diff options
| -rw-r--r-- | wqflask/wqflask/metadata_edits.py | 162 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 62 |
2 files changed, 130 insertions, 94 deletions
diff --git a/wqflask/wqflask/metadata_edits.py b/wqflask/wqflask/metadata_edits.py index 2be54620..85bd9b08 100644 --- a/wqflask/wqflask/metadata_edits.py +++ b/wqflask/wqflask/metadata_edits.py @@ -49,6 +49,45 @@ from gn3.db.traits import update_sample_data metadata_edit = Blueprint('metadata_edit', __name__) +def _get_diffs(diff_dir: str, + user_id: str, + redis_conn: redis.Redis, + gn_proxy_url: str): + def __get_file_metadata(file_name: str) -> Dict: + author, resource_id, time_stamp, *_ = file_name.split(".") + + return { + "resource_id": resource_id, + "file_name": file_name, + "author": json.loads(redis_conn.hget("users", + author)).get("full_name"), + "time_stamp": time_stamp, + "roles": get_highest_user_access_role( + resource_id=resource_id, + user_id=user_id, + gn_proxy_url=gn_proxy_url), + } + + approved, rejected, waiting = [], [], [] + if os.path.exists(diff_dir): + for name in os.listdir(diff_dir): + file_metadata = __get_file_metadata(file_name=name) + admin_status = file_metadata["roles"].get("admin") + append_p = (user_id in name or + admin_status > AdminRole.EDIT_ACCESS) + if name.endswith(".rejected") and append_p: + rejected.append(__get_file_metadata(file_name=name)) + elif name.endswith(".approved") and append_p: + approved.append(__get_file_metadata(file_name=name)) + elif append_p: # Normal file + waiting.append(__get_file_metadata(file_name=name)) + return { + "approved": approved, + "rejected": rejected, + "waiting": waiting, + } + + def edit_phenotype(conn, name, dataset_id): publish_xref = fetchone( conn=conn, @@ -185,7 +224,7 @@ def update_phenotype(dataset_id: str, name: str): data_ = request.form.to_dict() TMPDIR = current_app.config.get("TMPDIR") author = ((g.user_session.record.get(b"user_id") or b"").decode("utf-8") - or g.user_session.record.get("user_id") or "") + or g.user_session.record.get("user_id") or "") phenotype_id = str(data_.get('phenotype-id')) if not (file_ := request.files.get("file")): flash("No sample-data has been uploaded", "warning") @@ -201,13 +240,13 @@ def update_phenotype(dataset_id: str, name: str): os.makedirs(os.path.join(SAMPLE_DATADIR, "updated")) current_time = str(datetime.datetime.now().isoformat()) - _file_name = (f"{request.args.get('resource-id')}." - f"{current_time}.csv") + _file_name = (f"{author}.{request.args.get('resource-id')}." + f"{current_time}") new_file_name = (os.path.join(TMPDIR, f"sample-data/updated/{_file_name}.csv")) uploaded_file_name = (os.path.join( - TMPDIR, "sample-data/updated/updated.", - f"{_file_name}.csv")) + TMPDIR, "sample-data/updated/", + f"{_file_name}.csv.uploaded")) file_.save(new_file_name) publishdata_id = "" lines = [] @@ -331,7 +370,7 @@ def update_probeset(name: str): } diff_data = {} author = ((g.user_session.record.get(b"user_id") or b"").decode("utf-8") - or g.user_session.record.get("user_id") or "") + or g.user_session.record.get("user_id") or "") if (updated_probeset := update( conn, "ProbeSet", data=Probeset(**probeset_), @@ -371,29 +410,88 @@ def get_sample_data_as_csv(dataset_id: str, phenotype_id: int): ) -# @metadata_edit.route("/diffs") -# @login_required -# def display_diffs_admin(): -# TMPDIR = current_app.config.get("TMPDIR") -# DIFF_DIR = f"{TMPDIR}/sample-data/diffs" -# approved_files, rejected_files, files = {}, {}, {} -# user_id = ((g.user_session.record.get(b"user_id") or -# b"").decode("utf-8") -# or g.user_session.record.get("user_id") or "") -# redis_conn = redis.from_url(current_app.config["REDIS_URL"], -# decode_responses=True) -# if os.path.exists(DIFF_DIR): -# for name in os.listdir(DIFF_DIR): -# if name.endswith(".approved"): - -# approved_file.update{ - -# } -# approved_files.add(name) -# elif name.endswith(".rejected"): -# approved_files.add(name) -# else: -# files.append(name) -# return render_template("display_files_admin.html", -# files=files) -# http://localhost:5004/datasets/diffs/admin +@metadata_edit.route("/diffs") +@login_required +def list_diffs(): + files = _get_diffs( + diff_dir=f"{current_app.config.get('TMPDIR')}/sample-data/diffs", + user_id=((g.user_session.record.get(b"user_id") or + b"").decode("utf-8") + or g.user_session.record.get("user_id") or ""), + redis_conn=redis.from_url(current_app.config["REDIS_URL"], + decode_responses=True), + gn_proxy_url=current_app.config.get("GN2_PROXY")) + return render_template( + "display_files.html", + approved=files.get("approved"), + rejected=files.get("rejected"), + waiting=files.get("waiting")) + + +@metadata_edit.route("/diffs/<name>") +def