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Export ambiguous date strings for tips #1760

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Export ambiguous date strings for tips #1760

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8bda439
[refine] add 'date_inferred' boolean to output
jameshadfield Feb 18, 2025
bf1c02d
[export, num_date] use inferred / raw_date attrs
jameshadfield Feb 18, 2025
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8 changes: 8 additions & 0 deletions augur/data/schema-export-v2.json
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Original file line number Diff line number Diff line change
Expand Up @@ -167,6 +167,14 @@
{"type": "number"},
{"type": "number"}
]
},
"inferred": {
"type": "boolean",
"description": "[terminal nodes only] was the 'value' inferred or known?"
},
"raw_value": {
"type": "string",
"description": "[terminal nodes only, and only if inferred=true] the known (ambiguous) date string"
}
}
},
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8 changes: 8 additions & 0 deletions augur/export_v2.py
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Original file line number Diff line number Diff line change
Expand Up @@ -859,6 +859,13 @@ def _transfer_num_date(node, raw_data):
if is_valid(raw_data.get("num_date", None)): # it's ok not to have temporal information
node["node_attrs"]["num_date"] = {"value": format_number(raw_data["num_date"])}
node["node_attrs"]["num_date"].update(attr_confidence(node["name"], raw_data, "num_date"))
# For tips, transfer information about whether the date was inferred or known
# and if it was inferred then store the underlying (ambiguous) date string
if len(node.get('children', []))==0 and 'date_inferred' in raw_data:
node["node_attrs"]["num_date"]["inferred"] = raw_data['date_inferred']
if raw_data['date_inferred'] and raw_data.get('raw_date', False):
Comment on lines +865 to +866
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Why the check for raw_data['date_inferred'] in L866 after it's already been used in L865?

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It can be false (not inferred, i.e. known) and if so then date==raw_date so we don't export the raw date string.

node["node_attrs"]["num_date"]["raw_value"] = raw_data['raw_date']


def _transfer_url_accession(node, raw_data):
for prop in ["url", "accession"]:
Expand Down Expand Up @@ -918,6 +925,7 @@ def node_data_prop_is_normal_trait(name):
'clock_length',
'mutation_length',
'date',
'date_inferred',
'muts',
'aa_muts',
'sequence',
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6 changes: 5 additions & 1 deletion augur/refine.py
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Expand Up @@ -346,7 +346,11 @@ def run(args):
)
return 1

attributes.extend(['numdate', 'clock_length', 'mutation_length', 'raw_date', 'date'])
for node in T.find_clades():
inferred = node.raw_date_constraint is None or isinstance(node.raw_date_constraint, list)
setattr(node, 'date_inferred', inferred)

attributes.extend(['numdate', 'clock_length', 'mutation_length', 'raw_date', 'date', 'date_inferred'])
if args.date_confidence:
attributes.append('num_date_confidence')
else:
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