diff --git a/GeneticsCore/build.gradle b/GeneticsCore/build.gradle index 6cbd693fe..fdaada144 100644 --- a/GeneticsCore/build.gradle +++ b/GeneticsCore/build.gradle @@ -1,3 +1,18 @@ +/* + * Copyright (c) 2016-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ import org.labkey.gradle.util.BuildUtils; plugins { diff --git a/GeneticsCore/resources/queries/assay.GenotypeAssay.Genotype/Data.js b/GeneticsCore/resources/queries/assay.GenotypeAssay.Genotype/Data.js index 3a5229c82..be3f170f7 100644 --- a/GeneticsCore/resources/queries/assay.GenotypeAssay.Genotype/Data.js +++ b/GeneticsCore/resources/queries/assay.GenotypeAssay.Genotype/Data.js @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ var LABKEY = require("labkey"); var triggerHelper = new org.labkey.GeneticsCore.GeneticsCoreTriggerHelper(LABKEY.Security.currentUser.id, LABKEY.Security.currentContainer.id, this.schemaName, 'Data'); diff --git a/GeneticsCore/resources/queries/assay.SSP_assay.SSP/Data.js b/GeneticsCore/resources/queries/assay.SSP_assay.SSP/Data.js index 3a5229c82..be3f170f7 100644 --- a/GeneticsCore/resources/queries/assay.SSP_assay.SSP/Data.js +++ b/GeneticsCore/resources/queries/assay.SSP_assay.SSP/Data.js @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ var LABKEY = require("labkey"); var triggerHelper = new org.labkey.GeneticsCore.GeneticsCoreTriggerHelper(LABKEY.Security.currentUser.id, LABKEY.Security.currentContainer.id, this.schemaName, 'Data'); diff --git a/GeneticsCore/resources/queries/geneticscore/discordantCachedResults.sql b/GeneticsCore/resources/queries/geneticscore/discordantCachedResults.sql index 4df729de7..c26159574 100644 --- a/GeneticsCore/resources/queries/geneticscore/discordantCachedResults.sql +++ b/GeneticsCore/resources/queries/geneticscore/discordantCachedResults.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ SELECT COALESCE(t1.subjectId, t2.marker) as subjectId, COALESCE(t1.marker, t2.marker) as marker, diff --git a/GeneticsCore/resources/queries/geneticscore/discordantSubjectIds.sql b/GeneticsCore/resources/queries/geneticscore/discordantSubjectIds.sql index 9eb7f9322..64607fd66 100644 --- a/GeneticsCore/resources/queries/geneticscore/discordantSubjectIds.sql +++ b/GeneticsCore/resources/queries/geneticscore/discordantSubjectIds.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ SELECT a.rowId, a.subjectId, diff --git a/GeneticsCore/resources/queries/geneticscore/discordantSubjectIdsGrouped.sql b/GeneticsCore/resources/queries/geneticscore/discordantSubjectIdsGrouped.sql index a075be242..cb43f020c 100644 --- a/GeneticsCore/resources/queries/geneticscore/discordantSubjectIdsGrouped.sql +++ b/GeneticsCore/resources/queries/geneticscore/discordantSubjectIdsGrouped.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ SELECT a.subjectId, a.readsetSubjectId, diff --git a/GeneticsCore/resources/queries/geneticscore/mhc_data.js b/GeneticsCore/resources/queries/geneticscore/mhc_data.js index d5201c205..8edca6c6c 100644 --- a/GeneticsCore/resources/queries/geneticscore/mhc_data.js +++ b/GeneticsCore/resources/queries/geneticscore/mhc_data.js @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ var LABKEY = require("labkey"); function beforeInsert(row) { diff --git a/GeneticsCore/resources/queries/geneticscore/mhc_data_source.sql b/GeneticsCore/resources/queries/geneticscore/mhc_data_source.sql index 632c8a8db..d66017d3f 100644 --- a/GeneticsCore/resources/queries/geneticscore/mhc_data_source.sql +++ b/GeneticsCore/resources/queries/geneticscore/mhc_data_source.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ -- This is the source query for aggregating MHC data into geneticscore.mhc_data SELECT diff --git a/GeneticsCore/resources/queries/geneticscore/mhc_delete_source.sql b/GeneticsCore/resources/queries/geneticscore/mhc_delete_source.sql index 7c7c1bd1f..8c7e2342b 100644 --- a/GeneticsCore/resources/queries/geneticscore/mhc_delete_source.sql +++ b/GeneticsCore/resources/queries/geneticscore/mhc_delete_source.