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new env variable for setting Value set version #32

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new env variable for setting Value set version #32

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48fdc92
new env variable for setting Value set version
Shayan1375 Jul 4, 2024
040e585
new env variable for setting Value set version via a json file
Shayan1375 Jul 12, 2024
44cdd40
added try catch block and reading of mapping file from env
Shayan1375 Jul 18, 2024
27dcaf9
changed key to canonical adress
Shayan1375 Jul 18, 2024
e5d249f
ignore
Shayan1375 Jul 18, 2024
acad50a
new version for setting globaly setting the version of a value set
Shayan1375 Jul 19, 2024
cc15108
new version for setting globaly the version of a value set
Shayan1375 Jul 19, 2024
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8 changes: 8 additions & 0 deletions TerminologService/TermServerConstants.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,13 @@
import json
import os

TERMINOLOGY_SERVER_ADDRESS = os.environ.get('ONTOLOGY_SERVER_ADDRESS')
SERVER_CERTIFICATE = os.environ.get('SERVER_CERTIFICATE')
PRIVATE_KEY = os.environ.get('PRIVATE_KEY')

# Get the current working directory
current_working_dir = os.getcwd()
print(current_working_dir)
mapping_path = os.environ.get('ONTO_MAPPING_PATH', os.path.join(current_working_dir, '..', '..', 'mapping.json'))
with open(mapping_path, 'r') as file:
MAPPING_ONTO_VERSION = json.load(file)
2 changes: 1 addition & 1 deletion TerminologService/ValueSetResolver.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@

import requests

from TerminologService.TermServerConstants import TERMINOLOGY_SERVER_ADDRESS, SERVER_CERTIFICATE, PRIVATE_KEY
from TerminologService.TermServerConstants import TERMINOLOGY_SERVER_ADDRESS, SERVER_CERTIFICATE, PRIVATE_KEY, MAPPING_ONTO_VERSION
from TerminologService.valueSetToRoots import create_vs_tree, expand_value_set
from model.UiDataModel import TermCode

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22 changes: 19 additions & 3 deletions TerminologService/valueSetToRoots.py
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Original file line number Diff line number Diff line change
@@ -1,12 +1,13 @@
import bisect
import logging
from typing import List

import requests
import locale

from sortedcontainers import SortedSet

from TerminologService.TermServerConstants import TERMINOLOGY_SERVER_ADDRESS, SERVER_CERTIFICATE, PRIVATE_KEY
from TerminologService.TermServerConstants import TERMINOLOGY_SERVER_ADDRESS, SERVER_CERTIFICATE, PRIVATE_KEY, MAPPING_ONTO_VERSION
from model.UiDataModel import TermCode, TermEntry

locale.setlocale(locale.LC_ALL, 'de_DE')
Expand All @@ -22,7 +23,23 @@ def expand_value_set(url: str, onto_server: str = TERMINOLOGY_SERVER_ADDRESS):
if '|' in url:
url = url.replace('|', '&version=')
term_codes = SortedSet()
response = requests.get(onto_server + f"ValueSet/$expand?url={url}", cert=(SERVER_CERTIFICATE, PRIVATE_KEY))
version = MAPPING_ONTO_VERSION.get('canonical_address')
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Why use a file if you always get the same version?

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It ensures that the system remains adaptable and scalable as more version-specific requirements emerge.

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Sure but please a variable here and not a string in that case. Probably you want to use the actual canonical_adress not a string.

onto_server = TERMINOLOGY_SERVER_ADDRESS

if version:
canonical_address = f"ValueSet/$expand?url={url}&system-version={version}"
else:
canonical_address = f"ValueSet/$expand?url={url}"
logging.debug(f"No version found for canonical address: {canonical_address}")
Comment on lines +31 to +33
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The log output is not in line with the implementation. You never look up {canonical_address} but "canonical_address"

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Would that be a better logging message which clarifys the purpose of the error?
logging.debug(f"No version was provided.Using canonical address: {canonical_address}")

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yes


complete_url = onto_server + canonical_address
print(complete_url)
try:
response = requests.get(complete_url, cert=(SERVER_CERTIFICATE, PRIVATE_KEY))
response.raise_for_status()
except requests.exceptions.RequestException as e:
logging.error(f"An error occurred while requesting the ontology server: {e}")

print(response.status_code)
if response.status_code == 200:
value_set_data = response.json()
Expand Down Expand Up @@ -50,7 +67,6 @@ def expand_value_set(url: str, onto_server: str = TERMINOLOGY_SERVER_ADDRESS):
print(response.content)
return []
# raise Exception(response.status_code, response.content)
print(term_codes)
return term_codes


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1 change: 0 additions & 1 deletion ...Metric_Eingestellte_Gemessene_Parameter_Extrakorporale_Verfahren.StructureDefinition.json
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3 changes: 3 additions & 0 deletions mapping.json
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I can only assume this intended to be the canonical address of the valueset that requires the snomed version?
In that case you would have a change the key accordingly and also add all snomed based valuesets.

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The mapping.json file, which contains version information, has been updated as follows:
{ "snomed-version": "http%3A%2F%2Fsnomed.info%2Fsct%7Chttp%3A%2F%2Fsnomed.info%2Fsct%2F900000000000207008%2Fversion%2F20240101" }

Currently, only one version of SNOMED is provided in this file because this update specifically applies to ICU use cases. Additional versions will be added as they become available and relevant to other domains.

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Where do you get the key information from? It shouldn't be static.

Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
{
"canonical_address": "http%3A%2F%2Fsnomed.info%2Fsct%7Chttp%3A%2F%2Fsnomed.info%2Fsct%2F900000000000207008%2Fversion%2F20240101"
}