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remove unnecessary volumes of cbioportal

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juarez
2023-12-05 09:37:05 +01:00
committed by djuarezgf
parent 316398673d
commit 9f97792d6a
3 changed files with 20 additions and 786 deletions
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759
ccp/modules/cbioportal-cgds.sql
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@@ -1,759 +0,0 @@
--
-- Copyright (c) 2016 - 2022 Memorial Sloan Kettering Cancer Center.
--
-- This library is distributed in the hope that it will be useful, but WITHOUT
-- ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS
-- FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder
-- is on an "as is" basis, and Memorial Sloan Kettering Cancer Center has no
-- obligations to provide maintenance, support, updates, enhancements or
-- modifications. In no event shall Memorial Sloan Kettering Cancer Center be
-- liable to any party for direct, indirect, special, incidental or
-- consequential damages, including lost profits, arising out of the use of this
-- software and its documentation, even if Memorial Sloan Kettering Cancer
-- Center has been advised of the possibility of such damage.
--
-- This file is part of cBioPortal.
--
-- cBioPortal is free software: you can redistribute it and/or modify
-- it under the terms of the GNU Affero General Public License as
-- published by the Free Software Foundation, either version 3 of the
-- License.
--
-- This program is distributed in the hope that it will be useful,
-- but WITHOUT ANY WARRANTY; without even the implied warranty of
-- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-- GNU Affero General Public License for more details.
--
-- You should have received a copy of the GNU Affero General Public License
-- along with this program. If not, see <http://www.gnu.org/licenses/>.
-- ----------------------------------------------------------------------------
--
-- Database: `cgds`
--
-- --------------------------------------------------------
-- Database table schemas and version number
-- --------------------------------------------------------
-- The order of the following DROP TABLE statements is
-- significant. If a table has a FOREIGN_KEY referring to
-- another table, then it should be dropped before the
-- other table is dropped. The approach taken here is to
-- order the CREATE TABLE statements so that refererenced
-- tables are created before referring tables.
-- DROP TABLE statements are here in the reverse order.
-- --------------------------------------------------------
DROP TABLE IF EXISTS `info`;
DROP TABLE IF EXISTS `clinical_event_data`;
DROP TABLE IF EXISTS `clinical_event`;
DROP TABLE IF EXISTS `pdb_uniprot_residue_mapping`;
DROP TABLE IF EXISTS `pdb_uniprot_alignment`;
DROP TABLE IF EXISTS `cosmic_mutation`;
DROP TABLE IF EXISTS `copy_number_seg_file`;
