Skip inserting data when creating empty schemas - EHR-related tables (#254)

labkey-adam · web-flow · commit 2903c9e9fbf1 · 2025-08-01T14:48:34.000-07:00
diff --git a/LDK/resources/schemas/dbscripts/postgresql/ldk-0.01-0.02.sql b/LDK/resources/schemas/dbscripts/postgresql/ldk-0.01-0.02.sql
@@ -19,6 +19,7 @@ CREATE TABLE ldk.integers (
   CONSTRAINT PK_integers PRIMARY KEY (value)
 );
 
+-- @SkipOnEmptySchemasBegin
 INSERT INTO ldk.integers (value) VALUES (0);
 INSERT INTO ldk.integers (value) VALUES (1);
 INSERT INTO ldk.integers (value) VALUES (2);
@@ -120,4 +121,4 @@ INSERT INTO ldk.integers (value) VALUES (97);
 INSERT INTO ldk.integers (value) VALUES (98);
 INSERT INTO ldk.integers (value) VALUES (99);
 INSERT INTO ldk.integers (value) VALUES (100);
-
+-- @SkipOnEmptySchemasEnd
diff --git a/LDK/resources/schemas/dbscripts/postgresql/ldk-12.32-12.33.sql b/LDK/resources/schemas/dbscripts/postgresql/ldk-12.32-12.33.sql
@@ -1,3 +1,4 @@
+-- @SkipOnEmptySchemasBegin
 INSERT INTO ldk.integers (value) VALUES (101);
 INSERT INTO ldk.integers (value) VALUES (102);
 INSERT INTO ldk.integers (value) VALUES (103);
@@ -898,3 +899,4 @@ INSERT INTO ldk.integers (value) VALUES (997);
 INSERT INTO ldk.integers (value) VALUES (998);
 INSERT INTO ldk.integers (value) VALUES (999);
 INSERT INTO ldk.integers (value) VALUES (1000);
+-- @SkipOnEmptySchemasEnd
diff --git a/LDK/resources/schemas/dbscripts/postgresql/ldk-12.35-12.36.sql b/LDK/resources/schemas/dbscripts/postgresql/ldk-12.35-12.36.sql
@@ -5,10 +5,12 @@ CREATE TABLE ldk.daysOfWeek (
   CONSTRAINT PK_daysOfWeek PRIMARY KEY (idx)
 );
 
+-- @SkipOnEmptySchemasBegin
 INSERT INTO ldk.daysOfWeek (idx, name) VALUES (1, 'Sunday');
 INSERT INTO ldk.daysOfWeek (idx, name) VALUES (2, 'Monday');
 INSERT INTO ldk.daysOfWeek (idx, name) VALUES (3, 'Tuesday');
 INSERT INTO ldk.daysOfWeek (idx, name) VALUES (4, 'Wednesday');
 INSERT INTO ldk.daysOfWeek (idx, name) VALUES (5, 'Thursday');
 INSERT INTO ldk.daysOfWeek (idx, name) VALUES (6, 'Friday');
-INSERT INTO ldk.daysOfWeek (idx, name) VALUES (7, 'Saturday');
+INSERT INTO ldk.daysOfWeek (idx, name) VALUES (7, 'Saturday');
+-- @SkipOnEmptySchemasEnd
diff --git a/LDK/resources/schemas/dbscripts/postgresql/ldk-12.36-12.37.sql b/LDK/resources/schemas/dbscripts/postgresql/ldk-12.36-12.37.sql
@@ -6,6 +6,7 @@ CREATE TABLE ldk.months (
     CONSTRAINT PK_months PRIMARY KEY (rowid)
 );
 
