diff options
Diffstat (limited to 'gn2')
| -rw-r--r-- | gn2/wqflask/views.py | 64 |
1 files changed, 41 insertions, 23 deletions
diff --git a/gn2/wqflask/views.py b/gn2/wqflask/views.py index b70f5721..3b324719 100644 --- a/gn2/wqflask/views.py +++ b/gn2/wqflask/views.py @@ -155,6 +155,7 @@ def no_access_page(): @app.route("/") def index_page(): anon_id = session_info()["anon_id"] + def __render__(colls): return render_template("index_page.html", version=current_app.config.get("GN_VERSION"), gn_server_url=GN_SERVER_URL, @@ -261,27 +262,26 @@ def gsearchtable(): return flask.jsonify(current_page) - - -@app.route("/gnqna",methods =["POST","GET"]) +@app.route("/gnqna", methods=["POST", "GET"]) def gnqna(): if request.method == "POST": try: def __error__(resp): return resp.json() + def __success__(resp): - return render_template("gnqa_answer.html",**resp.json()) + return render_template("gnqa_answer.html", **resp.json()) return monad_requests.post( - urljoin(GN3_LOCAL_URL, - "/api/llm/gnqna"), + urljoin(current_app.config.get(GN_SERVER_URL), + "llm/gnqna"), json=dict(request.form), - ).then( - lambda resp: resp - ).either( - __error__, __success__) + ).then( + lambda resp: resp + ).either( + __error__, __success__) except Exception as error: - return flask.jsonify({"error":str(error)}) + return flask.jsonify({"error": str(error)}) return render_template("gnqa.html") @@ -526,7 +526,8 @@ def show_trait_page(): def __show_trait__(privileges_data): assert len(privileges_data) == 1 privileges_data = privileges_data[0] - trait_privileges = tuple(item for item in privileges_data["privileges"]) + trait_privileges = tuple( + item for item in privileges_data["privileges"]) with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor: user_id = ((g.user_session.record.get(b"user_id") or b"").decode("utf-8") @@ -573,7 +574,8 @@ def heatmap_page(): result = pickle.loads(result) else: - template_vars = heatmap.Heatmap(cursor, request.form, temp_uuid) + template_vars = heatmap.Heatmap( + cursor, request.form, temp_uuid) template_vars.js_data = json.dumps(template_vars.js_data, default=json_default_handler, indent=" ") @@ -851,6 +853,7 @@ def mapping_results_page(hash_of_inputs=None): return rendered_template + @app.route("/cache_mapping_inputs", methods=('POST',)) def cache_mapping_inputs(): cache_id = request.form.get("inputs_hash") @@ -859,6 +862,7 @@ def cache_mapping_inputs(): return "Success" + @app.route("/export_mapping_results", methods=('POST',)) def export_mapping_results(): file_path = request.form.get("results_path") @@ -916,25 +920,28 @@ def network_graph_page(): else: return render_template("empty_collection.html", **{'tool': 'Network Graph'}) + def __handle_correlation_error__(exc): return render_template( "correlation_error_page.html", - error = { + error={ "error-type": { "WrongCorrelationType": "Wrong Correlation Type" }[type(exc).__name__], "error-message": exc.args[0] }) + @app.route("/corr_compute", methods=('POST', 'GET')) def corr_compute_page(): with Redis.from_url(REDIS_URL, decode_responses=True) as rconn: if request.method == "POST": request_received = datetime.datetime.utcnow() - filename=hmac.hmac_creation(f"request_form_{request_received.isoformat()}") + filename = hmac.hmac_creation(f"request_form_{request_received.isoformat()}") filepath = f"{TMPDIR}{filename}" with open(filepath, "wb") as pfile: - pickle.dump(request.form, pfile, protocol=pickle.HIGHEST_PROTOCOL) + pickle.dump(request.form, pfile, + protocol=pickle.HIGHEST_PROTOCOL) job_id = jobs.queue( rconn, { "command": [ @@ -1135,6 +1142,7 @@ def get_dataset(name): dataset=metadata ) + @app.route("/datasets/search", methods=('POST',)) def search_for_dataset(): search = request.form.get('search') @@ -1143,6 +1151,7 @@ def search_for_dataset(): results=search ) + @app.route("/publications/<name>", methods=('GET',)) def get_publication(name): metadata = requests.get( @@ -1198,6 +1207,7 @@ def get_genotype(name): metadata=metadata, ) + @app.route("/case-attribute/<int:inbredset_id>/edit", methods=["GET", "POST"]) def edit_case_attributes(inbredset_id: int) -> Response: """ @@ -1205,8 +1215,10 @@ def edit_case_attributes(inbredset_id: int) -> Response: """ if request.method == "POST": form = request.form + def __process_data__(acc, item): - _new, strain, calabel = tuple(val.strip() for val in item[0].split(":")) + _new, strain, calabel = tuple(val.strip() + for val in item[0].split(":")) old_row = acc.get(strain, {}) return { **acc, @@ -1222,6 +1234,7 @@ def edit_case_attributes(inbredset_id: int) -> Response: "edit_case_attributes", inbredset_id=inbredset_id)) token = session_info()["user"]["token"].either( lambda err: err, lambda tok: tok["access_token"]) + def flash_success(resp): def __succ__(remote_resp): flash(f"Success: {remote_resp.json()['message']}", "alert-success") @@ -1236,8 +1249,8 @@ def edit_case_attributes(inbredset_id: int) -> Response: }, headers={ "Authorization": f"Bearer {token}"}).either( - with_flash_error(edit_case_attributes_page), - flash_success(edit_case_attributes_page)) + with_flash_error(edit_case_attributes_page), + flash_success(edit_case_attributes_page)) def __fetch_strains__(inbredset_group): return monad_requests.get(urljoin( @@ -1264,10 +1277,11 @@ def edit_case_attributes(inbredset_id: int) -> Response: lambda resp: {"inbredset_group": resp.json()}).then( __fetch_strains__).then(__fetch_names__).then( __fetch_values__).either( - lambda err: err, ## TODO: Handle error better + lambda err: err, # TODO: Handle error better lambda values: render_template( "edit_case_attributes.html", inbredset_id=inbredset_id, **values)) + @app.route("/case-attribute/<int:inbredset_id>/list-diffs", methods=["GET"]) def list_case_attribute_diffs(inbredset_id: int) -> Response: """List any diffs awaiting review.""" @@ -1280,12 +1294,13 @@ def list_case_attribute_diffs(inbredset_id: int) -> Response: inbredset_id=inbredset_id, error=err), lambda diffs: render_template( - "list_case_attribute_diffs.html", + "list_case_attribute_diffs.html", inbredset_id=inbredset_id, diffs=diffs)) + @app.route("/case-attribute/<int:inbredset_id>/diff/<int:diff_id>/view", methods=["GET"]) -def view_diff(inbredset_id:int, diff_id: int) -> Response: +def view_diff(inbredset_id: int, diff_id: int) -> Response: """View the pending diff.""" token = session_info()["user"]["token"].either( lambda err: err, lambda tok: tok["access_token"]) @@ -1299,6 +1314,7 @@ def view_diff(inbredset_id:int, diff_id: int) -> Response: lambda diff: render_template( "view_case_attribute_diff.html", diff=diff)) + @app.route("/case-attribute/diff/approve-reject", methods=["POST"]) def approve_reject_diff() -> Response: """Approve/Reject the diff.""" @@ -1319,12 +1335,14 @@ def approve_reject_diff() -> Response: inbredset_id=inbredset_id) token = session_info()["user"]["token"].either( lambda err: err, lambda tok: tok["access_token"]) + def __error__(resp): error = resp.json() flash((f"{resp.status_code} {error['error']}: " f"{error['error_description']}"), "alert-danger") return redirect(list_diffs_page) + def __success__(results): flash(results["message"], "alert-success") return redirect(list_diffs_page) @@ -1333,7 +1351,7 @@ def approve_reject_diff() -> Response: f"/api/case-attribute/{action}/{filename}"), headers={"Authorization": f"Bearer {token}"}).then( lambda resp: resp.json() - ).either( + ).either( __error__, __success__) except AssertionError as _ae: flash("Invalid action! Expected either 'approve' or 'reject'.", |