mirror of https://github.com/samply/bridgehead.git
Integrating cBioPortal
This commit is contained in:
MuhannadBaraghith
djuarezgf
parent
6da143f348
commit
4449beacb5
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--
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-- Copyright (c) 2016 - 2022 Memorial Sloan Kettering Cancer Center.
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--
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-- This library is distributed in the hope that it will be useful, but WITHOUT
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-- ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS
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-- FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder
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-- is on an "as is" basis, and Memorial Sloan Kettering Cancer Center has no
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-- obligations to provide maintenance, support, updates, enhancements or
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-- modifications. In no event shall Memorial Sloan Kettering Cancer Center be
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-- liable to any party for direct, indirect, special, incidental or
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-- consequential damages, including lost profits, arising out of the use of this
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-- software and its documentation, even if Memorial Sloan Kettering Cancer
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-- Center has been advised of the possibility of such damage.
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--
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-- This file is part of cBioPortal.
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--
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-- cBioPortal is free software: you can redistribute it and/or modify
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-- it under the terms of the GNU Affero General Public License as
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-- published by the Free Software Foundation, either version 3 of the
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-- License.
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--
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-- This program is distributed in the hope that it will be useful,
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-- but WITHOUT ANY WARRANTY; without even the implied warranty of
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-- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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-- GNU Affero General Public License for more details.
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--
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-- You should have received a copy of the GNU Affero General Public License
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-- along with this program. If not, see <http://www.gnu.org/licenses/>.
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-- ----------------------------------------------------------------------------
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--
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-- Database: `cgds`
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--
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-- --------------------------------------------------------
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-- Database table schemas and version number
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-- --------------------------------------------------------
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-- The order of the following DROP TABLE statements is
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-- significant. If a table has a FOREIGN_KEY referring to
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-- another table, then it should be dropped before the
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-- other table is dropped. The approach taken here is to
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-- order the CREATE TABLE statements so that refererenced
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-- tables are created before referring tables.
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-- DROP TABLE statements are here in the reverse order.
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-- --------------------------------------------------------
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DROP TABLE IF EXISTS `info`;
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DROP TABLE IF EXISTS `clinical_event_data`;
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DROP TABLE IF EXISTS `clinical_event`;
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DROP TABLE IF EXISTS `pdb_uniprot_residue_mapping`;
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DROP TABLE IF EXISTS `pdb_uniprot_alignment`;
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DROP TABLE IF EXISTS `cosmic_mutation`;
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DROP TABLE IF EXISTS `copy_number_seg_file`;
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DROP TABLE IF EXISTS `copy_number_seg`;
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DROP TABLE IF EXISTS `sample_cna_event`;
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DROP TABLE IF EXISTS `cna_event`;
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DROP TABLE IF EXISTS `gistic_to_gene`;
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DROP TABLE IF EXISTS `gistic`;
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DROP TABLE IF EXISTS `mut_sig`;
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DROP TABLE IF EXISTS `clinical_attribute_meta`;
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DROP TABLE IF EXISTS `clinical_sample`;
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DROP TABLE IF EXISTS `clinical_patient`;
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DROP TABLE IF EXISTS `resource_definition`;
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DROP TABLE IF EXISTS `resource_sample`;
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DROP TABLE IF EXISTS `resource_patient`;
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DROP TABLE IF EXISTS `resource_study`;
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DROP TABLE IF EXISTS `mutation_count_by_keyword`;
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DROP TABLE IF EXISTS `allele_specific_copy_number`;
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DROP TABLE IF EXISTS `mutation`;
