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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: 2021
**************************************************************************/
--1. Update latest_update field to new date
DO $_$
BEGIN
PERFORM VOCABULARY_PACK.SetLatestUpdate(
pVocabularyName => 'NDC',
pVocabularyDate => (SELECT vocabulary_date FROM sources.product LIMIT 1),
pVocabularyVersion => (SELECT vocabulary_version FROM sources.product LIMIT 1),
pVocabularyDevSchema => 'DEV_NDC'
);
PERFORM VOCABULARY_PACK.SetLatestUpdate(
pVocabularyName => 'SPL',
pVocabularyDate => (SELECT vocabulary_date FROM sources.product LIMIT 1),
pVocabularyVersion => (SELECT vocabulary_version FROM sources.product LIMIT 1),
pVocabularyDevSchema => 'DEV_NDC',
pAppendVocabulary => TRUE
);
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. Create necessary functions
--get aggregated dose
CREATE OR REPLACE FUNCTION GetAggrDose (active_numerator_strength IN VARCHAR, active_ingred_unit IN VARCHAR) RETURNS VARCHAR
AS
$BODY$
DECLARE
z VARCHAR(4000);
BEGIN
SELECT STRING_AGG(a_n_s||a_i_u, ' / ' ORDER BY LPAD(a_n_s||a_i_u,50,'0')) INTO z FROM
(
SELECT * FROM (
SELECT DISTINCT
UNNEST(regexp_matches(active_numerator_strength, '[^; ]+', 'g')) a_n_s,
UNNEST(regexp_matches(active_ingred_unit, '[^; ]+', 'g')) a_i_u
) AS s0
) AS s1;
RETURN z;
END;
$BODY$
LANGUAGE 'plpgsql' IMMUTABLE PARALLEL SAFE;
--get unique dose
CREATE OR REPLACE FUNCTION GetDistinctDose (active_numerator_strength IN VARCHAR, active_ingred_unit IN VARCHAR, p IN INT) RETURNS VARCHAR
AS
$BODY$
DECLARE
z VARCHAR(4000);
BEGIN
IF p=1 THEN --distinct active_numerator_strength values
SELECT STRING_AGG(a_n_s, '; ' ORDER BY LPAD(a_n_s,50,'0')) INTO z FROM
(
SELECT * FROM (
SELECT DISTINCT
UNNEST(regexp_matches(active_numerator_strength, '[^; ]+', 'g')) a_n_s,--::numeric::varchar a_n_s, --double cast to convert corrupted values e.g. '.7' to 0.7 (numeric) and then back to a text value /*disabled atm*/
UNNEST(regexp_matches(active_ingred_unit, '[^; ]+', 'g')) a_i_u
) AS s0
) AS s1;
ELSE --distinct active_ingred_unit values (but order by active_numerator_strength!)
SELECT STRING_AGG(a_i_u, '; ' ORDER BY LPAD(a_n_s,50,'0')) INTO z FROM
(
SELECT * FROM (
SELECT DISTINCT
UNNEST(regexp_matches(active_numerator_strength, '[^; ]+', 'g')) a_n_s,
UNNEST(regexp_matches(active_ingred_unit, '[^; ]+', 'g')) a_i_u
) AS s0
) AS s1;
END IF;
RETURN z;
END;
$BODY$
LANGUAGE 'plpgsql' IMMUTABLE PARALLEL SAFE;
--4. Load upgraded SPL concepts
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 vocabulary_pack.CutConceptName(spl_name) AS concept_name,
CASE
WHEN displayname IN ('COSMETIC')
THEN 'Observation'
WHEN displayname IN (
'MEDICAL DEVICE',
'OTC MEDICAL DEVICE LABEL',
'PRESCRIPTION MEDICAL DEVICE LABEL',
'MEDICAL FOOD',
'DIETARY SUPPLEMENT'
)
THEN 'Device'
ELSE 'Drug'
END AS domain_id,
'SPL' AS vocabulary_id,
CASE
WHEN displayname IN ('BULK INGREDIENT')
THEN 'Ingredient'
WHEN displayname IN (
'CELLULAR THERAPY',
