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Skip inserting data when creating empty schemas #258

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Merged
merged 1 commit into from
Aug 1, 2025
Merged

Skip inserting data when creating empty schemas #258

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4 changes: 3 additions & 1 deletion GenotypeAssays/resources/schemas/dbscripts/postgresql/genotypeassays-0.00-0.01.sql
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Expand Up @@ -23,6 +23,8 @@ CREATE TABLE genotypeassays.assaytypes (
CONSTRAINT pk_assaytypes PRIMARY KEY (name)
);

-- @SkipOnEmptySchemasBegin
INSERT INTO genotypeassays.assaytypes (name, description) VALUES ('SSP', 'Sequence-specific PCR');
INSERT INTO genotypeassays.assaytypes (name, description) VALUES ('STR', 'Microsatellite');
INSERT INTO genotypeassays.assaytypes (name, description) VALUES ('SBT', 'Sequence-based Genotyping');
INSERT INTO genotypeassays.assaytypes (name, description) VALUES ('SBT', 'Sequence-based Genotyping');
-- @SkipOnEmptySchemasEnd
4 changes: 3 additions & 1 deletion GenotypeAssays/resources/schemas/dbscripts/postgresql/genotypeassays-0.02-0.03.sql
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Expand Up @@ -26,7 +26,9 @@ CREATE TABLE genotypeassays.ssp_result_types
CONSTRAINT PK_ssp_result_types PRIMARY KEY (result)
);

-- @SkipOnEmptySchemasBegin
INSERT into genotypeassays.ssp_result_types (result, meaning, importAliases) VALUES ('POS', 'Positive', '+,1,Y');
INSERT into genotypeassays.ssp_result_types (result, meaning, importAliases) VALUES ('NEG', 'Negative', '-,0,N');
INSERT into genotypeassays.ssp_result_types (result, meaning, importAliases) VALUES ('IND', 'Indeterminate', null);
INSERT into genotypeassays.ssp_result_types (result, meaning, importAliases) VALUES ('FAIL', 'Fail', 'F');
INSERT into genotypeassays.ssp_result_types (result, meaning, importAliases) VALUES ('FAIL', 'Fail', 'F');
-- @SkipOnEmptySchemasEnd
2 changes: 2 additions & 0 deletions elispot_assay/resources/schemas/dbscripts/postgresql/elispot_assay-0.00-0.01.sql
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Expand Up @@ -56,7 +56,9 @@ CREATE TABLE elispot_assay.assay_types (
constraint PK_assay_types PRIMARY KEY (rowid)
);

-- @SkipOnEmptySchemasBegin
INSERT INTO elispot_assay.assay_types (name, description) VALUES ('IFN-Gamma', 'Interferon Gamma');
-- @SkipOnEmptySchemasEnd

CREATE TABLE elispot_assay.instruments
(
Expand Down
4 changes: 3 additions & 1 deletion elispot_assay/resources/schemas/dbscripts/postgresql/elispot_assay-0.02-0.03.sql
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@@ -1 +1,3 @@
INSERT INTO elispot_assay.instruments (instrument) VALUES ('AID Plate Reader');
-- @SkipOnEmptySchemasBegin
INSERT INTO elispot_assay.instruments (instrument) VALUES ('AID Plate Reader');
-- @SkipOnEmptySchemasEnd
2 changes: 2 additions & 0 deletions elispot_assay/resources/schemas/dbscripts/postgresql/elispot_assay-0.03-0.04.sql
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@@ -1,3 +1,4 @@
-- @SkipOnEmptySchemasBegin
TRUNCATE TABLE elispot_assay.peptide_pools;
INSERT INTO elispot_assay.peptide_pools (pool_name, category) VALUES ('SIVmac239 Env Pool A', 'SIV');
INSERT INTO elispot_assay.peptide_pools (pool_name, category) VALUES ('SIVmac239 Env Pool B', 'SIV');
Expand Down Expand Up @@ -909,3 +910,4 @@ INSERT INTO elispot_assay.peptide_pool_members (poolid, sequence) select rowid,
INSERT INTO elispot_assay.peptide_pool_members (poolid, sequence) select rowid, 'GKEVDSSSHMEDTGE' as sequence from elispot_assay.peptide_pools pp WHERE pp.pool_name = 'SIVmac239 Pol Pool Z';
INSERT INTO elispot_assay.peptide_pool_members (poolid, sequence) select rowid, 'DSSSHMEDTGEAREV' as sequence from elispot_assay.peptide_pools pp WHERE pp.pool_name = 'SIVmac239 Pol Pool Z';
INSERT INTO elispot_assay.peptide_pool_members (poolid, sequence) select rowid, 'HMEDTGEAREVA' as sequence from elispot_assay.peptide_pools pp WHERE pp.pool_name = 'SIVmac239 Pol Pool Z';
-- @SkipOnEmptySchemasEnd
16 changes: 11 additions & 5 deletions flowassays/resources/schemas/dbscripts/postgresql/flowassays-0.00-0.01.sql
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Expand Up @@ -30,6 +30,7 @@ CREATE TABLE flowassays.populations
CONSTRAINT PK_populations PRIMARY KEY (Name)
);

