Item #5606: Consolidate bootstrap scripts

nab/resources/schemas/dbscripts/postgresql/nab-0.00-17.10.sql

@@ -0,0 +1,188 @@
+/*
+ * Copyright (c) 2017-2018 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.
+ */
+
+/* nab-12.30-13.10.sql */
+
+CREATE SCHEMA nab;
+
+CREATE TABLE nab.cutoffvalue
+(
+    rowid SERIAL NOT NULL,
+    nabspecimenid INT NOT NULL,
+    cutoff DOUBLE PRECISION,
+    point DOUBLE PRECISION,
+    pointoorindicator VARCHAR(20),
+
+    ic_poly DOUBLE PRECISION,
+    ic_polyoorindicator VARCHAR(20),
+    ic_4pl DOUBLE PRECISION,
+    ic_4ploorindicator VARCHAR(20),
+    ic_5pl DOUBLE PRECISION,
+    ic_5ploorindicator VARCHAR(20),
+
+    CONSTRAINT pk_nab_cutoffvalue PRIMARY KEY (rowid)
+);
+
+CREATE TABLE nab.nabspecimen
+(
+    rowid SERIAL NOT NULL,
+    dataid INT,
+    runid INT NOT NULL,
+    specimenlsid lsidtype NOT NULL,
+    FitError DOUBLE PRECISION,
+    WellgroupName VARCHAR(100),
+
+    auc_poly DOUBLE PRECISION,
+    positiveauc_poly DOUBLE PRECISION,
+    auc_4pl DOUBLE PRECISION,
+    positiveauc_4pl DOUBLE PRECISION,
+    auc_5pl DOUBLE PRECISION,
+    positiveauc_5pl DOUBLE PRECISION,
+
+    -- For legacy migration purposes
+    objecturi VARCHAR(300),
+    objectid INT NOT NULL,
+    protocolid INT,
+    viruslsid lsidtype,
+
+    CONSTRAINT pk_nab_specimen PRIMARY KEY (rowid),
+    CONSTRAINT fk_nabspecimen_experimentrun FOREIGN KEY (runid)
+      REFERENCES exp.experimentrun (rowid) MATCH SIMPLE
+      ON UPDATE NO ACTION ON DELETE NO ACTION,
+    CONSTRAINT fk_nabspecimen_specimenlsid FOREIGN KEY (specimenlsid)
+      REFERENCES exp.material (lsid)
+      ON UPDATE NO ACTION ON DELETE NO ACTION
+);
+
+CREATE INDEX idx_nabspecimen_runid ON nab.nabspecimen(runid);
+CREATE INDEX idx_nabspecimen_objectid ON nab.nabspecimen(objectid);
+CREATE INDEX idx_nabspecimen_dataid ON nab.nabspecimen(dataid);
+
+ALTER TABLE nab.cutoffvalue ADD CONSTRAINT fk_cutoffvalue_nabspecimen FOREIGN KEY (nabspecimenid)
+        REFERENCES nab.nabspecimen (rowid) MATCH SIMPLE
+        ON UPDATE NO ACTION ON DELETE NO ACTION;
+ALTER TABLE nab.nabspecimen ADD CONSTRAINT fk_nabspecimen_protocolid FOREIGN KEY (protocolid)
+        REFERENCES exp.protocol (rowid) MATCH SIMPLE
+        ON UPDATE NO ACTION ON DELETE NO ACTION;
+
+
+CREATE INDEX IDX_NAbSpecimen_ProtocolId ON nab.NAbSpecimen(ProtocolId);
+CREATE INDEX IDX_CutoffValue_NabSpecimenId ON nab.cutoffvalue USING btree (NabSpecimenId);
+
+/* nab-14.20-14.30.sql */
+
+CREATE SCHEMA nabvirus;
+
+/* nab-15.10-15.11.sql */
+
+CREATE INDEX IDX_NAbSpecimen_SpecimenLSID ON nab.NAbSpecimen(SpecimenLSID);
+
+/* nab-15.20-15.21.sql */
+
+CREATE TABLE nab.dilutiondata
+(
+    RowId SERIAL NOT NULL,
+    Dilution DOUBLE PRECISION,
+    DilutionOrder INT,
+    PercentNeutralization DOUBLE PRECISION,
+    NeutralizationPlusMinus DOUBLE PRECISION,
+    Min DOUBLE PRECISION,
+    Max DOUBLE PRECISION,
+    Mean DOUBLE PRECISION,
+    StdDev DOUBLE PRECISION,
+    WellgroupName VARCHAR(100),
+    ReplicateName VARCHAR(100),
