diff --git a/ccp/modules/cbioportal-cgds.sql b/ccp/modules/cbioportal-cgds.sql deleted file mode 100644 index c0b20e8..0000000 --- a/ccp/modules/cbioportal-cgds.sql +++ /dev/null @@ -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 . --- ---------------------------------------------------------------------------- --- --- 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); - diff --git a/ccp/modules/cbioportal-compose.yml b/ccp/modules/cbioportal-compose.yml index eea98ff..08d49a8 100644 --- a/ccp/modules/cbioportal-compose.yml +++ b/ccp/modules/cbioportal-compose.yml @@ -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 diff --git a/ccp/modules/cbioportal-seed.sql.gz b/ccp/modules/cbioportal-seed.sql.gz deleted file mode 100644 index 876a26a..0000000 Binary files a/ccp/modules/cbioportal-seed.sql.gz and /dev/null differ