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load_stage.sql
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load_stage.sql
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/**************************************************************************
* Copyright 2016 Observational Health Data Sciences and Informatics (OHDSI)
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
* Authors: Timur Vakhitov, Christian Reich
* Date: 2017
**************************************************************************/
-- 1. Update latest_update field to new date
DO $_$
BEGIN
PERFORM VOCABULARY_PACK.SetLatestUpdate(
pVocabularyName => 'GCN_SEQNO',
pVocabularyDate => (SELECT vocabulary_date FROM sources.nddf_product_info LIMIT 1),
pVocabularyVersion => (SELECT vocabulary_version FROM sources.nddf_product_info LIMIT 1),
pVocabularyDevSchema => 'DEV_GCNSEQNO'
);
END $_$;
-- 2. Truncate all working tables
TRUNCATE TABLE concept_stage;
TRUNCATE TABLE concept_relationship_stage;
TRUNCATE TABLE concept_synonym_stage;
TRUNCATE TABLE pack_content_stage;
TRUNCATE TABLE drug_strength_stage;
--3. Add GCN_SEQNO to concept_stage from rxnconso
INSERT INTO concept_stage (
concept_name,
domain_id,
vocabulary_id,
concept_class_id,
standard_concept,
concept_code,
valid_start_date,
valid_end_date,
invalid_reason
)
SELECT SUBSTR(c.str, 1, 255) AS concept_name,
'Drug' AS domain_id,
'GCN_SEQNO' AS vocabulary_id,
'GCN_SEQNO' AS concept_class_id,
NULL AS standard_concept,
c.code AS concept_code,
(
SELECT v.latest_update
FROM vocabulary v
WHERE v.vocabulary_id = 'GCN_SEQNO'
) AS valid_start_date,
TO_DATE('20991231', 'yyyymmdd') AS valid_end_date,
NULL AS invalid_reason
FROM SOURCES.rxnconso c
WHERE c.sab = 'NDDF'
AND c.tty = 'CDC';
--4. Load into concept_relationship_stage
INSERT INTO concept_relationship_stage (
concept_code_1,
concept_code_2,
vocabulary_id_1,
vocabulary_id_2,
relationship_id,
valid_start_date,
valid_end_date,
invalid_reason
)
SELECT DISTINCT gcn.code AS concept_code_1,
rxn.code AS concept_code_2,
'GCN_SEQNO' AS vocabulary_id_1,
'RxNorm' AS vocabulary_id_2,
'Maps to' AS relationship_id,
(
SELECT v.latest_update
FROM vocabulary v
WHERE v.vocabulary_id = 'GCN_SEQNO'
) AS valid_start_date,
TO_DATE('20991231', 'yyyymmdd') AS valid_end_date,
NULL AS invalid_reason
FROM SOURCES.rxnconso gcn
JOIN SOURCES.rxnconso rxn ON rxn.rxcui = gcn.rxcui
AND rxn.sab = 'RXNORM'
WHERE gcn.sab = 'NDDF'
AND gcn.tty = 'CDC';
--5. Add mapping from deprecated to fresh concepts
DO $_$
BEGIN
PERFORM VOCABULARY_PACK.AddFreshMAPSTO();
END $_$;
--6. Deprecate 'Maps to' mappings to deprecated and upgraded concepts
DO $_$
BEGIN
PERFORM VOCABULARY_PACK.DeprecateWrongMAPSTO();
END $_$;
--7. Delete ambiguous 'Maps to' mappings
DO $_$
BEGIN
PERFORM VOCABULARY_PACK.DeleteAmbiguousMAPSTO();
END $_$;
-- At the end, the three tables concept_stage, concept_relationship_stage and concept_synonym_stage should be ready to be fed into the generic_update.sql script