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DROP TABLE IF EXISTS `mutation_event`;
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DROP TABLE IF EXISTS `structural_variant`;
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DROP TABLE IF EXISTS `sample_profile`;
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DROP TABLE IF EXISTS `gene_panel_list`;
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DROP TABLE IF EXISTS `gene_panel`;
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DROP TABLE IF EXISTS `genetic_profile_samples`;
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DROP TABLE IF EXISTS `genetic_alteration`;
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DROP TABLE IF EXISTS `genetic_profile_link`;
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DROP TABLE IF EXISTS `alteration_driver_annotation`;
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DROP TABLE IF EXISTS `genetic_profile`;
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DROP TABLE IF EXISTS `gene_alias`;
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DROP TABLE IF EXISTS `geneset_gene`;
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DROP TABLE IF EXISTS `reference_genome_gene`;
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DROP TABLE IF EXISTS `gene`;
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DROP TABLE IF EXISTS `sample_list_list`;
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DROP TABLE IF EXISTS `sample_list`;
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DROP TABLE IF EXISTS `sample`;
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DROP TABLE IF EXISTS `patient`;
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DROP TABLE IF EXISTS `authorities`;
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DROP TABLE IF EXISTS `data_access_tokens`;
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DROP TABLE IF EXISTS `users`;
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DROP TABLE IF EXISTS `cancer_study_tags`;
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DROP TABLE IF EXISTS `cancer_study`;
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DROP TABLE IF EXISTS `type_of_cancer`;
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DROP TABLE IF EXISTS `geneset_hierarchy_leaf`;
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DROP TABLE IF EXISTS `geneset_hierarchy_node`;
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DROP TABLE IF EXISTS `geneset`;
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DROP TABLE IF EXISTS `generic_entity_properties`;
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DROP TABLE IF EXISTS `genetic_entity`;
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DROP TABLE IF EXISTS `reference_genome`;
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-- --------------------------------------------------------
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CREATE TABLE `type_of_cancer` (
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`TYPE_OF_CANCER_ID` varchar(63) NOT NULL,
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`NAME` varchar(255) NOT NULL,
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`DEDICATED_COLOR` char(31) NOT NULL,
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`SHORT_NAME` varchar(127),
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`PARENT` varchar(63),
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PRIMARY KEY (`TYPE_OF_CANCER_ID`)
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);
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-- --------------------------------------------------------
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CREATE TABLE `reference_genome` (
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`REFERENCE_GENOME_ID` int(4) NOT NULL AUTO_INCREMENT,
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`SPECIES` varchar(64) NOT NULL,
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`NAME` varchar(64) NOT NULL,
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`BUILD_NAME` varchar(64) NOT NULL,
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`GENOME_SIZE` bigint(20) NULL,
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`URL` varchar(256) NOT NULL,
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`RELEASE_DATE` datetime DEFAULT NULL,
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PRIMARY KEY (`REFERENCE_GENOME_ID`),
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UNIQUE INDEX `BUILD_NAME_UNIQUE` (`BUILD_NAME` ASC)
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);
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-- --------------------------------------------------------
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CREATE TABLE `cancer_study` (
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`CANCER_STUDY_ID` int(11) NOT NULL auto_increment,
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`CANCER_STUDY_IDENTIFIER` varchar(255),
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`TYPE_OF_CANCER_ID` varchar(63) NOT NULL,
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`NAME` varchar(255) NOT NULL,
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`DESCRIPTION` varchar(1024) NOT NULL,
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`PUBLIC` BOOLEAN NOT NULL,
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`PMID` varchar(1024) DEFAULT NULL,
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`CITATION` varchar(200) DEFAULT NULL,
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`GROUPS` varchar(200) DEFAULT NULL,
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`STATUS` int(1) DEFAULT NULL,
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`IMPORT_DATE` datetime DEFAULT NULL,
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`REFERENCE_GENOME_ID` int(4) DEFAULT 1,
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PRIMARY KEY (`CANCER_STUDY_ID`),
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UNIQUE (`CANCER_STUDY_IDENTIFIER`),
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FOREIGN KEY (`TYPE_OF_CANCER_ID`) REFERENCES `type_of_cancer` (`TYPE_OF_CANCER_ID`),
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FOREIGN KEY (`REFERENCE_GENOME_ID`) REFERENCES `reference_genome` (`REFERENCE_GENOME_ID`) ON DELETE RESTRICT
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);
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-- --------------------------------------------------------
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CREATE TABLE `cancer_study_tags` (
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`CANCER_STUDY_ID` int(11) NOT NULL,
