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2024 migration #52

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2024 migration #52

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3c3ff75
frontend updates 2024
Aug 13, 2024
4df32b7
rye dependencies setup
Oct 6, 2024
ea0069c
ignore .DS_Store
Oct 6, 2024
536d1bf
className, key js warning fixes
Oct 7, 2024
f56572f
frontend update fixes WIP
Oct 29, 2024
32386d4
update limiter arg label; misc readme note; print dev aid
Oct 30, 2024
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1 change: 1 addition & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -145,3 +145,4 @@ opt/
TrainingScenarios/CaseFiles/*
TrainingScenarios/CaseFilesGeneBreaker.tar.gz

.DS_Store
4 changes: 2 additions & 2 deletions GeneBreaker/app/__init__.py
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Expand Up @@ -6,13 +6,13 @@
app = Flask(__name__)
app.config.from_pyfile('config.py')
limiter = Limiter(
app,
app=app,
key_func=get_remote_address,
default_limits=["500 per day", "5 per second"]
)

cors = CORS(app, resources={r"/*":
{"origins": ["http://localhost:3000", "http://genebreaker.cmmt.ubc.ca"]}})
{"origins": ["http://localhost:3000", "http://genebreaker.test", "http://genebreaker.cmmt.ubc.ca", "https://genebreaker.test", "https://genebreaker.cmmt.ubc.ca"]}})

import GeneBreaker.app.routes

1 change: 1 addition & 0 deletions GeneBreaker/src/api_helper.py
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Expand Up @@ -43,6 +43,7 @@ def get_all_results(request_url):

def get_all_transcripts(gene_name, genome):
url = host + '/api/v1/' + genome + '/genes?names='+gene_name
print("request to GUD",url) # TEMP dev aid
# &sources=ncbiRefSeqSelect
refSeqSelect = get_all_results(url + '&sources=ncbiRefSeqSelect')
refSeq = get_all_results(url + '&sources=ncbiRefSeq')
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16 changes: 15 additions & 1 deletion README.md
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Expand Up @@ -27,5 +27,19 @@ Downstream Benchmarking can either include full simulation of the variant(s) wit

For details on how to use the downstream benchmarking, please go to the [BenchmarkingTransition/](./BenchmarkingTransition) directory.


## dev notes

### config files:
- GeneBreaker/src/config.ini
```
[DEFAULT]
GUD_HOST = http://gud.host
```
- GeneBreaker/app/config.py
```
SECRET_KEY='a-secret-key'
GUD_HOST='http://gud.host'
```

`FLASK_APP=GeneBreaker.app python -m flask run`

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