fixed/updated licenses

sirius-ms · Jun 20, 2024 · 306731d · 306731d
1 parent a6b23a2
commit 306731d
Show file tree

Hide file tree

Showing 184 changed files with 1,102 additions and 1,278 deletions.
diff --git a/README.md b/README.md
@@ -27,13 +27,13 @@ Main developers of SIRIUS are the [Böcker group](https://bio.informatik.uni-jen
 
 <!--begin download-->
 
-### SIRIUS+CSI:FingerID GUI and CLI - Version 6.0.1-SNAPSHOT (2024-06-14)
+### SIRIUS+CSI:FingerID GUI and CLI - Version 6.0.1-SNAPSHOT (2024-06-20)
 ##### These versions include the Java Runtime Environment, so there is no need to install Java separately! Just download, install/unpack and execute.
 - for Windows (64bit): [msi](https://github.com/sirius-ms/sirius/releases/download/v6.0.1-SNAPSHOT/sirius-6.0.1-SNAPSHOT-win64.msi) / [zip](https://github.com/sirius-ms/sirius/releases/download/v6.0.1-SNAPSHOT/sirius-6.0.1-SNAPSHOT-win64.zip)
 - for Mac (64bit): [pkg](https://github.com/sirius-ms/sirius/releases/download/v6.0.1-SNAPSHOT/sirius-6.0.1-SNAPSHOT-osx64.pkg) / [zip](https://github.com/sirius-ms/sirius/releases/download/v6.0.1-SNAPSHOT/sirius-6.0.1-SNAPSHOT-osx64.zip)
 - for Linux (64bit): [zip](https://github.com/sirius-ms/sirius/releases/download/v6.0.1-SNAPSHOT/sirius-6.0.1-SNAPSHOT-linux64.zip)
 
-### SIRIUS+CSI:FingerID Command-Line Interface only - Version 6.0.1-SNAPSHOT (2024-06-14)
+### SIRIUS+CSI:FingerID Command-Line Interface only - Version 6.0.1-SNAPSHOT (2024-06-20)
 ##### These versions include the Java Runtime Environment, so there is no need to install Java separately! Just download, install/unpack and execute.
 - for Windows (64bit): [msi](https://github.com/sirius-ms/sirius/releases/download/v6.0.1-SNAPSHOT/sirius-6.0.1-SNAPSHOT-win64-headless.msi) / [zip](https://github.com/sirius-ms/sirius/releases/download/v6.0.1-SNAPSHOT/sirius-6.0.1-SNAPSHOT-win64-headless.zip)
 - for Mac (64bit): [pkg](https://github.com/sirius-ms/sirius/releases/download/v6.0.1-SNAPSHOT/sirius-6.0.1-SNAPSHOT-osx64-headless.pkg) / [zip](https://github.com/sirius-ms/sirius/releases/download/v6.0.1-SNAPSHOT/sirius-6.0.1-SNAPSHOT-osx64-headless.zip)

diff --git a/build.gradle b/build.gradle
@@ -182,12 +182,20 @@ subprojects {
  skip()
  }
  //build only artifacts from modules that contain code
- if (new File(projectDir, "src").isDirectory()) {
- println(new File(projectDir, "src"))
+ if (new File(projectDir, "src/main").isDirectory() && !"sirius_rest_service".equalsIgnoreCase(project.name) && !"buildSrc".equalsIgnoreCase(project.name)) {
  publishing {
  publications {
  mavenJava(MavenPublication) {
  from project.components.java
+
+ pom {
+ licenses {
+ license {
+ name = 'GNU Affero General Public License, Version 3.0'
+ url = 'https://www.gnu.org/licenses/agpl-3.0.txt'
+ }
+ }
+ }
  }
  }
  }

diff --git a/buildSrc/src/main/java/SiriusPlatform.java b/buildSrc/src/main/java/SiriusPlatform.java
@@ -4,7 +4,7 @@
  * This file is part of the SIRIUS library for analyzing MS and MS/MS data
  *
  * Copyright (C) 2013-2020 Kai Dührkop, Markus Fleischauer, Marcus Ludwig, Martin A. Hoffman, Fleming Kretschmer and Sebastian Böcker,
- * Chair of Bioinformatics, Friedrich-Schilller University.
+ * Chair of Bioinformatics, Friedrich-Schiller University.
  *
  * This library is free software; you can redistribute it and/or
  * modify it under the terms of the GNU Lesser General Public

