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-rw-r--r--qc_app/templates/rqtl2/create-geno-dataset-success.html57
-rw-r--r--qc_app/upload/rqtl2.py67
2 files changed, 115 insertions, 9 deletions
diff --git a/qc_app/templates/rqtl2/create-geno-dataset-success.html b/qc_app/templates/rqtl2/create-geno-dataset-success.html
new file mode 100644
index 0000000..7feb8d8
--- /dev/null
+++ b/qc_app/templates/rqtl2/create-geno-dataset-success.html
@@ -0,0 +1,57 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+
+{%block title%}Upload R/qtl2 Bundle{%endblock%}
+
+{%block contents%}
+<h2 class="heading">Select Genotypes Dataset</h2>
+
+<div class="explainer">
+ <p>You successfully created the genotype dataset with the following
+ information.
+ <dl>
+ <dt>ID</dt>
+ <dd>{{geno_dataset.id}}</dd>
+
+ <dt>Name</dt>
+ <dd>{{geno_dataset.name}}</dd>
+
+ <dt>Full Name</dt>
+ <dd>{{geno_dataset.fname}}</dd>
+
+ <dt>Short Name</dt>
+ <dd>{{geno_dataset.sname}}</dd>
+
+ <dt>Created On</dt>
+ <dd>{{geno_dataset.today}}</dd>
+
+ <dt>Public?</dt>
+ <dd>{%if geno_dataset.public == 0%}No{%else%}Yes{%endif%}</dd>
+ </dl>
+ </p>
+</div>
+
+<form id="frm-upload-rqtl2-bundle"
+ action="{{url_for('upload.rqtl2.select_dataset_info',
+ species_id=species.SpeciesId,
+ population_id=population.InbredSetId)}}"
+ method="POST"
+ enctype="multipart/form-data">
+ <legend class="heading">select from existing genotype datasets</legend>
+
+ <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
+ <input type="hidden" name="population_id"
+ value="{{population.InbredSetId}}" />
+ <input type="hidden" name="rqtl2_bundle_file"
+ value="{{rqtl2_bundle_file}}" />
+ <input type="hidden" name="geno-dataset-id"
+ value="{{geno_dataset.id}}" />
+
+ <fieldset>
+ <input type="submit"
+ value="continue"
+ class="btn btn-main form-col-2" />
+ </fieldset>
+</form>
+
+{%endblock%}
diff --git a/qc_app/upload/rqtl2.py b/qc_app/upload/rqtl2.py
index 9bed4f1..6ddc83f 100644
--- a/qc_app/upload/rqtl2.py
+++ b/qc_app/upload/rqtl2.py
@@ -1,14 +1,14 @@
"""Module to handle uploading of R/qtl2 bundles."""
from pathlib import Path
-from typing import Optional
+from datetime import date
from zipfile import ZipFile, is_zipfile
+from MySQLdb.cursors import DictCursor
from flask import (
flash,
request,
url_for,
redirect,
- Response,
Blueprint,
render_template,
current_app as app)
@@ -158,12 +158,12 @@ def upload_rqtl2_bundle(species_id: int, population_id: int):
"rqtl2/upload-rqtl2-bundle-step-02.html",
species=species,
population=population,
- rqtl2_bundle_file=the_file.name)
+ rqtl2_bundle_file=the_file.name)#type: ignore[union-attr]
except (InvalidFormat, __RequestError__) as exc:
flash("".join(exc.args), "alert-error alert-rqtl2")
return this_page_with_errors
-def check_errors(conn, *args, **kwargs) -> Optional[Response]:
+def check_errors(conn, *args, **kwargs):
"""Check for select errors in the forms and return a page to redirect to."""
species_id = kwargs.get("species_id") or request.form.get("species_id")
population_id = (kwargs.get("population_id")
@@ -199,7 +199,7 @@ def check_errors(conn, *args, **kwargs) -> Optional[Response]:
pgsrc="error"),
code=307)
- return False
+ return None
@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
"/rqtl2-bundle/dataset-info"),
@@ -230,7 +230,8 @@ def select_dataset_info(species_id: int, population_id: int):
datasets=geno_dataset_by_species_and_population(
conn, species_id, population_id))
- geno_dataset = geno_dataset_by_id(conn, form["geno-dataset-id"])
+ geno_dataset = geno_dataset_by_id(
+ conn, int(form["geno-dataset-id"]))
return render_template("rqtl2/summary-info.html",
species=species,
@@ -240,7 +241,7 @@ def select_dataset_info(species_id: int, population_id: int):
@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
"/rqtl2-bundle/select-geno-dataset"),
methods=["POST"])
-def select_geno_dataset(species_id: int, population_id: int) -> Response:
+def select_geno_dataset(species_id: int, population_id: int):
"""Select from existing geno datasets."""
with database_connection(app.config["SQL_URI"]) as conn:
error = check_errors(
@@ -269,6 +270,54 @@ def select_geno_dataset(species_id: int, population_id: int) -> Response:
@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
"/rqtl2-bundle/create-geno-dataset"),
methods=["POST"])
-def create_geno_dataset(species_id: int, population_id: int) -> Response:
+def create_geno_dataset(species_id: int, population_id: int):
"""Create a new geno dataset."""
- return "IMPLEMENT THIS!!!"
+ with database_connection(app.config["SQL_URI"]) as conn:
+ error = check_errors(conn, "species", "population", "rqtl2_bundle_file")
+ if bool(error):
+ return error
+
+ sgeno_page = redirect(url_for("upload.rqtl2.select_geno_dataset",
+ species_id=species_id,
+ population_id=population_id,
+ pgsrc="error"),
+ code=307)
+ if not bool(request.form.get("dataset-name")):
+ flash("You must provide the dataset name",
+ "alert-error alert-rqtl2")
+ return sgeno_page
+ if not bool(request.form.get("dataset-fullname")):
+ flash("You must provide the dataset full name",
+ "alert-error alert-rqtl2")
+ return sgeno_page
+ if not bool(request.form.get("dataset-shortname")):
+ flash("You must provide the dataset short name",
+ "alert-error alert-rqtl2")
+ return sgeno_page
+ public = 2 if request.form.get("dataset-public") == "on" else 0
+
+ with conn.cursor(cursorclass=DictCursor) as cursor:
+ new_dataset = {
+ "name": request.form.get("dataset-name"),
+ "fname": request.form.get("dataset-fullname"),
+ "sname": request.form.get("dataset-shortname"),
+ "today": date.today().isoformat(),
+ "pub": public,
+ "isetid": population_id
+ }
+ cursor.execute(
+ "INSERT INTO GenoFreeze("
+ "Name, FullName, ShortName, CreateTime, public, InbredSetId"
+ ") "
+ "VALUES("
+ "%(name)s, %(fname)s, %(sname)s, %(today)s, %(pub)s, %(isetid)s"
+ ")",
+ new_dataset)
+ flash("Created dataset successfully.", "alert-success")
+ return render_template(
+ "rqtl2/create-geno-dataset-success.html",
+ species=species_by_id(conn, species_id),
+ population=population_by_species_and_id(
+ conn, species_id, population_id),
+ rqtl2_bundle_file=request.form["rqtl2_bundle_file"],
+ geno_dataset={**new_dataset, "id": cursor.lastrowid})