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medco-deployment/docker-images/i2b2-medco/sql/60-local-medco-ontology.sh
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60-local-medco-ontology.sh
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#!/bin/bash
set -Eeuo pipefail
# set up local medco ontology
psql $PSQL_PARAMS -d "$I2B2_DB_NAME" <<-EOSQL
-- root nodes in table_access
insert into i2b2metadata_i2b2.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
('SENSITIVE_TAGGED', 'SENSITIVE_TAGGED', 'N', 1, '\medco\tagged\', 'MedCo Sensitive Tagged Ontology',
'N', 'CA', 'concept_cd', 'concept_dimension', 'concept_path', 'T', 'LIKE', '\medco\tagged\', 'MedCo Sensitive Tagged Ontology');
insert into i2b2metadata_i2b2.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
('NON_SENSITIVE_CLEAR', 'NON_SENSITIVE_CLEAR', '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');
-- medco-specific schemes (prefix to the concept codes)
insert into i2b2metadata_i2b2.schemes(c_key, c_name, c_description) values('TAG_ID:', 'TAG_ID', 'MedCo tag identifier');
insert into i2b2metadata_i2b2.schemes(c_key, c_name, c_description) values('ENC_ID:', 'ENC_ID', 'MedCo sensitive concept identifier (to be encrypted)');
insert into i2b2metadata_i2b2.schemes(c_key, c_name, c_description) values('CLEAR:', 'CLEAR', 'MedCo clear value');
insert into i2b2metadata_i2b2.schemes(c_key, c_name, c_description) values('GEN:', 'GEN', 'MedCo genomic annotations');
-- clear non sensitive ontology
CREATE TABLE i2b2metadata_i2b2.non_sensitive_clear (
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_i2b2.non_sensitive_clear ADD CONSTRAINT fullname_pk_10 PRIMARY KEY (c_fullname);
ALTER TABLE ONLY i2b2metadata_i2b2.non_sensitive_clear ADD CONSTRAINT basecode_un_10 UNIQUE (c_basecode);
--insert into i2b2metadata_i2b2.non_sensitive_clear (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()', 'CLEAR', '@');
-- tagged sensitive ontology
CREATE TABLE i2b2metadata_i2b2.sensitive_tagged (
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_i2b2.sensitive_tagged ADD CONSTRAINT fullname_pk_11 PRIMARY KEY (c_fullname);
ALTER TABLE ONLY i2b2metadata_i2b2.sensitive_tagged ADD CONSTRAINT basecode_un_11 UNIQUE (c_basecode);
--insert into i2b2metadata_i2b2.sensitive_tagged (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\tagged\', 'MedCo Sensitive Tagged Ontology', 'N', 'CA', '0', 'concept_cd', 'concept_dimension', 'concept_path',
--'T', 'LIKE', '\medco\tagged\', 'MedCo Sensitive Tagged Ontology', '\medco\tagged\', 'NOW()', 'NOW()', 'NOW()', 'TAG_ID', '@');
-- permissions
alter table i2b2metadata_i2b2.sensitive_tagged owner to $I2B2_DB_USER;
alter table i2b2metadata_i2b2.non_sensitive_clear owner to $I2B2_DB_USER;
grant all on schema i2b2metadata_i2b2 to $I2B2_DB_USER;
grant all privileges on all tables in schema i2b2metadata_i2b2 to $I2B2_DB_USER;
grant all privileges on all sequences in schema i2b2metadata_i2b2 to $I2B2_DB_USER;
grant all privileges on all functions in schema i2b2metadata_i2b2 to $I2B2_DB_USER;
EOSQL
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