Bulk Import via Firely Server Ingest

Note

This application is licensed separately from the core Firely Server distribution. Please contact Firely to get the license. Your license already permits the usage of FSI if it contains http://fire.ly/vonk/plugins/bulk-data-import. You can also try out Firely Server Ingest. It is limited to a maximum of 10000 resources in total in the connected Firely Server database.

Firely Server Ingest (FSI) is a CLI application designed to optimize massive resource ingestion into a Firely Server instance. In contrast to resource ingestion by sending HTTP requests to a running Firely Server instance, this tool writes data directly to the underlying FS database which increases the throughput significantly.

The tool supports ingestion into SQL Server and MongoDB databases.

Installation

To install the tool, you first need to have .NET Core SDK v6.x installed on your computer. You can download it here. Once it is installed, execute the following command:

dotnet tool install --global Firely.Server.Ingest

The command above will install FSI from this NuGet package.

Note

Make sure that the dotnet tools directory is added to your path, this makes it possible to run the fsi command from any directory.

Please find more information on where globally installed tools are located in this article.

For Linux and Mac, make sure you add your .profile or .bash_profile to your path.

General usage

Attention

Firely Server instances targeting the same database will be impacted severely by the workload that FSI puts on the database. We advise to stop the Firely Server instances while the import is performed.
Only one instance of FSI per database should be run at a time. FSI can utilize all the cores on the machine it is run on, and insert data over several connections to the database in parallel. Multiple instances would probably cause congestion in the database.

Prerequisites

The tool requires that the target database already exists and contains all required indexes and tables (for SQL Server). If you don’t have a database with the schema yet, you first need to run the Firely Server at least once as described in the articles Using SQL server and Using MongoDB.

Important

Each version of Firely Server Ingest is bound to a specific version of Firely Server. The following table shows which combinations of Firely Server (its database schema version respectively) and Firely Server Ingest can be used in combination.

Firely Server Version	Firely Server Ingest Version
v5.1.0 and later	v2.2.0 and v2.2.1
v5.0.0	v2.1.0
v5.0.0-beta1	v2.0.0
v4.10.0 and later	v1.4.0
v4.9.0	v1.3.0
v4.8.0	v1.2.0
v4.2.0 and later	v1.1.0
v4.2.0	v1.0.0

Input files formats

FSI supports the following input file formats:

FHIR collection bundles stored in *.json files, and
*.ndjson files where each line contains a separate FHIR resource in JSON format.

After the import

After ingesting massive amount of data, it is important to make sure the SQL Server indexes are in good shape. You can read more on this topic here: Index Maintenance.

Arguments

The execution of FSI can be configured using input parameters. These parameters can be supplied either as CLI arguments or specified in the file appsettings.instance.json which must be created in the same directory as the fsi executable.

If you want to specify input parameters in the file, you can use the snippet below as a base for your appsettings.instance.json. In this case, you need to update the values that you want to set yourself and delete all other records.

{
  "source": "./fsi-source", //valid directory
  "limit": -1,
  "fhirVersion": "R4",
  "license": "C:\\data\\deploy\\vonk\\license\\performance-test-license.json",
  "updateExistingResources": true,
  "databaseType": "SQL",
  "haltOnError": false,

  "absoluteUrlConversion": {
    "baseEndpoints": [
      // "http://localhost:4080/R4"
    ],
    "elements": [
      "DocumentReference.content.attachment.url"
    ]
  },

  "sqlserver": {
    "connectionString": "<connectionstring to the Firely Server SQL Server database>",
    "saveParallel": 2,
    "queryExistenceParallel": 4,
    "batchSize": 500,
    "commandTimeOut": 60 //seconds
  },

  "mongodb": {
    "entryCollection": "vonkentries",
    "connectionString": "<connectionstring to the Firely Server MongoDb database>",
    "saveParallel": 2,
    "queryExistenceParallel": 4,
    "batchSize": 500
  },

  "workflow": { //-1 = unbounded
    "readParallel": 3,
    "readBufferSize": 750,
    "metaParallel": 1,
    "metaBufferSize": 50,
    "typeParallel": 4,
    "typeBufferSize": 50,
    "absoluteToRelativeParallel": 1,
    "absoluteToRelativeBufferSize": 50,
    "indexParallel": -1, //this is usually the most time consuming process - give it as much CPU time as possible.
    "indexBufferSize": 50
  }
}

