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Features/handle gohan errors #49

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merged 7 commits into from
Jul 31, 2023
Merged

Features/handle gohan errors #49

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7ae357a
handle gohan errors in beacon overview
gsfk Jul 27, 2023
7934f89
empty variants table not necessarily an error
gsfk Jul 31, 2023
7b50264
add strip().lower(), to improve
gsfk Jul 31, 2023
3e0f0bc
if 'UseGohan", expect variants table to exist
gsfk Jul 31, 2023
362b927
merge master into features/handle-gohan-errors
gsfk Jul 31, 2023
293e666
rv .stip().lower(), this is already a bool
gsfk Jul 31, 2023
0b52ff2
fix beaconId in response meta
gsfk Jul 31, 2023
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6 changes: 2 additions & 4 deletions bento_beacon/utils/beacon_response.py
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Original file line number Diff line number Diff line change
Expand Up @@ -115,10 +115,9 @@ def received_request():
def build_response_meta():
returned_schemas = g.get("response_data", {}).get("returnedSchemas", [])
returned_granularity = g.get("response_data", {}).get("returnedGranularity", "count")
service_info = current_app.config["BEACON_CONFIG"].get("serviceInfo")
received_request_summary = received_request()
return {
"beaconId": service_info.get("id"),
"beaconId": current_app.config["BEACON_ID"],
"apiVersion": current_app.config["BEACON_SPEC_VERSION"],
"returnedSchemas": returned_schemas,
"returnedGranularity": returned_granularity,
Expand All @@ -127,9 +126,8 @@ def build_response_meta():


def build_info_response_meta():
service_info = current_app.config["BEACON_CONFIG"].get("serviceInfo")
return {
"beaconId": service_info.get("id"),
"beaconId": current_app.config["BEACON_ID"],
"apiVersion": current_app.config["BEACON_SPEC_VERSION"],
"returnedSchemas": []
}
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26 changes: 21 additions & 5 deletions bento_beacon/utils/gohan_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -195,7 +195,7 @@ def gohan_network_call(url, gohan_args):
gohan_response = r.json()

except requests.exceptions.RequestException as e:
current_app.logger.debug(f"gohan error: {e}")
current_app.logger.error(f"gohan error: {e}")
raise APIException(message="error calling gohan variants service")

return gohan_response
Expand Down Expand Up @@ -228,13 +228,29 @@ def gohan_counts_by_assembly_id():
return gohan_overview().get("assemblyIDs", {})


# gohan /variants/overview hangs when no variants table
# so check for a table before calling
# only runs if "useGohan" true
def gohan_counts_for_overview():
# gohan /variants/overview hangs when no variants table
# so check for tables before calling
tables_url = current_app.config["GOHAN_BASE_URL"] + "/tables?data-type=variant"
has_tables = gohan_network_call(tables_url, {})
if has_tables:
tables = None

try:
tables = gohan_network_call(tables_url, {})
except APIException:
# note this exception but don't rethrow
current_app.logger.error("cannot reach gohan for overview")

# non-empty tables
if tables:
return gohan_counts_by_assembly_id()

# empty tables (fresh instance or elasticsearch down)
# "useGohan" is true here so we expect variants to exist
if tables is not None:
return {"error": "no variants available"}

# else bad response from gohan
return {"error": "gohan unavailable"}

# --------------------------------------------
Expand Down