Improve AI topics for nextflow workflows (#488)

dockstore/dockstore#5748
https://ucsc-cgl.atlassian.net/browse/DOCK-2495
* Use main script for nextflow workflows
* Tweak prompt and record file checksum

THIRD-PARTY-LICENSES.txt

@@ -36,7 +36,7 @@ Lists of 417 third-party dependencies.
      (Apache License, Version 2.0) Apache HttpCore (org.apache.httpcomponents:httpcore:4.4.16 - http://hc.apache.org/httpcomponents-core-ga)
      (Apache License, Version 2.0) Apache HttpCore NIO (org.apache.httpcomponents:httpcore-nio:4.4.16 - http://hc.apache.org/httpcomponents-core-ga)
      (Apache License, Version 2.0) Apache Log4j API (org.apache.logging.log4j:log4j-api:2.17.1 - https://logging.apache.org/log4j/2.x/log4j-api/)
-     (The MIT License) api (com.theokanning.openai-gpt3-java:api:0.16.1 - https://github.com/theokanning/openai-java)
+     (The MIT License) api (com.theokanning.openai-gpt3-java:api:0.18.2 - https://github.com/theokanning/openai-java)
      (MIT) argparse4j (net.sourceforge.argparse4j:argparse4j:0.9.0 - https://argparse4j.github.io)
      (BSD) ASM Analysis (org.ow2.asm:asm-analysis:5.0.3 - http://asm.objectweb.org/asm-analysis/)
      (BSD) ASM Commons (org.ow2.asm:asm-commons:5.0.3 - http://asm.objectweb.org/asm-commons/)
@@ -103,7 +103,7 @@ Lists of 417 third-party dependencies.
      (Apache 2.0) circe-yaml (io.circe:circe-yaml_2.13:0.14.1 - https://github.com/circe/circe-yaml)
      (The MIT License (MIT)) ClassGraph (io.github.classgraph:classgraph:4.8.154 - https://github.com/classgraph/classgraph)
      (Apache License, Version 2.0) ClassMate (com.fasterxml:classmate:1.5.1 - https://github.com/FasterXML/java-classmate)
-     (The MIT License) client (com.theokanning.openai-gpt3-java:client:0.16.1 - https://github.com/theokanning/openai-java)
+     (The MIT License) client (com.theokanning.openai-gpt3-java:client:0.18.2 - https://github.com/theokanning/openai-java)
      (The Apache License, Version 2.0) com.helger:profiler (com.helger:profiler:1.1.1 - https://github.com/phax/profiler)
      (The Apache Software License, Version 2.0) Commons Digester (commons-digester:commons-digester:2.1 - http://commons.apache.org/digester/)
      (The Apache Software License, Version 2.0) Commons Lang (commons-lang:commons-lang:2.6 - http://commons.apache.org/lang/)
@@ -289,7 +289,7 @@ Lists of 417 third-party dependencies.
      (Revised BSD License) JSONLD Java :: Core (com.github.jsonld-java:jsonld-java:0.8.3 - http://github.com/jsonld-java/jsonld-java/jsonld-java/)
      (The MIT License) jsoup Java HTML Parser (org.jsoup:jsoup:1.10.2 - https://jsoup.org/)
      (Apache License, Version 2.0) JSR 354 (Money and Currency API) (javax.money:money-api:1.1 - https://javamoney.github.io/)
-     (MIT License) JTokkit (com.knuddels:jtokkit:0.6.1 - https://github.com/knuddelsgmbh/jtokkit)
+     (MIT License) JTokkit (com.knuddels:jtokkit:1.0.0 - https://github.com/knuddelsgmbh/jtokkit)
      (MIT License) JUL to SLF4J bridge (org.slf4j:jul-to-slf4j:2.0.9 - http://www.slf4j.org)
      (Eclipse Public License 1.0) JUnit (junit:junit:4.13.2 - http://junit.org)
      (Eclipse Public License v2.0) JUnit Jupiter (Aggregator) (org.junit.jupiter:junit-jupiter:5.10.0 - https://junit.org/junit5/)
@@ -381,7 +381,7 @@ Lists of 417 third-party dependencies.
      (MIT) scopt (com.github.scopt:scopt_2.13:4.1.0 - https://github.com/scopt/scopt)
      (MIT) Sentry SDK (io.sentry:sentry:5.7.4 - https://github.com/getsentry/sentry-java)
      (The Apache Software License, Version 2.0) server (org.elasticsearch:elasticsearch:7.10.2 - https://github.com/elastic/elasticsearch)
-     (The MIT License) service (com.theokanning.openai-gpt3-java:service:0.16.1 - https://github.com/theokanning/openai-java)
+     (The MIT License) service (com.theokanning.openai-gpt3-java:service:0.18.2 - https://github.com/theokanning/openai-java)
      (EPL 2.0) (GPL2 w/ CPE) ServiceLocator Default Implementation (org.glassfish.hk2:hk2-locator:3.0.4 - https://github.com/eclipse-ee4j/glassfish-hk2/hk2-locator)
      (MIT License) SLF4J API Module (org.slf4j:slf4j-api:2.0.9 - http://www.slf4j.org)
      (Apache License, Version 2.0) SnakeYAML (org.yaml:snakeyaml:2.0 - https://bitbucket.org/snakeyaml/snakeyaml)

topicgenerator/pom.xml

@@ -20,6 +20,7 @@
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
+        <openai-java.version>0.18.2</openai-java.version>
     </properties>
 
     <organization>
@@ -83,6 +84,11 @@
             <artifactId>openapi-java-client</artifactId>
             <version>${dockstore-core.version}</version>
         </dependency>
+        <dependency>
+            <groupId>io.dockstore</groupId>
+            <artifactId>dockstore-common</artifactId>
+            <version>${dockstore-core.version}</version>
+        </dependency>
         <dependency>
             <groupId>org.glassfish.jersey.inject</groupId>
             <artifactId>jersey-hk2</artifactId>
@@ -106,19 +112,19 @@
         <dependency>
             <groupId>com.knuddels</groupId>
             <artifactId>jtokkit</artifactId>
-            <version>0.6.1</version>
+            <version>1.0.0</version>
         </dependency>
         <dependency>
             <!-- https://github.com/TheoKanning/openai-java -->
             <groupId>com.theokanning.openai-gpt3-java</groupId>
             <artifactId>service</artifactId>
-            <version>0.16.1</version>
+            <version>${openai-java.version}</version>
         </dependency>
         <dependency>
             <!-- https://github.com/TheoKanning/openai-java -->
             <groupId>com.theokanning.openai-gpt3-java</groupId>
             <artifactId>api</artifactId>
-            <version>0.16.1</version>
+            <version>${openai-java.version}</version>
             <exclusions>
                 <exclusion>
                     <groupId>com.knuddels</groupId>