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`TAGS` text NOT NULL,
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PRIMARY KEY (`CANCER_STUDY_ID`),
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FOREIGN KEY (`CANCER_STUDY_ID`) REFERENCES `cancer_study` (`CANCER_STUDY_ID`) ON DELETE CASCADE
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);
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-- --------------------------------------------------------
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CREATE TABLE `users` (
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`EMAIL` varchar(128) NOT NULL,
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`NAME` varchar(255) NOT NULL,
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`ENABLED` BOOLEAN NOT NULL,
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PRIMARY KEY (`EMAIL`)
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);
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-- --------------------------------------------------------
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CREATE TABLE `authorities` (
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`EMAIL` varchar(128) NOT NULL,
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`AUTHORITY` varchar(255) NOT NULL
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);
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-- --------------------------------------------------------
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CREATE TABLE `patient` (
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`INTERNAL_ID` int(11) NOT NULL auto_increment,
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`STABLE_ID` varchar(50) NOT NULL,
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`CANCER_STUDY_ID` int(11) NOT NULL,
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PRIMARY KEY (`INTERNAL_ID`),
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FOREIGN KEY (`CANCER_STUDY_ID`) REFERENCES `cancer_study` (`CANCER_STUDY_ID`) ON DELETE CASCADE
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);
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-- --------------------------------------------------------
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CREATE TABLE `sample` (
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`INTERNAL_ID` int(11) NOT NULL auto_increment,
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`STABLE_ID` varchar(63) NOT NULL,
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`SAMPLE_TYPE` varchar(255) NOT NULL,
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`PATIENT_ID` int(11) NOT NULL,
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PRIMARY KEY (`INTERNAL_ID`),
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FOREIGN KEY (`PATIENT_ID`) REFERENCES `patient` (`INTERNAL_ID`) ON DELETE CASCADE
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);
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-- --------------------------------------------------------
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CREATE TABLE `sample_list` (
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`LIST_ID` int(11) NOT NULL auto_increment,
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`STABLE_ID` varchar(255) NOT NULL,
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`CATEGORY` varchar(255) NOT NULL,
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`CANCER_STUDY_ID` int(11) NOT NULL,
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`NAME` varchar(255) NOT NULL,
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`DESCRIPTION` mediumtext,
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PRIMARY KEY (`LIST_ID`),
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UNIQUE (`STABLE_ID`),
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FOREIGN KEY (`CANCER_STUDY_ID`) REFERENCES `cancer_study` (`CANCER_STUDY_ID`) ON DELETE CASCADE
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);
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-- --------------------------------------------------------
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CREATE TABLE `sample_list_list` (
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`LIST_ID` int(11) NOT NULL,
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`SAMPLE_ID` int(11) NOT NULL,
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PRIMARY KEY (`LIST_ID`,`SAMPLE_ID`),
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FOREIGN KEY (`SAMPLE_ID`) REFERENCES `sample` (`INTERNAL_ID`) ON DELETE CASCADE
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);
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-- --------------------------------------------------------
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CREATE TABLE `genetic_entity` (
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`ID` int(11) NOT NULL AUTO_INCREMENT,
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`ENTITY_TYPE` varchar(45) NOT NULL,
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`STABLE_ID` varchar(255) DEFAULT NULL,
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PRIMARY KEY (`ID`)
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);
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-- --------------------------------------------------------
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CREATE TABLE `gene` (
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`ENTREZ_GENE_ID` int(11) NOT NULL,
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`HUGO_GENE_SYMBOL` varchar(255) NOT NULL,
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`GENETIC_ENTITY_ID` int(11) NOT NULL,
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`TYPE` varchar(50),
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PRIMARY KEY (`ENTREZ_GENE_ID`),
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UNIQUE KEY `GENETIC_ENTITY_ID_UNIQUE` (`GENETIC_ENTITY_ID`),
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KEY `HUGO_GENE_SYMBOL` (`HUGO_GENE_SYMBOL`),
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FOREIGN KEY (`GENETIC_ENTITY_ID`) REFERENCES `genetic_entity` (`ID`) ON DELETE CASCADE
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);
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-- --------------------------------------------------------
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CREATE TABLE `gene_alias` (
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`ENTREZ_GENE_ID` int(11) NOT NULL,
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`GENE_ALIAS` varchar(255) NOT NULL,
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PRIMARY KEY (`ENTREZ_GENE_ID`,`GENE_ALIAS`),
