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Merged
labkey-adam merged 2 commits into from
May 29, 2026
Merged

Update copyrights and licenses #1219

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2fdda26
Update copyrights and licenses
labkey-adam May 28, 2026
eee7179
Fix weird spacing
labkey-adam May 28, 2026
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15 changes: 15 additions & 0 deletions api-src/org/labkey/api/targetedms/IModification.java
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/*
* Copyright (c) 2019-2026 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.
*/
package org.labkey.api.targetedms;

public interface IModification
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15 changes: 15 additions & 0 deletions api-src/org/labkey/api/targetedms/ISampleFile.java
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/*
* 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.
* 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.
*/
package org.labkey.api.targetedms;

import java.util.Date;
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15 changes: 15 additions & 0 deletions api-src/org/labkey/api/targetedms/ISpectrumLibrary.java
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/*
* Copyright (c) 2021-2026 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.
*/
package org.labkey.api.targetedms;

public interface ISpectrumLibrary
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2 changes: 1 addition & 1 deletion api-src/org/labkey/api/targetedms/ITargetedMSRun.java
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/*
* Copyright (c) 2015-2019 LabKey Corporation
* Copyright (c) 2015-2026 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion api-src/org/labkey/api/targetedms/RepresentativeDataState.java
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/*
* Copyright (c) 2012-2019 LabKey Corporation
* Copyright (c) 2012-2026 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
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15 changes: 15 additions & 0 deletions api-src/org/labkey/api/targetedms/RunRepresentativeDataState.java
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/*
* Copyright (c) 2021-2026 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.
*/
package org.labkey.api.targetedms;

public enum RunRepresentativeDataState
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2 changes: 1 addition & 1 deletion api-src/org/labkey/api/targetedms/SkylineAnnotation.java
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/*
* Copyright (c) 2015-2019 LabKey Corporation
* Copyright (c) 2015-2026 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
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15 changes: 15 additions & 0 deletions api-src/org/labkey/api/targetedms/SkylineDocumentImportListener.java
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/*
* Copyright (c) 2019-2026 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.
*/
package org.labkey.api.targetedms;

import org.labkey.api.data.Container;
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15 changes: 15 additions & 0 deletions api-src/org/labkey/api/targetedms/TargetedMSFolderTypeListener.java
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/*
* Copyright (c) 2019-2026 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.
*/
package org.labkey.api.targetedms;

import org.labkey.api.data.Container;
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2 changes: 1 addition & 1 deletion api-src/org/labkey/api/targetedms/TargetedMSService.java
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/*
* Copyright (c) 2015-2019 LabKey Corporation
* Copyright (c) 2015-2026 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
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15 changes: 15 additions & 0 deletions api-src/org/labkey/api/targetedms/TargetedMSUrls.java
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/*
* 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.
* 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.
*/
package org.labkey.api.targetedms;

import org.labkey.api.action.UrlProvider;
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15 changes: 15 additions & 0 deletions api-src/org/labkey/api/targetedms/model/OutlierCounts.java
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/*
* 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.
* 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.
*/
package org.labkey.api.targetedms.model;

import org.jetbrains.annotations.NotNull;
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2 changes: 1 addition & 1 deletion api-src/org/labkey/api/targetedms/model/QCMetricConfiguration.java
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/*
* Copyright (c) 2016-2019 LabKey Corporation
* 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.
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15 changes: 15 additions & 0 deletions api-src/org/labkey/api/targetedms/model/QCMetricStatus.java
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/*
* Copyright (c) 2024-2026 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.
*/
package org.labkey.api.targetedms.model;

public enum QCMetricStatus
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15 changes: 15 additions & 0 deletions api-src/org/labkey/api/targetedms/model/SampleFileInfo.java
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/*
* Copyright (c) 2019-2026 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.
*/
package org.labkey.api.targetedms.model;

import org.jetbrains.annotations.NotNull;
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15 changes: 15 additions & 0 deletions api-src/org/labkey/api/targetedms/model/SampleFilePath.java
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/*
* Copyright (c) 2022-2026 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.
*/
package org.labkey.api.targetedms.model;

import org.jetbrains.annotations.Nullable;
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15 changes: 15 additions & 0 deletions build.gradle
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/*
* 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
import org.labkey.gradle.util.ExternalDependency

