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ingest: Remove use of ncov-ingest geolocation rules #303

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ingest: Remove use of ncov-ingest geolocation rules #303

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df3aca6
ingest: Remove use of ncov-ingest geolocation rules
joverlee521 Feb 14, 2025
fd9dd06
color_ordering.tsv: Add "Puerto Rico" as country
joverlee521 Feb 14, 2025
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3 changes: 0 additions & 3 deletions ingest/defaults/config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -45,10 +45,7 @@ curate:
authors_default_value: '?'
# Field name for the generated abbreviated authors
abbr_authors_field: 'authors'
# General geolocation rules to apply to geolocation fields
geolocation_rules_url: 'https://raw.githubusercontent.com/nextstrain/ncov-ingest/master/source-data/gisaid_geoLocationRules.tsv'
# Local geolocation rules that are only applicable to mpox data
# Local rules can overwrite the general geolocation rules provided above
local_geolocation_rules: 'defaults/geolocation-rules.tsv'
# User annotations file
annotations: 'defaults/annotations.tsv'
Expand Down
27 changes: 2 additions & 25 deletions ingest/rules/curate.smk
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Expand Up @@ -13,29 +13,6 @@ Parameters are expected to be defined in `config.curate`.
"""


rule fetch_general_geolocation_rules:
output:
general_geolocation_rules="data/general-geolocation-rules.tsv",
params:
geolocation_rules_url=config["curate"]["geolocation_rules_url"],
shell:
"""
curl {params.geolocation_rules_url} > {output.general_geolocation_rules}
"""


rule concat_geolocation_rules:
input:
general_geolocation_rules="data/general-geolocation-rules.tsv",
local_geolocation_rules=config["curate"]["local_geolocation_rules"],
output:
all_geolocation_rules="data/all-geolocation-rules.tsv",
shell:
"""
cat {input.general_geolocation_rules} {input.local_geolocation_rules} >> {output.all_geolocation_rules}
"""


def format_field_map(field_map: dict[str, str]) -> str:
"""
Format dict to `"key1"="value1" "key2"="value2"...` for use in shell commands.
Expand All @@ -46,7 +23,7 @@ def format_field_map(field_map: dict[str, str]) -> str:
rule curate:
input:
sequences_ndjson="data/sequences.ndjson",
all_geolocation_rules="data/all-geolocation-rules.tsv",
geolocation_rules=config["curate"]["local_geolocation_rules"],
annotations=config["curate"]["annotations"],
output:
metadata="data/all_metadata.tsv",
Expand Down Expand Up @@ -92,7 +69,7 @@ rule curate:
--default-value {params.authors_default_value} \
--abbr-authors-field {params.abbr_authors_field} \
| augur curate apply-geolocation-rules \
--geolocation-rules {input.all_geolocation_rules} \
--geolocation-rules {input.geolocation_rules} \
| augur curate apply-record-annotations \
--annotations {input.annotations} \
--id-field {params.annotations_id} \
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2 changes: 1 addition & 1 deletion phylogenetic/defaults/color_ordering.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -16857,6 +16857,7 @@ country Bahamas
country North America
country Bermuda
country USA
country Puerto Rico
country Canada

################
Expand Down Expand Up @@ -16943,4 +16944,3 @@ lineage A.2.3
lineage A.3

################