DROP TABLE IF EXISTS `copy_number_seg`;
DROP TABLE IF EXISTS `sample_cna_event`;
DROP TABLE IF EXISTS `cna_event`;
DROP TABLE IF EXISTS `gistic_to_gene`;
DROP TABLE IF EXISTS `gistic`;
DROP TABLE IF EXISTS `mut_sig`;
DROP TABLE IF EXISTS `clinical_attribute_meta`;
DROP TABLE IF EXISTS `clinical_sample`;
DROP TABLE IF EXISTS `clinical_patient`;
DROP TABLE IF EXISTS `resource_definition`;
DROP TABLE IF EXISTS `resource_sample`;
DROP TABLE IF EXISTS `resource_patient`;
DROP TABLE IF EXISTS `resource_study`;
DROP TABLE IF EXISTS `mutation_count_by_keyword`;
DROP TABLE IF EXISTS `allele_specific_copy_number`;
DROP TABLE IF EXISTS `mutation`;
DROP TABLE IF EXISTS `mutation_event`;
DROP TABLE IF EXISTS `structural_variant`;
DROP TABLE IF EXISTS `sample_profile`;
DROP TABLE IF EXISTS `gene_panel_list`;
DROP TABLE IF EXISTS `gene_panel`;
DROP TABLE IF EXISTS `genetic_profile_samples`;
DROP TABLE IF EXISTS `genetic_alteration`;
DROP TABLE IF EXISTS `genetic_profile_link`;
DROP TABLE IF EXISTS `alteration_driver_annotation`;
DROP TABLE IF EXISTS `genetic_profile`;
DROP TABLE IF EXISTS `gene_alias`;
DROP TABLE IF EXISTS `geneset_gene`;
DROP TABLE IF EXISTS `reference_genome_gene`;
DROP TABLE IF EXISTS `gene`;
DROP TABLE IF EXISTS `sample_list_list`;
DROP TABLE IF EXISTS `sample_list`;
DROP TABLE IF EXISTS `sample`;
DROP TABLE IF EXISTS `patient`;
DROP TABLE IF EXISTS `authorities`;
DROP TABLE IF EXISTS `data_access_tokens`;
DROP TABLE IF EXISTS `users`;
DROP TABLE IF EXISTS `cancer_study_tags`;
DROP TABLE IF EXISTS `cancer_study`;
DROP TABLE IF EXISTS `type_of_cancer`;
DROP TABLE IF EXISTS `geneset_hierarchy_leaf`;
DROP TABLE IF EXISTS `geneset_hierarchy_node`;
DROP TABLE IF EXISTS `geneset`;
DROP TABLE IF EXISTS `generic_entity_properties`;
DROP TABLE IF EXISTS `genetic_entity`;
DROP TABLE IF EXISTS `reference_genome`;
-- --------------------------------------------------------
CREATE TABLE `type_of_cancer` (
`TYPE_OF_CANCER_ID` varchar(63) NOT NULL,
`NAME` varchar(255) NOT NULL,
`DEDICATED_COLOR` char(31) NOT NULL,
`SHORT_NAME` varchar(127),
`PARENT` varchar(63),
PRIMARY KEY (`TYPE_OF_CANCER_ID`)
);
-- --------------------------------------------------------
CREATE TABLE `reference_genome` (
`REFERENCE_GENOME_ID` int(4) NOT NULL AUTO_INCREMENT,
`SPECIES` varchar(64) NOT NULL,
`NAME` varchar(64) NOT NULL,
`BUILD_NAME` varchar(64) NOT NULL,
`GENOME_SIZE` bigint(20) NULL,
`URL` varchar(256) NOT NULL,
`RELEASE_DATE` datetime DEFAULT NULL,
PRIMARY KEY (`REFERENCE_GENOME_ID`),
UNIQUE INDEX `BUILD_NAME_UNIQUE` (`BUILD_NAME` ASC)
);
-- --------------------------------------------------------
CREATE TABLE `cancer_study` (
`CANCER_STUDY_ID` int(11) NOT NULL auto_increment,
`CANCER_STUDY_IDENTIFIER` varchar(255),
`TYPE_OF_CANCER_ID` varchar(63) NOT NULL,
`NAME` varchar(255) NOT NULL,
`DESCRIPTION` varchar(1024) NOT NULL,
`PUBLIC` BOOLEAN NOT NULL,
