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-rw-r--r--gn3/api/metadata.py2
-rw-r--r--gn3/api/metadata_api/wiki.py24
-rw-r--r--gn3/db/rdf.py124
-rw-r--r--gn3/db/rdf/__init__.py (renamed from gn3/db/constants.py)43
-rw-r--r--gn3/db/rdf/wiki.py168
-rw-r--r--gn3/db/wiki.py17
6 files changed, 242 insertions, 136 deletions
diff --git a/gn3/api/metadata.py b/gn3/api/metadata.py
index 3f28f5d..6110880 100644
--- a/gn3/api/metadata.py
+++ b/gn3/api/metadata.py
@@ -15,7 +15,7 @@ from gn3.db.datasets import (retrieve_metadata,
get_history)
from gn3.db.rdf import (query_frame_and_compact,
query_and_compact)
-from gn3.db.constants import (
+from gn3.db.rdf import (
RDF_PREFIXES, BASE_CONTEXT,
DATASET_CONTEXT,
DATASET_SEARCH_CONTEXT, PUBLICATION_CONTEXT,
diff --git a/gn3/api/metadata_api/wiki.py b/gn3/api/metadata_api/wiki.py
index a4abef6..9ea0d53 100644
--- a/gn3/api/metadata_api/wiki.py
+++ b/gn3/api/metadata_api/wiki.py
@@ -5,8 +5,9 @@ from typing import Any, Dict
from flask import Blueprint, request, jsonify, current_app, make_response
from gn3 import db_utils
from gn3.db import wiki
-from gn3.db.rdf import (query_frame_and_compact,
- get_wiki_entries_by_symbol)
+from gn3.db.rdf import query_frame_and_compact
+from gn3.db.rdf.wiki import (get_wiki_entries_by_symbol,
+ get_comment_history)
wiki_blueprint = Blueprint("wiki", __name__, url_prefix="wiki")
@@ -71,7 +72,6 @@ def edit_wiki(comment_id: int):
@wiki_blueprint.route("/<string:symbol>", methods=["GET"])
def get_wiki_entries(symbol: str):
"""Fetch wiki entries"""
- content_type = request.headers.get("Content-Type")
status_code = 200
response = get_wiki_entries_by_symbol(
symbol=symbol,
@@ -80,7 +80,7 @@ def get_wiki_entries(symbol: str):
if not data:
data = {}
status_code = 404
- if content_type == "application/ld+json":
+ if request.headers.get("Accept") == "application/ld+json":
payload = make_response(response)
payload.headers["Content-Type"] = "application/ld+json"
return payload, status_code
@@ -117,3 +117,19 @@ def get_species():
species_dict = wiki.get_species(cursor)
return jsonify(species_dict)
return jsonify(error="Error getting species, most likely due to DB error!"), 500
+
+
+@wiki_blueprint.route("/<int:comment_id>/history", methods=["GET"])
+def get_history(comment_id):
+ status_code = 200
+ response = get_comment_history(comment_id=comment_id,
+ sparql_uri=current_app.config["SPARQL_ENDPOINT"])
+ data = response.get("data")
+ if not data:
+ data = {}
+ status_code = 404
+ if request.headers.get("Accept") == "application/ld+json":
+ payload = make_response(response)
+ payload.headers["Content-Type"] = "application/ld+json"
+ return payload, status_code
+ return jsonify(data), status_code
diff --git a/gn3/db/rdf.py b/gn3/db/rdf.py
deleted file mode 100644
index 5a95683..0000000
--- a/gn3/db/rdf.py
+++ /dev/null
@@ -1,124 +0,0 @@
-"""RDF utilities
-
-This module is a collection of functions that handle SPARQL queries.
