Pass connection to `species_by_id` function.

To make `species_by_id` function reusable even outside of the
application context, pass in the database connection instead of
creating the connection inside the function.

1 files changed, 61 insertions, 59 deletions

diff --git a/qc_app/samples.py b/qc_app/samples.py
index 1063fb8..dee08e5 100644
--- a/qc_app/samples.py
+++ b/qc_app/samples.py
@@ -17,8 +17,8 @@ from flask import (
 from quality_control.parsing import take
 
 from .files import save_file
-from .db_utils import with_db_connection
 from .dbinsert import species_by_id, groups_by_species
+from .db_utils import with_db_connection, database_connection
 
 samples = Blueprint("samples", __name__)
 
@@ -29,7 +29,8 @@ def select_species():
     species_id = request.form.get("species_id")
     if bool(species_id):
         species_id = int(species_id)
-        species = species_by_id(species_id)
+        species = with_db_connection(
+            lambda conn: species_by_id(conn, species_id))
         if bool(species):
             return render_template(
                 "samples/select-population.html",
@@ -72,40 +73,42 @@ def population_by_id(conn: mdb.Connection, population_id: int) -> dict:
 def create_population():
     """Create new grouping/population."""
     species_page = redirect(url_for("samples.select_species"), code=307)
-    species = species_by_id(request.form.get("species_id"))
-    pop_name = request.form.get("inbredset_name").strip()
-    pop_fullname = request.form.get("inbredset_fullname").strip()
-
-    if not bool(species):
-        flash("Invalid species!", "alert-error error-create-population")
-        return species_page
-    if (not bool(pop_name)) or (not bool(pop_fullname)):
-        flash("You *MUST* provide a grouping/population name",
-              "alert-error error-create-population")
-        return species_page
-
-    pop_id = with_db_connection(lambda conn: save_population(conn, {
-        "SpeciesId": species["SpeciesId"],
-        "Name": pop_name,
-        "InbredSetName": pop_fullname,
-        "FullName": pop_fullname,
-        "Family": request.form.get("inbredset_family") or None,
-        "Description": request.form.get("description") or None
-    }))
-    flash("Grouping/Population created successfully.", "alert-success")
-    return render_template(
-        "samples/upload-samples.html",
-        species=species,
-        population=with_db_connection(
-            lambda conn: population_by_id(conn, pop_id)))
+    with database_connection(app.config["SQL_URI"]) as conn:
+        species = species_by_id(conn, request.form.get("species_id"))
+        pop_name = request.form.get("inbredset_name").strip()
+        pop_fullname = request.form.get("inbredset_fullname").strip()
+
+        if not bool(species):
+            flash("Invalid species!", "alert-error error-create-population")
+            return species_page
+        if (not bool(pop_name)) or (not bool(pop_fullname)):
+            flash("You *MUST* provide a grouping/population name",
+                  "alert-error error-create-population")
+            return species_page
+
+        pop_id = save_population(conn, {
+            "SpeciesId": species["SpeciesId"],
+            "Name": pop_name,
+            "InbredSetName": pop_fullname,
+            "FullName": pop_fullname,
+            "Family": request.form.get("inbredset_family") or None,
+            "Description": request.form.get("description") or None
+        })
+        flash("Grouping/Population created successfully.", "alert-success")
+        return render_template(
+            "samples/upload-samples.html",
+            species=species,
+            population=with_db_connection(
+                lambda conn: population_by_id(conn, pop_id)))
 
 @samples.route("/upload/select-population", methods=["POST"])
 def select_population():
     """Select from existing groupings/populations."""
     species_page = redirect(url_for("samples.select_species"), code=307)
-    species = species_by_id(request.form.get("species_id"))
-    pop_id = int(request.form.get("inbredset_id"))
-    population = with_db_connection(lambda conn: population_by_id(conn, pop_id))
+    with database_connection(app.config["SQL_URI"]) as conn:
+        species = species_by_id(conn, request.form.get("species_id"))
+        pop_id = int(request.form.get("inbredset_id"))
+        population = with_db_connection(lambda conn: population_by_id(conn, pop_id))
 
     if not bool(species):
         flash("Invalid species!", "alert-error error-select-population")
@@ -195,33 +198,33 @@ def upload_samples():
     samples_uploads_page = redirect(url_for("samples.select_population"),
                                     code=307)
 
-    species = species_by_id(request.form.get("species_id"))
-    if not bool(species):
-        flash("Invalid species!", "alert-error")
-        return samples_uploads_page
-
-    population = with_db_connection(
-        lambda conn: population_by_id(
-            conn, int(request.form.get("inbredset_id"))))
-    if not bool(population):
-        flash("Invalid grouping/population!", "alert-error")
-        return samples_uploads_page
-
-    samples_file = save_file(request.files["samples_file"], Path(app.config["UPLOAD_FOLDER"]))
-    if not bool(samples_file):
-        flash("You need to provide a file with the samples data.")
-        return samples_uploads_page
-
-    firstlineheading = (request.form.get("first_line_heading") == "on")
-
-    separator = request.form.get("separator")
-    if separator == "other":
-        separator = request.form.get("other_separator")
-    if not bool(separator):
-        flash("You need to provide a separator character.", "alert-error")
-        return samples_uploads_page
+    with database_connection(app.config["SQL_URI"]) as conn:
+        species = species_by_id(conn, request.form.get("species_id"))
+        if not bool(species):
+            flash("Invalid species!", "alert-error")
+            return samples_uploads_page
+
+        population = with_db_connection(
+            lambda conn: population_by_id(
+                conn, int(request.form.get("inbredset_id"))))
+        if not bool(population):
+            flash("Invalid grouping/population!", "alert-error")
+            return samples_uploads_page
+
+        samples_file = save_file(request.files["samples_file"], Path(app.config["UPLOAD_FOLDER"]))
+        if not bool(samples_file):
+            flash("You need to provide a file with the samples data.")
+            return samples_uploads_page
+
+        firstlineheading = (request.form.get("first_line_heading") == "on")
+
+        separator = request.form.get("separator")
+        if separator == "other":
+            separator = request.form.get("other_separator")
+        if not bool(separator):
+            flash("You need to provide a separator character.", "alert-error")
+            return samples_uploads_page
 
-    def __insert_samples__(conn: mdb.Connection):
         save_samples_data(
             conn,
             species["SpeciesId"],
@@ -232,5 +235,4 @@ def upload_samples():
             population["InbredSetId"],
             (row["Name"] for row in read_samples_file(samples_file, separator, firstlineheading)))
 
-    with_db_connection(__insert_samples__)
-    return "SUCCESS: Respond with a better UI than this."
+        return "SUCCESS: Respond with a better UI than this."