Supported arguments

CLI argument	Appsettings parameter name	Required	Description
`--settings <settingsJsonFile>`			Custom settings json file
`-f`, `--fhir-version <R3\|R4>`	fhirVersion		FHIR version of the input, R3 or R4 (not STU3)
`-s`, `--source <source>`	source	yes	Input directory for work (this directory is visited recursively including all the subdirectories)
`-l`, `--limit <limit>`	limit		Limit the number of resources to import. Use this for testing your setup
`--license <license>`	license	yes	Firely Server license file
`--update-existing-resources <true\|false\|onlyIfNewer>`	updateExistingResources		When true, a resource is updated in the database if it already exists and a history record is created. When false, existing records in the database are skipped. When onlyIfNewer, existing records with meta:LastUpdated greater in the database are skipped. `--dbType <MongoDb>` not supported for onlyIfNewer. Default = true.
`--dbType <MongoDb\|SQL>`	databaseType		Specifies the target database type
`--haltOnError <true\|false>`	haltOnError		When true, stop application on single error. Default = false.
`--convertAbsoluteUrlsToRelative:index url` with index ranging from 0 to 19	convertAbsoluteUrlsToRelative		This setting is deprecated. You should use `absoluteUrlConversion/baseEndpoints` instead.
`--urlConvBases:index url` with index ranging from 0 to 19	absoluteUrlConversion/baseEndpoints		Convert absolute URLs to relative for servers in this array. The array values must match exactly the base URL otherwise no changes are made. The conversion is done for all elements of type `reference` as well as the elements of type `Uri` or `Url` matching a FHIR path provided in `absoluteUrlConversion/elements` setting. Example: Setting of `http://example.org/R4` will convert an absolute URL `http://example.org/R4/Patient/123` to relative as `Patient/123` When using the command line argument, the entries of the array must be provided one by one by suffixing with the relevant index. For example: `--urlConvBases:0 https://host0/fhir --urlConvBases:1 https://host1/fhir`
`--urlConvElems:index FHIRPath` with index ranging from 0 to 19	absoluteUrlConversion/elements		List of FHIR paths specifying the list of `Uri` or `Url` elements that should be converted from absolute to relative URI if their base endpoints matches on of the base endpoint specified in `absoluteUrlConversion/baseEndpoints`. When using the command line argument, the entries of the array must be provided one by one by suffixing with the relevant index. For example: `--urlConvElems:0 some.path --urlConvElems:1 some.other.path`
`--mongoCollection <mongoCollection>`	mongodb/entryCollection		Collection name for entries
`--mongoConnectionstring <connectionstring>`	mongodb/connectionString	yes	Connection string to Firely Server MongoDb database
`--mongoPar <mongoPar>`	mongodb/saveParallel		The number of batches to save in parallel. Depends on your bandwidth to MongoDb and its processing power
`--mongoExistQryPar <mongoExistQryPar>`	mongodb/queryExistenceParallel		The number of parallel threads querying the DB to check whether a resource exists (only when `--update-existing-resources` is set to false)
`--mongoBatch <mongoBatch>`	mongodb/batchSize		The number of resources to save in each batch
`-c`, `--connectionstring <connectionstring>`	sqlServer/connectionString	yes	Connection string to Firely Server SQL Server database
`--sqlPar <sqlPar>`	sqlServer/saveParallel		The number of batches to save in parallel. Depends on your bandwidth to SQL Server and its processing power
`--sqlBatch <sqlBatch>`	sqlServer/saveBatchSize		The number of resources to save in each batch. SQL Server must be able to process it within the CommandTimeout. It is recommended to set this value to at least 500 for optimal performance
`--sqlTimeout <sqlTimeout>`	sqlServer/commandTimeOut		The time SQL Server is allowed to process a batch of resources
`--sqlExistQryPar <sqlExistQryPar>`	sqlserver/queryExistenceParallel		The number of parallel threads querying the DB to check whether a resource exists (only when `--update-existing-resources` is set to false).
`--readPar <readPar>`	workflow/readParallel		Number of threads to read from the source. Reading is quite fast so it need not be high
`--readBuffer <readBuffer>`	workflow/readBufferSize		Number of resources to buffer after reading
`--metaPar <metaPar>`	workflow/metaParallel		Number of threads to assign metadata. Should be higher than ReadParallel
`--metaBuffer <metaBuffer>`	workflow/metaBufferSize		Number of resources to buffer for assigning metadata
`--typePar <typePar>`	workflow/typeParallel		Number of threads to add type information. Should be higher than ReadParallel
`--typeBuffer <typeBuffer>`	workflow/typeBufferSize		Number of resources to buffer for adding type information
`--absRelPar <absRelPar>`	workflow/ absoluteToRelativeParallel		Number of threads when converting absolute to relative references. Should be higher than ReadParallel
`--absRelBuffer <absRelBuffer>`	workflow/ absoluteToRelativeBufferSize		Number of resources to buffer when converting absolute to relative references
`--indexPar <indexPar>`	workflow/indexParallel		Number of threads to index the search parameters. This is typically the most resource intensive step and should have the most threads
`--indexBuffer <indexBuffer>`	workflow/indexBufferSize		Number of resources to buffer for indexing the search parameters
`--version`			Show version information
`-?`, `-h`, `--help`			Show help and usage information

Examples

Specify a custom settings file /path/to/your/custom/settings/appsettings.instance.json.

fsi --settings ./path/to/your/custom/settings/appsettings.instance.json

Note

If --settings is omitted, FSI searches following folders sequentially and tries to find appsettings.instance.json. The first occurrence will be used if FSI finds one, otherwise the default appsettings.json will be used.