`PMID` varchar(1024) DEFAULT NULL,
`CITATION` varchar(200) DEFAULT NULL,
`GROUPS` varchar(200) DEFAULT NULL,
`STATUS` int(1) DEFAULT NULL,
`IMPORT_DATE` datetime DEFAULT NULL,
`REFERENCE_GENOME_ID` int(4) DEFAULT 1,
PRIMARY KEY (`CANCER_STUDY_ID`),
UNIQUE (`CANCER_STUDY_IDENTIFIER`),
FOREIGN KEY (`TYPE_OF_CANCER_ID`) REFERENCES `type_of_cancer` (`TYPE_OF_CANCER_ID`),
FOREIGN KEY (`REFERENCE_GENOME_ID`) REFERENCES `reference_genome` (`REFERENCE_GENOME_ID`) ON DELETE RESTRICT
);
-- --------------------------------------------------------
CREATE TABLE `cancer_study_tags` (
`CANCER_STUDY_ID` int(11) NOT NULL,
`TAGS` text NOT NULL,
PRIMARY KEY (`CANCER_STUDY_ID`),
FOREIGN KEY (`CANCER_STUDY_ID`) REFERENCES `cancer_study` (`CANCER_STUDY_ID`) ON DELETE CASCADE
);
-- --------------------------------------------------------
CREATE TABLE `users` (
`EMAIL` varchar(128) NOT NULL,
`NAME` varchar(255) NOT NULL,
`ENABLED` BOOLEAN NOT NULL,
PRIMARY KEY (`EMAIL`)
);
-- --------------------------------------------------------
CREATE TABLE `authorities` (
`EMAIL` varchar(128) NOT NULL,
`AUTHORITY` varchar(255) NOT NULL
);
-- --------------------------------------------------------
CREATE TABLE `patient` (
`INTERNAL_ID` int(11) NOT NULL auto_increment,
`STABLE_ID` varchar(50) NOT NULL,
`CANCER_STUDY_ID` int(11) NOT NULL,
PRIMARY KEY (`INTERNAL_ID`),
FOREIGN KEY (`CANCER_STUDY_ID`) REFERENCES `cancer_study` (`CANCER_STUDY_ID`) ON DELETE CASCADE
);
-- --------------------------------------------------------
CREATE TABLE `sample` (
`INTERNAL_ID` int(11) NOT NULL auto_increment,
`STABLE_ID` varchar(63) NOT NULL,
`SAMPLE_TYPE` varchar(255) NOT NULL,
`PATIENT_ID` int(11) NOT NULL,
PRIMARY KEY (`INTERNAL_ID`),
FOREIGN KEY (`PATIENT_ID`) REFERENCES `patient` (`INTERNAL_ID`) ON DELETE CASCADE
);
-- --------------------------------------------------------
CREATE TABLE `sample_list` (
`LIST_ID` int(11) NOT NULL auto_increment,
`STABLE_ID` varchar(255) NOT NULL,
`CATEGORY` varchar(255) NOT NULL,
`CANCER_STUDY_ID` int(11) NOT NULL,
`NAME` varchar(255) NOT NULL,
`DESCRIPTION` mediumtext,
PRIMARY KEY (`LIST_ID`),
UNIQUE (`STABLE_ID`),
FOREIGN KEY (`CANCER_STUDY_ID`) REFERENCES `cancer_study` (`CANCER_STUDY_ID`) ON DELETE CASCADE
);
-- --------------------------------------------------------
CREATE TABLE `sample_list_list` (
`LIST_ID` int(11) NOT NULL,
`SAMPLE_ID` int(11) NOT NULL,
PRIMARY KEY (`LIST_ID`,`SAMPLE_ID`),
FOREIGN KEY (`SAMPLE_ID`) REFERENCES `sample` (`INTERNAL_ID`) ON DELETE CASCADE
);
-- --------------------------------------------------------
CREATE TABLE `genetic_entity` (
`ID` int(11) NOT NULL AUTO_INCREMENT,
`ENTITY_TYPE` varchar(45) NOT NULL,
`STABLE_ID` varchar(255) DEFAULT NULL,
PRIMARY KEY (`ID`)
);
-- --------------------------------------------------------
CREATE TABLE `gene` (
`ENTREZ_GENE_ID` int(11) NOT NULL,
`HUGO_GENE_SYMBOL` varchar(255) NOT NULL,
