aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
Diffstat
-rw-r--r--gn2/utility/helper_functions.py45
-rw-r--r--gn2/wqflask/templates/gnqa.html72
-rw-r--r--gn2/wqflask/templates/gnqa_answer.html40
-rw-r--r--gn2/wqflask/templates/gsearch_gene.html9
-rw-r--r--gn2/wqflask/views.py12
5 files changed, 114 insertions, 64 deletions
diff --git a/gn2/utility/helper_functions.py b/gn2/utility/helper_functions.py
index fc101959..8c35df5f 100644
--- a/gn2/utility/helper_functions.py
+++ b/gn2/utility/helper_functions.py
@@ -8,6 +8,51 @@ from gn2.utility.tools import get_setting
from gn2.wqflask.database import database_connection
+
+def clean_xapian_query(query: str) -> str:
+ """
+ Clean and optimize a Xapian query string by removing filler words,
+ and ensuring the query is tailored for optimal results from Fahamu.
+
+ Args:
+ query (str): The original Xapian query string.
+
+ Returns:
+ str: The cleaned and optimized query string.
+ """
+ xapian_prefixes = {
+ "author",
+ "species",
+ "group",
+ "tissue",
+ "dataset",
+ "symbol",
+ "description",
+ "rif",
+ "wiki",
+ }
+ xapian_operators = {"AND", "NOT", "OR", "XOR", "NEAR", "ADJ"}
+ range_prefixes = {"mean", "peak", "position", "peakmb", "additive", "year"}
+ query_context = ["genes"]
+ cleaned_query_parts = []
+ for token in query.split():
+ if token in xapian_operators:
+ continue
+ prefix, _, suffix = token.partition(":")
+ if ".." in suffix and prefix in range_prefixes:
+ continue
+ if prefix in xapian_prefixes:
+ query_context.insert(0, prefix)
+ cleaned_query_parts.append(f"{prefix} {suffix}")
+ else:
+ cleaned_query_parts.append(prefix)
+ cleaned_query = " ".join(cleaned_query_parts)
+ context = ",".join(query_context)
+ return f"Provide answer on {cleaned_query} context {context}"
+
+
+
+
def get_species_dataset_trait(self, start_vars):
if "temp_trait" in list(start_vars.keys()):
if start_vars['temp_trait'] == "True":
diff --git a/gn2/wqflask/templates/gnqa.html b/gn2/wqflask/templates/gnqa.html
index 158b0b4e..371ad7b3 100644
--- a/gn2/wqflask/templates/gnqa.html
+++ b/gn2/wqflask/templates/gnqa.html
@@ -80,10 +80,15 @@
background-color: #ccf;
}
+.linux-libertine-font{
+ font-family: 'Linux Libertine','Georgia','Times','Source Serif Pro', 'serif'
+}
+
</style>
{% endblock %}
{% block search %}{% endblock %}
{% block content %}
+
<!-- Start of body -->
<section class="container-fluid">
<header class="row">
@@ -119,39 +124,44 @@
autocomplete="on"
required
placeholder="Ask More Questions or Topics (E.g Genes)"
+ {% if query %}
+ value='{{ query }}'
+ {% else %}
value=''
+ {% endif %}
name="querygnqa" />
</div>
</form>
<article id="swap" class="row">
- <div class="row gnqa-copy">
- <div class="col-sm-10 col-sm-offset-1 col-md-offset-3 col-md-6">
- <p>
- Welcome to the GeneNetwork Question and Answer (GNQA)system. We utilize a large language model and 3000 scientific publications to make GNQA a subject matter expert in three areas: <b><a href="/">GeneNetwork.org</a></b>, <b>genomics/genetics with regards to diabetes</b> and <b>genomics/genetics with regards to agin.</b>.
- </p>
- <p>
- At the moment when you ask GNQA something it will attempt to return a sensible answer with <q>real</q> references. To this end we aim to reduce hallucinations and provide a knowledge launchpad for a researcher to enhance their knowledge on the relevant subject matter.
