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ingest: Update geolocation_rules
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Add rules to switch the division and location for geolocations that
do not follow the expected GenBank geolocation format.

Following this change, the divisions are back down to 50 values which
are the expected US states.

Resolves <#134>
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joverlee521 committed Feb 20, 2025
1 parent 255a67d commit 928c23e
Showing 1 changed file with 68 additions and 0 deletions.
68 changes: 68 additions & 0 deletions ingest/defaults/geolocation_rules.tsv
Original file line number Diff line number Diff line change
Expand Up @@ -6,8 +6,76 @@ North America/USA/UNK/UNK North America/USA/?/?
North America/USA/CA/* North America/USA/California/*
North America/USA/CA/CA North America/USA/California/California
North America/USA/KS/KS North America/USA/Kansas/Kansas
North America/USA/MA/* North America/USA/Massachusetts/*
North America/USA/ME/* North America/USA/Maine/*
North America/USA/MI/MI North America/USA/Michigan/Michigan
North America/USA/NH/* North America/USA/New Hamphire/*
North America/USA/NM/NM North America/USA/New Mexico/New Mexico
North America/USA/OR/ North America/USA/Oregon/Oregon
North America/USA/RI/* North America/USA/Rhode Island/*
North America/USA/TX/TX North America/USA/Texas/Texas
North America/USA/VA/* North America/USA/Virginia/*
North America/USA/WY/WY North America/USA/Wyoming/Wyoming

# Switch location and divisions
North America/USA/Barnstable/MA North America/USA/MA/Barnstable
North America/USA/Barrington/RI North America/USA/RI/Barrington
North America/USA/Beverly/MA North America/USA/MA/Beverly
North America/USA/Boston/MA North America/USA/MA/Boston
North America/USA/Bourne/MA North America/USA/MA/Bourne
North America/USA/Brewster/MA North America/USA/MA/Brewster
North America/USA/Cambridge/MA North America/USA/MA/Cambridge
North America/USA/Centerville/MA North America/USA/MA/Centerville
North America/USA/Chatham/MA North America/USA/MA/Chatham
North America/USA/Chelsea/MA North America/USA/MA/Chelsea
North America/USA/Cohasset/MA North America/USA/MA/Cohasset
North America/USA/Cranston/RI North America/USA/RI/Cranston
North America/USA/Dennis/MA North America/USA/MA/Dennis
North America/USA/Dover/NH North America/USA/NH/Dover
North America/USA/Eastham/MA North America/USA/MA/Eastham
North America/USA/Easthampton/MA North America/USA/MA/Easthampton
North America/USA/Essex/MA North America/USA/MA/Essex
North America/USA/Falmouth/MA North America/USA/MA/Falmouth
North America/USA/Franklin/MA North America/USA/MA/Franklin
North America/USA/Hampton/MA North America/USA/MA/Hampton
North America/USA/Hampton/NH North America/USA/NH/Hampton
North America/USA/Harvard/MA North America/USA/MA/Harvard
North America/USA/Harwich/MA North America/USA/MA/Harwich
North America/USA/Hudson/MA North America/USA/MA/Hudson
North America/USA/Hull/MA North America/USA/MA/Hull
North America/USA/Ipswich/MA North America/USA/MA/Ipswich
North America/USA/Kennebunk/ME North America/USA/ME/Kennebunk
North America/USA/Kittery/ME North America/USA/ME/Kittery
North America/USA/Lynn/MA North America/USA/MA/Lynn
North America/USA/Lynnfield/MA North America/USA/MA/Lynnfield
North America/USA/Madbury/NH North America/USA/NH/Madbury
North America/USA/Manchester/MA North America/USA/MA/Manchester
North America/USA/Medford/MA North America/USA/MA/Medford
North America/USA/Nahant/MA North America/USA/MA/Nahant
North America/USA/Nantucket/MA North America/USA/MA/Nantucket
North America/USA/Newbury/MA North America/USA/MA/Newbury
North America/USA/Newburyport/MA North America/USA/MA/Newburyport
North America/USA/North Dartmouth/MA North America/USA/MA/North Dartmouth
North America/USA/North Grafton/MA North America/USA/MA/North Grafton
North America/USA/Northbridge/MA North America/USA/MA/Northbridge
North America/USA/Orleans/MA North America/USA/MA/Orleans
North America/USA/Pepperell/MA North America/USA/MA/Pepperell
North America/USA/Plum Island/MA North America/USA/MA/Plum Island
North America/USA/Plymouth/MA North America/USA/MA/Plymouth
North America/USA/Plympton/MA North America/USA/MA/Plympton
North America/USA/Provincetown/MA North America/USA/MA/Provincetown
North America/USA/Quantico/VA North America/USA/VA/Quantico
North America/USA/Quincy/MA North America/USA/MA/Quincy
North America/USA/Salisbury/MA North America/USA/MA/Salisbury
North America/USA/Scituate/MA North America/USA/MA/Scituate
North America/USA/Somerville/MA North America/USA/MA/Somerville
North America/USA/South Boston/MA North America/USA/MA/South Boston
North America/USA/South Orleans/MA North America/USA/MA/South Orleans
North America/USA/Stow/MA North America/USA/MA/Stow
North America/USA/Tiverton/RI North America/USA/RI/Tiverton
North America/USA/Unknown/VA North America/USA/VA/Unknown
North America/USA/Warwick/RI North America/USA/RI/Warwick
North America/USA/Wellfleet/MA North America/USA/MA/Wellfleet
North America/USA/Whitinsville/MA North America/USA/MA/Whitinsville
North America/USA/Winthrop/MA North America/USA/MA/Winthrop
North America/USA/Yarmouth/MA North America/USA/MA/Yarmouth

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