Add Stanford CoreNLP tool and data manager#8005
Open
ksuderman wants to merge 7 commits into
Open
Conversation
- Stanford CoreNLP tool wrapper supporting 8 languages - Multi-language support: English, Chinese, Arabic, French, German, Spanish, Italian, Hungarian - Multiple annotators: tokenization, POS, NER, parsing, coreference, sentiment - Output formats: JSON, CoNLL, CoNLL-U, XML, text - Docker containerization with Java 21 - Data manager for automated model downloads from Maven Central - Comprehensive tests and documentation - Fixed coreference resolution with common models JAR Tool: stanford_corenlp (v4.5.10+galaxy4) Data Manager: data_manager_corenlp_models Categories: Text Manipulation, Natural Language Processing
Co-Authored-By: Claude Sonnet 4 <noreply@anthropic.com>
RZ9082
reviewed
May 21, 2026
Member
There was a problem hiding this comment.
Should this file be an input/output of a tool test?
| - Text Manipulation | ||
| - Natural Language Processing | ||
| homepage_url: https://stanfordnlp.github.io/CoreNLP/ | ||
| remote_repository_url: https://github.com/galaxyproject/tools-iuc |
Member
There was a problem hiding this comment.
Suggested change
| remote_repository_url: https://github.com/galaxyproject/tools-iuc | |
| remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/corenlp |
RZ9082
reviewed
May 21, 2026
Member
There was a problem hiding this comment.
This should be in a sub-directory called data_manager
Member
There was a problem hiding this comment.
Also goes to the sub-directory data_manager.
Is it possible to write some tests here too?
- Fix remote_repository_url to point to specific tool directory - Reorganize data manager files into data_manager/ subdirectory structure - Both changes address reviewer feedback from RZ9082
Replace problematic has_json_property_with_text assertions with more robust has_text assertions to match successful pattern used in Stanza tool. This resolves JSON property path failures in Galaxy test framework. Co-Authored-By: Claude Sonnet 4 <noreply@anthropic.com>
bgruening
reviewed
Jun 7, 2026
| ln -s "\$(dirname '${language_model.fields.models_path}')/stanford-corenlp-@TOOL_VERSION@-models.jar" ./common.jar && | ||
| #end if | ||
| #if $language_model.fields.lang_code == "en" | ||
| echo 'pos.model = edu/stanford/nlp/models/pos-tagger/english-bidirectional-distsim.tagger' > corenlp.properties && |
Member
There was a problem hiding this comment.
instead of creating the "corenlp.properties" file with echo you can use <configfile> in Galaxy tool XML, this should make things much more readable and matainable.
bgruening
reviewed
Jun 7, 2026
| <inputs> | ||
| <param name="input" type="data" format="txt" label="Text"/> | ||
| <param name="language_model" type="select" label="Language Model"> | ||
| <options from_data_table="corenlp_models"> |
Member
There was a problem hiding this comment.
you are not filtering by version here, do you? So later versions of this tool will show all models, even if they are not combat?
| <command detect_errors="exit_code"><
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
CoreNLP Tool Features
Data Manager Features
Test plan
🤖 Generated with Claude Code