UI: Select from existing ProbeSet datasets.

1 files changed, 38 insertions, 6 deletions

diff --git a/qc_app/upload/rqtl2.py b/qc_app/upload/rqtl2.py
index 0d80776..fc4e0e8 100644
--- a/qc_app/upload/rqtl2.py
+++ b/qc_app/upload/rqtl2.py
@@ -172,7 +172,7 @@ def upload_rqtl2_bundle(species_id: int, population_id: int):
             flash("".join(exc.args), "alert-error alert-rqtl2")
             return this_page_with_errors
 
-def check_errors(conn, *args, **kwargs):
+def check_errors(conn, *args, **kwargs):#pylint: disable=[too-many-return-statements]
     """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")
@@ -208,14 +208,21 @@ def check_errors(conn, *args, **kwargs):
                                 pgsrc="error"),
                         code=307)
 
+    summary_page = redirect(url_for("upload.rqtl2.select_dataset_info",
+                                    species_id=species_id,
+                                    population_id=population_id,
+                                    pgsrc="error"),
+                            code=307)
+
     if ("probe-study-id" in args and
         not bool(request.form.get("probe-study-id"))):
         flash("No probeset study was selected!", "alert-error alert-rqtl2")
-        return redirect(url_for("upload.rqtl2.select_probeset_study",
-                                species_id=species_id,
-                                population_id=population_id,
-                                pgsrc="error"),
-                        code=307)
+        return summary_page
+
+    if ("probe-dataset-id" in args and
+        not bool(request.form.get("probe-dataset-id"))):
+        flash("No probeset dataset was selected!", "alert-error alert-rqtl2")
+        return summary_page
 
     return None
 
@@ -326,6 +333,28 @@ def select_probeset_study(species_id: int, population_id: int):
         return summary_page
 
 @rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
+              "/rqtl2-bundle/select-probeset-dataset"),
+             methods=["POST"])
+def select_probeset_dataset(species_id: int, population_id: int):
+    """Select or create a 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", "probe-dataset-id")
+        if bool(error):
+            return error
+
+        summary_page = redirect(url_for("upload.rqtl2.select_dataset_info",
+                                        species_id=species_id,
+                                        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")
+            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):
@@ -409,6 +438,8 @@ def select_dataset_info(species_id: int, population_id: int):
                             conn, species_id, population_id),
                     platforms=platforms_by_species(conn, species_id),
                     tissues=all_tissues(conn))
+            probeset_study = probeset_study_by_id(
+                conn, int(form["probe-study-id"]))
 
             if "pheno" in cdata and not bool(form.get("probe-dataset-id")):
                 return render_template(
@@ -417,6 +448,7 @@ def select_dataset_info(species_id: int, population_id: int):
                     population=population,
                     rqtl2_bundle_file=thefile.name,
                     geno_dataset=geno_dataset,
+                    probe_study=probeset_study,
                     datasets=probeset_datasets_by_study(
                         conn, int(form["probe-study-id"])))