From 6b3a5c861b7a4ce2910933b02faf5ad0cbc100a1 Mon Sep 17 00:00:00 2001 From: Adam Rauch Date: Sat, 26 Jul 2025 12:03:40 -0700 Subject: [PATCH 1/2] Skip inserting active modules if creating empty schemas --- .../src/org/labkey/openldapsync/OpenLdapSyncModule.java | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/OpenLdapSync/src/org/labkey/openldapsync/OpenLdapSyncModule.java b/OpenLdapSync/src/org/labkey/openldapsync/OpenLdapSyncModule.java index f66343c63..c5a39011f 100644 --- a/OpenLdapSync/src/org/labkey/openldapsync/OpenLdapSyncModule.java +++ b/OpenLdapSync/src/org/labkey/openldapsync/OpenLdapSyncModule.java @@ -23,6 +23,7 @@ import org.labkey.api.data.DbSchemaType; import org.labkey.api.module.Module; import org.labkey.api.module.ModuleContext; +import org.labkey.api.module.ModuleLoader; import org.labkey.api.module.SpringModule; import org.labkey.api.query.DefaultSchema; import org.labkey.api.query.DetailsURL; @@ -100,7 +101,8 @@ public boolean isAvailable(DefaultSchema schema, Module module) { modules = new HashSet<>(modules); modules.add(this); - ContainerManager.getSharedContainer().setActiveModules(modules); + if (ModuleLoader.getInstance().shouldInsertData()) + ContainerManager.getSharedContainer().setActiveModules(modules); } } From 78ffb3b5997250fddf878caacb0ecdf631e3519b Mon Sep 17 00:00:00 2001 From: Adam Rauch Date: Fri, 1 Aug 2025 13:40:00 -0700 Subject: [PATCH 2/2] Skip inserting data when creating empty schemas --- .../postgresql/SequenceAnalysis-0.00-11.20.sql | 16 ++++++++++++---- .../postgresql/SequenceAnalysis-11.20-11.30.sql | 4 ++++ .../postgresql/SequenceAnalysis-12.10-12.20.sql | 4 ++++ .../postgresql/SequenceAnalysis-12.12-12.13.sql | 2 ++ .../postgresql/SequenceAnalysis-12.20-12.21.sql | 2 ++ .../postgresql/SequenceAnalysis-12.25-12.26.sql | 2 ++ .../postgresql/SequenceAnalysis-12.26-12.261.sql | 6 ++++++ .../SequenceAnalysis-12.265-12.266.sql | 4 ++++ .../SequenceAnalysis-12.276-12.277.sql | 2 ++ .../SequenceAnalysis-12.292-12.293.sql | 4 +++- .../SequenceAnalysis-12.312-12.313.sql | 2 ++ .../SequenceAnalysis-12.316-12.317.sql | 4 +++- 12 files changed, 46 insertions(+), 6 deletions(-) diff --git a/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-0.00-11.20.sql b/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-0.00-11.20.sql index 18a155817..516088f3b 100644 --- a/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-0.00-11.20.sql +++ b/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-0.00-11.20.sql @@ -129,6 +129,7 @@ WITH (OIDS=FALSE); -- ---------------------------- -- Records of barcodes -- ---------------------------- +-- @SkipOnEmptySchemasBegin INSERT INTO sequenceanalysis.barcodes (tag_name, sequence, group_name) VALUES ('MID01', 'ACGAGTGCGT', 'GSMIDs'); INSERT INTO sequenceanalysis.barcodes (tag_name, sequence, group_name) VALUES ('MID02', 'ACGCTCGACA', 'GSMIDs'); INSERT INTO sequenceanalysis.barcodes (tag_name, sequence, group_name) VALUES ('MID03', 'AGACGCACTC', 'GSMIDs'); @@ -282,7 +283,7 @@ INSERT INTO sequenceanalysis.barcodes (tag_name, sequence, group_name) VALUES (' INSERT INTO sequenceanalysis.barcodes (tag_name, sequence, group_name) VALUES ('MID151', 'TGCTAGTCAG', 'GSMIDs'); INSERT INTO sequenceanalysis.barcodes (tag_name, sequence, group_name) VALUES ('MID152', 'TGTATCACAG', 'GSMIDs'); INSERT INTO sequenceanalysis.barcodes (tag_name, sequence, group_name) VALUES ('MID153', 'TGTGCGCGTG', 'GSMIDs'); - +-- @SkipOnEmptySchemasEnd -- ---------------------------- -- Table structure for