show_diff(name): + TMPDIR = current_app.config.get("TMPDIR") + with open(os.path.join(f"{TMPDIR}/sample-data/diffs", + name), 'r') as myfile: + content = myfile.read() + return Response(content, mimetype='text/json') + +# http://localhost:5004/datasets/diffs +@metadata_edit.route("<resource_id>/diffs/<file_name>/reject") +@edit_admins_access_required +@login_required +def reject_data(resource_id: str, file_name: str): + TMPDIR = current_app.config.get("TMPDIR") + os.rename(os.path.join(f"{TMPDIR}/sample-data/diffs", file_name), + os.path.join(f"{TMPDIR}/sample-data/diffs", + f"{file_name}.rejected")) + flash(f"{file_name} has been rejected!", "success") + return redirect(url_for('metadata_edit.list_diffs')) + + +@metadata_edit.route("<resource_id>/diffs/<file_name>/approve") +@edit_admins_access_required +@login_required +def approve_data(resource_id:str, file_name: str): + sample_data = {file_name: str} + conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"), + user=current_app.config.get("DB_USER"), + passwd=current_app.config.get("DB_PASS"), + host=current_app.config.get("DB_HOST")) + TMPDIR = current_app.config.get("TMPDIR") + with open(os.path.join(f"{TMPDIR}/sample-data/diffs", + file_name), 'r') as myfile: + sample_data = json.load(myfile) + PUBLISH_ID = sample_data.get("publishdata_id") + modifications = [d for d in sample_data.get("Modifications")] + row_counts = len(modifications) + for modification in modifications: + if modification.get("Current"): + (strain_id, + strain_name, + value, se, count) = modification.get("Current").split(",") + update_sample_data( + conn=conn, + strain_name=strain_name, + strain_id=int(strain_id), + publish_data_id=int(PUBLISH_ID), + value=value, + error=se, + count=count + ) + insert(conn, + table="metadata_audit", + data=MetadataAudit( + dataset_id=name.split(".")[0], # use the dataset name + editor=sample_data.get("author"), + json_data=json.dumps(sample_data))) + if modifications: + # Once data is approved, rename it! + os.rename(os.path.join(f"{TMPDIR}/sample-data/diffs", file_name), + os.path.join(f"{TMPDIR}/sample-data/diffs", + f"{file_name}.approved")) + flash((f"Just updated data from: {file_name}; {row_counts} " + "row(s) modified!"), + "success") + return redirect(url_for('metadata_edit.list_diffs')) + diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 3e53e4c5..2cbaffd6 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -1084,65 +1084,3 @@ def display_diffs_users(): files=files) -@app.route("/data-samples/approve/<name>") -def approve_data(name): - sample_data = {} - conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"), - user=current_app.config.get("DB_USER"), - passwd=current_app.config.get("DB_PASS"), - host=current_app.config.get("DB_HOST")) - TMPDIR = current_app.config.get("TMPDIR") - with open(os.path.join(f"{TMPDIR}/sample-data/diffs", - name), 'r') as myfile: - sample_data = json.load(myfile) - PUBLISH_ID = sample_data.get("publishdata_id") - modifications = [d for d in sample_data.get("Modifications")] - row_counts = len(modifications) - for modification in modifications: - if modification.get("Current"): - (strain_id, - strain_name, - value, se, count) = modification.get("Current").split(",") - update_sample_data( - conn=conn, - strain_name=strain_name, - strain_id=int(strain_id), - publish_data_id=int(PUBLISH_ID), - value=value, - error=se, - count=count - ) - insert(conn, - table="metadata_audit", - data=MetadataAudit( - dataset_id=name.split(".")[0], # use the dataset name - editor=sample_data.get("author"), - json_data=json.dumps(sample_data))) - if modifications: - # Once data is approved, rename it! - os.rename(os.path.join(f"{TMPDIR}/sample-data/diffs", name), - os.path.join(f"{TMPDIR}/sample-data/diffs", - f"{name}.approved")) - flash((f"Just updated data from: {name}; {row_counts} " - "row(s) modified!"), - "success") - return redirect("/admin/data-sample/diffs/") - - -@app.route("/data-samples/reject/<name>") -def reject_data(name): - TMPDIR = current_app.config.get("TMPDIR") - os.rename(os.path.join(f"{TMPDIR}/sample-data/diffs", name), - os.path.join(f"{TMPDIR}/sample-data/diffs", - f"{name}.rejected")) - flash(f"{name} has been rejected!", "success") - return redirect("/admin/data-sample/diffs/") - - -@app.route("/display-file/<name>") -def display_file(name): - TMPDIR = current_app.config.get("TMPDIR") - with open(os.path.join(f"{TMPDIR}/sample-data/diffs", - name), 'r') as myfile: - content = myfile.read() - return Response(content, mimetype='text/json') |