+    RunDataId INT,
+    MinDilution DOUBLE PRECISION,
+    MaxDilution DOUBLE PRECISION,
+    PlateNumber INT,
+    RunId INT,
+    ProtocolId INT,
+    Container ENTITYID NOT NULL,
+
+    CONSTRAINT pk_dilutiondata PRIMARY KEY (RowId)
+
+);
+
+ALTER TABLE nab.dilutiondata ADD CONSTRAINT fk_dilutiondata_experimentrun FOREIGN KEY (RunId)
+    REFERENCES exp.experimentrun (RowId) MATCH SIMPLE ON UPDATE NO ACTION ON DELETE NO ACTION;
+ALTER TABLE nab.dilutiondata ADD CONSTRAINT fk_dilutiondata_rundataid FOREIGN KEY (RunDataId)
+    REFERENCES nab.nabspecimen (RowId) ON UPDATE NO ACTION ON DELETE NO ACTION;
+
+CREATE INDEX IDX_DilutionData_RunId ON nab.DilutionData(RunId);
+
+CREATE TABLE nab.welldata
+(
+  RowId SERIAL NOT NULL,
+  RunId INT NOT NULL,
+  SpecimenLsid lsidtype,
+  RunDataId INT,
+  DilutionDataId INT,
+  ProtocolId INT,
+  "Row" INT,
+  "Column" INT,
+  Value REAL,
+  ControlWellgroup VARCHAR(100),
+  VirusWellgroup VARCHAR(100),
+  SpecimenWellgroup VARCHAR(100),
+  ReplicateWellgroup VARCHAR(100),
+  ReplicateNumber INT,
+  Container ENTITYID NOT NULL,
+  PlateNumber INT,
+  PlateVirusName VARCHAR(100),
+
+CONSTRAINT pk_welldata PRIMARY KEY (RowId),
+  CONSTRAINT fk_welldata_experimentrun FOREIGN KEY (RunId)
+    REFERENCES exp.experimentrun (RowId) MATCH SIMPLE
+    ON UPDATE NO ACTION ON DELETE NO ACTION,
+  CONSTRAINT fk_welldata_specimenlsid FOREIGN KEY (SpecimenLsid)
+    REFERENCES exp.material (Lsid)
+    ON UPDATE NO ACTION ON DELETE NO ACTION,
+  CONSTRAINT fk_welldata_rundataid FOREIGN KEY (RunDataId)
+    REFERENCES nab.nabspecimen (RowId)
+    ON UPDATE NO ACTION ON DELETE NO ACTION,
+  CONSTRAINT fk_welldata_dilutiondataid FOREIGN KEY (DilutionDataId)
+    REFERENCES nab.dilutiondata (RowId)
+    ON UPDATE NO ACTION ON DELETE NO ACTION
+
+);
+
+CREATE INDEX idx_welldata_runid ON nab.welldata(RunId);
+
+/* nab-16.20-16.30.sql */
+
+-- note : nab-16.20-nab-16.21 was backported to release 16.2 to fix issue : 27040
+-- when scripts are consolidated for 16.3 we will need to account for both 16.20-16.30 and 16.21-16.30 upgrade paths
+CREATE INDEX IDX_WellData_DilutionDataId ON nab.wellData(dilutionDataId);
+
+-- conditionally create the index, this is necessary because the index creation did not exist initially
+-- in script: nab-16.20-16.21 but was added later to fix issue 27040
+CREATE FUNCTION nab.ensureIndex() RETURNS void AS $$
+BEGIN
+  IF NOT EXISTS(SELECT * FROM pg_indexes WHERE SchemaName = 'nab' AND TableName = 'welldata' AND IndexName = 'idx_welldata_dilutiondataid') THEN
+    EXECUTE 'CREATE INDEX IDX_WellData_DilutionDataId ON nab.wellData(dilutionDataId)';
+  END IF;
+END
+$$ LANGUAGE plpgsql;
+
+SELECT nab.ensureIndex();
+DROP FUNCTION nab.ensureIndex();
+
+/* nab-16.30-17.10.sql */
+
+/* nab-16.30-16.31.sql */
+
+ALTER TABLE nab.WellData ADD Excluded BOOLEAN NOT NULL DEFAULT FALSE;

nab/resources/schemas/dbscripts/sqlserver/nab-0.00-17.10.sql

@@ -0,0 +1,194 @@
+/*
+ * Copyright (c) 2015-2017 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.