+-- @SkipOnEmptySchemasBegin
 INSERT into ldk.months (monthName, monthNum) VALUES ('January', 1);
 INSERT into ldk.months (monthName, monthNum) VALUES ('February', 2);
 INSERT into ldk.months (monthName, monthNum) VALUES ('March', 3);
@@ -18,3 +19,4 @@ INSERT into ldk.months (monthName, monthNum) VALUES ('September', 9);
 INSERT into ldk.months (monthName, monthNum) VALUES ('October', 10);
 INSERT into ldk.months (monthName, monthNum) VALUES ('November', 11);
 INSERT into ldk.months (monthName, monthNum) VALUES ('December', 12);
+-- @SkipOnEmptySchemasEnd
diff --git a/laboratory/resources/schemas/dbscripts/postgresql/laboratory-0.00-11.10.sql b/laboratory/resources/schemas/dbscripts/postgresql/laboratory-0.00-11.10.sql
@@ -216,11 +216,13 @@ WITH (OIDS=FALSE);
 -- ----------------------------
 -- Records of laboratory.dna_mol_type
 -- ----------------------------
+-- @SkipOnEmptySchemasBegin
 INSERT INTO laboratory.dna_mol_type VALUES ('mRNA');
 INSERT INTO laboratory.dna_mol_type VALUES ('vRNA');
 INSERT INTO laboratory.dna_mol_type VALUES ('gDNA');
 INSERT INTO laboratory.dna_mol_type VALUES ('Plasmid');
 INSERT INTO laboratory.dna_mol_type VALUES ('RNA');
+-- @SkipOnEmptySchemasEnd
 
 -- ----------------------------
 -- Table structure for laboratory.sample_type
@@ -236,6 +238,7 @@ WITH (OIDS=FALSE);
 -- ----------------------------
 -- Records of sample_type
 -- ----------------------------
+-- @SkipOnEmptySchemasBegin
 INSERT INTO laboratory.sample_type VALUES ('Nasal swab');
 INSERT INTO laboratory.sample_type VALUES ('PBMC');
 INSERT INTO laboratory.sample_type VALUES ('Plasma');
@@ -245,6 +248,7 @@ INSERT INTO laboratory.sample_type VALUES ('Total RNA');
 INSERT INTO laboratory.sample_type VALUES ('mRNA');
 INSERT INTO laboratory.sample_type VALUES ('vRNA');
 INSERT INTO laboratory.sample_type VALUES ('RNA');
+-- @SkipOnEmptySchemasEnd
 
 -- ----------------------------
 -- Table structure for laboratory.sample_additive
@@ -256,10 +260,12 @@ CREATE TABLE laboratory.sample_additive
     CONSTRAINT PK_sample_additive PRIMARY KEY (additive)
 ) WITH (OIDS=FALSE);
 
+-- @SkipOnEmptySchemasBegin
 INSERT INTO laboratory.sample_additive (Additive) VALUES
     ('EDTA'),
     ('Heparin'),
     ('RNA Later'),
     ('Sodium citrate');
 
-INSERT INTO laboratory.sample_type VALUES ('Cell Line');
+INSERT INTO laboratory.sample_type VALUES ('Cell Line');
+-- @SkipOnEmptySchemasEnd
diff --git a/laboratory/resources/schemas/dbscripts/postgresql/laboratory-11.10-11.20.sql b/laboratory/resources/schemas/dbscripts/postgresql/laboratory-11.10-11.20.sql
@@ -26,11 +26,13 @@ ALTER TABLE laboratory.inventory
 
 /* laboratory-11.13-11.14.sql */
 
+-- @SkipOnEmptySchemasBegin
 INSERT INTO laboratory.sample_type VALUES
 ('BLCL'),
 ('DNA'),
 ('Whole Blood')
 ;
+-- @SkipOnEmptySchemasEnd
 
 ALTER TABLE laboratory.inventory
   add column cell_number float
@@ -124,6 +126,7 @@ CREATE TABLE laboratory.report_types
   CONSTRAINT pk_report_types PRIMARY KEY (type )
 );
 
+-- @SkipOnEmptySchemasBegin
 INSERT INTO laboratory.report_types
 (type) VALUES
 ('query'),
@@ -132,7 +135,7 @@ INSERT INTO laboratory.report_types
 ('webpart'),
 ('details')
 ;
-
+-- @SkipOnEmptySchemasEnd
 
 -- ----------------------------
 -- Table structure for laboratory.subjects
@@ -181,6 +184,7 @@ WITH (OIDS=FALSE)
 -- ----------------------------
 -- Records of laboratory.species
 -- ----------------------------
+-- @SkipOnEmptySchemasBegin
 INSERT INTO laboratory.species
 (common_name, scientific_name, mhc_prefix)
 VALUES
@@ -197,7 +201,7 @@ VALUES
 ('Mouse', 'Mus musculus', null),
 ('Rat', 'Rattus norvegicus', null)
 ;
-
+-- @SkipOnEmptySchemasEnd
 
