aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorFrederick Muriuki Muriithi2024-09-24 14:23:13 -0500
committerFrederick Muriuki Muriithi2024-09-24 14:28:29 -0500
commit9eb0ea26879fcd10281611728b7f9ddfcb088121 (patch)
tree8c7915fbe26c64cfe56b8cf8a3dda3c86d31bc80
parent03b2ee98a1a2da648684e5a1a02c7f8c5b45ddd8 (diff)
downloadgn-uploader-9eb0ea26879fcd10281611728b7f9ddfcb088121.tar.gz
Implement creation of new platform.
-rw-r--r--uploader/platforms/models.py56
-rw-r--r--uploader/platforms/views.py46
-rw-r--r--uploader/templates/platforms/create-platform.html21
3 files changed, 119 insertions, 4 deletions
diff --git a/uploader/platforms/models.py b/uploader/platforms/models.py
index 4b690bb..199f2df 100644
--- a/uploader/platforms/models.py
+++ b/uploader/platforms/models.py
@@ -2,7 +2,7 @@
from typing import Optional
import MySQLdb as mdb
-from MySQLdb.cursors import DictCursor
+from MySQLdb.cursors import Cursor, DictCursor
def platforms_by_species(
conn: mdb.Connection,
@@ -29,6 +29,7 @@ def species_platforms_count(conn: mdb.Connection, species_id: int) -> int:
(species_id,))
return int(cursor.fetchone()["count"])
+
def platform_by_id(conn: mdb.Connection, platformid: int) -> Optional[dict]:
"""Retrieve a platform by its ID"""
with conn.cursor(cursorclass=DictCursor) as cursor:
@@ -39,3 +40,56 @@ def platform_by_id(conn: mdb.Connection, platformid: int) -> Optional[dict]:
return dict(result)
return None
+
+
+def platform_by_species_and_id(
+ conn: mdb.Connection, species_id: int, platformid: int
+) -> Optional[dict]:
+ """Retrieve a platform by its species and ID"""
+ with conn.cursor(cursorclass=DictCursor) as cursor:
+ cursor.execute("SELECT * FROM GeneChip WHERE SpeciesId=%s AND Id=%s",
+ (species_id, platformid))
+ result = cursor.fetchone()
+ if bool(result):
+ return dict(result)
+
+ return None
+
+
+def save_new_platform(# pylint: disable=[too-many-arguments]
+ cursor: Cursor,
+ species_id: int,
+ geo_platform: str,
+ platform_name: str,
+ platform_shortname: str,
+ platform_title: str,
+ go_tree_value: Optional[str]
+) -> dict:
+ """Save a new platform to the database."""
+ params = {
+ "species_id": species_id,
+ "GeoPlatform": geo_platform,
+ "GeneChipName": platform_name,
+ "Name": platform_shortname,
+ "Title": platform_title,
+ "GO_tree_value": go_tree_value
+ }
+ cursor.execute("SELECT SpeciesId, GeoPlatform FROM GeneChip")
+ assert (species_id, geo_platform) not in (
+ (row["SpeciesId"], row["GeoPlatform"]) for row in cursor.fetchall())
+ cursor.execute(
+ "INSERT INTO "
+ "GeneChip(SpeciesId, GeneChipName, Name, GeoPlatform, Title, GO_tree_value) "
+ "VALUES("
+ "%(species_id)s, %(GeneChipName)s, %(Name)s, %(GeoPlatform)s, "
+ "%(Title)s, %(GO_tree_value)s"
+ ")",
+ params)
+ new_id = cursor.lastrowid
+ cursor.execute("UPDATE GeneChip SET GeneChipId=%s WHERE Id=%s",
+ (new_id, new_id))
+ return {
+ **params,
+ "Id": new_id,
+ "GeneChipId": new_id
+ }
diff --git a/uploader/platforms/views.py b/uploader/platforms/views.py
index 1abf52e..1030b6c 100644
--- a/uploader/platforms/views.py
+++ b/uploader/platforms/views.py
@@ -1,4 +1,5 @@
"""The endpoints for the platforms"""
+from MySQLdb.cursors import DictCursor
from flask import (
flash,
request,
@@ -13,7 +14,10 @@ from uploader.db_utils import database_connection
from uploader.species.models import all_species, species_by_id
from uploader.datautils import safe_int, order_by_family, enumerate_sequence
-from .models import platforms_by_species, species_platforms_count
+from .models import (save_new_platform,
+ platforms_by_species,
+ species_platforms_count,
+ platform_by_species_and_id)
platformsbp = Blueprint("platforms", __name__)
render_template = make_template_renderer("platforms")
@@ -69,7 +73,8 @@ def list_platforms(species_id: int):
@require_login
def create_platform(species_id: int):
"""Create a new genetic sequencing platform."""