'LICENSED MINIMALLY MANIPULATED CELLS LABEL'
)
THEN 'Cellular Therapy'
WHEN displayname IN ('COSMETIC')
THEN 'Cosmetic'
WHEN displayname IN ('DIETARY SUPPLEMENT')
THEN 'Supplement'
WHEN displayname IN ('HUMAN OTC DRUG LABEL')
THEN 'OTC Drug'
WHEN displayname IN (
'MEDICAL DEVICE',
'OTC MEDICAL DEVICE LABEL',
'PRESCRIPTION MEDICAL DEVICE LABEL'
)
THEN 'Device'
WHEN displayname IN ('MEDICAL FOOD')
THEN 'Food'
WHEN displayname IN ('NON-STANDARDIZED ALLERGENIC LABEL')
THEN 'Non-Stand Allergenic'
WHEN displayname IN ('OTC ANIMAL DRUG LABEL')
THEN 'Animal Drug'
WHEN displayname IN ('PLASMA DERIVATIVE')
THEN 'Plasma Derivative'
WHEN displayname IN ('STANDARDIZED ALLERGENIC')
THEN 'Standard Allergenic'
WHEN displayname IN ('VACCINE LABEL')
THEN 'Vaccine'
ELSE 'Prescription Drug'
END AS concept_class_id,
NULL AS standard_concept,
replaced_spl AS concept_code,
TO_DATE('19700101', 'YYYYMMDD') AS valid_start_date,
spl_date - 1 AS valid_end_date,
'U' AS invalid_reason
FROM (
SELECT DISTINCT FIRST_VALUE(COALESCE(s2.concept_name, c.concept_name)) OVER (
PARTITION BY l.replaced_spl ORDER BY s.valid_start_date,
s.concept_code ROWS BETWEEN unbounded preceding
AND UNBOUNDED FOLLOWING
) spl_name,
FIRST_VALUE(s.displayname) OVER (
PARTITION BY l.replaced_spl ORDER BY s.valid_start_date,
s.concept_code ROWS BETWEEN unbounded preceding
AND UNBOUNDED FOLLOWING
) displayname,
FIRST_VALUE(s.valid_start_date) OVER (
PARTITION BY l.replaced_spl ORDER BY s.valid_start_date ROWS BETWEEN unbounded preceding
AND UNBOUNDED FOLLOWING
) spl_date,
l.replaced_spl
FROM (
SELECT s_int.concept_code,
s_int.replaced_spl,
s_int.displayname,
MIN(s_int.valid_start_date) AS valid_start_date
FROM sources.spl_ext s_int
WHERE s_int.replaced_spl IS NOT NULL -- if there is an SPL codes ( l ) that is mentioned in another record as replaced_spl (path /document/relatedDocument/relatedDocument/setId/@root)
GROUP BY s_int.concept_code,
s_int.replaced_spl,
s_int.displayname
) s
CROSS JOIN LATERAL(SELECT UNNEST(regexp_matches(s.replaced_spl, '[^;]+', 'g')) AS replaced_spl) l
LEFT JOIN concept c ON c.vocabulary_id = 'SPL'
AND c.concept_code = l.replaced_spl
LEFT JOIN sources.spl_ext s2 ON s2.concept_code = l.replaced_spl
) AS s0
WHERE spl_name IS NOT NULL
AND displayname NOT IN (
'IDENTIFICATION OF CBER-REGULATED GENERIC DRUG FACILITY',
'INDEXING - PHARMACOLOGIC CLASS',
'INDEXING - SUBSTANCE',
'WHOLESALE DRUG DISTRIBUTORS AND THIRD-PARTY LOGISTICS FACILITY REPORT'
);
--5. Load main SPL concepts into concept_stage
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 vocabulary_pack.CutConceptName(concept_name) concept_name,
CASE
WHEN displayname IN (
'COSMETIC',
'MEDICAL FOOD'
)
THEN 'Observation'
WHEN displayname IN (
'MEDICAL DEVICE',
'OTC MEDICAL DEVICE LABEL',
'PRESCRIPTION MEDICAL DEVICE LABEL'
)
THEN 'Device'
ELSE 'Drug'
END AS domain_id,
'SPL' AS vocabulary_id,
CASE
WHEN displayname IN ('BULK INGREDIENT')
THEN 'Ingredient'
WHEN displayname IN ('CELLULAR THERAPY')
THEN 'Cellular Therapy'
