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-rw-r--r--gn2/wqflask/templates/wiki/genewiki.html37
-rw-r--r--gn2/wqflask/views.py53
2 files changed, 60 insertions, 30 deletions
diff --git a/gn2/wqflask/templates/wiki/genewiki.html b/gn2/wqflask/templates/wiki/genewiki.html
index 06fa1f3a..740e93c9 100644
--- a/gn2/wqflask/templates/wiki/genewiki.html
+++ b/gn2/wqflask/templates/wiki/genewiki.html
@@ -11,26 +11,22 @@
<h5>
<strong>GeneNetwork:</strong>
</h5>
-
{% if wiki %}
-
<ol class="list-group">
{% for entry in wiki %}
<li class="list-group-item">
<div class="row">
- <div class="col-sm-1">{{ loop.index }}.</div>
<div class="col-sm-6">
- {{ entry.get("comment") }}
+ {{ loop.index }}. {{ entry.get("comment") }}
{% if entry.get("web_url") %}
<sup> <small> <a href = "{{ entry.web_url }}" target = "_blank"> <span class = "glyphicon glyphicon-globe" aria-hidden = "true"></span>web</a></small></sup>
{% endif %}
</div>
-
<div class="col-sm-2">
{% if is_logged_in %}
- <a href="{{ url_for('edit_wiki', comment_id=entry['id']) }}">
- <span class="glyphicon glyphicon-edit" aria-hidden="true"></span>
- </a>
+ <a href="{{ url_for('edit_wiki', comment_id=entry['id']) }}">
+ <span class="glyphicon glyphicon-edit" aria-hidden="true"></span>
+ </a>
{% endif %}
<sup><small>[<a href="/genewiki/{{ entry.id }}/history" target="_blank">history</a>]</small></sup>
</div>
@@ -43,5 +39,30 @@
<u> There are no GeneNetwork entries for <b> {{ symbol }}.</b></u>
</p>
{% endif %}
+ <h5>
+ <strong>GeneRIF from NCBI:</strong>
+ </h5>
+ {% if rif %}
+ <ol class="list-group">
+ {% for entry in rif %}
+ <li class="list-group-item">
+ <div class="row">
+ <div class="col-sm-12">
+ {{ loop.index }}. {{ entry.get("comment") }}
+ (<a href="http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids={{ entry.gene_id }}"
+ target="_blank">{{ entry.species }}</a>)
+ (<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids={{ entry.pubmed_id }}&dopt=Abstract"
+ target="_blank">PubMed</a>)
+ </div>
+ </div>
+ </li>
+ {% endfor %}
+ </ol>
+ {% else %}
+ <p class = "well">
+ <u> There are no NCBI RIF entries for this for<b> {{ symbol }}.</b></u>
+ </p>
+ {% endif %}
</div>
+ <div class="container"></div>
{% endblock %}
diff --git a/gn2/wqflask/views.py b/gn2/wqflask/views.py
index 6bd66940..ab151c59 100644
--- a/gn2/wqflask/views.py
+++ b/gn2/wqflask/views.py
@@ -248,7 +248,8 @@ def gsearchact():
search_type = request.args["type"]
is_user_logged_in = session_info().get("user", {}).get("logged_in", False)
- do_ai_search = current_app.config.get("AI_SEARCH_ENABLED") and is_user_logged_in
+ do_ai_search = current_app.config.get(
+ "AI_SEARCH_ENABLED") and is_user_logged_in
if search_type == "gene":
return render_template("gsearch_gene.html", **result, do_ai_search=do_ai_search, result=result)
elif search_type == "phenotype":
@@ -310,7 +311,8 @@ def gnqna():
else:
return render_template("gnqa.html")
if request.method == "POST":
- safe_query = urllib.parse.urlencode({"query": request.form.get("querygnqa")})
+ safe_query = urllib.parse.urlencode(
+ {"query": request.form.get("querygnqa")})
return monad_requests.get(
urljoin(GN3_LOCAL_URL, f"/api/llm/search?{safe_query}"),
headers={"Authorization": f"Bearer {token}"},
@@ -320,7 +322,8 @@ def gnqna():
@app.route("/editor/edit", methods=["GET"])
@require_oauth2
def edit_gn_doc_file():
- file_path = urllib.parse.urlencode({"file_path": request.args.get("file-path", "")})
+ file_path = urllib.parse.urlencode(
+ {"file_path": request.args.get("file-path", "")})
response = requests.get(f"http://localhost:8091/edit?{file_path}")
response.raise_for_status()
return render_template("gn_editor.html", **response.json())
