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20-medcodb-insidei2b2metadata.sh
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Sat, Nov 30, 22:46

20-medcodb-insidei2b2metadata.sh
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#!/bin/bash
set -e
psql -v ON_ERROR_STOP=1 --username "$POSTGRES_USER" -d "$I2B2_DOMAIN_NAME" <<-EOSQL
-- ################### medco_data ###################
create schema medco_data;
create table medco_data.enc_observation_fact (
encounter_id character varying(50) not null,
patient_id character varying(50) not null,
provider_id character varying(50) not null,
enc_concept_id character varying(500) not null
);
-- access rights
create role medco_data login password 'demouser';
grant all on schema medco_data to medco_data;
grant all privileges on all tables in schema medco_data to medco_data;
-- ################### medco_ontology ###################
-- i2b2 ontology medco: in postgresql i2b2 DB!
-- todo: currently added in i2b2metadata demo table
-- clinical sensitive ontology
CREATE TABLE i2b2metadata.clinical_sensitive (
c_hlevel numeric(22,0) not null,
c_fullname character varying(900) not null,
c_name character varying(2000) not null,
c_synonym_cd character(1) not null,
c_visualattributes character(3) not null,
c_totalnum numeric(22,0),
c_basecode character varying(450),
c_metadataxml text,
c_facttablecolumn character varying(50) not null,
c_tablename character varying(50) not null,
c_columnname character varying(50) not null,
c_columndatatype character varying(50) not null,
c_operator character varying(10) not null,
c_dimcode character varying(900) not null,
c_comment text,
c_tooltip character varying(900),
update_date date not null,
download_date date,
import_date date,
sourcesystem_cd character varying(50),
valuetype_cd character varying(50),
m_applied_path character varying(900) not null,
m_exclusion_cd character varying(900),
c_path character varying(700),
c_symbol character varying(50),
pcori_basecode character varying(50)
);
ALTER TABLE ONLY i2b2metadata.clinical_sensitive
ADD CONSTRAINT fullname_pk PRIMARY KEY (c_fullname);
ALTER TABLE ONLY i2b2metadata.clinical_sensitive
ADD CONSTRAINT basecode_un UNIQUE (c_basecode);
-- clinical non-sensitive ontology
CREATE TABLE i2b2metadata.clinical_non_sensitive (
c_hlevel numeric(22,0) not null,
c_fullname character varying(900) not null,
c_name character varying(2000) not null,
c_synonym_cd character(1) not null,
c_visualattributes character(3) not null,
c_totalnum numeric(22,0),
c_basecode character varying(450),
c_metadataxml text,
c_facttablecolumn character varying(50) not null,
c_tablename character varying(50) not null,
c_columnname character varying(50) not null,
c_columndatatype character varying(50) not null,
c_operator character varying(10) not null,
c_dimcode character varying(900) not null,
c_comment text,
c_tooltip character varying(900),
update_date date not null,
download_date date,
import_date date,
sourcesystem_cd character varying(50),
valuetype_cd character varying(50),
m_applied_path character varying(900) not null,
m_exclusion_cd character varying(900),
c_path character varying(700),
c_symbol character varying(50),
pcori_basecode character varying(50)
);
ALTER TABLE ONLY i2b2metadata.clinical_non_sensitive
ADD CONSTRAINT fullname_pk2 PRIMARY KEY (c_fullname);
ALTER TABLE ONLY i2b2metadata.clinical_non_sensitive
ADD CONSTRAINT basecode_un2 UNIQUE (c_basecode);
-- genomic ontology
CREATE TABLE i2b2metadata.genomic (
c_hlevel numeric(22,0) not null,
c_fullname character varying(900) not null,
c_name character varying(2000) not null,
c_synonym_cd character(1) not null,
c_visualattributes character(3) not null,
c_totalnum numeric(22,0),
c_basecode character varying(450),
c_metadataxml text,
c_facttablecolumn character varying(50) not null,
c_tablename character varying(50) not null,
c_columnname character varying(50) not null,
