From 8b5400fa04d4ca2e60d7e926800816245e2ab809 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Thu, 14 Jul 2022 06:20:44 +0300
Subject: Enable creation of new dataset
Enable the user to create a new dataset should the need arise.
A few extra fixes were done, such as:
- Provide list of average methods to choose from
- Provide input elements for some expected fields
- Add a new confirmation step before doing the actual data update
---
qc_app/dbinsert.py | 93 +++++++++++++++++-----
qc_app/static/css/styles.css | 2 +-
qc_app/templates/continue_from_create_dataset.html | 56 +++++++++++++
qc_app/templates/dbupdate_hidden_fields.html | 3 +
qc_app/templates/select_dataset.html | 82 +++++++++++++++----
5 files changed, 199 insertions(+), 37 deletions(-)
create mode 100644 qc_app/templates/continue_from_create_dataset.html
diff --git a/qc_app/dbinsert.py b/qc_app/dbinsert.py
index c106366..2b29749 100644
--- a/qc_app/dbinsert.py
+++ b/qc_app/dbinsert.py
@@ -1,8 +1,8 @@
"Handle inserting data into the database"
import os
import json
-import datetime
from functools import reduce
+from datetime import datetime
import requests
from redis import Redis
@@ -167,7 +167,7 @@ def create_study():
form["tissueid"], form["studyname"],
form.get("studyfullname", ""),
form.get("studyshortname", ""),
- datetime.datetime.now().date().strftime("%Y-%m-%d"),
+ datetime.now().date().strftime("%Y-%m-%d"),
form["inbredsetid"])
query = (
"INSERT INTO ProbeFreeze() "
@@ -188,12 +188,34 @@ def datasets_by_study(studyid:int) -> tuple:
with database_connection() as conn:
with conn.cursor(cursorclass=DictCursor) as cursor:
query = "SELECT * FROM ProbeSetFreeze WHERE ProbeFreezeId=%s"
- print(f"QUERY: {query}\n\tPARAMS: ({studyid},)")
cursor.execute(query, (studyid,))
return tuple(cursor.fetchall())
return tuple()
+def averaging_methods() -> tuple:
+ "Retrieve averaging methods from database"
+ with database_connection() as conn:
+ with conn.cursor(cursorclass=DictCursor) as cursor:
+ cursor.execute("SELECT * FROM AvgMethod")
+ return tuple(cursor.fetchall())
+
+ return tuple()
+
+def dataset_datascales() -> tuple:
+ "Retrieve datascales from database"
+ with database_connection() as conn:
+ with conn.cursor() as cursor:
+ cursor.execute(
+ 'SELECT DISTINCT DataScale FROM ProbeSetFreeze '
+ 'WHERE DataScale IS NOT NULL AND DataScale != ""')
+ return tuple(
+ item for item in
+ (res[0].strip() for res in cursor.fetchall())
+ if (item is not None and item != ""))
+
+ return tuple()
+
@dbinsertbp.route("/dataset", methods=["POST"])
def select_dataset():
"Select the dataset to add the file contents against"
@@ -210,27 +232,54 @@ def select_dataset():
return render_template(
"select_dataset.html", filename=form["filename"],
filetype=form["filetype"], species=form["species"],
- genechipid=form["genechipid"], studyid=studyid, datasets=datasets)
+ genechipid=form["genechipid"], studyid=studyid, datasets=datasets,
+ avgmethods=averaging_methods(), datascales=dataset_datascales())
except AssertionError as aserr:
return render_error(f"Missing data: {aserr.args[0]}")
+@dbinsertbp.route("/create-dataset", methods=["POST"])
+def create_dataset():
+ "Select the dataset to add the file contents against"
+ 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("avgid"), "averaging method"
+ assert form.get("datasetname2"), "Dataset Name 2"
+ assert form.get("datasetfullname"), "Dataset Full Name"
+ assert form.get("datasetshortname"), "Dataset Short Name"
+ assert form.get("datasetpublic"), "Dataset public specification"
