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labkey-adam merged 3 commits into from
Aug 1, 2025
Merged

Option to migrate SQL Server hard tables to PostgreSQL #1097

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9323d04
Option to migrate SQL Server hard tables to PostgreSQL
labkey-adam Jul 23, 2025
34cf2ea
Support skip annotations in comments for convenience
labkey-adam Jul 26, 2025
df4088e
No need for trailing semicolon
labkey-adam Jul 27, 2025
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14 changes: 12 additions & 2 deletions resources/schemas/dbscripts/postgresql/targetedms-0.000-24.000.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -1455,7 +1455,7 @@ CREATE TABLE targetedms.QCMetricConfiguration
CONSTRAINT UQ_QCMetricConfig_Name_Container UNIQUE (Name, Container)
);


-- @SkipOnEmptySchemasBegin
WITH rootIdentity as (select EntityId as theIdentity FROM core.Containers WHERE Parent is null)
INSERT INTO targetedms.QCMetricConfiguration (Container, Name,Series1Label,Series1SchemaName,Series1QueryName,Series2Label,Series2SchemaName,Series2QueryName) VALUES
((select theIdentity from rootIdentity), 'Retention Time','Retention Time','targetedms','QCMetric_retentionTime',NULL , NULL , NULL ),
Expand All @@ -1466,6 +1466,7 @@ INSERT INTO targetedms.QCMetricConfiguration (Container, Name,Series1Label,Serie
((select theIdentity from rootIdentity), 'Transition/Precursor Area Ratio','Transition/Precursor Area Ratio','targetedms','QCMetric_transitionPrecursorRatio',NULL , NULL , NULL ),
((select theIdentity from rootIdentity), 'Transition/Precursor Areas','Transition Area','targetedms','QCMetric_transitionArea','Precursor Area','targetedms','QCMetric_precursorArea'),
((select theIdentity from rootIdentity), 'Mass Accuracy','Mass Accuracy','targetedms','QCMetric_massAccuracy',NULL , NULL , NULL );
-- @SkipOnEmptySchemasEnd

-- Add column to ReplicateAnnotation to store the source of the annotation (e.g. Skyline or AutoQC)
ALTER TABLE targetedms.ReplicateAnnotation ADD COLUMN Source VARCHAR(20) NOT NULL DEFAULT 'Skyline';
Expand Down Expand Up @@ -1800,9 +1801,11 @@ ALTER TABLE targetedms.MeasuredDriftTime ADD IonMobilityUnits VARCHAR(30);

ALTER TABLE targetedms.Runs ADD COLUMN AuditLogEntriesCount INT4 DEFAULT 0 NOT NULL;

-- @SkipOnEmptySchemasBegin
WITH rootIdentity as (select EntityId as theIdentity FROM core.Containers WHERE Parent is null)
INSERT INTO targetedms.QCMetricConfiguration (Container, Name,Series1Label,Series1SchemaName,Series1QueryName,Series2Label,Series2SchemaName,Series2QueryName,PrecursorScoped) VALUES
((select theIdentity from rootIdentity), 'TIC Area','TIC Area','targetedms','QCRunMetric_ticArea',NULL , NULL , NULL , FALSE );
-- @SkipOnEmptySchemasEnd

ALTER TABLE targetedms.SampleFile ADD COLUMN TicArea DOUBLE PRECISION;

Expand Down Expand Up @@ -1860,6 +1863,7 @@ CREATE TABLE targetedms.ListItemValue
ALTER TABLE targetedms.QCMetricConfiguration ADD COLUMN EnabledQueryName VARCHAR(200);
ALTER TABLE targetedms.QCMetricConfiguration ADD COLUMN EnabledSchemaName VARCHAR(200);

-- @SkipOnEmptySchemasBegin
WITH rootIdentity as (select EntityId as theIdentity FROM core.Containers WHERE Parent is null)
INSERT INTO targetedms.QCMetricConfiguration (Container, Name,Series1Label,Series1SchemaName,Series1QueryName,Series2Label,Series2SchemaName,Series2QueryName,PrecursorScoped, EnabledQueryName, EnabledSchemaName) VALUES
((select theIdentity from rootIdentity), 'Isotopologue LOD', 'LOD','targetedms', 'QCMetric_IsotopologuePrecursorLOD', NULL, NULL, NULL, TRUE, 'QCMetricEnabled_IsotopologuePrecursorLOD', 'targetedms');
Expand All @@ -1877,6 +1881,7 @@ INSERT INTO targetedms.QCMetricConfiguration (Container, Name,Series1Label,Serie
((select theIdentity from rootIdentity), 'Isotopologue Regression RSquared', 'Coefficient', 'targetedms', 'QCMetric_IsotopologuePrecursorRSquared', NULL, NULL, NULL, TRUE, 'QCMetricEnabled_IsotopologuePrecursorRSquared', 'targetedms');