`GENETIC_ENTITY_ID` int(11) NOT NULL,
`TYPE` varchar(50),
PRIMARY KEY (`ENTREZ_GENE_ID`),
UNIQUE KEY `GENETIC_ENTITY_ID_UNIQUE` (`GENETIC_ENTITY_ID`),
KEY `HUGO_GENE_SYMBOL` (`HUGO_GENE_SYMBOL`),
FOREIGN KEY (`GENETIC_ENTITY_ID`) REFERENCES `genetic_entity` (`ID`) ON DELETE CASCADE
);
-- --------------------------------------------------------
CREATE TABLE `gene_alias` (
`ENTREZ_GENE_ID` int(11) NOT NULL,
`GENE_ALIAS` varchar(255) NOT NULL,
PRIMARY KEY (`ENTREZ_GENE_ID`,`GENE_ALIAS`),
FOREIGN KEY (`ENTREZ_GENE_ID`) REFERENCES `gene` (`ENTREZ_GENE_ID`)
);
-- --------------------------------------------------------
CREATE TABLE `geneset` (
`ID` INT(11) NOT NULL auto_increment,
`GENETIC_ENTITY_ID` INT NOT NULL,
`EXTERNAL_ID` VARCHAR(200) NOT NULL,
`NAME` VARCHAR(200) NOT NULL,
`DESCRIPTION` VARCHAR(300) NOT NULL,
`REF_LINK` TEXT,
PRIMARY KEY (`ID`),
UNIQUE INDEX `NAME_UNIQUE` (`NAME` ASC),
UNIQUE INDEX `EXTERNAL_ID_COLL_UNIQUE` (`EXTERNAL_ID` ASC),
UNIQUE INDEX `GENESET_GENETIC_ENTITY_ID_UNIQUE` (`GENETIC_ENTITY_ID` ASC),
FOREIGN KEY (`GENETIC_ENTITY_ID`) REFERENCES `genetic_entity` (`ID`) ON DELETE CASCADE
);
-- --------------------------------------------------------
CREATE TABLE `geneset_gene` (
`GENESET_ID` INT(11) NOT NULL,
`ENTREZ_GENE_ID` INT(11) NOT NULL,
PRIMARY KEY (`GENESET_ID`, `ENTREZ_GENE_ID`),
FOREIGN KEY (`ENTREZ_GENE_ID`) REFERENCES `gene` (`ENTREZ_GENE_ID`) ON DELETE CASCADE,
FOREIGN KEY (`GENESET_ID`) REFERENCES `geneset` (`ID`) ON DELETE CASCADE
);
-- --------------------------------------------------------
CREATE TABLE `geneset_hierarchy_node` (
`NODE_ID` BIGINT(20) NOT NULL auto_increment,
`NODE_NAME` VARCHAR(200) NOT NULL,
`PARENT_ID` BIGINT NULL DEFAULT NULL,
PRIMARY KEY (`NODE_ID`),
UNIQUE INDEX `NODE_NAME_UNIQUE` (`NODE_NAME` ASC, `PARENT_ID` ASC)
);
-- --------------------------------------------------------
CREATE TABLE `geneset_hierarchy_leaf` (
`NODE_ID` BIGINT NOT NULL,
`GENESET_ID` INT NOT NULL,
PRIMARY KEY (`NODE_ID`, `GENESET_ID`),
FOREIGN KEY (`NODE_ID`) REFERENCES `geneset_hierarchy_node` (`NODE_ID`) ON DELETE CASCADE,
FOREIGN KEY (`GENESET_ID`) REFERENCES `geneset` (`ID`) ON DELETE CASCADE
);
-- ------------------------------------------------------
CREATE TABLE `generic_entity_properties` (
`ID` INT(11) NOT NULL auto_increment,
`GENETIC_ENTITY_ID` INT NOT NULL,
`NAME` varchar(255) NOT NULL,
`VALUE` varchar(5000) NOT NULL,
UNIQUE (`GENETIC_ENTITY_ID`, `NAME`),
PRIMARY KEY (`ID`),
FOREIGN KEY (`GENETIC_ENTITY_ID`) REFERENCES `genetic_entity` (`ID`) ON DELETE CASCADE
);
-- --------------------------------------------------------
CREATE TABLE `genetic_profile` (
`GENETIC_PROFILE_ID` int(11) NOT NULL AUTO_INCREMENT,
`STABLE_ID` varchar(255) NOT NULL,
`CANCER_STUDY_ID` int(11) NOT NULL,
`GENETIC_ALTERATION_TYPE` varchar(255) NOT NULL,
`GENERIC_ASSAY_TYPE` varchar(255) DEFAULT NULL,
`DATATYPE` varchar(255) NOT NULL,
`NAME` varchar(255) NOT NULL,
