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Adds URL to constructor #9

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Adds URL to constructor #9

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8e51053
added named parameters to constructor
ciscorucinski Feb 7, 2023
d997d98
added url constructor test
ciscorucinski Feb 7, 2023
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10 changes: 5 additions & 5 deletions src/pango_aliasor/aliasor.py
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Original file line number Diff line number Diff line change
@@ -1,14 +1,15 @@
#%%
class Aliasor:
def __init__(self, alias_file=None):
def __init__(self, *, alias_file=None, alias_url=None):
import json

if alias_file is None:
import urllib.request, json

with urllib.request.urlopen(
"https://raw.githubusercontent.com/cov-lineages/pango-designation/master/pango_designation/alias_key.json"
) as data:
if not alias_url:
alias_url = "https://raw.githubusercontent.com/cov-lineages/pango-designation/master/pango_designation/alias_key.json"

with urllib.request.urlopen(alias_url) as data:
file = json.load(data)

else:
Expand Down Expand Up @@ -84,5 +85,4 @@ def partial_compress(self, name, up_to: int = 0, accepted_aliases: set = {}):
return alias
return alias + "." + ".".join(name_split[(3 * up_to + 1) :])


# %%
8 changes: 7 additions & 1 deletion tests/test_aliasor.py
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Original file line number Diff line number Diff line change
Expand Up @@ -58,9 +58,15 @@ def test_double_alias_uncompression():
assert aliasor.uncompress('BE.1') == 'B.1.1.529.5.3.1.1'

def test_read_from_file(datadir):
aliasor = Aliasor(datadir.join('alias_key.json'))
aliasor = Aliasor(alias_file=datadir.join('alias_key.json'))
assert aliasor.compress('B.1.1.529.1') == 'BA.1'

def test_read_from_url():
url = "https://raw.githubusercontent.com/cov-lineages/pango-designation/master/pango_designation/alias_key.json"
aliasor = Aliasor(alias_url=url)
assert aliasor.compress('B.1.1.529.1') == 'BA.1'
assert aliasor.uncompress('BE.1') == 'B.1.1.529.5.3.1.1'

def test_partial_alias_up_to():
aliasor = Aliasor()
assert aliasor.partial_compress('B.1.1.529.1.2', up_to = 0) == 'B.1.1.529.1.2'
Expand Down