 DROP TABLE IF EXISTS laboratory.geographic_origins;
 CREATE TABLE laboratory.geographic_origins (
@@ -226,6 +230,7 @@ CREATE TABLE laboratory.well_layout (
   CONSTRAINT PK_well_layout PRIMARY KEY (rowid)
 );
 
+-- @SkipOnEmptySchemasBegin
 INSERT INTO laboratory.well_layout
 (Plate,Well_96,Well_96_Padded,Well_384,Well_384_Padded,AddressByRow_96,AddressByColumn_96,AddressByColumn_384,AddressByRow_384)
 VALUES
@@ -614,7 +619,7 @@ VALUES
 (4, 'H11', 'H11', 'P23', 'P23', 95, 88, 368, 383),
 (4, 'H12', 'H12', 'P24', 'P24', 96, 96, 384, 384)
 ;
-
+-- @SkipOnEmptySchemasEnd
 
 -- ----------------------------
 -- Table structure for laboratory.genders
@@ -631,17 +636,22 @@ WITH (OIDS=FALSE)
 
 ;
 
+-- @SkipOnEmptySchemasBegin
 INSERT INTO laboratory.genders
 (code, meaning, numericvalue)
 VALUES
 ('m', 'Male', 1),
 ('f', 'Female', 2),
 ('u', 'Unknown', 0)
 ;
+-- @SkipOnEmptySchemasEnd
 
 drop table if exists laboratory.samples;
 
+-- @SkipOnEmptySchemasBegin
 insert into laboratory.sample_type (type) values ('gDNA');
+-- @SkipOnEmptySchemasEnd
+
 insert into laboratory.sample_source (source) values ('gDNA');
 insert into laboratory.sample_source (source) values ('DNA');
 
diff --git a/laboratory/resources/schemas/dbscripts/postgresql/laboratory-11.20-11.30.sql b/laboratory/resources/schemas/dbscripts/postgresql/laboratory-11.20-11.30.sql
@@ -21,7 +21,7 @@ alter table laboratory.samples
   add column subjectid varchar(200)
 ;
 
-
+-- @SkipOnEmptySchemasBegin
 insert into laboratory.species
 (common_name,scientific_name)
 values
@@ -35,6 +35,7 @@ values
 insert into laboratory.dna_mol_type
 (mol_type) values ('Vector')
 ;
+-- @SkipOnEmptySchemasEnd
 
 DROP TABLE IF EXISTS laboratory.site_module_properties;
 CREATE TABLE laboratory.site_module_properties (
diff --git a/laboratory/resources/schemas/dbscripts/postgresql/laboratory-12.20-12.21.sql b/laboratory/resources/schemas/dbscripts/postgresql/laboratory-12.20-12.21.sql
@@ -34,10 +34,12 @@ CREATE TABLE laboratory.qual_results
     CONSTRAINT PK_qual_results PRIMARY KEY (rowid)
 );
 
+-- @SkipOnEmptySchemasBegin
 INSERT INTO laboratory.qual_results (meaning, description) VALUES ('POS', 'Positive');
 INSERT INTO laboratory.qual_results (meaning, description) VALUES ('NEG', 'Negative');
 INSERT INTO laboratory.qual_results (meaning, description) VALUES ('OUTLIER', 'Outlier');
 INSERT INTO laboratory.qual_results (meaning, description) VALUES ('ND', 'No Data');
+-- @SkipOnEmptySchemasEnd
 