c_columndatatype character varying(50) not null,
c_operator character varying(10) not null,
c_dimcode character varying(900) not null,
c_comment text,
c_tooltip character varying(900),
update_date date not null,
download_date date,
import_date date,
sourcesystem_cd character varying(50),
valuetype_cd character varying(50),
m_applied_path character varying(900) not null,
m_exclusion_cd character varying(900),
c_path character varying(700),
c_symbol character varying(50),
pcori_basecode character varying(50)
);
ALTER TABLE ONLY i2b2metadata.genomic
ADD CONSTRAINT fullname_pk3 PRIMARY KEY (c_fullname);
ALTER TABLE ONLY i2b2metadata.genomic
ADD CONSTRAINT basecode_un3 UNIQUE (c_basecode);
-- schemes table
insert into i2b2metadata.schemes(c_key, c_name, c_description) values
('MEDCO_ENC:', 'MEDCO_ENC', 'MedCo encrypted values');
insert into i2b2metadata.schemes(c_key, c_name, c_description) values
('MEDCO_CLEAR:', 'MEDCO_CLEAR', 'MedCo clear values');
insert into i2b2metadata.schemes(c_key, c_name, c_description) values
('MEDCO_ADMIN:', 'MEDCO_ADMIN', 'MedCo administrative entries');
insert into i2b2metadata.schemes(c_key, c_name, c_description) values
('MEDCO_GEN:', 'MEDCO_GEN', 'MedCo genomic entries');
-- table_access table
insert into i2b2metadata.table_access (c_table_cd, c_table_name, c_protected_access, c_hlevel, c_fullname, c_name,
c_synonym_cd, c_visualattributes, c_facttablecolumn, c_dimtablename,
c_columnname, c_columndatatype, c_operator, c_dimcode, c_tooltip) VALUES
('CLINICAL_SENSITIVE', 'CLINICAL_SENSITIVE', 'N', 2, '\\medco\\clinical\\sensitive\\', 'MedCo Clinical Sensitive Ontology',
'N', 'CA', 'concept_cd', 'concept_dimension', 'concept_path', 'T', 'LIKE', '\\medco\\clinical\\sensitive\\', 'MedCo Clinical Sensitive Ontology');
insert into i2b2metadata.table_access (c_table_cd, c_table_name, c_protected_access, c_hlevel, c_fullname, c_name,
c_synonym_cd, c_visualattributes, c_facttablecolumn, c_dimtablename,
c_columnname, c_columndatatype, c_operator, c_dimcode, c_tooltip) VALUES
('CLINICAL_NON_SENSITIVE', 'CLINICAL_NON_SENSITIVE', 'N', 2, '\\medco\\clinical\\nonsensitive\\', 'MedCo Clinical Non-Sensitive Ontology',
'N', 'CA', 'concept_cd', 'concept_dimension', 'concept_path', 'T', 'LIKE', '\\medco\\clinical\\nonsensitive\\', 'MedCo Clinical Non-Sensitive Ontology');
insert into i2b2metadata.table_access (c_table_cd, c_table_name, c_protected_access, c_hlevel, c_fullname, c_name,
c_synonym_cd, c_visualattributes, c_facttablecolumn, c_dimtablename,
c_columnname, c_columndatatype, c_operator, c_dimcode, c_tooltip) VALUES
('GENOMIC', 'GENOMIC', 'N', 2, '\\medco\\genomic\\', 'MedCo Genomic Entries',
'N', 'CA', 'concept_cd', 'concept_dimension', 'concept_path', 'T', 'LIKE', '\\medco\\genomic\\', 'MedCo Genomic Entries');
-- access rights
-- tables ont init
insert into i2b2metadata.clinical_sensitive (c_hlevel, c_fullname, c_name, c_synonym_cd, c_visualattributes, c_totalnum,
c_facttablecolumn, c_tablename, c_columnname, c_columndatatype, c_operator, c_dimcode, c_comment, c_tooltip, update_date,
download_date, import_date, valuetype_cd, m_applied_path) values
('2', '\medco\clinical\sensitive\', 'MedCo Clinical Sensitive Ontology', 'N', 'CA', '0', 'concept_cd', 'concept_dimension', 'concept_path',
'T', 'LIKE', '\medco\clinical\sensitive\', 'MedCo Clinical Sensitive Ontology', '\medco\clinical\sensitive\',
'NOW()', 'NOW()', 'NOW()', 'MEDCO_ENC', '@');
insert into i2b2metadata.clinical_non_sensitive (c_hlevel, c_fullname, c_name, c_synonym_cd, c_visualattributes, c_totalnum,
c_facttablecolumn, c_tablename, c_columnname, c_columndatatype, c_operator, c_dimcode, c_comment, c_tooltip, update_date,
download_date, import_date, valuetype_cd, m_applied_path) values
('2', '\medco\clinical\nonsensitive\', 'MedCo Clinical Non-Sensitive Ontology', 'N', 'CA', '0', 'concept_cd', 'concept_dimension', 'concept_path',