-
-"""
-import json
-from string import Template
-from SPARQLWrapper import SPARQLWrapper
-from pyld import jsonld # type: ignore
-from gn3.db.constants import (
- RDF_PREFIXES, BASE_CONTEXT
-)
-
-
-def sparql_construct_query(query: str, endpoint: str) -> dict:
- """Query virtuoso using a CONSTRUCT query and return a json-ld
- dictionary"""
- sparql = SPARQLWrapper(endpoint)
- sparql.setQuery(query)
- results = sparql.queryAndConvert()
- return json.loads(results.serialize(format="json-ld")) # type: ignore
-
-
-def query_frame_and_compact(query: str, context: dict, endpoint: str) -> dict:
- """Frame and then compact the results given a context"""
- results = sparql_construct_query(query, endpoint)
- return jsonld.compact(jsonld.frame(results, context), context)
-
-
-def query_and_compact(query: str, context: dict, endpoint: str) -> dict:
- """Compact the results given a context"""
- results = sparql_construct_query(query, endpoint)
- return jsonld.compact(results, context)
-
-
-def query_and_frame(query: str, context: dict, endpoint: str) -> dict:
- """Frame the results given a context"""
- results = sparql_construct_query(query, endpoint)
- return jsonld.frame(results, context)
-
-
-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("""
-$prefix
-
-CONSTRUCT {
- ?uid rdfs:label ?symbolName;
- gnt:reason ?reason ;
- gnt:species ?species ;
- dct:references ?pmid ;
- foaf:homepage ?weburl ;
- rdfs:comment ?comment ;
- foaf:mbox ?email ;
- gnt:initial ?usercode ;
- gnt:belongsToCategory ?category ;
- gnt:hasVersion ?versionId ;
- dct:created ?created ;
- dct:identifier ?identifier .
-} WHERE {
- ?symbolId rdfs:label ?symbolName .
- ?uid rdfs:comment ?comment ;
- gnt:symbol ?symbolId ;
- rdf:type gnc:GNWikiEntry ;
- dct:created ?createTime .
- FILTER ( LCASE(?symbolName) = LCASE('$symbol') ) .
- {
- SELECT (MAX(?vers) AS ?max) ?id_ WHERE {
- ?symbolId rdfs:label ?symbolName .
- ?uid dct:identifier ?id_ ;
- dct:hasVersion ?vers ;
- dct:identifier ?id_ ;
- gnt:symbol ?symbolId .
- FILTER ( LCASE(?symbolName) = LCASE('$symbol') ) .
- }
- }
- ?uid dct:hasVersion ?max ;
- dct:identifier ?id_ .
- OPTIONAL { ?uid gnt:reason ?reason } .
- OPTIONAL {
- ?uid gnt:belongsToSpecies ?speciesId .
- ?speciesId gnt:shortName ?species .
- } .
- OPTIONAL { ?uid dct:references ?pubmedId . } .
- OPTIONAL { ?uid foaf:homepage ?weburl . } .
- OPTIONAL { ?uid gnt:initial ?usercode . } .
- OPTIONAL { ?uid gnt:mbox ?email . } .
- OPTIONAL { ?uid gnt:belongsToCategory ?category . } .
- BIND (str(?version) AS ?versionId) .
- BIND (str(?id_) AS ?identifier) .
- BIND (str(?pubmedId) AS ?pmid) .
- BIND (str(?createTime) AS ?created) .
-}
-""").substitute(prefix=RDF_PREFIXES, symbol=symbol,)
- context = BASE_CONTEXT | {
- "foaf": "http://xmlns.com/foaf/0.1/",
- "dct": "http://purl.org/dc/terms/",
- "categories": "gnt:belongsToCategory",
- "web_url": "foaf:homepage",
- "version": "gnt:hasVersion",
- "symbol": "rdfs:label",
- "reason": "gnt:reason",
- "species": "gnt:species",
- "pubmed_id": "dct:references",
- "email": "foaf:mbox",
- "initial": "gnt:initial",
- "comment": "rdfs:comment",
- "created": "dct:created",
- "id": "dct:identifier",
- # This points to the RDF Node which is the unique identifier
- # for this triplet. It's constructed using the comment-id and
- # the comment-versionId
- "wiki_identifier": "@id",
- }
- results = query_frame_and_compact(
- query, context,
- sparql_uri
- )
- data = results.get("data")
- if not data:
- return results
- return results
diff --git a/gn3/db/constants.py b/gn3/db/rdf/__init__.py
index 45e3bfc..ffb75e5 100644
--- a/gn3/db/constants.py
+++ b/gn3/db/rdf/__init__.py
@@ -1,6 +1,15 @@
+"""RDF
+
+Constants for prefixes and contexts; and wrapper functions around
+creating contexts to be used by jsonld when framing and/or compacting.