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ SELECT q.RowPk as objectid, q.created, diff --git a/GeneticsCore/resources/queries/study/dnaFlagSummary.sql b/GeneticsCore/resources/queries/study/dnaFlagSummary.sql index 74525845c..f91d7709b 100644 --- a/GeneticsCore/resources/queries/study/dnaFlagSummary.sql +++ b/GeneticsCore/resources/queries/study/dnaFlagSummary.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2013-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ -- NOTE: any changes to the logic the this query should also modify processingGeneticsBloodDraws.sql in ONPRC_Reports SELECT t.Id, diff --git a/GeneticsCore/resources/queries/study/mhcFlagSummary.sql b/GeneticsCore/resources/queries/study/mhcFlagSummary.sql index 017e9d223..defbef728 100644 --- a/GeneticsCore/resources/queries/study/mhcFlagSummary.sql +++ b/GeneticsCore/resources/queries/study/mhcFlagSummary.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2013-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ -- NOTE: any changes to the logic the this query should also modify processingGeneticsBloodDraws.sql in ONPRC_Reports SELECT d.Id, diff --git a/GeneticsCore/resources/queries/study/parentageFlagSummary.sql b/GeneticsCore/resources/queries/study/parentageFlagSummary.sql index 7346b9942..ace88fee1 100644 --- a/GeneticsCore/resources/queries/study/parentageFlagSummary.sql +++ b/GeneticsCore/resources/queries/study/parentageFlagSummary.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2013-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ -- NOTE: any changes to the logic the this query should also modify processingGeneticsBloodDraws.sql in ONPRC_Reports SELECT d.Id, diff --git a/GeneticsCore/resources/schemas/dbscripts/postgresql/geneticscore-0.03-17.10.sql b/GeneticsCore/resources/schemas/dbscripts/postgresql/geneticscore-0.03-17.10.sql index c4ece5d9e..d62dd8daf 100644 --- a/GeneticsCore/resources/schemas/dbscripts/postgresql/geneticscore-0.03-17.10.sql +++ b/GeneticsCore/resources/schemas/dbscripts/postgresql/geneticscore-0.03-17.10.sql @@ -1,5 +1,5 @@ /* - * Copyright (c) 2011 LabKey Corporation + * Copyright (c) 2017-2026 LabKey Corporation * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/GeneticsCore/resources/schemas/dbscripts/postgresql/geneticscore-17.10-17.11.sql b/GeneticsCore/resources/schemas/dbscripts/postgresql/geneticscore-17.10-17.11.sql index f3a6a3455..03a3df72c 100644 --- a/GeneticsCore/resources/schemas/dbscripts/postgresql/geneticscore-17.10-17.11.sql +++ b/GeneticsCore/resources/schemas/dbscripts/postgresql/geneticscore-17.10-17.11.sql @@ -1,5 +1,5 @@ /* - * Copyright (c) 2011 LabKey Corporation + * Copyright (c) 2020-2026 LabKey Corporation * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/GeneticsCore/resources/schemas/dbscripts/postgresql/geneticscore-17.11-17.12.sql b/GeneticsCore/resources/schemas/dbscripts/postgresql/geneticscore-17.11-17.12.sql index 11ceff7b2..b170f2def 100644 --- a/GeneticsCore/resources/schemas/dbscripts/postgresql/geneticscore-17.11-17.12.sql +++ b/GeneticsCore/resources/schemas/dbscripts/postgresql/geneticscore-17.11-17.12.sql @@ -1,2 +1,7 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ ALTER TABLE geneticscore.mhc_data ADD objectid ENTITYID; ALTER TABLE geneticscore.mhc_data ADD totalTests int; \ No newline at end of file diff --git a/GeneticsCore/resources/schemas/dbscripts/postgresql/geneticscore-17.12-17.13.sql b/GeneticsCore/resources/schemas/dbscripts/postgresql/geneticscore-17.12-17.13.sql index a195b2897..1f4fd94dd 100644 --- a/GeneticsCore/resources/schemas/dbscripts/postgresql/geneticscore-17.12-17.13.sql +++ b/GeneticsCore/resources/schemas/dbscripts/postgresql/geneticscore-17.12-17.13.