diff options
| -rw-r--r-- | uploader/phenotypes/views.py | 47 |
1 files changed, 44 insertions, 3 deletions
diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py index f10ba09..8ae3ae4 100644 --- a/uploader/phenotypes/views.py +++ b/uploader/phenotypes/views.py @@ -369,12 +369,53 @@ def process_phenotypes_rqtl2_bundle( job_id=str(_job["jobid"]))) -def process_phenotypes_individual_files(rconn, species, population, dataset): +def process_phenotypes_individual_files(rconn, species, population, dataset, error_uri): """Process the uploaded individual files.""" - ## Handle huge file uploads here... + form = request.form + cdata = { + "sep": form["file-separator"], + "comment.char": form["file-comment-character"], + "na.strings": form["file-na"].split(" "), + } + with ZipFile( + Path(app.config["UPLOAD_FOLDER"], + f"{str(uuid.uuid4()).replace('-', '')}.zip"), + mode="w" + ) as zfile: + for rqtlkey, formkey in (("phenocovar", "phenotype-descriptions"), + ("pheno", "phenotype-data"), + ("phenose", "phenotype-se"), + ("phenonum", "phenotype-n")): + if form.get("resumable-upload", False): + # Chunked upload of large files was used + filedata = json.loads(form[formkey]) + zfile.write( + Path(app.config["UPLOAD_FOLDER"], filedata["uploaded-file"]), + arcname=filedata["original-name"]) + cdata[rqtlkey] = cdata.get(rqtlkey, []) + [filedata["original-name"]] + else: + # TODO: Check this path: fix any bugs. + _sentfile = request.files[formkey] + if not bool(_sentfile): + flash(f"Expected file ('{formkey}') was not provided.", + "alert-danger") + return error_uri + + filepath = save_file( + _sentfile, Path(app.config["UPLOAD_FOLDER"])) + zfile.write( + Path(app.config["UPLOAD_FOLDER"], filepath), + arcname=filepath.name) + cdata[rqtlkey] = cdata.get(rqtlkey, []) + [filepath.name] + + zfile.writestr("control_data.json", data=json.dumps(cdata, indent=2)) + ## Convert files and settings to R/qtl2 bundle ## Use same processing as R/qtl2 bundle (after some refactoring) - raise NotImplementedError("Implement this!") + print(f"FORM: {request.form}") + print(f"FILES: {request.files}") + print(f"CDATA: {cdata}") + return "Would process individual files…" @phenotypesbp.route( |