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FOREIGN KEY (`ENTREZ_GENE_ID`) REFERENCES `gene` (`ENTREZ_GENE_ID`)
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);
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-- --------------------------------------------------------
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CREATE TABLE `geneset` (
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`ID` INT(11) NOT NULL auto_increment,
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`GENETIC_ENTITY_ID` INT NOT NULL,
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`EXTERNAL_ID` VARCHAR(200) NOT NULL,
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`NAME` VARCHAR(200) NOT NULL,
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`DESCRIPTION` VARCHAR(300) NOT NULL,
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`REF_LINK` TEXT,
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PRIMARY KEY (`ID`),
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UNIQUE INDEX `NAME_UNIQUE` (`NAME` ASC),
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UNIQUE INDEX `EXTERNAL_ID_COLL_UNIQUE` (`EXTERNAL_ID` ASC),
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UNIQUE INDEX `GENESET_GENETIC_ENTITY_ID_UNIQUE` (`GENETIC_ENTITY_ID` ASC),
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FOREIGN KEY (`GENETIC_ENTITY_ID`) REFERENCES `genetic_entity` (`ID`) ON DELETE CASCADE
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);
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-- --------------------------------------------------------
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CREATE TABLE `geneset_gene` (
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`GENESET_ID` INT(11) NOT NULL,
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`ENTREZ_GENE_ID` INT(11) NOT NULL,
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PRIMARY KEY (`GENESET_ID`, `ENTREZ_GENE_ID`),
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FOREIGN KEY (`ENTREZ_GENE_ID`) REFERENCES `gene` (`ENTREZ_GENE_ID`) ON DELETE CASCADE,
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FOREIGN KEY (`GENESET_ID`) REFERENCES `geneset` (`ID`) ON DELETE CASCADE
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);
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-- --------------------------------------------------------
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CREATE TABLE `geneset_hierarchy_node` (
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`NODE_ID` BIGINT(20) NOT NULL auto_increment,
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`NODE_NAME` VARCHAR(200) NOT NULL,
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`PARENT_ID` BIGINT NULL DEFAULT NULL,
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PRIMARY KEY (`NODE_ID`),
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UNIQUE INDEX `NODE_NAME_UNIQUE` (`NODE_NAME` ASC, `PARENT_ID` ASC)
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);
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-- --------------------------------------------------------
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CREATE TABLE `geneset_hierarchy_leaf` (
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`NODE_ID` BIGINT NOT NULL,
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`GENESET_ID` INT NOT NULL,
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PRIMARY KEY (`NODE_ID`, `GENESET_ID`),
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FOREIGN KEY (`NODE_ID`) REFERENCES `geneset_hierarchy_node` (`NODE_ID`) ON DELETE CASCADE,
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FOREIGN KEY (`GENESET_ID`) REFERENCES `geneset` (`ID`) ON DELETE CASCADE
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);
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-- ------------------------------------------------------
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CREATE TABLE `generic_entity_properties` (
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`ID` INT(11) NOT NULL auto_increment,
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`GENETIC_ENTITY_ID` INT NOT NULL,
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`NAME` varchar(255) NOT NULL,
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`VALUE` varchar(5000) NOT NULL,
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UNIQUE (`GENETIC_ENTITY_ID`, `NAME`),
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PRIMARY KEY (`ID`),
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FOREIGN KEY (`GENETIC_ENTITY_ID`) REFERENCES `genetic_entity` (`ID`) ON DELETE CASCADE
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|
);
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-- --------------------------------------------------------
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CREATE TABLE `genetic_profile` (
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`GENETIC_PROFILE_ID` int(11) NOT NULL AUTO_INCREMENT,
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`STABLE_ID` varchar(255) NOT NULL,
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`CANCER_STUDY_ID` int(11) NOT NULL,
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`GENETIC_ALTERATION_TYPE` varchar(255) NOT NULL,
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`GENERIC_ASSAY_TYPE` varchar(255) DEFAULT NULL,
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`DATATYPE` varchar(255) NOT NULL,
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`NAME` varchar(255) NOT NULL,
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`DESCRIPTION` mediumtext,
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`SHOW_PROFILE_IN_ANALYSIS_TAB` tinyint(1) NOT NULL,
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`PIVOT_THRESHOLD` FLOAT DEFAULT NULL,
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`SORT_ORDER` ENUM('ASC','DESC') DEFAULT NULL,
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`PATIENT_LEVEL` boolean DEFAULT 0,
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PRIMARY KEY (`GENETIC_PROFILE_ID`),
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UNIQUE (`STABLE_ID`),
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FOREIGN KEY (`CANCER_STUDY_ID`) REFERENCES `cancer_study` (`CANCER_STUDY_ID`) ON DELETE CASCADE
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);
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-- --------------------------------------------------------
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CREATE TABLE `genetic_profile_link` (
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`REFERRING_GENETIC_PROFILE_ID` INT NOT NULL,
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`REFERRED_GENETIC_PROFILE_ID` INT NOT NULL,