sequenceAnalysis.ref_nt_sequences @@ -1061,6 +1062,7 @@ WITH (OIDS=FALSE) -- ---------------------------- -- Records of sequenceAnalysis.dna_adapters -- ---------------------------- +-- @SkipOnEmptySchemasBegin INSERT INTO sequenceanalysis.dna_adapters (name, group_name, sequence) VALUES ('Roche-454 FLX Amplicon A', 'Roche-454 FLX Amplicon', 'GCCTCCCTCGCGCCATCAG'), ('Roche-454 FLX Amplicon B', 'Roche-454 FLX Amplicon', 'GCCTTGCCAGCCCGCTCAG'), @@ -1070,7 +1072,7 @@ INSERT INTO sequenceanalysis.dna_adapters (name, group_name, sequence) VALUES ('Roche-454 Titanium Library A', 'Roche-454 Titanium Library', 'CCATCTCATCCCTGCGTGTCTCCGACTCAG'), ('Roche-454 Titanium Library B', 'Roche-454 Titanium Library', 'CCTATCCCCTGTGTGCCTTGGCAGTCTCAG'), ('Nextera Transposon Adapter A', 'Nextera Adapters', 'AGATGTGTATAAGAGACAG'); - +-- @SkipOnEmptySchemasEnd -- ---------------------------- @@ -1089,6 +1091,7 @@ WITH (OIDS=FALSE) -- ---------------------------- -- Records of sequenceanalysis.dna_loci -- ---------------------------- +-- @SkipOnEmptySchemasBegin INSERT INTO sequenceanalysis.dna_loci VALUES ('MHC-A', '-a'), @@ -1111,7 +1114,7 @@ VALUES ('HLA-A', 'hla-a'), ('HLA-B', 'hla-b'), ('HLA-C', 'hla-c'); - +-- @SkipOnEmptySchemasEnd @@ -1130,7 +1133,9 @@ WITH (OIDS=FALSE) -- ---------------------------- -- Records of sequenceAnalysis.ref_nt_category -- ---------------------------- +-- @SkipOnEmptySchemasBegin INSERT INTO sequenceAnalysis.ref_nt_category (category) VALUES ('Virus'), ('DNA'); +-- @SkipOnEmptySchemasEnd -- ---------------------------- -- Table structure for sequenceanalysis.dna_region @@ -1146,7 +1151,9 @@ WITH (OIDS=FALSE); -- ---------------------------- -- Records of sequenceAnalysis.dna_region -- ---------------------------- +-- @SkipOnEmptySchemasBegin INSERT INTO sequenceAnalysis.dna_region (region) VALUES ('KIR'), ('MHC'); +-- @SkipOnEmptySchemasEnd -- ---------------------------- -- Table structure for sequenceanalysis.geographic_origins @@ -1657,12 +1664,13 @@ CREATE TABLE sequenceanalysis.analysis_types ( WITH (OIDS=FALSE) ; +-- @SkipOnEmptySchemasBegin INSERT INTO sequenceanalysis.analysis_types (type) VALUES ('Virus'), ('SBT') ; - +-- @SkipOnEmptySchemasEnd --foreign keys not necessary. diff --git a/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-11.20-11.30.sql b/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-11.20-11.30.sql index 545f173ec..b4149cd65 100644 --- a/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-11.20-11.30.sql +++ b/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-11.20-11.30.sql @@ -51,6 +51,7 @@ WITH (OIDS=FALSE) -- ---------------------------- -- Records of sequenceAnalysis.sequence_platforms -- ---------------------------- +-- @SkipOnEmptySchemasBegin INSERT INTO sequenceanalysis.sequence_platforms (platform,aliases) VALUES @@ -62,11 +63,14 @@ VALUES ('ION_TORRENT', 'IONTORRENT'), ('SANGER', null) ; +-- @SkipOnEmptySchemasEnd update sequenceAnalysis.sequence_reads set chemistry = 'LS454' where chemistry = 'Pyrosequencing'; delete from sequenceAnalysis.site_module_properties where prop_name = 'contactEmail'; +-- @SkipOnEmptySchemasBegin insert into sequenceAnalysis.site_module_properties (prop_name, stringValue) VALUES ('contactEmail', 'bbimber@labkey.com'); +-- @SkipOnEmptySchemasEnd DROP TABLE IF EXISTS sequenceAnalysis.sequence_readsets; CREATE TABLE sequenceAnalysis.sequence_readsets ( diff --git a/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.10-12.20.sql