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ ALTER TABLE geneticscore.mhc_data DROP CONSTRAINT PK_mhc_data; ALTER TABLE geneticscore.mhc_data ALTER COLUMN objectid SET NOT NULL; ALTER TABLE geneticscore.mhc_data ADD CONSTRAINT PK_mhc_data PRIMARY KEY (objectid); \ No newline at end of file diff --git a/GeneticsCore/resources/schemas/dbscripts/postgresql/geneticscore-17.13-17.14.sql b/GeneticsCore/resources/schemas/dbscripts/postgresql/geneticscore-17.13-17.14.sql index f4c56c05f..afcbafbb2 100644 --- a/GeneticsCore/resources/schemas/dbscripts/postgresql/geneticscore-17.13-17.14.sql +++ b/GeneticsCore/resources/schemas/dbscripts/postgresql/geneticscore-17.13-17.14.sql @@ -1 +1,6 @@ +/* + * Copyright (c) 2023-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ ALTER TABLE geneticscore.mhc_data ALTER COLUMN marker TYPE varchar(1000); diff --git a/GeneticsCore/resources/schemas/dbscripts/sqlserver/geneticscore-0.03-17.10.sql b/GeneticsCore/resources/schemas/dbscripts/sqlserver/geneticscore-0.03-17.10.sql index a91e64d5e..7c050b655 100644 --- a/GeneticsCore/resources/schemas/dbscripts/sqlserver/geneticscore-0.03-17.10.sql +++ b/GeneticsCore/resources/schemas/dbscripts/sqlserver/geneticscore-0.03-17.10.sql @@ -1,5 +1,5 @@ /* - * Copyright (c) 2011 LabKey Corporation + * Copyright (c) 2017-2026 LabKey Corporation * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/GeneticsCore/resources/schemas/dbscripts/sqlserver/geneticscore-17.10-17.11.sql b/GeneticsCore/resources/schemas/dbscripts/sqlserver/geneticscore-17.10-17.11.sql index 1dd7283be..7df125ad3 100644 --- a/GeneticsCore/resources/schemas/dbscripts/sqlserver/geneticscore-17.10-17.11.sql +++ b/GeneticsCore/resources/schemas/dbscripts/sqlserver/geneticscore-17.10-17.11.sql @@ -1,5 +1,5 @@ /* - * Copyright (c) 2011 LabKey Corporation + * Copyright (c) 2020-2026 LabKey Corporation * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/GeneticsCore/resources/schemas/dbscripts/sqlserver/geneticscore-17.11-17.12.sql b/GeneticsCore/resources/schemas/dbscripts/sqlserver/geneticscore-17.11-17.12.sql index 11ceff7b2..b170f2def 100644 --- a/GeneticsCore/resources/schemas/dbscripts/sqlserver/geneticscore-17.11-17.12.sql +++ b/GeneticsCore/resources/schemas/dbscripts/sqlserver/geneticscore-17.11-17.12.sql @@ -1,2 +1,7 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ ALTER TABLE geneticscore.mhc_data ADD objectid ENTITYID; ALTER TABLE geneticscore.mhc_data ADD totalTests int; \ No newline at end of file diff --git a/GeneticsCore/resources/schemas/dbscripts/sqlserver/geneticscore-17.12-17.13.sql b/GeneticsCore/resources/schemas/dbscripts/sqlserver/geneticscore-17.12-17.13.sql index 1c982801c..79109313e 100644 --- a/GeneticsCore/resources/schemas/dbscripts/sqlserver/geneticscore-17.12-17.13.sql +++ b/GeneticsCore/resources/schemas/dbscripts/sqlserver/geneticscore-17.12-17.13.sql @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ ALTER TABLE geneticscore.mhc_data DROP CONSTRAINT PK_mhc_data; ALTER TABLE geneticscore.mhc_data ALTER COLUMN objectid entityid NOT NULL; GO diff --git a/GeneticsCore/resources/schemas/dbscripts/sqlserver/geneticscore-17.13-17.14.sql b/GeneticsCore/resources/schemas/dbscripts/sqlserver/geneticscore-17.13-17.14.sql index 377056baf..839e6dbd9 100644 --- a/GeneticsCore/resources/schemas/dbscripts/sqlserver/geneticscore-17.13-17.14.sql +++ b/GeneticsCore/resources/schemas/dbscripts/sqlserver/geneticscore-17.13-17.14.sql @@ -1 +1,6 @@ +/* + * Copyright (c) 2023-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ ALTER TABLE geneticscore.mhc_data ALTER COLUMN marker nvarchar(1000); diff --git a/GeneticsCore/resources/schemas/geneticscore.xml b/GeneticsCore/resources/schemas/geneticscore.xml index 209606e59..edd583b0f 100644 --- a/GeneticsCore/resources/schemas/geneticscore.xml +++ b/GeneticsCore/resources/schemas/geneticscore.xml @@ -1,7 +1,7 @@