From 6222ebc5ca0fdeaac9ce7addd07ee4dd900a1afb Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Tue, 16 Jan 2024 12:48:43 +0300
Subject: UI: Create UI to select from existing genotype datasets.

---
 qc_app/upload/rqtl2.py | 73 ++++++++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 71 insertions(+), 2 deletions(-)

(limited to 'qc_app/upload/rqtl2.py')

diff --git a/qc_app/upload/rqtl2.py b/qc_app/upload/rqtl2.py
index 0eca6ae..e020d5a 100644
--- a/qc_app/upload/rqtl2.py
+++ b/qc_app/upload/rqtl2.py
@@ -1,5 +1,6 @@
 """Module to handle uploading of R/qtl2 bundles."""
 from pathlib import Path
+from typing import Optional
 from zipfile import ZipFile, is_zipfile
 
 from flask import (
@@ -7,6 +8,7 @@ from flask import (
     request,
     url_for,
     redirect,
+    Response,
     Blueprint,
     render_template,
     current_app as app)
@@ -14,14 +16,15 @@ from flask import (
 from r_qtl import r_qtl2
 from r_qtl.errors import InvalidFormat
 
-from qc_app.files import save_file
+from qc_app.files import save_file, fullpath
 from qc_app.dbinsert import species as all_species
 from qc_app.db_utils import with_db_connection, database_connection
 from qc_app.db import (
     species_by_id,
     save_population,
     populations_by_species,
-    population_by_species_and_id)
+    population_by_species_and_id,
+    geno_dataset_by_species_and_population)
 
 rqtl2 = Blueprint("rqtl2", __name__)
 
@@ -158,3 +161,69 @@ def upload_rqtl2_bundle(species_id: int, population_id: int):
         except (InvalidFormat, __RequestError__) as exc:
             flash("".join(exc.args), "alert-error alert-danger error-rqtl2")
             return this_page_with_errors
+
+def check_errors(conn, *args, **kwargs) -> Optional[Response]:
+    """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")
+                     or request.form.get("population_id"))
+    species = species_by_id(conn, species_id)
+    population = population_by_species_and_id(conn, species_id, population_id)
+
+    if "species" in args and not bool(species):
+        flash("Invalid species!", "alert-error error-rqtl2")
+        return redirect(url_for("upload.rqtl2.select_species"))
+
+    if "population" in args and not bool(population):
+        flash("Invalid Population!", "alert-error error-rqtl2")
+        return redirect(
+            url_for("upload.rqtl2.select_population", pgsrc="error"),
+            code=307)
+
+    if ("rqtl2_bundle_file" in args
+        and not bool(request.form.get("rqtl2_bundle_file"))):
+        flash("There is no file to process.",
+              "alert-error alert-danger error-rqtl2")
+        return redirect(url_for("upload.rqtl2.upload_rqtl2_bundle",
+                                species_id=species_id,
+                                population_id=population_id,
+                                pgsrc="error"),
+                        code=307)
+
+    return False
+
+@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
+              "/rqtl2-bundle/dataset-info"),
+             methods=["POST"])
+def select_dataset_info(species_id: int, population_id: int):
+    """
+    If `geno` files exist in the R/qtl2 bundle, prompt user to provide the
+    dataset the genotypes belong to.
+    """
+    form = request.form
+    with database_connection(app.config["SQL_URI"]) as conn:
+        error_page = check_errors(conn, "species", "population", "rqtl2_bundle_file")
+        if bool(error_page):
+            return error_page
+
+        thefile = fullpath(form["rqtl2_bundle_file"])
+        with ZipFile(str(thefile), "r") as zfile:
+            cdata = r_qtl2.control_data(zfile)
+            if "geno" in cdata and not bool(form.get("geno_datasetid")):
+                return render_template(
+                    "rqtl2/select-geno-dataset.html",
+                    species=species_by_id(conn, species_id),
+                    population=population_by_species_and_id(
+                        conn, species_id, population_id),
+                    rqtl2_bundle_file=thefile.name,
+                    datasets=geno_dataset_by_species_and_population(
+                        conn, species_id, population_id))
+
+    return "All data points collected. Should proceed to launching the job."
+
+@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:
+    """Select from existing geno datasets."""
+    return "IMPLEMENT THIS!!!"
-- 
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