b/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.10-12.20.sql index 500627ebe..526ae70a7 100644 --- a/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.10-12.20.sql +++ b/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.10-12.20.sql @@ -74,12 +74,14 @@ CREATE TABLE sequenceanalysis.quality_metrics_types ( CONSTRAINT PK_quality_metrics_types PRIMARY KEY (type) ); +-- @SkipOnEmptySchemasBegin INSERT INTO sequenceanalysis.quality_metrics_types (type) VALUES ('Total Sequences'); INSERT INTO sequenceanalysis.quality_metrics_types (type) VALUES ('Filtered Sequences'); INSERT INTO sequenceanalysis.quality_metrics_types (type) VALUES ('Avg Sequence Length'); INSERT INTO sequenceanalysis.quality_metrics_types (type) VALUES ('Min Sequence Length'); INSERT INTO sequenceanalysis.quality_metrics_types (type) VALUES ('Max Sequence Length'); INSERT INTO sequenceanalysis.quality_metrics_types (type) VALUES ('%GC'); +-- @SkipOnEmptySchemasEnd ALTER TABLE sequenceanalysis.sequence_readsets DROP COLUMN machine_run_id; ALTER TABLE sequenceanalysis.sequence_readsets ADD COLUMN instrument_run_id integer; @@ -187,7 +189,9 @@ UPDATE sequenceanalysis.ref_nt_sequences set genbank = 'SIVmac239' WHERE name = UPDATE sequenceanalysis.ref_nt_sequences set genbank = 'SIVmac251' WHERE name = 'M19499'; UPDATE sequenceanalysis.ref_nt_sequences set genbank = 'SIVsmE543' WHERE name = 'U72748.2'; +-- @SkipOnEmptySchemasBegin INSERT INTO sequenceanalysis.sequence_platforms (platform) VALUES ('MIXED'); +-- @SkipOnEmptySchemasEnd --delete duplicate epitopes accidentally entered update sequenceanalysis.ref_aa_features set comment = null where comment = ''; diff --git a/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.12-12.13.sql b/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.12-12.13.sql index cc6cc3d87..6e3b94681 100644 --- a/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.12-12.13.sql +++ b/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.12-12.13.sql @@ -38,7 +38,9 @@ UPDATE sequenceanalysis.ref_nt_sequences set genbank = 'SIVmac239' WHERE name = UPDATE sequenceanalysis.ref_nt_sequences set genbank = 'SIVmac251' WHERE name = 'M19499'; UPDATE sequenceanalysis.ref_nt_sequences set genbank = 'SIVsmE543' WHERE name = 'U72748.2'; +-- @SkipOnEmptySchemasBegin INSERT INTO sequenceanalysis.sequence_platforms (platform) VALUES ('MIXED'); +-- @SkipOnEmptySchemasEnd --delete duplicate epitopes accidentally entered update sequenceanalysis.ref_aa_features set comment = null where comment = ''; diff --git a/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.20-12.21.sql b/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.20-12.21.sql index 2a6131e7d..c58895a9c 100644 --- a/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.20-12.21.sql +++ b/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.20-12.21.sql @@ -13,6 +13,7 @@ * See the License for the specific language governing permissions and * limitations under the License. */ +-- @SkipOnEmptySchemasBegin INSERT INTO sequenceanalysis.barcodes (tag_name, sequence, group_name) VALUES ('N701', 'TCGCCTTA', 'Illumina'); INSERT INTO sequenceanalysis.barcodes (tag_name, sequence, group_name) VALUES ('N702', 'CTAGTACG', 'Illumina'); INSERT INTO sequenceanalysis.barcodes (tag_name, sequence, group_name) VALUES ('N703', 'TTCTGCCT', 'Illumina'); @@ -420,3 +421,4 @@ INSERT into sequenceanalysis.barcodes (tag_name, sequence, group_name) VALUES (' INSERT into sequenceanalysis.barcodes (tag_name, sequence, group_name) VALUES ('FLD0382', 'AAGGTATGAG', 