Extract common pattern into generic function.

6 files changed, 85 insertions, 114 deletions

diff --git a/uploader/genotypes/views.py b/uploader/genotypes/views.py
index 5105730..54c2444 100644
--- a/uploader/genotypes/views.py
+++ b/uploader/genotypes/views.py
@@ -12,12 +12,12 @@ from flask import (flash,
 from uploader.ui import make_template_renderer
 from uploader.oauth2.client import oauth2_post
 from uploader.authorisation import require_login
+from uploader.route_utils import generic_select_population
+from uploader.datautils import safe_int, enumerate_sequence
 from uploader.species.models import all_species, species_by_id
 from uploader.monadic_requests import make_either_error_handler
 from uploader.request_checks import with_species, with_population
-from uploader.datautils import safe_int, order_by_family, enumerate_sequence
-from uploader.population.models import (populations_by_species,
-                                        population_by_species_and_id)
+from uploader.population.models import population_by_species_and_id
 
 from .models import (genotype_markers,
                      genotype_dataset,
@@ -57,34 +57,16 @@ def index():
                    methods=["GET"])
 @require_login
 @with_species(redirect_uri="species.populations.genotypes.index")
-def select_population(species: dict, species_id: int):
+def select_population(species: dict, species_id: int):# pylint: disable=[unused-argument]
     """Select the population under which the genotypes go."""
-    with database_connection(app.config["SQL_URI"]) as conn:
-        if not bool(request.args.get("population_id")):
-            return render_template("genotypes/select-population.html",
-                                   species=species,
-                                   populations=populations_by_species(
-                                       conn, species_id),
-                                   activelink="genotypes")
-
-        population_id = request.args["population_id"]
-        if population_id == "CREATE-POPULATION":
-            return redirect(url_for(
-                "species.populations.create_population",
-                species_id=species["SpeciesId"],
-                return_to="species.populations.samples.list_genotypes"))
-
-        population = population_by_species_and_id(
-            conn, species_id, request.args.get("population_id"))
-        if not bool(population):
-            flash("Invalid population selected!", "alert-danger")
-            return redirect(url_for(
-                "species.populations.genotypes.select_population",
-                species_id=species_id))
-
-        return redirect(url_for("species.populations.genotypes.list_genotypes",
-                                species_id=species_id,
-                                population_id=population["Id"]))
+    return generic_select_population(
+        species,
+        "genotypes/select-population.html",
+        request.args.get("population_id") or "",
+        "species.populations.genotypes.select_population",
+        "species.populations.genotypes.list_genotypes",
+        "genotypes",
+        "Invalid population selected!")
 
 
 @genotypesbp.route(
diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py
index bcbb3a9..dc2df8f 100644
--- a/uploader/phenotypes/views.py
+++ b/uploader/phenotypes/views.py
@@ -31,12 +31,11 @@ from uploader.files import save_file#, fullpath
 from uploader.ui import make_template_renderer
 from uploader.oauth2.client import oauth2_post
 from uploader.authorisation import require_login
+from uploader.route_utils import generic_select_population
+from uploader.datautils import safe_int, enumerate_sequence
 from uploader.species.models import all_species, species_by_id
 from uploader.monadic_requests import make_either_error_handler
 from uploader.request_checks import with_species, with_population
-from uploader.datautils import safe_int, order_by_family, enumerate_sequence
-from uploader.population.models import (populations_by_species,
-                                        population_by_species_and_id)
 from uploader.input_validation import (encode_errors,
                                        decode_errors,
                                        is_valid_representative_name)
@@ -85,31 +84,14 @@ def index():
 @with_species(redirect_uri="species.populations.phenotypes.index")
 def select_population(species: dict, **kwargs):# pylint: disable=[unused-argument]
     """Select the population for your phenotypes."""
-    with database_connection(app.config["SQL_URI"]) as conn:
-        if not bool(request.args.get("population_id")):
-            return render_template("phenotypes/select-population.html",
-                                   species=species,
-                                   populations=populations_by_species(
-                                       conn, species["SpeciesId"]),
-                                   activelink="phenotypes")
-
-        population_id = request.args["population_id"]
-        if population_id == "CREATE-POPULATION":
-            return redirect(url_for(
-                "species.populations.create_population",
-                species_id=species["SpeciesId"],
-                return_to="species.populations.phenotypes.list_datasets"))
-        population = population_by_species_and_id(
-            conn, species["SpeciesId"], int(population_id))
-        if not bool(population):
-            flash("No such population found!", "alert-danger")
-            return redirect(url_for(
-                "species.populations.phenotypes.select_population",
-                species_id=species["SpeciesId"]))
-
-        return redirect(url_for("species.populations.phenotypes.list_datasets",
-                                species_id=species["SpeciesId"],
-                                population_id=population["Id"]))
+    return generic_select_population(
+        species,
+        "phenotypes/select-population.html",
+        request.args.get("population_id") or "",
+        "species.populations.phenotypes.select_population",
+        "species.populations.phenotypes.list_datasets",
+        "phenotypes",
+        "No such population found!")
 