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`REFERENCE_TYPE` VARCHAR(45) NULL, -- COMMENT 'Values: AGGREGATION (e.g. for GSVA) or STATISTIC (e.g. for Z-SCORES)
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PRIMARY KEY (`REFERRING_GENETIC_PROFILE_ID`, `REFERRED_GENETIC_PROFILE_ID`),
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FOREIGN KEY (`REFERRING_GENETIC_PROFILE_ID` ) REFERENCES `genetic_profile` (`GENETIC_PROFILE_ID`) ON DELETE CASCADE,
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FOREIGN KEY (`REFERRED_GENETIC_PROFILE_ID` ) REFERENCES `genetic_profile` (`GENETIC_PROFILE_ID`) ON DELETE NO ACTION ON UPDATE NO ACTION
|
||||||
|
);
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-- --------------------------------------------------------
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CREATE TABLE `genetic_alteration` (
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`GENETIC_PROFILE_ID` int(11) NOT NULL,
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||||||
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`GENETIC_ENTITY_ID` int(11) NOT NULL,
|
||||||
|
`VALUES` longtext NOT NULL,
|
||||||
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PRIMARY KEY (`GENETIC_PROFILE_ID`,`GENETIC_ENTITY_ID`),
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||||||
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FOREIGN KEY (`GENETIC_PROFILE_ID`) REFERENCES `genetic_profile` (`GENETIC_PROFILE_ID`) ON DELETE CASCADE,
|
||||||
|
FOREIGN KEY (`GENETIC_ENTITY_ID`) REFERENCES `genetic_entity` (`ID`) ON DELETE CASCADE
|
||||||
|
);
|
||||||
|
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|
-- --------------------------------------------------------
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CREATE TABLE `genetic_profile_samples` (
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`GENETIC_PROFILE_ID` int(11) NOT NULL,
|
||||||
|
`ORDERED_SAMPLE_LIST` longtext NOT NULL,
|
||||||
|
UNIQUE (`GENETIC_PROFILE_ID`),
|
||||||
|
FOREIGN KEY (`GENETIC_PROFILE_ID`) REFERENCES `genetic_profile` (`GENETIC_PROFILE_ID`) ON DELETE CASCADE
|
||||||
|
);
|
||||||
|
|
||||||
|
-- --------------------------------------------------------
|
||||||
|
CREATE TABLE `gene_panel` (
|
||||||
|
`INTERNAL_ID` int(11) NOT NULL auto_increment,
|
||||||
|
`STABLE_ID` varchar(255) NOT NULL,
|
||||||
|
`DESCRIPTION` mediumtext,
|
||||||
|
PRIMARY KEY (`INTERNAL_ID`),
|
||||||
|
UNIQUE (`STABLE_ID`)
|
||||||
|
);
|
||||||
|
|
||||||
|
-- --------------------------------------------------------
|
||||||
|
CREATE TABLE `gene_panel_list` (
|
||||||
|
`INTERNAL_ID` int(11) NOT NULL,
|
||||||
|
`GENE_ID` int(11) NOT NULL,
|
||||||
|
PRIMARY KEY (`INTERNAL_ID`, `GENE_ID`),
|
||||||
|
FOREIGN KEY (`INTERNAL_ID`) REFERENCES `gene_panel` (`INTERNAL_ID`) ON DELETE CASCADE,
|
||||||
|
FOREIGN KEY (`GENE_ID`) REFERENCES `gene` (`ENTREZ_GENE_ID`) ON DELETE CASCADE
|
||||||
|
);
|
||||||
|
|
||||||
|
-- --------------------------------------------------------
|
||||||
|
CREATE TABLE `sample_profile` (
|
||||||
|
`SAMPLE_ID` int(11) NOT NULL,
|
||||||
|
`GENETIC_PROFILE_ID` int(11) NOT NULL,
|
||||||
|
`PANEL_ID` int(11) DEFAULT NULL,
|
||||||
|
UNIQUE KEY `UQ_SAMPLE_ID_GENETIC_PROFILE_ID` (`SAMPLE_ID`,`GENETIC_PROFILE_ID`), -- Constraint to allow each sample only once in each profile
|
||||||
|
KEY (`SAMPLE_ID`),
|
||||||
|
FOREIGN KEY (`GENETIC_PROFILE_ID`) REFERENCES `genetic_profile` (`GENETIC_PROFILE_ID`) ON DELETE CASCADE,
|
||||||
|
FOREIGN KEY (`SAMPLE_ID`) REFERENCES `sample` (`INTERNAL_ID`) ON DELETE CASCADE,
|
||||||
|
FOREIGN KEY (`PANEL_ID`) REFERENCES `gene_panel` (`INTERNAL_ID`) ON DELETE RESTRICT
|
||||||
|
);
|
||||||
|
|
||||||
|
-- --------------------------------------------------------
|
||||||
|
CREATE TABLE `structural_variant` (
|
||||||
|
`INTERNAL_ID` int(11) NOT NULL auto_increment,
|
||||||
|
`GENETIC_PROFILE_ID` int(11) NOT NULL,
|
||||||
|
`SAMPLE_ID` int(11) NOT NULL,
|
||||||
|
`SITE1_ENTREZ_GENE_ID` int(11),
|
||||||
|
`SITE1_ENSEMBL_TRANSCRIPT_ID` varchar(25),
|
||||||
|
`SITE1_CHROMOSOME` varchar(5),
|
||||||
|
`SITE1_REGION` varchar(25),
|
||||||
|
`SITE1_REGION_NUMBER` int(11),
|
||||||
|
`SITE1_CONTIG` varchar(100),
|
||||||
|
`SITE1_POSITION` int(11),
|
||||||
|
`SITE1_DESCRIPTION` varchar(255),
|
||||||
|
`SITE2_ENTREZ_GENE_ID` int(11),
|
||||||
|
`SITE2_ENSEMBL_TRANSCRIPT_ID` varchar(25),
|
||||||
|
`SITE2_CHROMOSOME` varchar(5),
|
||||||
|
`SITE2_REGION` varchar(25),
|
||||||
|
`SITE2_REGION_NUMBER` int(11),
|
||||||
|
`SITE2_CONTIG` varchar(100),
|
||||||
|
`SITE2_POSITION` int(11),
|
||||||
|
`SITE2_DESCRIPTION` varchar(255),
|
||||||
|
`SITE2_EFFECT_ON_FRAME` varchar(25),
|
||||||
|
`NCBI_BUILD` varchar(10),
|
||||||
|
`DNA_SUPPORT` varchar(3),
|
||||||
|
`RNA_SUPPORT` varchar(3),
|
||||||
|
`NORMAL_READ_COUNT` int(11),
|
||||||
|
`TUMOR_READ_COUNT` int(11),
|
||||||
|
`NORMAL_VARIANT_COUNT` int(11),
|
||||||
|
`TUMOR_VARIANT_COUNT` int(11),
|
||||||
|
`NORMAL_PAIRED_END_READ_COUNT` int(11),
|
||||||
|
`TUMOR_PAIRED_END_READ_COUNT` int(11),
|
||||||
|
`NORMAL_SPLIT_READ_COUNT` int(11),
|
||||||
|
`TUMOR_SPLIT_READ_COUNT` int(11),
|
||||||
|
`ANNOTATION` varchar(255),
|
||||||
|
`BREAKPOINT_TYPE` varchar(25),
|
||||||
|
`CONNECTION_TYPE` varchar(25),
|
||||||
|
`EVENT_INFO` varchar(255),
|
||||||
|
`CLASS` varchar(25),
|
||||||
|
`LENGTH` int(11),
|
||||||
|
`COMMENTS` varchar(255),
|
||||||
|
`SV_STATUS` varchar(25) NOT NULL DEFAULT 'SOMATIC' COMMENT 'GERMLINE or SOMATIC.',
|
||||||
|
`ANNOTATION_JSON` JSON,
|
||||||
|
PRIMARY KEY (`INTERNAL_ID`),
|
||||||
|
FOREIGN KEY (`SAMPLE_ID`) REFERENCES `sample` (`INTERNAL_ID`) ON DELETE CASCADE,
|
||||||
|
FOREIGN KEY (`SITE1_ENTREZ_GENE_ID`) REFERENCES `gene` (`ENTREZ_GENE_ID`) ON DELETE CASCADE,
|
||||||
|
FOREIGN KEY (`SITE2_ENTREZ_GENE_ID`) REFERENCES `gene` (`ENTREZ_GENE_ID`) ON DELETE CASCADE,
|
||||||
|
FOREIGN KEY (`GENETIC_PROFILE_ID`) REFERENCES `genetic_profile` (`GENETIC_PROFILE_ID`) ON DELETE CASCADE
|
||||||
|
);
|
||||||
|
|
||||||
|
-- --------------------------------------------------------
|
||||||
|
CREATE TABLE `alteration_driver_annotation` (
|
||||||
|
`ALTERATION_EVENT_ID` int(255) NOT NULL,
|
||||||
|
`GENETIC_PROFILE_ID` int(11) NOT NULL,
|
||||||
|
`SAMPLE_ID` int(11) NOT NULL,
|
||||||
|
`DRIVER_FILTER` VARCHAR(20),
|
||||||
|
`DRIVER_FILTER_ANNOTATION` VARCHAR(80),
|
||||||
|
`DRIVER_TIERS_FILTER` VARCHAR(50),
|
||||||
|
`DRIVER_TIERS_FILTER_ANNOTATION` VARCHAR(80),
|
||||||
|
PRIMARY KEY (`ALTERATION_EVENT_ID`, `GENETIC_PROFILE_ID`, `SAMPLE_ID`),
|
||||||
|
FOREIGN KEY (`GENETIC_PROFILE_ID`) REFERENCES `genetic_profile` (`GENETIC_PROFILE_ID`) ON DELETE CASCADE,
|
||||||