WHEN displayname IN ('COSMETIC')
THEN 'Cosmetic'
WHEN displayname IN ('DIETARY SUPPLEMENT')
THEN 'Supplement'
WHEN displayname IN ('HUMAN OTC DRUG LABEL')
THEN 'OTC Drug'
WHEN displayname IN ('LICENSED MINIMALLY MANIPULATED CELLS LABEL')
THEN 'Cellular Therapy'
WHEN displayname IN (
'MEDICAL DEVICE',
'OTC MEDICAL DEVICE LABEL',
'PRESCRIPTION MEDICAL DEVICE LABEL'
)
THEN 'Device'
WHEN displayname IN ('MEDICAL FOOD')
THEN 'Food'
WHEN displayname IN ('NON-STANDARDIZED ALLERGENIC LABEL')
THEN 'Non-Stand Allergenic'
WHEN displayname IN ('OTC ANIMAL DRUG LABEL')
THEN 'Animal Drug'
WHEN displayname IN ('PLASMA DERIVATIVE')
THEN 'Plasma Derivative'
WHEN displayname IN ('STANDARDIZED ALLERGENIC')
THEN 'Standard Allergenic'
WHEN displayname IN ('VACCINE LABEL')
THEN 'Vaccine'
ELSE 'Prescription Drug'
END AS concept_class_id,
'C' AS standard_concept,
concept_code,
valid_start_date,
TO_DATE('20991231', 'YYYYMMDD') AS valid_end_date,
NULL AS invalid_reason
FROM (
SELECT DISTINCT ON (s_int.concept_code)
s_int.concept_code,
s_int.concept_name,
s_int.displayname,
s_int.valid_start_date
FROM sources.spl_ext s_int
ORDER BY s_int.concept_code,
s_int.valid_start_date DESC
) s
WHERE displayname NOT IN (
'IDENTIFICATION OF CBER-REGULATED GENERIC DRUG FACILITY',
'INDEXING - PHARMACOLOGIC CLASS',
'INDEXING - SUBSTANCE',
'WHOLESALE DRUG DISTRIBUTORS AND THIRD-PARTY LOGISTICS FACILITY REPORT'
)
AND NOT EXISTS (
SELECT 1
FROM concept_stage cs_int
WHERE LOWER(s.concept_code) = LOWER(cs_int.concept_code)
);
--6. Load other SPL into concept_stage (from 'product')
CREATE OR REPLACE VIEW prod --for using INDEX 'idx_f_product'
AS
(
SELECT SUBSTR(productid, devv5.INSTR(productid, '_') + 1) AS concept_code,
dosageformname,
routename,
proprietaryname,
nonproprietaryname,
TRIM(proprietarynamesuffix) AS proprietarynamesuffix,
active_numerator_strength,
active_ingred_unit
FROM sources.product
);
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
)
WITH good_spl AS (
SELECT CASE -- add [brandname] if proprietaryname exists and not identical to nonproprietaryname
WHEN brand_name IS NULL
THEN vocabulary_pack.CutConceptName(concept_name)
ELSE vocabulary_pack.CutConceptName(CONCAT (
TRIM(concept_name),
' [',
brand_name,
']'
))
END AS concept_name,
'Drug' AS domain_id,
'SPL' AS vocabulary_id,
concept_class_id,
'C' AS standard_concept,
concept_code,
COALESCE(valid_start_date, latest_update) AS valid_start_date,
TO_DATE('20991231', 'yyyymmdd') AS valid_end_date,
NULL AS invalid_reason
FROM --get unique and aggregated data from source
(
SELECT concept_code,
concept_class_id,
CASE
WHEN multi_nonproprietaryname IS NULL
THEN CONCAT (
SUBSTR(nonproprietaryname, 1, 100),
CASE
WHEN LENGTH(nonproprietaryname) > 100
THEN '...'
END,
' ' || TRIM(SUBSTR(aggr_dose, 1, 100)),
' ' || TRIM(SUBSTR(routename, 1, 100)),
' ',
TRIM(SUBSTR(dosageformname, 1, 100))
)
ELSE CONCAT (
'Multiple formulations: ',
SUBSTR(nonproprietaryname, 1, 100),
CASE
WHEN LENGTH(nonproprietaryname) > 100
THEN '...'
