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-rw-r--r--uploader/genotypes/views.py22
-rw-r--r--uploader/monadic_requests.py32
-rw-r--r--uploader/population/views.py28
3 files changed, 37 insertions, 45 deletions
diff --git a/uploader/genotypes/views.py b/uploader/genotypes/views.py
index 9f08ca6..0821eca 100644
--- a/uploader/genotypes/views.py
+++ b/uploader/genotypes/views.py
@@ -1,5 +1,4 @@
"""Views for the genotypes."""
-from requests.models import Response
from MySQLdb.cursors import DictCursor
from flask import (flash,
request,
@@ -14,6 +13,7 @@ from uploader.oauth2.client import oauth2_post
from uploader.authorisation import require_login
from uploader.db_utils import database_connection
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,
@@ -186,21 +186,6 @@ def create_dataset(species: dict, population: dict, **kwargs):# pylint: disable=
species_id=species["SpeciesId"],
population_id=population["Id"]))
- def __fail__(error):
- msg = "There was an error creating the genotype dataset."
- if issubclass(type(error), Exception):
- app.logger.debug("\n\n%s (Exception)\n\n", msg, exc_info=True)
- raise error
- if issubclass(type(error), Response):
- try:
- _data = error.json()
- except Exception as _exc:
- raise Exception(error.content) from _exc
- raise Exception(_data)
-
- app.logger.debug("\n\n%s\n\n", msg)
- raise Exception(error)
-
return oauth2_post(
"auth/resource/genotypes/create",
json={
@@ -213,4 +198,7 @@ def create_dataset(species: dict, population: dict, **kwargs):# pylint: disable=
"dataset_shortname": form["geno-dataset-shortname"],
"public": "on"
}
- ).either(__fail__, __success__)
+ ).either(
+ make_either_error_handler(
+ "There was an error creating the genotype dataset."),
+ __success__)
diff --git a/uploader/monadic_requests.py b/uploader/monadic_requests.py
index aa34951..c492df5 100644
--- a/uploader/monadic_requests.py
+++ b/uploader/monadic_requests.py
@@ -5,13 +5,12 @@ from typing import Union, Optional, Callable
import requests
from requests.models import Response
from pymonad.either import Left, Right, Either
-from flask import (
- flash,
- request,
- redirect,
- render_template,
- current_app as app,
- escape as flask_escape)
+from flask import (flash,
+ request,
+ redirect,
+ render_template,
+ current_app as app,
+ escape as flask_escape)
# HTML Status codes indicating a successful request.
SUCCESS_CODES = (200, 201, 202, 203, 204, 205, 206, 207, 208, 226)
@@ -84,3 +83,22 @@ def post(url, data=None, json=None, **kwargs) -> Either:
return Left(resp)
except requests.exceptions.RequestException as exc:
return Left(exc)
+
+
+def make_either_error_handler(msg):
+ """Make generic error handler for pymonads Either objects."""
+ def __fail__(error):
+ if issubclass(type(error), Exception):
+ app.logger.debug("\n\n%s (Exception)\n\n", msg, exc_info=True)
+ raise error
+ if issubclass(type(error), Response):
+ try:
+ _data = error.json()
+ except Exception as _exc:
+ raise Exception(error.content) from _exc
+ raise Exception(_data)
+
+ app.logger.debug("\n\n%s\n\n", msg)
+ raise Exception(error)
+
+ return __fail__
diff --git a/uploader/population/views.py b/uploader/population/views.py
index 23bf242..3638453 100644
--- a/uploader/population/views.py
+++ b/uploader/population/views.py
@@ -2,9 +2,7 @@
import re
import json
import base64
-import traceback
-from requests.models import Response
from MySQLdb.cursors import DictCursor
from flask import (flash,
request,
@@ -18,10 +16,11 @@ from uploader.oauth2.client import oauth2_post
from uploader.ui import make_template_renderer
from uploader.authorisation import require_login
from uploader.genotypes.views import genotypesbp
-from uploader.phenotypes.views import phenotypesbp
-from uploader.expression_data.views import exprdatabp
from uploader.db_utils import database_connection
from uploader.datautils import enumerate_sequence
+from uploader.phenotypes.views import phenotypesbp
+from uploader.expression_data.views import exprdatabp
+from uploader.monadic_requests import make_either_error_handler
from uploader.species.models import (all_species,
species_by_id,
order_species_by_family)
@@ -174,22 +173,6 @@ def create_population(species_id: int):
"GeneticType": request.form.get("population_genetic_type") or None
})
- def __handle_error__(error):
- error_format = (
- "\n\nThere was an error creating the population:\n\t%s\n\n")
- if issubclass(type(error), Exception):
- app.logger.debug(error_format, traceback.format_exc())
- raise error
- if issubclass(type(error), Response):
- try:
- _data = error.json()
- except Exception as _exc:
- raise Exception(error.content) from _exc
- raise Exception(_data)
-
- app.logger.debug(error_format, error)
- raise Exception(error)
-
def __flash_success__(_success):
flash("Successfully created resource.", "alert-success")
return redirect(url_for(
@@ -206,7 +189,10 @@ def create_population(species_id: int):
"population_id": new_population["Id"],
"public": "on"
}
- ).either(__handle_error__, __flash_success__)
+ ).either(
+ make_either_error_handler(
+ "There was an error creating the population"),
+ __flash_success__)
@popbp.route("/<int:species_id>/populations/<int:population_id>",