Remove Jira Issue Attachments by MD5 Hash Redux

In my previous post Remove Jira Issue Attachments by MD5 Hash I showed how to remove attachments from JIRA based on the MD5 hash of the attachment.

I was feeling pretty good after writing that post and having eaten my doughnut. So, I went to tell a couple of my colleagues about it. This was their reaction …

So, you expect me to …

  1. know what an MD5 hash is?
  2. know how to get the MD5 hash of a file?
  3. know where to find this script to add the hash to?
  4. not mess the whole thing up in the process?

Um … uhh … yes? Ok, so maybe my approach isn’t super easy except to the programmer type. And now that I think about it I don’t want to have to be the one to always fix these. So, back to the drawing board. Let’s get this right.

So, I need to make it easy for others than myself to help maintain. Maybe if I made a way for my colleagues to take an attachment from an issue ticket and simply drop to a centralized storage location that could be scanned by the script … yeah that could work. It involves no knowledge of MD5 hashes or scripting and should be easy for pretty much anyone to do.

Now if I only had a location where we could place these attachments. A place that JIRA is able to scan. A place that all my colleagues have easy access to. If only such a place actually existed … hmm … oh, wait!! I could just have them attach the files to another JIRA ticket that will be used as a control ticket of sorts. Any attachments attached to this ticket would be compared against by the script and if a match is found then the issue attachment is deleted. (insert Handel’s Messiah playing in my head here)

The great thing is that most of my script doesn’t really need to be changed. All I need to do is specify a control ticket key in the script and have the script build the list of hashes based on that ticket. Here is my ticket …

And here is the new script. I’ve cleaned it up a little from the last version and removed a call to a method that is currently set as deprecated. It still worked even with the call, but best to get rid of that call before Atlassian removes the method altogether. Simply replace “{Project Key}-{Issue Number}” on line 12 with the issue key that holds your attachments to remove. So, if for instance the issue is in the FOO project and the issue number is 789 then that line would look like this …

def controlIssue = “FOO-789”;

And now my colleagues sing my praises (in my dreams) instead of cursing my name (which maybe still happens when I make hard to update workflows). Oh well, you live and learn.

Remove Jira Issue Attachments by MD5 Hash

Recently, we started using Jira at work to track some IT related things. Thus, I have quickly had to learn how to administer Jira. One thing that I really wanted to get set up and working well was the ability to respond to an email sent by the system via a reply email and have that filed in the ticket. That wasn’t too terribly hard to set up. First I created a mailbox for Jira to check in our mail system. Then I set up a mail handler to pull the reply emails in. I settled for using a “Add a comment before a specified marker or separator in the email body” handler so that I could provide a regular expression to define how to extract just the reply. The below screenshots show my setup for this.

The Split Regex field below is this /[Ff]{1}rom:[^\n]+{myuser}@{mydomain}\.{extention}/. Replace the {myuser}, {mydomain}, and {extention} parts with the email address of the account that Jira mails as. So, if your Jira system sends email as [email protected] the above expressions would look like this /[Ff]{1}rom:[^\n][email protected]\.org/. This will split the email where it sees the first line that looks something like this From: Jira [mailto:[email protected]] or from: Jira [mailto:[email protected]] … which is how Outlook formats its replies.

So, I got that part working great now I can go get a doughnut right? Nope! Turns out every time I would reply the issue icon and the image attachment in my email signature would get attached to the issue … over and over and over. So, before long I had a veritable glut of the same images attached to the issue. Grrrr!! So, I asked myself “Self, what can we do about this?” To which I so helpfully replied to myself, “Go check the Atlassian Marketplace, Atlassian Community, and Google for an answer.” After a couple grueling hours of trying to find the answer I came to the stark conclusion that there wasn’t one. Double grrrr!!

After a bit of thinking I decided I could just scan the images against a set of MD5 hashes to exclude when the issue is updated and here is the fruit of my labor. This solution requires having ScriptRunner for Jira installed. If you don’t have it … well, you should. The possibilities are pretty endless with what you can do with it. I created a Script Listener that would respond to the “Issue Updated” event.

And the actual contents of the script file.

Now, when I respond to an issue via email if any of the attachments on the issue match any of the MD5 hashes at the top of the script that attachment will get deleted from the issue. And if I find that there are other attachments we start seeing like this on a regular basis all I have to do is add the MD5 hash to the list and save the script … problem solved.

Now, about that doughnut.

Update: So, the whole editing the script and having others put in MD5 hashes part … yeah, that went over like a lead balloon. Here is an updated version that is much easier to administer.

Parsing HL7 with Splunk

At my job I do a fair amount of work with HL7. If you work in the medical field you probably know that HL7 is the language that medical systems use to talk with each other. It’s a fairly simple format that uses carriage returns and pipes to delimit fields … ok there are a few other delimiters as well, but the carriage returns and pipes are the big ones. Below is an example HL7 message.

