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authorMunyoki Kilyungi2024-09-10 10:34:42 +0300
committerBonfaceKilz2024-09-11 10:30:57 +0300
commit091b3d02af3ef3f1ed1c910fe3b10a9efd5c0473 (patch)
treef91023dab297dc0cfc08342fed76222019a7cee7 /gn3/db
parentbceb5ce98c14dc64ef3980caf23f975278f63d50 (diff)
downloadgenenetwork3-091b3d02af3ef3f1ed1c910fe3b10a9efd5c0473.tar.gz
Run python-black against file.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Diffstat (limited to 'gn3/db')
-rw-r--r--gn3/db/rdf/wiki.py42
1 files changed, 20 insertions, 22 deletions
diff --git a/gn3/db/rdf/wiki.py b/gn3/db/rdf/wiki.py
index f3a56da..f082096 100644
--- a/gn3/db/rdf/wiki.py
+++ b/gn3/db/rdf/wiki.py
@@ -10,8 +10,7 @@ NOTE: In the CONSTRUCT queries below, we manually sort the arrays from
<https://www.w3.org/TR/rdf-sparql-query/#modOrderBy>
"""
from string import Template
-from gn3.db.rdf import (BASE_CONTEXT, RDF_PREFIXES,
- query_frame_and_compact)
+from gn3.db.rdf import BASE_CONTEXT, RDF_PREFIXES, query_frame_and_compact
WIKI_CONTEXT = BASE_CONTEXT | {
@@ -33,9 +32,7 @@ WIKI_CONTEXT = BASE_CONTEXT | {
def __sanitize_result(result: dict):
- """Make sure `categories` and `pubmed_ids` are always arrays
-
- """
+ """Make sure `categories` and `pubmed_ids` are always arrays"""
categories = result.get("categories")
if isinstance(categories, str):
result["categories"] = [categories] if categories else []
@@ -44,8 +41,10 @@ def __sanitize_result(result: dict):
result["pubmed_ids"] = [pmids] if pmids else []
if isinstance(pmids, int):
result["pubmed_ids"] = [pmids]
- result["pubmed_ids"] = [int(pmid.split("/")[-1]) if isinstance(pmid, str) else pmid
- for pmid in result["pubmed_ids"]]
+ result["pubmed_ids"] = [
+ int(pmid.split("/")[-1]) if isinstance(pmid, str) else pmid
+ for pmid in result["pubmed_ids"]
+ ]
return result
@@ -53,7 +52,8 @@ def get_wiki_entries_by_symbol(symbol: str, sparql_uri: str) -> dict:
"""Fetch all the Wiki entries using the symbol"""
# This query uses a sub-query to fetch the latest comment by the
# version id.
- query = Template("""
+ query = Template(
+ """
$prefix
CONSTRUCT {
@@ -105,13 +105,13 @@ CONSTRUCT {
BIND (COALESCE(?species_, "") AS ?species) .
BIND (COALESCE(?category_, "") AS ?category) .
}
-""").substitute(prefix=RDF_PREFIXES, symbol=symbol,)
- results = query_frame_and_compact(
- query, WIKI_CONTEXT,
- sparql_uri
+"""
+ ).substitute(
+ prefix=RDF_PREFIXES,
+ symbol=symbol,
)
- data = [__sanitize_result(result)
- for result in results.get("data")]
+ results = query_frame_and_compact(query, WIKI_CONTEXT, sparql_uri)
+ data = [__sanitize_result(result) for result in results.get("data")]
# See note above in the doc-string
results["data"] = sorted(data, key=lambda d: d["created"])
if not data:
@@ -121,7 +121,8 @@ CONSTRUCT {
def get_comment_history(comment_id: int, sparql_uri: str) -> dict:
"""Get all the historical data for a given id"""
- query = Template("""
+ query = Template(
+ """
$prefix
CONSTRUCT {
@@ -165,13 +166,10 @@ CONSTRUCT {
BIND (COALESCE(?species_, "") AS ?species) .
BIND (COALESCE(?category_, "") AS ?category) .
}
-""").substitute(prefix=RDF_PREFIXES, comment_id=comment_id)
- results = query_frame_and_compact(
- query, WIKI_CONTEXT,
- sparql_uri
- )
- data = [__sanitize_result(result)
- for result in results.get("data")]
+"""
+ ).substitute(prefix=RDF_PREFIXES, comment_id=comment_id)
+ results = query_frame_and_compact(query, WIKI_CONTEXT, sparql_uri)
+ data = [__sanitize_result(result) for result in results.get("data")]
# See note above in the doc-string
results["data"] = sorted(data, key=lambda d: d["version"], reverse=True)
return results