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[REF] Refactor httpx.post call to Stardog and context creation (#195)
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* refactor Stardog post request into separate function

* create function to handle context generation

* update docstring

* more graph backend-generic function names and docstrings
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@alyssadai
alyssadai authored Oct 4, 2023
1 parent 8a5efa1 commit f00a1ff
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Showing 3 changed files with 73 additions and 87 deletions.
134 changes: 62 additions & 72 deletions app/api/crud.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,48 @@
]


def post_query_to_graph(query: str, timeout: float = 5.0) -> dict:
"""
Makes a post request to the graph API to perform a query, using parameters from the environment.
Parameters
----------
query : str
The full SPARQL query string.
timeout : float, optional
The maximum duration for the request, by default 5.0 seconds.
Returns
-------
dict
The response from the graph API, encoded as json.
"""
try:
response = httpx.post(
url=util.QUERY_URL,
content=query,
headers=util.QUERY_HEADER,
auth=httpx.BasicAuth(
os.environ.get(util.GRAPH_USERNAME.name),
os.environ.get(util.GRAPH_PASSWORD.name),
),
timeout=timeout,
)
# Provide more informative error message for a timeout in the connection to the host.
except httpx.ConnectTimeout as exc:
raise HTTPException(
status_code=status.HTTP_500_INTERNAL_SERVER_ERROR,
detail="Timed out while connecting to the server. You may not be on an authorized network to perform this request.",
) from exc

if not response.is_success:
raise HTTPException(
status_code=response.status_code,
detail=f"{response.reason_phrase}: {response.text}",
)

return response.json()


async def get(
min_age: float,
max_age: float,
Expand All @@ -40,7 +82,7 @@ async def get(
image_modal: str,
):
"""
Makes a POST request to Stardog API using httpx where the payload is a SPARQL query generated by the create_query function.
Makes a POST request to graph API using httpx where the payload is a SPARQL query generated by the create_query function.
Parameters
----------
Expand All @@ -67,40 +109,20 @@ async def get(
Response of the POST request.
"""
try:
response = httpx.post(
url=util.QUERY_URL,
content=util.create_query(
return_agg=util.RETURN_AGG.val,
age=(min_age, max_age),
sex=sex,
diagnosis=diagnosis,
is_control=is_control,
min_num_sessions=min_num_sessions,
assessment=assessment,
image_modal=image_modal,
),
headers=util.QUERY_HEADER,
auth=httpx.BasicAuth(
os.environ.get(util.GRAPH_USERNAME.name),
os.environ.get(util.GRAPH_PASSWORD.name),
),
# TODO: Revisit timeout value when query performance is improved
timeout=30.0,
)
except httpx.ConnectTimeout as exc:
raise HTTPException(
status_code=status.HTTP_500_INTERNAL_SERVER_ERROR,
detail="Timed out while connecting to the server. Please confirm that you are connected to the McGill network and try again.",
) from exc

if not response.is_success:
raise HTTPException(
status_code=response.status_code,
detail=f"{response.reason_phrase}: {response.text}",
)

results = response.json()
results = post_query_to_graph(
util.create_query(
return_agg=util.RETURN_AGG.val,
age=(min_age, max_age),
sex=sex,
diagnosis=diagnosis,
is_control=is_control,
min_num_sessions=min_num_sessions,
assessment=assessment,
image_modal=image_modal,
),
# TODO: Revisit timeout value when query performance is improved
timeout=30.0,
)

# Reformat SPARQL results into more human-readable form
results_dicts = [
Expand Down Expand Up @@ -160,7 +182,7 @@ async def get(

async def get_terms(data_element_URI: str):
"""
Makes a POST request to Stardog API using httpx where the payload is a SPARQL query generated by the create_terms_query function.
Makes a POST request to graph API using httpx where the payload is a SPARQL query generated by the create_terms_query function.
Parameters
----------
Expand All @@ -172,23 +194,7 @@ async def get_terms(data_element_URI: str):
httpx.response
Response of the POST request.
"""
response = httpx.post(
url=util.QUERY_URL,
content=util.create_terms_query(data_element_URI),
headers=util.QUERY_HEADER,
auth=httpx.BasicAuth(
os.environ.get(util.GRAPH_USERNAME.name),
os.environ.get(util.GRAPH_PASSWORD.name),
),
)

