the database!! This is only for demo purpose, the data isn't meaningful.
'storageTypes', COALESCE((SELECT json_agg(json_build_object('code',
stor.type_of_germplasm_storage_code,
'description', 'TODO'))
FROM germplasm_entity_type_of_germplasm_storage_code stor
WHERE stor.germplasm_entity_id = g.id), '[]'::json),
'subtaxa', g.subtaxa,
'subtaxaAuthority', g.subtaxa_authority,
'synonyms',
COALESCE((SELECT json_agg(json_build_object('synonym', s.synonym, 'type', s.type))
FROM germplasm_synonym s
WHERE s.germplasm_id = g.id), '[]'::json),
'taxonIds', COALESCE(
(SELECT json_agg(json_build_object('sourceName', taxon.source_name,
'taxonId', taxon.taxon_id))
FROM germplasm_taxon taxon
WHERE taxon.germplasm_id = g.id), '[]'::json)
)
)
,
'[]'::json
)
)

)



FROM
germplasm g
LEFT JOIN
breeding_method bm ON g.breeding_method_id = bm.id
LEFT JOIN
crop c ON g.crop_id = c.id
LEFT JOIN
germplasm_institute gi ON g.id = gi.germplasm_id
LEFT JOIN
pedigree_node this_node ON g.id = this_node.germplasm_id
WHERE
(accessionNumbers IS NULL OR accessionNumbers @> ARRAY[g.accession_number])
AND
(binomialNames IS NULL OR
binomialNames @> ARRAY[g.genus || ' ' || g.species]) -- TODO: potentially expand.
AND
(collections IS NULL OR collections @> ARRAY[g.collection])
AND
(commonCropNames IS NULL OR commonCropNames @> ARRAY[c.crop_name])
AND
(
COALESCE(externalReferenceIds, externalReferenceSources) IS NULL
OR
(
g.id IN
(SELECT germplasm_entity_id
FROM germplasm_external_references gxr
JOIN external_reference xr ON gxr.external_references_id = xr.id
WHERE externalReferenceIds @> ARRAY[xr.external_reference_id]
AND externalReferenceSources @> ARRAY[xr.external_reference_source])
)
)
AND
(familyCodes IS NULL OR familyCodes @> ARRAY[family_code]) -- TODO: double check this.
AND
(genus_list IS NULL OR genus_list @> ARRAY[g.genus])
AND
(germplasmDbIds IS NULL OR germplasmDbIds @> ARRAY[g.id])
AND
(germplasmNames IS NULL OR germplasmNames @> ARRAY[g.germplasm_name])
AND
(germplasmPUIs IS NULL OR germplasmPUIs @> ARRAY[g.germplasmpui])
AND
(instituteCodes IS NULL OR instituteCodes @> ARRAY[gi.institute_code])
AND
(
parentDbIds IS NULL
OR
-- Get germplasm by parentDbIds. -- TODO: hardcoded EdgeType (parent=0, child=1, sibling=2)
g.id IN (SELECT child.germplasm_id
FROM pedigree_node parent
JOIN pedigree_edge e ON parent.id = e.connceted_node_id AND e.edge_type = 0
JOIN pedigree_node child ON e.this_node_id = child.id
WHERE parentDbIds @> ARRAY[parent.id])
)
AND
(
progenyDbIds IS NULL
OR
-- Get germplasm by progenyDbIds. -- TODO: hardcoded EdgeType (parent=0, child=1, sibling=2)
g.id IN (SELECT parent.germplasm_id
FROM pedigree_node parent
JOIN pedigree_edge e ON parent.id = e.connceted_node_id AND e.edge_type = 0
JOIN pedigree_node child ON e.this_node_id = child.id
WHERE progenyDbIds @> ARRAY[child.id])
)
-- TODO: germplasm doesn't seem to have relationship to program.
-- AND
-- (programDbIds IS NULL OR programDbIds @> ARRAY[])
-- AND
-- (programNames IS NULL OR programNames @> ARRAY[])
AND
(species_list IS NULL OR species_list @> ARRAY[g.species])
-- TODO: germplasm doesn't seem to have relationship to study.
-- AND
-- (studyDbIds IS NULL OR studyDbIds @> ARRAY[])
-- AND
-- (studyNames IS NULL OR studyNames @> ARRAY[])
AND
(
synonyms IS NULL
OR
g.id IN
(SELECT gs.germplasm_id FROM germplasm_synonym gs WHERE synonyms @> ARRAY[gs.synonym])
)
-- TODO: germplasm doesn't seem to have relationship to program.
-- AND
-- (trialDbIds IS NULL OR trialDbIds @> ARRAY[])
-- AND
-- (trialNames IS NULL OR trialNames @> ARRAY[])
);
END;
$$ LANGUAGE plpgsql;