From 19e781e9f8dc8bfaeacfb3f86c3823fe4f6f1218 Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Tue, 14 May 2024 12:56:43 +0300 Subject: Revert "Disable gnqa functionality." This reverts commit 01eba6e9b54e45bc937983e33b439a353118de2c. --- gn2/wqflask/templates/base.html | 3 +-- gn2/wqflask/views.py | 6 +----- 2 files changed, 2 insertions(+), 7 deletions(-) diff --git a/gn2/wqflask/templates/base.html b/gn2/wqflask/templates/base.html index 14b484a5..26b75230 100644 --- a/gn2/wqflask/templates/base.html +++ b/gn2/wqflask/templates/base.html @@ -183,11 +183,10 @@ - + diff --git a/gn2/wqflask/views.py b/gn2/wqflask/views.py index 9f403ace..843ed07a 100644 --- a/gn2/wqflask/views.py +++ b/gn2/wqflask/views.py @@ -255,12 +255,8 @@ def gsearchtable(): return flask.jsonify(current_page) -"""@app.route("/gnqna", methods=["POST", "GET"]) ;;feature currently disabled -;;use ga.genenetwork.org +@app.route("/gnqna", methods=["POST", "GET"]) @require_oauth2 -""" - - def gnqna(): if request.method == "POST": -- cgit v1.2.3 From 1202ce35e22ec765deacf65724fbaa235aeafb20 Mon Sep 17 00:00:00 2001 From: Alexander_Kabui Date: Tue, 14 May 2024 13:17:39 +0300 Subject: Bug: fix issue form submission happening twice --- gn2/wqflask/templates/gnqa.html | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/gn2/wqflask/templates/gnqa.html b/gn2/wqflask/templates/gnqa.html index 1268ef39..8b50fe43 100644 --- a/gn2/wqflask/templates/gnqa.html +++ b/gn2/wqflask/templates/gnqa.html @@ -118,12 +118,8 @@ type="text" autocomplete="on" required placeholder="Ask More Questions or Topics (E.g Genes)" - value='' + value='' name="querygnqa" - hx-post="/gnqna" - hx-target="#swap" - hx-swap="innerHTML" - hx-indicator="#indicator" /> -- cgit v1.2.3 From 16f978ecdaf450cfa700bd6e78194831ed9a8f57 Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Tue, 14 May 2024 15:33:00 +0300 Subject: Use correct URL when redirecting user after a new registration. Signed-off-by: Munyoki Kilyungi --- gn2/wqflask/oauth2/users.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gn2/wqflask/oauth2/users.py b/gn2/wqflask/oauth2/users.py index 2407703c..8a935170 100644 --- a/gn2/wqflask/oauth2/users.py +++ b/gn2/wqflask/oauth2/users.py @@ -116,7 +116,7 @@ def register_user(): return redirect(url_for("oauth2.user.register_user")) flash("Registration successful! Please login to continue.", "alert-success") - return redirect(url_for("/")) + return redirect("/") @users.route("/masquerade", methods=["GET", "POST"]) def masquerade(): -- cgit v1.2.3 From cfbb1a847d20a726ff286734cba3fa429b4e93c4 Mon Sep 17 00:00:00 2001 From: Alexander_Kabui Date: Wed, 22 May 2024 13:53:32 +0300 Subject: Refactor template code for gnqa search history --- gn2/wqflask/templates/gnqa.html | 4 ++-- gn2/wqflask/templates/gnqa_search_history.html | 10 ++++------ 2 files changed, 6 insertions(+), 8 deletions(-) diff --git a/gn2/wqflask/templates/gnqa.html b/gn2/wqflask/templates/gnqa.html index 8b50fe43..b3bc74fd 100644 --- a/gn2/wqflask/templates/gnqa.html +++ b/gn2/wqflask/templates/gnqa.html @@ -93,7 +93,7 @@ AI Search - @@ -107,7 +107,7 @@ - {% endfor %} -- cgit v1.2.3 From 292f4ab25508ef2e72a0caac6e609317113be232 Mon Sep 17 00:00:00 2001 From: Alexander_Kabui Date: Wed, 22 May 2024 14:00:30 +0300 Subject: View file code cleanup for gnqa. --- gn2/wqflask/views.py | 46 ++++++++++------------------------------------ 1 file changed, 10 insertions(+), 36 deletions(-) diff --git a/gn2/wqflask/views.py b/gn2/wqflask/views.py index 843ed07a..5d0075c5 100644 --- a/gn2/wqflask/views.py +++ b/gn2/wqflask/views.py @@ -258,23 +258,14 @@ def gsearchtable(): @app.route("/gnqna", methods=["POST", "GET"]) @require_oauth2 def gnqna(): - if request.method == "POST": try: - def __error__(resp): - return resp.json() - def error_page(resp): return render_template("gnqa_errors.html", **{"status_code": resp.status_code, **resp.json()}) def __success__(resp): return render_template("gnqa_answer.html", **{"gn_server_url": GN3_LOCAL_URL, **(resp.json())}) - """ - disable gn-auth currently not stable - if not user_logged_in(): - return error_page("Please Login/Register to Genenetwork to access this Service") - """ token = session_info()["user"]["token"].either( lambda err: err, lambda tok: tok["access_token"]) return monad_requests.post( @@ -290,44 +281,27 @@ def gnqna(): error_page, __success__) except Exception as error: return flask.jsonify({"error": str(error)}) - prev_queries = (monad_requests.get( - urljoin(GN3_LOCAL_URL, - "/api/llm/get_hist_names") - ).then( - lambda resp: resp - ).either(lambda x: [], lambda x: x.json()["prev_queries"])) - - return render_template("gnqa.html", prev_queries=prev_queries) - - -@app.route("/gnqna/hist/", methods=["GET"]) -@require_oauth2 -def get_hist_titles(): - token = session_info()["user"]["token"].either( - lambda err: err, lambda tok: tok["access_token"]) - response = monad_requests.get(urljoin(GN3_LOCAL_URL, - "/api/llm/hist/titles"), - headers={ - "Authorization": f"Bearer {token}" - } - ).then(lambda resp: resp).either( - lambda x: x.json(), lambda x: x.json()) - return render_template("gnqa_search_history.html", **response) + return render_template("gnqa.html") -@app.route("/gnqna/hist/search/", methods=["GET"]) +@app.route("/gnqna/hist", methods=["GET"]) @require_oauth2 -def fetch_hist_records(search_term): +def get_gnqa_history(): token = session_info()["user"]["token"].either( lambda err: err, lambda tok: tok["access_token"]) response = monad_requests.get(urljoin(GN3_LOCAL_URL, - f"/api/llm/history/{search_term}"), + (f"/api/llm/history?search_term={request.args.get('search_term')}" + if request.args.get("search_term") else "/api/llm/history")), headers={ "Authorization": f"Bearer {token}" } ).then(lambda resp: resp).either( lambda x: x.json(), lambda x: x.json()) - return render_template("gnqa_answer.html", **response) + if request.args.get("search_term"): + return render_template("gnqa_answer.html", + **{"gn_server_url": "GN3_LOCAL_URL", **response}) + return render_template("gnqa_search_history.html", + prev_queries=response) @app.route("/gnqna/rating//", -- cgit v1.2.3 From 13a554a9744bc70da9606c0348ec675276147a29 Mon Sep 17 00:00:00 2001 From: Alexander_Kabui Date: Thu, 23 May 2024 14:47:27 +0300 Subject: Update endpoints and add search history functionality. --- gn2/wqflask/templates/gnqa_search_history.html | 29 +++++++++++++------------- gn2/wqflask/views.py | 11 ++++++---- 2 files changed, 22 insertions(+), 18 deletions(-) diff --git a/gn2/wqflask/templates/gnqa_search_history.html b/gn2/wqflask/templates/gnqa_search_history.html index af38392a..890a3995 100644 --- a/gn2/wqflask/templates/gnqa_search_history.html +++ b/gn2/wqflask/templates/gnqa_search_history.html @@ -1,39 +1,40 @@
-
-

