Tweak readme, update multi-module support.

THIRD-PARTY-LICENSES.txt

@@ -167,7 +167,7 @@ Lists of 402 third-party dependencies.
      (The Apache Software License, Version 2.0) Google OAuth Client Library for Java (com.google.oauth-client:google-oauth-client:1.34.0 - https://github.com/googleapis/google-oauth-java-client/google-oauth-client)
      (The Apache Software License, Version 2.0) Google OAuth2 API v2-rev151-1.25.0 (com.google.apis:google-api-services-oauth2:v2-rev151-1.25.0 - http://nexus.sonatype.org/oss-repository-hosting.html/google-api-services-oauth2)
      (The Apache Software License, Version 2.0) Graph Core (org.scala-graph:graph-core_2.13:1.13.1 - http://scala-graph.org)
-     (Apache-2.0) Gson (com.google.code.gson:gson:2.9.0 - https://github.com/google/gson/gson)
+     (Apache-2.0) Gson (com.google.code.gson:gson:2.10.1 - https://github.com/google/gson/gson)
      (The Apache Software License, Version 2.0) GSON extensions to the Google HTTP Client Library for Java. (com.google.http-client:google-http-client-gson:1.41.8 - https://github.com/googleapis/google-http-java-client/google-http-client-gson)
      (The Apache Software License, Version 2.0) Guava InternalFutureFailureAccess and InternalFutures (com.google.guava:failureaccess:1.0.1 - https://github.com/google/guava/failureaccess)
      (The Apache Software License, Version 2.0) Guava ListenableFuture only (com.google.guava:listenablefuture:9999.0-empty-to-avoid-conflict-with-guava - https://github.com/google/guava/listenablefuture)
@@ -198,9 +198,9 @@ Lists of 402 third-party dependencies.
      (The Apache Software License, Version 2.0) Jackson module: Blackbird (com.fasterxml.jackson.module:jackson-module-blackbird:2.14.2 - https://github.com/FasterXML/jackson-modules-base)
      (The Apache Software License, Version 2.0) Jackson module: Jakarta XML Bind Annotations (jakarta.xml.bind) (com.fasterxml.jackson.module:jackson-module-jakarta-xmlbind-annotations:2.14.2 - https://github.com/FasterXML/jackson-modules-base)
      (The Apache Software License, Version 2.0) Jackson module: Old JAXB Annotations (javax.xml.bind) (com.fasterxml.jackson.module:jackson-module-jaxb-annotations:2.14.2 - https://github.com/FasterXML/jackson-modules-base)
-     (The Apache Software License, Version 2.0) Jackson-annotations (com.fasterxml.jackson.core:jackson-annotations:2.14.2 - https://github.com/FasterXML/jackson)
-     (The Apache Software License, Version 2.0) Jackson-core (com.fasterxml.jackson.core:jackson-core:2.14.2 - https://github.com/FasterXML/jackson-core)
-     (The Apache Software License, Version 2.0) jackson-databind (com.fasterxml.jackson.core:jackson-databind:2.14.2 - https://github.com/FasterXML/jackson)
+     (The Apache Software License, Version 2.0) Jackson-annotations (com.fasterxml.jackson.core:jackson-annotations:2.13.4 - http://github.com/FasterXML/jackson)
+     (The Apache Software License, Version 2.0) Jackson-core (com.fasterxml.jackson.core:jackson-core:2.13.4 - https://github.com/FasterXML/jackson-core)
+     (The Apache Software License, Version 2.0) jackson-databind (com.fasterxml.jackson.core:jackson-databind:2.13.4.2 - http://github.com/FasterXML/jackson)
      (The Apache Software License, Version 2.0) Jackson-dataformat-YAML (com.fasterxml.jackson.dataformat:jackson-dataformat-yaml:2.14.2 - https://github.com/FasterXML/jackson-dataformats-text)
      (The Apache Software License, Version 2.0) Jackson-datatype-Hibernate5-jakarta (com.fasterxml.jackson.datatype:jackson-datatype-hibernate5-jakarta:2.14.2 - https://github.com/FasterXML/jackson-datatype-hibernate)
      (The Apache Software License, Version 2.0) Jackson-JAXRS: base (com.fasterxml.jackson.jaxrs:jackson-jaxrs-base:2.14.2 - https://github.com/FasterXML/jackson-jaxrs-providers/jackson-jaxrs-base)

jira_automation/README.md

@@ -1,4 +1,25 @@
-Generates a JQL query to find JIRA issues that are done, but the GitHub issue is open.
+There are three applications in here to facilitate our JIRA/GitHub interaction
+
+1. io.dockstore.jira.ResolutionChecker - used to help find issues open in GitHub that are closed in JIRA. This was to diagnose an issue where 
+Unito was seemingly mysteriously closing JIRA issues at random. It turned out to be because we hadn't properly configured
+a GitHub and JIRA user in Unito -- it's the Unito intended behavior. We currently don't need to run this, although if we have
+a configuration issue again, it could be useful in the future.
+2. io.dockstore.jira.MilestoneChecker - generates GitHub and JQL queries to find mismatches in the JIRA fix version and GitHub milestone. The JIRA fix version is
+a multi-value field; the GitHub milestone is a single-value field, so Unito doesn't sync them. We have to remember to manually
+keep them in sync; this program identifies cases we've missed.
+3. SprintStart - an barely started work in progress to automatically generate review tickets at the beginning of a sprint, which
+is currently a manual and tedious process.
+
+# Auth
+
+* ResolutionChecker and MilestoneCheck require environment variable `GITHUB_TOKEN` be set to a GitHub personal access token.
+* SprintStart requires the environment variable `JIRA_TOKEN` be set to a JIRA token.
+
+# Usage
+
+I usually run in IntelliJ with a Run Configuration
+
+1. In Run Configuration, set the main class to io.dockstore.jira.MilestoneChecker or io.dockstore.jira.ResolutionChecker
+2. Add the environment variable `GITHUB_TOKEN` to your GitHub token.
+3. The console will print out generated queries, which you then paste into your browser.
 
-Set the environment variable `GITHUB_TOKEN` to a personal access token prior to running it, or you'll likely hit the
-GitHub rate limit.

jira_automation/src/main/java/io/dockstore/jira/App.java → jira_automation/src/main/java/io/dockstore/jira/ResolutionChecker.java

@@ -3,8 +3,6 @@
 import java.io.IOException;
 import java.util.List;
 import java.util.Objects;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
 import java.util.stream.Collectors;
 import org.kohsuke.github.GHIssue;
 import org.kohsuke.github.GHRepository;
@@ -15,7 +13,7 @@
  * Does not generate a url, because the url will be too long for the browser; you need to input
  * the query in JIRA so it can be POSTed.
  */
-public class App
+public class ResolutionChecker
 {
     public static void main( String[] args ) throws IOException {
         final GHRepository repository = Utils.getDockstoreRepository();

pom.xml

@@ -125,6 +125,7 @@
         <module>toolbackup</module>
         <module>tooltester</module>
         <module>dockstore-support-reports</module>
+        <module>jira_automation</module>
     </modules>