+
"""
-This module contains some constants used in other modules.
-"""
+import json
+
+from SPARQLWrapper import SPARQLWrapper
+from pyld import jsonld # type: ignore
+
+
PREFIXES = {
"dcat": "http://www.w3.org/ns/dcat#",
"dct": "http://purl.org/dc/terms/",
@@ -150,3 +159,33 @@ PHENOTYPE_CONTEXT = BASE_CONTEXT | PUBLICATION_CONTEXT | {
"species": "gnt:belongsToSpecies",
"group": "gnt:belongsToGroup",
}
+
+
+def sparql_construct_query(query: str, endpoint: str) -> dict:
+ """Query virtuoso using a CONSTRUCT query and return a json-ld
+ dictionary"""
+ sparql = SPARQLWrapper(endpoint)
+ sparql.setQuery(query)
+ results = sparql.queryAndConvert()
+ return json.loads(results.serialize(format="json-ld")) # type: ignore
+
+
+def query_frame_and_compact(query: str, context: dict, endpoint: str) -> dict:
+ """Frame and then compact the results given a context"""
+ results = sparql_construct_query(query, endpoint)
+ return jsonld.compact(
+ jsonld.frame(results, context),
+ context,
+ options={"graph": True})
+
+
+def query_and_compact(query: str, context: dict, endpoint: str) -> dict:
+ """Compact the results given a context"""
+ results = sparql_construct_query(query, endpoint)
+ return jsonld.compact(results, context, options={"graph": True})
+
+
+def query_and_frame(query: str, context: dict, endpoint: str) -> dict:
+ """Frame the results given a context"""
+ results = sparql_construct_query(query, endpoint)
+ return jsonld.frame(results, context)
diff --git a/gn3/db/rdf/wiki.py b/gn3/db/rdf/wiki.py
new file mode 100644
index 0000000..f7bec47
--- /dev/null
+++ b/gn3/db/rdf/wiki.py
@@ -0,0 +1,168 @@
+"""Sparql queries to get metadata about WIKI and RIF metadata.
+
+"""
+from string import Template
+from gn3.db.rdf import (BASE_CONTEXT, RDF_PREFIXES,
+ query_frame_and_compact)
+
+
+WIKI_CONTEXT = BASE_CONTEXT | {
+ "foaf": "http://xmlns.com/foaf/0.1/",
+ "dct": "http://purl.org/dc/terms/",
+ "categories": "gnt:belongsToCategory",
+ "web_url": "foaf:homepage",
+ "version": "gnt:hasVersion",
+ "symbol": "rdfs:label",
+ "reason": "gnt:reason",
+ "species": "gnt:species",
+ "pubmed_ids": "dct:references",
+ "email": "foaf:mbox",
+ "initial": "gnt:initial",
+ "comment": "rdfs:comment",
+ "created": "dct:created",
+ "id": "dct:identifier",
+ # This points to the RDF Node which is the unique identifier
+ # for this triplet. It's constructed using the comment-id and
+ # the comment-versionId
+ "wiki_identifier": "@id",
+}
+
+
+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("""
+$prefix
+
+CONSTRUCT {
+ ?uid rdfs:label ?symbolName;
+ gnt:reason ?reason ;
+ gnt:species ?species ;
+ dct:references ?pmid ;
+ foaf:homepage ?weburl ;
+ rdfs:comment ?comment ;
+ foaf:mbox ?email ;
+ gnt:initial ?usercode ;
+ gnt:belongsToCategory ?category ;
+ gnt:hasVersion ?versionId ;
+ dct:created ?created ;
+ dct:identifier ?identifier .