'Fluidigm'); INSERT into sequenceanalysis.barcodes (tag_name, sequence, group_name) VALUES ('FLD0383', 'ATGGAGCACT', 'Fluidigm'); INSERT into sequenceanalysis.barcodes (tag_name, sequence, group_name) VALUES ('FLD0384', 'ACGGTGCTAG', 'Fluidigm'); +-- @SkipOnEmptySchemasEnd diff --git a/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.25-12.26.sql b/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.25-12.26.sql index 4aed07f37..b7b2934e1 100644 --- a/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.25-12.26.sql +++ b/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.25-12.26.sql @@ -17,7 +17,9 @@ ALTER TABLE sequenceanalysis.quality_metrics add column analysis_id integer; ALTER TABLE sequenceanalysis.aa_snps_by_codon add column ref_nt_positions varchar(200); +-- @SkipOnEmptySchemasBegin INSERT into sequenceanalysis.quality_metrics_types (type) VALUES ('%Reads Aligned In Pairs'); INSERT into sequenceanalysis.quality_metrics_types (type) VALUES ('Total Sequences Passed Filter'); INSERT into sequenceanalysis.quality_metrics_types (type) VALUES ('Reads Aligned'); INSERT into sequenceanalysis.quality_metrics_types (type) VALUES ('%Reads Aligned'); +-- @SkipOnEmptySchemasEnd diff --git a/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.26-12.261.sql b/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.26-12.261.sql index 2ebf4fc17..5651c4c68 100644 --- a/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.26-12.261.sql +++ b/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.26-12.261.sql @@ -2,9 +2,11 @@ -- insert into sequenceanalysis.aligners (haplotype,displayhaplotype,description,jsonconfig) values -- ('mosaik', 'Mosaik', 'Mosaik is suitable for longer reads and has the option to retain multiple hits per read. The only downside is that it can be slower. When this pipeline was first written, this aligner was preferred for sequence-based genotyping and similar applications which require retaining multiple hits. It supports paired end reads. The aligner is still good; however, Lastz also seems to perform well for SBT.', '[{"xtype":"hidden","name":"pairedEnd","value":"true"},{"name":"mosaik.output_multiple","fieldLabel":"Retain All Hits","xtype":"checkbox","renderData":{"helpPopup":"If selected, all hits above thresholds will be reported. If not, only a single hit will be retained."},"checked":true},{"name":"mosaik.max_mismatch_pct","fieldLabel":"Max Mismatch Pct","renderData":{"helpPopup":"The maximum percent of bases allowed to mismatch per alignment. Note: Ns are counted as mismatches"},"value":0.02,"minValue":0,"maxValue":1},{"name":"mosaik.hash_size","fieldLabel":"Hash Size","renderData":{"helpPopup":"The hash size used in alignment (see Mosaik documentation). A large value is preferred for sequences expected to be highly similar to the reference"},"minValue":0,"value":32},{"name":"mosaik.local_alignment","fieldLabel":"Local Alignment Radius","renderData":{"helpPopup":"This option is only used for paired end data. If a value is supplied, a local alignment will be performed around paired end reads in order to attempt to rescue mates"},"minValue":0},{"name":"mosaik.max_hash_positions","fieldLabel":"Max Hash Positions","renderData":{"helpPopup":"The maximum number of hash matches that are passed to local alignment."},"minValue":0,"value":200},{"name":"mosaik.align_threshold","fieldLabel":"Alignment Threshold","renderData":{"helpPopup":"The alignment score required for an alignment to continue to local alignment. Because the latter is slow, a higher value can improve speed."