diff options
Diffstat (limited to 'gn3/db/rdf/wiki.py')
| -rw-r--r-- | gn3/db/rdf/wiki.py | 42 |
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 |