Use extracted functions and fix bugs

5 files changed, 29 insertions, 15 deletions

diff --git a/qc_app/dbinsert.py b/qc_app/dbinsert.py
index 881c913..a878ff5 100644
--- a/qc_app/dbinsert.py
+++ b/qc_app/dbinsert.py
@@ -11,8 +11,10 @@ from flask import (
     flash, request, url_for, Blueprint, redirect, render_template,
     current_app as app)
 
+from qc_app.db_utils import with_db_connection, database_connection
+from qc_app.db import species, species_by_id, populations_by_species
+
 from . import jobs
-from .db_utils import with_db_connection, database_connection
 
 dbinsertbp = Blueprint("dbinsert", __name__)
 
@@ -91,7 +93,8 @@ def tissues() -> tuple:
 def select_platform():
     "Select the platform (GeneChipId) used for the data."
     job_id = request.form["job_id"]
-    with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn:
+    with (Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn,
+          database_connection(app.config["SQL_URI"]) as conn):
         job = jobs.job(rconn, job_id)
         if job:
             filename = job["filename"]
@@ -102,7 +105,7 @@ def select_platform():
                 return render_template(
                     "select_platform.html", filename=filename,
                     filetype=job["filetype"], totallines=int(job["currentline"]),
-                    default_species=default_species, species=species(),
+                    default_species=default_species, species=species(conn),
                     genechips=gchips[default_species],
                     genechips_data=json.dumps(gchips))
             return render_error(f"File '{filename}' no longer exists.")
@@ -124,7 +127,10 @@ def select_study():
 
         the_studies = studies_by_species_and_platform(speciesid, genechipid)
         the_groups = reduce(
-            organise_groups_by_family, groups_by_species(speciesid), {})
+            organise_groups_by_family,
+            with_db_connection(
+                lambda conn: populations_by_species(conn, speciesid)),
+            {})
         return render_template(
             "select_study.html", filename=form["filename"],
             filetype=form["filetype"], totallines=form["totallines"],
diff --git a/qc_app/entry.py b/qc_app/entry.py
index bf78037..0cd34c5 100644
--- a/qc_app/entry.py
+++ b/qc_app/entry.py
@@ -14,7 +14,8 @@ from flask import (
     render_template,
     current_app as app)
 
-from .dbinsert import species
+from qc_app.db import species
+from qc_app.db_utils import with_db_connection
 
 entrybp = Blueprint("entry", __name__)
 
@@ -78,14 +79,16 @@ def zip_file_errors(filepath, upload_dir) -> Tuple[str, ...]:
 def upload_file():
     """Enables uploading the files"""
     if request.method == "GET":
-        return render_template("index.html", species = species())
+        return render_template(
+            "index.html", species=with_db_connection(species))
 
     upload_dir = app.config["UPLOAD_FOLDER"]
     request_errors = errors(request)
     if request_errors:
         for error in request_errors:
             flash(error, "alert-error")
-        return render_template("index.html", species = species()), 400
+        return render_template(
+            "index.html", species=with_db_connection(species)), 400
 
     filename = secure_filename(request.files["qc_text_file"].filename)
     if not os.path.exists(upload_dir):
@@ -98,7 +101,8 @@ def upload_file():
     if zip_errors:
         for error in zip_errors:
             flash(error, "alert-error")
-        return render_template("index.html", species = species()), 400
+        return render_template(
+            "index.html", species=with_db_connection(species)), 400
 
     return redirect(url_for(
         "parse.parse", filename=filename,
diff --git a/qc_app/samples.py b/qc_app/samples.py
index 107e889..8f56ee1 100644
--- a/qc_app/samples.py
+++ b/qc_app/samples.py
@@ -22,11 +22,15 @@ from quality_control.parsing import take
 
 from qc_app import jobs
 from qc_app.files import save_file
-from qc_app.dbinsert import species_by_id, groups_by_species
 from qc_app.db_utils import (
     with_db_connection,
     database_connection,
     with_redis_connection)
+from qc_app.db import (
+    species_by_id,
+    save_population,
+    population_by_id,
+    populations_by_species)
 
 samples = Blueprint("samples", __name__)
 
@@ -43,7 +47,8 @@ def select_species():
             return render_template(
                 "samples/select-population.html",
                 species=species,
-                populations=groups_by_species(species_id))
+                populations=with_db_connection(
+                    lambda conn: populations_by_species(conn, species_id)))
         flash("Invalid species selected!", "alert-error")
     flash("You need to select a species", "alert-error")
     return index_page
@@ -65,7 +70,7 @@ def create_population():
                   "alert-error error-create-population")
             return species_page
 
-        pop_id = save_population(conn, {
+        pop = save_population(conn, {
             "SpeciesId": species["SpeciesId"],
             "Name": pop_name,
             "InbredSetName": pop_fullname,
@@ -79,7 +84,7 @@ def create_population():
         "samples/upload-samples.html",
         species=species,
         population=with_db_connection(
-            lambda conn: population_by_id(conn, pop_id)))
+            lambda conn: population_by_id(conn, pop["population_id"])))
 
 @samples.route("/upload/select-population", methods=["POST"])
 def select_population():
diff --git a/qc_app/upload/rqtl2.py b/qc_app/upload/rqtl2.py
index 06edfee..aabcea9 100644
--- a/qc_app/upload/rqtl2.py
+++ b/qc_app/upload/rqtl2.py
@@ -19,7 +19,7 @@ rqtl2 = Blueprint("rqtl2", __name__)
 def select_species():
     """Select the species."""
     if request.method == "GET":
-        return render_template("rqtl2/index.html", species=all_species())
+        return render_template("rqtl2/index.html", species=with_db_connection(all_species))
 
     species_id = request.form.get("species_id")
     species = with_db_connection(
diff --git a/scripts/insert_samples.py b/scripts/insert_samples.py
index 6b6faf1..8431462 100644
--- a/scripts/insert_samples.py
+++ b/scripts/insert_samples.py
@@ -9,9 +9,8 @@ from redis import Redis
 
 from qc_app.db_utils import database_connection
 from qc_app.check_connections import check_db, check_redis
+from qc_app.db import species_by_id, population_by_id
 from qc_app.samples import (
-    species_by_id,
-    population_by_id,
     save_samples_data,
     read_samples_file,
     cross_reference_samples)