aboutsummaryrefslogtreecommitdiff
path: root/qc_app/dbinsert.py
diff options
context:
space:
mode:
authorFrederick Muriuki Muriithi2022-07-14 08:25:52 +0300
committerFrederick Muriuki Muriithi2022-07-19 05:08:17 +0300
commit1711bbad1409a4def4099d8721deb894a0d5e21c (patch)
treee7cd992a808061ed03fdad84dc30d29a54be9ca7 /qc_app/dbinsert.py
parent8b5400fa04d4ca2e60d7e926800816245e2ab809 (diff)
downloadgn-uploader-1711bbad1409a4def4099d8721deb894a0d5e21c.tar.gz
Implement confirmation stage
Provide user with a confirmation stage where they can verify all the data before inserting into the database.
Diffstat (limited to 'qc_app/dbinsert.py')
-rw-r--r--qc_app/dbinsert.py78
1 files changed, 77 insertions, 1 deletions
diff --git a/qc_app/dbinsert.py b/qc_app/dbinsert.py
index 2b29749..eee7a56 100644
--- a/qc_app/dbinsert.py
+++ b/qc_app/dbinsert.py
@@ -1,6 +1,7 @@
"Handle inserting data into the database"
import os
import json
+from typing import Union
from functools import reduce
from datetime import datetime
@@ -41,6 +42,18 @@ def species() -> tuple:
return tuple()
+def species_by_id(speciesid) -> Union[dict, None]:
+ "Retrieve the species from the database by id."
+ with database_connection() as conn:
+ with conn.cursor(cursorclass=DictCursor) as cursor:
+ cursor.execute(
+ (
+ "SELECT "
+ "SpeciesId, SpeciesName, LOWER(Name) AS Name, MenuName "
+ "FROM Species WHERE SpeciesId=%s"),
+ (speciesid,))
+ return cursor.fetchone()
+
def genechips():
"Retrieve the genechip information from the database"
def __organise_by_species__(acc, chip):
@@ -56,6 +69,15 @@ def genechips():
return {}
+def platform_by_id(genechipid:int) -> Union[dict, None]:
+ "Retrieve the gene platform by id"
+ with database_connection() as conn:
+ with conn.cursor(cursorclass=DictCursor) as cursor:
+ cursor.execute(
+ "SELECT * FROM GeneChip WHERE GeneChipId=%s",
+ (genechipid,))
+ return cursor.fetchone()
+
def studies_by_species_and_platform(speciesid:int, genechipid:int) -> tuple:
"Retrieve the studies by the related species and gene platform"
with database_connection() as conn:
@@ -279,7 +301,61 @@ def create_dataset():
flash(f"Missing data {aserr.args[0]}", "alert-error")
return redirect(url_for("dbinsert.select_dataset"), code=307)
+def study_by_id(studyid:int) -> Union[dict, None]:
+ "Get a study by its Id"
+ with database_connection() as conn:
+ with conn.cursor(cursorclass=DictCursor) as cursor:
+ cursor.execute(
+ "SELECT * FROM ProbeFreeze WHERE ProbeFreezeId=%s",
+ (studyid,))
+ return cursor.fetchone()
+
+def dataset_by_id(datasetid:int) -> Union[dict, None]:
+ "Retrieve a dataset by its id"
+ with database_connection() as conn:
+ with conn.cursor(cursorclass=DictCursor) as cursor:
+ cursor.execute(
+ ("SELECT AvgMethod.Name AS AvgMethodName, ProbeSetFreeze.* "
+ "FROM ProbeSetFreeze INNER JOIN AvgMethod "
+ "ON ProbeSetFreeze.AvgId=AvgMethod.AvgMethodId "
+ "WHERE ProbeSetFreeze.Id=%s"),
+ (datasetid,))
+ return cursor.fetchone()
+
+def selected_keys(original: dict, keys: tuple) -> dict:
+ "Return a new dict from the `original` dict with only `keys` present."
+ return {key: value for key,value in original.items() if key in keys}
+
@dbinsertbp.route("/final-confirmation", methods=["POST"])
def final_confirmation():
"Preview the data before triggering entry into the database"
- return str(request.form)
+ form = request.form
+ try:
+ assert form.get("filename"), "filename"
+ assert form.get("filetype"), "filetype"
+ assert form.get("species"), "species"
+ assert form.get("genechipid"), "platform"
+ assert form.get("studyid"), "study"
+ assert form.get("datasetid"), "dataset"
+
+ speciesid = form["species"]
+ genechipid = form["genechipid"]
+ studyid = form["studyid"]
+ datasetid=form["datasetid"]
+ return render_template(
+ "final_confirmation.html", filename=form["filename"],
+ filetype=form["filetype"], species=speciesid, genechipid=genechipid,
+ studyid=studyid, datasetid=datasetid,
+ the_species=selected_keys(
+ species_by_id(speciesid), ("SpeciesName", "Name", "MenuName")),
+ platform=selected_keys(
+ platform_by_id(genechipid),
+ ("GeneChipName", "Name", "GeoPlatform", "Title", "GO_tree_value")),
+ study=selected_keys(
+ study_by_id(studyid), ("Name", "FullName", "ShortName")),
+ dataset=selected_keys(
+ dataset_by_id(datasetid),
+ ("AvgMethodName", "Name", "Name2", "FullName", "ShortName",
+ "DataScale")))
+ except AssertionError as aserr:
+ return render_error(f"Missing data: {aserr.args[0]}")