diff --git a/sirius_cli/src/main/java/de/unijena/bioinf/ms/frontend/core/Workspace.java b/sirius_cli/src/main/java/de/unijena/bioinf/ms/frontend/core/Workspace.java
@@ -3,19 +3,19 @@
  * This file is part of the SIRIUS library for analyzing MS and MS/MS data
  *
  * Copyright (C) 2013-2020 Kai Dührkop, Markus Fleischauer, Marcus Ludwig, Martin A. Hoffman, Fleming Kretschmer and Sebastian Böcker,
- * Chair of Bioinformatics, Friedrich-Schilller University.
+ * Chair of Bioinformatics, Friedrich-Schiller University.
  *
- * This library is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public
- * License as published by the Free Software Foundation; either
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Affero General Public License
+ * as published by the Free Software Foundation; either
  * version 3 of the License, or (at your option) any later version.
  *
- * This library is distributed in the hope that it will be useful,
+ * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
+ * Affero General Public License for more details.
  *
- * You should have received a copy of the GNU Lesser General Public License along with SIRIUS. If not, see <https://www.gnu.org/licenses/lgpl-3.0.txt>
+ * You should have received a copy of the GNU Affero General Public License along with SIRIUS.  If not, see <https://www.gnu.org/licenses/agpl-3.0.txt>
  */
 
 package de.unijena.bioinf.ms.frontend.core;

diff --git a/sirius_cli/src/main/java/de/unijena/bioinf/ms/frontend/subtools/decomp/AlphabetParser.java b/sirius_cli/src/main/java/de/unijena/bioinf/ms/frontend/subtools/decomp/AlphabetParser.java
@@ -16,24 +16,6 @@
  *
  * You should have received a copy of the GNU Affero General Public License along with SIRIUS. If not, see <https://www.gnu.org/licenses/agpl-3.0.txt>
  */
-
-/*
- * This file is part of the SIRIUS library for analyzing MS and MS/MS data
- *
- * Copyright (C) 2013-2015 Kai Dührkop
- *
- * This library is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public
- * License as published by the Free Software Foundation; either
- * version 2.1 of the License, or (at your option) any later version.
- *
- * This library is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with SIRIUS. If not, see <http:https://www.gnu.org/licenses/>.
- */
 package de.unijena.bioinf.ms.frontend.subtools.decomp;
 
 

diff --git a/...n/java/de/unijena/bioinf/ms/frontend/subtools/export/tables/ExportPredictionsOptions.java b/...n/java/de/unijena/bioinf/ms/frontend/subtools/export/tables/ExportPredictionsOptions.java
@@ -2,7 +2,7 @@
  * This file is part of the SIRIUS library for analyzing MS and MS/MS data
  *
  * Copyright (C) 2013-2020 Kai Dührkop, Markus Fleischauer, Marcus Ludwig, Martin A. Hoffman and Sebastian Böcker,
- * Chair of Bioinformatics, Friedrich-Schilller University.
+ * Chair of Bioinformatics, Friedrich-Schiller University.
  *
  * This library is free software; you can redistribute it and/or
  * modify it under the terms of the GNU Lesser General Public

diff --git a/...rc/main/java/de/unijena/bioinf/ms/frontend/subtools/export/tables/PredictionsOptions.java b/...rc/main/java/de/unijena/bioinf/ms/frontend/subtools/export/tables/PredictionsOptions.java
@@ -3,19 +3,19 @@
  * This file is part of the SIRIUS library for analyzing MS and MS/MS data
  *
  * Copyright (C) 2013-2020 Kai Dührkop, Markus Fleischauer, Marcus Ludwig, Martin A. Hoffman, Fleming Kretschmer and Sebastian Böcker,
- * Chair of Bioinformatics, Friedrich-Schilller University.
+ * Chair of Bioinformatics, Friedrich-Schiller University.
  *
- * This library is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public
- * License as published by the Free Software Foundation; either
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Affero General Public License
+ * as published by the Free Software Foundation; either
  * version 3 of the License, or (at your option) any later version.
  *
- * This library is distributed in the hope that it will be useful,
+ * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
+ * Affero General Public License for more details.
  *
- * You should have received a copy of the GNU Lesser General Public License along with SIRIUS. If not, see <https://www.gnu.org/licenses/lgpl-3.0.txt>
+ * You should have received a copy of the GNU Affero General Public License along with SIRIUS.  If not, see <https://www.gnu.org/licenses/agpl-3.0.txt>
  */
 
 package de.unijena.bioinf.ms.frontend.subtools.export.tables;

