diff options
Diffstat (limited to 'uploader/genotypes')
| -rw-r--r-- | uploader/genotypes/views.py | 23 |
1 files changed, 23 insertions, 0 deletions
diff --git a/uploader/genotypes/views.py b/uploader/genotypes/views.py index e475986..454fee7 100644 --- a/uploader/genotypes/views.py +++ b/uploader/genotypes/views.py @@ -1,5 +1,6 @@ """Views for the genotypes.""" import logging +from uuid import uuid4 from MySQLdb.cursors import DictCursor from pymonad.either import Left, Right, Either @@ -214,6 +215,12 @@ def create_dataset(species: dict, population: dict, **kwargs):# pylint: disable= __success__) +def genotype_csv_to_r_qtl2(uploadsdir: Path, csvfile, csv_meta: dict) -> Path: + """Convert given CSV genotype file into the R/qtl2 format.""" + bundlepath = Path(uploadsdir, f"{uuid.uuid4()}.zip".replace("-", "")) + raise NotImplementedError("This is not implemented yet.") + + @genotypesbp.route( "/<int:species_id>/populations/<int:population_id>/genotypes/datasets/" "<int:dataset_id>/add-records", @@ -234,6 +241,22 @@ def add_genotype_records(species: dict, population: dict, dataset: dict, **kwarg dataset=dataset, activelink="add-genotypes-records") + # request.method is POST from here + # T0D0: Handle direct uploads (i.e. Not via javascript) + form = dict(request.form) # Request comes in as multipart/formdata + + bundlepath = genotype_csv_to_r_qtl2( + # T0D0: Actually, rather than generating the R/qtl2 bundle here, first + # off, do basic check through the data to collect the alleles and other + # necessary information. Also do basic QC. + Path(uploads_dir(app)), + form["uploaded-file"], + csv_meta: { + "sep": form.get("file-separator", ","), + "comment.char": form.get("file-comment-char", "#"), + "na.strings": form.get("file-na", "- NA N/A").split(" ") + }) + if "application/json" in request.headers.get("Accept"): return make_response( jsonify({ |