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Add new grpc endpoint to get genome id from accession id #63
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17fbf7d
Add new grpc endpoint to get genome id from accession id
jyothishnt 019bdf6
review comments update
jyothishnt 026335f
update url endpoint
jyothishnt ef29bfe
add 404
jyothishnt e8fd064
logging
jyothishnt dcccbf9
review comment
jyothishnt 01a2481
update api spec doc
jyothishnt 7584965
update api spec; return json response
jyothishnt e6cd8ef
add 404 in api spec
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Original file line number | Diff line number | Diff line change |
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@@ -14,6 +14,7 @@ | |
See the License for the specific language governing permissions and | ||
limitations under the License. | ||
""" | ||
import json | ||
import logging | ||
from typing import Annotated | ||
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@@ -25,7 +26,7 @@ | |
from api.models.statistics import GenomeStatistics, ExampleObjectList | ||
from api.models.popular_species import PopularSpeciesGroup | ||
from api.models.karyotype import Karyotype | ||
from api.models.genome import BriefGenomeDetails, GenomeDetails, DatasetAttributes | ||
from api.models.genome import BriefGenomeDetails, GenomeDetails, DatasetAttributes, GenomeByKeyword | ||
from api.models.ftplinks import FTPLinks | ||
|
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from core.config import GRPC_HOST, GRPC_PORT | ||
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@@ -238,3 +239,19 @@ async def get_genome_dataset_attributes( | |
except Exception as ex: | ||
logging.error(ex) | ||
return response_error_handler({"status": 500}) | ||
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@router.get("/genomeid/{assembly_accession_id}", name="genome_id") | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. This does not look like a great pathname. Something like |
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async def get_uuid(request: Request, assembly_accession_id: str): | ||
try: | ||
genome_array = grpc_client.get_genome_by_specific_keyword(assembly_accession_id) | ||
latest_genome_by_keyword_object = GenomeByKeyword() | ||
for arr in genome_array: | ||
arr = MessageToDict(arr) | ||
genome_by_keyword_object = GenomeByKeyword(**arr) | ||
if (genome_by_keyword_object.release_version > latest_genome_by_keyword_object.release_version): | ||
latest_genome_by_keyword_object = genome_by_keyword_object | ||
return latest_genome_by_keyword_object | ||
except Exception as ex: | ||
logging.error(ex) | ||
return response_error_handler({"status": 500}) | ||
return response_data |
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It seems that you are looking up genome id specifically by assembly accession id. If so, you probably shouldn't say
by_specific_keyword
in the function name, and in the class name inmodels/genome.py
.Both thoas and the grpc service allow various fields to be used as a "keyword"; but here you are only using a specific one.