Smuggler is a Web-based work queue to shovel images into OMERO. Still rough but coming alive: soon he’ll learn how to interact properly with OMERO and, with a bit of luck, tackle many other data processing tasks.
Say what?! Smuggler is a Java Web app to import images on behalf of OMERO clients. Using Smuggler’s REST API, any program P can POST a request to add an import task to Smuggler’s work queue; P can then carry on with its life without having to wait for the import to complete. If P wants to know what’s going on with its import, it can GET a status update from Smuggler. The catch is that P’s process doesn’t have to wait for the image data to trek to OMERO and being imported; P could even exit or crash (ouch!) but the data would still be imported. (Hope all these P’s won’t make you want to go to the loo now.) In fact, Smuggler will run the import and if it fails, he’ll try again, and again, until he hopefully manages to shovel all the data into OMERO. Or he’ll eventually give up if it’s a lost cause. (Retry behaviour is configurable.) Come hell or high water, Smuggler sends an email to the user who requested the import to fill them in on the outcome: either a success message (their image data is safely stored in OMERO) or a failure alert; the sys admin gets this email alert too so that some techie can work out the issue. (You have an issue? Here’s a tissue…) To help the techies, Smuggler comes with a full-blown management & monitoring interface, available both over HTTP and JMX.
Oh, I should mention this site is intended as a programmer’s notebook, hence the relaxed and colloquial style of writing. Unless you’re a programmer interested in joining development, you’re unlikely to find anything interesting here. Rather check out the OME Web site. Or maybe you’re just a bot prowling the interwebs…then go ahead and knock yourself out!
If a picture is worth a thousand words, how many words are worth five pictures? Hope at least most of the above description of how Smuggler works. So here are five slides to turn words into figures.
Feel adventurous? You can deploy Smuggler quite easily. But bear in mind you’re trying out a tech preview at this stage, so please be safe and wear a crash helmet. Also, why not take our whirlwind tour to see Smuggler in action?
Come hack with us! Smuggler is open source and hosted on GitHub so feel free to open a pull request if there’s functionality you’d like to add, something you’d do differently, or you’ve found a bug. Have ideas or suggestions? Let them come our way! And naturally, constructive criticism is always appreciated.
Here’s a possible way to get started with Smuggler.
- Fork the repo on GitHub.
- Read the README (excuse the pun!) and do a full build. Did the tests pass? Yes? Phew! Move on. No? Well, lucky you, you’ve just found something to help us with!
- See Smuggler in action. Run the server and go through failure and success scenarios as explained in this example.
- Head over to the design section to get a feel of the lay of the the land. As you do that, keep the source code handy so it’s easier to map design concepts and ideas to actual code.
Most of the code is commented and comes with test cases, but it’s probably easier to chat directly with us if something is not immediately obvious as, admittedly, it’s not always easy to figure out what the heck was buzzing in someone else’s skull when they wrote the code! If, after testing the waters, you feel like you’d like to get your hands dirty, here’s a TODO list you can look at. Finally, you may want to have a look at our Condensed Use Cases to get an idea of what were our initial requirements and what we’re planning to do next.
About the Name
Smuggler. Really?! Why?! Well, if you’ve read about how the project started, you know our users at MRI have to pay for the time they’re logged on any acquisition workstation; if an OMERO import happens within a login session, you pay for the time it takes to run the import. But we love our users and want to save them some money. So we’ve come up with this mechanism to import image goodies into OMERO sneakily, outside of login sessions, without paying MRI session duties…we’re smuggling data into OMERO!
Smuggler is obviously just a codename. We’ll come up with a proper, dignified product name when we release. How about OMERO.Smuggler ? Uh? No? OMERO.Runner ? Okay, fine, got it, don’t shout…