'T', 'LIKE', '\medco\clinical\nonsensitive\', 'MedCo Clinical Non-Sensitive Ontology', '\medco\clinical\nonsensitive\',
'NOW()', 'NOW()', 'NOW()', 'MEDCO_CLEAR', '@');
insert into i2b2metadata.genomic (c_hlevel, c_fullname, c_name, c_synonym_cd, c_visualattributes, c_totalnum,
c_facttablecolumn, c_tablename, c_columnname, c_columndatatype, c_operator, c_dimcode, c_comment, c_tooltip, update_date,
download_date, import_date, valuetype_cd, m_applied_path) values
('1', '\medco\genomic\', 'MedCo Genomic Entries', 'N', 'CA', '0', 'concept_cd', 'concept_dimension', 'concept_path',
'T', 'LIKE', '\medco\genomic\', 'MedCo Genomic Entries', '\medco\genomic\',
'NOW()', 'NOW()', 'NOW()', 'MEDCO_GEN', '@');
-- next usable id init
insert into i2b2metadata.clinical_sensitive (c_hlevel, c_fullname, c_name, c_synonym_cd, c_visualattributes, c_totalnum,
c_facttablecolumn, c_tablename, c_columnname, c_columndatatype, c_operator, c_dimcode, c_comment, c_tooltip, update_date,
download_date, import_date, valuetype_cd, m_applied_path) values
('3', '\medco\clinical\sensitive\next_usable_id\', 'nextEncUsableId', 'N', 'LH', '0', 'concept_cd', 'concept_dimension', 'concept_path',
'T', 'LIKE', '\medco\clinical\sensitive\next_usable_id\', 'The next usable id for Unlynx encryption.', '\medco\clinical\sensitive\next_usable_id\',
'NOW()', 'NOW()', 'NOW()', 'MEDCO_ADMIN', '@');
insert into i2b2metadata.clinical_non_sensitive (c_hlevel, c_fullname, c_name, c_synonym_cd, c_visualattributes, c_totalnum,
c_facttablecolumn, c_tablename, c_columnname, c_columndatatype, c_operator, c_dimcode, c_comment, c_tooltip, update_date,
download_date, import_date, valuetype_cd, m_applied_path) values
('3', '\medco\clinical\nonsensitive\next_usable_id\', 'nextClearUsableId', 'N', 'LH', '0', 'concept_cd', 'concept_dimension', 'concept_path',
'T', 'LIKE', '\medco\clinical\nonsensitive\next_usable_id\', 'The next usable id for non sensitive clinical data.', '\medco\clinical\nonsensitive\next_usable_id\',
'NOW()', 'NOW()', 'NOW()', 'MEDCO_ADMIN', '@');
insert into i2b2metadata.clinical_sensitive (c_hlevel, c_fullname, c_name, c_synonym_cd, c_visualattributes, c_totalnum, c_basecode,
c_facttablecolumn, c_tablename, c_columnname, c_columndatatype, c_operator, c_dimcode, c_comment, update_date,
download_date, import_date, valuetype_cd, m_applied_path) values
('4', '\medco\clinical\sensitive\next_usable_id\1\', '1', 'N', 'LH', '0', 'MEDCO_ADMIN:nextEncUsableId', 'concept_cd', 'concept_dimension', 'concept_path',
'T', 'LIKE', '\medco\clinical\sensitive\next_usable_id\1\', 'The next usable id for Unlynx encryption.',
'NOW()', 'NOW()', 'NOW()', 'MEDCO_ADMIN', '@');
insert into i2b2metadata.clinical_non_sensitive (c_hlevel, c_fullname, c_name, c_synonym_cd, c_visualattributes, c_totalnum, c_basecode,
c_facttablecolumn, c_tablename, c_columnname, c_columndatatype, c_operator, c_dimcode, c_comment, update_date,
download_date, import_date, valuetype_cd, m_applied_path) values
('4', '\medco\clinical\nonsensitive\next_usable_id\1\', '1', 'N', 'LH', '0', 'MEDCO_ADMIN:nextClearUsableId', 'concept_cd', 'concept_dimension', 'concept_path',
'T', 'LIKE', '\medco\clinical\nonsensitive\next_usable_id\1\', 'The next usable id for non sensitive clinical data.',
'NOW()', 'NOW()', 'NOW()', 'MEDCO_ADMIN', '@');
-- todo: db lookup for medco?? yes in i2b2hive.ont_db_lookup add entry
-- setup i2b2-medco ontology todo: when setting up shrine, change to the schema of medco/shrine ontology !!
-- fix permissions
alter table i2b2metadata.clinical_sensitive owner to i2b2metadata;
alter table i2b2metadata.clinical_non_sensitive owner to i2b2metadata;
alter table i2b2metadata.genomic owner to i2b2metadata;
grant all on schema i2b2metadata to i2b2metadata;
grant all privileges on all tables in schema i2b2metadata to i2b2metadata;
alter table medco_data.enc_observation_fact owner to medco_data;
EOSQL

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