You search History

+

Your AI search History

-
- {% for (key,val) in prev_queries.items() %} -
-
- +
+
+
    + {% for item in prev_queries %} +
  • +
    -
    -
-
- {% endfor %} +
+ + {% endfor %} +
diff --git a/gn2/wqflask/views.py b/gn2/wqflask/views.py index 5d0075c5..5bb443c1 100644 --- a/gn2/wqflask/views.py +++ b/gn2/wqflask/views.py @@ -270,7 +270,7 @@ def gnqna(): lambda err: err, lambda tok: tok["access_token"]) return monad_requests.post( urljoin(GN3_LOCAL_URL, - "/api/llm/gnqna"), + "/api/llm/search"), json=dict(request.form), headers={ "Authorization": f"Bearer {token}" @@ -287,6 +287,10 @@ def gnqna(): @app.route("/gnqna/hist", methods=["GET"]) @require_oauth2 def get_gnqa_history(): + def _error_(resp): + return render_template("gnqa_errors.html", + **{"status_code": resp.status_code, + **resp.json()}) token = session_info()["user"]["token"].either( lambda err: err, lambda tok: tok["access_token"]) response = monad_requests.get(urljoin(GN3_LOCAL_URL, @@ -296,10 +300,9 @@ def get_gnqa_history(): "Authorization": f"Bearer {token}" } ).then(lambda resp: resp).either( - lambda x: x.json(), lambda x: x.json()) + _error_, lambda x: x.json()) if request.args.get("search_term"): - return render_template("gnqa_answer.html", - **{"gn_server_url": "GN3_LOCAL_URL", **response}) + return render_template("gnqa_answer.html", **response) return render_template("gnqa_search_history.html", prev_queries=response) -- cgit v1.2.3 From 066adb63d2a539693a60fd2d120922de324a65ea Mon Sep 17 00:00:00 2001 From: Alexander_Kabui Date: Fri, 24 May 2024 18:04:25 +0300 Subject: Add UI code for gnqa history search delete functionality. --- gn2/wqflask/templates/gnqa_search_history.html | 25 +++++++++++++++++++++---- 1 file changed, 21 insertions(+), 4 deletions(-) diff --git a/gn2/wqflask/templates/gnqa_search_history.html b/gn2/wqflask/templates/gnqa_search_history.html index 890a3995..c1e66541 100644 --- a/gn2/wqflask/templates/gnqa_search_history.html +++ b/gn2/wqflask/templates/gnqa_search_history.html @@ -11,12 +11,17 @@
-
+
+
+ +
+
+
-
    +
      {% for item in prev_queries %}
    • -
-
+ +{% block js %} + + +{% endblock %} -- cgit v1.2.3 From eff7011aa002aea41cd71d7cb0b21b9ab938ffc4 Mon Sep 17 00:00:00 2001 From: Alexander_Kabui Date: Mon, 27 May 2024 17:39:40 +0300 Subject: Mark answer and references as safe to render a tags. --- gn2/wqflask/templates/gnqa_answer.html | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gn2/wqflask/templates/gnqa_answer.html b/gn2/wqflask/templates/gnqa_answer.html index 0ddcfde7..62ce70d9 100644 --- a/gn2/wqflask/templates/gnqa_answer.html +++ b/gn2/wqflask/templates/gnqa_answer.html @@ -3,7 +3,7 @@

{{ query }}
- {{ answer }} + {{ answer|safe }}

@@ -32,7 +32,7 @@
-

{{ reference.comboTxt }}

+

{{ reference.comboTxt|safe }}

{% if reference.pubmed %}
@@ -60,7 +60,7 @@
-

{{reference.comboTxt}}

+

{{ reference.comboTxt|safe }}

{% if reference.pubmed %}
-- cgit v1.2.3 From 8edf35d35b91ca27f70d958f668589cfda201f52 Mon Sep 17 00:00:00 2001 From: Alexander_Kabui Date: Tue, 28 May 2024 17:35:49 +0300 Subject: Fix bug: Update DOM correctly when rating error occurs. --- gn2/wqflask/templates/gnqa_answer.html | 27 +++++++++++++++++---------- 1 file changed, 17 insertions(+), 10 deletions(-) diff --git a/gn2/wqflask/templates/gnqa_answer.html b/gn2/wqflask/templates/gnqa_answer.html index 62ce70d9..41c1b338 100644 --- a/gn2/wqflask/templates/gnqa_answer.html +++ b/gn2/wqflask/templates/gnqa_answer.html @@ -6,7 +6,7 @@ {{ answer|safe }}

