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-rw-r--r--etc/default_config.py2
-rw-r--r--manifest.scm3
-rw-r--r--qc_app/dbinsert.py46
-rw-r--r--qc_app/static/css/styles.css27
-rw-r--r--qc_app/static/js/dbinsert.js55
-rw-r--r--qc_app/templates/select_dataset.html40
6 files changed, 153 insertions, 20 deletions
diff --git a/etc/default_config.py b/etc/default_config.py
index fcb17d9..5bafd1a 100644
--- a/etc/default_config.py
+++ b/etc/default_config.py
@@ -11,3 +11,5 @@ UPLOAD_FOLDER = "/tmp/qc_app_files"
REDIS_URL = "redis://"
JOBS_TTL_SECONDS = 1209600 # 14 days
GN3_URL="http://localhost:8080"
+SQL_URI = os.getenv(
+ "SQL_URI", "mysql://gn2:mysql_password@localhost/db_webqtl_s")
diff --git a/manifest.scm b/manifest.scm
index 407834a..d18be5b 100644
--- a/manifest.scm
+++ b/manifest.scm
@@ -8,4 +8,5 @@
"python-pylint"
"python-pytest"
"python-hypothesis"
- "python-jsonpickle"))
+ "python-jsonpickle"
+ "python-mysqlclient"))
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.")
diff --git a/qc_app/static/css/styles.css b/qc_app/static/css/styles.css
index 4d0fa8c..922924c 100644
--- a/qc_app/static/css/styles.css
+++ b/qc_app/static/css/styles.css
@@ -1,3 +1,7 @@
+* {
+ box-sizing: border-box;
+}
+
label, legend {
text-transform: capitalize;
}
@@ -57,14 +61,11 @@ fieldset {
table {
border-collapse: collapse;
-}
-
-.reports-table {
border: 1px solid;
border-color: #336699;
}
-.reports-table thead {
+table thead {
color: #FEFEFE;
background-color: #336699;
border-width: 0 1px 0 1px;
@@ -72,12 +73,12 @@ table {
border-color: #336699;
}
-.reports-table thead tr th {
+table thead tr th {
text-transform: capitalize;
}
-.reports-table th,td {
- border-width: 0 1px 0 1px;
+table th,td {
+ border-width: 0 1px 1px 1px;
border-style: solid;
border-color: #336699;
padding: 0 0.3em 0.3em 0.3em;
@@ -102,10 +103,6 @@ table {
border-radius: 1em;
}
-form {
- width: 30%;
-}
-
fieldset {
border-style: none;
display: grid;
@@ -117,6 +114,12 @@ label {
grid-column: 1 / 2;
}
-input,select,button {
+fieldset input,select,button {
grid-column: 2 / 3;
+ width: 20%;
+}
+
+input[disabled="true"],input[disabled="disabled"] {
+ border-color: #878787;
+ background-color: #A9A9A9;
}
diff --git a/qc_app/static/js/dbinsert.js b/qc_app/static/js/dbinsert.js
index 3c0be54..63d2c86 100644
--- a/qc_app/static/js/dbinsert.js
+++ b/qc_app/static/js/dbinsert.js
@@ -62,7 +62,6 @@ function setup_types(type_data) {
}
function setup_datasets(dataset_data) {
- console.info("DATASET DATA:", dataset_data);
elt = document.getElementById("dataset");
remove_children(elt);
dataset_data.forEach(dataset => {
@@ -75,14 +74,65 @@ function setup_datasets(dataset_data) {
trigger_change_event(elt);
}
+function radio_column(chip) {
+ col = document.createElement("td");
+ radio = document.createElement("input");
+ radio.setAttribute("type", "radio");
+ radio.setAttribute("name", "genechipid");
+ radio.setAttribute("value", chip["GeneChipId"]);
+ radio.setAttribute("required", "required");
+ col.appendChild(radio);
+ return col;
+}
+
+function setup_genechips(genechip_data) {
+ columns = ["GeneChipName", "Name", "GeoPlatform", "GO_tree_value"]
+ submit_button = document.querySelector(
