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Fix /summarize #94

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Merged
asherpasha merged 2 commits into from
Nov 9, 2021
Merged

Fix /summarize #94

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cd9f91b
Fix bug in /summarize
brucosper Nov 8, 2021
b602614
Merge branch 'BioAnalyticResource:dev' into dev
brucosper Nov 8, 2021
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8 changes: 2 additions & 6 deletions api/resources/summarization_gene_expression.py
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Original file line number Diff line number Diff line change
Expand Up @@ -149,6 +149,7 @@ def post(self):
"workflowInputs": ("rpkm_inputs.json", file.read()),
}
id_and_status = requests.post(CROMWELL_URL + "/api/workflows/v1", files=files)
id_and_status = id_and_status.json()
file.close()
gkey = os.environ.get("DRIVE_LIST_KEY")
cipher_suite = Fernet(gkey)
Expand All @@ -165,7 +166,7 @@ def post(self):
fs = [x["name"] for x in r.json()['files'] if ".bam" in x["name"]]
else:
fs = r.status_code
return BARUtils.success_exit((id_and_status.id, fs)), 200
return BARUtils.success_exit((id_and_status["id"], fs)), 200
else:
return BARUtils.error_exit("Invalid API key")

Expand Down Expand Up @@ -219,14 +220,12 @@ def post(self):
if "file" not in request.files:
return BARUtils.error_exit("No file attached"), 400
file = request.files["file"]
print(file)
if file:
filename = secure_filename(file.filename)
key = request.headers.get("X-Api-Key")
overwrite = request.form.get("overwrite")
addToDb = request.form.get("addToDb")
email = request.form.get("email")
print(overwrite, addToDb, email)
if(overwrite is True):
overwrite = "replace"
else:
Expand Down Expand Up @@ -260,7 +259,6 @@ def post(self):
}
"""
)
print(inputs)
path = os.path.join(SUMMARIZATION_FILES_PATH, "tsvUpload.wdl")
files = {
"workflowSource": ("tsvUpload.wdl", open(path, "rb")),
Expand Down Expand Up @@ -288,7 +286,6 @@ def post(self):
overwrite = request.form.get("overwrite")
addToDb = request.form.get("addToDb")
email = request.form.get("email")
print(addToDb)
if(overwrite is True):
overwrite = "replace"
else:
Expand Down Expand Up @@ -491,7 +488,6 @@ def post(self):
elif SummarizationGeneExpressionUtils.decrement_uses(api_key):
if "file" in request.files:
file = request.files["file"]
print(file)
if file.content_type == "text/json":
extension = ".json"
elif file.content_type == "image/svg+xml":
Expand Down