- + @@ -93,20 +93,27 @@ {% block js %} {% endblock %} -- cgit v1.2.3 From c7b1210c1a8716ef045a1291bca76c1d822c134f Mon Sep 17 00:00:00 2001 From: Alexander_Kabui Date: Tue, 28 May 2024 17:51:59 +0300 Subject: BugFix: return correct status code for generic exceptions handler. --- gn2/wqflask/views.py | 1 + 1 file changed, 1 insertion(+) diff --git a/gn2/wqflask/views.py b/gn2/wqflask/views.py index 5bb443c1..5bfcce83 100644 --- a/gn2/wqflask/views.py +++ b/gn2/wqflask/views.py @@ -137,6 +137,7 @@ def handle_generic_exceptions(e): stack={formatted_lines}, error_image=animation, version=current_app.config.get("GN_VERSION"))) + resp.status_code = exc_type.code or 500 resp.set_cookie(err_msg[:32], animation) return resp -- cgit v1.2.3 From 034b50502a6d15bccd52211a8bb282d46ac1558e Mon Sep 17 00:00:00 2001 From: Alexander_Kabui Date: Wed, 29 May 2024 12:47:12 +0300 Subject: Handle attributeError when getting error codes. --- gn2/wqflask/views.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/gn2/wqflask/views.py b/gn2/wqflask/views.py index 5bfcce83..8f1c62ff 100644 --- a/gn2/wqflask/views.py +++ b/gn2/wqflask/views.py @@ -137,7 +137,10 @@ def handle_generic_exceptions(e): stack={formatted_lines}, error_image=animation, version=current_app.config.get("GN_VERSION"))) - resp.status_code = exc_type.code or 500 + try: + resp.status_code = exc_type.code + except AttributeError: + resp.status_code = 500 resp.set_cookie(err_msg[:32], animation) return resp -- cgit v1.2.3 From 30e5a84940bd9715bea02d07c5092bbfd717f7c5 Mon Sep 17 00:00:00 2001 From: Alexander_Kabui Date: Wed, 29 May 2024 14:05:44 +0300 Subject: integrate gnqa history delete functionality. --- gn2/wqflask/views.py | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/gn2/wqflask/views.py b/gn2/wqflask/views.py index 8f1c62ff..666e765a 100644 --- a/gn2/wqflask/views.py +++ b/gn2/wqflask/views.py @@ -288,7 +288,8 @@ def gnqna(): return render_template("gnqa.html") -@app.route("/gnqna/hist", methods=["GET"]) + +@app.route("/gnqna/hist", methods=["GET", "DELETE"]) @require_oauth2 def get_gnqa_history(): def _error_(resp): @@ -297,6 +298,14 @@ def get_gnqa_history(): **resp.json()}) token = session_info()["user"]["token"].either( lambda err: err, lambda tok: tok["access_token"]) + if request.method == "DELETE": + monad_requests.post(urljoin(GN3_LOCAL_URL, "/api/llm/history"), + json=dict(request.form), + headers={ + "Authorization": f"Bearer {token}" + } + ).either( + _error_, lambda x: x.json()) response = monad_requests.get(urljoin(GN3_LOCAL_URL, (f"/api/llm/history?search_term={request.args.get('search_term')}" if request.args.get("search_term") else "/api/llm/history")), -- cgit v1.2.3 From 842a758f31143a5934b2798a4d0f40f11a402919 Mon Sep 17 00:00:00 2001 From: Alexander_Kabui Date: Wed, 29 May 2024 14:27:40 +0300 Subject: Add htmx js api for delete functionality. --- gn2/wqflask/templates/gnqa_search_history.html | 18 ++++++------------ 1 file changed, 6 insertions(+), 12 deletions(-) diff --git a/gn2/wqflask/templates/gnqa_search_history.html b/gn2/wqflask/templates/gnqa_search_history.html index c1e66541..976fd7fd 100644 --- a/gn2/wqflask/templates/gnqa_search_history.html +++ b/gn2/wqflask/templates/gnqa_search_history.html @@ -1,4 +1,4 @@ -
+
@@ -15,8 +15,8 @@
-
-
+
+
    {% for item in prev_queries %} @@ -44,15 +44,9 @@
-{% block js %} - - -{% endblock %} -- cgit v1.2.3 From 0f4c9fbe37ed74022d9fad35352b59d948789818 Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Wed, 28 Aug 2024 14:58:16 +0300 Subject: Revert "Feature/gnqa search history" --- gn2/wqflask/templates/gnqa.html | 4 +- gn2/wqflask/templates/gnqa_answer.html | 33 ++++++------- gn2/wqflask/templates/gnqa_search_history.html | 46 ++++++++---------- gn2/wqflask/views.py | 64 +++++++++++++++----------- 4 files changed, 70 insertions(+), 77 deletions(-) diff --git a/gn2/wqflask/templates/gnqa.html b/gn2/wqflask/templates/gnqa.html index b3bc74fd..8b50fe43 100644 --- a/gn2/wqflask/templates/gnqa.html +++ b/gn2/wqflask/templates/gnqa.html @@ -93,7 +93,7 @@ AI Search - @@ -107,7 +107,7 @@ + @@ -32,7 +32,7 @@
-

{{ reference.comboTxt|safe }}

+

{{ reference.comboTxt }}

{% if reference.pubmed %}
@@ -60,7 +60,7 @@
-

{{ reference.comboTxt|safe }}

+

{{reference.comboTxt}}

{% if reference.pubmed %}
@@ -93,27 +93,20 @@ {% block js %} {% endblock %} diff --git a/gn2/wqflask/templates/gnqa_search_history.html b/gn2/wqflask/templates/gnqa_search_history.html index 976fd7fd..2c07b8c0 100644 --- a/gn2/wqflask/templates/gnqa_search_history.html +++ b/gn2/wqflask/templates/gnqa_search_history.html @@ -1,52 +1,42 @@ -
+
+
-