UPDATE targetedms.QCMetricConfiguration SET EnabledQueryName = 'QCMetricEnabled_lhRatio', EnabledSchemaName ='targetedms' WHERE Series1QueryName = 'QCMetric_lhRatio';
-- @SkipOnEmptySchemasEnd

ALTER TABLE targetedms.runs ALTER COLUMN SoftwareVersion TYPE VARCHAR(200);

Expand Down Expand Up @@ -2229,6 +2234,7 @@ CREATE TABLE targetedms.keywords (
CONSTRAINT keywords_keywordid_key UNIQUE (keywordid)
);

-- @SkipOnEmptySchemasBegin
INSERT INTO targetedms.keywordcategories VALUES (1, 'KW-9999', 'Biological process');
INSERT INTO targetedms.keywordcategories VALUES (2, 'KW-9998', 'Cellular component');
INSERT INTO targetedms.keywordcategories VALUES (3, 'KW-9997', 'Coding sequence diversity');
Expand Down Expand Up @@ -3423,6 +3429,7 @@ INSERT INTO targetedms.keywords VALUES ( DEFAULT, 'KW-1268', 'Autism spectrum di
INSERT INTO targetedms.keywords VALUES ( DEFAULT, 'KW-1269', 'Autism', 'KW-9995');
INSERT INTO targetedms.keywords VALUES ( DEFAULT, 'KW-1270', 'Asperger syndrome', 'KW-9995');
INSERT INTO targetedms.keywords VALUES ( DEFAULT, 'KW-1271', 'Inflammasome', 'KW-9998');
-- @SkipOnEmptySchemasEnd

ALTER TABLE targetedms.Runs ALTER COLUMN Id TYPE bigint;

Expand Down Expand Up @@ -3924,6 +3931,7 @@ ALTER TABLE targetedms.SampleFile ADD IRTSlope REAL;
ALTER TABLE targetedms.SampleFile ADD IRTIntercept REAL;
ALTER TABLE targetedms.SampleFile ADD IRTCorrelation REAL;

-- @SkipOnEmptySchemasBegin
WITH rootIdentity as (select EntityId as theIdentity FROM core.Containers WHERE Parent is null)
INSERT INTO targetedms.QCMetricConfiguration (Container, Name, Series1Label, Series1SchemaName, Series1QueryName, PrecursorScoped, EnabledQueryName, EnabledSchemaName) VALUES
((select theIdentity from rootIdentity), 'iRT Slope', 'iRT Slope', 'targetedms', 'QCRunMetric_iRTSlope', false, 'QCRunMetricEnabled_iRTSlope', 'targetedms');
Expand All @@ -3943,7 +3951,6 @@ WITH rootIdentity as (select EntityId as theIdentity FROM core.Containers WHERE
INSERT INTO targetedms.QCMetricConfiguration (Container, Name, Series1Label, Series1SchemaName, Series1QueryName, PrecursorScoped) VALUES
((select theIdentity from rootIdentity), 'Precursor Area', 'Precursor Area', 'targetedms', 'QCMetric_precursorArea', true);


WITH rootIdentity as (select EntityId as theIdentity FROM core.Containers WHERE Parent is null)
INSERT INTO targetedms.QCMetricConfiguration (Container, Name, Series1Label, Series1SchemaName, Series1QueryName, PrecursorScoped, EnabledQueryName, EnabledSchemaName) VALUES
((select theIdentity from rootIdentity), 'Transition Area', 'Transition Area', 'targetedms', 'QCMetric_transitionArea', true, 'QCMetricEnabled_transitionArea', 'targetedms');
Expand All @@ -3970,6 +3977,7 @@ SET
EnabledQueryName = 'QCMetricEnabled_transitionArea',
EnabledSchemaName = 'targetedms'
WHERE Name = 'Transition & Precursor Areas';
-- @SkipOnEmptySchemasEnd

ALTER TABLE targetedms.PrecursorChromInfo
ADD COLUMN TotalAreaMs1 REAL,
Expand Down Expand Up @@ -4025,13 +4033,15 @@ SELECT core.fn_dropifexists('AuditLogEntry', 'targetedms', 'CONSTRAINT', 'fk_aud
ALTER TABLE targetedms.AuditLogEntry
DROP COLUMN VersionId;

