Link to admin on yeast sample page.

Makefile

@@ -0,0 +1,142 @@
+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

config/gunicorn_config.py

@@ -0,0 +1,217 @@
+# 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")

config/settings.py

@@ -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 = [

yeast/migrations/0028_alter_batch_id_alter_manufacturer_id_and_more.py

@@ -0,0 +1,39 @@
+# 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),
+        ),
+    ]

yeast/migrations/0029_alter_manufacturer_id_alter_storage_id_and_more.py

@@ -0,0 +1,28 @@
+# 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'),
+        ),
+    ]

yeast/migrations/0030_alter_batch_id_alter_yeast_id.py

@@ -0,0 +1,24 @@
+# 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),
+        ),
+    ]

yeast/templates/yeast/sample.html

@@ -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>