END,
' ' || TRIM(SUBSTR(aggr_dose, 1, 100)),
' ' || TRIM(SUBSTR(routename, 1, 100)),
' ',
TRIM(SUBSTR(dosageformname, 1, 100))
)
END AS concept_name,
vocabulary_pack.CutConceptName(brand_name) AS brand_name,
valid_start_date
FROM (
WITH t AS (
SELECT concept_code,
concept_class_id,
valid_start_date,
GetAggrDose(active_numerator_strength, active_ingred_unit) aggr_dose
FROM (
SELECT concept_code,
concept_class_id,
STRING_AGG(active_numerator_strength, '; ' ORDER BY CONCAT (
active_numerator_strength,
active_ingred_unit
)) AS active_numerator_strength,
STRING_AGG(active_ingred_unit, '; ' ORDER BY CONCAT (
active_numerator_strength,
active_ingred_unit
)) AS active_ingred_unit,
valid_start_date
FROM (
SELECT concept_code,
concept_class_id,
active_numerator_strength,
active_ingred_unit,
MIN(valid_start_date) OVER (PARTITION BY concept_code) AS valid_start_date
FROM (
SELECT GetDistinctDose(active_numerator_strength, active_ingred_unit, 1) AS active_numerator_strength,
GetDistinctDose(active_numerator_strength, active_ingred_unit, 2) AS active_ingred_unit,
SUBSTR(productid, devv5.INSTR(productid, '_') + 1) AS concept_code,
CASE producttypename
WHEN 'VACCINE'
THEN 'Vaccine'
WHEN 'LICENSED VACCINE BULK INTERMEDIATE'
THEN 'Vaccine'
WHEN 'STANDARDIZED ALLERGENIC'
THEN 'Standard Allergenic'
WHEN 'HUMAN PRESCRIPTION DRUG'
THEN 'Prescription Drug'
WHEN 'HUMAN OTC DRUG'
THEN 'OTC Drug'
WHEN 'PLASMA DERIVATIVE'
THEN 'Plasma Derivative'
WHEN 'NON-STANDARDIZED ALLERGENIC'
THEN 'Non-Stand Allergenic'
WHEN 'CELLULAR THERAPY'
THEN 'Cellular Therapy'
END AS concept_class_id,
startmarketingdate AS valid_start_date
FROM sources.product
) AS s0
GROUP BY concept_code,
concept_class_id,
active_numerator_strength,
active_ingred_unit,
valid_start_date
) AS s1
GROUP BY concept_code,
concept_class_id,
valid_start_date
) AS s2
)
SELECT t1.*,
--aggregated unique dosageformname
(
SELECT STRING_AGG(dosageformname, ', ' ORDER BY dosageformname)
FROM (
SELECT DISTINCT p.dosageformname
FROM prod p
WHERE p.concept_code = t1.concept_code
) AS s3
) AS dosageformname,
--aggregated unique routename
(
SELECT STRING_AGG(routename, ', ' ORDER BY routename)
FROM (
SELECT DISTINCT P.routename
FROM prod p
WHERE p.concept_code = t1.concept_code
) AS s4
) AS routename,
--aggregated unique nonproprietaryname
(
SELECT STRING_AGG(nonproprietaryname, ', ' ORDER BY nonproprietaryname)
FROM (
SELECT DISTINCT LOWER(p.nonproprietaryname) nonproprietaryname
FROM prod p
WHERE p.concept_code = t1.concept_code
ORDER BY nonproprietaryname LIMIT 14
) AS s5
) AS nonproprietaryname,
--multiple formulations flag
(
SELECT COUNT(LOWER(p.nonproprietaryname))
FROM prod p
WHERE p.concept_code = t1.concept_code
HAVING COUNT(DISTINCT LOWER(p.nonproprietaryname)) > 1
) AS multi_nonproprietaryname,
(
SELECT STRING_AGG(brand_name, ', ' ORDER BY brand_name)
FROM (
SELECT DISTINCT CASE
WHEN (
LOWER(proprietaryname) <> LOWER(nonproprietaryname)
OR nonproprietaryname IS NULL
)
THEN LOWER(TRIM(CONCAT (
proprietaryname,
' ',
proprietarynamesuffix
)))
ELSE NULL
END AS brand_name
FROM prod p
WHERE p.concept_code = t1.concept_code
ORDER BY brand_name LIMIT 49 --brand_name may be too long for concatenation
) AS s6
) AS brand_name
FROM t t1
) AS s7
) s,
vocabulary v
WHERE v.vocabulary_id = 'SPL'
)
SELECT *
FROM good_spl s
WHERE NOT EXISTS (
SELECT 1
FROM concept_stage cs_int
WHERE LOWER(s.concept_code) = LOWER(cs_int.concept_code)
