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-rw-r--r--qc_app/dbinsert.py46
1 files changed, 44 insertions, 2 deletions
diff --git a/qc_app/dbinsert.py b/qc_app/dbinsert.py
index 0733e5f..5381fb5 100644
--- a/qc_app/dbinsert.py
+++ b/qc_app/dbinsert.py
@@ -5,9 +5,11 @@ from functools import reduce
import requests
from redis import Redis
+from MySQLdb.cursors import DictCursor
from flask import request, Blueprint, render_template, current_app as app
from . import jobs
+from .db_utils import database_connection
dbinsertbp = Blueprint("dbinsert", __name__)
@@ -25,6 +27,24 @@ def make_menu_items_grouper(grouping_fn=lambda item: item):
return {**acc, grouping: (acc[grouping] + (row_values,))}
return __grouper__
+def genechips():
+ "Retrieve the genechip information from the database"
+ def __organise_by_species__(acc, chip):
+ species = chip["species_name"]
+ if acc.get(species) is None:
+ return {**acc, species: (chip,)}
+ return {**acc, species: acc[species] + (chip,)}
+
+ with database_connection() as conn:
+ with conn.cursor(cursorclass=DictCursor) as cursor:
+ cursor.execute(
+ "SELECT GeneChip.*, LOWER(Species.Name) AS species_name "
+ "FROM GeneChip INNER JOIN Species "
+ "ON GeneChip.SpeciesId=Species.SpeciesId")
+ return reduce(__organise_by_species__, cursor.fetchall(), {})
+
+ return {}
+
@dbinsertbp.route("/select-dataset", methods=["POST"])
def select_dataset():
"Select the dataset to add the file contents against"
@@ -52,12 +72,34 @@ def select_dataset():
"datasets"][default_species][default_group][
default_type]
+ gchips = genechips()
+
return render_template(
- "select_dataset.html", job_id=job_id, job_name=filename,
+ "select_dataset.html", filename=filename,
species=menu_contents["species"],
default_species=default_species, groups=mouse_groups,
types=group_types, datasets=datasets,
- menu_contents=json.dumps(menu_contents))
+ menu_contents=json.dumps(menu_contents),
+ genechips_data=json.dumps(gchips),
+ genechips=gchips.get(default_species, []))
return render_error(f"File '{filename}' no longer exists.")
return render_error(f"Job '{job_id}' no longer exists.")
return render_error("Unknown error")
+
+
+@dbinsertbp.route("/insert_data", methods=["POST"])
+def insert_data():
+ "Preview the data before triggering entry into the database"
+ form = request.form
+ filename = form["filename"]
+ filepath = f"{app.config['UPLOAD_FOLDER']}/{filename}"
+ if os.path.exists(filepath):
+ try:
+ dataset_id = int(form["dataset"])
+ return (f"Would insert data in file '{filepath}' "
+ "into the database with the dataset "
+ f"{dataset_id}")
+ except ValueError as ve:
+ msg = "::".join(ve.args)
+ return render_error(f"Invalid value: {msg}")
+ return render_error(f"File '{filename}' no longer exists.")