diff options
Diffstat (limited to 'gn2/wqflask')
| -rw-r--r-- | gn2/wqflask/templates/gsearch_gene.html | 19 | ||||
| -rw-r--r-- | gn2/wqflask/views.py | 112 |
2 files changed, 85 insertions, 46 deletions
diff --git a/gn2/wqflask/templates/gsearch_gene.html b/gn2/wqflask/templates/gsearch_gene.html index ecb8de8f..091cc435 100644 --- a/gn2/wqflask/templates/gsearch_gene.html +++ b/gn2/wqflask/templates/gsearch_gene.html @@ -272,8 +272,9 @@ }); </script> + {% if do_ai_search %} <script type='text/javascript'> - function ai_content_div(search_term, search_result) { + function ai_content_div(search_term, search_result, search_uri) { return ` <div class="col-sm-6"> <div class="panel panel-info"> @@ -287,7 +288,7 @@ <div id="ai_results" class="panel-collapse collapse" role="tabpanel" aria-labelledby="ai_heading"> <div class="panel-body"> <p>${ search_result }</p> - <p><a class="btn btn-default" href="${search_term}" role="button">See References</a></p> + <p><a class="btn btn-default" href="${ search_uri }" role="button">See References</a></p> </div> </div> </div> @@ -296,9 +297,19 @@ } $(document).ready( function () { - let ai_div = ai_content_div("this is a test", "test contains some text"); - $("#ai_result").append(ai_div); + $.ajax({url: "gnqna", + contentType: "application/json", + data: { + query: "{{ terms }}", + type: "xapian", + }, + success: function(result) { + let ai_div = ai_content_div(result.search_term, result.search_result, result.search_url) + $("#ai_result").append(ai_div); + } + }) }) </script> + {% endif %} {% endblock %} diff --git a/gn2/wqflask/views.py b/gn2/wqflask/views.py index 6cc4f2a7..7e63f165 100644 --- a/gn2/wqflask/views.py +++ b/gn2/wqflask/views.py @@ -18,6 +18,7 @@ import sys import traceback import math import uuid +import urllib.parse import xlsxwriter from functools import reduce @@ -33,6 +34,7 @@ from gn2.wqflask import app from gn3.computations.gemma import generate_hash_of_string from flask import current_app +from flask import jsonify from flask import g from flask import Response from flask import request @@ -239,20 +241,17 @@ def search_page_table(): return flask.jsonify(current_page) -@app.route("/gsearch", methods=('GET',)) +@app.route("/gsearch", methods=("GET",)) def gsearchact(): result = GSearch(request.args).__dict__ - search_type = request.args['type'] - ai_result = None - if current_app.config.get("AI_SEARCH_ENABLED"): - ai_result = { - "search_term": "glioma human gtex_v8", - "search_result": "The Bama miniature pig has the same number of chromosomes as humans", - # we need to modify the search to use url params so that we can easily link - "search_url": "https://qa.genenetwork.org/gnqna" - } + search_type = request.args["type"] + is_user_logged_in = session_info().get("user", {}).get("logged_in", False) + + do_ai_search = False + if current_app.config.get("AI_SEARCH_ENABLED") and is_user_logged_in: + do_ai_search = True if search_type == "gene": - return render_template("gsearch_gene.html", **result, ai_result=ai_result) + return render_template("gsearch_gene.html", **result, do_ai_search=do_ai_search, result=result) elif search_type == "phenotype": return render_template("gsearch_pheno.html", **result) @@ -269,32 +268,57 @@ def gsearchtable(): return flask.jsonify(current_page) +def clean_xapian_query(query: str) -> str: + """ Remove filler words in xapian query + TODO: FIXME + """ + return query + @app.route("/gnqna", methods=["POST", "GET"]) @require_oauth2 def gnqna(): - """ Main endpoint to call gn3 gnqna Api endpoint""" + """Main endpoint to call gn3 gnqna Api endpoint""" + def _error_(resp): - return render_template("gnqa_errors.html", - **{"status_code": resp.status_code, - **resp.json()}) + return render_template( + "gnqa_errors.html", **{"status_code": resp.status_code, **resp.json()} + ) def _success_(resp): - return render_template("gnqa_answer.html", - **resp.json()) + return render_template("gnqa_answer.html", **resp.json()) + + content_type = request.headers.get("Content-Type") + token = session_info()["user"]["token"].either( + lambda err: err, lambda tok: tok["access_token"] + ) + if request.method == "GET": + query = request.args.get("query") + query_type = request.args.get("type") + if query_type == "xapian": + query = clean_xapian_query(query) + safe_query = urllib.parse.urlencode({"query": query}) + search_result = requests.put( + urljoin(GN3_LOCAL_URL, f"/api/llm/search?{safe_query}"), + headers={"Authorization": f"Bearer {token}"}, + ) + search_result.raise_for_status() + search_result = search_result.json() + if content_type == "application/json": + ai_result = { + "search_term": query, + "search_result": search_result["answer"], + "search_url": f"/gnqna?{safe_query}", + } + return jsonify(ai_result) + return render_template("gnqa_answer.html", **search_result) + if request.method == "POST": - token = session_info()["user"]["token"].either( - lambda err: err, lambda tok: tok["access_token"]) + safe_query = urlib.parse.urlencode({"query": request.form.get("querygnqa")}) return monad_requests.put( - urljoin(GN3_LOCAL_URL, - f"/api/llm/search?query={request.form.get('querygnqa')}"), - headers={ - "Authorization": f"Bearer {token}" - } - ).then( - lambda resp: resp - ).either( - _error_, _success_) + urljoin(GN3_LOCAL_URL, f"/api/llm/search?{safe_query}"), + headers={"Authorization": f"Bearer {token}"}, + ).either(_error_, _success_) return render_template("gnqa.html") @@ -1302,19 +1326,13 @@ def display_wiki_history(comment_id: str): entries = [] try: entries = requests.get( - urljoin( - GN3_LOCAL_URL, - f"/api/metadata/wiki/{comment_id}/history" - ) + urljoin(GN3_LOCAL_URL, f"/api/metadata/wiki/{comment_id}/history") ) entries.raise_for_status() entries = entries.json() except requests.RequestException as excp: flash(excp, "alert-warning") - return render_template( - "wiki/history.html", - entries=entries - ) + return render_template("wiki/history.html", entries=entries) @app.route("/datasets/<name>", methods=('GET',)) @@ -1580,18 +1598,26 @@ def edit_wiki(comment_id: int): """fetch generif metadata from gn3 and display it""" # FIXME: better error handling if request.method == "GET": - last_wiki_resp = requests.get(urljoin(GN3_LOCAL_URL, f"/api/metadata/wiki/{comment_id}")) + last_wiki_resp = requests.get( + urljoin(GN3_LOCAL_URL, f"/api/metadata/wiki/{comment_id}") + ) last_wiki_resp.raise_for_status() last_wiki_content = last_wiki_resp.json() - species_dict_resp = requests.get(urljoin(GN3_LOCAL_URL, "/api/metadata/wiki/species")) + species_dict_resp = requests.get( + urljoin(GN3_LOCAL_URL, "/api/metadata/wiki/species") + ) species_dict_resp.raise_for_status() species_dict = species_dict_resp.json() - categories_resp = requests.get(urljoin(GN3_LOCAL_URL, "/api/metadata/wiki/categories")) + categories_resp = requests.get( + urljoin(GN3_LOCAL_URL, "/api/metadata/wiki/categories") + ) categories_resp.raise_for_status() categories = list(categories_resp.json().keys()) - grouped_categories = [categories[i : i + 3] for i in range(0, len(categories), 3)] + grouped_categories = [ + categories[i : i + 3] for i in range(0, len(categories), 3) + ] return render_template( "wiki/edit_wiki.html", @@ -1611,8 +1637,10 @@ def edit_wiki(comment_id: int): "initial": post_data["initial"], "categories": post_data.getlist("genecategory"), "reason": post_data["reason"], - } - post_response = requests.post(urljoin(GN3_LOCAL_URL, f"api/metadata/wiki/{comment_id}/edit"), json=payload) + } + post_response = requests.post( + urljoin(GN3_LOCAL_URL, f"api/metadata/wiki/{comment_id}/edit"), json=payload + ) post_response.raise_for_status() post_res = post_response.json() |