- </p>
- <p>GNQA is not a finished product as we are working diligently to improve it daily.</p>
- <p>
- <b>Thanks for using GNQA!</b>
- </p>
- <div></div>
- </article>
- </section>
- {% endblock %}
- {% block js %}
- <script src="{{ url_for('js', filename='jquery/jquery.min.js') }}"
- type="text/javascript"></script>
- <script language="javascript"
- type="text/javascript"
- src="{{ url_for('js', filename='jquery-ui/jquery-ui.min.js') }}"></script>
- <script language="javascript"
- type="text/javascript"
- src="{{ url_for('js', filename='htmx.min.js') }}"></script>
- <script type="text/javascript">
- document.addEventListener('DOMContentLoaded', function() {
- $('footer').hide()
- });
- </script>
- {% endblock %}
+ {% if answer %}
+ {% include 'gnqa_answer.html' %}
+ {% else %}
+
+ <div class="row gnqa-copy">
+ <div class="col-sm-10 col-sm-offset-1 col-md-offset-3 col-md-6">
+ <p>
+ Welcome to the GeneNetwork Question and Answer (GNQA)system. We utilize a large language model and 3000 scientific publications to make GNQA a subject matter expert in three areas: <b><a href="/">GeneNetwork.org</a></b>, <b>genomics/genetics with regards to diabetes</b> and <b>genomics/genetics with regards to agin.</b>.
+ </p>
+ <p>
+ At the moment when you ask GNQA something it will attempt to return a sensible answer with <q>real</q> references. To this end we aim to reduce hallucinations and provide a knowledge launchpad for a researcher to enhance their knowledge on the relevant subject matter.
+ </p>
+ <p>GNQA is not a finished product as we are working diligently to improve it daily.</p>
+ <p>
+ <b>Thanks for using GNQA!</b>
+ </p>
+ </div>
+ </div>
+ {% endif %}
+ </article>
+ </section>
+ {% endblock %}
+ {% block js %}
+ <script src="{{ url_for('js', filename='jquery/jquery.min.js') }}" type="text/javascript"></script>
+ <script src="{{ url_for('js', filename='jquery-ui/jquery-ui.min.js') }}" type="text/javascript"></script>
+ <script src="{{ url_for('js', filename='htmx.min.js') }}" type="text/javascript" ></script>
+ <script type="text/javascript">
+document.addEventListener('DOMContentLoaded', function() {
+ $('footer').hide()
+});
+ </script>
+ {% endblock %}
diff --git a/gn2/wqflask/templates/gnqa_answer.html b/gn2/wqflask/templates/gnqa_answer.html
index 91fa4981..2e182375 100644
--- a/gn2/wqflask/templates/gnqa_answer.html
+++ b/gn2/wqflask/templates/gnqa_answer.html
@@ -1,7 +1,7 @@
<section class="container-fluid answers gnqa-copy">
<div class="row container gnqa-answer" style="margin-bottom: 1em">
<p class="row lead">
- <mark style="font-family: 'Linux Libertine','Georgia','Times','Source Serif Pro',serif"><b><i>{{ query }}</i></b></mark>
+ <mark class="linux-libertine-font"><b><i>{{ query }}</i></b></mark>
<br />
<span style="white-space: pre-line">{{ answer|safe }}</span>
</p>
@@ -20,32 +20,24 @@
title="Vote Down">
<i class="fa fa-thumbs-down fa-sm fa-1x" aria-hidden="true"></i>
</button>
- <sub id="rate" class="text-info">
- </sub>
+ <sub id="rate" class="text-info"></sub>
</div>
</div>
<div class="row container">
<details open>
<summary>
- <h3 style="font-family: 'Linux Libertine','Georgia','Times','Source Serif Pro',serif">References</h3>
+ <h3 class="linux-libertine-font">References</h3>
</summary>
{% if references %}
<ul class="list-unstyled">
{% for reference in references %}
<li>
- <div class="panel-group"
- role="tablist"
- aria-multiselectable="true"
- style="margin-bottom:0">
+ <div class="panel-group" role="tablist" aria-multiselectable="true" style="margin-bottom:0">
<div class="panel panel-default">
{% if loop.first %}
- <div class="panel-heading active"
- role="tab"
- id="heading{{ reference.doc_id }}">
- <h4 class="panel-title"
- style="font-family: 'Linux Libertine','Georgia','Times','Source Serif Pro',serif">
- <a class="collapsed"
- role="button"