);
--7. Add full SPL names into concept_synonym_stage
INSERT INTO concept_synonym_stage (
synonym_concept_code,
synonym_vocabulary_id,
synonym_name,
language_concept_id
)
SELECT concept_code AS synonym_concept_code,
'SPL' AS vocabulary_id,
vocabulary_pack.CutConceptSynonymName(CASE
WHEN brand_name IS NULL
THEN TRIM(long_concept_name)
ELSE CONCAT (
TRIM(long_concept_name),
' [',
brand_name,
']'
)
END) AS synonym_name,
4180186 AS language_concept_id -- English
FROM --get unique and aggregated data from source
(
SELECT concept_code,
CASE
WHEN multi_nonproprietaryname IS NULL
THEN CONCAT (
nonproprietaryname,
' ' || aggr_dose,
' ' || routename,
' ',
dosageformname
)
ELSE CONCAT (
'Multiple formulations: ',
nonproprietaryname,
' ' || aggr_dose,
' ' || routename,
' ',
dosageformname
)
END AS long_concept_name,
vocabulary_pack.CutConceptName(brand_name) AS brand_name
FROM (
WITH t AS (
SELECT concept_code,
GetAggrDose(active_numerator_strength, active_ingred_unit) aggr_dose
FROM (
SELECT concept_code,
STRING_AGG(active_numerator_strength, '; ' ORDER BY CONCAT (
active_numerator_strength,
active_ingred_unit
)) AS active_numerator_strength,
STRING_AGG(active_ingred_unit, '; ' ORDER BY CONCAT (
active_numerator_strength,
active_ingred_unit
)) AS active_ingred_unit
FROM (
SELECT DISTINCT GetDistinctDose(active_numerator_strength, active_ingred_unit, 1) AS active_numerator_strength,
GetDistinctDose(active_numerator_strength, active_ingred_unit, 2) AS active_ingred_unit,
SUBSTR(productid, devv5.INSTR(productid, '_') + 1) AS concept_code
FROM sources.product
) AS s0
GROUP BY concept_code
) AS s2
)
SELECT t1.*,
--aggregated unique dosageformname
(
SELECT STRING_AGG(dosageformname, ', ' ORDER BY dosageformname)
FROM (
SELECT DISTINCT p.dosageformname
FROM prod p
WHERE p.concept_code = t1.concept_code
) AS s3
) AS dosageformname,
--aggregated unique routename
(
SELECT STRING_AGG(routename, ', ' ORDER BY routename)
FROM (
SELECT DISTINCT p.routename
FROM prod p
WHERE p.concept_code = t1.concept_code
) AS s4
) AS routename,
--aggregated unique nonproprietaryname
(
SELECT STRING_AGG(nonproprietaryname, ', ' ORDER BY nonproprietaryname)
FROM (
SELECT DISTINCT LOWER(p.nonproprietaryname) nonproprietaryname
FROM prod p
WHERE p.concept_code = t1.concept_code
ORDER BY nonproprietaryname LIMIT 14
) AS s5
) AS nonproprietaryname,
--multiple formulations flag
(
SELECT COUNT(LOWER(P.nonproprietaryname))
FROM prod p
WHERE p.concept_code = t1.concept_code
HAVING COUNT(DISTINCT LOWER(P.nonproprietaryname)) > 1
) AS multi_nonproprietaryname,
(
SELECT STRING_AGG(brand_name, ', ' ORDER BY brand_name)
FROM (
SELECT DISTINCT CASE
WHEN (
LOWER(proprietaryname) <> LOWER(nonproprietaryname)
OR nonproprietaryname IS NULL
)
THEN LOWER(TRIM(CONCAT (
proprietaryname,
' ',
proprietarynamesuffix
)))
ELSE NULL
END AS brand_name
FROM prod p
WHERE p.concept_code = t1.concept_code
ORDER BY brand_name LIMIT 49 --brand_name may be too long for concatenation
) AS s6
) AS brand_name
FROM t t1
) AS s7
) s;
DROP VIEW prod;
--7. Add upgrade SPL relationships
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 replaced_spl AS concept_code_1,
spl_code AS concept_code_2,
'SPL' AS vocabulary_id_1,
'SPL' AS vocabulary_id_2,
'Concept replaced by' AS relationship_id,
spl_date - 1 AS valid_start_date,
TO_DATE('20991231', 'YYYYMMDD') AS valid_end_date,
NULL AS invalid_reason
FROM (