+ */
+
+/* nab-12.30-13.10.sql */
+
+CREATE SCHEMA nab;
+GO
+
+CREATE TABLE nab.CutoffValue
+(
+    RowId INT IDENTITY (1, 1) NOT NULL,
+    NAbSpecimenId INT NOT NULL,
+    Cutoff DOUBLE PRECISION,
+    Point DOUBLE PRECISION,
+    PointOORIndicator NVARCHAR(20),
+
+    IC_Poly DOUBLE PRECISION,
+    IC_PolyOORIndicator NVARCHAR(20),
+    IC_4pl DOUBLE PRECISION,
+    IC_4plOORIndicator NVARCHAR(20),
+    IC_5pl DOUBLE PRECISION,
+    IC_5plOORIndicator NVARCHAR(20),
+
+    CONSTRAINT PK_NAb_CutoffValue PRIMARY KEY (RowId)
+);
+
+CREATE TABLE nab.NAbSpecimen
+(
+    RowId INT IDENTITY (1, 1) NOT NULL,
+    DataId INT,
+    RunId INT NOT NULL,
+    SpecimenLSID LSIDtype NOT NULL,
+    FitError DOUBLE PRECISION,
+    WellgroupName NVARCHAR(100),
+
+    AUC_poly DOUBLE PRECISION,
+    PositiveAUC_Poly DOUBLE PRECISION,
+    AUC_4pl DOUBLE PRECISION,
+    PositiveAUC_4pl DOUBLE PRECISION,
+    AUC_5pl DOUBLE PRECISION,
+    PositiveAUC_5pl DOUBLE PRECISION,
+
+    -- For legacy migration purposes
+    ObjectUri NVARCHAR(300),
+    ObjectId INT NOT NULL,
+    ProtocolId INT,
+	viruslsid lsidtype,
+
+    CONSTRAINT PK_NAb_Specimen PRIMARY KEY (RowId),
+    CONSTRAINT FK_NAbSpecimen_ExperimentRun FOREIGN KEY (RunId)
+      REFERENCES Exp.ExperimentRun (RowId)
+      ON UPDATE NO ACTION ON DELETE NO ACTION,
+    CONSTRAINT FK_NAbSpecimen_SpecimenLSID FOREIGN KEY (SpecimenLSID)
+      REFERENCES Exp.Material (LSID)
+      ON UPDATE NO ACTION ON DELETE NO ACTION
+);
+
+CREATE INDEX IDX_NAbSpecimen_RunId ON nab.NAbSpecimen(RunId);
+CREATE INDEX IDX_NAbSpecimen_ObjectId ON nab.NAbSpecimen(ObjectId);
+CREATE INDEX IDX_NAbSpecimen_DataId ON nab.NAbSpecimen(DataId);
+
+ALTER TABLE nab.CutoffValue ADD CONSTRAINT FK_CutoffValue_NAbSpecimen FOREIGN KEY (NAbSpecimenId)
+        REFERENCES nab.NAbSpecimen (rowid);
+ALTER TABLE nab.NAbSpecimen ADD CONSTRAINT FK_NAbSpecimen_ProtocolId FOREIGN KEY (ProtocolId)
+        REFERENCES Exp.Protocol (rowid);
+
+
+CREATE INDEX IDX_NAbSpecimen_ProtocolId ON nab.NAbSpecimen(ProtocolId);
+CREATE INDEX IDX_CutoffValue_NabSpecimenId ON nab.cutoffvalue(NabSpecimenId);
+GO
+
+/* nab-14.20-14.30.sql */
+
+CREATE SCHEMA nabvirus;
+GO
+
+/* nab-15.10-15.11.sql */
+
+CREATE INDEX IDX_NAbSpecimen_SpecimenLSID ON nab.NAbSpecimen(SpecimenLSID);
+
+/* nab-15.20-15.21.sql */
+
+CREATE TABLE nab.DilutionData
+(
+  RowId INT IDENTITY (1, 1) NOT NULL,
+  Dilution DOUBLE PRECISION,
+  DilutionOrder INT,
+  PercentNeutralization DOUBLE PRECISION,
+  NeutralizationPlusMinus DOUBLE PRECISION,
+  Min DOUBLE PRECISION,
+  Max DOUBLE PRECISION,
+  Mean DOUBLE PRECISION,
+  StdDev DOUBLE PRECISION,
+  WellgroupName NVARCHAR(100),
+  ReplicateName NVARCHAR(100),
+  RunDataId INT,