+ <div class="panel-heading active" role="tab" id="heading{{ reference.doc_id }}">
+ <h4 class="panel-title linux-libertine-font">
+ <a class="collapsed" role="button"
data-toggle="collapse"
data-parent="#accordion"
href="#collapse{{ reference.doc_id }}"
@@ -65,8 +57,7 @@
{% if reference.pubmed %}
<details open>
<summary>See PubMed Info</summary>
- <div style="font-family: 'Linux Libertine','Georgia','Times','Source Serif Pro',serif;
- margin-top:1.4em">
+ <div class="linux-libertine-font" style="margin-top:1.4em">
<h3>
<b>{{ reference.pubmed[0].get("title") }}:</b>
</h3>
@@ -90,8 +81,7 @@
</div>
{% else %}
<div class="panel-heading" role="tab" id="heading{{ reference.doc_id }}">
- <h4 class="panel-title"
- style="font-family: 'Linux Libertine','Georgia','Times','Source Serif Pro',serif">
+ <h4 class="panel-title linux-libertine-font">
<a class="collapsed"
role="button"
data-toggle="collapse"
@@ -113,8 +103,7 @@
{% if reference.pubmed %}
<details>
<summary>See PubMed Info</summary>
- <div style="font-family: 'Linux Libertine','Georgia','Times','Source Serif Pro',serif;
- margin-top:1.4em">
+ <div class="linux-libertine-font" style="margin-top:1.4em">
<h3>
<b>{{ reference.pubmed[0].get("title") }}:</b>
</h3>
@@ -154,8 +143,9 @@
</div>
</div>
</section>
-{% block js %}
- <script>
+
+<script>
+$(document).ready(function() {
function updateRatingHandler(target, responseObj, args){
let {status, response} = responseObj.xhr
if (status == 200 && args == "upvote"){
@@ -187,5 +177,5 @@ htmx.on("#upvote", "click", function(evt){
handler: (target, obj)=> updateRatingHandler(target,obj, "downvote"),
swap:"innerHTML",
values: {'query': query, 'answer': answer}})});
- </script>
-{% endblock %}
+})
+</script>
diff --git a/gn2/wqflask/templates/gsearch_gene.html b/gn2/wqflask/templates/gsearch_gene.html
index 091cc435..80ed8b47 100644
--- a/gn2/wqflask/templates/gsearch_gene.html
+++ b/gn2/wqflask/templates/gsearch_gene.html
@@ -16,8 +16,14 @@
</h3>
</div>
+
+ {% if do_ai_search %}
<div class="row" id="ai_result">
+ <div class="text-center" id="spinner">
+ <i class="fa fa-spinner fa-spin fa-3x"></i>
+ </div>
</div>
+ {% endif %}
<p>To study a record, click on its Record ID below.<br />Check records below and click Add button to add to selection.</p>
<div>
@@ -306,6 +312,9 @@
success: function(result) {
let ai_div = ai_content_div(result.search_term, result.search_result, result.search_url)
$("#ai_result").append(ai_div);
+ },
+ complete: function() {
+ $("#spinner").hide();
}
})
})
diff --git a/gn2/wqflask/views.py b/gn2/wqflask/views.py
index ec1c2b74..d5fcedfe 100644
--- a/gn2/wqflask/views.py
+++ b/gn2/wqflask/views.py
@@ -89,6 +89,7 @@ from gn2.utility.tools import GN3_LOCAL_URL
from gn2.utility.tools import JS_TWITTER_POST_FETCHER_PATH
from gn2.utility.tools import JS_GUIX_PATH
from gn2.utility.helper_functions import get_species_groups
+from gn2.utility.helper_functions import clean_xapian_query
from gn2.utility.redis_tools import get_redis_conn
import gn2.utility.hmac as hmac
@@ -268,12 +269,6 @@ 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
@@ -298,8 +293,9 @@ def gnqna():
query_type = request.args.get("type")
if query_type == "xapian":
query = clean_xapian_query(query)
+ # todo; check if is empty
safe_query = urllib.parse.urlencode({"query": query})
- search_result = requests.put(
+ search_result = requests.get(
urljoin(GN3_LOCAL_URL, f"/api/llm/search?{safe_query}"),
headers={"Authorization": f"Bearer {token}"},
)
@@ -312,7 +308,7 @@ def gnqna():
"search_url": f"/gnqna?{safe_query}",
}
return jsonify(ai_result)
- return render_template("gnqa_answer.html", **search_result)
+ return render_template("gnqa.html", **search_result)
else:
return render_template("gnqa.html")
if request.method == "POST":
generated by cgit v1.2.3 (git 2.46.2) at 2025-02-16 19:11:35 +0000