From af485aff7d25c1f5128586c550ca36debe24fd66 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Thu, 18 Jan 2024 14:43:00 +0300
Subject: UI: Create new ProbeSet dataset.

---
 qc_app/upload/rqtl2.py | 65 ++++++++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 63 insertions(+), 2 deletions(-)

(limited to 'qc_app/upload')

diff --git a/qc_app/upload/rqtl2.py b/qc_app/upload/rqtl2.py
index fc4e0e8..0b446ac 100644
--- a/qc_app/upload/rqtl2.py
+++ b/qc_app/upload/rqtl2.py
@@ -22,6 +22,7 @@ from qc_app.db_utils import with_db_connection, database_connection
 
 from qc_app.db.tissues import all_tissues, tissue_by_id
 from qc_app.db.platforms import platform_by_id, platforms_by_species
+from qc_app.db.averaging import averaging_methods, averaging_method_by_id
 from qc_app.db import (
     species_by_id,
     save_population,
@@ -33,6 +34,7 @@ from qc_app.db.datasets import (
 
     probeset_study_by_id,
     probeset_create_study,
+    probeset_create_dataset,
     probeset_datasets_by_study,
     probeset_studies_by_species_and_population)
 
@@ -349,7 +351,7 @@ def select_probeset_dataset(species_id: int, population_id: int):
                                         population_id=population_id),
                                 code=307)
         if not bool(probeset_study_by_id(conn, int(request.form["probe-study-id"]))):
-            flash("Invalid dataset selected!", "alert-error alert-rqtl2")
+            flash("Invalid study selected!", "alert-error alert-rqtl2")
             return summary_page
 
         return summary_page
@@ -397,6 +399,64 @@ def create_probeset_study(species_id: int, population_id: int):
                 int(request.form["geno-dataset-id"])),
             study=study)
 
+@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
+              "/rqtl2-bundle/create-probeset-dataset"),
+             methods=["POST"])
+def create_probeset_dataset(species_id: int, population_id: int):#pylint: disable=[too-many-return-statements]
+    """Create a new probeset dataset."""
+    with database_connection(app.config["SQL_URI"]) as conn:
+        error = check_errors(
+            conn, "species", "population", "rqtl2_bundle_file", "geno-dataset",
+            "probe-study-id")
+        if bool(error):
+            return error
+
+        form = request.form
+        summary_page = redirect(url_for("upload.rqtl2.select_dataset_info",
+                                        species_id=species_id,
+                                        population_id=population_id),
+                                code=307)
+        if not bool(form.get("averageid")):
+            flash("Averaging method not selected!", "alert-error alert-rqtl2")
+            return summary_page
+        if not bool(form.get("datasetname")):
+            flash("Dataset name not provided!", "alert-error alert-rqtl2")
+            return summary_page
+        if not bool(form.get("datasetfullname")):
+            flash("Dataset full name not provided!", "alert-error alert-rqtl2")
+            return summary_page
+
+        study = probeset_study_by_id(conn, int(form["probe-study-id"]))
+        if not bool(study):
+            flash("Invalid ProbeSet study provided!", "alert-error alert-rqtl2")
+            return summary_page
+
+        avgmethod = averaging_method_by_id(conn, int(form["averageid"]))
+        if not bool(avgmethod):
+            flash("Invalid averaging method provided!", "alert-error alert-rqtl2")
+            return summary_page
+
+        dset = probeset_create_dataset(conn,
+                                       int(form["probe-study-id"]),
+                                       int(form["averageid"]),
+                                       form["datasetname"],
+                                       form["datasetfullname"],
+                                       form["datasetshortname"],
+                                       form["datasetpublic"] == "on",
+                                       form.get("datasetdatascale", "log2"))
+        return render_template(
+            "rqtl2/create-probe-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=geno_dataset_by_id(
+                conn,
+                int(request.form["geno-dataset-id"])),
+            study=study,
+            avgmethod=avgmethod,
+            dataset=dset)
+
 @rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
               "/rqtl2-bundle/dataset-info"),
              methods=["POST"])
@@ -450,7 +510,8 @@ def select_dataset_info(species_id: int, population_id: int):
                     geno_dataset=geno_dataset,
                     probe_study=probeset_study,
                     datasets=probeset_datasets_by_study(
-                        conn, int(form["probe-study-id"])))
+                        conn, int(form["probe-study-id"])),
+                    avgmethods=averaging_methods(conn))
 
     return render_template("rqtl2/summary-info.html",
                            species=species,
-- 
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