Link to admin on yeast sample page.

This commit is contained in:
Chris Giacofei 2024-06-02 08:33:13 -04:00
parent 7d503d6ae4
commit bd73ec2a80
7 changed files with 454 additions and 3 deletions

142
Makefile Normal file
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SHELL:=/bin/bash
UNAME:=$(shell uname)
export LOG_DIR:=logs
# full installation of all the software and config setup
install: conda-install django conf-setup
# starts the web server and app server
# wait a second for gunicorn to start before starting nginx
start: gunicorn-start
sleep 1
$(MAKE) nginx-start
# stop all the servers
stop: gunicorn-kill nginx-stop
# ~~~~~ Setup Conda ~~~~~ #
# this sets the system PATH to ensure we are using in included 'conda' installation for all software
PATH:=$(CURDIR)/conda/bin:$(PATH)
unexport PYTHONPATH
unexport PYTHONHOME
# install versions of conda for Mac or Linux
ifeq ($(UNAME), Darwin)
CONDASH:=Miniconda3-4.5.4-MacOSX-x86_64.sh
endif
ifeq ($(UNAME), Linux)
CONDASH:=Miniconda3-4.5.4-Linux-x86_64.sh
endif
CONDAURL:=https://repo.continuum.io/miniconda/$(CONDASH)
# install conda
conda:
@echo ">>> Setting up conda..."
@wget "$(CONDAURL)" && \
bash "$(CONDASH)" -b -p conda && \
rm -f "$(CONDASH)"
# install the conda packages required
conda-install: conda
conda install -y -c anaconda \
django=2.1.2 \
gunicorn=19.9.0 \
nginx=1.15.5
# ~~~~~ SETUP DJANGO APP ~~~~~ #
# create the app for development; only need to run this when first creating repo
# django-start:
# django-admin startproject webapp .
# python manage.py startapp helloworld
# all the steps needed to set up the django app
django: django-init django-import django-collectstatic
# setup the app for the first time
django-init:
python manage.py makemigrations
python manage.py migrate
python manage.py createsuperuser
# import items to the database
django-import:
python db_import.py
# copy static files over for web hosting
django-collectstatic:
python manage.py collectstatic
# run the Django dev server
django-runserver:
python manage.py runserver
# ~~~~~~ setup Gunicorn WSGI server ~~~~~ #
# set the path to the Unix socket to bind Gunicorn to
SOCKET_FILE:=$(CURDIR)/django.sock
SOCKET:=unix:$(SOCKET_FILE)
GUNICORN_CONFIG:=config/gunicorn_config.py
GUNICORN_PIDFILE:=$(LOG_DIR)/gunicorn.pid
GUNICORN_ACCESS_LOG:=$(LOG_DIR)/gunicorn.access.log
GUNICORN_ERROR_LOG:=$(LOG_DIR)/gunicorn.error.log
GUNICORN_LOG:=$(LOG_DIR)/gunicorn.log
GUNICORN_PID:=
# start gunicorn as a background process; direct paths to the logs and pid files
gunicorn-start:
gunicorn config.wsgi \
--bind "$(SOCKET)" \
--config "$(GUNICORN_CONFIG)" \
--pid "$(GUNICORN_PIDFILE)" \
--access-logfile "$(GUNICORN_ACCESS_LOG)" \
--error-logfile "$(GUNICORN_ERROR_LOG)" \
--log-file "$(GUNICORN_LOG)" \
--daemon
# check to see if gunicorn is running
gunicorn-check:
ps -ax | grep gunicorn
# stop gunicorn; get the process ID from the pid file
gunicorn-kill: GUNICORN_PID=$(shell head -1 $(GUNICORN_PIDFILE))
gunicorn-kill: $(GUNICORN_PIDFILE)
kill "$(GUNICORN_PID)"
# ~~~~~ set nginx web sever ~~~~~ #
# location of nginx "prefix" directory in this repo
NGINX_PREFIX:=$(CURDIR)/nginx
# conf file is located inside the prefix dir
NGINX_CONF:=nginx.conf
# need to edit the myapp.conf file to update it with the paths for this directory
OLD_CONF:=nginx/myapp.conf.og
NEW_CONF:=nginx/myapp.conf
conf-setup: $(NEW_CONF)
$(NEW_CONF):
cat "$(OLD_CONF)" | \
sed 's|unix:/usr/local/bin/apps/myapp/myapp.sock|$(SOCKET)|' | \
sed 's|/usr/local/bin/apps/myapp/|$(CURDIR)|' > "$(NEW_CONF)"
# start nginx; make sure the socket and config files exist first
nginx-start: $(NEW_CONF) $(SOCKET_FILE)
nginx -p "$(NGINX_PREFIX)" -c "$(NGINX_CONF)"
# stop nginx
nginx-stop:
nginx -p "$(NGINX_PREFIX)" -c "$(NGINX_CONF)" -s quit
# reload any updates to the nginx config files
nginx-reload:
nginx -p "$(NGINX_PREFIX)" -c "$(NGINX_CONF)" -s reload
# test to make sure nginx config files can be found and look valid
nginx-test:
nginx -p "$(NGINX_PREFIX)" -c "$(NGINX_CONF)" -t
# check to see if nginx is running
nginx-check:
ps -ax | grep nginx