SELECT DISTINCT FIRST_VALUE(s.concept_code) OVER (
PARTITION BY l.replaced_spl ORDER BY s.valid_start_date,
s.concept_code ROWS BETWEEN UNBOUNDED PRECEDING
AND UNBOUNDED FOLLOWING
) spl_code,
FIRST_VALUE(s.valid_start_date) OVER (
PARTITION BY l.replaced_spl ORDER BY s.valid_start_date,
s.concept_code ROWS BETWEEN UNBOUNDED PRECEDING
AND UNBOUNDED FOLLOWING
) spl_date,
l.replaced_spl
FROM (
SELECT s_int.concept_code,
s_int.replaced_spl,
MIN(s_int.valid_start_date) AS valid_start_date
FROM sources.spl_ext s_int
WHERE s_int.replaced_spl IS NOT NULL -- if there is an SPL codes ( l ) that is mentioned in another record as replaced_spl (path /document/relatedDocument/relatedDocument/setId/@root)
GROUP BY s_int.concept_code,
s_int.replaced_spl
) s
CROSS JOIN LATERAL(SELECT UNNEST(regexp_matches(s.replaced_spl, '[^;]+', 'g')) AS replaced_spl) l
) AS s0;
ANALYZE concept_stage;
ANALYZE concept_relationship_stage;
--8. Working with replacement mappings
DO $_$
BEGIN
PERFORM VOCABULARY_PACK.CheckReplacementMappings();
END $_$;
--9. Add mapping from deprecated to fresh concepts
DO $_$
BEGIN
PERFORM VOCABULARY_PACK.AddFreshMAPSTO('SPL');
END $_$;
--10. Deprecate 'Maps to' mappings to deprecated and upgraded concepts
DO $_$
BEGIN
PERFORM VOCABULARY_PACK.DeprecateWrongMAPSTO();
END $_$;
--11. Delete ambiguous 'Maps to' mappings
DO $_$
BEGIN
PERFORM VOCABULARY_PACK.DeleteAmbiguousMAPSTO();
END $_$;
--12. Load NDC into temporary table from 'product'
DROP TABLE IF EXISTS main_ndc;
CREATE UNLOGGED TABLE main_ndc (
concept_name TEXT,
long_concept_name TEXT,
domain_id TEXT,
vocabulary_id TEXT,
concept_class_id TEXT,
standard_concept TEXT,
concept_code TEXT,
valid_start_date DATE,
valid_end_date DATE,
invalid_reason TEXT,
is_diluent BOOLEAN DEFAULT FALSE
);
CREATE OR REPLACE VIEW prod --for using INDEX 'idx_f1_product'
AS
(
SELECT CASE
WHEN devv5.INSTR(productndc, '-') = 5
THEN '0' || SUBSTR(productndc, 1, devv5.INSTR(productndc, '-') - 1)
ELSE SUBSTR(productndc, 1, devv5.INSTR(productndc, '-') - 1)
END || CASE
WHEN LENGTH(SUBSTR(productndc, devv5.INSTR(productndc, '-'))) = 4
THEN '0' || SUBSTR(productndc, devv5.INSTR(productndc, '-') + 1)
ELSE SUBSTR(productndc, devv5.INSTR(productndc, '-') + 1)
END AS concept_code,
dosageformname,
routename,
proprietaryname,
nonproprietaryname,
TRIM(proprietarynamesuffix) AS proprietarynamesuffix,
active_numerator_strength,
active_ingred_unit
FROM sources.product
);
INSERT INTO main_ndc
SELECT CASE -- add [brandname] if proprietaryname exists and not identical to nonproprietaryname
WHEN brand_name IS NULL
THEN vocabulary_pack.CutConceptName(concept_name)
ELSE vocabulary_pack.CutConceptName(CONCAT (
TRIM(concept_name),
' [',
brand_name,
']'
))
END AS concept_name,
CASE -- same for long concept name
WHEN brand_name IS NULL
THEN TRIM(long_concept_name)
ELSE CONCAT (
TRIM(long_concept_name),
' [',
brand_name,
']'
)
END AS long_concept_name,
'Drug' AS domain_id,
'NDC' AS vocabulary_id,
'9-digit NDC' AS concept_class_id,
NULL AS standard_concept,
concept_code,
COALESCE(valid_start_date, latest_update) AS valid_start_date,
TO_DATE('20991231', 'yyyymmdd') AS valid_end_date,
NULL AS invalid_reason,
is_diluent
FROM --get unique and aggregated data from source
(
SELECT concept_code,
CASE
WHEN multi_nonproprietaryname IS NULL
THEN CONCAT (
SUBSTR(nonproprietaryname, 1, 100),
CASE
WHEN LENGTH(nonproprietaryname) > 100
THEN '...'
