fhir_db

Description:

fhir db

FHIR_DB #
This is the newest iteration of this package. I've started to look into using Dart and a small, lightweight database on the server side, and this prompted a number of updates. The biggest is that I think I'm going to change this over to Hive. It seems to be faster and works in pure dart. If you don't like the changes or really want me to keep some of the old stuf, feel free to email me [email protected] or join our slack and let me know. I can bring it back, but if there's no big arguments, it's obviously easier to just maintain one version.
Changes #
Hive - Hive has been around a while, but I've finally started looking into it because it's what the Atsign Folks use as their backend database. So far I like it, and it is really, really fast. I've tried uploading ~1GB of FHIR resources (totals about a million) and it takes about 20 seconds.
Other Considerations

Sembast_SQFLite - Old school, but it doesn't handle the same volume that Hive does (at least not as quickly), and it requires Flutter. Still want to give kudos to Alex Tekartik for all of his continued work maintaining all of these. I highly recommend that if you have any questions about working with this package that you take a look at Sembast. He's also just a super nice guy, and even answered a question for me when I was deciding which sembast version to use.
Isar - is the newest database from the creator of Hive. However, it requires everything to have an integer ID (which tbh is part of the reason I added a dbId entry for Resources), but it doesn't handle maps very well. And I couldn't ever get it work the way I wanted to. Could still be an option for the future.
ObjectBox - another db that a lot of people use and like, and is supposed to be fast. However, it doesn't seem to work very well with Freezed, and the FHIR structure is complicated enough that they have issues with it.
ServerPod - so not an option for local db, but possibly if you're trying to run a lightweight server/database on your own. However, still a little too cumbersome for me to feel like it was worthwhile at this point.

Functionality and methods needed - this is everything I want this package to be able to do #


Create

Add new Resource
Add a list of Resources



Read

Active version of a Resource
A historical version of a Resource
All historical versions of a Resource
All versions of a Resource
All active versions of a Type of Resource
All historical version of a Type of Resource
All versions of a Type of Resource
All active versions of all Resources
All historical versions of all Resources
Everything



Update

Update a Resource (identified by ID)
Update a Resource (identified by a Filter/Search)
Update multiple Resources (identified by ID)
Update multiple Resources (identified by a Filter/Search)



Delete

Delete a Resource (identified by ID)
Delete a Resource (identified by a Filter/Search)
Delete multiple Resources (identified by ID)
Delete multiple Resources (identified by a Filter/Search)
Delete all of a Type of Resource
Everything



Using the Db #
2 idiosnycrasies to be aware of surrounding encryption #

Passwords and ciphers. Hive uses a 256-bit AES Cipher for encryption. This can be generated from a password, and I've included a function that does just this. However, it's important to always pass in the same password/cipher. If you open a box with the wrong password, you won't get any data, but you may mess up the box, even when you try and use it later with the correct password. I'm working on ways to fix this, but it may involve storing the cipher using flutter_secure_storage so we're always sure we pass the correct one in.

So, while not absolutely necessary, I highly recommend that you use some sort of interface class. This adds the benefit of more easily handling errors, plus if you change to a different database in the future, you don't have to change the rest of your app, just the interface.
I've used something like this in my projects:
class IFhirDb {
IFhirDb();
final ResourceDao resourceDao = ResourceDao();

Future<Either<DbFailure, Resource>> save(Resource resource) async {
Resource resultResource;
try {
resultResource = await resourceDao.save(resource);
} catch (error) {
return left(DbFailure.unableToSave(error: error.toString()));
}
return right(resultResource);
}

Future<Either<DbFailure, List<Resource>>> returnListOfSingleResourceType(
String resourceType) async {
List<Resource> resultList;
try {
resultList =
await resourceDao.getAllSortedById(resourceType: resourceType);
} catch (error) {
return left(DbFailure.unableToObtainList(error: error.toString()));
}
return right(resultList);
}

