- And open the 'Mirth Connect Formatter.xml' file. Ensure that 'Mirth' is selected as the Active profile, then click 'Apply' and then 'OK'. To run the formatter, select Source Format from the Eclipse menu bar or press Control-Shift-F (Command-Shift-F in Mac OS X).
- Mirth is multi-platfrom and could work across Windows, Linux and Mac environments. Posted in Healthcare IT Tagged DICOM, DICOM Router, India, Linux, Middle East, Mirth Connect, Multiplatform, Singapore, Wide area network.
- Along with the Mirth Connect installation, also download and install the Mirth Connect command line interface. For information about installation and initial configuration steps, see the Mirth Connect Getting Started Guide. After it's installed, ensure that the Mirth Connect service starts up automatically on reboot, and then start the service.
- 2) While you can load JAR files with the SDK into Mirth, utilizing the REST API seemed easier at the onset than needing to load a new framework onto our Nextgen Connect server. 2 days, and 5 hours later, I had the functionality built out.
As part of my work to document the process of building a health data platform on Azure, I decided that I should build NextGen Connect connectivity to CosmosDB. Cosmos is a globally distributed, multi-model database that can take the shape and function of various database types (traditional SQL, NoSQL, Columnar, Graph). This new database type allows users to pick and choose between different database technologies and rely on their strengths for the appropriate situations. Cosmos is a pragmatic choice for building a new health data platform solution, with strong out of the box options for running highly available applications (which most health apps are) with strong tooling for analytics and built directly into the Azure framework. JSON is a first-class citizen on CosmosDB, so it is a logical location to store FHIR-based data.
Import iText into Mirth Connect - Mac (0:44) Start Download, Import, and Save 'PDF Extract to Text' Mirth Channel - Mac (0:42).
Going into writing up this chapter, I was a relative CosmosDB newbie. I had spun up a few databases and walked through a few tutorials in the past, but this is the first time I had plugged the data into a solid, open-source health data transformation tool of choice, Nextgen (Mirth) connect. I went into the project with two assumptions:
1) Since we are setting up CosmosDB in a HIPAA compliant fashion, we likely do not want users accessing the database through the internet (the Azure portal). As such, we should perform most administrative actions (creating databases, creating containers) using the CLI on a server behind the VNet our database is connected to instead of using the GUI. You may opt into letter a very small subset of users use the data explorer to run analytics, but that wouldn't be the developers who would be managing
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2) While you can load JAR files with the SDK into Mirth, utilizing the REST API seemed easier at the onset than needing to load a new framework onto our Nextgen Connect server.
2 days, and 5 hours later, I had the functionality built out. How to citrix receiver for mac. But, I found a lot of nuances to the setup of CosmosDB REST API to be tricky to implement without the SDK. If I had to do it again (which I will), I would definitely recommend using the SDK. But, if you want to implement this with the REST API, here's a guide on how. If you want to skip the prep and lessons learned and head straight to a channel you can download, the channel is located in our GitHub repo for the project. This assumes you have gone through some of the basic CosmosDB reading and understand the basic terminology and concepts of the database.
Create a Database and Container using the CLI
First, create a database. Install the Azure CLI onto your local machine and run the following command to create a database:
Next we want to create our container. One of the first hard lessons learned is that while Partition Keys are not required when creating a container with the CLI, a partition key must be provided when writing documents to a container. This is different than creating a container with the Azure Portal GUI, which requires a partition key upfront. It seems like requirements on this have changed over time, so it's likely the CLI requirements may be dictated by backwards compatibility needs. While I've needed to manage partitions and sharding with Postgres and MongoDB in the past, these were always tasks that could be delegated to later in the design and architecture process. However, given the use case for CosmosDB as a large scale, globally-redundant data store, it makes sense that you would want to determine how to partition data upfront. The challenge with a container that holds patients, like the one we are about to create, is that data access patterns can vary. You can always just set your initial partition key to ‘/id', especially if you are just poking around with CosmosDB. But, that doesn't make sense unless you plan on accessing patients directly by ID from another table (patient census, today's appointments, etc). It's more likely that you would want to partition patients by DOB, ZIP Code, national identifier or some other groupable data element. You should entirely grok this concept before tossing a ton of data at this. At any rate, knowing that we need to specify a partition key, we can create our container with this CLI command using ‘/id' as our partition key:
Now that we have a database and container. Let's move to the REST API and Nextgen Connect to insert our documents into our container. Cummins insite manager.
Creating an Authorization Signature.
The first challenge of using the REST API is that you are responsible for managing the authentication mechanism to connect to the API. Heading into this, I assumed that this would be some Active Directory-type oAuth token retrieval workflow. Instead, your server-based application can retrieve data by signing the specific request to CosmosDB.
There were samples in JavaScript and C# on the website, but since we needed to implement this in Rhino (JavaScript on the JVM) we needed to manage some of the encryption pieces ourselves. You can do this by importing these packages into the top of the source transformer with these declarations:
The next thing we need to do is to obtain our key for our account from either the Azure Dashboard or the CLI. Microsoft recommends using the Secondary Key instead of the primary key in downstream applications. You can do this from the Azure dashboard here
Based on your appetite for storing secrets in NextGen Connect, you can either invoke the secret from an environment variable or store the key directly in the NextGen Connect channel.
Next, we need to generate our statement which we will hash with our key. The guide to this indicates that our 'String to Sign' should follow a format like this:
This means that to insert a document into CosmosDB, we would generate our String to Sign in NextGen Connect like this. Generating a time-stamp in RFC-1123 format was a new one for me, but it's pretty easy to do using Connect's built in DateUtil. We need to use the date generated as a header in our request, so save it in a channelMap in the code for later:
The next part was actually hashing this string with our key. I tried this with a bunch of methods recommended for Java and Azure kept rejecting my authorization. Of course, it's bad practice to tell a hacker why they are messing up hacking you, but there's nothing like staring at base64-encoded strings and seeing if they match or look right. This is good reason #1 to just use the Java CosmosDB SDK. I caught a break when I found a great blog from Swapnil Salunke at Spherigen, who needed to do something similar to create an authorization statement for Azure Queue Storage. When I used Swapnil's implementation, my hashes began to be accepted. The code looks like this, using the NextGen Connect channelMap to store our hash for troubleshooting purposes and our completed authorization statement:
Mirth Connect For Mac Software
Finally, we need to make sure that we generate an ID for our object and store our value for our partition Key in a channel Map since this also needs to be included in our request (we'll talk about this in a bit). CosmosDB is more like MongoDB in that each document in a container requires a unique ID. While the documentation alludes to CosmosDB generating a GUID in the event that an ID is not provided directly within the document sent to CosmosDB, this does not seem to be the case for documents generated from the REST API. As such, ensure that your document (a JSON object):
1) Has a unique ID in a field named 'id'. You can generate this yourself using the UUID tools in NextGen Connect like:
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2) We need to include our partition key as a string in an array (for reasons?) in a header, we can do this with this snippet of code (assuming you are using your ID as both ID and partition key for now):
Now that we've completed this, we can move onto the HTTP Request itself.
Creating the HTTP Request
Since we've done all the necessary workup beforehand, this is relatively straightforward. Not knowing the requirements around the partition key led to most of my 'make request, get an error, google error' based workflow until I got it right. But I struggled so you can coast.
Enter the URL of your CosmosDB database, set the Method to POST, and the Content-Type to application/json.
Next we need to set all of our headers. There should be four headers set. In NextGen Connect, we'll set them using the variables we set in our ChannelMap by entering the Header name on the left hand side of the activity and then dragging the variable from the left hand nav with channelMap names into the field on the right. We've hardcoded our API version here as the latest version at the time of writing (it's required), but check here to see if there is something more recent required in the event that this API version is no longer accepted in the future
With this all built, we can now save and deploy our channel. With a tuned channel, passing a message to the channel should generate the following success statement from the Dashboard.
It all seems straightforward now, but if I could go back again, I think I'd stick with the SDK. Especially when our use cases become more complicated with upserts and queries, being able to use something with fewer sharp edges seems like a good move. But, if you are looking to get started and need something fast, feel free to fork our sample channel.
Skip to end of metadataGo to start of metadataWhen developing Mirth Connect in Eclipse, it is recommended to use the Mirth Connect code formatter to ensure that the source code is formatted consistently. Batman the dark knight rises blu ray 1080p torrent.
- Download the Mirth Connect code formatter XML file: Mirth Connect Formatter.xml.
- From Eclipse, open the Eclipse preferences window.
- From the menu hierarchy, select Java > Code Style > Formatter.
- Click 'Import..' and open the 'Mirth Connect Formatter.xml' file.
- Ensure that 'Mirth' is selected as the Active profile, then click 'Apply' and then 'OK'.
- To run the formatter, select Source > Format from the Eclipse menu bar or press Control-Shift-F (Command-Shift-F in Mac OS X).