Current launched folder
e.g. C:\Users\Bob\Desktop
FSI installation folder
e.g. C:\Users\Bob\.dotnet\tools
FSI installation dll folder
e.g. C:\Users\Bob\.dotnet\tools\.store\firely.server.ingest\version\firely.server.ingest\version\tools\net6.0\any

Run the import for files located in directory /path/to/your/input/files and its subdirectories using license file /path/to/your/license/fsi-license.json targeting the database defined by the connection string. In case a resource being imported already exists in the target database, it gets skipped.

fsi \
-s ./path/to/your/input/files \
--license /path/to/your/license/fsi-license.json \
-c 'Initial Catalog=VonkData;Data Source=server.hostname,1433;User ID=username;Password=PaSSSword!' \
--update-existing-resources false

Same as above but if a resource being imported already exists in the target database, it gets updated. The old resource gets preserved as a historical record.

fsi \
-s ./path/to/your/input/files \
--license /path/to/your/license/fsi-license.json \
-c 'Initial Catalog=VonkData;Data Source=server.hostname,1433;User ID=username;Password=PaSSSword!'

Same as above but targeting a MongoDB database.

fsi \
--dbType MongoDb
-s ./path/to/your/input/files \
--license /path/to/your/license/fsi-license.json \
--mongoConnectionstring 'mongodb://username:password@localhost:27017/vonkdata'

Packages cache

Upon its first execution, FSI requires internet access to download and cache packages with core FHIR conformance resources (such as StructureDefinitions and SearchParameters, etc.) The internet connection is not required for the subsequent runs.

It is possible to copy the cached files from one computer to another. It is also possible to mount the cached files to a Docker container if you run FSI in Docker.

The cached files can be found in the following locations:

for v. ≥ v2.2.1
- Windows: %USERPROFILE%\.fhir\packages
- Linux/MacOS: $HOME/.fhir/packages
for v. ≥ v1.4.1
- Windows: %APPDATA%\.fhir_packages
- Linux/MacOS: $XDG_CONFIG_HOME/.fhir_packages if the environment variable XDG_CONFIG_HOME is defined otherwise $HOME/.config/.fhir_packages

Monitoring

Logs

When importing the data, it is handy to have the logging enabled, as it would capture any issues if they occur. By default, the log messages are written both to the console window and to the log files in the %temp% directory.

You can configure the log settings the same way as you do for Firely Server: Log settings.

Performance counters

You can get insights into the tool performance by means of performance counters. There are many ways to monitor the performance counters. One of the options is using dotnet-counters.

To monitor the counters for FSI, you can execute the following command:

dotnet-counters monitor --counters 'System.Runtime','FSI Processing'  --process-id <process_id>

where <process_id> is the PID of the running FSI tool.

Note

If you think the ingestion process is going too slow for your amount of data and the hardware specifications, please contact us for advice.

Known issues

FSI does not support scenarios where resources of different FHIR versions are stored in the same database;
When importing data from large *.ndjson files, the memory consumption may be quite high.
When importing STU3 resources, the field Patient.deceased will always be set to true if it exists. This is caused by an error in the FHIR STU3 specification. In case you would like to use FSI with STU3 resources, please contact us.
If a resource is present in a workload more than once, the entries may get processed in parallel and a version that is different from the latest may be set as current.

Release notes

Note

You can pull the latest version of Firely Server Ingest using the following instructions:

dotnet tool update --global Firely.Server.Ingest

Release 2.3.0, November 23rd, 2023

Feature: the mode --update-existing-resources onlyIfNewer is now supported for MongoDB.
Feature: Serilog.Sinks.MongoDB was added to the list of supported log sinks.
Fix: the SqlClient dependency package has been updated to version v5.1.1 to address the vulnerability: CVE-2022-41064.
Fix: the rare exception System.InvalidOperationException: Cannot change state from Skipped to Error does not get thrown anymore.
Internal: the way of handling command line arguments has been refactored.

Release 2.2.1, September 19th, 2023

Added support for running FSI without the internet connection (see Packages cache)
This release includes a new setting for handling the conversion of absolute to relative references: absoluteUrlConversion. This setting replaces the old convertAbsoluteUrlsToRelative setting. With this setting you can specify the FHIR Path of the elements that you would like to see converted. See also the urlConvBases:index url and urlConvElems:index FHIRPath arguments in the Supported arguments section for more information.

