Add entity geocoding tool by ksuderman · Pull Request #8003 · galaxyproject/tools-iuc

ksuderman · 2026-05-20T00:56:48Z

Summary

Adds entity geocoding tool to convert NER output to GeoJSON format
Uses Nominatim geocoding service for location resolution
Outputs interactive GeoJSON datasets for map visualization in Galaxy
Works with JSON output from spaCy, Stanza, and CoreNLP NER tools
Includes entity aggregation and coordinate mapping capabilities

Test plan

Tool passes planemo lint validation
Test data included with spaCy NER JSON input
README documentation provided
.shed.yml configured for IUC submission
GeoJSON output format properly configured

🤖 Generated with Claude Code

- Extracts location entities from NLP-annotated JSON (spaCy/Stanza) - Geocodes GPE, LOC, FAC, and ORG entities using Nominatim - Dual output: GeoJSON for interactive maps + tabular summary - Galaxy OpenLayers integration for map visualization - Configurable Nominatim server (public or self-hosted) - Entity type selection and deduplication - Pure Python with urllib.request (no geopy dependency) - Rate-limited public API or unlimited self-hosted options - Comprehensive tests and documentation - Enables spatial analysis of text corpora Tool: geocode_entities (v1.0.0+galaxy1) Categories: Text Manipulation, Natural Language Processing Citation: OpenStreetMap contributors

- Geocodes named entities from NER JSON to GeoJSON format - Uses Nominatim geocoding service for location resolution - Outputs interactive GeoJSON for map visualization in Galaxy - Works with JSON output from spaCy, Stanza, and CoreNLP NER - Includes entity aggregation and coordinate mapping Co-Authored-By: Claude Sonnet 4 <noreply@anthropic.com>

RZ9082

This PR is adding two different directories with identical content! So please let's start by removing one of them.

Keep only tools/geocode/ to resolve duplicate tools issue

- Update profile from 21.05 to 24.1 - Remove macros.xml and inline version - Fix homepage_url and remote_repository_url to point to IUC repository - Add Galaxy copyright notice to Python script - Add ftype attributes and has_n_rows to test assertions

ksuderman · 2026-05-20T16:37:51Z

Addressed review issues - removed duplicate tools/geocode_entities/ directory and applied standard IUC fixes

Co-Authored-By: Claude Sonnet 4 <noreply@anthropic.com>

- Changed version suffix from 1 to 0 (bgruening) - Added requests requirement for Pulsar compatibility (bgruening) - Updated to use JSON asserts for GeoJSON output (bgruening) - Removed version history section from README (bgruening) - Updated homepage_url to point to specific tool directory (RZ9082) - Updated remote_repository_url to point to specific tool directory (RZ9082) Co-Authored-By: Claude Sonnet 4 <noreply@anthropic.com>

Co-Authored-By: Claude Sonnet 4 <noreply@anthropic.com>

- Changed required_files type from 'file' to 'literal' - Added version to requests requirement Co-Authored-By: Claude Sonnet 4 <noreply@anthropic.com>

Replaced complex JSON path with simple text assertions for GeoJSON output Co-Authored-By: Claude Sonnet 4 <noreply@anthropic.com>

…etic operators Co-Authored-By: Claude Sonnet 4 <noreply@anthropic.com>

Add comment to ensure file is properly recognized by CI linter. Co-Authored-By: Claude Sonnet 4 <noreply@anthropic.com>

- Add required 2 blank lines before function definition - Update comment to trigger clean GitHub Actions environment - Addresses both flake8 and planemo lint CI environment issues Co-Authored-By: Claude Sonnet 4 <noreply@anthropic.com>

bgruening · 2026-05-23T21:01:27Z

I filled an issue here: galaxyproject/planemo#1646

ksuderman · 2026-05-24T00:16:02Z

I filled an issue here: galaxyproject/planemo#1646

And I also opened galaxyproject/planemo#1645

bgruening

Thanks @ksuderman just two tiny things

Sch-Da · 2026-07-06T10:09:12Z

Since the two referenced Issues are now closed, is this tool good to go?

…ement, use profile macro

ksuderman · 2026-07-06T16:51:54Z

Thanks @ksuderman just two tiny things

Done.

