From 8e4e15ae62989f07d3ca8512165ba2a93c42aa94 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Fri, 12 Apr 2024 09:17:49 +0300
Subject: Consistently check for possibly non-existent data

The "geno-dataset", "tissue", "pheno-study" and "pheno-dataset" data
"objects" might not exist for a particular uploaded bundle, so we
check in a consistent manner to ensure they are provided when needed.
---
 qc_app/upload/rqtl2.py | 35 ++++++++++++++---------------------
 1 file changed, 14 insertions(+), 21 deletions(-)

(limited to 'qc_app/upload')

diff --git a/qc_app/upload/rqtl2.py b/qc_app/upload/rqtl2.py
index bf392a9..8c80ef3 100644
--- a/qc_app/upload/rqtl2.py
+++ b/qc_app/upload/rqtl2.py
@@ -525,7 +525,7 @@ def create_geno_dataset(species_id: int, population_id: int):
 
         return with_errors(__thunk__,
                            partial(check_species, conn=conn),
-                           partial(check_population, conn=conn),
+                           partial(check_population, conn=conn, species_id=species_id),
                            partial(check_r_qtl2_bundle,
                                    species_id=species_id,
                                    population_id=population_id))
@@ -765,6 +765,8 @@ def create_probeset_dataset(species_id: int, population_id: int):#pylint: disabl
                 flash("Dataset full name not provided!", errorclasses)
                 return summary_page
 
+            tissue = tissue_by_id(conn, form.get("tissueid", "").strip())
+
             study = probeset_study_by_id(conn, int(form["probe-study-id"]))
             if not bool(study):
                 flash("Invalid ProbeSet study provided!", errorclasses)
@@ -806,6 +808,7 @@ def create_probeset_dataset(species_id: int, population_id: int):#pylint: disabl
                 geno_dataset=geno_dataset_by_id(
                     conn,
                     int(request.form["geno-dataset-id"])),
+                tissue=tissue,
                 study=study,
                 avgmethod=avgmethod,
                 dataset=dset)
@@ -846,6 +849,9 @@ 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)
+
+                geno_dataset = geno_dataset_by_id(
+                    conn,form.get("geno-dataset-id", "").strip())
                 if "geno" in cdata and not bool(form.get("geno-dataset-id")):
                     return render_template(
                         "rqtl2/select-geno-dataset.html",
@@ -854,21 +860,6 @@ def select_dataset_info(species_id: int, population_id: int):
                         rqtl2_bundle_file=thefile.name,
                         datasets=geno_datasets_by_species_and_population(
                             conn, species_id, population_id))
-                geno_dataset = geno_dataset_by_id(conn, int(form["geno-dataset-id"]))
-
-                if "pheno" in cdata and not bool(form.get("probe-study-id")):
-                    tissue = tissue_by_id(conn, form.get("tissueid", "").strip())
-                    if not bool(tissue):
-                        return render_template(
-                            "rqtl2/select-tissue.html",
-                            species=species,
-                            population=population,
-                            rqtl2_bundle_file=thefile.name,
-                            geno_dataset=geno_dataset,
-                            studies=probeset_studies_by_species_and_population(
-                                conn, species_id, population_id),
-                            platforms=platforms_by_species(conn, species_id),
-                            tissues=all_tissues(conn))
 
                 tissue = tissue_by_id(conn, form.get("tissueid", "").strip())
                 if "pheno" in cdata and not bool(tissue):
@@ -883,6 +874,9 @@ def select_dataset_info(species_id: int, population_id: int):
                         platforms=platforms_by_species(conn, species_id),
                         tissues=all_tissues(conn))
 
+                probeset_study = probeset_study_by_id(
+                    conn, form.get("probe-study-id", "").strip())
+                if "pheno" in cdata and not bool(probeset_study):
                     return render_template(
                         "rqtl2/select-probeset-study-id.html",
                         species=species,
@@ -896,7 +890,9 @@ def select_dataset_info(species_id: int, population_id: int):
                 probeset_study = probeset_study_by_id(
                     conn, int(form["probe-study-id"]))
 
-                if "pheno" in cdata and not bool(form.get("probe-dataset-id")):
+                probeset_dataset = probeset_dataset_by_id(
+                    conn, form.get("probe-dataset-id", "").strip())
+                if "pheno" in cdata and not bool(probeset_dataset):
                     return render_template(
                         "rqtl2/select-probeset-dataset.html",
                         species=species,
@@ -908,16 +904,13 @@ def select_dataset_info(species_id: int, population_id: int):
                         datasets=probeset_datasets_by_study(
                             conn, int(form["probe-study-id"])),
                         avgmethods=averaging_methods(conn))
-                probeset_study = probeset_study_by_id(
-                    conn, int(form["probe-study-id"]))
-                probeset_dataset = probeset_dataset_by_id(
-                    conn, int(form["probe-dataset-id"]))
 
             return render_template("rqtl2/summary-info.html",
                                    species=species,
                                    population=population,
                                    rqtl2_bundle_file=thefile.name,
                                    geno_dataset=geno_dataset,
+                                   tissue=tissue,
                                    probe_study=probeset_study,
                                    probe_dataset=probeset_dataset)
 
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