Your AI search History

+

You search History

-
-
- -
-
-
-
-
    - {% for item in prev_queries %} -
  • - +
    + {% for record in prev_queries %} +
    +
    +
    + {% for id,val in record.items() %} -
    -
    • - {% endfor %} -
+ {% endfor %} +
+
+
+ {% endfor %}
- - + diff --git a/gn2/wqflask/views.py b/gn2/wqflask/views.py index 666e765a..843ed07a 100644 --- a/gn2/wqflask/views.py +++ b/gn2/wqflask/views.py @@ -137,10 +137,6 @@ def handle_generic_exceptions(e): stack={formatted_lines}, error_image=animation, version=current_app.config.get("GN_VERSION"))) - try: - resp.status_code = exc_type.code - except AttributeError: - resp.status_code = 500 resp.set_cookie(err_msg[:32], animation) return resp @@ -262,19 +258,28 @@ def gsearchtable(): @app.route("/gnqna", methods=["POST", "GET"]) @require_oauth2 def gnqna(): + if request.method == "POST": try: + def __error__(resp): + return resp.json() + def error_page(resp): return render_template("gnqa_errors.html", **{"status_code": resp.status_code, **resp.json()}) def __success__(resp): return render_template("gnqa_answer.html", **{"gn_server_url": GN3_LOCAL_URL, **(resp.json())}) + """ + disable gn-auth currently not stable + if not user_logged_in(): + return error_page("Please Login/Register to Genenetwork to access this Service") + """ token = session_info()["user"]["token"].either( lambda err: err, lambda tok: tok["access_token"]) return monad_requests.post( urljoin(GN3_LOCAL_URL, - "/api/llm/search"), + "/api/llm/gnqna"), json=dict(request.form), headers={ "Authorization": f"Bearer {token}" @@ -285,39 +290,44 @@ def gnqna(): error_page, __success__) except Exception as error: return flask.jsonify({"error": str(error)}) - return render_template("gnqa.html") + prev_queries = (monad_requests.get( + urljoin(GN3_LOCAL_URL, + "/api/llm/get_hist_names") + ).then( + lambda resp: resp + ).either(lambda x: [], lambda x: x.json()["prev_queries"])) + return render_template("gnqa.html", prev_queries=prev_queries) -@app.route("/gnqna/hist", methods=["GET", "DELETE"]) +@app.route("/gnqna/hist/", methods=["GET"]) @require_oauth2 -def get_gnqa_history(): - def _error_(resp): - return render_template("gnqa_errors.html", - **{"status_code": resp.status_code, - **resp.json()}) +def get_hist_titles(): + token = session_info()["user"]["token"].either( + lambda err: err, lambda tok: tok["access_token"]) + response = monad_requests.get(urljoin(GN3_LOCAL_URL, + "/api/llm/hist/titles"), + headers={ + "Authorization": f"Bearer {token}" + } + ).then(lambda resp: resp).either( + lambda x: x.json(), lambda x: x.json()) + return render_template("gnqa_search_history.html", **response) + + +@app.route("/gnqna/hist/search/", methods=["GET"]) +@require_oauth2 +def fetch_hist_records(search_term): token = session_info()["user"]["token"].either( lambda err: err, lambda tok: tok["access_token"]) - if request.method == "DELETE": - monad_requests.post(urljoin(GN3_LOCAL_URL, "/api/llm/history"), - json=dict(request.form), - headers={ - "Authorization": f"Bearer {token}" - } - ).either( - _error_, lambda x: x.json()) response = monad_requests.get(urljoin(GN3_LOCAL_URL, - (f"/api/llm/history?search_term={request.args.get('search_term')}" - if request.args.get("search_term") else "/api/llm/history")), + f"/api/llm/history/{search_term}"), headers={ "Authorization": f"Bearer {token}" } ).then(lambda resp: resp).either( - _error_, lambda x: x.json()) - if request.args.get("search_term"): - return render_template("gnqa_answer.html", **response) - return render_template("gnqa_search_history.html", - prev_queries=response) + lambda x: x.json(), lambda x: x.json()) + return render_template("gnqa_answer.html", **response) @app.route("/gnqna/rating//", -- cgit v1.2.3 From 9671e9ef4bc20d562b831f97c52b40e91b1d4c20 Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Mon, 20 May 2024 12:55:52 +0300 Subject: Check metadata exists before setting 'editable' field in get_dataset. Signed-off-by: Munyoki Kilyungi --- gn2/wqflask/views.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gn2/wqflask/views.py b/gn2/wqflask/views.py index 843ed07a..a7bc8fa2 100644 --- a/gn2/wqflask/views.py +++ b/gn2/wqflask/views.py @@ -1230,8 +1230,8 @@ def get_dataset(name): lambda err: {"roles": []}, lambda val: val ) - - metadata["editable"] = "group:resource:edit-resource" in result["roles"] + if metadata: + metadata["editable"] = "group:resource:edit-resource" in result["roles"] return render_template( "dataset.html", name=name, -- cgit v1.2.3 From dc1485253ef4b9a4c2c1af45a56eff4018bc6d07 Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Mon, 20 May 2024 12:56:03 +0300 Subject: Remove styling for search field. Signed-off-by: Munyoki Kilyungi --- gn2/wqflask/templates/dataset.html | 27 +-------------------------- 1 file changed, 1 insertion(+), 26 deletions(-) diff --git a/gn2/wqflask/templates/dataset.html b/gn2/wqflask/templates/dataset.html index 096a3724..62fac650 100644 --- a/gn2/wqflask/templates/dataset.html +++ b/gn2/wqflask/templates/dataset.html @@ -40,31 +40,6 @@ .panel-metadata dt::after { content: ":"; } - - .search { - width: 50%; - margin: 1em auto; - } - .has-search .form-control-feedback { - right: initial; - left: 0; - color: #ccc; - } - - .has-search .form-control { - padding-right: 12px; - padding-left: 34px; - } - - .search { - transform: scale(1.5, 1.5); - } - .search input { - min-width: 17em; - } - .dataset-search { - padding: 0 17%; - } {% endblock %} @@ -348,7 +323,7 @@
{% else %} -
+

We appreciate your interest, but unfortunately, we don't have any additional information available for: {{ name }}. If you have other inquiries or need assistance with something else, please don't hesitate to get in touch with us.