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config/gunicorn_config.py Normal file
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# Sample Gunicorn configuration file.
# https://raw.githubusercontent.com/benoitc/gunicorn/master/examples/example_config.py
#
# Server socket
#
# bind - The socket to bind.
#
# A string of the form: 'HOST', 'HOST:PORT', 'unix:PATH'.
# An IP is a valid HOST.
#
# backlog - The number of pending connections. This refers
# to the number of clients that can be waiting to be
# served. Exceeding this number results in the client
# getting an error when attempting to connect. It should
# only affect servers under significant load.
#
# Must be a positive integer. Generally set in the 64-2048
# range.
#
bind = 'myserver.com:1234'
backlog = 2048
#
# Worker processes
#
# workers - The number of worker processes that this server
# should keep alive for handling requests.
#
# A positive integer generally in the 2-4 x $(NUM_CORES)
# range. You'll want to vary this a bit to find the best
# for your particular application's work load.
#
# worker_class - The type of workers to use. The default
# sync class should handle most 'normal' types of work
# loads. You'll want to read
# http://docs.gunicorn.org/en/latest/design.html#choosing-a-worker-type
# for information on when you might want to choose one
# of the other worker classes.
#
# A string referring to a Python path to a subclass of
# gunicorn.workers.base.Worker. The default provided values
# can be seen at
# http://docs.gunicorn.org/en/latest/settings.html#worker-class
#
# worker_connections - For the eventlet and gevent worker classes
# this limits the maximum number of simultaneous clients that
# a single process can handle.
#
# A positive integer generally set to around 1000.
#
# timeout - If a worker does not notify the master process in this
# number of seconds it is killed and a new worker is spawned
# to replace it.
#
# Generally set to thirty seconds. Only set this noticeably
# higher if you're sure of the repercussions for sync workers.
# For the non sync workers it just means that the worker
# process is still communicating and is not tied to the length
# of time required to handle a single request.
#
# keepalive - The number of seconds to wait for the next request
# on a Keep-Alive HTTP connection.
#
# A positive integer. Generally set in the 1-5 seconds range.
#
workers = 1
worker_class = 'sync'
worker_connections = 1000
timeout = 30
keepalive = 2
#
# spew - Install a trace function that spews every line of Python
# that is executed when running the server. This is the
# nuclear option.
#
# True or False
#
spew = False
#
# Server mechanics
#
# daemon - Detach the main Gunicorn process from the controlling
# terminal with a standard fork/fork sequence.
#
# True or False
#
# raw_env - Pass environment variables to the execution environment.
#
# pidfile - The path to a pid file to write
#
# A path string or None to not write a pid file.
#
# user - Switch worker processes to run as this user.
#
# A valid user id (as an integer) or the name of a user that
# can be retrieved with a call to pwd.getpwnam(value) or None
# to not change the worker process user.
#
# group - Switch worker process to run as this group.
#
# A valid group id (as an integer) or the name of a user that
# can be retrieved with a call to pwd.getgrnam(value) or None
# to change the worker processes group.
#
# umask - A mask for file permissions written by Gunicorn. Note that
# this affects unix socket permissions.
#
# A valid value for the os.umask(mode) call or a string
# compatible with int(value, 0) (0 means Python guesses
# the base, so values like "0", "0xFF", "0022" are valid
# for decimal, hex, and octal representations)
#
# tmp_upload_dir - A directory to store temporary request data when
# requests are read. This will most likely be disappearing soon.
#
# A path to a directory where the process owner can write. Or
# None to signal that Python should choose one on its own.
#
daemon = False
# raw_env = [
# 'DJANGO_SECRET_KEY=something',
# 'SPAM=eggs',
# ]
pidfile = None
umask = 0
user = None
group = None
tmp_upload_dir = None
#
# Logging
#
# logfile - The path to a log file to write to.
#
# A path string. "-" means log to stdout.
#
# loglevel - The granularity of log output
#
# A string of "debug", "info", "warning", "error", "critical"
#
errorlog = '-'
loglevel = 'info'
accesslog = '-'
access_log_format = '%(h)s %(l)s %(u)s %(t)s "%(r)s" %(s)s %(b)s "%(f)s" "%(a)s"'
#
# Process naming
#
# proc_name - A base to use with setproctitle to change the way
# that Gunicorn processes are reported in the system process
# table. This affects things like 'ps' and 'top'. If you're
# going to be running more than one instance of Gunicorn you'll
# probably want to set a name to tell them apart. This requires
# that you install the setproctitle module.
#
# A string or None to choose a default of something like 'gunicorn'.
#
proc_name = None
#
# Server hooks
#
# post_fork - Called just after a worker has been forked.
#
# A callable that takes a server and worker instance
# as arguments.
#
# pre_fork - Called just prior to forking the worker subprocess.
#
# A callable that accepts the same arguments as after_fork
#
# pre_exec - Called just prior to forking off a secondary
# master process during things like config reloading.
#
# A callable that takes a server instance as the sole argument.
#
def post_fork(server, worker):
server.log.info("Worker spawned (pid: %s)", worker.pid)
def pre_fork(server, worker):
pass
def pre_exec(server):
server.log.info("Forked child, re-executing.")
def when_ready(server):
server.log.info("Server is ready. Spawning workers")
def worker_int(worker):
worker.log.info("worker received INT or QUIT signal")
## get traceback info
import threading, sys, traceback
id2name = {th.ident: th.name for th in threading.enumerate()}
code = []
for threadId, stack in sys._current_frames().items():
code.append("\n# Thread: %s(%d)" % (id2name.get(threadId,""),
threadId))
for filename, lineno, name, line in traceback.extract_stack(stack):
code.append('File: "%s", line %d, in %s' % (filename,
lineno, name))
if line:
code.append(" %s" % (line.strip()))
worker.log.debug("\n".join(code))
def worker_abort(worker):
worker.log.info("worker received SIGABRT signal")