-- @SkipOnEmptySchemasBegin
INSERT INTO flowassays.populations (Name) VALUES
('NK'),
('CD14 Mono'),
Expand All @@ -38,7 +39,7 @@ INSERT INTO flowassays.populations (Name) VALUES
('CD4'),
('CD14'),
('CD8');

-- @SkipOnEmptySchemasEnd

CREATE TABLE flowassays.units
(
Expand All @@ -47,15 +48,16 @@ CREATE TABLE flowassays.units
CONSTRAINT PK_units PRIMARY KEY (unit)
);

-- @SkipOnEmptySchemasBegin
INSERT INTO flowassays.units VALUES ('cells/uL'), ('Tc/uL');

-- @SkipOnEmptySchemasEnd

UPDATE flowassays.populations SET Name = 'CD4 T-cells' WHERE Name = 'CD4';
UPDATE flowassays.populations SET Name = 'CD8 T-cells' WHERE Name = 'CD8';


-- @SkipOnEmptySchemasBegin
INSERT INTO flowassays.units VALUES ('%');

-- @SkipOnEmptySchemasEnd

CREATE TABLE flowassays.instruments
(
Expand All @@ -64,7 +66,9 @@ CREATE TABLE flowassays.instruments
CONSTRAINT PK_instruments PRIMARY KEY (instrument)
);

-- @SkipOnEmptySchemasBegin
INSERT INTO flowassays.instruments VALUES ('BD LSR II');
-- @SkipOnEmptySchemasEnd

CREATE TABLE flowassays.assay_types (
rowid serial,
Expand All @@ -74,6 +78,7 @@ CREATE TABLE flowassays.assay_types (
constraint pk_assay_types PRIMARY KEY (rowid)
);

-- @SkipOnEmptySchemasBegin
DELETE FROM flowassays.populations WHERE name = 'NK';
DELETE FROM flowassays.populations WHERE name = 'CD4';
DELETE FROM flowassays.populations WHERE name = 'CD8';
Expand All @@ -97,4 +102,5 @@ DELETE FROM flowassays.populations WHERE name = 'T-cells';
INSERT INTO flowassays.populations(name) VALUES ('T-cells');


INSERT INTO flowassays.assay_types(name) VALUES ('TruCount');
INSERT INTO flowassays.assay_types(name) VALUES ('TruCount');
-- @SkipOnEmptySchemasEnd
4 changes: 3 additions & 1 deletion flowassays/resources/schemas/dbscripts/postgresql/flowassays-0.02-0.03.sql
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Expand Up @@ -13,11 +13,13 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-- @SkipOnEmptySchemasBegin
DELETE FROM flowassays.populations WHERE name = 'T-cells';
DELETE FROM flowassays.populations WHERE name = 'T-Cells';
INSERT INTO flowassays.populations (name) VALUES ('T-cells');

DELETE FROM flowassays.populations WHERE name = 'Lymphocytes';
INSERT INTO flowassays.populations (name) VALUES ('Lymphocytes');

INSERT INTO flowassays.assay_types (name) VALUES ('Phenotyping');
INSERT INTO flowassays.assay_types (name) VALUES ('Phenotyping');
-- @SkipOnEmptySchemasEnd
4 changes: 3 additions & 1 deletion flowassays/resources/schemas/dbscripts/postgresql/flowassays-12.21-12.22.sql
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@@ -1,7 +1,9 @@
DELETE FROM flowassays.populations WHERE name = 'Lymphocytes';
-- @SkipOnEmptySchemasBegin
DELETE FROM flowassays.populations WHERE name = 'Lymphocytes';
INSERT INTO flowassays.populations (name) VALUES ('Lymphocytes');

DELETE FROM flowassays.assay_types WHERE name = 'Tetramer';
DELETE FROM flowassays.assay_types WHERE name = 'Phenotyping';
INSERT INTO flowassays.assay_types(name) VALUES ('Tetramer');
INSERT INTO flowassays.assay_types(name) VALUES ('Phenotyping');
-- @SkipOnEmptySchemasEnd
2 changes: 2 additions & 0 deletions tcrdb/resources/schemas/dbscripts/postgresql/tcrdb-15.31-15.32.sql
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Expand Up @@ -4,6 +4,7 @@ CREATE TABLE tcrdb.loci (
constraint PK_loci PRIMARY KEY (locus)
);

-- @SkipOnEmptySchemasBegin
INSERT INTO tcrdb.loci (locus) VALUES ('IGH');
INSERT INTO tcrdb.loci (locus) VALUES ('IGL');
INSERT INTO tcrdb.loci (locus) VALUES ('IGK');
Expand All @@ -14,3 +15,4 @@ INSERT INTO tcrdb.loci (locus) VALUES ('TRD');
INSERT INTO tcrdb.loci (locus) VALUES ('IG');
INSERT INTO tcrdb.loci (locus) VALUES ('TCR');
INSERT INTO tcrdb.loci (locus) VALUES ('ALL');
-- @SkipOnEmptySchemasEnd