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Allow for handling multiple uploaded TSV files #125

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Merged
asherpasha merged 3 commits into from
Jan 29, 2022
Merged

Allow for handling multiple uploaded TSV files #125

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a075189
Update TSV upload to use multiple files
brucosper Jan 27, 2022
ab3207a
Fix folders
brucosper Jan 27, 2022
cc8893a
Merge branch 'BioAnalyticResource:dev' into dev
brucosper Jan 28, 2022
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89 changes: 45 additions & 44 deletions api/resources/summarization_gene_expression.py
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Original file line number Diff line number Diff line change
Expand Up @@ -226,53 +226,51 @@ class SummarizationGeneExpressionTsvUpload(Resource):
def post(self):
"""Takes a TSV file from Kallisto converts to RPKM"""
if request.method == "POST":
if "file" not in request.files:
return BARUtils.error_exit("No file attached"), 400
file = request.files["file"]
if file:
filename = secure_filename(file.filename)
key = request.headers.get("X-Api-Key")
overwrite = request.form.get("overwrite")
email = request.form.get("email")
if overwrite == "true":
overwrite = "replace"
else:
overwrite = "append"
# Create folder for user data if it doesn't exist
key = request.headers.get("X-Api-Key")
overwrite = request.form.get("overwrite")
email = request.form.get("email")
if overwrite == "true":
overwrite = "replace"
else:
overwrite = "append"
# Create folder for user data if it doesn't exist
files = request.files.items()
for i in files:
filename = secure_filename(i[0])
dirName = os.path.join("/DATA/users/www-data/", secure_filename(key))
if not os.path.exists(dirName):
os.makedirs(dirName)
file.save(os.path.join(dirName, secure_filename(filename)))
if SummarizationGeneExpressionUtils.decrement_uses(key):
inputs = (
i[1].save(os.path.join(dirName, filename))
if SummarizationGeneExpressionUtils.decrement_uses(key):
inputs = (
"""
{
"tsvUpload.insertDataScript": "./insertData.py",
"tsvUpload.conversionScript": "./kallistoToRpkm.R",
"tsvUpload.id": """
+ key
+ """,
"tsvUpload.tsv": """
+ str(os.listdir(dirName))
+ """,
"tsvUpload.overwrite": """
+ overwrite
+ """,
"tsvUpload.email": """
+ email
+ """
}
"""
{
"tsvUpload.insertDataScript": "./insertData.py",
"tsvUpload.conversionScript": "./kallistoToRpkm.R",
"tsvUpload.id": """
+ key
+ """,
"tsvUpload.tsv": """
+ os.path.join(dirName, secure_filename(filename))
+ """,
"tsvUpload.overwrite": """
+ overwrite
+ """,
"tsvUpload.email": """
+ email
+ """
}
"""
)
path = os.path.join(SUMMARIZATION_FILES_PATH, "tsvUpload.wdl")
files = {
"workflowSource": ("tsvUpload.wdl", open(path, "rb")),
"workflowInputs": ("rpkm_inputs.json", inputs),
}
requests.post(CROMWELL_URL + "/api/workflows/v1", files=files)
return BARUtils.success_exit(key)
else:
return BARUtils.error_exit("Invalid API key")
)
path = os.path.join(SUMMARIZATION_FILES_PATH, "tsvUpload.wdl")
files = {
"workflowSource": ("tsvUpload.wdl", open(path, "rb")),
"workflowInputs": ("rpkm_inputs.json", inputs),
}
requests.post(CROMWELL_URL + "/api/workflows/v1", files=files)
return BARUtils.success_exit(key)
else:
return BARUtils.error_exit("Invalid API key")


@summarization_gene_expression.route("/csv_upload", methods=["POST"], doc=False)
Expand Down Expand Up @@ -495,9 +493,12 @@ def post(self):
extension = ".svg"
else:
return BARUtils.error_exit("Invalid file type"), 400
dirName = os.path.join(DATA_FOLDER, api_key)
filename = os.path.join(
DATA_FOLDER, api_key, file.filename + extension
dirName, file.filename + extension
)
if not os.path.exists(dirName):
os.makedirs(dirName)
file.save(filename)
return BARUtils.success_exit(True)
else:
Expand Down