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DIG-1686: Update query to work with updated katsu endpoints #45

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merged 4 commits into from
Aug 9, 2024

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OrdiNeu
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@OrdiNeu OrdiNeu commented Jul 18, 2024

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Description

This addresses changes from the Katsu Model 3 PR

To Test:

  1. Check out this branch, CanDIGv2-ingest's model_3 branch, and Katsu's model_3 branch
  2. Run Katsu ingest with the following:
conda activate candig

# Be in the root CanDIG directory for the following
python settings.py
source env.sh
cp env.sh lib/candig-ingest/candigv2-ingest/
cd lib/candig-ingest/candigv2-ingest/

export KATSU_URL=$CANDIG_URL/katsu

export CLINICAL_DATA_LOCATION=/home/fnguyen/Documents/CanDIGv2/lib/candig-ingest/candigv2-ingest/tests/clinical_ingest.json
python katsu_ingest.py
  1. Modify candig-data-portal with the following: search and replace all instances of v2/ with v3/ except for the ones in package-lock.json, the Footer's index.js, the random line in the .svg file, and the ones that are /beacon/v2/g_variants`.
  2. Load up the front page

@OrdiNeu OrdiNeu marked this pull request as ready for review August 8, 2024 14:20
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@CourtneyGosselin CourtneyGosselin left a comment

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Along with the /query call that occurs when you load the clinical and genomic search page getting a 500 for key error on primary_diagnosis. There is also some 400 errors when I try and do some filtering

query_server/query_operations.py Outdated Show resolved Hide resolved
@OrdiNeu OrdiNeu changed the base branch from develop to model3 August 8, 2024 19:22
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@CourtneyGosselin CourtneyGosselin left a comment

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LGTM works now with the data-portal PR

@OrdiNeu OrdiNeu changed the base branch from model3 to model_3 August 9, 2024 13:25
@OrdiNeu OrdiNeu merged commit 6ed047e into model_3 Aug 9, 2024
@OrdiNeu OrdiNeu deleted the feature/model3 branch August 9, 2024 13:26
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2 participants