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@ -72,7 +72,7 @@ MIDDLEWARE = [
MEDIA_ROOT = '/tmp/media/'
MEDIA_URL = '/media/'
STATIC_ROOT = os.path.join(BASE_DIR,'sitestatic')
STATIC_ROOT = secrets.get('STATIC_ROOT',os.path.join(BASE_DIR,'sitestatic'))
STATIC_URL = '/static/'
TEMPLATES = [

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# Generated by Django 5.0.6 on 2024-05-31 11:40
import config.extras
from django.db import migrations
class Migration(migrations.Migration):
dependencies = [
('yeast', '0027_alter_batch_source_batch_alter_batch_strain_and_more'),
]
operations = [
migrations.AlterField(
model_name='batch',
name='id',
field=config.extras.DateUUIDField(blank=True, editable=False, max_length=22, primary_key=True, serialize=False, unique=True),
),
migrations.AlterField(
model_name='manufacturer',
name='id',
field=config.extras.DateUUIDField(blank=True, editable=False, max_length=22, primary_key=True, serialize=False, unique=True),
),
migrations.AlterField(
model_name='storage',
name='id',
field=config.extras.DateUUIDField(blank=True, editable=False, max_length=22, primary_key=True, serialize=False, unique=True),
),
migrations.AlterField(
model_name='strain',
name='id',
field=config.extras.DateUUIDField(blank=True, editable=False, max_length=22, primary_key=True, serialize=False, unique=True),
),
migrations.AlterField(
model_name='yeast',
name='id',
field=config.extras.DateUUIDField(blank=True, editable=False, max_length=22, primary_key=True, serialize=False, unique=True),
),
]

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# Generated by Django 5.0.6 on 2024-05-31 11:43
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('yeast', '0028_alter_batch_id_alter_manufacturer_id_and_more'),
]
operations = [
migrations.AlterField(
model_name='manufacturer',
name='id',
field=models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
),
migrations.AlterField(
model_name='storage',
name='id',
field=models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
),
migrations.AlterField(
model_name='strain',
name='id',
field=models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
),
]

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# Generated by Django 5.0.6 on 2024-05-31 12:03
import config.extras
from django.db import migrations
class Migration(migrations.Migration):
dependencies = [
('yeast', '0029_alter_manufacturer_id_alter_storage_id_and_more'),
]
operations = [
migrations.AlterField(
model_name='batch',
name='id',
field=config.extras.DateUUIDField(blank=True, editable=False, primary_key=True, serialize=False, unique=True),
),
migrations.AlterField(
model_name='yeast',
name='id',
field=config.extras.DateUUIDField(blank=True, editable=False, primary_key=True, serialize=False, unique=True),
),
]

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@ -16,7 +16,8 @@
<h3>{{ batch.strain.name }}</h3>
Batch Source: {{ batch.get_source_display }}<br>
Production Date: {{ sample.batch.production_date }}
Production Date: {{ sample.batch.production_date }}<br>
<a href="{% url 'admin:yeast_yeast_change' sample.id %}">Admin Page</a>
<p><p>
{% for sample in batch.remaining_samples %}
<ul>