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Fix broken pages when sequence data not available #39

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Fix broken pages when sequence data not available #39

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f103afe
add option to skip loading dash
Oct 4, 2024
70dc876
remove gunicorn from frontend requirements
Oct 4, 2024
9f7b768
safely handle missing seq data
Oct 4, 2024
7849a60
handle missing sequence data
Oct 4, 2024
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1 change: 1 addition & 0 deletions README.md
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Expand Up @@ -38,6 +38,7 @@ cd webstr
# optionally, checkout a specific branch to test
export BASEPATH=*full data directory path*
export FLASK_DEBUG=1 # run in debug mode
export NODASH=1 # optional, skip loading dash modules
python ./WebSTR/WebSTR.py --host 0.0.0.0 --port <port>
```

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8 changes: 6 additions & 2 deletions WebSTR/WebSTR.py
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Expand Up @@ -16,11 +16,11 @@
from locus_view import *
from region_view import *
from gene_plots import *
from dash_graphs import add_dash_graphs_to_flask_server

# Grab environment variables
API_URL = os.environ.get("WEBSTR_API_URL",'http://webstr-api.ucsd.edu')
BASEPATH = os.environ.get("BASEPATH", "/storage/resources/dbase/human/")
NODASH = os.environ.get("NODASH", 0) == "1"

#################### Data paths ###############
RefFaPath_hg19 = os.path.join(BASEPATH, "hg19", "hg19.fa")
Expand All @@ -29,7 +29,11 @@
#################### Set up flask server ###############
server = Flask(__name__)
server.secret_key = 'dbSTR'
add_dash_graphs_to_flask_server(server)

#################### Set up dash ###############
if not NODASH:
from dash_graphs import add_dash_graphs_to_flask_server
add_dash_graphs_to_flask_server(server)

#################### Render region page ###############
@server.route('/search')
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2 changes: 2 additions & 0 deletions WebSTR/locus_view.py
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Expand Up @@ -319,6 +319,8 @@ def GetSeqDataAPI(repeat_id):
sys.stderr.write("WARNING: could not access allseq table from API\n")
return None
df = pd.DataFrame.from_records(resp.json())
if df.empty:
return None
agg_df = df.pivot_table(index='sequence', columns='population', values='frequency', aggfunc='first').reset_index()
agg_df = agg_df.fillna(0)

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1 change: 0 additions & 1 deletion requirements.txt
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Expand Up @@ -19,5 +19,4 @@ tenacity==8.1.0
urllib3==1.26.13
Werkzeug==2.2.2
zipp==3.11.0
gunicorn==20.1.0
dash_bio==1.0.2