From cf8d133b110d87aed5cb6695711616625a6669fd Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Thu, 18 Jan 2024 05:52:52 +0300
Subject: Create new ProbeSet study.

---
 qc_app/upload/rqtl2.py | 75 +++++++++++++++++++++++++++++++++++++++++---------
 1 file changed, 62 insertions(+), 13 deletions(-)

(limited to 'qc_app/upload')

diff --git a/qc_app/upload/rqtl2.py b/qc_app/upload/rqtl2.py
index 3411f98..0d80776 100644
--- a/qc_app/upload/rqtl2.py
+++ b/qc_app/upload/rqtl2.py
@@ -19,6 +19,9 @@ from r_qtl.errors import InvalidFormat
 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.tissues import all_tissues, tissue_by_id
+from qc_app.db.platforms import platform_by_id, platforms_by_species
 from qc_app.db import (
     species_by_id,
     save_population,
@@ -28,6 +31,8 @@ from qc_app.db.datasets import (
     geno_dataset_by_id,
     geno_datasets_by_species_and_population,
 
+    probeset_study_by_id,
+    probeset_create_study,
     probeset_datasets_by_study,
     probeset_studies_by_species_and_population)
 
@@ -311,16 +316,58 @@ def select_probeset_study(species_id: int, population_id: int):
             return error
 
         summary_page = redirect(url_for("upload.rqtl2.select_dataset_info",
-                                        species=species_by_id(conn, species_id),
-                                        population=population_by_species_and_id(
-                                            conn, species_id, population_id)),
+                                        species_id=species_id,
+                                        population_id=population_id),
                                 code=307)
-        if not bool(probe_study_by_id(conn, int(request.form["probe-study-id"]))):
+        if not bool(probeset_study_by_id(conn, int(request.form["probe-study-id"]))):
             flash("Invalid study selected!", "alert-error alert-rqtl2")
             return summary_page
 
         return summary_page
 
+@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
+              "/rqtl2-bundle/create-probeset-study"),
+             methods=["POST"])
+def create_probeset_study(species_id: int, population_id: int):
+    """Create a new probeset study."""
+    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
+
+        form = request.form
+        select_study_page = redirect(
+            url_for("upload.rqtl2.select_probeset_study",
+                    species_id=species_id,
+                    population_id=population_id),
+            code=307)
+
+        if not (bool(form.get("platformid")) and
+                bool(platform_by_id(conn, int(form["platformid"])))):
+            flash("Invalid platform selected.", "alert-error alert-rqtl2")
+            return select_study_page
+
+        if not (bool(form.get("tissueid")) and
+                bool(tissue_by_id(conn, int(form["tissueid"])))):
+            flash("Invalid tissue selected.", "alert-error alert-rqtl2")
+            return select_study_page
+
+        study = probeset_create_study(
+            conn, population_id, int(form["platformid"]), int(form["tissueid"]),
+            form["studyname"], form.get("studyfullname") or "",
+            form.get("studyshortname") or "")
+        return render_template(
+            "rqtl2/create-probe-study-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)
+
 @rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
               "/rqtl2-bundle/dataset-info"),
              methods=["POST"])
@@ -359,17 +406,19 @@ def select_dataset_info(species_id: int, population_id: int):
                     rqtl2_bundle_file=thefile.name,
                     geno_dataset=geno_dataset,
                     studies=probeset_studies_by_species_and_population(
-                            conn, species_id, population_id))
+                            conn, species_id, population_id),
+                    platforms=platforms_by_species(conn, species_id),
+                    tissues=all_tissues(conn))
 
             if "pheno" in cdata and not bool(form.get("probe-dataset-id")):
-                    return render_template(
-                        "rqtl2/select-probeset-dataset.html",
-                        species=species,
-                        population=population,
-                        rqtl2_bundle_file=thefile.name,
-                        geno_dataset=geno_dataset,
-                        datasets=probeset_datasets_by_study(
-                            conn, int(form["probe-study-id"])))
+                return render_template(
+                    "rqtl2/select-probeset-dataset.html",
+                    species=species,
+                    population=population,
+                    rqtl2_bundle_file=thefile.name,
+                    geno_dataset=geno_dataset,
+                    datasets=probeset_datasets_by_study(
+                        conn, int(form["probe-study-id"])))
 
     return render_template("rqtl2/summary-info.html",
                            species=species,
-- 
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