},"value":55}]'); +-- @SkipOnEmptySchemasBegin INSERT INTO sequenceanalysis.haplotype_types (type) VALUES ('MHC-IA'); INSERT INTO sequenceanalysis.haplotype_types (type) VALUES ('MHC-IB'); INSERT INTO sequenceanalysis.haplotype_types (type) VALUES ('MHC-II'); +-- @SkipOnEmptySchemasEnd ALTER table sequenceanalysis.haplotype_sequences DROP column haplotypeid; ALTER table sequenceanalysis.haplotype_sequences ADD column haplotype varchar(100); @@ -12,6 +14,7 @@ ALTER table sequenceanalysis.haplotype_sequences ADD column required boolean; UPDATE sequenceanalysis.haplotype_sequences SET required = true; TRUNCATE sequenceanalysis.haplotypes; +-- @SkipOnEmptySchemasBegin INSERT INTO sequenceanalysis.haplotypes (name,type) VALUES ('A001', 'MHC-IA'); INSERT INTO sequenceanalysis.haplotypes (name,type) VALUES ('A002a', 'MHC-IA'); INSERT INTO sequenceanalysis.haplotypes (name,type) VALUES ('A003', 'MHC-IA'); @@ -46,8 +49,10 @@ INSERT INTO sequenceanalysis.haplotypes (name,type) VALUES ('B048', 'MHC-IB'); INSERT INTO sequenceanalysis.haplotypes (name,type) VALUES ('B055', 'MHC-IB'); INSERT INTO sequenceanalysis.haplotypes (name,type) VALUES ('B069a', 'MHC-IB'); INSERT INTO sequenceanalysis.haplotypes (name,type) VALUES ('B069b', 'MHC-IB'); +-- @SkipOnEmptySchemasEnd TRUNCATE sequenceanalysis.haplotype_sequences; +-- @SkipOnEmptySchemasBegin INSERT INTO sequenceanalysis.haplotype_sequences (haplotype,lineage,required) VALUES ('A001', 'Mamu-A1*001g', TRUE); INSERT INTO sequenceanalysis.haplotype_sequences (haplotype,lineage,required) VALUES ('A001', 'Mamu-A2*05g', FALSE); INSERT INTO sequenceanalysis.haplotype_sequences (haplotype,lineage,required) VALUES ('A002a', 'Mamu-A1*002g', TRUE); @@ -210,4 +215,5 @@ INSERT INTO sequenceanalysis.haplotype_sequences (haplotype,lineage,required) VA INSERT INTO sequenceanalysis.haplotype_sequences (haplotype,lineage,required) VALUES ('B069b', 'Mamu-B*046g', FALSE); INSERT INTO sequenceanalysis.haplotype_sequences (haplotype,lineage,required) VALUES ('B069b', 'Mamu-B*060g', FALSE); INSERT INTO sequenceanalysis.haplotype_sequences (haplotype,lineage,required) VALUES ('B069b', 'Mamu-B*072g', FALSE); +-- @SkipOnEmptySchemasEnd UPDATE sequenceanalysis.haplotype_sequences SET present = true; \ No newline at end of file diff --git a/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.265-12.266.sql b/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.265-12.266.sql index 51cc6bd99..d8a4694d8 100644 --- a/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.265-12.266.sql +++ b/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.265-12.266.sql @@ -11,6 +11,7 @@ CREATE TABLE sequenceanalysis.illumina_applications ( ); DELETE FROM sequenceanalysis.illumina_applications; +-- @SkipOnEmptySchemasBegin INSERT INTO sequenceanalysis.illumina_applications (name,version,workflowname,compatiblekits,settings,workflowparams,json) VALUES ('Assembly', 1, 'Assembly', 'TruSeq LT,Nextera XT,Nextera,TruSeq HT', '{"OptionalGenome":null}', '', ''); INSERT INTO sequenceanalysis.illumina_applications (name,version,workflowname,compatiblekits,settings,workflowparams,json) VALUES ('ChIP-Seq', 1, 'GenerateFASTQ', 'TruSeq LT', '', '', ''); INSERT INTO sequenceanalysis.illumina_applications (name,version,workflowname,compatiblekits,settings,workflowparams,json) VALUES ('Clone Checking', 1, 'GenerateFASTQ', 'Nextera XT,Nextera,TruSeq HT,TruSeq LT', '', '', ''); @@ -23,6 +24,7 @@ INSERT INTO