Link to admin on yeast sample page.
This commit is contained in:
parent
7d503d6ae4
commit
bd73ec2a80
142
Makefile
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142
Makefile
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SHELL:=/bin/bash
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UNAME:=$(shell uname)
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export LOG_DIR:=logs
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# full installation of all the software and config setup
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install: conda-install django conf-setup
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# starts the web server and app server
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# wait a second for gunicorn to start before starting nginx
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start: gunicorn-start
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sleep 1
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$(MAKE) nginx-start
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# stop all the servers
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stop: gunicorn-kill nginx-stop
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# ~~~~~ Setup Conda ~~~~~ #
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# this sets the system PATH to ensure we are using in included 'conda' installation for all software
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PATH:=$(CURDIR)/conda/bin:$(PATH)
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unexport PYTHONPATH
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unexport PYTHONHOME
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# install versions of conda for Mac or Linux
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ifeq ($(UNAME), Darwin)
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CONDASH:=Miniconda3-4.5.4-MacOSX-x86_64.sh
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endif
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ifeq ($(UNAME), Linux)
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CONDASH:=Miniconda3-4.5.4-Linux-x86_64.sh
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endif
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CONDAURL:=https://repo.continuum.io/miniconda/$(CONDASH)
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# install conda
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conda:
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@echo ">>> Setting up conda..."
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@wget "$(CONDAURL)" && \
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bash "$(CONDASH)" -b -p conda && \
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rm -f "$(CONDASH)"
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# install the conda packages required
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conda-install: conda
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conda install -y -c anaconda \
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django=2.1.2 \
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gunicorn=19.9.0 \
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nginx=1.15.5
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# ~~~~~ SETUP DJANGO APP ~~~~~ #
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# create the app for development; only need to run this when first creating repo
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# django-start:
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# django-admin startproject webapp .
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# python manage.py startapp helloworld
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# all the steps needed to set up the django app
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django: django-init django-import django-collectstatic
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# setup the app for the first time
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django-init:
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python manage.py makemigrations
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python manage.py migrate
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python manage.py createsuperuser
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# import items to the database
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django-import:
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python db_import.py
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# copy static files over for web hosting
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django-collectstatic:
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python manage.py collectstatic
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# run the Django dev server
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django-runserver:
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python manage.py runserver
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# ~~~~~~ setup Gunicorn WSGI server ~~~~~ #
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# set the path to the Unix socket to bind Gunicorn to
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SOCKET_FILE:=$(CURDIR)/django.sock
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SOCKET:=unix:$(SOCKET_FILE)
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GUNICORN_CONFIG:=config/gunicorn_config.py
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GUNICORN_PIDFILE:=$(LOG_DIR)/gunicorn.pid
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GUNICORN_ACCESS_LOG:=$(LOG_DIR)/gunicorn.access.log
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GUNICORN_ERROR_LOG:=$(LOG_DIR)/gunicorn.error.log
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GUNICORN_LOG:=$(LOG_DIR)/gunicorn.log
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GUNICORN_PID:=
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# start gunicorn as a background process; direct paths to the logs and pid files
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gunicorn-start:
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gunicorn config.wsgi \
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--bind "$(SOCKET)" \
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--config "$(GUNICORN_CONFIG)" \
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--pid "$(GUNICORN_PIDFILE)" \
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--access-logfile "$(GUNICORN_ACCESS_LOG)" \
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--error-logfile "$(GUNICORN_ERROR_LOG)" \
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--log-file "$(GUNICORN_LOG)" \
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--daemon
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# check to see if gunicorn is running
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gunicorn-check:
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ps -ax | grep gunicorn
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# stop gunicorn; get the process ID from the pid file
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gunicorn-kill: GUNICORN_PID=$(shell head -1 $(GUNICORN_PIDFILE))
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gunicorn-kill: $(GUNICORN_PIDFILE)
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kill "$(GUNICORN_PID)"
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# ~~~~~ set nginx web sever ~~~~~ #
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# location of nginx "prefix" directory in this repo
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NGINX_PREFIX:=$(CURDIR)/nginx
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# conf file is located inside the prefix dir
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NGINX_CONF:=nginx.conf