END,
' ' || TRIM(SUBSTR(aggr_dose, 1, 100)),
' ' || TRIM(SUBSTR(routename, 1, 100)),
' ',
TRIM(SUBSTR(dosageformname, 1, 100))
)
ELSE CONCAT (
'Multiple formulations: ',
SUBSTR(nonproprietaryname, 1, 100),
CASE
WHEN LENGTH(nonproprietaryname) > 100
THEN '...'
END,
' ' || TRIM(SUBSTR(aggr_dose, 1, 100)),
' ' || TRIM(SUBSTR(routename, 1, 100)),
' ',
TRIM(SUBSTR(dosageformname, 1, 100))
)
END AS concept_name,
CASE
WHEN multi_nonproprietaryname IS NULL
THEN CONCAT (
nonproprietaryname,
' ' || aggr_dose,
' ' || routename,
' ',
dosageformname
)
ELSE CONCAT (
'Multiple formulations: ',
nonproprietaryname,
' ' || aggr_dose,
' ' || routename,
' ',
dosageformname
)
END AS long_concept_name,
vocabulary_pack.CutConceptName(brand_name) AS brand_name,
valid_start_date,
is_diluent
FROM (
WITH t AS (
SELECT concept_code,
valid_start_date,
GetAggrDose(active_numerator_strength, active_ingred_unit) aggr_dose,
is_diluent
FROM (
SELECT concept_code,
STRING_AGG(active_numerator_strength, '; ' ORDER BY CONCAT (
active_numerator_strength,
active_ingred_unit
)) AS active_numerator_strength,
STRING_AGG(active_ingred_unit, '; ' ORDER BY CONCAT (
active_numerator_strength,
active_ingred_unit
)) AS active_ingred_unit,
valid_start_date,
is_diluent
FROM (
SELECT concept_code,
active_numerator_strength,
active_ingred_unit,
MIN(valid_start_date) OVER (PARTITION BY concept_code) AS valid_start_date,
is_diluent
FROM (
SELECT GetDistinctDose(active_numerator_strength, active_ingred_unit, 1) AS active_numerator_strength,
GetDistinctDose(active_numerator_strength, active_ingred_unit, 2) AS active_ingred_unit,
CASE
WHEN devv5.INSTR(productndc, '-') = 5
THEN '0' || SUBSTR(productndc, 1, devv5.INSTR(productndc, '-') - 1)
ELSE SUBSTR(productndc, 1, devv5.INSTR(productndc, '-') - 1)
END || CASE
WHEN LENGTH(SUBSTR(productndc, devv5.INSTR(productndc, '-'))) = 4
THEN '0' || SUBSTR(productndc, devv5.INSTR(productndc, '-') + 1)
ELSE SUBSTR(productndc, devv5.INSTR(productndc, '-') + 1)
END AS concept_code,
startmarketingdate AS valid_start_date,
CASE
WHEN proprietaryname ILIKE '%diluent%'
THEN TRUE
ELSE FALSE
END AS is_diluent
FROM sources.product
) AS s0
GROUP BY concept_code,
active_numerator_strength,
active_ingred_unit,
valid_start_date,
is_diluent
) AS s1
GROUP BY concept_code,
valid_start_date,
is_diluent
) AS s2
)
SELECT t1.*,
--aggregated unique dosageformname
(
SELECT STRING_AGG(dosageformname, ', ' ORDER BY dosageformname)
FROM (
SELECT DISTINCT p.dosageformname
FROM prod p
WHERE p.concept_code = t1.concept_code
) AS s3
) AS dosageformname,
--aggregated unique routename
(
SELECT STRING_AGG(routename, ', ' ORDER BY routename)
FROM (
SELECT DISTINCT p.routename
FROM prod p
WHERE p.concept_code = t1.concept_code