|
FOREIGN KEY (`SAMPLE_ID`) REFERENCES `sample` (`INTERNAL_ID`) ON DELETE CASCADE,
|
||||||
|
INDEX (`DRIVER_FILTER`),
|
||||||
|
INDEX (`DRIVER_TIERS_FILTER`)
|
||||||
|
) COMMENT='Alteration driver annotation';
|
||||||
|
|
||||||
|
-- --------------------------------------------------------
|
||||||
|
CREATE TABLE `mutation_event` (
|
||||||
|
`MUTATION_EVENT_ID` int(255) NOT NULL auto_increment,
|
||||||
|
`ENTREZ_GENE_ID` int(11) NOT NULL,
|
||||||
|
`CHR` varchar(5),
|
||||||
|
`START_POSITION` bigint(20),
|
||||||
|
`END_POSITION` bigint(20),
|
||||||
|
`REFERENCE_ALLELE` text,
|
||||||
|
`TUMOR_SEQ_ALLELE` text,
|
||||||
|
`PROTEIN_CHANGE` varchar(255),
|
||||||
|
`MUTATION_TYPE` varchar(255) COMMENT 'e.g. Missense, Nonsence, etc.',
|
||||||
|
`NCBI_BUILD` varchar(10),
|
||||||
|
`STRAND` varchar(2),
|
||||||
|
`VARIANT_TYPE` varchar(15),
|
||||||
|
`DB_SNP_RS` varchar(25),
|
||||||
|
`DB_SNP_VAL_STATUS` varchar(255),
|
||||||
|
`REFSEQ_MRNA_ID` varchar(64),
|
||||||
|
`CODON_CHANGE` varchar(255),
|
||||||
|
`UNIPROT_ACCESSION` varchar(64),
|
||||||
|
`PROTEIN_POS_START` int(11),
|
||||||
|
`PROTEIN_POS_END` int(11),
|
||||||
|
`CANONICAL_TRANSCRIPT` boolean,
|
||||||
|
`KEYWORD` varchar(255) DEFAULT NULL COMMENT 'e.g. truncating, V200 Missense, E338del, ',
|
||||||
|
KEY (`KEYWORD`),
|
||||||
|
PRIMARY KEY (`MUTATION_EVENT_ID`),
|
||||||
|
KEY `KEY_MUTATION_EVENT_DETAILS` (`CHR`, `START_POSITION`, `END_POSITION`, `TUMOR_SEQ_ALLELE`(240), `ENTREZ_GENE_ID`, `PROTEIN_CHANGE`, `MUTATION_TYPE`),
|
||||||
|
FOREIGN KEY (`ENTREZ_GENE_ID`) REFERENCES `gene` (`ENTREZ_GENE_ID`),
|
||||||
|
INDEX (`MUTATION_TYPE`)
|
||||||
|
) COMMENT='Mutation Data';
|
||||||
|
|
||||||
|
-- --------------------------------------------------------
|
||||||
|
CREATE TABLE `mutation` (
|
||||||
|
`MUTATION_EVENT_ID` int(255) NOT NULL,
|
||||||
|
`GENETIC_PROFILE_ID` int(11) NOT NULL,
|
||||||
|
`SAMPLE_ID` int(11) NOT NULL,
|
||||||
|
`ENTREZ_GENE_ID` int(11) NOT NULL,
|
||||||
|
`CENTER` varchar(100),
|
||||||
|
`SEQUENCER` varchar(255),
|
||||||
|
`MUTATION_STATUS` varchar(25) COMMENT 'Germline, Somatic or LOH.',
|
||||||
|
`VALIDATION_STATUS` varchar(25),
|
||||||
|
`TUMOR_SEQ_ALLELE1` TEXT,
|
||||||
|
`TUMOR_SEQ_ALLELE2` TEXT,
|
||||||
|
`MATCHED_NORM_SAMPLE_BARCODE` varchar(255),
|
||||||
|
`MATCH_NORM_SEQ_ALLELE1` TEXT,
|
||||||
|
`MATCH_NORM_SEQ_ALLELE2` TEXT,
|
||||||
|
`TUMOR_VALIDATION_ALLELE1` TEXT,
|
||||||
|
`TUMOR_VALIDATION_ALLELE2` TEXT,
|
||||||
|
`MATCH_NORM_VALIDATION_ALLELE1` TEXT,
|
||||||
|
`MATCH_NORM_VALIDATION_ALLELE2` TEXT,
|
||||||
|
`VERIFICATION_STATUS` varchar(10),
|
||||||
|
`SEQUENCING_PHASE` varchar(100),
|
||||||
|
`SEQUENCE_SOURCE` varchar(255) NOT NULL,
|
||||||
|
`VALIDATION_METHOD` varchar(255),
|
||||||
|
`SCORE` varchar(100),
|
||||||
|
`BAM_FILE` varchar(255),
|
||||||
|
`TUMOR_ALT_COUNT` int(11),
|
||||||
|
`TUMOR_REF_COUNT` int(11),
|
||||||
|
`NORMAL_ALT_COUNT` int(11),
|
||||||
|
`NORMAL_REF_COUNT` int(11),
|
||||||
|
`AMINO_ACID_CHANGE` varchar(255),
|
||||||
|
`ANNOTATION_JSON` JSON,
|
||||||
|
UNIQUE KEY `UQ_MUTATION_EVENT_ID_GENETIC_PROFILE_ID_SAMPLE_ID` (`MUTATION_EVENT_ID`,`GENETIC_PROFILE_ID`,`SAMPLE_ID`), -- Constraint to block duplicated mutation entries
|
||||||
|
KEY (`GENETIC_PROFILE_ID`,`ENTREZ_GENE_ID`),
|
||||||
|
KEY (`GENETIC_PROFILE_ID`,`SAMPLE_ID`),
|
||||||
|
KEY (`GENETIC_PROFILE_ID`),
|
||||||
|
KEY (`ENTREZ_GENE_ID`),
|
||||||
|
KEY (`SAMPLE_ID`),
|
||||||
|
KEY (`MUTATION_EVENT_ID`),
|
||||||
|
FOREIGN KEY (`MUTATION_EVENT_ID`) REFERENCES `mutation_event` (`MUTATION_EVENT_ID`),
|
||||||
|
FOREIGN KEY (`ENTREZ_GENE_ID`) REFERENCES `gene` (`ENTREZ_GENE_ID`),
|
||||||
|
FOREIGN KEY (`GENETIC_PROFILE_ID`) REFERENCES `genetic_profile` (`GENETIC_PROFILE_ID`) ON DELETE CASCADE,
|
||||||
|
FOREIGN KEY (`SAMPLE_ID`) REFERENCES `sample` (`INTERNAL_ID`) ON DELETE CASCADE
|
||||||
|
) COMMENT='Mutation Data Details';
|
||||||
|
|
||||||
|
-- --------------------------------------------------------
|
||||||
|
CREATE TABLE `mutation_count_by_keyword` (
|
||||||
|
`GENETIC_PROFILE_ID` int(11) NOT NULL,
|
||||||
|
`KEYWORD` varchar(255) DEFAULT NULL,
|
||||||
|
`ENTREZ_GENE_ID` int(11) NOT NULL,
|
||||||
|
`KEYWORD_COUNT` int NOT NULL,
|
||||||
|
`GENE_COUNT` int NOT NULL,
|
||||||
|
KEY (`GENETIC_PROFILE_ID`,`KEYWORD`),
|
||||||
|
FOREIGN KEY (`GENETIC_PROFILE_ID`) REFERENCES `genetic_profile` (`GENETIC_PROFILE_ID`) ON DELETE CASCADE,
|
||||||
|
FOREIGN KEY (`ENTREZ_GENE_ID`) REFERENCES `gene` (`ENTREZ_GENE_ID`) ON DELETE CASCADE
|
||||||
|
);
|
||||||
|
|
||||||
|
-- --------------------------------------------------------
|
||||||
|
CREATE TABLE `clinical_patient` (
|
||||||
|
`INTERNAL_ID` int(11) NOT NULL,
|
||||||
|
`ATTR_ID` varchar(255) NOT NULL,
|
||||||
|
`ATTR_VALUE` varchar(255) NOT NULL,
|
||||||
|
PRIMARY KEY (`INTERNAL_ID`, `ATTR_ID`),
|
||||||
|
FOREIGN KEY (`INTERNAL_ID`) REFERENCES `patient` (`INTERNAL_ID`) ON DELETE CASCADE
|
||||||
|
);
|
||||||
|
|
||||||
|
-- --------------------------------------------------------
|
||||||
|
CREATE TABLE `clinical_sample` (
|
||||||
|
`INTERNAL_ID` int(11) NOT NULL,
|
||||||
|
`ATTR_ID` varchar(255) NOT NULL,
|
||||||
|
`ATTR_VALUE` varchar(255) NOT NULL,
|
||||||
|
PRIMARY KEY (`INTERNAL_ID`,`ATTR_ID`),
|
||||||
|
FOREIGN KEY (`INTERNAL_ID`) REFERENCES `sample` (`INTERNAL_ID`) ON DELETE CASCADE
|
||||||
|
);
|
||||||
|
|
||||||
|
-- --------------------------------------------------------
|
||||||
|
CREATE TABLE `clinical_attribute_meta` (
|
||||||
|
`ATTR_ID` varchar(255) NOT NULL,
|
||||||
|
`DISPLAY_NAME` varchar(255) NOT NULL,
|
||||||
|
`DESCRIPTION` varchar(2048) NOT NULL,
|
||||||
|
`DATATYPE` varchar(255) NOT NULL COMMENT 'NUMBER, BOOLEAN, or STRING',
|
||||||
|
`PATIENT_ATTRIBUTE` BOOLEAN NOT NULL,
|
||||||
|
`PRIORITY` varchar(255) NOT NULL,
|
||||||
|
`CANCER_STUDY_ID` int(11) NOT NULL,
|
||||||
|
PRIMARY KEY (`ATTR_ID`,`CANCER_STUDY_ID`),
|
||||||
|
FOREIGN KEY (`CANCER_STUDY_ID`) REFERENCES `cancer_study` (`CANCER_STUDY_ID`) ON DELETE CASCADE
|
||||||
|
);
|
||||||
|
|
||||||
|
-- --------------------------------------------------------
|
||||||
|
CREATE TABLE `mut_sig` (
|
||||||
|
`CANCER_STUDY_ID` int(11) NOT NULL,
|
||||||
|
`ENTREZ_GENE_ID` int(11) NOT NULL,
|
||||||
|
`RANK` int(11) NOT NULL,
|
||||||
|
`NumBasesCovered` int(11) NOT NULL,
|
||||||
|
`NumMutations` int(11) NOT NULL,
|
||||||
|
`P_VALUE` float NOT NULL,
|
||||||
|
`Q_VALUE` float NOT NULL,
|
||||||
|
PRIMARY KEY (`CANCER_STUDY_ID`, `ENTREZ_GENE_ID`),
|
||||||
|
FOREIGN KEY (`CANCER_STUDY_ID`) REFERENCES `cancer_study` (`CANCER_STUDY_ID`) ON DELETE CASCADE,
|
||||||
|
FOREIGN KEY (`ENTREZ_GENE_ID`) REFERENCES `gene` (`ENTREZ_GENE_ID`)
|
||||||
|
);
