diff options
| -rw-r--r-- | wqflask/wqflask/views.py | 55 |
1 files changed, 51 insertions, 4 deletions
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 6e8d1e78..73829bb2 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -27,6 +27,7 @@ from zipfile import ZIP_DEFLATED from wqflask import app +from gn3.commands import run_cmd from gn3.db import diff_from_dict from gn3.db import fetchall from gn3.db import fetchone @@ -43,6 +44,7 @@ from gn3.db.traits import get_trait_csv_sample_data from flask import current_app from flask import g +from flask import flash from flask import Response from flask import request from flask import make_response @@ -541,6 +543,52 @@ def update_phenotype(): passwd=current_app.config.get("DB_PASS"), host=current_app.config.get("DB_HOST")) data_ = request.form.to_dict() + author = g.user_session.record.get(b'user_name') + if 'file' not in request.files: + flash("No sample data has been uploaded") + else: + file_ = request.files['file'] + trait_name = str(data_.get('dataset-name')) + phenotype_id = str(data_.get('phenotype-id', 35)) + SAMPLE_DATADIR = "/tmp/sample-data/" + if not os.path.exists(SAMPLE_DATADIR): + os.makedirs(SAMPLE_DATADIR) + if not os.path.exists(os.path.join(SAMPLE_DATADIR, + "diffs")): + os.makedirs(os.path.join(SAMPLE_DATADIR, + "diffs")) + if not os.path.exists(os.path.join(SAMPLE_DATADIR, + "updated")): + os.makedirs(os.path.join(SAMPLE_DATADIR, + "updated")) + current_time = str(datetime.datetime.now().isoformat()) + new_file_name = ("/tmp/sample-data/updated/" + f"{author.decode('utf-8')}." + f"{trait_name}.{phenotype_id}." + f"{current_time}.csv") + uploaded_file_name = ("/tmp/sample-data/updated/" + f"updated.{author.decode('utf-8')}." + f"{trait_name}.{phenotype_id}." + f"{current_time}.csv") + file_.save(new_file_name) + csv_ = get_trait_csv_sample_data(conn=conn, + trait_name=str(trait_name), + phenotype_id=str(phenotype_id)) + with open(uploaded_file_name, "w") as f_: + f_.write(csv_) + r = run_cmd(cmd=("/home/bonface/opt/genenetwork3/bin/csvdiff " + f"'{uploaded_file_name}' '{new_file_name}' " + "--format json")) + diff_output = ("/tmp/sample-data/diffs/" + f"{trait_name}." + f"{phenotype_id}.{current_time}.json") + with open(diff_output, "w") as f: + print(r.get("output")) + dict_ = json.loads(r.get("output")) + dict_.update({"author": author.decode('utf-8')}) + dict_.update({"timestamp": datetime.datetime.now().strftime( + "%Y-%m-%d %H:%M:%S")}) + f.write(json.dumps(dict_)) # Run updates: phenotype_ = { "pre_pub_description": data_.get("pre-pub-desc"), @@ -582,7 +630,6 @@ def update_phenotype(): diff_data.update({"Publication": diff_from_dict(old={ k: data_.get(f"old_{k}") for k, v in publication_.items() if v is not None}, new=publication_)}) - author = g.user_session.record.get(b'user_name') if diff_data: diff_data.update({"dataset_id": data_.get("dataset-name")}) diff_data.update({"author": author.decode('utf-8')}) @@ -1320,10 +1367,10 @@ def get_sample_data_as_csv(trait_name: int, phenotype_id: int): user=current_app.config.get("DB_USER"), passwd=current_app.config.get("DB_PASS"), host=current_app.config.get("DB_HOST")) - csv_data = get_trait_csv_sample_data(conn, str(trait_name), - str(phenotype_id)) + csv_ = get_trait_csv_sample_data(conn, str(trait_name), + str(phenotype_id)) return Response( - csv_data, + csv_, mimetype="text/csv", headers={"Content-disposition": "attachment; filename=myplot.csv"} |