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-rw-r--r--uploader/__init__.py8
-rw-r--r--uploader/publications/datatables.py52
-rw-r--r--uploader/publications/models.py10
-rw-r--r--uploader/publications/views.py29
-rw-r--r--uploader/static/css/styles.css6
-rw-r--r--uploader/templates/phenotypes/add-phenotypes-base.html43
6 files changed, 112 insertions, 36 deletions
diff --git a/uploader/__init__.py b/uploader/__init__.py
index 97b9af5..8b49ad5 100644
--- a/uploader/__init__.py
+++ b/uploader/__init__.py
@@ -67,7 +67,13 @@ def setup_logging(app: Flask) -> Flask:
def setup_modules_logging(app_logger):
"""Setup module-level loggers to the same log-level as the application."""
loglevel = logging.getLevelName(app_logger.getEffectiveLevel())
- logging.getLogger("uploader.publications.models").setLevel(loglevel)
+
+ def __setup__(logger_name):
+ _logger = logging.getLogger(logger_name)
+ _logger.setLevel(loglevel)
+
+ __setup__("uploader.publications.models")
+ __setup__("uploader.publications.datatables")
def create_app(config: Optional[dict] = None):
diff --git a/uploader/publications/datatables.py b/uploader/publications/datatables.py
new file mode 100644
index 0000000..e07fafd
--- /dev/null
+++ b/uploader/publications/datatables.py
@@ -0,0 +1,52 @@
+"""Fetch data for datatables."""
+import logging
+from typing import Optional
+
+from MySQLdb.cursors import DictCursor
+
+from gn_libs.mysqldb import Connection, debug_query
+
+logger = logging.getLogger(__name__)
+
+def fetch_publications(
+ conn: Connection,
+ search: Optional[str] = None,
+ offset: int = 0,
+ limit: int = -1
+) -> tuple[dict, int, int, int]:
+ """Fetch publications from the database."""
+ _query = "SELECT * FROM Publication"
+ _count_query = "SELECT COUNT(*) FROM Publication"
+ _params = None
+ _where_clause = ""
+ _limit_clause = ""
+ if search is not None and bool(search):
+ _where_clause = ("WHERE PubMed_ID LIKE %s "
+ "OR Authors LIKE %s "
+ "OR Title LIKE %s")
+ _params = (f"%{search}%",) * 3
+
+ if limit > 0:
+ _limit_clause = f"LIMIT {limit} OFFSET {offset}"
+
+ with conn.cursor(cursorclass=DictCursor) as cursor:
+ cursor.execute("SELECT COUNT(*) FROM Publication")
+ _total_rows = int(cursor.fetchone()["COUNT(*)"])
+
+ cursor.execute(f"{_count_query} {_where_clause}", _params)
+ debug_query(cursor, logger)
+ _result = cursor.fetchone()
+ _total_filtered = int(_result["COUNT(*)"] if bool(_result) else 0)
+
+ cursor.execute(f"{_query} {_where_clause} {_limit_clause}", _params)
+ debug_query(cursor, logger)
+ _current_filtered = tuple(
+ {**dict(row), "index": idx}
+ for idx, row
+ in enumerate(cursor.fetchall(), start=offset+1))
+
+ return (
+ _current_filtered,
+ len(_current_filtered),
+ _total_filtered,
+ _total_rows)
diff --git a/uploader/publications/models.py b/uploader/publications/models.py
index 2b0339b..b199991 100644
--- a/uploader/publications/models.py
+++ b/uploader/publications/models.py
@@ -1,6 +1,6 @@
"""Module to handle persistence and retrieval of publication to/from MariaDB"""
import logging
-from typing import Iterable
+from typing import Iterable, Optional
from MySQLdb.cursors import DictCursor
@@ -69,14 +69,6 @@ def update_publications(conn: Connection , publications: tuple[dict, ...]) -> tu
return tuple()
-def fetch_publications(conn: Connection) -> Iterable[dict]:
- """Fetch publications from the database."""
- with conn.cursor(cursorclass=DictCursor) as cursor:
- cursor.execute("SELECT * FROM Publication")
- for row in cursor.fetchall():
- yield dict(row)
-
-
def fetch_publication_by_id(conn: Connection, publication_id: int) -> dict:
"""Fetch a specific publication from the database."""
