Add upload-topics command to topicgenerator #489
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## develop #489 +/- ##
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- Coverage 56.02% 54.44% -1.59%
- Complexity 297 307 +10
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Files 33 37 +4
Lines 2001 2173 +172
Branches 163 177 +14
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+ Hits 1121 1183 +62
- Misses 796 903 +107
- Partials 84 87 +3
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pom.xml
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| <github.url>scm:git:git@github.com:dockstore/dockstore-support.git</github.url> | |||
| <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding> | |||
| <dockstore-core.version>1.16.0-alpha.2</dockstore-core.version> | |||
| <dockstore-core.version>1.16.0-SNAPSHOT</dockstore-core.version> | |||
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Will update to tag when webservice PR is merged
| # networks: | ||
| # - elastic | ||
| postgres_db: | ||
| image: postgres:16.1 |
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We're going to have a bunch of these scattered around, maybe a follow-up ticket to create a shared resource in https://github.com/dockstore/.github
This one in particular looks a lot like https://github.com/dockstore/dockstore-cli/blob/develop/docker-compose.yml with the right postgres version
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One idea, could download during build via https://github.com/maven-download-plugin/maven-download-plugin
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topicgenerator/src/test/java/io/dockstore/topicgenerator/client/cli/package-info.java
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| try (CSVPrinter csvPrinter = new CSVPrinter(new FileWriter(outputFileName, StandardCharsets.UTF_8), CSVFormat.DEFAULT.builder().setHeader(OutputCsvHeaders.class).build())) { | ||
| for (CSVRecord entry: entriesCsvRecords) { | ||
| final String trsId = entry.get(InputCsvHeaders.trsId); | ||
| final String versionId = entry.get(InputCsvHeaders.version); | ||
| final String trsId = entry.get(GenerateTopicsCommand.InputCsvHeaders.trsId); |
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The lowercase enum value names confuse me every time. No need to change, but I needed to vent that. :) It would be great if the apache csv library calculated the column name as the toString() of the enum value, so the enum names themselves could be capitalized correctly (with a little extra work/code). Or maybe it does? If it did, you could do something like:
public enum CsvColumns {
ID("id"),
SOME_VALUE("someValue");
private final String value;
public CsvColumns(String value) {
this.value = value;
}
public String toString() {
return value;
}
}
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Description
Related PR: dockstore/dockstore#5847
This PR adds an
upload-topicscommand to the topic generator so it can upload the topics generated by thegenerate-topicscommand to Dockstore.Review Instructions
Run the
upload-topicscommand against QA to upload the generated topics in this file https://github.com/dockstore/dockstore-support/blob/develop/topicgenerator/results/generated-topics_GPT_3_5_TURBO_16K_20231113T135602Z.csv. Steps below:Can create a new directory called
topic-generatorlocally to do this testingCreate a
topic-generator.configfile. See the topicgenerator README for instructions on how to get set up. Note that you do not need theopenai-api-keyto run theupload-topicscommand.Download the topicgenerator 1.16.0-alpha.1 JAR using
Download the generated topics file
Upload the topics
Go to the search page on QA and select the Workflows tab.
Verify that the first few workflows have topics with an AI bubble.
View this tool (should have permission to view it if you're a part of the dockstore GitHub organization, if not, run the Discover Existing Workflows button) https://qa.dockstore.org/my-tools/github.com/dockstore/dockstore-tool-bamstats/bamstats_sort_cwl and verify that the AI generated topic shows up.
Verify that the Topic Selection is not AI because the entry has an automatic topic.
Select AI Generated as the Topic Selection.
View the tool's public page and verify that the AI topic shows up. There should be an AI bubble.
Find the tool in the search table and verify that the AI topic shows up and that there's an AI bubble.
Issue
SEAB-6007
Security
If there are any concerns that require extra attention from the security team, highlight them here.
Please make sure that you've checked the following before submitting your pull request. Thanks!
mvn clean installin the project that you have modified (until https://ucsc-cgl.atlassian.net/browse/SEAB-5300 adds multi-module support properly)