Remove SQL Server upgrade scripts and code

GenotypeAssays/module.properties

@@ -1,3 +1,2 @@
 ModuleClass: org.labkey.genotypeassays.GenotypeAssaysModule
 ManageVersion: false
-SupportedDatabases: mssql, pgsql

GenotypeAssays/src/org/labkey/genotypeassays/GeneticsTableCustomizer.java

@@ -167,7 +167,6 @@ private void customizeSummaryGrouped(AbstractTableInfo ti)
             }
 
             Domain d = ap.getResultsDomain(protocols.get(0));
-            String chr = ti.getSqlDialect().isPostgreSQL() ? "chr" : "char";
             SQLFragment sql3 = new SQLFragment("(select ").append(ti.getSqlDialect().getGroupConcat(new SQLFragment("hs.haplotype"), true, true, getNewlineSql(ti))).append(" as expr FROM assayresult." + d.getStorageTableName() + " a JOIN sequenceanalysis.haplotype_sequences hs ON (a.marker = hs.haplotype AND hs.type = 'Lineage' AND hs.present = " + ti.getSqlDialect().getBooleanTRUE() + ") WHERE a.analysisId = " + ExprColumn.STR_TABLE_ALIAS + ".analysis_id AND a.result IS NULL AND hs.name = " + ExprColumn.STR_TABLE_ALIAS + ".lineages)");
             ExprColumn newCol3 = new ExprColumn(ti, "cachedHaplotypes", sql3, JdbcType.VARCHAR, ti.getColumn("analysis_id"), ti.getColumn("lineages"));
             newCol3.setLabel("Matching Cached Haplotypes");

IDR/module.properties

@@ -4,4 +4,3 @@ Description: This module will support the ONPRC IDR
 License: Apache 2.0
 LicenseURL: http://www.apache.org/licenses/LICENSE-2.0
 ManageVersion: false
-SupportedDatabases: mssql, pgsql

LabPurchasing/module.properties

@@ -4,4 +4,3 @@ Description: A module designed to assist with purchasing supplies for academic l
 License: Apache 2.0
 LicenseURL: http://www.apache.org/licenses/LICENSE-2.0
 ManageVersion: false
-SupportedDatabases: mssql, pgsql

MccColony/module.properties

@@ -3,5 +3,4 @@ Label: Module to manage MCC Colony Study Folders
 Description: This module is designed to provide views and resources specific to MCC colony folders.
 License: Apache 2.0
 LicenseURL: http://www.apache.org/licenses/LICENSE-2.0
-SupportedDatabases: mssql, pgsql
 ManageVersion: false

PMR/module.properties

@@ -4,4 +4,3 @@ Description: This is the ONPRC Precision Medicine Resource (PMR) module
 License: Apache 2.0
 LicenseURL: http://www.apache.org/licenses/LICENSE-2.0
 ManageVersion: false
-SupportedDatabases: mssql, pgsql

SivStudies/module.properties

@@ -4,4 +4,3 @@ Description: A module designed to manage data from SIV and related studies.
 License: Apache 2.0
 LicenseURL: http://www.apache.org/licenses/LICENSE-2.0
 ManageVersion: false
-SupportedDatabases: mssql, pgsql

covidseq/module.properties

@@ -3,5 +3,4 @@ Label: CovidSeq
 Description: A module to assist with SARS-CoV-2 genomic sequencing
 License: Apache 2.0
 LicenseURL: http://www.apache.org/licenses/LICENSE-2.0
-SupportedDatabases: mssql
 ManageVersion: false

covidseq/resources/schemas/dbscripts/sqlserver/covidseq-0.00-21.000.sql → covidseq/resources/schemas/dbscripts/postgresql/covidseq-0.00-21.000.sql

@@ -17,13 +17,12 @@
 -- Create schema, tables, indexes, and constraints used for Covidseq module here
 -- All SQL VIEW definitions should be created in covidseq-create.sql and dropped in covidseq-drop.sql
 CREATE SCHEMA covidseq;
-GO
 
 CREATE TABLE covidseq.samples (
-  rowid int identity(1,1),
+  rowid serial,
   sampleName varchar(2000),
   patientId varchar(2000),
-  sampleDate datetime,
+  sampleDate timestamp,
   sampleSource varchar(2000),
   sampleType varchar(2000),
   comment varchar(4000),
@@ -33,10 +32,10 @@ CREATE TABLE covidseq.samples (
   country varchar(2000),
 
   container entityid,
-  created datetime,
+  created timestamp,
   createdby int,
-  modified datetime,
+  modified timestamp,
   modifiedby int,
 
-  constraint PK_samples PRIMARY KEY (rowid)
-);
+  CONSTRAINT PK_samples PRIMARY KEY (rowid)
+);

covidseq/resources/schemas/dbscripts/postgresql/covidseq-21.000-21.001.sql

@@ -0,0 +1,32 @@
+ALTER TABLE covidseq.samples ADD COLUMN assayType varchar(200);
+ALTER TABLE covidseq.samples ADD COLUMN N1_or_S double precision;
+ALTER TABLE covidseq.samples ADD COLUMN N2_orN double precision;
+ALTER TABLE covidseq.samples ADD COLUMN RP_or_ORF1ab double precision;
+ALTER TABLE covidseq.samples ADD COLUMN MS2 double precision;
+ALTER TABLE covidseq.samples ADD COLUMN cDNA_Plate_ID varchar(200);
+ALTER TABLE covidseq.samples ADD COLUMN cDNA_Plate_Location varchar(200);
+
+ALTER TABLE covidseq.samples DROP COLUMN country;
+ALTER TABLE covidseq.samples DROP COLUMN county;
+
+ALTER TABLE covidseq.samples DROP COLUMN patientId;
+ALTER TABLE covidseq.samples ADD COLUMN patientId ENTITYID;
+
+CREATE TABLE covidseq.patients (
+    rowid serial,
+    identifier varchar(1000),
+    patientId ENTITYID,
+
+    "state" varchar(1000),
+    county varchar(2000),
+    country varchar(2000),
+    age double precision,
+
+    container entityid,
+    created timestamp,
+    createdby int,
+    modified timestamp,
+    modifiedby int,
+
+    CONSTRAINT PK_patients PRIMARY KEY (patientId)
+);

covidseq/resources/schemas/dbscripts/postgresql/covidseq-21.001-21.002.sql

@@ -0,0 +1 @@
+ALTER TABLE covidseq.patients ADD COLUMN gender varchar(200);

covidseq/resources/schemas/dbscripts/postgresql/covidseq-21.002-21.003.sql

@@ -0,0 +1 @@
+ALTER TABLE covidseq.patients ADD COLUMN ageQualifier varchar(200);

covidseq/resources/schemas/dbscripts/postgresql/covidseq-21.003-21.004.sql

@@ -0,0 +1 @@
+ALTER TABLE covidseq.samples ADD COLUMN rqg_alt_id varchar(200);