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monarch-initiative / dipper

Data Ingestion Pipeline for Monarch
https://dipper.readthedocs.io/en/latest/
BSD 3-Clause "New" or "Revised" License
57 stars 26 forks source link

Google Code references #268

Closed TomConlin closed 8 years ago

TomConlin commented 8 years ago

References to Google Code should be removed

This one has been commented out but it would be nice to know if it can be replaced before it is deleted 

dipper/sources/ZFIN.py:  
# old     'url': 'https://phenotype-ontologies.googlecode.com/svn/trunk/src/ontology/zp/zp-mapping.txt',},

This one is in a comment but it would be nice to know if it can be replaced before it is deleted 

dipper/sources/EOM.py:    
Monarch-curated data for the HP to EOM mapping is stored at
 https://phenotype-ontologies.googlecode.com

This one is in code and cannot be right. 

dipper/sources/EOM.py:           
'url': 'https://phenotype-ontologies.googlecode.com/svn/trunk/src/ontology/hp/mappings/hp-to-eom-mapping.tsv'

guessing something like this would work instead: 

https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/master/src/mappings/hp-to-eom-mapping.tsv
TomConlin commented 8 years ago

@mbrush do you have the new names/locations for the ontologies mentioned?

TomConlin commented 8 years ago

changing the one in dipper/sources/EOM.py to https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/master/src/mappings/hp-to-eom-mapping.tsv

as it appears to work

jmcmurry commented 8 years ago

@TomConlin can this be closed then?

TomConlin commented 8 years ago

I took the reference out of the comment in EOM.py will push it eventually

no resolution on the deadwood in
dipper/sources/ZFIN.py:
# old 'url': 'https://phenotype-ontologies.googlecode.com/svn/trunk/src/ontology/zp/zp-mapping.txt',},

it has been removed, but no word on what it should have been

closing