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* LinuxForHealth rename

Signed-off-by: Berkant KARDUMAN <karduman.berkant@gmail.com>

* LinuxForHealth rename

Signed-off-by: Berkant KARDUMAN <karduman.berkant@gmail.com>

* Fix 'the' to 'The' where applicable

Signed-off-by: Lee Surprenant <lmsurpre@merative.com>

Signed-off-by: Berkant KARDUMAN <karduman.berkant@gmail.com>
Signed-off-by: Lee Surprenant <lmsurpre@merative.com>
Co-authored-by: Lee Surprenant <lmsurpre@merative.com>
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berkant-k and lmsurpre authored Sep 6, 2022
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4 changes: 2 additions & 2 deletions CONTRIBUTING.md
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```

## Communication
Connect with us through https://chat.fhir.org/ or open an [issue](https://github.com/LinuxForHealth/FHIR/issues). The IBM FHIR Server has a dedicated "stream" at https://chat.fhir.org/#narrow/stream/212434-ibm (`#ibm`).
Connect with us through https://chat.fhir.org/ or open an [issue](https://github.com/LinuxForHealth/FHIR/issues). The LinuxForHealth FHIR Server has a dedicated "stream" at https://chat.fhir.org/#narrow/stream/212434-ibm (`#ibm`).

## Setup
See the [Setting up for development](https://github.com/LinuxForHealth/FHIR/wiki/Setting-up-for-development) in the wiki.
Expand All @@ -78,7 +78,7 @@ See the [Setting up for development](https://github.com/LinuxForHealth/FHIR/wiki
To ensure a working build, please run the full build from the root of the project before submitting your pull request.

## Coding style guidelines
The IBM FHIR Server has been written by many individuals over many years. Formatting has not been strictly enforced, but we'd like to improve it over time, so please consider the following points as you change the code:
The LinuxForHealth FHIR Server has been written by many individuals over many years. Formatting has not been strictly enforced, but we'd like to improve it over time, so please consider the following points as you change the code:

1. Write tests. Pull Requests should include necessary updates to unit tests (src/test/java of the corresponding project) and integration tests (in the fhir-server-test project)