-- cgit v1.2.3 From 8734f97b1d2c6dd20ec42de513009252d214f38b Mon Sep 17 00:00:00 2001 From: zsloan Date: Tue, 21 May 2024 17:27:18 +0000 Subject: Change default for Mean Expr filter to OR for correlations to avoid excluding any results when the page first loads --- gn2/wqflask/templates/correlation_page.html | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gn2/wqflask/templates/correlation_page.html b/gn2/wqflask/templates/correlation_page.html index 24eaff1f..07118145 100644 --- a/gn2/wqflask/templates/correlation_page.html +++ b/gn2/wqflask/templates/correlation_page.html @@ -69,8 +69,8 @@ , with mean > mean < -- cgit v1.2.3 From 31c8f14df9f354ea3cef82c28ce3d9006d424b65 Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 22 May 2024 19:58:50 +0000 Subject: Check if case attribute for RRID is a list, to prevent it being added twice in situations where a sample appears in both the parent/f1 file and the .geno file --- gn2/wqflask/show_trait/SampleList.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gn2/wqflask/show_trait/SampleList.py b/gn2/wqflask/show_trait/SampleList.py index 64fc8fe6..64909d6e 100644 --- a/gn2/wqflask/show_trait/SampleList.py +++ b/gn2/wqflask/show_trait/SampleList.py @@ -81,7 +81,8 @@ class SampleList: sample.extra_attributes['36'].append( webqtlConfig.RRID_MOUSE_URL % the_rrid) elif self.dataset.group.species == "rat": - if len(rrid_string): + # Check if it's a list just in case a parent/f1 strain also shows up in the .geno file, to avoid being added twice + if len(rrid_string) and not isinstance(sample.extra_attributes['36'], list): the_rrid = rrid_string.split("_")[1] sample.extra_attributes['36'] = [ rrid_string] -- cgit v1.2.3 From c871b5019ebaf1c57e7c9666b741cfa6a5393942 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Thu, 23 May 2024 09:40:16 -0500 Subject: Bug: Compute numeric timestamp for the claims. --- gn2/wqflask/oauth2/toplevel.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gn2/wqflask/oauth2/toplevel.py b/gn2/wqflask/oauth2/toplevel.py index 23965cc1..f0179250 100644 --- a/gn2/wqflask/oauth2/toplevel.py +++ b/gn2/wqflask/oauth2/toplevel.py @@ -47,7 +47,7 @@ def authorisation_code(): "iss": str(oauth2_clientid()), "sub": request.args["user_id"], "aud": urljoin(authserver_uri(), "auth/token"), - "exp": (issued + datetime.timedelta(minutes=5)), + "exp": (issued + datetime.timedelta(minutes=5)).timestamp(), "nbf": int(issued.timestamp()), "iat": int(issued.timestamp()), "jti": str(uuid.uuid4())}, -- cgit v1.2.3 From 32832d2a78485b1180c4bebb16aa8f3723851b6d Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 31 May 2024 20:24:30 +0000 Subject: Restore collections endpoints Import was removed in commit 7c77ff91f6530aca0865bd13025811f2f93e3541 because it wasn't being used in views.py, but it was providing the collections endpoints albeit indirectly. This commit makes it somewhat explicit that it is a needed module. --- gn2/gn2_main.py | 1 + 1 file changed, 1 insertion(+) diff --git a/gn2/gn2_main.py b/gn2/gn2_main.py index 38444620..197eed83 100644 --- a/gn2/gn2_main.py +++ b/gn2/gn2_main.py @@ -15,5 +15,6 @@ from gn2.wqflask import search_results from gn2.wqflask import resource_manager from gn2.wqflask import update_search_results +import gn2.wqflask.collect import gn2.wqflask.views import gn2.wqflask.partial_correlations_views -- cgit v1.2.3 From 385b6b861e6586bf1dd985b3aa416124835f07a1 Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 31 May 2024 21:17:30 +0000 Subject: Enable NA sorting for case attributes The NA-excluding sort functions were moved to table_functions.js (and removed from search_results.js) so they can be used by other pages (in this case the show_trait page) --- .../new/javascript/initialize_show_trait_tables.js | 2 +- .../static/new/javascript/search_results.js | 47 ---------------------- .../static/new/javascript/table_functions.js | 47 ++++++++++++++++++++++ 3 files changed, 48 insertions(+), 48 deletions(-) diff --git a/gn2/wqflask/static/new/javascript/initialize_show_trait_tables.js b/gn2/wqflask/static/new/javascript/initialize_show_trait_tables.js index 44076c17..970a49a3 100644 --- a/gn2/wqflask/static/new/javascript/initialize_show_trait_tables.js +++ b/gn2/wqflask/static/new/javascript/initialize_show_trait_tables.js @@ -141,7 +141,7 @@ buildColumns = function() { columnList.push( { 'title': "
" + js_data.attributes[attrKeys[i]].name + "
", - 'type': "natural", + 'type': "natural-minus-na", 'data': null, 'targets': attrStart + i, 'render': function(data, type, row, meta) { diff --git a/gn2/wqflask/static/new/javascript/search_results.js b/gn2/wqflask/static/new/javascript/search_results.js index c263ef49..29050c2b 100644 --- a/gn2/wqflask/static/new/javascript/search_results.js +++ b/gn2/wqflask/static/new/javascript/search_results.js @@ -325,53 +325,6 @@ $(function() { $("#export_traits").click(exportTraits); $("#export_collection").click(exportCollection); - let naturalAsc = $.fn.dataTableExt.oSort["natural-ci-asc"] - let naturalDesc = $.fn.dataTableExt.oSort["natural-ci-desc"] - - let na_equivalent_vals = ["N/A", "--", ""]; //ZS: Since there are multiple values that should be treated the same as N/A - - function extractInnerText(the_string){ - var span = document.createElement('span'); - span.innerHTML = the_string; - return span.textContent || span.innerText; - } - - function sortNAs(a, b, sort_function){ - if ( na_equivalent_vals.includes(a) && na_equivalent_vals.includes(b)) { - return 0; - } - if (na_equivalent_vals.includes(a)){ - return 1 - } - if (na_equivalent_vals.includes(b)) { - return -1; - } - return sort_function(a, b) - } - - $.extend( $.fn.dataTableExt.oSort, { - "natural-minus-na-asc": function (a, b) { - return sortNAs(extractInnerText(a), extractInnerText(b), naturalAsc) - }, - "natural-minus-na-desc": function (a, b) { - return sortNAs(extractInnerText(a), extractInnerText(b), naturalDesc) - } - }); - - $.fn.dataTable.ext.order['dom-checkbox'] = function ( settings, col ) - { - return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) { - return $('input', td).prop('checked') ? '1' : '0'; - } ); - }; - - $.fn.dataTable.ext.order['dom-inner-text'] = function ( settings, col ) - { - return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) { - return $(td).text(); - } ); - } - applyDefault = function() { let default_collection_id = $.cookie('default_collection'); if (default_collection_id) { diff --git a/gn2/wqflask/static/new/javascript/table_functions.js b/gn2/wqflask/static/new/javascript/table_functions.js index 62888cd9..a648778e 100644 --- a/gn2/wqflask/static/new/javascript/table_functions.js +++ b/gn2/wqflask/static/new/javascript/table_functions.js @@ -88,3 +88,50 @@ function saveColumnSettings(tableId, traitTable) { // Save (or update) the settings in localStorage localStorage.setItem(tableId, JSON.stringify(userColumnDefs)); } + +let naturalAsc = $.fn.dataTableExt.oSort["natural-ci-asc"] +let naturalDesc = $.fn.dataTableExt.oSort["natural-ci-desc"] + +let na_equivalent_vals = ["N/A", "--", "", "NULL"]; //ZS: Since there are multiple values