Update source file SPDX headers and fix typos

CONTRIBUTING.md

@@ -1,7 +1,11 @@
+---
+SPDX-FileType: DOCUMENTATION
 SPDX-License-Identifier: CC-BY-4.0
+---
 
 Contributing
 ============
+
 Thank you for your interest in `tools-java`. The project is open-source software, and bug reports, suggestions, and most especially patches are welcome.
 
 All contributions must include a "Signed-off-by" line in the commit message.
@@ -10,12 +14,14 @@ This indicates that the contribution is made pursuant to the [Developer Certific
 
 Issues
 ------
+
 `tools-java` has a [project page on GitHub](https://github.com/spdx/tools-java/) where you can [create an issue](https://github.com/spdx/tools-java/issues/new) to report a bug, make a suggestion, or propose a substantial change or improvement that you might like to make. You may also wish to contact the SPDX working group technical team through its mailing list, [spdx-tech@lists.spdx.org](mailto:spdx-tech@lists.spdx.org).
 
 If you would like to work on a fix for any issue, please assign the issue to yourself prior to creating a patch.
 
 Patches
 -------
+
 The source code for `spdx-tools` is hosted on [github.com/spdx/tools-java](https://github.com/spdx/tools-java). Please review [open pull requests](https://github.com/spdx/tools-java/pulls) and [active branches](https://github.com/spdx/tools-java/branches) before committing time to a substantial revision. Work along similar lines may already be in progress.
 
 To submit a patch via GitHub, fork the repository, create a topic branch from `master` for your work, and send a pull request when ready. If you would prefer to send a patch or grant access to pull from your own Git repository, please contact the project's contributors by e-mail.
@@ -24,20 +30,19 @@ To contribute an implementation of a feature defined by a version of the SPDX sp
 
 Once implemented, submit a pull request with `spec/X.X` branch as the parent branch.
 
-
 Licensing
 ---------
 
 New **code files** should include a [short-form SPDX ID](https://spdx.org/ids) at the top, indicating the project license for code, which is Apache-2.0. This should look like the following:
 
-```
+```java
 // SPDX-License-Identifier: Apache-2.0
 ```
 
 Developer Certificate of Origin (DCO)
 -------------------------------------
 
-```
+```text
 Developer Certificate of Origin
 Version 1.1
 
@@ -76,4 +81,3 @@ By making a contribution to this project, I certify that:
     maintained indefinitely and may be redistributed consistent with
     this project or the open source license(s) involved.
 ```
-

examples/org/spdx/examples/ExistingSpdxDocumentV2Compat.java

@@ -1,6 +1,7 @@
 /**
+ * SPDX-FileCopyrightText: Copyright (c) 2021 Source Auditor Inc.
+ * SPDX-FileType: SOURCE
  * SPDX-License-Identifier: Apache-2.0
- * Copyright (c) 2021 Source Auditor Inc.
  */
 package org.spdx.examples;
 
@@ -33,7 +34,6 @@
  * This example depends on the Spdx-Java-Library and the spdx-java-jackson store libraries
  * 
  * @author Gary O'Neall
- *
  */
 public class ExistingSpdxDocumentV2Compat {
 
@@ -52,7 +52,7 @@ public static void main(String[] args) {
 		}
 
 		/*
-		 * First thing we need is a store deseralize the SPDX document into.
+		 * First thing we need is a store deserialize the SPDX document into.
 		 * We'll chose the MultiFormatStore since it supports serializing to JSON files
 		 * It takes an underlying model store as the first parameter - the inMemSpdxStore is a simple
 		 * built in store included in the Spdx-Java-Library.  The second parameter is the format
@@ -74,7 +74,7 @@ public static void main(String[] args) {
 		 * license information over to the document model store
 		 */
 		ModelCopyManager copyManager = new ModelCopyManager();
-		// Let's deseralize the document
+		// Let's deserialize the document
 		try (InputStream stream = new FileInputStream(inputFile)) {
 			modelStore.deSerialize(stream, false);
 

examples/org/spdx/examples/SimpleSpdxDocumentV2Compat.java

@@ -1,6 +1,7 @@
 /**
+ * SPDX-FileCopyrightText: Copyright (c) 2021 Source Auditor Inc.
+ * SPDX-FileType: SOURCE
  * SPDX-License-Identifier: Apache-2.0
- * Copyright (c) 2021 Source Auditor Inc.
  */
 package org.spdx.examples;
 