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10 changes: 5 additions & 5 deletions README.md
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Expand Up @@ -67,15 +67,15 @@ Note, if you are using a local repository or private host, you must add the repo
...
```

For versions prior to 4.7.0, the IBM FHIR Server modules are only available from the [Releases tab](https://github.com/LinuxForHealth/FHIR/releases) in an archived Maven repository format.
For versions prior to 4.7.0, the LinuxForHealth FHIR Server modules are only available from the [Releases tab](https://github.com/LinuxForHealth/FHIR/releases) in an archived Maven repository format.

### LinuxForHealth FHIR modules
The LinuxForHealth FHIR Server is modular and extensible. The following tables provide an overview of all the modules, along with an indicator of the stability of the Java APIs defined in each module. This indicator is only applicable to the direct usage of the modules, not for usage of the LinuxForHealth FHIR Server as a whole.

#### Core
|Module|Description|Java API-stable|
|------|-----------|----------|
|fhir-parent|The parent project for all projects which make up the IBM FHIR Server|false|
|fhir-parent|The parent project for all projects which make up the LinuxForHealth FHIR Server|false|
|fhir-core|Core helpers and utilities|false|
|fhir-cache|Cache-related helpers and utilities|false|

Expand Down Expand Up @@ -139,7 +139,7 @@ The LinuxForHealth FHIR Server is modular and extensible. The following tables p
#### Client
|Module|Description|Java API-stable|
|------|-----------|----------|
|fhir-client|A FHIR Client that re-uses the IBM FHIR Server model and its JAX-RS Providers|false|
|fhir-client|A FHIR Client that re-uses the LinuxForHealth FHIR Server model and its JAX-RS Providers|false|

#### Clinical Quality

Expand All @@ -163,9 +163,9 @@ The LinuxForHealth FHIR Server is modular and extensible. The following tables p
|fhir-swagger-generator|Utilities for generating Swagger 2.0 and OpenAPI 3.0 definitions for a subset of the FHIR HTTP interface|false|
|fhir-openapi|A web application that provides a simplified OpenAPI 3.0 definition of the FHIR HTTP interface|false|
|fhir-install|Packaging and installation scripts for creating the fhir-distribution zip and the corresponding IBM FHIR Server Docker image|false|
|fhir-benchmark|Java Microbenchmark Harness (JMH) tests for measuring read/write/validation performance for the IBM FHIR Server and the HL7 FHIR Java Reference Implementation|false|
|fhir-benchmark|Java Microbenchmark Harness (JMH) tests for measuring read/write/validation performance for the LinuxForHealth FHIR Server and the HL7 FHIR Java Reference Implementation|false|
|fhir-bucket|Scans cloud object storage buckets and uploads data using the FHIR REST API|false|
|fhir-persistence-schema|Classes for deploying and updating the IBM FHIR Server relational database schema|false|
|fhir-persistence-schema|Classes for deploying and updating the LinuxForHealth FHIR Server relational database schema|false|
|fhir-persistence-cassandra-app|CLI utility application supporting payload storage to Cassandra *experimental* |false|

### Contributing to the LinuxForHealth FHIR Server
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2 changes: 1 addition & 1 deletion build/audit/README.md
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Expand Up @@ -48,6 +48,6 @@ Also, be sure to add an example `fhir-server-config-<audit-name>.json` configura
## Test the Automation

To test the build, be sure to pre-set `WORKSPACE` with `export WORKSPACE=$(pwd)`.
You must also start Docker, so the image is built that supports the IBM FHIR Server.
You must also start Docker, so the image is built that supports the LinuxForHealth FHIR Server.

If you have any questions, please reach out on Zulip.
2 changes: 1 addition & 1 deletion build/certificates/README.md
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# Server: Continuous Integration Certificates

The following certificates are used with the IBM FHIR Server.
The following certificates are used with the LinuxForHealth FHIR Server.

```
fhir-server-webapp/src/main/liberty/config/resources/security/fhirKeyStore.p12
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2 changes: 1 addition & 1 deletion build/migration/README.md
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Expand Up @@ -91,6 +91,6 @@ Consult the reference implementation (`postgres`) to start a new migration job.
## Testing the Automation

To test the build, be sure to pre-set the environment variable `WORKSPACE` with `export WORKSPACE=$(pwd)`.
You must also start Docker, so the image is built that supports the IBM FHIR Server.
You must also start Docker, so the image is built that supports the LinuxForHealth FHIR Server.

If you have any questions, please reach out on Zulip.
2 changes: 1 addition & 1 deletion build/notifications/README.md
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Expand Up @@ -48,6 +48,6 @@ Also, be sure to add an example `fhir-server-config-notifications-<notifications
## Test the Automation

To test the build, be sure to pre-set `WORKSPACE` with `export WORKSPACE=$(pwd)`.
You must also start Docker, so the image is built that supports the IBM FHIR Server.
You must also start Docker, so the image is built that supports the LinuxForHealth FHIR Server.

If you have any questions, please reach out on Zulip.
2 changes: 1 addition & 1 deletion build/persistence/README.md
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Expand Up @@ -48,6 +48,6 @@ Also, be sure to add an example `fhir-server-config-<persistence-name>.json` con
## Test the Automation

To test the build, be sure to pre-set `WORKSPACE` with `export WORKSPACE=\`pwd\``/
You must also start Docker, so the image is built that supports the IBM FHIR Server.
You must also start Docker, so the image is built that supports the LinuxForHealth FHIR Server.

If you have any questions, please reach out on Zulip.
2 changes: 1 addition & 1 deletion build/reindex/README.md
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Expand Up @@ -43,6 +43,6 @@ Consult the reference implementation (`postgres`) to start a new reindex tests.
## