From 95e8846a25c8dce74fc9fa93dfaeb535c0418c5f Mon Sep 17 00:00:00 2001 From: Adam Rauch Date: Tue, 18 Mar 2025 12:54:27 -0700 Subject: [PATCH] Remove SQL Server scripts from PostgreSQL-only modules --- .../oconnorexperiments-0.00-14.30.sql | 109 ------ .../sqlserver/genotyping-0.00-15.30.sql | 333 ------------------ 2 files changed, 442 deletions(-) delete mode 100644 OConnorExperiments/resources/schemas/dbscripts/sqlserver/oconnorexperiments-0.00-14.30.sql delete mode 100644 genotyping/resources/schemas/dbscripts/sqlserver/genotyping-0.00-15.30.sql diff --git a/OConnorExperiments/resources/schemas/dbscripts/sqlserver/oconnorexperiments-0.00-14.30.sql b/OConnorExperiments/resources/schemas/dbscripts/sqlserver/oconnorexperiments-0.00-14.30.sql deleted file mode 100644 index 8cfdf9c8..00000000 --- a/OConnorExperiments/resources/schemas/dbscripts/sqlserver/oconnorexperiments-0.00-14.30.sql +++ /dev/null @@ -1,109 +0,0 @@ -/* - * Copyright (c) 2013-2016 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ - -/* oconnorexperiments-0.00-13.10.sql */ - -CREATE SCHEMA oconnorexperiments; -GO - --- Experiments table has 1 row per workbook container -CREATE TABLE OConnorExperiments.Experiments -( - Container EntityID NOT NULL, - ModifiedBy USERID NOT NULL, - Modified TIMESTAMP NOT NULL, - - ExperimentType VARCHAR(255), - - CONSTRAINT PK_Experiments PRIMARY KEY (Container), - CONSTRAINT FK_Experiments_Container FOREIGN KEY (Container) REFERENCES core.Containers (EntityID) -); - --- ParentExperiments multi-value FK -CREATE TABLE OConnorExperiments.ParentExperiments -( - RowId INT IDENTITY(1,1) NOT NULL, - Container EntityID NOT NULL, - - ParentExperiment EntityID NOT NULL, - - CONSTRAINT PK_ParentExperiments PRIMARY KEY (RowId), - CONSTRAINT FK_ParentExperiments_Container FOREIGN KEY (ParentExperiment) REFERENCES OConnorExperiments.Experiments (Container) -); - -/* oconnorexperiments-13.10-13.20.sql */ - --- Modified column was mistakenly created as TIMESTAMP -ALTER TABLE oconnorexperiments.Experiments - DROP COLUMN Modified; -GO -ALTER TABLE oconnorexperiments.Experiments - ADD Modified DATETIME; -GO - -UPDATE oconnorexperiments.Experiments SET Modified = CURRENT_TIMESTAMP; -GO - --- drop ParentExperiments.Container FK to allow bulk folder delete -EXEC core.fn_dropifexists 'ParentExperiments', 'OConnorExperiments', 'constraint', 'FK_ParentExperiments_Container'; -GO - -/* oconnorexperiments-13.20-13.30.sql */ - -ALTER TABLE OConnorExperiments.Experiments ADD GrantId INT; - -/* oconnorexperiments-14.10-14.20.sql */ - -CREATE TABLE OConnorExperiments.ExperimentType -( - RowId INT IDENTITY (1, 1) NOT NULL, - Container ENTITYID NOT NULL, - Name NVARCHAR(255) -); - -ALTER TABLE OConnorExperiments.ExperimentType ADD CONSTRAINT PK_ExperimentType PRIMARY KEY (RowId); -ALTER TABLE OConnorExperiments.ExperimentType ADD CONSTRAINT UQ_ExperimentType_Container_Name UNIQUE (Container, Name); -ALTER TABLE OConnorExperiments.ExperimentType ADD - CONSTRAINT FK_ExperimentType_Container FOREIGN KEY - (Container) REFERENCES core.Containers (EntityId); - -INSERT INTO OConnorExperiments.ExperimentType (Name, Container) SELECT DISTINCT e.ExperimentType, c.Parent FROM - OConnorExperiments.Experiments e, core.Containers c WHERE e.Container = c.EntityId; - -ALTER TABLE OConnorExperiments.Experiments ADD ExperimentTypeId INT -GO - -UPDATE OConnorExperiments.Experiments SET ExperimentTypeId = - (SELECT t.RowId FROM OConnorExperiments.ExperimentType t, core.Containers c - WHERE t.Container = c.Parent AND Experiments.Container = c.EntityId and Experiments.ExperimentType = t.Name); - -ALTER TABLE OConnorExperiments.Experiments DROP COLUMN ExperimentType; - -ALTER TABLE OConnorExperiments.Experiments ADD - CONSTRAINT FK_Experiments_ExperimentTypeId FOREIGN KEY - (ExperimentTypeId) REFERENCES OConnorExperiments.ExperimentType (RowId); - -CREATE INDEX idx_parent_experiment_container ON oconnorexperiments.parentexperiments(container); -CREATE INDEX idx_parent_experiment_parent_experiment ON oconnorexperiments.parentexperiments(parentexperiment); -CREATE INDEX idx_experiments_experimenttypeid ON oconnorexperiments.experiments(experimenttypeid); -CREATE INDEX idx_experiments_grantid ON oconnorexperiments.experiments(grantid); - -/* oconnorexperiments-14.20-14.30.sql */ - -ALTER TABLE OConnorExperiments.ExperimentType ADD Enabled BIT DEFAULT 1; -GO -UPDATE OConnorExperiments.ExperimentType SET Enabled = 1; -ALTER TABLE OConnorExperiments.ExperimentType ALTER COLUMN Enabled BIT NOT NULL; \ No newline at end of file diff --git a/genotyping/resources/schemas/dbscripts/sqlserver/genotyping-0.00-15.30.sql b/genotyping/resources/schemas/dbscripts/sqlserver/genotyping-0.00-15.30.sql deleted file mode 100644 index fb2a57a8..00000000 --- a/genotyping/resources/schemas/dbscripts/sqlserver/genotyping-0.00-15.30.sql +++ /dev/null @@ -1,333 +0,0 @@ -/* - * Copyright (c) 2010-2017 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ - -/* genotyping-0.00-15.20.sql */ - -/* genotyping-0.00-11.20.sql */ - -CREATE SCHEMA genotyping; -GO - -CREATE TABLE genotyping.Dictionaries -( - RowId INT IDENTITY(1, 1) NOT NULL, - Container ENTITYID NOT NULL, - CreatedBy USERID NOT NULL, - Created DATETIME NOT NULL, - - CONSTRAINT PK_Dictionaries PRIMARY KEY (RowId) -); - -CREATE TABLE genotyping.Sequences -( - RowId INT IDENTITY(1, 1) NOT NULL, - Dictionary INT NOT NULL, - Uid INT NOT NULL, - AlleleName VARCHAR(100) NOT NULL, - Initials VARCHAR(45) NULL, - GenbankId VARCHAR(100) NULL, - ExptNumber VARCHAR(45) NULL, - Comments VARCHAR(4000) NULL, - Locus VARCHAR(45) NULL, - Species VARCHAR(45) NULL, - Origin VARCHAR(100) NULL, - Sequence TEXT NOT NULL, - PreviousName VARCHAR(100) NULL, - LastEdit DATETIME NOT NULL, - Version INT NOT NULL, - ModifiedBy VARCHAR(45) NOT NULL, - Translation TEXT NULL, - Type VARCHAR(45) NULL, - IpdAccession VARCHAR(100) NULL, - Reference INT NOT NULL, - RegIon VARCHAR(45) NULL, - Id INT NOT NULL, - Variant INT NOT NULL, - UploadId VARCHAR(45), - FullLength INT NOT NULL, - AlleleFamily VARCHAR(45), - - CONSTRAINT PK_Sequences PRIMARY KEY (RowId), - CONSTRAINT UQ_AlleleName UNIQUE (Dictionary, AlleleName), - CONSTRAINT UQ_Uid UNIQUE (Dictionary, Uid), - CONSTRAINT FK_Sequences_Dictionary FOREIGN KEY (Dictionary) REFERENCES genotyping.Dictionaries(RowId) -); - -CREATE TABLE genotyping.Runs -( - RowId INT IDENTITY (1,1) NOT NULL, - MetaDataId INT NULL, -- Optional row ID of record with additional meta data about this run - Container ENTITYID NOT NULL, - CreatedBy USERID NOT NULL, - Created DATETIME NOT NULL, - Path VARCHAR(1000) NOT NULL, - FileName VARCHAR(200) NOT NULL, - Status INT NOT NULL, - Platform VARCHAR(200) - - CONSTRAINT PK_Runs PRIMARY KEY (RowId) -); - -ALTER TABLE genotyping.Runs ADD CONSTRAINT UNIQUE_Runs UNIQUE (RowId, Container, MetaDataId) - -CREATE TABLE genotyping.Reads -( - RowId INT IDENTITY(1, 1) NOT NULL, - Run INT NOT NULL, - Name VARCHAR(20) NOT NULL, - Mid INT NULL, -- NULL == Mid could not be isolated from sequence - Sequence VARCHAR(8000) NOT NULL, - Quality VARCHAR(8000) NOT NULL, - -- Link reads directly to sample ids; SampleId replaces the Mid column, though we'll leave Mid in place for one release - SampleId INT NULL, - - CONSTRAINT PK_Reads PRIMARY KEY NONCLUSTERED (RowId), - CONSTRAINT FK_Reads_Runs FOREIGN KEY (Run) REFERENCES genotyping.Runs (RowId), - CONSTRAINT UQ_Reads_Name UNIQUE (Name) -); - --- Create clustered index to help with base sort on reads table -CREATE CLUSTERED INDEX IDX_ReadsRunRowId ON genotyping.Reads (Run, RowId); - -CREATE TABLE genotyping.Analyses -( - RowId INT IDENTITY(1, 1) NOT NULL, - Run INT NOT NULL, - CreatedBy USERID NOT NULL, - Created DATETIME NOT NULL, - Description VARCHAR(8000) NULL, - Path VARCHAR(1000) NULL, - FileName VARCHAR(200) NULL, - Status INT NOT NULL, - SequenceDictionary INT NOT NULL, - SequencesView VARCHAR(200) NULL, -- NULL => default view - - CONSTRAINT PK_Analyses PRIMARY KEY (RowId), - CONSTRAINT FK_Analyses_Runs FOREIGN KEY (Run) REFERENCES genotyping.Runs (RowId), - CONSTRAINT FK_Analyses_Dictionaries FOREIGN KEY (SequenceDictionary) REFERENCES genotyping.Dictionaries(RowId) -); - -CREATE TABLE genotyping.AnalysisSamples -( - Analysis INT NOT NULL, - SampleId INT NOT NULL, - - CONSTRAINT PK_AnalysisSamples PRIMARY KEY (Analysis, SampleId), - CONSTRAINT FK_AnalysisSamples_Analyses FOREIGN KEY (Analysis) REFERENCES genotyping.Analyses(RowId) -); - -CREATE TABLE genotyping.Matches -( - RowId INT IDENTITY(1, 1) NOT NULL, - Analysis INT NOT NULL, - SampleId INT NOT NULL, - Reads INT NOT NULL, - "Percent" REAL NOT NULL, - AverageLength REAL NOT NULL, - PosReads INT NOT NULL, - NegReads INT NOT NULL, - PosExtReads INT NOT NULL, - NegExtReads INT NOT NULL, - -- Add ParentId column -- when matches are combined or altered this is set to the new match's row id - -- We then filter out combined matches (ParentId IS NOT NULL) from normal analysis views. - ParentId INT NULL, - - CONSTRAINT PK_Matches PRIMARY KEY (RowId), - CONSTRAINT FK_Matches_Analyses FOREIGN KEY (Analysis) REFERENCES genotyping.Analyses(RowId), - CONSTRAINT FK_Matches_AnalysisSamples FOREIGN KEY (Analysis, SampleId) REFERENCES genotyping.AnalysisSamples(Analysis, SampleId) -); - --- Junction table that links each row of Matches to one or more allele sequences in Sequences table -CREATE TABLE genotyping.AllelesJunction -( - MatchId INT NOT NULL, - SequenceId INT NOT NULL, - Analysis INT NOT NULL, - - CONSTRAINT FK_AllelesJunction_Matches FOREIGN KEY (MatchId) REFERENCES genotyping.Matches(RowId), - CONSTRAINT FK_AllelesJunction_Reads FOREIGN KEY (SequenceId) REFERENCES genotyping.Sequences(RowId), - CONSTRAINT FK_AllelesJunction_Analyses FOREIGN KEY (Analysis) REFERENCES genotyping.Analyses (RowId) -); - -CREATE INDEX IX_Analysis ON genotyping.AllelesJunction(Analysis); - --- Junction table that links each row of Matches to one or more rows in Reads table -CREATE TABLE genotyping.ReadsJunction -( - MatchId INT NOT NULL, - ReadId INT NOT NULL, - - CONSTRAINT FK_ReadsJunction_Matches FOREIGN KEY (MatchId) REFERENCES genotyping.Matches(RowId), - CONSTRAINT FK_ReadsJunction_Reads FOREIGN KEY (ReadId) REFERENCES genotyping.Reads(RowId) -); - - - --- Add indexes on all junction table columns to speed up deletes. -CREATE INDEX IX_ReadsJunction_MatchId ON genotyping.ReadsJunction (MatchId); -CREATE INDEX IX_ReadsJunction_ReadId ON genotyping.ReadsJunction (ReadId); -CREATE INDEX IX_AllelesJunction_MatchId ON genotyping.AllelesJunction (MatchId); -CREATE INDEX IX_AllelesJunction_SequenceId ON genotyping.AllelesJunction (SequenceId); - -/* genotyping-12.10-12.20.sql */ - - -CREATE TABLE genotyping.SequenceFiles ( - RowId INT IDENTITY(1, 1), - Run INTEGER NOT NULL, - DataId INTEGER NOT NULL, - SampleId INTEGER, - ReadCount INTEGER, - PoolNum INT NULL, - - CONSTRAINT FK_SequenceFiles_Runs FOREIGN KEY (Run) REFERENCES genotyping.Runs (RowId), - CONSTRAINT FK_SequenceFiles_DataId FOREIGN KEY (DataId) REFERENCES exp.Data (RowId), - CONSTRAINT PK_SequenceFiles PRIMARY KEY (rowid) -); - -create table genotyping.IlluminaTemplates ( - name varchar(100) not null, - json varchar(4000), - editable bit default 1, - - CreatedBy USERID, - Created datetime, - ModifiedBy USERID, - Modified datetime, - - constraint PK_illumina_templates PRIMARY KEY (name) -); - -insert into genotyping.IlluminaTemplates (name, json, editable) -VALUES -('Default', '{' + - '"Header": [["Template",""],["IEMFileVersion","3"],["Assay",""],["Chemistry","Default"]],' + - '"Reads": [["151",""], ["151",""]]' + - '}', 0 -); - -insert into genotyping.IlluminaTemplates (name, json, editable) -VALUES -('Resequencing', '{' + - '"Header": [["Template","Resequencing"],["IEMFileVersion","3"],["Assay","TruSeq DNA/RNA"],["Chemistry","Default"]],' + - '"Reads": [["151",""], ["151",""]],' + - '"Settings": [["OnlyGenerateFASTQ","1"]]' + - '}', 1 -); - - -/* genotyping-12.20-12.30.sql */ - -CREATE TABLE genotyping.Species -( - RowId INT IDENTITY(1, 1) NOT NULL, - Name NVARCHAR(10), - FullName NVARCHAR(45), - - CONSTRAINT PK_Species PRIMARY KEY (RowId), - CONSTRAINT Unique_Species_Name UNIQUE (Name), - CONSTRAINT Unique_Species_FullName UNIQUE (FullName) -); -GO - -INSERT INTO genotyping.Species (Name, FullName) VALUES ('mamu', 'Macaca mulatta (rhesus)'); -INSERT INTO genotyping.Species (Name, FullName) VALUES ('mane', 'Macaca nemestrina (pigtail)'); -INSERT INTO genotyping.Species (Name, FullName) VALUES ('mafa', 'Macaca fascicularis (cynomolgus)'); - -CREATE TABLE genotyping.Animal -( - RowId INT IDENTITY(1, 1) NOT NULL, - Container ENTITYID NOT NULL, - LabAnimalId NVARCHAR(100), - ClientAnimalId NVARCHAR(100), - Lsid LsidType, - CreatedBy USERID NOT NULL, - Created DATETIME NOT NULL, - ModifiedBy USERID NOT NULL, - Modified DATETIME NOT NULL, - SpeciesId INT NOT NULL, - - CONSTRAINT PK_Animal PRIMARY KEY (RowId), - CONSTRAINT UQ_Animal_LabAnimalId UNIQUE (Container, LabAnimalId), - CONSTRAINT FK_Animal_Container FOREIGN KEY (Container) REFERENCES core.Containers(EntityId), - CONSTRAINT FK_Animal_Lsid FOREIGN KEY (Lsid) REFERENCES exp.Object(ObjectURI), - CONSTRAINT FK_Animal_SpeciesId FOREIGN KEY (SpeciesId) REFERENCES genotyping.Species(RowId) -); - -CREATE INDEX IDX_Animal_Container ON genotyping.Animal(Container); - -CREATE TABLE genotyping.Haplotype -( - RowId INT IDENTITY(1, 1) NOT NULL, - Container ENTITYID NOT NULL, - Name NVARCHAR(50), - CreatedBy USERID NOT NULL, - Created DATETIME NOT NULL, - ModifiedBy USERID NOT NULL, - Modified DATETIME NOT NULL, - Lsid LsidType NULL, - Type NVARCHAR(20), - SpeciesId INT NOT NULL, - - CONSTRAINT PK_Haplotype PRIMARY KEY (RowId), - CONSTRAINT FK_Haplotype_Container FOREIGN KEY (Container) REFERENCES core.Containers(EntityId), - CONSTRAINT FK_Haplotype_Lsid FOREIGN KEY (Lsid) REFERENCES exp.Object(ObjectURI), - CONSTRAINT FK_Haplotype_SpeciesId FOREIGN KEY (SpeciesId) REFERENCES genotyping.Species(RowId) -); - -CREATE INDEX IDX_Haplotype_Container ON genotyping.Haplotype(Container); - -CREATE TABLE genotyping.AnimalAnalysis -( - RowId INT IDENTITY(1, 1) NOT NULL, - AnimalId INT NOT NULL, - RunId INT NOT NULL, - TotalReads INT, - IdentifiedReads INT, - Enabled BIT NOT NULL DEFAULT 1, - CreatedBy USERID NOT NULL, - Created DATETIME NOT NULL, - ModifiedBy USERID NOT NULL, - Modified DATETIME NOT NULL, - - CONSTRAINT PK_AnimalAnalysis PRIMARY KEY (RowId), - CONSTRAINT UQ_AnimalAnalysis UNIQUE (AnimalId, RunId), - CONSTRAINT FK_AnimalAnalysis_Animal FOREIGN KEY (AnimalId) REFERENCES genotyping.Animal(RowId), - CONSTRAINT FK_AnimalAnalysis_Run FOREIGN KEY (RunId) REFERENCES exp.ExperimentRun(RowId) -); - -CREATE INDEX IDX_AnimalAnalysis_Run ON genotyping.AnimalAnalysis(RunId); -CREATE INDEX IDX_AnimalAnalysis_Animal ON genotyping.AnimalAnalysis(AnimalId); - -CREATE TABLE genotyping.AnimalHaplotypeAssignment -( - RowId INT IDENTITY(1, 1) NOT NULL, - AnimalAnalysisId INT NOT NULL, - HaplotypeId INT NOT NULL, - CreatedBy USERID NOT NULL, - Created DATETIME NOT NULL, - ModifiedBy USERID NOT NULL, - Modified DATETIME NOT NULL, - DiploidNumber INT NOT NULL, - DiploidNumberInferred BIT NOT NULL, - - CONSTRAINT PK_AnimalHaplotypeAssignment PRIMARY KEY (RowId), - CONSTRAINT FK_AnimalHaplotypeAssignment_Haplotype FOREIGN KEY (HaplotypeId) REFERENCES genotyping.Haplotype(RowId), - CONSTRAINT FK_AnimalHaplotypeAssignment_AnimalAnalysis FOREIGN KEY (AnimalAnalysisId) REFERENCES genotyping.AnimalAnalysis(RowId) -); - -CREATE INDEX IDX_AnimalHaplotypeAssignment_Haplotype ON genotyping.AnimalHaplotypeAssignment(HaplotypeId); -CREATE INDEX idx_animalhaplotypeassignment_animalanalysisid ON genotyping.animalhaplotypeassignment (animalanalysisid);