Add entity geocoding tool#8003
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- 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
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May 20, 2026
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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
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Addressed review issues - removed duplicate tools/geocode_entities/ directory and applied standard IUC fixes |
Co-Authored-By: Claude Sonnet 4 <noreply@anthropic.com>
bgruening
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May 20, 2026
| <tool id="geocode_entities" name="Geocode Named Entities" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.1"> | ||
| <macros> | ||
| <token name="@TOOL_VERSION@">1.0.0</token> | ||
| <token name="@VERSION_SUFFIX@">1</token> |
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| <token name="@VERSION_SUFFIX@">1</token> | |
| <token name="@VERSION_SUFFIX@">0</token> |
bgruening
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May 20, 2026
| <requirement type="package" version="3.12">python</requirement> | ||
| </requirements> | ||
| <command detect_errors="exit_code"><
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