@@ -35,7 +36,6 @@
  * This example depends on the Spdx-Java-Library and the spdx-java-jackson store libraries
  * 
  * @author Gary O'Neall
- *
  */
 public class SimpleSpdxDocumentV2Compat {
 

src/main/java/org/spdx/tools/CONTRIBUTING.md

@@ -1,15 +1,18 @@
 Contributing
 ============
+
 Thank you for your interest in `Spdx-Java-Library`. The project is open-source software, and bug reports, suggestions, and most especially patches are welcome.
 
 Issues
 ------
+
 `Spdx-Java-Library` has a [project page on GitHub](https://github.com/spdx/Spdx-Java-Library) where you can [create an issue](https://github.com/spdx/Spdx-Java-Library/issues/new/choose) to report a bug, make a suggestion, or propose a substantial change or improvement that you might like to make. You may also wish to contact the SPDX working group technical team through its mailing list, [spdx-tech@lists.spdx.org](mailto:spdx-tech@lists.spdx.org).
 
 If you would like to work on a fix for any issue, please assign the issue to yourself prior to creating a Pull Request.
 
 Pull Requests
 -------
+
 The source code for `Spdx-Java-Library` is hosted on [github.com/spdx/Spdx-Java-Library](https://github.com/spdx/Spdx-Java-Library). Please review [open pull requests](https://github.com/spdx/Spdx-Java-Library/pulls) and [active branches](https://github.com/spdx/Spdx-Java-Library/branches) before committing time to a substantial revision. Work along similar lines may already be in progress.
 
 To submit a pull request via GitHub, fork the repository, create a topic branch from `master` for your work, and send a pull request when ready. If you would prefer to send a patch or grant access to pull from your own Git repository, please contact the project's contributors by e-mail.
@@ -20,4 +23,5 @@ Once implemented, submit a pull request with `spec/X.X` branch as the parent bra
 
 Licensing
 ---------
-However you choose to contribute, please sign-off in each of your commits that you license your contributions under the terms of [the Developer Certificate of Origin](https://developercertificate.org/). Git has utilities for signing off on commits: `git commit -s` signs a current commit, and `git rebase --signoff <revision-range>` retroactively signs a range of past commits.
+
+However you choose to contribute, please sign-off in each of your commits that you license your contributions under the terms of [the Developer Certificate of Origin](https://developercertificate.org/). Git has utilities for signing off on commits: `git commit -s` signs a current commit, and `git rebase --signoff <revision-range>` retroactively signs a range of past commits.

src/main/java/org/spdx/tools/CompareSpdxDocs.java

@@ -1,20 +1,22 @@
 /**
- * Copyright (c) 2013 Source Auditor Inc.
- * Copyright (c) 2013 Black Duck Software Inc.
+ * SPDX-FileCopyrightText: Copyright (c) 2013 Source Auditor Inc.
+ * SPDX-FileCopyrightText: Copyright (c) 2013 Black Duck Software Inc.
+ * SPDX-FileType: SOURCE
+ * SPDX-License-Identifier: Apache-2.0
  *
  *   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
+ *       https://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.spdx.tools;
 
 import java.io.File;
@@ -44,7 +46,6 @@
  * Document files can be either in RDF/XML  or tag/value format
  *
  * @author Gary O'Neall
- *
  */
 public class CompareSpdxDocs {
 	static final int MIN_ARGS = 2;
@@ -77,6 +78,7 @@ public static void main(String[] args) {
 	}
 