sequenceanalysis.illumina_applications (name,version,workflowname,co INSERT INTO sequenceanalysis.illumina_applications (name,version,workflowname,compatiblekits,settings,workflowparams,json) VALUES ('RNA-Seq', 1, 'GenerateFASTQ', 'TruSeq LT,TruSeq HT', '', '', ''); INSERT INTO sequenceanalysis.illumina_applications (name,version,workflowname,compatiblekits,settings,workflowparams,json) VALUES ('Small RNA', 1, 'SmallRNA', 'Small RNA', '', '[{"Label":"Genome Folder","Type":"GENOME","LabelInSampleSheet":"GenomeFolder","TrueVal":"-","FalseVal":"-","DefaultVal":"","Required":"FALSE","DisplayAsCol":"TRUE","DisplayEvenIfEmpty":"TRUE"},{"Label":"Contaminants","Type":"STRING","LabelInSampleSheet":"Contaminants","TrueVal":"-","FalseVal":"-","DefaultVal":"","Required":"TRUE","DisplayAsCol":"TRUE","DisplayEvenIfEmpty":"FALSE"},{"Label":"RNA","Type":"STRING","LabelInSampleSheet":"RNA","TrueVal":"-","FalseVal":"-","DefaultVal":"","Required":"TRUE","DisplayAsCol":"TRUE","DisplayEvenIfEmpty":"FALSE"},{"Label":"miRNA","Type":"STRING","LabelInSampleSheet":"miRNA","TrueVal":"-","FalseVal":"-","DefaultVal":"","Required":"TRUE","DisplayAsCol":"TRUE","DisplayEvenIfEmpty":"FALSE"}]', ''); INSERT INTO sequenceanalysis.illumina_applications (name,version,workflowname,compatiblekits,settings,workflowparams,json) VALUES ('TruSeq Amplicon', 1, 'Amplicon', 'TruSeq Amplicon', '{"Genome":null,"Manifest":null,"NoCustomPrimers":null}', '[{"Label":"Use Somatic Variant Caller (Recommended for Cancer Panel)","Type":"BOOL","LabelInSampleSheet":"VariantCaller","TrueVal":"Somatic","FalseVal":"NULL","DefaultVal":"FALSE","Required":"FALSE","DisplayAsCol":"FALSE"}]', ''); +-- @SkipOnEmptySchemasEnd CREATE TABLE sequenceanalysis.illumina_genome_folders ( label varchar(200), @@ -45,6 +47,7 @@ CREATE TABLE sequenceanalysis.illumina_sample_kits ( ); DELETE FROM sequenceanalysis.illumina_sample_kits; +-- @SkipOnEmptySchemasBegin INSERT INTO sequenceanalysis.illumina_sample_kits (name,json) VALUES ('Nextera', '{"Settings":[["NexteraManifest"],["Adapter","CTGTCTCTTATACACATCT"],["ManifestExtension","AmpliconManifest"]]}'); INSERT INTO sequenceanalysis.illumina_sample_kits (name,json) VALUES ('Nextera Enrichment', '{"Settings":[["Adapter","CTGTCTCTTATACACATCT"]]}'); INSERT INTO sequenceanalysis.illumina_sample_kits (name,json) VALUES ('Nextera XT', '{"Settings":[["NexteraManifest"],["Adapter","CTGTCTCTTATACACATCT"],["ManifestExtension","AmpliconManifest"]]}'); @@ -52,5 +55,6 @@ INSERT INTO sequenceanalysis.illumina_sample_kits (name,json) VALUES ('Small RNA INSERT INTO sequenceanalysis.illumina_sample_kits (name,json) VALUES ('TruSeq Amplicon', '{"Settings":[["CAT"],["IndexOnly"],["PairedEndOnly"],["ManifestExtension","txt"]]}'); INSERT INTO sequenceanalysis.illumina_sample_kits (name,json) VALUES ('TruSeq HT', '{"Settings":[["Adapter","AGATCGGAAGAGCACACGTC"]]}'); INSERT INTO sequenceanalysis.illumina_sample_kits (name,json) VALUES ('TruSeq LT', '{"Settings":[["Adapter","AGATCGGAAGAGCACACGTC"]]}'); +-- @SkipOnEmptySchemasEnd DROP TABLE sequenceanalysis.illumina_templates; \ No newline at end of file diff --git a/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.276-12.277.sql b/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.276-12.277.sql index f59095ec3..dd8aba444 100644 --- a/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.276-12.277.sql +++ b/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.276-12.277.sql @@ -6,7 +6,9 @@ CREATE TABLE sequenceanalysis.sequence_applications ( ALTER TABLE