If you've ever worked with scientific software you will know that installing them is not necessarily straightforward. I think this is changing quite a bit with tools like conda and docker, but sometimes we need to just sit down and debug an installation. There is hope here, because if you can get it working just once, and put it in a docker container, you don't ever have to worry about getting it working on another server!
CellProfiler is a free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. More information can be found in the CellProfiler Wiki.
Cool stuff. CellProfiler is an industry standard, and beyond useful for many scientists. It's totally worth packaging up into a docker container, and there is in fact one available from the wonderful people at CellProfiler. I needed to...
If you are anything like me, you heavily rely on a debugger. Likewise, you install all your development environments into a docker container because installing things on your own computer is FOR THE BIRDS. I cannot tell you what a relief it is to have all my development environments safely in docker containers. I break operating systems frequently. It's a serious problem for me and I needed an intervention. For me, this intervention was docker. I do not care how often I break a docker container, because 1. it's versioned, and 2. I can always just rebuilt it. MAGICAL.
Many IDEs and editors assume you are working from a local environment. I think this is changing with so many people moving towards cloud computing and technologies like docker. I don't have an exact list of IDEs that do and do not have use an interpreter from a docker or docker-compose environment.
The JetBrains IDEs support...
During the previous parts in this series, I introduced Apache Airflow in general, demonstrated my docker dev stack, and built out a simple linear DAG definition. I want to wrap up the series by showing a few other common DAG patterns I regularly use.
In order to follow along, get the source code!
unzip airflow-template.zip cd airflow-template docker-compose up -d docker-compose logs airflow_webserver
This will take a few minutes to get everything initialized, but once its up you will see something like this:
If you've read this far you should have a reasonable understanding of the Apache Airflow layout and be up and running with your own docker dev environment. Well done! This part in the series will cover building an actual simple pipeline in Airflow.
Start building by getting the source code!
The simplest DAG is simply having a list of tasks, where each task depends upon its previous task. If you've spun up the airflow instance and taken a look, it looks like this:
Now, if you're asking why I would choose making an ice cream sundae as my DAG, you may need to reevaluate your priorities.
Generally, if you order ice cream, the lovely deliverer of the ice cream will first as you what kind of cone (or cup, you heathen) you want, then your flavor (or flavors!), what toppings, and then will put them all together into sweet, creamy, cold, deliciousness.
You would accomplish this awesomeness with the following Airflow code:
In this part of the series I will cover how to get a nice Apache Airflow instance up and running with docker. You won't need to have anything installed locally besides docker, which is fantastic, because configuring all these pieces individually would be kind of awful!
This is the exact same setup and configuration I use for my own Apache Airflow instances. When I run Apache Airflow in production I don't use Postgres in a docker container, as that is not recommended, but this setup is absolutely perfect for dev and will very closely match your production requirements!
Following along with a blog post is great, but the best way to learn is to just jump in and start building. Get the Apache Airflow Docker Dev Stack here.
Getting an instance Apache Airflow up and running looks very similar to a Celery instance. This is because Airflow uses Celery behind the scenes to execute tasks. Read more...
Briefly, Apache Airflow is a workflow management system (WMS). It groups tasks into analyses, and defines a logical template for when these analyses should be run. Then it gives you all kinds of amazing logging, reporting, and a nice graphical view of your analyses. I'll let you hear it directly from the folks at Apache Airflow
Apache Airflow is a platform to programmatically author, schedule and monitor workflows.
Use airflow to author workflows as directed acyclic graphs (DAGs) of tasks. The airflow scheduler executes your tasks on an array of workers while following the specified dependencies. Rich command line utilities make performing complex surgeries on DAGs a snap. The rich user interface makes it easy to visualize pipelines running in production, monitor progress, and troubleshoot issues when needed.
When workflows are defined as code, they become more maintainable, versionable, testable, and collaborative.
Source - ...
Every time I want to get started with new tech I figure out how to get a stack up and running that closely resembles a real-world production instance as much as possible.
This is a get up and running post. It does not get into the nitty gritty details of developing with Spark, since I am only just getting comfortable with Spark myself. Mostly I wanted to get up and running, and write a post about some of the issues that came up along the way.
Spark is a distributed computing library with support for Java, Scala, Python, and R. It's what I refer to as a world domination technology, where you want to do lots of computations, and you want to do it fast. You can run computations from the embarrassingly parallel, such as parallelizing a for loop to complex workflows, and support for distributed machine learning as well. You can transparently scale out your computations to not only multiple cores, but even multiple machines by creating a spark cluster....
In Part 1 of this series we went over the Celery Architecture, how to separate out the components in a docker-compose file, and laid the ground for deployment.
This portion of the blog post assumes you have a ssh key setup. If you don't go to the AWS docs here.
AWS CloudFormation is an infrastructure design tool that allows users to design their infrastructure by defining file systems, compute requirements, networking, etc. If you have no interest in designing infrastructure, y0u probably don't need to worry. Cloudformation configurations are shareable through templates.
Docker has come to our rescue here, with a Docker for AWS CloudFormation template. This will, with the click of a few buttons, deploy a docker swarm on AWS for us!!
Click on the page, and scroll down to quick start. Under 'Stable Channel' select '...
In this post I will hopefully show you how to organize a large docker-compose project, specifically a project related to a job queue. In this instance we will use Celery, but hopefully you can see how the concepts relate to any project with a job queue, or just a large number of moving pieces.
This post will be in two parts. The first will give a very brief overview of celery, the architecture of a celery job queue, and how to setup a celery task, worker, and celery flower interface with docker and docker-compose. Part 2 will go over deployment using docker-swarm.
Celery is a distributed job queuing system that allows us queue up oodles of tasks, and execute them as we have resources.
From celeryproject.org -
Celery is an asynchronous task queue/job queue based on distributed message passing.It is focused on real-time operation, but supports scheduling as well.The execution units, called tasks, are executed...
Have you ever had to deploy a full stack web application? With different services, some mapping to different ports, some static html, maybe a couple databases thrown in there? Have you ever banged your head against your desk trying to figure out how to expose different ports on a remote server, or through a cloud platform?
If you have, you understand.
I'm going to go over how I deploy such an application, with nice path names instead of annoying port numbers, using traefik and docker. I'm not going to go into the specific code so much, but I may go crazy and do that at a later time. This setup makes it much easier to deploy your application to cloud platforms that don't expose ports besides 80 by default, because you don't need any other ports!
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