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2 changes: 1 addition & 1 deletion resources/queries/targetedms/CalibrationCurveMoleculePrecursors.sql
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/*
* Copyright (c) 2017-2019 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.
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2 changes: 1 addition & 1 deletion resources/queries/targetedms/CalibrationCurvePrecursors.sql
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/*
* Copyright (c) 2017-2019 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.
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5 changes: 5 additions & 0 deletions resources/queries/targetedms/DefaultGuideSet.sql
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/*
* Copyright (c) 2019-2026 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
*/

SELECT
0 AS RowId,
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5 changes: 5 additions & 0 deletions resources/queries/targetedms/GuideSetForOutliers.sql
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/*
* Copyright (c) 2019-2026 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
*/

SELECT RowId,
TrainingStart,
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2 changes: 1 addition & 1 deletion resources/queries/targetedms/InstrumentBilling.sql
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/*
* Copyright (c) 2019 LabKey Corporation
* Copyright (c) 2025-2026 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion resources/queries/targetedms/InstrumentBillingByMonth.sql
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/*
* Copyright (c) 2019 LabKey Corporation
* Copyright (c) 2025-2026 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
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5 changes: 5 additions & 0 deletions resources/queries/targetedms/InstrumentSummaryByFolder.sql
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/*
* Copyright (c) 2021-2026 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
*/
SELECT
COUNT(DISTINCT ReplicateId.RunId) AS SkylineDocumentCount,
COUNT(DISTINCT ReplicateId) AS ReplicateCount,
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5 changes: 5 additions & 0 deletions resources/queries/targetedms/PTMPercents.sql
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/*
* Copyright (c) 2020-2026 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
*/

SELECT
StructuralModId AS Modification,
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5 changes: 5 additions & 0 deletions resources/queries/targetedms/PTMPercentsGrouped.sql
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/*
* Copyright (c) 2023-2026 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
*/
SELECT
PeptideGroupId,
SiteLocation,
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5 changes: 5 additions & 0 deletions resources/queries/targetedms/PTMPercentsGroupedPrepivot.sql
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/*
* Copyright (c) 2023-2026 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
*/
--Calculate the percentage for each individual modification
WITH InitialGrouping AS (
(SELECT StructuralModId AS Modification,
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5 changes: 5 additions & 0 deletions resources/queries/targetedms/PTMPercentsPrepivot.sql
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/*
* Copyright (c) 2020-2026 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
*/
SELECT ci.ModifiedAreaProportion,
ci.PeptideId AS Id,
ci.PeptideId.PeptideModifiedSequence,
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5 changes: 5 additions & 0 deletions resources/queries/targetedms/PassportMxN.sql
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/*
* Copyright (c) 2021-2026 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
*/
SELECT * FROM (

SELECT
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5 changes: 5 additions & 0 deletions resources/queries/targetedms/Passport_TotalPrecursorArea.sql
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/*
* Copyright (c) 2020-2026 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
*/
SELECT PrecursorId.Id,
SampleFileId.ReplicateId.Name AS Replicate,
SampleFileId.AcquiredTime AS AcquiredTime,
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5 changes: 5 additions & 0 deletions resources/queries/targetedms/Passport_proteins.sql
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/*
* Copyright (c) 2020-2026 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
*/
SELECT
sequenceid,
min(sequenceid.description) AS name,
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5 changes: 5 additions & 0 deletions resources/queries/targetedms/PeptideIds.sql
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/*
* Copyright (c) 2020-2026 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
*/
SELECT
PrecursorId.PeptideId.PeptideGroupId @hidden,
ROUND(AVG(BestRetentionTime), 1) AS RetentionTime,
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5 changes: 5 additions & 0 deletions resources/queries/targetedms/QCAnnotation.js
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/*
* Copyright (c) 2023-2026 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
*/
function beforeInsert(row, errors) {
if (row.date && row.date.getTime && row.enddate && row.enddate.getTime) {
if (row.enddate.getTime() < row.date.getTime()) {
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