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# need to edit the myapp.conf file to update it with the paths for this directory
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OLD_CONF:=nginx/myapp.conf.og
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NEW_CONF:=nginx/myapp.conf
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conf-setup: $(NEW_CONF)
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$(NEW_CONF):
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cat "$(OLD_CONF)" | \
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sed 's|unix:/usr/local/bin/apps/myapp/myapp.sock|$(SOCKET)|' | \
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sed 's|/usr/local/bin/apps/myapp/|$(CURDIR)|' > "$(NEW_CONF)"
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# start nginx; make sure the socket and config files exist first
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nginx-start: $(NEW_CONF) $(SOCKET_FILE)
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nginx -p "$(NGINX_PREFIX)" -c "$(NGINX_CONF)"
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# stop nginx
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nginx-stop:
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nginx -p "$(NGINX_PREFIX)" -c "$(NGINX_CONF)" -s quit
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# reload any updates to the nginx config files
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nginx-reload:
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nginx -p "$(NGINX_PREFIX)" -c "$(NGINX_CONF)" -s reload
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# test to make sure nginx config files can be found and look valid
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nginx-test:
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nginx -p "$(NGINX_PREFIX)" -c "$(NGINX_CONF)" -t
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# check to see if nginx is running
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nginx-check:
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ps -ax | grep nginx
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217
config/gunicorn_config.py
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config/gunicorn_config.py
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# Sample Gunicorn configuration file.
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# https://raw.githubusercontent.com/benoitc/gunicorn/master/examples/example_config.py
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#
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# Server socket
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#
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# bind - The socket to bind.
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#
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# A string of the form: 'HOST', 'HOST:PORT', 'unix:PATH'.
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# An IP is a valid HOST.
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#
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# backlog - The number of pending connections. This refers
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# to the number of clients that can be waiting to be
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# served. Exceeding this number results in the client
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# getting an error when attempting to connect. It should
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# only affect servers under significant load.
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#
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# Must be a positive integer. Generally set in the 64-2048
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# range.
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#
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bind = 'myserver.com:1234'
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backlog = 2048
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#
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# Worker processes
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#
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# workers - The number of worker processes that this server
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# should keep alive for handling requests.
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#
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# A positive integer generally in the 2-4 x $(NUM_CORES)
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# range. You'll want to vary this a bit to find the best
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# for your particular application's work load.
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#
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# worker_class - The type of workers to use. The default
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# sync class should handle most 'normal' types of work
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# loads. You'll want to read
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# http://docs.gunicorn.org/en/latest/design.html#choosing-a-worker-type
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# for information on when you might want to choose one
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# of the other worker classes.
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#
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# A string referring to a Python path to a subclass of
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# gunicorn.workers.base.Worker. The default provided values
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# can be seen at
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# http://docs.gunicorn.org/en/latest/settings.html#worker-class
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#
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# worker_connections - For the eventlet and gevent worker classes
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# this limits the maximum number of simultaneous clients that
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# a single process can handle.
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#
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# A positive integer generally set to around 1000.
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#
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# timeout - If a worker does not notify the master process in this
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# number of seconds it is killed and a new worker is spawned
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# to replace it.
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#
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# Generally set to thirty seconds. Only set this noticeably
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# higher if you're sure of the repercussions for sync workers.
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# For the non sync workers it just means that the worker
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# process is still communicating and is not tied to the length
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# of time required to handle a single request.
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#
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# keepalive - The number of seconds to wait for the next request
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# on a Keep-Alive HTTP connection.
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#
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# A positive integer. Generally set in the 1-5 seconds range.