that should be treated the same as N/A + +function extractInnerText(the_string){ + var span = document.createElement('span'); + span.innerHTML = the_string; + return span.textContent || span.innerText; +} + +function sortNAs(a, b, sort_function){ + if ( na_equivalent_vals.includes(a) && na_equivalent_vals.includes(b)) { + return 0; + } + if (na_equivalent_vals.includes(a)){ + return 1 + } + if (na_equivalent_vals.includes(b)) { + return -1; + } + return sort_function(a, b) +} + +$.extend( $.fn.dataTableExt.oSort, { + "natural-minus-na-asc": function (a, b) { + return sortNAs(extractInnerText(a), extractInnerText(b), naturalAsc) + }, + "natural-minus-na-desc": function (a, b) { + return sortNAs(extractInnerText(a), extractInnerText(b), naturalDesc) + } +}); + +$.fn.dataTable.ext.order['dom-checkbox'] = function ( settings, col ) +{ + return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) { + return $('input', td).prop('checked') ? '1' : '0'; + } ); +}; + +$.fn.dataTable.ext.order['dom-inner-text'] = function ( settings, col ) +{ + return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) { + return $(td).text(); + } ); +} \ No newline at end of file -- cgit v1.2.3 From 111593d7e1685db33188eb03685210db6656c0c8 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Mon, 3 Jun 2024 16:10:01 -0500 Subject: Ensure endpoint returns a response. --- gn2/wqflask/oauth2/users.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gn2/wqflask/oauth2/users.py b/gn2/wqflask/oauth2/users.py index 8a935170..ed88aaa4 100644 --- a/gn2/wqflask/oauth2/users.py +++ b/gn2/wqflask/oauth2/users.py @@ -84,7 +84,8 @@ def logout(): f"{the_session['masquerading']['name']} " f"({the_session['masquerading']['email']})", "alert-success") - return redirect("/") + + return redirect("/") @users.route("/register", methods=["GET", "POST"]) def register_user(): -- cgit v1.2.3 From dd4fd626ad763a890e130ac48087c40525dac207 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Mon, 3 Jun 2024 16:10:39 -0500 Subject: Handle generic OAuthError gracefully --- gn2/wqflask/app_errors.py | 25 ++++++++++++++++++++++++- 1 file changed, 24 insertions(+), 1 deletion(-) diff --git a/gn2/wqflask/app_errors.py b/gn2/wqflask/app_errors.py index 503f4e1c..5b85bd53 100644 --- a/gn2/wqflask/app_errors.py +++ b/gn2/wqflask/app_errors.py @@ -6,7 +6,8 @@ import traceback from uuid import uuid4 from werkzeug.exceptions import InternalServerError -from authlib.integrations.base_client.errors import InvalidTokenError +from authlib.integrations.base_client.errors import ( + OAuthError, InvalidTokenError) from flask import ( flash, request, redirect, current_app, render_template, make_response) @@ -46,13 +47,35 @@ def handle_authorisation_error(exc: AuthorisationError): "authorisation_error.html", error_type=type(exc).__name__, error=exc) def handle_invalid_token_error(exc: InvalidTokenError): + """Handle InvalidTokenError""" flash("An invalid session token was detected. " "You have been logged out of the system.", "alert-danger") session.clear_session_info() return redirect("/") +def __build_message__(exc: OAuthError) -> str: + """Build up the message to flash for any OAuthError""" + match exc.args[0]: + case "ForbiddenAccess: Token does not belong to client.": + return "An invalid token was used. The session has been cleared." + case "ForbiddenAccess: Token is expired.": + return "The session has expired." + case "ForbiddenAccess: Token has previously been revoked.": + return "Revoked token was used. The session has been cleared." + case _: + return exc.args[0] + +def handle_oauth_error(exc: OAuthError): + """Handle generic OAuthError""" + flash((f"{type(exc).__name__}: {__build_message__(exc)} " + "Please log in again to continue."), + "alert-danger") + session.clear_session_info() + return redirect("/") + __handlers__ = { + OAuthError: handle_oauth_error, AuthorisationError: handle_authorisation_error, ExternalRequestError: lambda exc: render_error(exc), InternalServerError: lambda exc: render_error(exc), -- cgit v1.2.3 From 67df44ac2df9f05da22634f04eaaf29393710e9f Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Tue, 4 Jun 2024 12:05:08 -0500 Subject: Provide client data used for user verification. --- gn2/wqflask/oauth2/users.py | 21 +++++++++++++++------ 1 file changed, 15 insertions(+), 6 deletions(-) diff --git a/gn2/wqflask/oauth2/users.py b/gn2/wqflask/oauth2/users.py index ed88aaa4..520a13c5 100644 --- a/gn2/wqflask/oauth2/users.py +++ b/gn2/wqflask/oauth2/users.py @@ -1,6 +1,6 @@ import requests from uuid import UUID -from urllib.parse import urljoin +from urllib.parse import urljoin, urlparse from authlib.integrations.base_client.errors import OAuthError from flask import ( @@ -11,10 +11,16 @@ from . import client from . import session from .ui import render_ui from .checks import require_oauth2 -from .client import (oauth2_get, oauth2_post, oauth2_client, - authserver_uri, user_logged_in) -from .request_utils import ( - user_details, request_error, process_error, with_flash_error) +from .client import (oauth2_get, + oauth2_post, + oauth2_client, + authserver_uri, + user_logged_in) +from .request_utils import (user_details, + request_error, + process_error, + with_flash_error, + authserver_authorise_uri) users = Blueprint("user", __name__) @@ -106,7 +112,10 @@ def register_user(): "user_name": form.get("user_name"), "email": form.get("email_address"), "password": form.get("password"), - "confirm_password": form.get("confirm_password")}) + "confirm_password": form.get("confirm_password"), + **dict( + item.split("=") for item in + urlparse(authserver_authorise_uri()).query.split("&"))}) results = response.json() if "error" in results: error_messages = tuple( -- cgit v1.2.3 From 2439a4a0af29a57adc55fec093e4231c7b320ff6 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Wed, 5 Jun 2024 16:12:35 -0500 Subject: Build phenotype results template URI on backend Build the template URI on the backend to remove the need to remember to update the javascript if the URI changes in the future. --- gn2/wqflask/oauth2/data.py | 4 +++- gn2/wqflask/static/new/javascript/auth/search_phenotypes.js | 4 ++-- gn2/wqflask/templates/oauth2/data-list-phenotype.html | 2 +- 3 files changed, 6 insertions(+), 4 deletions(-) diff --git a/gn2/wqflask/oauth2/data.py b/gn2/wqflask/oauth2/data.py index 29d68be0..b7c7800c 100644 --- a/gn2/wqflask/oauth2/data.py +++ b/gn2/wqflask/oauth2/data.py @@ -70,7 +70,9 @@ def __search_phenotypes__(query, template, **kwargs): selected_traits=selected_traits, search_results=search_results, search_endpoint=urljoin( authserver_uri(), "auth/data/search"), - gn_server_url = authserver_uri(), + auth_server_url=authserver_uri(), + pheno_results_template=urljoin( + authserver_uri(), "auth/data/search/phenotype/"), results_endpoint=urljoin( authserver_uri(), f"auth/data/search/phenotype/{job_id}"), diff --git a/gn2/wqflask/static/new/javascript/auth/search_phenotypes.js b/gn2/wqflask/static/new/javascript/auth/search_phenotypes.js index 99ecb16e..e9ef2683 100644 --- a/gn2/wqflask/static/new/javascript/auth/search_phenotypes.js +++ b/gn2/wqflask/static/new/javascript/auth/search_phenotypes.js @@ -96,8 +96,8 @@ function display_search_results(data, textStatus, jqXHR) { * @param {UUID}: The job id to fetch data for */ function fetch_search_results(job_id, success, error=default_error_fn) { - host = $("#frm-search-traits").attr("data-gn-server-url"); - endpoint = host + "auth/data/search/phenotype/" + job_id + endpoint = $("#frm-search-traits").attr( + "data-pheno-results-template").replace("", job_id); $("#txt-search").prop("disabled", true); $.ajax( endpoint, diff --git a/gn2/wqflask/templates/oauth2/data-list-phenotype.html b/gn2/wqflask/templates/oauth2/data-list-phenotype.html index e5172c70..b23c16e2 100644 --- a/gn2/wqflask/templates/oauth2/data-list-phenotype.html +++ b/gn2/wqflask/templates/oauth2/data-list-phenotype.html @@ -113,7 +113,7 @@