diff --git a/.../main/java/de/unijena/bioinf/ms/frontend/subtools/fingerprinter/FingerprinterOptions.java b/.../main/java/de/unijena/bioinf/ms/frontend/subtools/fingerprinter/FingerprinterOptions.java
@@ -3,19 +3,19 @@
  * This file is part of the SIRIUS library for analyzing MS and MS/MS data
  *
  * Copyright (C) 2013-2020 Kai Dührkop, Markus Fleischauer, Marcus Ludwig, Martin A. Hoffman, Fleming Kretschmer and Sebastian Böcker,
- * Chair of Bioinformatics, Friedrich-Schilller University.
+ * Chair of Bioinformatics, Friedrich-Schiller University.
  *
- * This library is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public
- * License as published by the Free Software Foundation; either
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Affero General Public License
+ * as published by the Free Software Foundation; either
  * version 3 of the License, or (at your option) any later version.
  *
- * This library is distributed in the hope that it will be useful,
+ * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
+ * Affero General Public License for more details.
  *
- * You should have received a copy of the GNU Lesser General Public License along with SIRIUS. If not, see <https://www.gnu.org/licenses/lgpl-3.0.txt>
+ * You should have received a copy of the GNU Affero General Public License along with SIRIUS.  If not, see <https://www.gnu.org/licenses/agpl-3.0.txt>
  */
 
 package de.unijena.bioinf.ms.frontend.subtools.fingerprinter;

diff --git a/...main/java/de/unijena/bioinf/ms/frontend/subtools/fingerprinter/FingerprinterWorkflow.java b/...main/java/de/unijena/bioinf/ms/frontend/subtools/fingerprinter/FingerprinterWorkflow.java
@@ -3,19 +3,19 @@
  * This file is part of the SIRIUS library for analyzing MS and MS/MS data
  *
  * Copyright (C) 2013-2020 Kai Dührkop, Markus Fleischauer, Marcus Ludwig, Martin A. Hoffman, Fleming Kretschmer and Sebastian Böcker,
- * Chair of Bioinformatics, Friedrich-Schilller University.
+ * Chair of Bioinformatics, Friedrich-Schiller University.
  *
- * This library is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public
- * License as published by the Free Software Foundation; either
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Affero General Public License
+ * as published by the Free Software Foundation; either
  * version 3 of the License, or (at your option) any later version.
  *
- * This library is distributed in the hope that it will be useful,
+ * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
+ * Affero General Public License for more details.
  *
- * You should have received a copy of the GNU Lesser General Public License along with SIRIUS. If not, see <https://www.gnu.org/licenses/lgpl-3.0.txt>
+ * You should have received a copy of the GNU Affero General Public License along with SIRIUS.  If not, see <https://www.gnu.org/licenses/agpl-3.0.txt>
  */
 
 package de.unijena.bioinf.ms.frontend.subtools.fingerprinter;

diff --git a/sirius_cli/src/main/java/de/unijena/bioinf/ms/frontend/subtools/login/LoginOptions.java b/sirius_cli/src/main/java/de/unijena/bioinf/ms/frontend/subtools/login/LoginOptions.java
@@ -3,19 +3,19 @@
  * This file is part of the SIRIUS library for analyzing MS and MS/MS data
  *
  * Copyright (C) 2013-2020 Kai Dührkop, Markus Fleischauer, Marcus Ludwig, Martin A. Hoffman, Fleming Kretschmer and Sebastian Böcker,
- * Chair of Bioinformatics, Friedrich-Schilller University.
+ * Chair of Bioinformatics, Friedrich-Schiller University.
  *
- * This library is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public
- * License as published by the Free Software Foundation; either
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Affero General Public License
+ * as published by the Free Software Foundation; either
  * version 3 of the License, or (at your option) any later version.
  *
- * This library is distributed in the hope that it will be useful,
+ * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
+ * Affero General Public License for more details.
  *
- * You should have received a copy of the GNU Lesser General Public License along with SIRIUS. If not, see <https://www.gnu.org/licenses/lgpl-3.0.txt>
+ * You should have received a copy of the GNU Affero General Public License along with SIRIUS.  If not, see <https://www.gnu.org/licenses/agpl-3.0.txt>
  */
 
 package de.unijena.bioinf.ms.frontend.subtools.login;

diff --git a/.../java/de/unijena/bioinf/ms/frontend/subtools/msnovelist/NumberOfMsNovelistCandidates.java b/.../java/de/unijena/bioinf/ms/frontend/subtools/msnovelist/NumberOfMsNovelistCandidates.java
@@ -3,19 +3,19 @@
  * This file is part of the SIRIUS library for analyzing MS and MS/MS data
  *
  * Copyright (C) 2013-2020 Kai Dührkop, Markus Fleischauer, Marcus Ludwig, Martin A. Hoffman, Fleming Kretschmer and Sebastian Böcker,
- * Chair of Bioinformatics, Friedrich-Schilller University.
+ * Chair of Bioinformatics, Friedrich-Schiller University.
  *
- * This library is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public
- * License as published by the Free Software Foundation; either
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Affero General Public License
+ * as published by the Free Software Foundation; either
  * version 3 of the License, or (at your option) any later version.
  *
- * This library is distributed in the hope that it will be useful,
+ * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
+ * Affero General Public License for more details.
  *
- * You should have received a copy of the GNU Lesser General Public License along with SIRIUS. If not, see <https://www.gnu.org/licenses/lgpl-3.0.txt>
+ * You should have received a copy of the GNU Affero General Public License along with SIRIUS.  If not, see <https://www.gnu.org/licenses/agpl-3.0.txt>
  */
 