 	/**
+	 * Invoke SPDX document processing functions from the online tool
 	 *
 	 * @param args args[0] is the output Excel file name, all other args are SPDX document file names
 	 * @throws OnlineToolException Exception caught by JPype and displayed to the user

src/main/java/org/spdx/tools/GenerateVerificationCode.java

@@ -1,19 +1,21 @@
 /**
- * Copyright (c) 2011 Source Auditor Inc.
+ * SPDX-FileCopyrightText: Copyright (c) 2011 Source Auditor Inc.
+ * SPDX-FileType: SOURCE
+ * SPDX-License-Identifier: Apache-2.0
  *
  *   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
+ *       https://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.spdx.tools;
 
 import java.io.File;
@@ -36,7 +38,6 @@
 /**
  * Generates a verification code for a specific directory
  * @author Gary O'Neall
- *
  */
 public class GenerateVerificationCode {
 

src/main/java/org/spdx/tools/InvalidFileNameException.java

@@ -1,26 +1,26 @@
 /**
- * Copyright (c) 2020 Source Auditor Inc.
- *
+ * SPDX-FileCopyrightText: Copyright (c) 2020 Source Auditor Inc.
+ * SPDX-FileType: SOURCE
  * SPDX-License-Identifier: Apache-2.0
- * 
+ *
  *   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
+ *       https://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.spdx.tools;
 
 /**
- * Illegal paramater fro a file name
+ * Illegal parameter fro a file name
  * @author Gary O'Neall
- *
  */
 public class InvalidFileNameException extends Exception {
 

src/main/java/org/spdx/tools/Main.java

@@ -1,21 +1,20 @@
 /**
- * Copyright (c) 2020 Source Auditor Inc.
- *
+ * SPDX-FileCopyrightText: Copyright (c) 2020 Source Auditor Inc.
+ * SPDX-FileType: SOURCE
  * SPDX-License-Identifier: Apache-2.0
- * 
+ *
  *   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
+ *       https://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.
  *
- * SPDX-License-Identifier: Apache-2.0
  */
 package org.spdx.tools;
 
@@ -26,7 +25,6 @@
  * Dispatch individual tools
  * 
  * @author Gary O'Neall
- *
  */
 public class Main {
 

src/main/java/org/spdx/tools/MatchingStandardLicenses.java

@@ -1,19 +1,21 @@
 /**
- * Copyright (c) 2014 Source Auditor Inc.
+ * SPDX-FileCopyrightText: Copyright (c) 2014 Source Auditor Inc.
+ * SPDX-FileType: SOURCE
+ * SPDX-License-Identifier: Apache-2.0
  *
  *   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
+ *       https://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.spdx.tools;
 
 import java.io.File;
@@ -30,7 +32,6 @@
  * license ID's that are equivalent using the SPDX Legal team's license matching
  * guidelines (http://spdx.org/spdx-license-list/matching-guidelines)
  * @author Gary O'Neall
- *
  */
 public class MatchingStandardLicenses {
 

src/main/java/org/spdx/tools/OnlineToolException.java

@@ -1,59 +1,59 @@
 /**
- * Copyright (c) 2017 Source Auditor Inc.
+ * SPDX-FileCopyrightText: Copyright (c) 2017 Source Auditor Inc.
+ * SPDX-FileType: SOURCE
+ * SPDX-License-Identifier: Apache-2.0
  *
  *   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
+ *       https://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.spdx.tools;
 
 /**
  * Default Exception thrown to the Online Tool
  *
  * @author Rohit Lodha
- *
  */
-
 public class OnlineToolException extends Exception {
 
 	/**
-	 * 
+	 * Serial version UID
 	 */
 	private static final long serialVersionUID = 1L;
 
 	/**
-	 *
+	 * Default constructor for OnlineToolException.
 	 */
 	public OnlineToolException() {
 	}
 
 	/**
-	 *
+	 * Constructs an OnlineToolException with the specified message.
 	 * @param arg0
 	 */
 	public OnlineToolException(String arg0) {
 		super(arg0);
 	}
 
 	/**
-	 *
+	 * Constructs an OnlineToolException with the specified throwable.
 	 * @param arg0
 	 */
 	public OnlineToolException(Throwable arg0) {
 		super(arg0);
 	}
 
 	/**
-	 *
+	 * Constructs an OnlineToolException with the specified message and throwable.
 	 * @param arg0
 	 * @param arg1
 	 */
@@ -62,7 +62,7 @@ public OnlineToolException(String arg0, Throwable arg1) {
 	}
 
 	/**
-	 *
+	 * Constructs an OnlineToolException with the specified message, throwable, and booleans.
 	 * @param arg0
 	 * @param arg1
 	 * @param arg2