+ data-pheno-results-template="{{pheno_results_template}}"> {%if dataset_type == "mrna"%} mRNA: Search {%else%} -- cgit v1.2.3 From 16b9ccc56a99f1290825c36b3788590a585920a6 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Wed, 5 Jun 2024 16:37:12 -0500 Subject: Build search URI endpoint on server rather than on JS To help with maintenance, build the search URI on the server rather than in the javascript. --- gn2/wqflask/oauth2/data.py | 2 +- gn2/wqflask/static/new/javascript/auth/search_phenotypes.js | 2 +- gn2/wqflask/templates/oauth2/data-list-phenotype.html | 1 + 3 files changed, 3 insertions(+), 2 deletions(-) diff --git a/gn2/wqflask/oauth2/data.py b/gn2/wqflask/oauth2/data.py index b7c7800c..767de1a3 100644 --- a/gn2/wqflask/oauth2/data.py +++ b/gn2/wqflask/oauth2/data.py @@ -69,7 +69,7 @@ def __search_phenotypes__(query, template, **kwargs): template, traits=[], per_page=per_page, query=query, selected_traits=selected_traits, search_results=search_results, search_endpoint=urljoin( - authserver_uri(), "auth/data/search"), + request.host_url, "oauth2/data/phenotype/search"), auth_server_url=authserver_uri(), pheno_results_template=urljoin( authserver_uri(), "auth/data/search/phenotype/"), diff --git a/gn2/wqflask/static/new/javascript/auth/search_phenotypes.js b/gn2/wqflask/static/new/javascript/auth/search_phenotypes.js index e9ef2683..8689af75 100644 --- a/gn2/wqflask/static/new/javascript/auth/search_phenotypes.js +++ b/gn2/wqflask/static/new/javascript/auth/search_phenotypes.js @@ -119,7 +119,7 @@ function search_phenotypes() { per_page = document.getElementById("txt-per-page").value search_table = new TableDataSource( "#tbl-phenotypes", "data-traits", search_checkbox); - endpoint = "/auth/data/phenotype/search" + endpoint = endpoint = $("#frm-search-traits").attr("data-search-endpoint"); $.ajax( endpoint, { diff --git a/gn2/wqflask/templates/oauth2/data-list-phenotype.html b/gn2/wqflask/templates/oauth2/data-list-phenotype.html index b23c16e2..d355f3f9 100644 --- a/gn2/wqflask/templates/oauth2/data-list-phenotype.html +++ b/gn2/wqflask/templates/oauth2/data-list-phenotype.html @@ -113,6 +113,7 @@ {%if dataset_type == "mrna"%} mRNA: Search -- cgit v1.2.3 From b22d5baffb236c522ff8469f3495b63912201094 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Wed, 5 Jun 2024 16:38:21 -0500 Subject: Bug: Add missing data to search query. --- gn2/wqflask/oauth2/data.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gn2/wqflask/oauth2/data.py b/gn2/wqflask/oauth2/data.py index 767de1a3..16e5f60c 100644 --- a/gn2/wqflask/oauth2/data.py +++ b/gn2/wqflask/oauth2/data.py @@ -124,6 +124,7 @@ def json_search_mrna() -> Response: @data.route("/phenotype/search", methods=["POST"]) def json_search_phenotypes() -> Response: """Search for phenotypes.""" + from gn2.utility.tools import GN_SERVER_URL form = request.json def __handle_error__(err): error = process_error(err) @@ -138,6 +139,7 @@ def json_search_phenotypes() -> Response: "per_page": int(form.get("per_page", 50)), "page": int(form.get("page", 1)), "auth_server_uri": authserver_uri(), + "gn3_server_uri": GN_SERVER_URL, "selected_traits": form.get("selected_traits", []) }).either(__handle_error__, jsonify) -- cgit v1.2.3 From 503795f16fbed1b5e6ea7ecffeb1a25cf3548d8e Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Thu, 6 Jun 2024 10:10:38 -0500 Subject: Deactivate the "create_role" function The `create_role` function could lead to privilege escalation. This commit deactivates it completely to prevent the chance of that happening. --- gn2/wqflask/oauth2/roles.py | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/gn2/wqflask/oauth2/roles.py b/gn2/wqflask/oauth2/roles.py index 2fe35f9b..ee75475e 100644 --- a/gn2/wqflask/oauth2/roles.py +++ b/gn2/wqflask/oauth2/roles.py @@ -93,7 +93,12 @@ def create_role(): def __create_success__(*args): flash("Role created successfully.", "alert-success") return redirect(url_for("oauth2.role.user_roles")) - return oauth2_post( - "auth/group/role/create",data={ - "role_name": role_name, "privileges[]": privileges}).either( - __create_error__,__create_success__) + + raise DeprecationWarning( + f"The `{__name__}.create_role(…)` function, as is currently, can " + "lead to unbounded privilege escalation. See " + "https://issues.genenetwork.org/issues/gn-auth/problems-with-roles") + # return oauth2_post( + # "auth/group/role/create",data={ + # "role_name": role_name, "privileges[]": privileges}).either( + # __create_error__,__create_success__) -- cgit v1.2.3 From e4fc0eb4ed80931bbd36f3777b06d9343a2008d0 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Thu, 6 Jun 2024 10:14:02 -0500 Subject: Remove the "Roles" page. --- gn2/wqflask/oauth2/roles.py | 25 ------------------------- gn2/wqflask/templates/oauth2/profile_nav.html | 7 ------- 2 files changed, 32 deletions(-) diff --git a/gn2/wqflask/oauth2/roles.py b/gn2/wqflask/oauth2/roles.py index ee75475e..b0f990c7 100644 --- a/gn2/wqflask/oauth2/roles.py +++ b/gn2/wqflask/oauth2/roles.py @@ -10,31 +10,6 @@ from .request_utils import request_error, process_error roles = Blueprint("role", __name__) -@roles.route("/user", methods=["GET"]) -@require_oauth2 -def user_roles(): - def __grerror__(roles, user_privileges, error): - return render_ui( - "oauth2/list_roles.html", roles=roles, - user_privileges=user_privileges, - group_roles_error=process_error(error)) - - def __grsuccess__(roles, user_privileges, group_roles): - return render_ui( - "oauth2/list_roles.html", roles=roles, - user_privileges=user_privileges, group_roles=group_roles) - - def __role_success__(roles): - uprivs = tuple( - privilege["privilege_id"] for role in roles - for privilege in role["privileges"]) - return oauth2_get("auth/group/roles").either( - lambda err: __grerror__(roles, uprivs, err), - lambda groles: __grsuccess__(roles, uprivs, groles)) - - return oauth2_get("auth/system/roles").either( - request_error, __role_success__) - @roles.route("/role/", methods=["GET"]) @require_oauth2 def role(role_id: uuid.UUID): diff --git a/gn2/wqflask/templates/oauth2/profile_nav.html b/gn2/wqflask/templates/oauth2/profile_nav.html index aa752905..c79bccbc 100644 --- a/gn2/wqflask/templates/oauth2/profile_nav.html +++ b/gn2/wqflask/templates/oauth2/profile_nav.html @@ -16,13 +16,6 @@ Group - -