sequenceanalysis.sequence_readsets add column application varchar(200); +-- @SkipOnEmptySchemasBegin INSERT INTO sequenceanalysis.sequence_applications (application) values ('RNA-seq'); INSERT INTO sequenceanalysis.sequence_applications (application) values ('DNA Sequencing (Genome)'); INSERT INTO sequenceanalysis.sequence_applications (application) values ('DNA Sequencing (Amplicon)'); INSERT INTO sequenceanalysis.sequence_applications (application) values ('Other'); +-- @SkipOnEmptySchemasEnd diff --git a/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.292-12.293.sql b/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.292-12.293.sql index 3e2cbce4e..67a96edbf 100644 --- a/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.292-12.293.sql +++ b/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.292-12.293.sql @@ -74,5 +74,7 @@ CREATE TABLE sequenceanalysis.analysisSetMembers ( ALTER TABLE sequenceanalysis.outputfiles drop column intermediate; +-- @SkipOnEmptySchemasBegin INSERT INTO sequenceanalysis.sequence_applications (application) VALUES ('DNA Sequencing (Exome)'); -INSERT INTO sequenceanalysis.sequence_applications (application) VALUES ('DNA Sequencing (GBS)'); \ No newline at end of file +INSERT INTO sequenceanalysis.sequence_applications (application) VALUES ('DNA Sequencing (GBS)'); +-- @SkipOnEmptySchemasEnd diff --git a/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.312-12.313.sql b/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.312-12.313.sql index 7747bfae2..92d731e59 100644 --- a/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.312-12.313.sql +++ b/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.312-12.313.sql @@ -6,9 +6,11 @@ CREATE TABLE sequenceanalysis.sequence_chemistries ( CONSTRAINT PK_sequence_chemistries PRIMARY KEY (chemistry) ); +-- @SkipOnEmptySchemasBegin INSERT INTO sequenceanalysis.sequence_chemistries (chemistry) VALUES ('Illumina HiSeq3000'); INSERT INTO sequenceanalysis.sequence_chemistries (chemistry) VALUES ('Illumina MiSeq 2x250'); INSERT INTO sequenceanalysis.sequence_chemistries (chemistry) VALUES ('Illumina MiSeq 2x300'); INSERT INTO sequenceanalysis.sequence_chemistries (chemistry) VALUES ('Illumina XTen'); INSERT INTO sequenceanalysis.sequence_chemistries (chemistry) VALUES ('Illumina NextSeq MidOutput'); INSERT INTO sequenceanalysis.sequence_chemistries (chemistry) VALUES ('Illumina NextSeq HighOutput'); +-- @SkipOnEmptySchemasEnd diff --git a/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.316-12.317.sql b/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.316-12.317.sql index c82c404d6..1716b4a88 100644 --- a/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.316-12.317.sql +++ b/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.316-12.317.sql @@ -6,7 +6,9 @@ ALTER TABLE sequenceanalysis.instrument_runs DROP instrumentid; ALTER TABLE sequenceanalysis.saved_analyses ALTER COLUMN json TYPE text; +-- @SkipOnEmptySchemasBegin INSERT into sequenceanalysis.instruments (displayname, platform) VALUES ('MiSeq', 'ILLUMINA'); INSERT into sequenceanalysis.instruments (displayname, platform) VALUES ('HiSeq3000', 'ILLUMINA'); INSERT into sequenceanalysis.instruments (displayname, platform) VALUES ('HiSeq2500', 'ILLUMINA'); -INSERT into sequenceanalysis.instruments (displayname, platform) VALUES ('NovaSeq', 'ILLUMINA'); \ No newline at end of file +INSERT into sequenceanalysis.instruments (displayname, platform) VALUES ('NovaSeq', 'ILLUMINA'); +-- @SkipOnEmptySchemasEnd