-- @SkipOnEmptySchemasBegin
WITH rootIdentity as (select EntityId as theIdentity FROM core.Containers WHERE Parent is null)
INSERT INTO targetedms.QCMetricConfiguration (Container, Name, Series1Label, Series1SchemaName, Series1QueryName, PrecursorScoped, EnabledQueryName, EnabledSchemaName) VALUES
((select theIdentity from rootIdentity), 'Library dotp', 'Library dotp', 'targetedms', 'QCMetric_libraryDotp', true, 'QCMetricEnabled_libraryDotp', 'targetedms');

WITH rootIdentity as (select EntityId as theIdentity FROM core.Containers WHERE Parent is null)
INSERT INTO targetedms.QCMetricConfiguration (Container, Name, Series1Label, Series1SchemaName, Series1QueryName, PrecursorScoped, EnabledQueryName, EnabledSchemaName) VALUES
((select theIdentity from rootIdentity), 'Isotope dotp', 'Isotope dotp', 'targetedms', 'QCMetric_isotopeDotp', true, 'QCMetricEnabled_isotopeDotp', 'targetedms');
-- @SkipOnEmptySchemasEnd

-- Reparent table if it exists in PanoramaPremium schema
ALTER TABLE IF EXISTS PanoramaPremium.QCEmailNotifications SET SCHEMA targetedms;
Expand Down
5 changes: 3 additions & 2 deletions resources/schemas/dbscripts/postgresql/targetedms-24.000-24.001.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,8 @@ UPDATE targetedms.QCMetricConfiguration SET
YAxisLabel1 = 'Mass Error PPM'
WHERE Name = 'Mass Accuracy';

-- @SkipOnEmptySchemasBegin
WITH rootIdentity AS (SELECT EntityId AS theIdentity FROM core.Containers WHERE Parent IS NULL)
INSERT INTO targetedms.QCMetricConfiguration (Container, Name, Series1Label, Series1SchemaName, Series1QueryName, EnabledSchemaName, EnabledQueryName, YAxisLabel1) VALUES
((SELECT theIdentity FROM rootIdentity), 'Transition Mass Error','Transition Mass Error','targetedms','QCMetric_massErrorTransition', 'targetedms', 'QCMetricEnabled_massErrorTransition', 'Mass Error PPM')
;
((SELECT theIdentity FROM rootIdentity), 'Transition Mass Error','Transition Mass Error','targetedms','QCMetric_massErrorTransition', 'targetedms', 'QCMetricEnabled_massErrorTransition', 'Mass Error PPM');
-- @SkipOnEmptySchemasEnd
22 changes: 14 additions & 8 deletions src/org/labkey/targetedms/TargetedMSUpgradeCode.java
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Expand Up @@ -54,21 +54,27 @@ public class TargetedMSUpgradeCode implements UpgradeCode
@SuppressWarnings({"UnusedDeclaration"})
public void populateDefaultAnnotationTypes(final ModuleContext moduleContext)
{
insertAnnotationType("Instrumentation Change", "FF0000", moduleContext.getUpgradeUser());
insertAnnotationType("Reagent Change", "00FF00", moduleContext.getUpgradeUser());
insertAnnotationType("Technician Change", "0000FF", moduleContext.getUpgradeUser());
if (ModuleLoader.getInstance().shouldInsertData())
{
insertAnnotationType("Instrumentation Change", "FF0000", moduleContext.getUpgradeUser());
insertAnnotationType("Reagent Change", "00FF00", moduleContext.getUpgradeUser());
insertAnnotationType("Technician Change", "0000FF", moduleContext.getUpgradeUser());

// Enable the module in the /Shared container so that it can be resolved
Set<Module> activeModules = new HashSet<>(ContainerManager.getSharedContainer().getActiveModules());
activeModules.add(ModuleLoader.getInstance().getModule(TargetedMSModule.class));
ContainerManager.getSharedContainer().setActiveModules(activeModules);
// Enable the module in the /Shared container so that it can be resolved
Set<Module> activeModules = new HashSet<>(ContainerManager.getSharedContainer().getActiveModules());
activeModules.add(ModuleLoader.getInstance().getModule(TargetedMSModule.class));
ContainerManager.getSharedContainer().setActiveModules(activeModules);
}
}

// initialization code called at 0.000-24.000 to add a new type. Can eventually be consolidated into the bootstrap insert above
@SuppressWarnings({"UnusedDeclaration"})
public void addInstrumentDowntimeAnnotationType(final ModuleContext moduleContext)
{
insertAnnotationType(QCAnnotationTypeTable.INSTRUMENT_DOWNTIME, "CCCC00", moduleContext.getUpgradeUser());
if (ModuleLoader.getInstance().shouldInsertData())
{
insertAnnotationType(QCAnnotationTypeTable.INSTRUMENT_DOWNTIME, "CCCC00", moduleContext.getUpgradeUser());
}
}

private void insertAnnotationType(String name, String color, User user)
Expand Down