-- cgit v1.2.3 From eed64341c758e7f39b8f9ff2d7aee46f0fccd630 Mon Sep 17 00:00:00 2001 From: Alexander_Kabui Date: Mon, 2 Sep 2024 14:05:20 +0300 Subject: Fix issue for rendering error template for gnqa history. --- gn2/wqflask/views.py | 36 ++++++++++++++++++++---------------- 1 file changed, 20 insertions(+), 16 deletions(-) diff --git a/gn2/wqflask/views.py b/gn2/wqflask/views.py index 7b1fb22d..68fcb489 100644 --- a/gn2/wqflask/views.py +++ b/gn2/wqflask/views.py @@ -330,6 +330,14 @@ def get_gnqa_history(): return render_template("gnqa_errors.html", **{"status_code": resp.status_code, **resp.json()}) + + def _success_(resp): + response = resp.json() + if request.args.get("search_term"): + return render_template("gnqa_answer.html", **response) + else: + return render_template("gnqa_search_history.html", + prev_queries=response) token = session_info()["user"]["token"].either( lambda err: err, lambda tok: tok["access_token"]) if request.method == "DELETE": @@ -341,22 +349,18 @@ def get_gnqa_history(): ).either( _error_, lambda x: x.json()) - search_term = request.args.get('search_term') - if search_term: - response_url = f"/api/llm/history?search_term={request.args.get('search_term')}" - else: - response_url = "/api/llm/history" - response = monad_requests.get(urljoin(GN3_LOCAL_URL, response_url), - headers={ - "Authorization": f"Bearer {token}" - } - ).then(lambda resp: resp).either( - _error_, lambda x: x.json()) - if request.args.get("search_term"): - return render_template("gnqa_answer.html", **response) - return render_template("gnqa_search_history.html", - prev_queries=response) - + if request.method == "GET": + search_term = request.args.get('search_term') + if search_term: + response_url = f"/api/llm/history?search_term={request.args.get('search_term')}" + else: + response_url = "/api/llm/history" + return (monad_requests.get(urljoin(GN3_LOCAL_URL, response_url), + headers={ + "Authorization": f"Bearer {token}" + } + ).then(lambda resp: resp).either( + _error_, _success_)) @app.route("/gnqna/rating//", methods=["POST"]) -- cgit v1.2.3 From 54ac32749469be9c2e07ed941383341922f9e017 Mon Sep 17 00:00:00 2001 From: Alexander_Kabui Date: Thu, 5 Sep 2024 13:55:59 +0300 Subject: Use new endpoints for fetching gnqna history records. --- gn2/wqflask/views.py | 94 ++++++++++++++++++++++++++++++++++++++-------------- 1 file changed, 70 insertions(+), 24 deletions(-) diff --git a/gn2/wqflask/views.py b/gn2/wqflask/views.py index 68fcb489..4164c604 100644 --- a/gn2/wqflask/views.py +++ b/gn2/wqflask/views.py @@ -323,9 +323,10 @@ def commit_gn_doc(): return render_template("gn_editor_results_page.html", **data) -@app.route("/gnqna/hist", methods=["GET", "DELETE"]) +@app.route("/gnqna/records", methods=["GET"]) @require_oauth2 -def get_gnqa_history(): +def get_gnqa_records(): + """Call the Api endpoint for fetching all gnqa records""" def _error_(resp): return render_template("gnqa_errors.html", **{"status_code": resp.status_code, @@ -333,35 +334,80 @@ def get_gnqa_history(): def _success_(resp): response = resp.json() - if request.args.get("search_term"): - return render_template("gnqa_answer.html", **response) - else: - return render_template("gnqa_search_history.html", - prev_queries=response) + return render_template("gnqa_search_history.html", + prev_queries=response) token = session_info()["user"]["token"].either( lambda err: err, lambda tok: tok["access_token"]) - if request.method == "DELETE": - monad_requests.delete(urljoin(GN3_LOCAL_URL, "/api/llm/history"), - json=dict(request.form), - headers={ - "Authorization": f"Bearer {token}" - } - ).either( - _error_, lambda x: x.json()) - - if request.method == "GET": - search_term = request.args.get('search_term') - if search_term: - response_url = f"/api/llm/history?search_term={request.args.get('search_term')}" - else: - response_url = "/api/llm/history" - return (monad_requests.get(urljoin(GN3_LOCAL_URL, response_url), - headers={ + response_url = "/api/llm/search/records" + return (monad_requests.get(urljoin(GN3_LOCAL_URL, response_url), + headers={ "Authorization": f"Bearer {token}" } ).then(lambda resp: resp).either( _error_, _success_)) + +@app.route("/gnqna/record", methods=["GET"]) +@require_oauth2 +def get_gnqa_record_by_task_id(): + """Get specific record using task""" + def _error_(resp): + return render_template("gnqa_errors.html", + **{"status_code": resp.status_code, + **resp.json()}) + + def _success_(resp): + response = resp.json() + return render_template("gnqa_answer.html", **response) + token = session_info()["user"]["token"].either( + lambda err: err, lambda tok: tok["access_token"]) + response_url = f"api/llm/search/record/{request.args.get('search_task_id')}" + return (monad_requests.get(urljoin(GN3_LOCAL_URL, response_url), + headers={ + "Authorization": f"Bearer {token}" + }).then(lambda resp: resp).either( + _error_, _success_)) + + +@app.route("/gnqna/records", methods=["DELETE"]) +@require_oauth2 +def delete_gnqa_records(): + """Call the Api endpoint for fetching all gnqa records""" + def _error_(resp): + return render_template("gnqa_errors.html", + **{"status_code": resp.status_code, + **resp.json()}) + + token = session_info()["user"]["token"].either( + lambda err: err, lambda tok: tok["access_token"]) + return (monad_requests.delete(urljoin(GN3_LOCAL_URL, + "/api/llm/search/records"), + json=dict(request.form), + headers={ + "Authorization": f"Bearer {token}"}) + .then(lambda resp: resp).either( + _error_, lambda x: x.json())) + + +@app.route("/gnqna/record", methods=["DELETE"]) +@require_oauth2 +def delete_gnqa_record_by_task_id(): + """Get specific record using task""" + def _error_(resp): + return render_template("gnqa_errors.html", + **{"status_code": resp.status_code, + **resp.json()}) + + token = session_info()["user"]["token"].either( + lambda err: err, lambda tok: tok["access_token"]) + response_url = f"api/llm/search/record/{request.args.get('search_task_id')}" + return (monad_requests.get(urljoin(GN3_LOCAL_URL, response_url), + headers={ + "Authorization": f"Bearer {token}"}).then(lambda resp: resp) + .either( + _error_, lambda x: x.json())) + + @app.route("/gnqna/rating//", methods=["POST"]) @require_oauth2 -- cgit v1.2.3 From 93f91be029e62fbd96ca71f0cfc8792f564f899a Mon Sep 17 00:00:00 2001 From: Alexander_Kabui Date: Thu, 5 Sep 2024 13:56:27 +0300 Subject: Modify UI url to fetch from correct history records. --- gn2/wqflask/templates/gnqa.html | 2 +- gn2/wqflask/templates/gnqa_search_history.html | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/gn2/wqflask/templates/gnqa.html b/gn2/wqflask/templates/gnqa.html index 6969bad9..a2c1c276 100644 --- a/gn2/wqflask/templates/gnqa.html +++ b/gn2/wqflask/templates/gnqa.html @@ -92,7 +92,7 @@ diff --git a/gn2/wqflask/templates/gnqa_search_history.html b/gn2/wqflask/templates/gnqa_search_history.html index 6042afe3..2019cb3b 100644 --- a/gn2/wqflask/templates/gnqa_search_history.html +++ b/gn2/wqflask/templates/gnqa_search_history.html @@ -30,13 +30,13 @@ style="height: 20px; width: 20px">
-