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-rw-r--r--uploader/genotypes/views.py42
-rw-r--r--uploader/phenotypes/views.py38
-rw-r--r--uploader/platforms/views.py2
-rw-r--r--uploader/population/views.py4
-rw-r--r--uploader/route_utils.py41
-rw-r--r--uploader/samples/views.py72
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)
generated by cgit v1.2.3 (git 2.46.2) at 2025-02-23 22:14:50 +0000