 package de.unijena.bioinf.ms.frontend.subtools.msnovelist;

diff --git a/...us_cli/src/main/java/de/unijena/bioinf/ms/frontend/subtools/settings/SettingsOptions.java b/...us_cli/src/main/java/de/unijena/bioinf/ms/frontend/subtools/settings/SettingsOptions.java
@@ -3,19 +3,19 @@
  * This file is part of the SIRIUS library for analyzing MS and MS/MS data
  *
  * Copyright (C) 2013-2020 Kai Dührkop, Markus Fleischauer, Marcus Ludwig, Martin A. Hoffman, Fleming Kretschmer and Sebastian Böcker,
- * Chair of Bioinformatics, Friedrich-Schilller University.
+ * Chair of Bioinformatics, Friedrich-Schiller University.
  *
- * This library is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public
- * License as published by the Free Software Foundation; either
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Affero General Public License
+ * as published by the Free Software Foundation; either
  * version 3 of the License, or (at your option) any later version.
  *
- * This library is distributed in the hope that it will be useful,
+ * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
+ * Affero General Public License for more details.
  *
- * You should have received a copy of the GNU Lesser General Public License along with SIRIUS. If not, see <https://www.gnu.org/licenses/lgpl-3.0.txt>
+ * You should have received a copy of the GNU Affero General Public License along with SIRIUS.  If not, see <https://www.gnu.org/licenses/agpl-3.0.txt>
  */
 
 package de.unijena.bioinf.ms.frontend.subtools.settings;

diff --git a/...main/java/de/unijena/bioinf/ms/frontend/subtools/summaries/NoSqlCanopusSummaryWriter.java b/...main/java/de/unijena/bioinf/ms/frontend/subtools/summaries/NoSqlCanopusSummaryWriter.java
@@ -3,19 +3,19 @@
  * This file is part of the SIRIUS library for analyzing MS and MS/MS data
  *
  * Copyright (C) 2013-2020 Kai Dührkop, Markus Fleischauer, Marcus Ludwig, Martin A. Hoffman, Fleming Kretschmer and Sebastian Böcker,
- * Chair of Bioinformatics, Friedrich-Schilller University.
+ * Chair of Bioinformatics, Friedrich-Schiller University.
  *
- * This library is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public
- * License as published by the Free Software Foundation; either
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Affero General Public License
+ * as published by the Free Software Foundation; either
  * version 3 of the License, or (at your option) any later version.
  *
- * This library is distributed in the hope that it will be useful,
+ * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
+ * Affero General Public License for more details.
  *
- * You should have received a copy of the GNU Lesser General Public License along with SIRIUS. If not, see <https://www.gnu.org/licenses/lgpl-3.0.txt>
+ * You should have received a copy of the GNU Affero General Public License along with SIRIUS.  If not, see <https://www.gnu.org/licenses/agpl-3.0.txt>
  */
 
 package de.unijena.bioinf.ms.frontend.subtools.summaries;

diff --git a/.../main/java/de/unijena/bioinf/ms/frontend/subtools/summaries/NoSqlDeNovoSummaryWriter.java b/.../main/java/de/unijena/bioinf/ms/frontend/subtools/summaries/NoSqlDeNovoSummaryWriter.java
@@ -3,19 +3,19 @@
  * This file is part of the SIRIUS library for analyzing MS and MS/MS data
  *
  * Copyright (C) 2013-2020 Kai Dührkop, Markus Fleischauer, Marcus Ludwig, Martin A. Hoffman, Fleming Kretschmer and Sebastian Böcker,
- * Chair of Bioinformatics, Friedrich-Schilller University.
+ * Chair of Bioinformatics, Friedrich-Schiller University.
  *
- * This library is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public
- * License as published by the Free Software Foundation; either
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Affero General Public License
+ * as published by the Free Software Foundation; either
  * version 3 of the License, or (at your option) any later version.
  *
- * This library is distributed in the hope that it will be useful,
+ * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
+ * Affero General Public License for more details.
  *
- * You should have received a copy of the GNU Lesser General Public License along with SIRIUS. If not, see <https://www.gnu.org/licenses/lgpl-3.0.txt>
+ * You should have received a copy of the GNU Affero General Public License along with SIRIUS.  If not, see <https://www.gnu.org/licenses/agpl-3.0.txt>
  */
 
 package de.unijena.bioinf.ms.frontend.subtools.summaries;