 CREATE TABLE laboratory.assay_requests
 (
diff --git a/laboratory/resources/schemas/dbscripts/postgresql/laboratory-12.22-12.23.sql b/laboratory/resources/schemas/dbscripts/postgresql/laboratory-12.22-12.23.sql
@@ -14,6 +14,7 @@
  * limitations under the License.
  */
 delete from laboratory.reference_peptides;
+-- @SkipOnEmptySchemasBegin
 INSERT INTO laboratory.reference_peptides (sequence, mhc_restriction) VALUES ('AAAQQRGPRK', null);
 INSERT INTO laboratory.reference_peptides (sequence, mhc_restriction) VALUES ('AADWDLQHPQ', null);
 INSERT INTO laboratory.reference_peptides (sequence, mhc_restriction) VALUES ('AADWDLQHPQPAPQQGQLRE', null);
@@ -5017,3 +5018,4 @@ INSERT INTO laboratory.reference_peptides (sequence, mhc_restriction) VALUES ('Y
 INSERT INTO laboratory.reference_peptides (sequence, mhc_restriction) VALUES ('YYREGRDQLWKGPGE', null);
 INSERT INTO laboratory.reference_peptides (sequence, mhc_restriction) VALUES ('YYSARRHRIL', null);
 INSERT INTO laboratory.reference_peptides (sequence, mhc_restriction) VALUES ('YYSARRHRILDIYLE', null);
+-- @SkipOnEmptySchemasEnd
diff --git a/laboratory/resources/schemas/dbscripts/postgresql/laboratory-12.24-12.25.sql b/laboratory/resources/schemas/dbscripts/postgresql/laboratory-12.24-12.25.sql
@@ -13,12 +13,15 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
+
+-- @SkipOnEmptySchemasBegin
 DELETE FROM laboratory.sample_type WHERE type = 'Serum';
 INSERT INTO laboratory.sample_type (type) VALUES ('Serum');
 DELETE FROM laboratory.sample_type WHERE type = 'Tissue';
 INSERT INTO laboratory.sample_type (type) VALUES ('Tissue');
 DELETE FROM laboratory.sample_type WHERE type = 'Supernatant';
 INSERT INTO laboratory.sample_type (type) VALUES ('Supernatant');
+-- @SkipOnEmptySchemasEnd
 
 -- NOTE: SQLServer will not allow 2 FKs pointing to the same table with update cascade
 -- therefore rather than let 1 field update and the other not, we get rid of both
diff --git a/laboratory/resources/schemas/dbscripts/postgresql/laboratory-12.25-12.26.sql b/laboratory/resources/schemas/dbscripts/postgresql/laboratory-12.25-12.26.sql
@@ -17,4 +17,7 @@ DROP TABLE laboratory.site_module_properties;
 DROP TABLE laboratory.module_properties;
 
 INSERT INTO laboratory.samplecategory (category) VALUES ('NTC');
-INSERT INTO laboratory.samplecategory (category) VALUES ('Unknown');
+
+-- @SkipOnEmptySchemasBegin
+INSERT INTO laboratory.samplecategory (category) VALUES ('Unknown');
+-- @SkipOnEmptySchemasEnd
diff --git a/laboratory/resources/schemas/dbscripts/postgresql/laboratory-12.273-12.274.sql b/laboratory/resources/schemas/dbscripts/postgresql/laboratory-12.273-12.274.sql
@@ -9,11 +9,13 @@ DELETE FROM laboratory.samplecategory WHERE category = 'Pos Control';
 DELETE FROM laboratory.samplecategory WHERE category = 'Neg Control';
 DELETE FROM laboratory.samplecategory WHERE category = 'Control';
 
+-- @SkipOnEmptySchemasBegin
 INSERT INTO laboratory.samplecategory (category) VALUES ('Pos Control');
 INSERT INTO laboratory.samplecategory (category) VALUES ('Neg Control');
 INSERT INTO laboratory.samplecategory (category) VALUES ('Control');
 INSERT INTO laboratory.samplecategory (category) VALUES ('Blank');
 INSERT INTO laboratory.samplecategory (category) VALUES ('Standard');
+-- @SkipOnEmptySchemasEnd
 
 ALTER TABLE laboratory.samplecategory ADD control boolean;
 UPDATE laboratory.samplecategory SET control = true;
diff --git a/laboratory/resources/schemas/dbscripts/postgresql/laboratory-12.279-12.280.sql b/laboratory/resources/schemas/dbscripts/postgresql/laboratory-12.279-12.280.sql
@@ -18,6 +18,7 @@ CREATE TABLE laboratory.workbook_group_members (
   CONSTRAINT pk_workbook_group_members PRIMARY KEY (rowid)
 );
 