) AS s4
) AS routename,
--aggregated unique nonproprietaryname
(
SELECT STRING_AGG(nonproprietaryname, ', ' ORDER BY nonproprietaryname)
FROM (
SELECT DISTINCT LOWER(p.nonproprietaryname) nonproprietaryname
FROM prod p
WHERE p.concept_code = t1.concept_code
ORDER BY nonproprietaryname LIMIT 14
) AS s5
) AS nonproprietaryname,
--multiple formulations flag
(
SELECT COUNT(LOWER(p.nonproprietaryname))
FROM prod p
WHERE p.concept_code = t1.concept_code
HAVING COUNT(DISTINCT LOWER(p.nonproprietaryname)) > 1
) AS multi_nonproprietaryname,
(
SELECT STRING_AGG(brand_name, ', ' ORDER BY brand_name)
FROM (
SELECT DISTINCT CASE
WHEN (
LOWER(proprietaryname) <> LOWER(nonproprietaryname)
OR nonproprietaryname IS NULL
)
THEN LOWER(TRIM(proprietaryname || ' ' || proprietarynamesuffix))
ELSE NULL
END AS brand_name
FROM prod p
WHERE p.concept_code = t1.concept_code
ORDER BY brand_name LIMIT 49 --brand_name may be too long for concatenation
) AS s6
) AS brand_name
FROM t t1
) AS s7
) AS s8,
vocabulary v
WHERE v.vocabulary_id = 'NDC';
DROP VIEW prod;
--13. Add NDC to MAIN_NDC from rxnconso
INSERT INTO main_ndc (
concept_name,
long_concept_name,
domain_id,
vocabulary_id,
concept_class_id,
standard_concept,
concept_code,
valid_start_date,
valid_end_date,
invalid_reason
)
SELECT DISTINCT vocabulary_pack.CutConceptName(c.str) AS concept_name,
TRIM(c.str) AS long_concept_name,
'Drug' AS domain_id,
'NDC' AS vocabulary_id,
'11-digit NDC' AS concept_class_id,
NULL AS standard_concept,
s.atv AS concept_code,
latest_update AS valid_start_date,
TO_DATE ('20991231', 'yyyymmdd') AS valid_end_date,
NULL AS invalid_reason
FROM sources.rxnsat s
JOIN sources.rxnconso c ON c.sab = 'RXNORM'
AND c.rxaui = s.rxaui
AND c.rxcui = s.rxcui
JOIN vocabulary v ON v.vocabulary_id = 'NDC'
WHERE s.sab = 'RXNORM'
AND s.atn = 'NDC';
CREATE INDEX idx_main_ndc ON main_ndc (concept_code);
ANALYZE main_ndc;
--14. Add additional NDC with fresh dates and active mapping to RxCUI (source: http://rxnav.nlm.nih.gov/REST/ndcstatus?history=1&ndc=xxx) [part 1 of 3]
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 vocabulary_pack.CutConceptName(concept_name) AS concept_name,
'Drug' AS domain_id,
'NDC' AS vocabulary_id,
'11-digit NDC' AS concept_class_id,
NULL AS standard_concept,
concept_code,
startDate AS valid_start_date,
endDate AS valid_end_date,
invalid_reason
FROM (
SELECT DISTINCT ON (n.concept_code)
n.concept_code,
n.startDate,
n.endDate,
n.invalid_reason,
COALESCE(mn.concept_name, c.concept_name, spl.concept_name) concept_name
FROM (
SELECT ndc.concept_code,
startDate,
CASE
WHEN LOWER(status) = 'active'
THEN TO_DATE('20991231', 'yyyymmdd')
ELSE endDate
END endDate,
CASE
WHEN LOWER(status) = 'active'
THEN NULL