Each line in the message is called a segment and each segment can be divided into fields based on the pipes. For instance the third line is the PID segment which has patient information such as the MRN (PID 3), patient name (PID 5), birth date (PID 7), etc. The PV1 segment has information that relates to the patient visit. It is a fairly concise format without much overhead and as such is perfect for medical institutions where these kinds of messages are flowing constantly throughout the day.

The Problem

In a typical medical environment there will be a system called the HL7 routing engine that serves as an intermediary between all the various medical systems in the clinic or hospital. The HL7 engine can route messages to one or various systems and transforms them en-route based on rules. Most HL7 engines have the ability to log the messages sent through them in some format.

Often times there may be a need to lookup what messages were sent to various system to troubleshoot problems. In many cases there is no great means of searching through the thousands or even hundreds of thousands of messages sent each day to troubleshoot these issues.

The Solution

About a year ago I was approached by some folks from Splunk about creating a Technical Add-on (TA) for Splunk for parsing HL7. After many months of working with one of their engineers named Joe Welsh we were able to release the free ‘HL7 Add-On for Splunk“. We tested the add-on by throwing millions of our HL7 messages at it to make sure it parsed the messages correctly.

With this TA we can have Splunk monitor our HL7 logs and in real-time are able to quickly search those logs to troubleshoot issues, report on failed messages, and view dashboards to monitor the health of our HL7 environment. I have been super pleased with the results.

If you are a medical institution that uses Splunk check out the add-on … it’s free. See what awesome things you can do with Splunk and HL7. Let me know in the comments if you have found it useful.

Splunkbase Link

Doing a select on a stored procedure

I came across a scenario today where I just wished that I could do a SQL select on a stored procedure. Akin to something like this …

Alas, this is not possible … urg! However, I did manage to find a workaround that gives me basically what I wanted. It involves turning on some insecure settings in SQL sever. So we want to make sure we turn them back off after the fact.

The gist of the below SQL is as follows. We  first enable the insecure settings. Next we execute the stored procedure using openrowset and store the results into a temp table. Once we have the data in a temp table we can work with it just like any other table, yeay!! Finally, we want to make sure to turn off the openrowset feature again.


Powered by WordPress, running on raspberries

The Issue

My Raspbery Pi running WordPressMeet my new web server! Isn’t it cute? Up till recently I have been running my website on my home machine. This has worked fine as this site doesn’t get a ton of traffic and my home machine is fairly beefy. However, I’ve always been slightly leery about running my web server on my main computer just for security reasons. If it were to get hacked I could be potentially opening up everything to the hackers. Not only that, in order for the site to be up I had to leave my home machine running 24/7. This is not great on the electricity bill. Also, during the summer months in our not so air-conditioned house it actually adds significantly to the heat. Which is not too fun for my wife who has to been home all day in the heat while I sit at work in the air-conditioning.

The Solution

So, I started looking around for a not too expensive solution to this. As I researched I started seeing more and more people running WordPress on a Raspberry Pi. Now, I can muck my way around Linux, but it’s certainly not my forté. Fortunately, I found a great tutorial for installing WordPress on a Raspberry Pi that even a Linux noob like me can follow.

It worked great! I was able to get WordPress set up, move my content over and flip the port forwarding over to the Pi within a few hours. I also set up a dynamic DNS client on the PI to keep my address current with my domain registrar. I now have a separate server, that runs on pennies, puts out little to no heat, is completely quiet, and cost very little to purchase. I could not be happier.

Confluence Macro Usage Report

When it comes to upgrading Confluence it is handy to know which macros are being used throughout the site so that you can test the upgrade and check that the used macros still work correctly. The below user macro will generate a Confluence macro usage report that lists all of the macros and user macros that are used in your Confluence installation along with a link for each macro so that you can spot check the pages that use that macro … or you could check all the pages if you are that thorough. This requires at least Confluence 5.5 as the MacroBrowserManager.getMacroSummaries() method was added in 5.5.

Report Example:Macro Usage Report

Macro Body Processing:
No macro body


Referenced on

Bookmarklet for Creating a CSV From an HTML Table

We have a wiki at work that we use for documentation called Confluence. It has the ability to export pages to Word or PDF, but a lacking feature is the ability to take a table and export it for Excel. So, I decided to create a bookmarklet that will allow you to select an HTML table on any web page and create a CSV file from that table that can be downloaded to your machine. Below is the bookmarklet. Just drag it to your bookmarks toolbar. Then give it a shot by clicking the bookmarklet and the below example table should get a link right before it that says “Export to CSV”. Click that link and you will be prompted to download the CSV version of that table. Let me know if it is useful for you.

On thing of note, this will not work correctly in Internet Explorer 9 and below as IE will not allow data uri’s for anything other than images.