with conn.cursor(cursorclass=DictCursor) as cursor:
diff --git a/uploader/publications/views.py b/uploader/publications/views.py
index ebb8740..0608a35 100644
--- a/uploader/publications/views.py
+++ b/uploader/publications/views.py
@@ -1,6 +1,7 @@
"""Endpoints for publications"""
import json
+from MySQLdb.cursors import DictCursor
from gn_libs.mysqldb import database_connection
from flask import (
flash,
@@ -14,11 +15,12 @@ from flask import (
from uploader.authorisation import require_login
from .models import (
- fetch_publications,
fetch_publication_by_id,
create_new_publications,
fetch_publication_phenotypes)
+from .datatables import fetch_publications
+
from gn_libs.debug import __pk__
pubbp = Blueprint("publications", __name__)
@@ -35,12 +37,25 @@ def index():
@pubbp.route("/list", methods=["GET"])
@require_login
def list_publications():
- with database_connection(app.config["SQL_URI"]) as conn:
+ # request breakdown:
+ # https://datatables.net/manual/server-side
+ _page = int(request.args.get("draw"))
+ _length = int(request.args.get("length") or '-1')
+ _start = int(request.args.get("start") or '0')
+ _search = request.args["search[value]"]
+ with (database_connection(app.config["SQL_URI"]) as conn,
+ conn.cursor(cursorclass=DictCursor) as cursor):
+ _publications, _current_rows, _totalfiltered, _totalrows = fetch_publications(
+ conn,
+ _search,
+ offset=_start,
+ limit=_length)
+
return json.dumps({
- "publications": tuple({
- **row, "index": idx
- } for idx,row in enumerate(
- fetch_publications(conn), start=1)),
+ "draw": _page,
+ "recordsTotal": _totalrows,
+ "recordsFiltered": _totalfiltered,
+ "publications": _publications,
"status": "success"
})
@@ -71,7 +86,7 @@ def create_publication():
with database_connection(app.config["SQL_URI"]) as conn:
publications = create_new_publications(conn, ({
- "pubmed_id": form.get("pubmed-id"),
+ "pubmed_id": form.get("pubmed-id") or None,
"abstract": form.get("publication-abstract").encode("utf8") or None,
"authors": authors,
"title": form.get("publication-title").encode("utf8") or None,
diff --git a/uploader/static/css/styles.css b/uploader/static/css/styles.css
index 826ac41..df50dec 100644
--- a/uploader/static/css/styles.css
+++ b/uploader/static/css/styles.css
@@ -179,3 +179,9 @@ table.dataTable thead th, table.dataTable tfoot th{
table.dataTable tbody tr.selected td {
background-color: #ffee99 !important;
}
+
+.form-group {
+ margin-bottom: 2em;
+ padding-bottom: 0.2em;
+ border-bottom: solid gray 1px;
+}
diff --git a/uploader/templates/phenotypes/add-phenotypes-base.html b/uploader/templates/phenotypes/add-phenotypes-base.html
index a7aaeb0..01cd0fe 100644
--- a/uploader/templates/phenotypes/add-phenotypes-base.html
+++ b/uploader/templates/phenotypes/add-phenotypes-base.html
@@ -92,48 +92,53 @@
[
{data: "index"},
{
+ searchable: true,
data: (pub) => {
- if(pub.PubMed_ID) {
- return `<a href="https://pubmed.ncbi.nlm.nih.gov/` +
- `${pub.PubMed_ID}/" target="_blank" ` +
- `title="Link to publication on NCBI.">` +
- `${pub.PubMed_ID}</a>`;
- }
- return "";
+ if(pub.PubMed_ID) {
+ return `<a href="https://pubmed.ncbi.nlm.nih.gov/` +
+ `${pub.PubMed_ID}/" target="_blank" ` +
+ `title="Link to publication on NCBI.">` +
+ `${pub.PubMed_ID}</a>`;
+ }
+ return "";
}
},
{
+ searchable: true,
data: (pub) => {
- var title = "⸻";
- if(pub.Title) {
- title = pub.Title
- }
- return `<a href="/publications/view/${pub.Id}" ` +
+ var title = "⸻";
+ if(pub.Title) {
+ title = pub.Title
+ }
+ return `<a href="/publications/view/${pub.Id}" ` +
`target="_blank" ` +
`title="Link to view publication details">` +
`${title}</a>`;
}
},
{
+ searchable: true,
data: (pub) => {
- authors = pub.Authors.split(",").map(
- (item) => {return item.trim();});
- if(authors.length > 1) {
- return authors[0] + ", et. al.";
- }
- return authors[0];
+ authors = pub.Authors.split(",").map(
+ (item) => {return item.trim();});
+ if(authors.length > 1) {
+ return authors[0] + ", et. al.";
+ }
+ return authors[0];
}
}
],
{
+ serverSide: true,
ajax: {
url: "/publications/list",
dataSrc: "publications"
},
select: "single",
+ paging: true,
scrollY: 700,
- paging: false,
deferRender: true,
+ scroller: true,
layout: {
topStart: "info",
topEnd: "search"
generated by cgit v1.2.3 (git 2.47.1) at 2025-06-15 21:59:50 +0000