+} WHERE {
+ ?symbolId rdfs:label ?symbolName .
+ ?uid rdfs:comment ?comment ;
+ gnt:symbol ?symbolId ;
+ rdf:type gnc:GNWikiEntry ;
+ dct:created ?createTime .
+ FILTER ( LCASE(?symbolName) = LCASE('$symbol') ) .
+ {
+ SELECT (MAX(?vers) AS ?max) ?id_ WHERE {
+ ?symbolId rdfs:label ?symbolName .
+ ?uid dct:identifier ?id_ ;
+ dct:hasVersion ?vers ;
+ dct:identifier ?id_ ;
+ gnt:symbol ?symbolId .
+ FILTER ( LCASE(?symbolName) = LCASE('$symbol') ) .
+ }
+ }
+ ?uid dct:hasVersion ?max ;
+ dct:identifier ?id_ .
+ OPTIONAL { ?uid gnt:reason ?reason } .
+ OPTIONAL {
+ ?uid gnt:belongsToSpecies ?speciesId .
+ ?speciesId gnt:shortName ?species .
+ } .
+ OPTIONAL { ?uid dct:references ?pubmedId . } .
+ OPTIONAL { ?uid foaf:homepage ?weburl . } .
+ OPTIONAL { ?uid gnt:initial ?usercode . } .
+ OPTIONAL { ?uid foaf:mbox ?email . } .
+ OPTIONAL { ?uid gnt:belongsToCategory ?category . } .
+ BIND (str(?version) AS ?versionId) .
+ BIND (str(?id_) AS ?identifier) .
+ BIND (str(?pubmedId) AS ?pmid) .
+ BIND (str(?createTime) AS ?created) .
+}
+""").substitute(prefix=RDF_PREFIXES, symbol=symbol,)
+ results = query_frame_and_compact(
+ query, WIKI_CONTEXT,
+ sparql_uri
+ )
+ data = results.get("data")
+ if not data:
+ return results
+ return results
+
+
+def get_comment_history(comment_id: int, sparql_uri: str) -> dict:
+ """Get all the historical data for a given id"""
+ query = Template("""
+$prefix
+
+CONSTRUCT {
+ ?uid rdfs:label ?symbolName ;
+ gnt:reason ?reason ;
+ gnt:species ?species ;
+ dct:references ?pmid ;
+ foaf:homepage ?weburl ;
+ rdfs:comment ?comment ;
+ foaf:mbox ?email ;
+ gnt:initial ?usercode ;
+ gnt:belongsToCategory ?category ;
+ gnt:hasVersion ?versionId ;
+ dct:created ?created .
+} WHERE {
+ ?symbolId rdfs:label ?symbolName .
+ ?uid rdf:type gnc:GNWikiEntry ;
+ rdfs:comment ?comment ;
+ gnt:symbol ?symbolId ;
+ dct:created ?createTime ;
+ dct:hasVersion ?version ;
+ dct:identifier $comment_id ;
+ dct:identifier ?id_ .
+ OPTIONAL { ?uid gnt:reason ?reason_ } .
+ OPTIONAL {
+ ?uid gnt:belongsToSpecies ?speciesId .
+ ?speciesId gnt:shortName ?species_ .
+ } .
+ OPTIONAL { ?uid dct:references ?pmid . } .
+ OPTIONAL { ?uid foaf:homepage ?weburl_ . } .
+ OPTIONAL { ?uid gnt:initial ?usercode_ . } .
+ OPTIONAL { ?uid foaf:mbox ?email_ . } .
+ OPTIONAL { ?uid gnt:belongsToCategory ?category_ . } .
+ BIND (str(?version) AS ?versionId) .
+ BIND (str(?createTime) AS ?created) .
+ BIND (COALESCE(?reason_, "") AS ?reason) .
+ BIND (COALESCE(?weburl_, "") AS ?weburl) .
+ BIND (COALESCE(?usercode_, "") AS ?usercode) .