Export to CSV <- drag this to your bookmarks toolbar

09/16/2016 – Now works with IE 10+.
04/19/2016 – Fixed issue with tables that have header cells not on top.

Example Table:

Heading 1 Heading 2 Heading 3 Heading 4 Heading 5 Heading 6
Data 1, 1 Data 1, 2 Data 1, 3 Data 1, 4 Data 1, 5 Data 1, 6
Data 2, 1 Data 2, 2 Data 2, 3 Data 2, 4 Data 2, 5 Data 2, 6
Data 3, 1 Data 3, 2 Data 3, 3 Data 3, 4 Data 3, 5 Data 3, 6
Data 4, 1 Data 4, 2 Data 4, 3 Data 4, 4 Data 4, 5 Data 4, 6
Data 5, 1 Data 5, 2 Data 5, 3 Data 5, 4 Data 5, 5 Data 5, 6
Data 6, 1 Data 6, 2 Data 6, 3 Data 6, 4 Data 6, 5 Data 6, 6

Bookmarklet Source: 

Microsoft, the 90’s wants its security policy back!

Today, I went to change the password on my Microsoft account from a shortish hard to remember and type password to a nice and secure long and easy to type passphrase. With all of the hubbub these days around hacked accounts I want to make sure that my accounts are nice and secure. I just wish Microsoft was on-board with that.

Phrase1I went to my account and put in a pass phrase that seems pretty decent to me. Here is the first message I got. It seems that my nineteen character passphrase is too long. Why is this an issue I ask? Why does Microsoft care if I want to have a long password? If I want to take on the burden of typing those extra characters what is it to them? This is not a limitation with any other Microsoft system I have ever used (personal machine and work machines). I’m sure their own systems are based on their own stack, so this is an artificial limit that they have put in that has no real value except to make my account easier to hack.

Phrase2Ok, since I can only have up to sixteen characters in my password I guess I’ll have to comply. Sixteen characters is still pretty long right? So, I swapped out some words and made a few tweaks only to be presented with this. REALLY!? By the way, the character that they do not like is a space. So, I thought I would see what characters they do allow. They allow A-Z, a-z, 0-9, and every special character printed on your keyboard … just not space. Ugh!! It seems they are going out of their way to discourage pass phrases when it has been shown time, and again, and again, and again that pass phrases are more secure than passwords.

So, in the end, I am forced to bow to their ridiculous security policy that excludes one character and forces me to 16 characters. What do you think?

Confluence Profile Photo Uploader

Small disclaimer: this works great on my setup. I have not tested it outside of my setup. It should work just fine as I am using the standard API’s that come with Confluence, but it is an open source project and I’m not getting paid for it, so I haven’t done extensive testing in all scenarios.

At the Vancouver Clinic we use a wiki product called Confluence. It is a fantastic product that is super customizable via add-ons, extensions, custom html/js/css, and SOAP and REST APIs.

Unfortunately, Confluence does not have a way for administrators to bulk upload user profile photos into it. For corporate organizations that want to make sure that user photos are uniform and professional this is somewhat cumbersome. As a result Confluence may have user profiles with Mickey Mouse, Wolverine, or worse as the photo … don’t get me wrong Wolverine is pretty cool, just not professional.

Because of this I decided to write a utility that allows an administrator to sweep in photos in a specified folder with a file mask of “%username%.%extension%” into Confluence. The utility will accept .jpg, .jpeg, .tif, .tiff, .png, and .bmp files. Optionally, you can specify a folder to archive the swept-in photos to after they have been uploaded. Confluence profile photos are 48×48 pixels and since most photos are not square the utility will attempt to do face detection and crop the photo to the largest face in the photo. If the photo is already square you can opt to have the utility not perform the face detection. I am personally not smart enough to write face detection algorithms, so I am using EMGU/OpenCV to do the face detection (which is why the compiled version is so freakin big). Hey, I got no problem standing on the shoulders of giants.

For automation purposes there is a command line switch /headless that will do the upload without any GUI using the configured settings. This works great with Windows Task Scheduler.

This is working awesomely for the clinic and fortunately my manager has allowed me to open source the code. So, I have uploaded it to Bitbucket for anyone to use, or make fun of my code. : ) Seriously, have at it if it will help your organization. And by all means let me know if there you run into any bugs along the way.

Confluence Speakeasy Favorite Menu Extension

So, lately I’ve been doing a lot of customization at work on a product we use called Confluence. It is quite possibly the slickest wiki I have ever used. It has an awesome plugin model and pretty huge market for community developed plugins. One plugin that Atlassian has created allows for creating modular client based extensions to the wiki. It is called Speakeasy.

menuI happen to have a few favorite pages in the wiki that I refer to all the time and I have been wanting a favorite menu that shows up on every page. Alas, I couldn’t find one that existed, so I decided to make my own.

Feel free to download the extension and modify it to your needs.

I have released this on the Atlassian Marketplace for free.