`DESCRIPTION` mediumtext,
`SHOW_PROFILE_IN_ANALYSIS_TAB` tinyint(1) NOT NULL,
`PIVOT_THRESHOLD` FLOAT DEFAULT NULL,
`SORT_ORDER` ENUM('ASC','DESC') DEFAULT NULL,
`PATIENT_LEVEL` boolean DEFAULT 0,
PRIMARY KEY (`GENETIC_PROFILE_ID`),
UNIQUE (`STABLE_ID`),
FOREIGN KEY (`CANCER_STUDY_ID`) REFERENCES `cancer_study` (`CANCER_STUDY_ID`) ON DELETE CASCADE
);
-- --------------------------------------------------------
CREATE TABLE `genetic_profile_link` (
`REFERRING_GENETIC_PROFILE_ID` INT NOT NULL,
`REFERRED_GENETIC_PROFILE_ID` INT NOT NULL,
`REFERENCE_TYPE` VARCHAR(45) NULL, -- COMMENT 'Values: AGGREGATION (e.g. for GSVA) or STATISTIC (e.g. for Z-SCORES)
PRIMARY KEY (`REFERRING_GENETIC_PROFILE_ID`, `REFERRED_GENETIC_PROFILE_ID`),
FOREIGN KEY (`REFERRING_GENETIC_PROFILE_ID` ) REFERENCES `genetic_profile` (`GENETIC_PROFILE_ID`) ON DELETE CASCADE,
FOREIGN KEY (`REFERRED_GENETIC_PROFILE_ID` ) REFERENCES `genetic_profile` (`GENETIC_PROFILE_ID`) ON DELETE NO ACTION ON UPDATE NO ACTION
);
-- --------------------------------------------------------
CREATE TABLE `genetic_alteration` (
`GENETIC_PROFILE_ID` int(11) NOT NULL,
`GENETIC_ENTITY_ID` int(11) NOT NULL,
`VALUES` longtext NOT NULL,
PRIMARY KEY (`GENETIC_PROFILE_ID`,`GENETIC_ENTITY_ID`),
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
);
-- --------------------------------------------------------
CREATE TABLE `genetic_profile_samples` (
`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);

47
ccp/modules/cbioportal-compose.yml
View File

@@ -1,25 +1,26 @@
version: '3.7'
services:
cbioportal:
image: docker.verbis.dkfz.de/ccp/dktk-cbioportal:latest
container_name: bridgehead-cbioportal
environment:
DB_PASSWORD: ${CBIOPORTAL_DB_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:
# image: docker.verbis.dkfz.de/ccp/dktk-cbioportal:latest
# container_name: bridgehead-cbioportal
# environment:
# DB_PASSWORD: ${CBIOPORTAL_DB_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
#image: docker.verbis.dkfz.de/ccp/dktk-cbioportal-database:latest
image: dktk-cbioportal-database
container_name: bridgehead-cbioportal-database
environment:
MYSQL_DATABASE: cbioportal
@@ -27,10 +28,7 @@ services:
MYSQL_PASSWORD: ${CBIOPORTAL_DB_PASSWORD}
MYSQL_ROOT_PASSWORD: ${CBIOPORTAL_DB_ROOT_PASSWORD}
volumes:
- /var/cache/bridgehead/ccp/cbioportal_mysql_data:/var/lib/mysql
# 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_db_data:/var/lib/mysql
cbioportal-session:
image: cbioportal/session-service:0.6.1
@@ -47,9 +45,4 @@ services:
environment:
MONGO_INITDB_DATABASE: session_service
volumes:
- /var/cache/bridgehead/ccp/cbioportal_mongo_data:/data/db
volumes:
cbioportal_mysql_data:
cbioportal_mongo_data:
- /var/cache/bridgehead/ccp/cbioportal_session_db_data:/data/db

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ccp/modules/cbioportal-seed.sql.gz
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