"absoluteUrlConversion": {
  "baseEndpoints": [
    // "http://localhost:4080/R4"
  ],
  "elements": [
    "DocumentReference.content.attachment.url"
  ]
}

Release 1.4.1, August 28th, 2023

Note

It is a hotfix release for the latest FSI that supports Firely Server v.4

Added support for running FSI without the internet connection (see Packages cache)

Release 2.2.0, June 20th, 2023

Fix: Composite parameters are more accurately indexed for SQL Server, to align with Firely Server 5.1.0. See Release 5.1.0, June 20th, 2023 and the accompanying warnings.
Feature: FSI is now open to evaluation, just like Firely Server itself. It is limited though, to a maximum of 10.000 resources in the database, including history.
Feature: FSI is updated to Firely .NET SDK 5.1.0, see its releasenotes

Release 2.1.0, March 9th, 2023

Fix: Eliminated deadlocks in FSI when writing data in parallel.
Settings: The setting maxActiveResources and the related CLI argument --maxActiveRes are no longer needed and have been removed.

Release 2.0.1, February 12th, 2023

Fix: Add support for schema version 25 for MongoDb

Release 2.0.0, January 26th, 2023

Upgraded to work with the database schemas for Firely Server 5.0.0-beta1
Indexing has been updated to support searching for version-specific references.

Release 1.4.0, October 6th, 2022

Added new setting convertAbsoluteUrlsToRelative which is an array of server URL base values. This feature converts absolute URL references to relative references for the given server URL base array. Example: Setting of http://example.org/R4 will convert an absolute URL http://example.org/R4/Patient/123 to relative as Patient/123.
Added a new mode onlyIfNewer for option --update-existing-resources (see the CLI options above)

Note

This option is currently supported only for SQL Server
The setting --useUcum has been removed. From now on, all quantitative values get automatically canonicalized to UCUM values
Indexing has been fixed for search parameters of type reference that index resource elements of type uri. The following SearchParameters were affected by the bug:
- FHIR4: ConceptMap-source-uri, ConceptMap-target-uri, PlanDefinition-definition
- STU3: ImplementationGuide-resource, Provenance-agent
Consider re-indexing your database for these search parameters if you use them.

Note

Please note that due to a mistake in the official STU3 specification, search parameters ConceptMap-source-uri, ConceptMap-target-uri still do not work as expected. The correct search parameter expressions would be ConceptMap.source.as(uri) and ConceptMap.target.as(uri) while the specification contains ConceptMap.source.as(Uri) and ConceptMap.target.as(Uri) respectively. The issue has been addressed in R4.

Release 1.3.1

Corrected an exception when multiple batch threads are processing and saving in parallel to SQL Server.

Release 1.3.0

Add configuration haltOnError. When true, the FSI will be stopped on a single error. Otherwise, it will log error and continue.
Changed the serialization format of decimal from string to use the native decimal type in MongoDB to improve performance.
Bugfix: Fixed Money.currency indexing for FHIR STU3 and R4

Release 1.2.0

Ability to provide a path to a custom appsettings.json file via a command-line argument (see examples above)
Bugfix: ensure FSI uses all available values from the SQL PK-generating sequences when inserting data to the vonk.entry and component tables

Release 1.1.0

Feature: added support for MongoDb!
Feature: added support for performance counters using dotnet-counters. See Performance counters on how to setup and use dotnet-counters.
FSI has been upgraded to .NET 6. To install the tool, you first need to have .NET Core SDK v6.x installed on your computer. See Installation for more information.
The Firely .NET SDK that FSI uses has been upgraded to 3.7.0. The release notes for the SDK v3.7.0 can be found here.
Multiple smaller fixes to improve reliability and performance of the tool.

Release 1.0.0

First public release
Performance: optimized memory consumption (especially, when reading large *.ndjson files)
Feature: quantitative values can be automatically canonicalized to UCUM values (see –useUcum CLI option)
Multiple smaller fixes to improve reliability and performance of the tool

Bill of Materials

Firely Server Ingest is mainly built using libraries from Microsoft .Net Core and ASP.NET Core, along with a limited list of other libraries. This is the full list of direct dependencies that Firely Server Ingest has on other libraries, along with their licenses.

This list uses the NuGet package names (or prefixes of them) so you can easily lookup further details of those packages on NuGet.org if needed.

Microsoft.Extensions.* - MIT
Serilog(.*) - Apache-2.0
System.CommandLine.Hosting - MIT
System.ComponentModel.Annotations - MIT
System.Threading.Tasks.Dataflow - MIT
Hl7.Fhir.* - Firely OSS license
Firely.Fhir.* - Firely OSS license
Simplifier.Licensing - as Hl7.Fhir

For MongoDB:

MongoDB.* - Apache 2.0

For SQL Server:

Microsoft.Data.SqlClient - MIT
Microsoft.SqlServer.SqlManagementObjects - MIT