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#
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workers = 1
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worker_class = 'sync'
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worker_connections = 1000
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timeout = 30
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keepalive = 2
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#
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# spew - Install a trace function that spews every line of Python
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# that is executed when running the server. This is the
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# nuclear option.
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#
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# True or False
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#
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spew = False
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#
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# Server mechanics
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#
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# daemon - Detach the main Gunicorn process from the controlling
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# terminal with a standard fork/fork sequence.
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#
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# True or False
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#
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# raw_env - Pass environment variables to the execution environment.
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#
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# pidfile - The path to a pid file to write
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#
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# A path string or None to not write a pid file.
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#
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# user - Switch worker processes to run as this user.
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#
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# A valid user id (as an integer) or the name of a user that
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# can be retrieved with a call to pwd.getpwnam(value) or None
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# to not change the worker process user.
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#
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# group - Switch worker process to run as this group.
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#
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# A valid group id (as an integer) or the name of a user that
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# can be retrieved with a call to pwd.getgrnam(value) or None
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# to change the worker processes group.
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#
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# umask - A mask for file permissions written by Gunicorn. Note that
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# this affects unix socket permissions.
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#
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# A valid value for the os.umask(mode) call or a string
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# compatible with int(value, 0) (0 means Python guesses
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# the base, so values like "0", "0xFF", "0022" are valid
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# for decimal, hex, and octal representations)
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#
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# tmp_upload_dir - A directory to store temporary request data when
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# requests are read. This will most likely be disappearing soon.
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#
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# A path to a directory where the process owner can write. Or
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# None to signal that Python should choose one on its own.
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#
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daemon = False
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# raw_env = [
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# 'DJANGO_SECRET_KEY=something',
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# 'SPAM=eggs',
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# ]
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pidfile = None
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umask = 0
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user = None
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group = None
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tmp_upload_dir = None
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#
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# Logging
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#
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# logfile - The path to a log file to write to.
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#
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# A path string. "-" means log to stdout.
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#
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# loglevel - The granularity of log output
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#
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# A string of "debug", "info", "warning", "error", "critical"
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#
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errorlog = '-'
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loglevel = 'info'
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accesslog = '-'
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access_log_format = '%(h)s %(l)s %(u)s %(t)s "%(r)s" %(s)s %(b)s "%(f)s" "%(a)s"'
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#
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# Process naming
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#
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# proc_name - A base to use with setproctitle to change the way
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# that Gunicorn processes are reported in the system process
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# table. This affects things like 'ps' and 'top'. If you're
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# going to be running more than one instance of Gunicorn you'll
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# probably want to set a name to tell them apart. This requires
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# that you install the setproctitle module.
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#
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# A string or None to choose a default of something like 'gunicorn'.
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#
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proc_name = None
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#
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# Server hooks
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#
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# post_fork - Called just after a worker has been forked.
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#
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# A callable that takes a server and worker instance
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# as arguments.
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#
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# pre_fork - Called just prior to forking the worker subprocess.
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#
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# A callable that accepts the same arguments as after_fork
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#
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# pre_exec - Called just prior to forking off a secondary
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# master process during things like config reloading.
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#
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# A callable that takes a server instance as the sole argument.
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#
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def post_fork(server, worker):
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server.log.info("Worker spawned (pid: %s)", worker.pid)
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def pre_fork(server, worker):
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pass
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def pre_exec(server):
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server.log.info("Forked child, re-executing.")
