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medco-deployment/docker-images/i2b2-medco/sql/75-genomic-annotations.sh
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75-genomic-annotations.sh
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#!/bin/bash
set -Eeuo pipefail
# set up common medco ontology
psql $PSQL_PARAMS -d "$I2B2_DB_NAME" <<-EOSQL
-- genomic entries in i2b2/medco ontology
insert into medco_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 medco_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 medco_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 tables
create table genomic_annotations.genomic_annotations(
variant_id character varying(255) NOT NULL,
variant_name character varying(255) NOT NULL,
protein_change character varying(255) NOT NULL,
hugo_gene_symbol character varying(255) NOT NULL,
annotations text NOT NULL
);
create table genomic_annotations.annotation_names(
annotation_name character varying(255) NOT NULL PRIMARY KEY
);
create table genomic_annotations.gene_values(
gene_value character varying(255) NOT NULL PRIMARY KEY
);
-- permissions
ALTER TABLE genomic_annotations.genomic_annotations OWNER TO $I2B2_DB_USER;
ALTER TABLE genomic_annotations.annotation_names OWNER TO $I2B2_DB_USER;
ALTER TABLE genomic_annotations.gene_values OWNER TO $I2B2_DB_USER;
grant all on schema genomic_annotations to $I2B2_DB_USER;
grant all privileges on all tables in schema genomic_annotations to $I2B2_DB_USER;
EOSQL
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