if not response.is_success:
raise HTTPException(
status_code=response.status_code,
detail=f"{response.reason_phrase}: {response.text}",
)

results = response.json()
results = post_query_to_graph(util.create_terms_query(data_element_URI))

results_dict = {
data_element_URI: [
Expand All @@ -202,39 +208,23 @@ async def get_terms(data_element_URI: str):

async def get_controlled_term_attributes():
"""
Makes a POST query to Stardog API for all Neurobagel classes representing controlled term attributes.
Makes a POST query to graph API for all Neurobagel classes representing controlled term attributes.
Returns
-------
dict
Dictionary with value corresponding to all available controlled term attributes.
"""
attributes_query = f"""
{util.DEFAULT_CONTEXT}
{util.create_context()}
SELECT DISTINCT ?attribute
WHERE {{
?attribute rdfs:subClassOf nb:ControlledTerm .
}}
"""
results = post_query_to_graph(attributes_query)

response = httpx.post(
url=util.QUERY_URL,
content=attributes_query,
headers=util.QUERY_HEADER,
auth=httpx.BasicAuth(
os.environ.get(util.GRAPH_USERNAME.name),
os.environ.get(util.GRAPH_PASSWORD.name),
),
)

if not response.is_success:
raise HTTPException(
status_code=response.status_code,
detail=f"{response.reason_phrase}: {response.text}",
)

results = response.json()
results_list = [
util.replace_namespace_uri(result["attribute"]["value"])
for result in results["results"]["bindings"]
Expand Down
24 changes: 10 additions & 14 deletions app/api/utility.py
View file
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
"""Constants for Stardog graph connection and utility functions for writing the SPARQL query."""
"""Constants for graph server connection and utility functions for writing the SPARQL query."""

import os
from collections import namedtuple
Expand Down Expand Up @@ -37,17 +37,6 @@
"Accept": "application/sparql-results+json",
}

# SPARQL query context
# TODO: Refactor into a function.
DEFAULT_CONTEXT = """
PREFIX cogatlas: <https://www.cognitiveatlas.org/task/id/>
PREFIX nb: <http://neurobagel.org/vocab/>
PREFIX nbg: <http://neurobagel.org/graph/>
PREFIX ncit: <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#>
PREFIX nidm: <http://purl.org/nidash/nidm#>
PREFIX snomed: <http://purl.bioontology.org/ontology/SNOMEDCT/>
"""

CONTEXT = {
"cogatlas": "https://www.cognitiveatlas.org/task/id/",
"nb": "http://neurobagel.org/vocab/",
Expand Down Expand Up @@ -79,6 +68,13 @@ def parse_origins_as_list(allowed_origins: str) -> list:
return list(allowed_origins.split(" "))


def create_context() -> str:
"""Creates a SPARQL query context string from the CONTEXT dictionary."""
return "\n".join(
[f"PREFIX {prefix}: <{uri}>" for prefix, uri in CONTEXT.items()]
)


def create_query(
return_agg: bool,
age: Optional[tuple] = (None, None),
Expand Down Expand Up @@ -213,7 +209,7 @@ def create_query(
\n}} GROUP BY ?dataset_uuid ?dataset_name ?dataset_portal_uri ?sub_id ?session_file_path ?image_modal
"""

return "\n".join([DEFAULT_CONTEXT, query_string])
return "\n".join([create_context(), query_string])


def create_terms_query(data_element_URI: str) -> str:
Expand Down Expand Up @@ -243,7 +239,7 @@ def create_terms_query(data_element_URI: str) -> str:
}}
"""

return "\n".join([DEFAULT_CONTEXT, query_string])
return "\n".join([create_context(), query_string])


def replace_namespace_uri(url: str) -> str:
Expand Down
2 changes: 1 addition & 1 deletion tests/test_query.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
"""Test API to query subjects from the Stardog graph who match user-specified criteria."""
"""Test API to query subjects from the graph database who match user-specified criteria."""

import os
import warnings
Expand Down

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