+  MaxDilution DOUBLE PRECISION,
+  MinDilution DOUBLE PRECISION,
+  PlateNumber INT,
+  RunId INT,
+  ProtocolId INT,
+  Container ENTITYID NOT NULL,
+
+  CONSTRAINT PK_NAb_DilutionData PRIMARY KEY (RowId)
+);
+
+ALTER TABLE nab.DilutionData ADD CONSTRAINT FK_DilutionData_ExperimentRun FOREIGN KEY (RunId)
+	REFERENCES Exp.ExperimentRun (RowId)
+	ON UPDATE NO ACTION ON DELETE NO ACTION;
+ALTER TABLE nab.DilutionData ADD CONSTRAINT FK_DilutionData_RunDataId FOREIGN KEY (RunDataId)
+	REFERENCES nab.NAbSpecimen (RowId)
+	ON UPDATE NO ACTION ON DELETE NO ACTION;
+
+CREATE INDEX IDX_DilutionData_RunId ON nab.DilutionData(RunId);
+
+CREATE TABLE nab.WellData
+(
+  RowId INT IDENTITY (1, 1) NOT NULL,
+  RunId INT NOT NULL,
+  SpecimenLsid LSIDtype NULL,
+  RunDataId INT NULL,
+  DilutionDataId INT,
+  ProtocolId INT,
+  "Row" INT,
+  "Column" INT,
+  Value REAL,
+  ControlWellgroup NVARCHAR(100),
+  VirusWellgroup NVARCHAR(100),
+  SpecimenWellgroup NVARCHAR(100),
+  ReplicateWellgroup NVARCHAR(100),
+  ReplicateNumber INT,
+  Container EntityId NOT NULL,
+  PlateNumber INT,
+  PlateVirusName NVARCHAR(100),
+
+  CONSTRAINT PK_NAb_WellData PRIMARY KEY (RowId),
+  CONSTRAINT FK_WellData_ExperimentRun FOREIGN KEY (RunId)
+    REFERENCES Exp.ExperimentRun (RowId)
+    ON UPDATE NO ACTION ON DELETE NO ACTION,
+  CONSTRAINT FK_WellData_SpecimenLSID FOREIGN KEY (SpecimenLSID)
+    REFERENCES Exp.Material (LSID)
+    ON UPDATE NO ACTION ON DELETE NO ACTION,
+  CONSTRAINT FK_WellData_RunDataId FOREIGN KEY (RunDataId)
+    REFERENCES NAb.NAbSpecimen (RowId)
+    ON UPDATE NO ACTION ON DELETE NO ACTION,
+  CONSTRAINT FK_WellData_DilutionDataId FOREIGN KEY (DilutionDataId)
+    REFERENCES NAb.DilutionData (RowId)
+    ON UPDATE NO ACTION ON DELETE NO ACTION
+
+);
+
+CREATE INDEX IDX_WellData_RunId ON nab.WellData(RunId);
+
+/* nab-16.20-16.30.sql */
+
+-- note : nab-16.20-nab-16.21 was backported to release 16.2 to fix issue : 27040
+-- when scripts are consolidated for 16.3 we will need to account for both 16.20-16.30 and 16.21-16.30 upgrade paths
+CREATE INDEX IDX_WellData_DilutionDataId ON nab.wellData(dilutionDataId);
+
+GO
+
+-- conditionally create the index, this is necessary because the index creation did not exist initially
+-- in script: nab-16.20-16.21 but was added later to fix issue 27040
+CREATE PROCEDURE nab.ensureIndex AS
+  BEGIN
+    IF NOT EXISTS(SELECT * FROM sys.indexes WHERE name = 'IDX_WellData_DilutionDataId')
+      BEGIN
+        execute('CREATE INDEX IDX_WellData_DilutionDataId ON nab.wellData(dilutionDataId)');
+      END
+  END;
+GO
+
+EXEC nab.ensureIndex
+GO
+
+DROP PROCEDURE nab.ensureIndex
+GO
+
+/* nab-16.30-17.10.sql */
+
+ALTER TABLE nab.WellData ADD Excluded BIT NOT NULL DEFAULT 0;