+ assert form.get("datasetconfidentiality"), "Dataset confidentiality"
+ assert form.get("datasetdatascale"), "Dataset Datascale"
+
+ with database_connection() as conn:
+ with conn.cursor(cursorclass=DictCursor) as cursor:
+ cursor.execute("SELECT MAX(Id) AS last_id FROM ProbeSetFreeze")
+ new_datasetid = cursor.fetchone()["last_id"] + 1
+ values = (
+ new_datasetid, new_datasetid, form["avgid"],
+ form.get("datasetname",""), form["datasetname2"],
+ form["datasetfullname"], form["datasetshortname"],
+ datetime.now().date().strftime("%Y-%m-%d"),
+ form["datasetpublic"], form["datasetconfidentiality"],
+ form["datasetdatascale"])
+ query = (
+ "INSERT INTO ProbeSetFreeze VALUES"
+ "(%s, %s, %s, %s, %s, %s, %s, %s, NULL, %s, %s, NULL, %s)")
+ cursor.execute(query, values)
+ return render_template(
+ "continue_from_create_dataset.html",
+ filename=form["filename"], filetype=form["filetype"],
+ species=form["species"], genechipid=form["genechipid"],
+ studyid=form["studyid"], datasetid=new_datasetid)
+ except AssertionError as aserr:
+ flash(f"Missing data {aserr.args[0]}", "alert-error")
+ return redirect(url_for("dbinsert.select_dataset"), code=307)
-@dbinsertbp.route("/insert_data", methods=["POST"])
-def insert_data():
+@dbinsertbp.route("/final-confirmation", methods=["POST"])
+def final_confirmation():
"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:
- species = form["species"]
- filetype = form["filetype"]
- datasetid = int(form["dataset"])
- genechipid = int(form["genechipid"])
- return (f"Would insert '{species}' data in '{filetype}' file "
- f"'{filepath}' into the database with the dataset "
- f"'{datasetid}' and genechip '{genechipid}'.")
- except ValueError as verr:
- msg = "::".join(verr.args)
- return render_error(f"Invalid value: {msg}")
- return render_error(f"File '{filename}' no longer exists.")
+ return str(request.form)
diff --git a/qc_app/static/css/styles.css b/qc_app/static/css/styles.css
index a42ffb0..5340701 100644
--- a/qc_app/static/css/styles.css
+++ b/qc_app/static/css/styles.css
@@ -107,7 +107,7 @@ table th,td {
fieldset {
border-style: none;
display: grid;
- grid-template-columns: 1fr 9fr;
+ grid-template-columns: 2fr 8fr;
column-gap: 5px;
}
diff --git a/qc_app/templates/continue_from_create_dataset.html b/qc_app/templates/continue_from_create_dataset.html
new file mode 100644
index 0000000..1e493c5
--- /dev/null
+++ b/qc_app/templates/continue_from_create_dataset.html
@@ -0,0 +1,56 @@
+{%extends "base.html"%}
+{%from "dbupdate_hidden_fields.html" import hidden_fields%}
+
+{%block title%}Create Study{%endblock%}
+
+{%block css%}
+
+{%endblock%}
+
+{%block contents%}
+{{filename}}: create study
+
+{%with messages = get_flashed_messages(with_categories=true)%}
+{%if messages:%}
+
+ {%for category, message in messages:%}
+ - {{message}}
+ {%endfor%}
+
+{%endif%}
+{%endwith%}
+
+
+{%endblock%}
diff --git a/qc_app/templates/dbupdate_hidden_fields.html b/qc_app/templates/dbupdate_hidden_fields.html
index c66ebba..5a95cbb 100644
--- a/qc_app/templates/dbupdate_hidden_fields.html
+++ b/qc_app/templates/dbupdate_hidden_fields.html
@@ -19,5 +19,8 @@
{%if kwargs.get("studyid"):%}
{%endif%}
+{%if kwargs.get("datasetid"):%}
+
+{%endif%}
{%endmacro%}
diff --git a/qc_app/templates/select_dataset.html b/qc_app/templates/select_dataset.html
index 59ead59..a16fc75 100644
--- a/qc_app/templates/select_dataset.html
+++ b/qc_app/templates/select_dataset.html
@@ -8,10 +8,10 @@
{%endblock%}
{%block contents%}
-{{filename}}: select dataset
+{{filename}}: select dataset