- with database_connection(app.config["SQL_URI"]) as conn:
+ with (database_connection(app.config["SQL_URI"]) as conn,
+ conn.cursor(cursorclass=DictCursor) as cursor):
species = species_by_id(conn, species_id)
if not bool(species):
flash("No species provided.", "alert-danger")
@@ -81,4 +86,39 @@ def create_platform(species_id: int):
species=species,
activelink="create-platform")
- raise NotImplementedError("This still needs to be implemented.")
+ try:
+ form = request.form
+ new_platform = save_new_platform(
+ cursor,
+ species_id,
+ form["geo-platform"],
+ form["platform-name"],
+ form["platform-shortname"],
+ form["platform-title"],
+ form.get("go-tree-value") or None)
+ except KeyError as _kerr:
+ flash(f"Required value for field {_kerr.args[0]} was not provided.",
+ "alert-danger")
+ return redirect(url_for("species.platforms.create_platform",
+ species_id=species_id))
+ except AssertionError as _aerr:
+ flash(f"Platform with GeoPlatform value of '{form['geo-platform']}'"
+ f" already existst for species '{species['FullName']}'.",
+ "alert-danger")
+ return redirect(url_for("species.platforms.create_platform",
+ species_id=species_id))
+
+ flash("Platform created successfully", "alert-success")
+ return redirect(url_for("species.platforms.view_platform",
+ species_id=species_id,
+ platform_id=new_platform["Id"]))
+
+
+@platformsbp.route("<int:species_id>/platforms/<int:platform_id>/view",
+ methods=["GET"])
+@require_login
+def view_platform(species_id: int, platform_id: int):
+ """View details for a specific platform."""
+ with database_connection(app.config["SQL_URI"]) as conn:
+ return platform_by_species_and_id(
+ conn, species_id, platform_id)
diff --git a/uploader/templates/platforms/create-platform.html b/uploader/templates/platforms/create-platform.html
index b5961ce..0866d5e 100644
--- a/uploader/templates/platforms/create-platform.html
+++ b/uploader/templates/platforms/create-platform.html
@@ -90,6 +90,27 @@
</div>
<div class="form-group">
+ <label for="txt-go-tree-value" class="form-label">GO Tree Value</label>
+ <input type="text"
+ id="txt-go-tree-value"
+ name="go-tree-value"
+ class="form-control" />
+ <small class="form-text text-muted">
+ <p>This is a Chip identification value useful for analysis with the
+ <strong>
+ <a href="https://www.geneweaver.org/"
+ title="Go to the GeneWeaver site."
+ target="_blank">GeneWeaver</a></strong>
+ and
+ <strong>
+ <a href="https://www.webgestalt.org/"
+ title="Go to the WEB-based GEne SeT AnaLysis Toolkit site."
+ target="_blank">WebGestalt</a></strong>
+ tools.<br />
+ This can be left blank for custom platforms.</p></small>
+ </div>
+
+ <div class="form-group">
<input type="submit"
value="create new platform"
class="btn btn-primary" />