|
||||||
|
|
||||||
|
-- --------------------------------------------------------
|
||||||
|
CREATE TABLE `gistic` (
|
||||||
|
`GISTIC_ROI_ID` bigint(20) NOT NULL auto_increment,
|
||||||
|
`CANCER_STUDY_ID` int(11) NOT NULL,
|
||||||
|
`CHROMOSOME` int(11) NOT NULL,
|
||||||
|
`CYTOBAND` varchar(255) NOT NULL,
|
||||||
|
`WIDE_PEAK_START` int(11) NOT NULL,
|
||||||
|
`WIDE_PEAK_END` int(11) NOT NULL,
|
||||||
|
`Q_VALUE` double NOT NULL,
|
||||||
|
`AMP` tinyint(1) NOT NULL,
|
||||||
|
PRIMARY KEY (`GISTIC_ROI_ID`),
|
||||||
|
FOREIGN KEY (`CANCER_STUDY_ID`) REFERENCES `cancer_study` (`CANCER_STUDY_ID`) ON DELETE CASCADE
|
||||||
|
);
|
||||||
|
|
||||||
|
-- --------------------------------------------------------
|
||||||
|
CREATE TABLE `gistic_to_gene` (
|
||||||
|
`GISTIC_ROI_ID` bigint(20) NOT NULL,
|
||||||
|
`ENTREZ_GENE_ID` int(11) NOT NULL,
|
||||||
|
PRIMARY KEY(`GISTIC_ROI_ID`, `ENTREZ_GENE_ID`),
|
||||||
|
FOREIGN KEY (`ENTREZ_GENE_ID`) REFERENCES `gene` (`ENTREZ_GENE_ID`),
|
||||||
|
FOREIGN KEY (`GISTIC_ROI_ID`) REFERENCES `gistic` (`GISTIC_ROI_ID`) ON DELETE CASCADE
|
||||||
|
);
|
||||||
|
|
||||||
|
-- --------------------------------------------------------
|
||||||
|
CREATE TABLE `cna_event` (
|
||||||
|
`CNA_EVENT_ID` int(255) NOT NULL auto_increment,
|
||||||
|
`ENTREZ_GENE_ID` int(11) NOT NULL,
|
||||||
|
`ALTERATION` tinyint NOT NULL,
|
||||||
|
PRIMARY KEY (`CNA_EVENT_ID`),
|
||||||
|
UNIQUE (`ENTREZ_GENE_ID`, `ALTERATION`),
|
||||||
|
FOREIGN KEY (`ENTREZ_GENE_ID`) REFERENCES `gene` (`ENTREZ_GENE_ID`),
|
||||||
|
INDEX (`ALTERATION`)
|
||||||
|
);
|
||||||
|
|
||||||
|
-- --------------------------------------------------------
|
||||||
|
CREATE TABLE `sample_cna_event` (
|
||||||
|
`CNA_EVENT_ID` int(255) NOT NULL,
|
||||||
|
`SAMPLE_ID` int(11) NOT NULL,
|
||||||
|
`GENETIC_PROFILE_ID` int(11) NOT NULL,
|
||||||
|
`ANNOTATION_JSON` JSON,
|
||||||
|
KEY (`GENETIC_PROFILE_ID`,`SAMPLE_ID`),
|
||||||
|
PRIMARY KEY (`CNA_EVENT_ID`, `SAMPLE_ID`, `GENETIC_PROFILE_ID`),
|
||||||
|
FOREIGN KEY (`CNA_EVENT_ID`) REFERENCES `cna_event` (`CNA_EVENT_ID`),
|
||||||
|
FOREIGN KEY (`GENETIC_PROFILE_ID`) REFERENCES `genetic_profile` (`GENETIC_PROFILE_ID`) ON DELETE CASCADE,
|
||||||
|
FOREIGN KEY (`SAMPLE_ID`) REFERENCES `sample` (`INTERNAL_ID`) ON DELETE CASCADE
|
||||||
|
);
|
||||||
|
|
||||||
|
-- --------------------------------------------------------
|
||||||
|
CREATE TABLE `copy_number_seg` (
|
||||||
|
`SEG_ID` bigint(20) NOT NULL auto_increment,
|
||||||
|
`CANCER_STUDY_ID` int(11) NOT NULL,
|
||||||
|
`SAMPLE_ID` int(11) NOT NULL,
|
||||||
|
`CHR` varchar(5) NOT NULL,
|
||||||
|
`START` int(11) NOT NULL,
|
||||||
|
`END` int(11) NOT NULL,
|
||||||
|
`NUM_PROBES` int(11) NOT NULL,
|
||||||
|
`SEGMENT_MEAN` double NOT NULL,
|
||||||
|
KEY (`CANCER_STUDY_ID`,`SAMPLE_ID`),
|
||||||
|
PRIMARY KEY (`SEG_ID`),
|
||||||
|
FOREIGN KEY (`CANCER_STUDY_ID`) REFERENCES `cancer_study` (`CANCER_STUDY_ID`) ON DELETE CASCADE,
|
||||||
|
FOREIGN KEY (`SAMPLE_ID`) REFERENCES `sample` (`INTERNAL_ID`) ON DELETE CASCADE
|
||||||
|
);
|
||||||
|
|
||||||
|
-- --------------------------------------------------------
|
||||||
|
CREATE TABLE `copy_number_seg_file` (
|
||||||
|
`SEG_FILE_ID` int(11) NOT NULL auto_increment,
|
||||||
|
`CANCER_STUDY_ID` int(11) NOT NULL,
|
||||||
|
`REFERENCE_GENOME_ID` varchar(10) NOT NULL,
|
||||||
|
`DESCRIPTION` varchar(255) NOT NULL,
|
||||||
|
`FILENAME` varchar(255) NOT NULL,
|
||||||
|
PRIMARY KEY(`SEG_FILE_ID`),
|
||||||
|
FOREIGN KEY (`CANCER_STUDY_ID`) REFERENCES `cancer_study` (`CANCER_STUDY_ID`) ON DELETE CASCADE
|
||||||
|
);
|
||||||
|
|
||||||
|
-- --------------------------------------------------------
|
||||||
|
CREATE TABLE `cosmic_mutation` (
|
||||||
|
`COSMIC_MUTATION_ID` varchar(30) NOT NULL,
|
||||||
|
`CHR` varchar(5),
|
||||||
|
`START_POSITION` bigint(20),
|
||||||
|
`REFERENCE_ALLELE` varchar(255),
|
||||||
|
`TUMOR_SEQ_ALLELE` varchar(255),
|
||||||
|
`STRAND` varchar(2),
|
||||||
|
`CODON_CHANGE` varchar(255),
|
||||||
|
`ENTREZ_GENE_ID` int(11) NOT NULL,
|
||||||
|
`PROTEIN_CHANGE` varchar(255) NOT NULL,
|
||||||
|
`COUNT` int(11) NOT NULL,
|
||||||
|
`KEYWORD` varchar(50) DEFAULT NULL,
|
||||||
|
KEY (`KEYWORD`),
|
||||||
|
PRIMARY KEY (`COSMIC_MUTATION_ID`),
|
||||||
|
FOREIGN KEY (`ENTREZ_GENE_ID`) REFERENCES `gene` (`ENTREZ_GENE_ID`)
|
||||||
|
);
|
||||||
|
|
||||||
|
-- --------------------------------------------------------
|
||||||
|
CREATE TABLE `clinical_event` (
|
||||||
|
`CLINICAL_EVENT_ID` int NOT NULL auto_increment,
|
||||||
|
`PATIENT_ID` int(11) NOT NULL,
|
||||||
|
`START_DATE` int NOT NULL,
|
||||||
|
`STOP_DATE` int,
|
||||||
|
`EVENT_TYPE` varchar(20) NOT NULL,
|
||||||
|
PRIMARY KEY (`CLINICAL_EVENT_ID`),
|
||||||
|
KEY (`PATIENT_ID`, `EVENT_TYPE`),
|
||||||
|
FOREIGN KEY (`PATIENT_ID`) REFERENCES `patient` (`INTERNAL_ID`) ON DELETE CASCADE
|
||||||
|
);
|
||||||
|
|
||||||
|
-- --------------------------------------------------------
|
||||||
|
CREATE TABLE `clinical_event_data` (
|
||||||
|
`CLINICAL_EVENT_ID` int(255) NOT NULL,
|
||||||
|
`KEY` varchar(255) NOT NULL,
|
||||||
|
`VALUE` varchar(5000) NOT NULL,
|
||||||
|
FOREIGN KEY (`CLINICAL_EVENT_ID`) REFERENCES `clinical_event` (`CLINICAL_EVENT_ID`) ON DELETE CASCADE
|
||||||
|
);
|
||||||
|
|
||||||
|
-- --------------------------------------------------------
|
||||||
|
CREATE TABLE `reference_genome_gene` (
|
||||||
|
`ENTREZ_GENE_ID` int(11) NOT NULL,
|
||||||
|
`REFERENCE_GENOME_ID` int(4) NOT NULL,
|
||||||
|
`CHR` varchar(5) DEFAULT NULL,
|
||||||
|
`CYTOBAND` varchar(64) DEFAULT NULL,
|
||||||
|
`START` bigint(20) DEFAULT NULL,
|
||||||
|
`END` bigint(20) DEFAULT NULL,
|
||||||
|
PRIMARY KEY (`ENTREZ_GENE_ID`,`REFERENCE_GENOME_ID`),
|
||||||
|
FOREIGN KEY (`REFERENCE_GENOME_ID`) REFERENCES `reference_genome` (`REFERENCE_GENOME_ID`) ON DELETE CASCADE,
|
||||||
|
FOREIGN KEY (`ENTREZ_GENE_ID`) REFERENCES `gene` (`ENTREZ_GENE_ID`) ON DELETE CASCADE
|
||||||
|
);
|
||||||
|
|
||||||
|
-- --------------------------------------------------------
|
||||||
|
CREATE TABLE `data_access_tokens` (
|
||||||
|
`TOKEN` varchar(50) NOT NULL,
|
||||||
|
`USERNAME` varchar(128) NOT NULL,
|
||||||
|
`EXPIRATION` datetime NOT NULL,
|
||||||
|
`CREATION` datetime NOT NULL,
|
||||||
|
PRIMARY KEY (`TOKEN`),
|
||||||
|
FOREIGN KEY (`USERNAME`) REFERENCES `users` (`EMAIL`) ON DELETE CASCADE
|
||||||
|
);
|
||||||
|
-- --------------------------------------------------------
|
||||||
|
CREATE TABLE `allele_specific_copy_number` (
|
||||||
|
`MUTATION_EVENT_ID` int(255) NOT NULL,
|
||||||
|
`GENETIC_PROFILE_ID` int(11) NOT NULL,
|
||||||
|
`SAMPLE_ID` int(11) NOT NULL,
|
||||||
|
`ASCN_INTEGER_COPY_NUMBER` int DEFAULT NULL,