…param help, correct input example and ORG mentions, fold README into tool help Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

mvdbeek · 2026-07-09T08:07:17Z

Deployment status: skipped

https://github.com/galaxyproject/tools-iuc/actions/runs/29002795920

bgruening · 2026-07-09T08:24:14Z

Thanks @ksuderman

mvdbeek · 2026-07-09T08:26:47Z

Deployment status: success

https://github.com/galaxyproject/tools-iuc/actions/runs/29002795920

Sch-Da · 2026-07-09T11:48:08Z

Thanks so much @ksuderman!

ksuderman and others added 2 commits May 19, 2026 19:16

RZ9082 reviewed May 20, 2026

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ksuderman added 2 commits May 20, 2026 12:30

Remove duplicate geocode_entities directory

53559cc

Keep only tools/geocode/ to resolve duplicate tools issue

Fixed macro inlining for geocoding tool

54759a9

Co-Authored-By: Claude Sonnet 4 <noreply@anthropic.com>

bgruening reviewed May 20, 2026

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Comment thread tools/geocode/geocode_entities.xml Outdated

bgruening reviewed May 20, 2026

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Comment thread tools/geocode/geocode_entities.xml

bgruening reviewed May 20, 2026

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Comment thread tools/geocode/geocode_entities.xml Outdated

bgruening reviewed May 20, 2026

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Comment thread tools/geocode/README.md Outdated

RZ9082 reviewed May 21, 2026

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Comment thread tools/geocode/.shed.yml Outdated

Comment thread tools/geocode/.shed.yml Outdated

Comment thread tools/geocode/geocode_entities.xml Outdated

ksuderman and others added 8 commits May 21, 2026 15:30

Fixed invalid test assertion: has_n_rows → has_n_lines

7d31d93

Co-Authored-By: Claude Sonnet 4 <noreply@anthropic.com>

Added required_files section for Pulsar compatibility

195204d

Co-Authored-By: Claude Sonnet 4 <noreply@anthropic.com>

Fixed planemo lint issues

c51928e

- Changed required_files type from 'file' to 'literal' - Added version to requests requirement Co-Authored-By: Claude Sonnet 4 <noreply@anthropic.com>

Fixed JSON assertion syntax in tests

75d396a

Replaced complex JSON path with simple text assertions for GeoJSON output Co-Authored-By: Claude Sonnet 4 <noreply@anthropic.com>

Fix flake8 E226 errors in geocode tool - add whitespace around arithm…

6be64a5

…etic operators Co-Authored-By: Claude Sonnet 4 <noreply@anthropic.com>

Force CI refresh for geocode tool

0f8f322

Add comment to ensure file is properly recognized by CI linter. Co-Authored-By: Claude Sonnet 4 <noreply@anthropic.com>

Fix flake8 E302 error and force fresh CI run

20f154c

- Add required 2 blank lines before function definition - Update comment to trigger clean GitHub Actions environment - Addresses both flake8 and planemo lint CI environment issues Co-Authored-By: Claude Sonnet 4 <noreply@anthropic.com>

nsoranzo reviewed May 23, 2026

View reviewed changes

Comment thread tools/geocode/geocode_entities.xml Outdated

Remove required_files for now

da2ae93

ksuderman requested a review from bgruening May 23, 2026 20:58

bgruening reviewed Jun 7, 2026

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Comment thread tools/geocode/geocode_entities.xml Outdated

bgruening reviewed Jun 7, 2026

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Comment thread tools/geocode/geocode_entities.xml

bgruening reviewed Jun 7, 2026

View reviewed changes

Add nlp_ prefix to geocode tool id/name, drop redundant python requir…

d439b84

…ement, use profile macro

ksuderman requested a review from bgruening July 6, 2026 18:11

ksuderman and others added 2 commits July 8, 2026 22:03

Fix geocode docs: replace dead requests requirement with python, add …

f18eb4c

…param help, correct input example and ORG mentions, fold README into tool help Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

add required-files

48fff87

bgruening approved these changes Jul 9, 2026

View reviewed changes

bgruening merged commit 553496c into galaxyproject:main Jul 9, 2026
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ksuderman commented May 20, 2026

Summary

Test plan

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ksuderman commented May 20, 2026

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Sch-Da commented Jul 6, 2026

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mvdbeek commented Jul 9, 2026

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