From 09b4b70aae5e65516c766882118a897c75a44974 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Fri, 12 Apr 2024 09:13:20 +0300
Subject: Provide tissue-id details to probeset dataset templates

---
 qc_app/db/tissues.py                                     |  5 ++---
 qc_app/templates/rqtl2/create-probe-dataset-success.html |  1 +
 qc_app/templates/rqtl2/select-probeset-dataset.html      |  4 +++-
 qc_app/upload/rqtl2.py                                   | 14 ++++++++++++++
 4 files changed, 20 insertions(+), 4 deletions(-)

(limited to 'qc_app')

diff --git a/qc_app/db/tissues.py b/qc_app/db/tissues.py
index 062e824..9fe7bab 100644
--- a/qc_app/db/tissues.py
+++ b/qc_app/db/tissues.py
@@ -11,11 +11,10 @@ def all_tissues(conn: mdb.Connection) -> tuple[dict, ...]:
         return tuple(dict(row) for row in cursor.fetchall())
 
 
-def tissue_by_id(conn: mdb.Connection, tissueid: int) -> Optional[dict]:
+def tissue_by_id(conn: mdb.Connection, tissueid) -> Optional[dict]:
     """Retrieve a tissue by its ID"""
     with conn.cursor(cursorclass=DictCursor) as cursor:
-        cursor.execute("SELECT * FROM Tissue WHERE Id=%s",
-                       (tissueid,))
+        cursor.execute("SELECT * FROM Tissue WHERE Id=%s", (tissueid,))
         result = cursor.fetchone()
         if bool(result):
             return dict(result)
diff --git a/qc_app/templates/rqtl2/create-probe-dataset-success.html b/qc_app/templates/rqtl2/create-probe-dataset-success.html
index 33612c4..71ff7ac 100644
--- a/qc_app/templates/rqtl2/create-probe-dataset-success.html
+++ b/qc_app/templates/rqtl2/create-probe-dataset-success.html
@@ -47,6 +47,7 @@
 	 value="{{population.InbredSetId}}" />
   <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2_bundle_file}}" />
   <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
+  <input type="hidden" name="tissueid" value="{{tissue.Id}}" />
   <input type="hidden" name="probe-study-id" value="{{study.Id}}" />
   <input type="hidden" name="probe-dataset-id" value="{{dataset.datasetid}}" />
 
diff --git a/qc_app/templates/rqtl2/select-probeset-dataset.html b/qc_app/templates/rqtl2/select-probeset-dataset.html
index d00d6aa..0b2a8f2 100644
--- a/qc_app/templates/rqtl2/select-probeset-dataset.html
+++ b/qc_app/templates/rqtl2/select-probeset-dataset.html
@@ -18,7 +18,7 @@
 	      species_id=species.SpeciesId, population_id=population.Id)}}"
       id="frm:select-probeset-dataset">
   <legend class="heading">Select from existing ProbeSet datasets</legend>
-  {{flash_messages("error-rqtl2-select-probeset-dataset")}}
+  {{flash_messages("error-rqtl2")}}
 
   <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
   <input type="hidden" name="population_id"
@@ -26,6 +26,7 @@
   <input type="hidden" name="rqtl2_bundle_file"
 	 value="{{rqtl2_bundle_file}}" />
   <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
+  <input type="hidden" name="tissueid" value="{{tissue.Id}}" />
   <input type="hidden" name="probe-study-id" value="{{probe_study.Id}}" />
 
   <fieldset>
@@ -75,6 +76,7 @@
   <input type="hidden" name="rqtl2_bundle_file"
 	 value="{{rqtl2_bundle_file}}" />
   <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
+  <input type="hidden" name="tissueid" value="{{tissue.Id}}" />
   <input type="hidden" name="probe-study-id" value="{{probe_study.Id}}" />
 
   <fieldset>
diff --git a/qc_app/upload/rqtl2.py b/qc_app/upload/rqtl2.py
index 66c95b9..bf392a9 100644
--- a/qc_app/upload/rqtl2.py
+++ b/qc_app/upload/rqtl2.py
@@ -870,6 +870,19 @@ def select_dataset_info(species_id: int, population_id: int):
                             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):
+                    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))
+
                     return render_template(
                         "rqtl2/select-probeset-study-id.html",
                         species=species,
@@ -891,6 +904,7 @@ def select_dataset_info(species_id: int, population_id: int):
                         rqtl2_bundle_file=thefile.name,
                         geno_dataset=geno_dataset,
                         probe_study=probeset_study,
+                        tissue=tissue,
                         datasets=probeset_datasets_by_study(
                             conn, int(form["probe-study-id"])),
                         avgmethods=averaging_methods(conn))
-- 
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