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def when_ready(server):
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server.log.info("Server is ready. Spawning workers")
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def worker_int(worker):
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worker.log.info("worker received INT or QUIT signal")
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## get traceback info
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import threading, sys, traceback
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id2name = {th.ident: th.name for th in threading.enumerate()}
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code = []
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for threadId, stack in sys._current_frames().items():
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code.append("\n# Thread: %s(%d)" % (id2name.get(threadId,""),
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threadId))
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for filename, lineno, name, line in traceback.extract_stack(stack):
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code.append('File: "%s", line %d, in %s' % (filename,
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lineno, name))
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if line:
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code.append(" %s" % (line.strip()))
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worker.log.debug("\n".join(code))
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def worker_abort(worker):
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worker.log.info("worker received SIGABRT signal")
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@ -72,7 +72,7 @@ MIDDLEWARE = [
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MEDIA_ROOT = '/tmp/media/'
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MEDIA_URL = '/media/'
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STATIC_ROOT = os.path.join(BASE_DIR,'sitestatic')
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STATIC_ROOT = secrets.get('STATIC_ROOT',os.path.join(BASE_DIR,'sitestatic'))
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STATIC_URL = '/static/'
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TEMPLATES = [
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@ -0,0 +1,39 @@
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# Generated by Django 5.0.6 on 2024-05-31 11:40
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import config.extras
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from django.db import migrations
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class Migration(migrations.Migration):
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dependencies = [
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('yeast', '0027_alter_batch_source_batch_alter_batch_strain_and_more'),
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]
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operations = [
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migrations.AlterField(
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model_name='batch',
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name='id',
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field=config.extras.DateUUIDField(blank=True, editable=False, max_length=22, primary_key=True, serialize=False, unique=True),
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),
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migrations.AlterField(
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model_name='manufacturer',
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name='id',
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field=config.extras.DateUUIDField(blank=True, editable=False, max_length=22, primary_key=True, serialize=False, unique=True),
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),
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migrations.AlterField(
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model_name='storage',
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name='id',
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field=config.extras.DateUUIDField(blank=True, editable=False, max_length=22, primary_key=True, serialize=False, unique=True),
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),
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migrations.AlterField(
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model_name='strain',
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name='id',
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field=config.extras.DateUUIDField(blank=True, editable=False, max_length=22, primary_key=True, serialize=False, unique=True),
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),
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migrations.AlterField(
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model_name='yeast',
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name='id',
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field=config.extras.DateUUIDField(blank=True, editable=False, max_length=22, primary_key=True, serialize=False, unique=True),
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),
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]
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# Generated by Django 5.0.6 on 2024-05-31 11:43
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from django.db import migrations, models
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class Migration(migrations.Migration):
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dependencies = [
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('yeast', '0028_alter_batch_id_alter_manufacturer_id_and_more'),
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]
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operations = [
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migrations.AlterField(
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model_name='manufacturer',
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name='id',
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field=models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
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),
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migrations.AlterField(
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model_name='storage',
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name='id',
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field=models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
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),
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migrations.AlterField(
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model_name='strain',
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name='id',
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field=models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
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),
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]
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24
yeast/migrations/0030_alter_batch_id_alter_yeast_id.py
Normal file
24
yeast/migrations/0030_alter_batch_id_alter_yeast_id.py
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# Generated by Django 5.0.6 on 2024-05-31 12:03
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import config.extras
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from django.db import migrations
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class Migration(migrations.Migration):
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dependencies = [
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('yeast', '0029_alter_manufacturer_id_alter_storage_id_and_more'),
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]
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operations = [
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migrations.AlterField(
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model_name='batch',
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name='id',
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field=config.extras.DateUUIDField(blank=True, editable=False, primary_key=True, serialize=False, unique=True),
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),
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migrations.AlterField(
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model_name='yeast',
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name='id',
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field=config.extras.DateUUIDField(blank=True, editable=False, primary_key=True, serialize=False, unique=True),
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),
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]
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@ -16,7 +16,8 @@
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<h3>{{ batch.strain.name }}</h3>
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Batch Source: {{ batch.get_source_display }}<br>
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Production Date: {{ sample.batch.production_date }}
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Production Date: {{ sample.batch.production_date }}<br>
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<a href="{% url 'admin:yeast_yeast_change' sample.id %}">Admin Page</a>
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<p><p>
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{% for sample in batch.remaining_samples %}
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<ul>
|
||||
|
Loading…
Reference in New Issue
Block a user