+ BIND (COALESCE(?email_, "") AS ?email) .
+ 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 = results.get("data")
+ for result in data:
+ categories = result.get("categories") or []
+ if categories and isinstance(categories, str):
+ result["categories"] = [categories]
+ pmids = result.get("pubmed_ids")
+ if pmids and isinstance(pmids, str):
+ result["pubmed_ids"] = [pmids]
+ elif pmids:
+ result["pubmed_ids"] = [int(pmid) for pmid in pmids]
+ else:
+ result["pubmed_ids"] = []
+ result["version"] = int(result["version"])
+
+ # We manually sort the array, since the SPARQL engine does not
+ # provide a guarantee that it will support an ORDER BY clause in a
+ # CONSTRUCT. Using ORDER BY on a solution sequence for a CONSTRUCT
+ # or DESCRIBE query has no direct effect because only SELECT
+ # returns a sequence of results. See:
+ # <https://stackoverflow.com/questions/78186393>
+ # <https://www.w3.org/TR/rdf-sparql-query/#modOrderBy>
+ results["data"] = sorted(data, key=lambda d: d["version"], reverse=True)
+ return results
diff --git a/gn3/db/wiki.py b/gn3/db/wiki.py
index abb1644..7ef5e68 100644
--- a/gn3/db/wiki.py
+++ b/gn3/db/wiki.py
@@ -9,7 +9,7 @@ class MissingDBDataException(Exception):
"""Error due to DB missing some data"""
-def get_latest_comment(connection, comment_id: str) -> int:
+def get_latest_comment(connection, comment_id: int) -> int:
""" Latest comment is one with the highest versionId """
cursor = connection.cursor(DictCursor)
query = """ SELECT versionId AS version, symbol, PubMed_ID AS pubmed_ids, sp.Name AS species,
@@ -19,7 +19,7 @@ def get_latest_comment(connection, comment_id: str) -> int:
WHERE gr.Id = %s
ORDER BY versionId DESC LIMIT 1;
"""
- cursor.execute(query, (comment_id,))
+ cursor.execute(query, (str(comment_id),))
result = cursor.fetchone()
result["pubmed_ids"] = [x.strip() for x in result["pubmed_ids"].split()]
categories_query = """
@@ -36,7 +36,8 @@ def get_latest_comment(connection, comment_id: str) -> int:
def get_species_id(cursor, species_name: str) -> int:
"""Find species id given species `Name`"""
- cursor.execute("SELECT SpeciesID from Species WHERE Name = %s", (species_name,))
+ cursor.execute(
+ "SELECT SpeciesID from Species WHERE Name = %s", (species_name,))
species_ids = cursor.fetchall()
if len(species_ids) != 1:
raise MissingDBDataException(
@@ -52,7 +53,8 @@ def get_next_comment_version(cursor, comment_id: int) -> int:
)
latest_version = cursor.fetchone()[0]
if latest_version is None:
- raise MissingDBDataException(f"No comment found with comment_id={comment_id}")
+ raise MissingDBDataException(
+ f"No comment found with comment_id={comment_id}")
return latest_version + 1
@@ -63,17 +65,22 @@ def get_categories_ids(cursor, categories: List[str]) -> List[int]:
for category in set(categories):
cat_id = dict_cats.get(category.strip())
if cat_id is None:
- raise MissingDBDataException(f"Category with Name={category} not found")
+ raise MissingDBDataException(
+ f"Category with Name={category} not found")
category_ids.append(cat_id)
return category_ids
+
def get_categories(cursor) -> Dict[str, int]:
+ """Get all categories"""
cursor.execute("SELECT Name, Id from GeneCategory")
raw_categories = cursor.fetchall()
dict_cats = dict(raw_categories)
return dict_cats
+
def get_species(cursor) -> Dict[str, str]:
+ """Get all species"""
cursor.execute("SELECT Name, SpeciesName from Species")
raw_species = cursor.fetchall()
dict_cats = dict(raw_species)
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 19:19:15 +0000