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medco-deployment/docker-images/i2b2-database/initdb-data/25-medco-shrine-ontology.sh
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25-medco-shrine-ontology.sh
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#!/bin/bash
set -e
psql -v ON_ERROR_STOP=1 --username "$POSTGRES_USER" -d "$I2B2_DOMAIN_NAME" <<-EOSQL
-- ################### SHRINE ONT DB ###################
-- user and schema
create user shrine_ont with password '$DB_PASSWORD';
create schema authorization shrine_ont;
-- table access (ontologies list)
CREATE TABLE shrine_ont.table_access
(
C_TABLE_CD VARCHAR(50),
C_TABLE_NAME VARCHAR(50),
C_PROTECTED_ACCESS CHAR(1),
C_HLEVEL NUMERIC(22,0),
C_FULLNAME VARCHAR(900),
C_NAME VARCHAR(2000),
C_SYNONYM_CD CHAR(1),
C_VISUALATTRIBUTES CHAR(3),
C_TOTALNUM NUMERIC(22,0),
C_BASECODE VARCHAR(450),
C_METADATAXML TEXT,
C_FACTTABLECOLUMN VARCHAR(50),
C_DIMTABLENAME VARCHAR(50),
C_COLUMNNAME VARCHAR(50),
C_COLUMNDATATYPE VARCHAR(50),
C_OPERATOR VARCHAR(10),
C_DIMCODE VARCHAR(900),
C_COMMENT TEXT,
C_TOOLTIP VARCHAR(900),
C_ENTRY_DATE DATE,
C_CHANGE_DATE DATE,
C_STATUS_CD CHAR(1),
VALUETYPE_CD VARCHAR(50)
);
ALTER TABLE shrine_ont.table_access OWNER TO shrine_ont;
insert into shrine_ont.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 shrine_ont.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 shrine_ont.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', 1, '\medco\genomic\', 'MedCo Genomic Ontology',
'N', 'CA', 'concept_cd', 'concept_dimension', 'concept_path', 'T', 'LIKE', '\medco\genomic\', 'MedCo Genomic Ontology');
-- schemes
CREATE TABLE shrine_ont.schemes
(
C_KEY VARCHAR(50) NOT NULL,
C_NAME VARCHAR(50) NOT NULL,
C_DESCRIPTION VARCHAR(100),
CONSTRAINT SCHEMES_PK PRIMARY KEY (C_KEY)
);
ALTER TABLE shrine_ont.schemes OWNER TO shrine_ont;
insert into shrine_ont.schemes(c_key, c_name, c_description) values
('TAG_ID:', 'TAG_ID', 'MedCo tag identifier');
insert into shrine_ont.schemes(c_key, c_name, c_description) values
('ENC_ID:', 'ENC_ID', 'MedCo sensitive concept identifier (to be encrypted)');
insert into shrine_ont.schemes(c_key, c_name, c_description) values
('CLEAR:', 'CLEAR', 'MedCo clear value');
insert into shrine_ont.schemes(c_key, c_name, c_description) values
('GEN:', 'GEN', 'MedCo genomic annotations');
-- clinical sensitive ontology
CREATE TABLE shrine_ont.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 shrine_ont.clinical_sensitive OWNER TO shrine_ont;
ALTER TABLE ONLY shrine_ont.clinical_sensitive
ADD CONSTRAINT fullname_pk_20 PRIMARY KEY (c_fullname);
ALTER TABLE ONLY shrine_ont.clinical_sensitive
ADD CONSTRAINT basecode_un_20 UNIQUE (c_basecode);
insert into shrine_ont.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()', 'ENC_ID', '@');
-- clinical non-sensitive ontology
CREATE TABLE shrine_ont.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 shrine_ont.clinical_non_sensitive OWNER TO shrine_ont;
ALTER TABLE ONLY shrine_ont.clinical_non_sensitive
ADD CONSTRAINT fullname_pk_21 PRIMARY KEY (c_fullname);
ALTER TABLE ONLY shrine_ont.clinical_non_sensitive
ADD CONSTRAINT basecode_un_21 UNIQUE (c_basecode);
insert into shrine_ont.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()', 'CLEAR', '@');
-- genomic ontology
CREATE TABLE shrine_ont.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 shrine_ont.genomic OWNER TO shrine_ont;
ALTER TABLE ONLY shrine_ont.genomic
ADD CONSTRAINT fullname_pk_22 PRIMARY KEY (c_fullname);
ALTER TABLE ONLY shrine_ont.genomic
ADD CONSTRAINT basecode_un_22 UNIQUE (c_basecode);
-- todo: hard-coded genomic entries
insert into shrine_ont.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 Ontology', 'N', 'CA', '0', 'concept_cd', 'concept_dimension', 'concept_path',
'T', 'LIKE', '\medco\genomic\', 'MedCo Genomic Ontology', '\medco\genomic\',
'NOW()', 'NOW()', 'NOW()', 'GEN', '@');
insert into shrine_ont.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
('2', '\medco\genomic\annotations_Hugo_Symbol\', 'Gene Name', 'N', 'LA', '0', 'concept_cd', 'concept_dimension', 'concept_path',
'T', 'LIKE', '\medco\genomic\annotations_Hugo_Symbol\', 'Gene Name', '\medco\genomic\annotations_Hugo_Symbol\',
'NOW()', 'NOW()', 'NOW()', 'GEN', '@');
insert into shrine_ont.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
('2', '\medco\genomic\annotations_Protein_position\', 'Protein Position', 'N', 'LA', '0', 'concept_cd', 'concept_dimension', 'concept_path',
'T', 'LIKE', '\medco\genomic\annotations_Protein_position\', 'Protein Position', '\medco\genomic\annotations_Protein_position\',
'NOW()', 'NOW()', 'NOW()', 'GEN', '@');
insert into shrine_ont.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
('2', '\medco\genomic\variant\', 'Variant Name', 'N', 'LA', '0', 'concept_cd', 'concept_dimension', 'concept_path',
'T', 'LIKE', '\medco\genomic\variant\', 'Variant Name', '\medco\genomic\variant\',
'NOW()', 'NOW()', 'NOW()', 'GEN', '@');
-- genomic annotations table
CREATE TABLE shrine_ont.genomic_annotations (
variant_id bigint not null,
variant_annotations json not null
);
ALTER TABLE shrine_ont.genomic_annotations OWNER TO shrine_ont;
ALTER TABLE ONLY shrine_ont.genomic_annotations
ADD CONSTRAINT variant_id_pk PRIMARY KEY (variant_id);
-- authorizations
grant all on schema shrine_ont to shrine_ont;
grant all on schema shrine_ont to i2b2metadata;
grant all on schema i2b2metadata to shrine_ont;
grant all privileges on all tables in schema shrine_ont to shrine_ont;
grant all privileges on all sequences in schema shrine_ont to shrine_ont;
grant all privileges on all functions in schema shrine_ont to shrine_ont;
grant all privileges on all tables in schema shrine_ont to i2b2metadata;
grant all privileges on all sequences in schema shrine_ont to i2b2metadata;
grant all privileges on all functions in schema shrine_ont to i2b2metadata;
grant all privileges on all tables in schema i2b2metadata to shrine_ont;
grant all privileges on all sequences in schema i2b2metadata to shrine_ont;
grant all privileges on all functions in schema i2b2metadata to shrine_ont;
EOSQL
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