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remove unneeded references to old tables #10875

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remove unneeded references to old tables #10875

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2 changes: 0 additions & 2 deletions src/main/resources/db-scripts/cgds.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -45,8 +45,6 @@
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`;
Expand Down
36 changes: 16 additions & 20 deletions src/main/resources/db-scripts/migration.sql
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Expand Up @@ -294,7 +294,6 @@ INSERT INTO mutation_count_by_keyword
GROUP BY g2.`GENETIC_PROFILE_ID` , mutation_event.`KEYWORD` , m2.`ENTREZ_GENE_ID`;
UPDATE info SET DB_SCHEMA_VERSION="2.2.0";


##version: 2.3.0
-- ========================== new geneset related tables =============================================

Expand Down Expand Up @@ -419,17 +418,17 @@ CREATE TABLE `reference_genome_gene` (

INSERT INTO reference_genome_gene (ENTREZ_GENE_ID, CYTOBAND, EXONIC_LENGTH, CHR, REFERENCE_GENOME_ID)
(SELECT
ENTREZ_GENE_ID,
CYTOBAND,
LENGTH,
ENTREZ_GENE_ID,
CYTOBAND,
LENGTH,
SUBSTRING_INDEX(
SUBSTRING_INDEX(
SUBSTRING_INDEX(
SUBSTRING_INDEX(gene.CYTOBAND, 'p', 1),
'q', 1),
'cen', 1),
' ', 1),
1
1
FROM `gene`);

UPDATE info SET DB_SCHEMA_VERSION="2.4.1";
Expand Down Expand Up @@ -854,16 +853,16 @@ UPDATE `info` SET `DB_SCHEMA_VERSION`="2.12.4";
##version: 2.12.5
-- survival data migration
-- create temporary table to store survival attributes
CREATE TEMPORARY TABLE IF NOT EXISTS survival_attributes AS
(SELECT DISTINCT Concat(Substr(ATTR_ID, 1, Char_length(ATTR_ID) - 7),
"_STATUS") AS ATTR_ID
FROM clinical_attribute_meta
WHERE ATTR_ID LIKE "%_STATUS"
AND Substr(ATTR_ID, 1, Char_length(ATTR_ID) - 7)IN (SELECT DISTINCT
Substr(ATTR_ID, 1, Char_length(ATTR_ID) - 7) AS
SurvivalDataStatusPrefix
FROM clinical_attribute_meta
WHERE ATTR_ID LIKE "%_MONTHS"));
CREATE TEMPORARY TABLE IF NOT EXISTS survival_attributes AS
(SELECT DISTINCT Concat(Substr(ATTR_ID, 1, Char_length(ATTR_ID) - 7),
"_STATUS") AS ATTR_ID
FROM clinical_attribute_meta
WHERE ATTR_ID LIKE "%_STATUS"
AND Substr(ATTR_ID, 1, Char_length(ATTR_ID) - 7)IN (SELECT DISTINCT
Substr(ATTR_ID, 1, Char_length(ATTR_ID) - 7) AS
SurvivalDataStatusPrefix
FROM clinical_attribute_meta
WHERE ATTR_ID LIKE "%_MONTHS"));

-- mapping to 0/1
UPDATE clinical_patient SET ATTR_VALUE = CONCAT("1:",ATTR_VALUE) WHERE ATTR_ID in (SELECT ATTR_ID FROM survival_attributes) AND ATTR_VALUE in ('DECEASED','Recurred/Progressed','Recurred','Progressed','Yes','yes','1','PROGRESSION','Event','DEAD OF MELANOMA','DEAD WITH TUMOR','Metastatic Relapse','Localized Relapse');
Expand Down Expand Up @@ -932,7 +931,7 @@ UPDATE `info` SET `DB_SCHEMA_VERSION`="2.12.7";

##version: 2.12.8
CREATE INDEX idx_mutation_type ON mutation_event (`MUTATION_TYPE`);
CREATE INDEX idx_cna_type ON cna_event (`ALTERATION`);
CREATE INDEX idx_cna_type ON cna_event (`ALTERATION`);
CREATE INDEX idx_driver_filter ON alteration_driver_annotation (`DRIVER_FILTER`);
CREATE INDEX idx_driver_tiers_filter ON alteration_driver_annotation (`DRIVER_TIERS_FILTER`);
UPDATE `info` SET `DB_SCHEMA_VERSION`="2.12.8";
Expand Down Expand Up @@ -978,8 +977,6 @@ UPDATE `info` SET `DB_SCHEMA_VERSION`="2.12.12";
ALTER TABLE `sample` MODIFY COLUMN `STABLE_ID` VARCHAR(63) NOT NULL;
UPDATE `info` SET `DB_SCHEMA_VERSION`="2.12.13";



##version: 2.12.14
ALTER TABLE `structural_variant` MODIFY COLUMN `SITE1_ENTREZ_GENE_ID` int(11);
ALTER TABLE `structural_variant` ADD COLUMN `SITE1_REGION` varchar(25) AFTER `SITE1_CHROMOSOME`;
Expand Down Expand Up @@ -1021,10 +1018,9 @@ ALTER TABLE `mutation_event` CHANGE COLUMN `ONCOTATOR_PROTEIN_POS_START` `PROTEI
ALTER TABLE `mutation_event` CHANGE COLUMN `ONCOTATOR_PROTEIN_POS_END` `PROTEIN_POS_END` int(11);
UPDATE `info` SET `DB_SCHEMA_VERSION`="2.13.0";


##version: 2.13.1
ALTER TABLE `clinical_event_data` MODIFY COLUMN `VALUE` varchar(3000) NOT NULL;
CREATE INDEX idx_clinical_event_key ON clinical_event_data (`KEY`);
CREATE INDEX idx_clinical_event_value ON clinical_event_data (`VALUE`);
CREATE INDEX idx_sample_stable_id ON sample (`STABLE_ID`);
UPDATE `info` SET `DB_SCHEMA_VERSION`="2.13.1";
UPDATE `info` SET `DB_SCHEMA_VERSION`="2.13.1";
2 changes: 0 additions & 2 deletions src/test/resources/cgds-h2.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -45,8 +45,6 @@
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`;
Expand Down
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