 
 
diff --git a/uploader/platforms/views.py b/uploader/platforms/views.py
index 114c1a9..d12a9ef 100644
--- a/uploader/platforms/views.py
+++ b/uploader/platforms/views.py
@@ -12,7 +12,7 @@ from flask import (
 from uploader.ui import make_template_renderer
 from uploader.authorisation import require_login
 from uploader.species.models import all_species, species_by_id
-from uploader.datautils import safe_int, order_by_family, enumerate_sequence
+from uploader.datautils import safe_int, enumerate_sequence
 
 from .models import (save_new_platform,
                      platforms_by_species,
diff --git a/uploader/population/views.py b/uploader/population/views.py
index f42e547..bc233a2 100644
--- a/uploader/population/views.py
+++ b/uploader/population/views.py
@@ -20,11 +20,9 @@ from uploader.genotypes.views import genotypesbp
 from uploader.datautils import enumerate_sequence
 from uploader.phenotypes.views import phenotypesbp
 from uploader.expression_data.views import exprdatabp
+from uploader.species.models import all_species, species_by_id
 from uploader.monadic_requests import make_either_error_handler
 from uploader.input_validation import is_valid_representative_name
-from uploader.species.models import (all_species,
-                                     species_by_id,
-                                     order_species_by_family)
 
 from .models import (save_population,
                      population_families,
diff --git a/uploader/route_utils.py b/uploader/route_utils.py
new file mode 100644
index 0000000..18eadda
--- /dev/null
+++ b/uploader/route_utils.py
@@ -0,0 +1,41 @@
+"""Generic routing utilities."""
+from flask import flash, url_for, redirect, render_template, current_app as app
+
+from gn_libs.mysqldb import database_connection
+
+from uploader.population.models import (populations_by_species,
+                                        population_by_species_and_id)
+
+def generic_select_population(# pylint: disable=[too-many-arguments]
+        species: dict,
+        template: str,
+        population_id: str,
+        back_to: str,
+        forward_to: str,
+        activelink: str,
+        error_message: str = "No such population found!"
+):
+    """Handles common flow for 'select population' step."""
+    with database_connection(app.config["SQL_URI"]) as conn:
+        if not bool(population_id):
+            return render_template(
+                template,
+                species=species,
+                populations=populations_by_species(conn, species["SpeciesId"]),
+                activelink=activelink)
+
+        if population_id == "CREATE-POPULATION":
+            return redirect(url_for(
+                "species.populations.create_population",
+                species_id=species["SpeciesId"],
+                return_to=forward_to))
+
+        population = population_by_species_and_id(
+            conn, species["SpeciesId"], int(population_id))
+        if not bool(population):
+            flash(error_message, "alert-danger")
+            return redirect(url_for(back_to, species_id=species["SpeciesId"]))
+
+        return redirect(url_for(forward_to,
+                                species_id=species["SpeciesId"],
+                                population_id=population["Id"]))
diff --git a/uploader/samples/views.py b/uploader/samples/views.py
index 95a6f8c..27e5d3c 100644
--- a/uploader/samples/views.py
+++ b/uploader/samples/views.py
@@ -16,16 +16,15 @@ from uploader import jobs
 from uploader.files import save_file
 from uploader.ui import make_template_renderer
 from uploader.authorisation import require_login
-from uploader.request_checks import with_population
 from uploader.input_validation import is_integer_input
-from uploader.datautils import safe_int, order_by_family, enumerate_sequence
-from uploader.population.models import population_by_id, populations_by_species
+from uploader.population.models import population_by_id
+from uploader.route_utils import generic_select_population
+from uploader.datautils import safe_int, enumerate_sequence
+from uploader.species.models import all_species, species_by_id
+from uploader.request_checks import with_species, with_population
 from uploader.db_utils import (with_db_connection,
                                database_connection,
                                with_redis_connection)
-from uploader.species.models import (all_species,
-                                     species_by_id,
-                                     order_species_by_family)
 