+ "#select-dataset-form input[type='submit']");
+ elt = document.getElementById(
+ "genechips-table").getElementsByTagName("tbody")[0];
+ remove_children(elt);
+ if((genechip_data === undefined) || genechip_data.length === 0) {
+ row = document.createElement("tr");
+ col = document.createElement("td");
+ col.setAttribute("colspan", "5");
+ text = document.createTextNode("No chips found for selected species");
+ col.appendChild(text);
+ row.appendChild(col);
+ elt.appendChild(row);
+ submit_button.setAttribute("disabled", true);
+ return false;
+ }
+
+ submit_button.removeAttribute("disabled")
+ genechip_data.forEach(chip => {
+ row = document.createElement("tr");
+ row.appendChild(radio_column(chip));
+ columns.forEach(column => {
+ col = document.createElement("td");
+ content = document.createTextNode(chip[column]);
+ col.appendChild(content);
+ row.appendChild(col);
+ });
+ elt.appendChild(row);
+ });
+}
+
function menu_contents() {
return JSON.parse(
- document.getElementsByTagName("form")[0].getAttribute(
+ document.getElementById("select-dataset-form").getAttribute(
"data-menu-content"));
}
+function genechips() {
+ return JSON.parse(
+ document.getElementById("select-dataset-form").getAttribute(
+ "data-genechips"));
+}
+
function update_menu(event) {
menu = menu_contents();
+ genec = genechips();
species_elt = document.getElementById("species");
group_elt = document.getElementById("group");
@@ -91,6 +141,7 @@ function update_menu(event) {
if(event.target == species_elt) {
setup_groups(menu["groups"][species_elt.value]);
+ setup_genechips(genec[species_elt.value.toLowerCase()]);
}
if(event.target == group_elt) {
diff --git a/qc_app/templates/select_dataset.html b/qc_app/templates/select_dataset.html
index 5fefccc..db48694 100644
--- a/qc_app/templates/select_dataset.html
+++ b/qc_app/templates/select_dataset.html
@@ -3,10 +3,13 @@
{%block title%}Select Dataset{%endblock%}
{%block contents%}
-<h1 class="heading">{{job_name}}: select dataset</h2>
+<h1 class="heading">{{filename}}: select dataset</h2>
-<form method="POST" data-menu-content="{{menu_contents}}">
- <input type="hidden" name="job_id" value="{{job_id}}" />
+<form method="POST" action="{{url_for('dbinsert.insert_data')}}"
+ id="select-dataset-form"
+ data-menu-content="{{menu_contents}}"
+ data-genechips="{{genechips_data}}">
+ <input type="hidden" name="filename" value="{{filename}}" />
<fieldset>
<label for="species">species:</label>
@@ -57,6 +60,37 @@
</select>
</fieldset>
+ <table id="genechips-table">
+ <thead>
+ <tr>
+ <th>Select</th>
+ <th>GeneChip Name</th>
+ <th>Name</th>
+ <th>GeoPlatform</th>
+ <th>GO Tree Value</th>
+ </tr>
+ </thead>
+
+ <tbody>
+ {%for chip in genechips:%}
+ <tr>
+ <td>
+ <input type="radio" name="genechipid" value="{{chip['GeneChipId']}}"
+ required="required" />
+ </td>
+ <td>{{chip["GeneChipName"]}}</td>
+ <td>{{chip["Name"]}}</td>
+ <td>{{chip["GeoPlatform"]}}</td>
+ <td>{{chip["GO_tree_value"]}}</td>
+ </tr>
+ {%else%}
+ <tr>
+ <td colspan="5">No chips found for selected species</td>
+ </tr>
+ {%endfor%}
+ </tbody>
+ </table>
+
<fieldset>
<input type="submit" class="btn btn-main" value="update database" />
</fieldset>