|
||||||
|
`ASCN_METHOD` varchar(24) NOT NULL,
|
||||||
|
`CCF_EXPECTED_COPIES_UPPER` float DEFAULT NULL,
|
||||||
|
`CCF_EXPECTED_COPIES` float DEFAULT NULL,
|
||||||
|
`CLONAL` varchar(16) DEFAULT NULL,
|
||||||
|
`MINOR_COPY_NUMBER` int DEFAULT NULL,
|
||||||
|
`EXPECTED_ALT_COPIES` int DEFAULT NULL,
|
||||||
|
`TOTAL_COPY_NUMBER` int DEFAULT NULL,
|
||||||
|
UNIQUE KEY `UQ_ASCN_MUTATION_EVENT_ID_GENETIC_PROFILE_ID_SAMPLE_ID` (`MUTATION_EVENT_ID`,`GENETIC_PROFILE_ID`,`SAMPLE_ID`), -- Constraint to block duplicated mutation entries
|
||||||
|
FOREIGN KEY (`MUTATION_EVENT_ID`) REFERENCES `mutation_event` (`MUTATION_EVENT_ID`),
|
||||||
|
FOREIGN KEY (`GENETIC_PROFILE_ID`) REFERENCES `genetic_profile` (`GENETIC_PROFILE_ID`) ON DELETE CASCADE,
|
||||||
|
FOREIGN KEY (`SAMPLE_ID`) REFERENCES `sample` (`INTERNAL_ID`) ON DELETE CASCADE
|
||||||
|
);
|
||||||
|
-- --------------------------------------------------------
|
||||||
|
CREATE TABLE `info` (
|
||||||
|
`DB_SCHEMA_VERSION` varchar(24),
|
||||||
|
`GENESET_VERSION` varchar(24)
|
||||||
|
);
|
||||||
|
|
||||||
|
-- --------------------------------------------------------
|
||||||
|
CREATE TABLE `resource_definition` (
|
||||||
|
`RESOURCE_ID` varchar(255) NOT NULL,
|
||||||
|
`DISPLAY_NAME` varchar(255) NOT NULL,
|
||||||
|
`DESCRIPTION` varchar(2048) DEFAULT NULL,
|
||||||
|
`RESOURCE_TYPE` ENUM('STUDY', 'PATIENT', 'SAMPLE') NOT NULL,
|
||||||
|
`OPEN_BY_DEFAULT` BOOLEAN DEFAULT 0,
|
||||||
|
`PRIORITY` int(11) NOT NULL,
|
||||||
|
`CANCER_STUDY_ID` int(11) NOT NULL,
|
||||||
|
PRIMARY KEY (`RESOURCE_ID`,`CANCER_STUDY_ID`),
|
||||||
|
FOREIGN KEY (`CANCER_STUDY_ID`) REFERENCES `cancer_study` (`CANCER_STUDY_ID`) ON DELETE CASCADE
|
||||||
|
);
|
||||||
|
|
||||||
|
-- --------------------------------------------------------
|
||||||
|
CREATE TABLE `resource_sample` (
|
||||||
|
`INTERNAL_ID` int(11) NOT NULL,
|
||||||
|
`RESOURCE_ID` varchar(255) NOT NULL,
|
||||||
|
`URL` varchar(255) NOT NULL,
|
||||||
|
PRIMARY KEY (`INTERNAL_ID`, `RESOURCE_ID`, `URL`),
|
||||||
|
FOREIGN KEY (`INTERNAL_ID`) REFERENCES `sample` (`INTERNAL_ID`) ON DELETE CASCADE
|
||||||
|
);
|
||||||
|
|
||||||
|
-- --------------------------------------------------------
|
||||||
|
CREATE TABLE `resource_patient` (
|
||||||
|
`INTERNAL_ID` int(11) NOT NULL,
|
||||||
|
`RESOURCE_ID` varchar(255) NOT NULL,
|
||||||
|
`URL` varchar(255) NOT NULL,
|
||||||
|
PRIMARY KEY (`INTERNAL_ID`, `RESOURCE_ID`, `URL`),
|
||||||
|
FOREIGN KEY (`INTERNAL_ID`) REFERENCES `patient` (`INTERNAL_ID`) ON DELETE CASCADE
|
||||||
|
);
|
||||||
|
|
||||||
|
-- --------------------------------------------------------
|
||||||
|
CREATE TABLE `resource_study` (
|
||||||
|
`INTERNAL_ID` int(11) NOT NULL,
|
||||||
|
`RESOURCE_ID` varchar(255) NOT NULL,
|
||||||
|
`URL` varchar(255) NOT NULL,
|
||||||
|
PRIMARY KEY (`INTERNAL_ID`, `RESOURCE_ID`, `URL`),
|
||||||
|
FOREIGN KEY (`INTERNAL_ID`) REFERENCES `cancer_study` (`CANCER_STUDY_ID`) ON DELETE CASCADE
|
||||||
|
);
|
||||||
|
|
||||||
|
-- THIS MUST BE KEPT IN SYNC WITH db.version PROPERTY IN pom.xml
|
||||||
|
INSERT INTO info VALUES ('2.13.0', NULL);
|
||||||
|
|
||||||
|
|
@ -0,0 +1,56 @@
|
||||||
|
version: '3.7'
|
||||||
|
|
||||||
|
services:
|
||||||
|
cbioportal:
|
||||||
|
#image: docker.verbis.dkfz.de/ccp/dktk-cbioportal:latest
|
||||||
|
image: dktk-cbioportal
|
||||||
|
container_name: bridgehead-cbioportal
|
||||||
|
environment:
|
||||||
|
generate_password: ${MYSQL_PASSWORD}
|
||||||
|
depends_on:
|
||||||
|
- cbioportal-database
|
||||||
|
- cbioportal-session
|
||||||
|
labels:
|
||||||
|
- "traefik.enable=true"
|
||||||
|
- "traefik.http.routers.cbioportal.rule=PathPrefix(`/cbioportal`)"
|
||||||
|
- "traefik.http.services.cbioportal.loadbalancer.server.port=8080"
|
||||||
|
- "traefik.http.routers.cbioportal.tls=true"
|
||||||
|
- "traefik.http.routers.cbioportal-update.rule=PathPrefix(`/cbioportal-update`)"
|
||||||
|
- "traefik.http.services.cbioportal-update.loadbalancer.server.port=8001"
|
||||||
|
- "traefik.http.routers.cbioportal-update.tls=true"
|
||||||
|
|
||||||
|
cbioportal-database:
|
||||||
|
image: mysql:5.7
|
||||||
|
container_name: bridgehead-cbioportal-database
|
||||||
|
environment:
|
||||||
|
MYSQL_DATABASE: cbioportal
|
||||||
|
MYSQL_USER: cbio_user
|
||||||
|
generate_password: ${MYSQL_PASSWORD}
|
||||||
|
generate_root_password: ${MYSQL_ROOT_PASSWORD}
|
||||||
|
volumes:
|
||||||
|
# TODO: Move sql files to image. Are they really necessary?
|
||||||
|
- ./cbioportal-cgds.sql:/docker-entrypoint-initdb.d/cgds.sql:ro
|
||||||
|
- ./cbioportal-seed.sql.gz:/docker-entrypoint-initdb.d/seed.sql.gz:ro
|
||||||
|
- /var/cache/bridgehead/ccp/cbioportal_mysql_data:/var/lib/mysql
|
||||||
|
|
||||||
|
cbioportal-session:
|
||||||
|
image: cbioportal/session-service:0.6.1
|
||||||
|
container_name: bridgehead-cbioportal-session
|
||||||
|
environment:
|
||||||
|
SERVER_PORT: 5000
|
||||||
|
JAVA_OPTS: -Dspring.data.mongodb.uri=mongodb://cbioportal-session-database:27017/session-service
|
||||||
|
depends_on:
|
||||||
|
- cbioportal-session-database
|
||||||
|
|
||||||
|
cbioportal-session-database:
|
||||||
|
image: mongo:4.2
|
||||||
|
container_name: bridgehead-cbioportal-session-database
|
||||||
|
environment:
|
||||||
|
MONGO_INITDB_DATABASE: session_service
|
||||||
|
volumes:
|
||||||
|
- /var/cache/bridgehead/ccp/cbioportal_mongo_data:/data/db
|
||||||
|
|
||||||
|
|
||||||
|
volumes:
|
||||||
|
cbioportal_mysql_data:
|
||||||
|
cbioportal_mongo_data:
|
||||||
Binary file not shown.
|
|
@ -0,0 +1,8 @@
|
||||||
|
#!/bin/bash -e
|
||||||
|
|
||||||
|
if [ "$ENABLE_CBIOPORTAL" == true ]; then
|
||||||
|
log INFO "cBioPortal setup detected -- will start cBioPortal service."
|
||||||
|
OVERRIDE+=" -f ./$PROJECT/modules/cbioportal-compose.yml"
|
||||||
|
generate_password="$(echo \"This is a salt string to generate one consistent password for the cbioportal database. It is not required to be secret.\" | openssl rsautl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
|
||||||
|
generate_root_password="$(echo \"This is a salt string to generate one consistent root password for the cbioportal database. It is not required to be secret.\" | openssl rsautl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 64)"
|
||||||
|
fi
|
||||||
|
|
@ -0,0 +1,10 @@
|
||||||
|
# CBioPortal Data uploader
|
||||||
|
|
||||||
|
|
||||||
|
## Usage
|
||||||
|
|
||||||
|
We have integrated an API that allows you to upload data directly to cbioportal without the need to have cbioportal installed in your system.
|
||||||
|
|
||||||
|
## Tech stack
|
||||||
|
|
||||||
|
We used Flask to add this feature
|
||||||
Loading…
Reference in New Issue