 from .models import samples_by_species_and_population
 
@@ -59,62 +58,31 @@ def index():
 
 @samplesbp.route("<int:species_id>/samples/select-population", methods=["GET"])
 @require_login
-def select_population(species_id: int):
+@with_species(redirect_uri="species.populations.samples.index")
+def select_population(species: dict, **kwargs):# pylint: disable=[unused-argument]
     """Select the population to use for the samples."""
-    with database_connection(app.config["SQL_URI"]) as conn:
-        species = species_by_id(conn, species_id)
-        if not bool(species):
-            flash("Invalid species!", "alert-danger")
-            return redirect(url_for("species.populations.samples.index"))
-
-        if not bool(request.args.get("population_id")):
-            return render_template("samples/select-population.html",
-                                   species=species,
-                                   populations=populations_by_species(
-                                       conn,
-                                       species_id),
-                                   activelink="samples")
-
-        population_id = request.args["population_id"]
-        if population_id == "CREATE-POPULATION":
-            return redirect(url_for(
-                "species.populations.create_population",
-                species_id=species["SpeciesId"],
-                return_to="species.populations.samples.list_samples"))
-
-        population = population_by_id(conn, request.args.get("population_id"))
-        if not bool(population):
-            flash("Population not found!", "alert-danger")
-            return redirect(url_for(
-                "species.populations.samples.select_population",
-                species_id=species_id))
-
-        return redirect(url_for("species.populations.samples.list_samples",
-                                species_id=species_id,
-                                population_id=population["Id"]))
+    return generic_select_population(
+        species,
+        "samples/select-population.html",
+        request.args.get("population_id") or "",
+        "species.populations.samples.select_population",
+        "species.populations.samples.list_samples",
+        "samples",
+        "Population not found!")
 
 @samplesbp.route("<int:species_id>/populations/<int:population_id>/samples")
 @require_login
-def list_samples(species_id: int, population_id: int):
+@with_population(
+    species_redirect_uri="species.populations.samples.index",
+    redirect_uri="species.populations.samples.select_population")
+def list_samples(species: dict, population: dict, **kwargs):# pylint: disable=[unused-argument]
     """
     List the samples in a particular population and give the ability to upload
     new ones.
     """
     with database_connection(app.config["SQL_URI"]) as conn:
-        species = species_by_id(conn, species_id)
-        if not bool(species):
-            flash("Invalid species!", "alert-danger")
-            return redirect(url_for("species.populations.samples.index"))
-
-        population = population_by_id(conn, population_id)
-        if not bool(population):
-            flash("Population not found!", "alert-danger")
-            return redirect(url_for(
-                "species.populations.samples.select_population",
-                species_id=species_id))
-
         all_samples = enumerate_sequence(samples_by_species_and_population(
-            conn, species_id, population_id))
+            conn, species["SpeciesId"], population["Id"]))
         total_samples = len(all_samples)
         offset = max(safe_int(request.args.get("from") or 0), 0)
         count = int(request.args.get("count") or 20)