@@ -339,12 +342,12 @@ def commit_gn_doc():
if request.method == "GET":
return render_template("gn_editor_commit.html")
results = requests.post("http://localhost:8091/commit", json={
- "content": request.form.get("content"),
- "filename": request.form.get("file_path"),
- "username": session_info()["user"]["name"],
- "email": session_info()["user"]["email"],
- "commit_message": request.form.get("msg"),
- "prev_commit": request.form.get("hash")})
+ "content": request.form.get("content"),
+ "filename": request.form.get("file_path"),
+ "username": session_info()["user"]["name"],
+ "email": session_info()["user"]["email"],
+ "commit_message": request.form.get("msg"),
+ "prev_commit": request.form.get("hash")})
data = results.json()
data["filename"] = request.form.get("file_path")
return render_template("gn_editor_results_page.html", **data)
@@ -371,7 +374,8 @@ def get_gnqa_records():
prev_n_queries = get_chunk(response, page, pagination_size)
return render_template("gnqa_search_history.html",
prev_queries=prev_n_queries,
- num_pages=math.ceil(len(response)/pagination_size),
+ num_pages=math.ceil(
+ len(response)/pagination_size),
current=page)
token = session_info()["user"]["token"].either(
lambda err: err, lambda tok: tok["access_token"])
@@ -379,9 +383,9 @@ def get_gnqa_records():
return (monad_requests.get(urljoin(GN3_LOCAL_URL, response_url),
headers={
"Authorization": f"Bearer {token}"
- }
- ).then(lambda resp: resp).either(
- _error_, _success_))
+ }
+ ).then(lambda resp: resp).either(
+ _error_, _success_))
@app.route("/gnqna/record", methods=["GET"])
@@ -402,7 +406,7 @@ def get_gnqa_record_by_task_id():
return (monad_requests.get(urljoin(GN3_LOCAL_URL, response_url),
headers={
"Authorization": f"Bearer {token}"
- }).then(lambda resp: resp).either(
+ }).then(lambda resp: resp).either(
_error_, _success_))
@@ -1296,18 +1300,22 @@ def display_diffs_users():
@app.route("/genewiki/<string:symbol>")
def display_genewiki_page(symbol: str):
- """Fetch GeneRIF metadata from GN3 and display it"""
- wiki = {}
+ """Display RIF metadata from NCBI"""
+ wiki, rif = [], []
try:
- wiki = requests.get(urljoin(GN3_LOCAL_URL, f"/api/metadata/wiki/{symbol}"))
+ wiki = requests.get(
+ urljoin(GN3_LOCAL_URL, f"/api/metadata/wiki/{symbol}"))
+ rif = requests.get(
+ urljoin(GN3_LOCAL_URL, f"/api/metadata/rif/{symbol}"))
wiki.raise_for_status()
- wiki = wiki.json()
+ rif.raise_for_status()
+ wiki, rif = wiki.json(), rif.json()
except requests.RequestException as excp:
flash(excp, "alert-warning")
sess_info = session_info()
is_logged_in = sess_info.get("user", {}).get("logged_in", False)
-
- return render_template("wiki/genewiki.html", symbol=symbol, wiki=wiki, is_logged_in=is_logged_in)
+ return render_template("wiki/genewiki.html",
+ symbol=symbol, wiki=wiki, rif=rif, is_logged_in=is_logged_in)
@app.route("/genewiki/<int:comment_id>/history")
@@ -1605,7 +1613,7 @@ def edit_wiki(comment_id: int):
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)
+ categories[i: i + 3] for i in range(0, len(categories), 3)
]
session_email = session_info()["user"]["email"]
@@ -1619,7 +1627,7 @@ def edit_wiki(comment_id: int):
if request.method == "POST":
post_data = request.form
web_url = post_data["web_url"]
- if web_url == "http://": # default prefilled value in form
+ if web_url == "http://": # default prefilled value in form
web_url = ""
payload = {
"symbol": post_data["symbol"],
@@ -1632,6 +1640,7 @@ def edit_wiki(comment_id: int):
"categories": post_data.getlist("genecategory"),
"reason": post_data["reason"],
}
+
def _invalid_token(err):
raise ValueError(f"Error finding user token, got: {err}")
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-25 21:15:07 +0000