Future<Either<DbFailure, List<Resource>>> searchFunction(
String resourceType, String searchString, String reference) async {
List<Resource> resultList;
try {
resultList =
await resourceDao.searchFor(resourceType, searchString, reference);
} catch (error) {
return left(DbFailure.unableToObtainList(error: error.toString()));
}
return right(resultList);
}
}
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I like this because in case there's an i/o error or something, it won't crash your app. Then, you can call this interface in your app like the following:
final patient = Patient(
resourceType: 'Patient',
name: [HumanName(text: 'New Patient Name')],
birthDate: Date(DateTime.now()),
);

final saveResult = await IFhirDb().save(patient);
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This will save your newly created patient to the locally embedded database.
IMPORTANT: this database will expect that all previously created resources have an id. When you save a resource, it will check to see if that resource type has already been stored. (Each resource type is saved in its own store in the database). It will then check if there is an ID. If there is no ID, it will create a new one for that resource (along with metadata on version number and creation time). It will save it, and return the resource. If it already has an ID, it will copy the the old version of the resource into a _history store. It will then update the metadata of the new resource and save that version into the appropriate store for that resource. If, for instance, we have a previously created patient:
{
"resourceType": "Patient",
"id": "fhirfli-294057507-6811107",
"meta": {
"versionId": "1",
"lastUpdated": "2020-10-16T19:41:28.054369Z"
},
"name": [
{
"given": ["New"],
"family": "Patient"
}
],
"birthDate": "2020-10-16"
}
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And we update the last name to 'Provider'. The above version of the patient will be kept in _history, while in the 'Patient' store in the db, we will have the updated version:
{
"resourceType": "Patient",
"id": "fhirfli-294057507-6811107",
"meta": {
"versionId": "2",
"lastUpdated": "2020-10-16T19:45:07.316698Z"
},
"name": [
{
"given": ["New"],
"family": "Provider"
}
],
"birthDate": "2020-10-16"
}
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This way we can keep track of all previous version of all resources (which is obviously important in medicine).
For most of the interactions (saving, deleting, etc), they work the way you'd expect. The only difference is search. Because Sembast is NoSQL, we can search on any of the fields in a resource. If in our interface class, we have the following function:
Future<Either<DbFailure, List<Resource>>> searchFunction(
String resourceType, String searchString, String reference) async {
List<Resource> resultList;
try {
resultList =
await resourceDao.searchFor(resourceType, searchString, reference);
} catch (error) {
return left(DbFailure.unableToObtainList(error: error.toString()));
}
return right(resultList);
}
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You can search for all immunizations of a certain patient:
searchFunction(
'Immunization', 'patient.reference', 'Patient/$patientId');
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This function will search through all entries in the 'Immunization' store. It will look at all 'patient.reference' fields, and return any that match 'Patient/$patientId'.
The last thing I'll mention is that this is a password protected db, using AES-256 encryption (although it can also use Salsa20). Anytime you use the db, you have the option of using a password for encryption/decryption. Remember, if you setup the database using encryption, you will only be able to access it using that same password. When you're ready to change the password, you will need to call the update password function. If we again assume we created a change password method in our interface, it might look something like this:
class IFhirDb {
IFhirDb();
final ResourceDao resourceDao = ResourceDao();
...
Future<Either<DbFailure, Unit>> updatePassword(String oldPassword, String newPassword) async {
try {
await resourceDao.updatePw(oldPassword, newPassword);
} catch (error) {
return left(DbFailure.unableToUpdatePassword(error: error.toString()));
}
return right(Unit);
}
}
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You don't have to use a password, and in that case, it will save the db file as plain text. If you want to add a password later, it will encrypt it at that time.
General Store #
After using this for a while in an app, I've realized that it needs to be able to store data apart from just FHIR resources, at least on occasion. For this, I've added a second class for all versions of the database called GeneralDao. This is similar to the ResourceDao, but fewer options. So, in order to save something, it would look like this:
await GeneralDao().save('password', {'new':'map'});
await GeneralDao().save('password', {'new':'map'}, 'key');
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The difference between these two options is that the first one will generate a key for the map being stored, while the second will store the map using the key provided. Both will return the key after successfully storing the map.
Other functions available include:
// deletes everything in the general store
await GeneralDao().deleteAllGeneral('password');

// delete specific entry
await GeneralDao().delete('password','key');

// returns map with that key
await GeneralDao().find('password', 'key');
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FHIR® is a registered trademark of Health Level Seven International (HL7) and its use does not constitute an endorsement of products by HL7®