+-- @SkipOnEmptySchemasBegin
 DELETE FROM laboratory.sample_type  WHERE type = 'Brain';
 INSERT INTO laboratory.sample_type (type) VALUES ('Brain');
 
@@ -29,6 +30,7 @@ INSERT INTO laboratory.sample_type (type) VALUES ('Spleen');
 
 DELETE FROM laboratory.sample_additive  WHERE additive = 'Filter Paper';
 INSERT INTO laboratory.sample_additive (additive) VALUES ('Filter Paper');
+-- @SkipOnEmptySchemasEnd
 
 ALTER TABLE laboratory.workbooks ADD folder entityid;
 
diff --git a/laboratory/resources/schemas/dbscripts/postgresql/laboratory-12.286-12.287.sql b/laboratory/resources/schemas/dbscripts/postgresql/laboratory-12.286-12.287.sql
@@ -5,6 +5,8 @@ CREATE TABLE laboratory.result_status (
   CONSTRAINT PK_result_status PRIMARY KEY (status)
 );
 
+-- @SkipOnEmptySchemasBegin
 INSERT INTO laboratory.result_status (status, not_trusted) VALUES ('Definitive', false);
 INSERT INTO laboratory.result_status (status, not_trusted) VALUES ('Outlier', true);
-INSERT INTO laboratory.result_status (status, not_trusted) VALUES ('Replaced', true);
+INSERT INTO laboratory.result_status (status, not_trusted) VALUES ('Replaced', true);
+-- @SkipOnEmptySchemasEnd
diff --git a/laboratory/resources/schemas/dbscripts/postgresql/laboratory-12.296-12.297.sql b/laboratory/resources/schemas/dbscripts/postgresql/laboratory-12.296-12.297.sql
@@ -1 +1,3 @@
-INSERT INTO laboratory.result_status (status) VALUES ('Exclude');
+-- @SkipOnEmptySchemasBegin
+INSERT INTO laboratory.result_status (status) VALUES ('Exclude');
+-- @SkipOnEmptySchemasEnd
diff --git a/laboratory/resources/schemas/dbscripts/postgresql/laboratory-12.297-12.298.sql b/laboratory/resources/schemas/dbscripts/postgresql/laboratory-12.297-12.298.sql
@@ -1,2 +1,4 @@
+-- @SkipOnEmptySchemasBegin
 DELETE FROM laboratory.result_status WHERE status = 'No Data';
-INSERT INTO laboratory.result_status (status) VALUES ('No Data');
+INSERT INTO laboratory.result_status (status) VALUES ('No Data');
+-- @SkipOnEmptySchemasEnd
diff --git a/laboratory/resources/schemas/dbscripts/postgresql/laboratory-12.299-12.300.sql b/laboratory/resources/schemas/dbscripts/postgresql/laboratory-12.299-12.300.sql
@@ -1,2 +1,4 @@
+-- @SkipOnEmptySchemasBegin
 DELETE FROM laboratory.species WHERE common_name = 'Rabbit';
-INSERT INTO laboratory.species (common_name, scientific_name) VALUES ('Rabbit', 'Lepus curpaeums');
+INSERT INTO laboratory.species (common_name, scientific_name) VALUES ('Rabbit', 'Lepus curpaeums');
+-- @SkipOnEmptySchemasEnd

Original file line number	Diff line number	Diff line change
`@@ -21,7 +21,7 @@ alter table laboratory.samples`
`21`	`21`	`add column subjectid varchar(200)`
`22`	`22`	`;`
`23`	`23`
`24`		`-`
	`24`	`+-- @SkipOnEmptySchemasBegin`
`25`	`25`	`insert into laboratory.species`
`26`	`26`	`(common_name,scientific_name)`
`27`	`27`	`values`
`@@ -35,6 +35,7 @@ values`
`35`	`35`	`insert into laboratory.dna_mol_type`
`36`	`36`	`(mol_type) values ('Vector')`
`37`	`37`	`;`
	`38`	`+-- @SkipOnEmptySchemasEnd`
`38`	`39`
`39`	`40`	`DROP TABLE IF EXISTS laboratory.site_module_properties;`
`40`	`41`	`CREATE TABLE laboratory.site_module_properties (`