From 4e3f6e51b92d9c56f77452bd4b723323a526bc52 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Wed, 17 Jan 2024 05:02:34 +0300
Subject: Enable selecting from existing genotype datasets.

---
 qc_app/templates/rqtl2/select-geno-dataset.html |  2 +-
 qc_app/upload/rqtl2.py                          | 35 +++++++++++++++++++++++--
 2 files changed, 34 insertions(+), 3 deletions(-)

(limited to 'qc_app')

diff --git a/qc_app/templates/rqtl2/select-geno-dataset.html b/qc_app/templates/rqtl2/select-geno-dataset.html
index 3487b6e..64f886e 100644
--- a/qc_app/templates/rqtl2/select-geno-dataset.html
+++ b/qc_app/templates/rqtl2/select-geno-dataset.html
@@ -33,7 +33,7 @@
     <legend>Datasets</legend>
     <label for="select:geno-datasets">Dataset</label>
     <select id="select:geno-datasets"
-	    name="geno-datasets"
+	    name="geno-dataset-id"
 	    required="required"
 	    {%if datasets | length == 0%}
 	    disabled="disabled"
diff --git a/qc_app/upload/rqtl2.py b/qc_app/upload/rqtl2.py
index 146c301..7db005c 100644
--- a/qc_app/upload/rqtl2.py
+++ b/qc_app/upload/rqtl2.py
@@ -189,6 +189,15 @@ def check_errors(conn, *args, **kwargs) -> Optional[Response]:
                                 pgsrc="error"),
                         code=307)
 
+    if ("geno-dataset" in args and
+        not bool(request.form.get("geno-dataset-id"))):
+        flash("No genotype dataset was provided!", "alert-error alert-rqtl2")
+        return redirect(url_for("upload.rqtl2.select_geno_dataset",
+                                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>"
@@ -208,7 +217,7 @@ def select_dataset_info(species_id: int, population_id: int):
         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")):
+            if "geno" in cdata and not bool(form.get("geno-dataset-id")):
                 return render_template(
                     "rqtl2/select-geno-dataset.html",
                     species=species_by_id(conn, species_id),
@@ -225,7 +234,29 @@ def select_dataset_info(species_id: int, population_id: int):
              methods=["POST"])
 def select_geno_dataset(species_id: int, population_id: int) -> Response:
     """Select from existing geno datasets."""
-    return "IMPLEMENT THIS!!!"
+    with database_connection(app.config["SQL_URI"]) as conn:
+        error = check_errors(
+            conn, "species", "population", "rqtl2_bundle_file", "geno-dataset")
+        if bool(error):
+            return error
+
+        geno_dset = geno_dataset_by_species_and_population(
+            conn, species_id, population_id)
+        if not bool(geno_dset):
+            flash("No genotype dataset was provided!",
+                  "alert-error alert-rqtl2")
+            return redirect(url_for("upload.rqtl2.select_geno_dataset",
+                                    species_id=species_id,
+                                    population_id=population_id,
+                                    pgsrc="error"),
+                            code=307)
+
+        flash("Genotype accepted", "alert-success alert-rqtl2")
+        return redirect(url_for("upload.rqtl2.select_dataset_info",
+                                species_id=species_id,
+                                population_id=population_id,
+                                pgsrc="upload.rqtl2.select_geno_dataset"),
+                        code=307)
 
 @rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
               "/rqtl2-bundle/create-geno-dataset"),
-- 
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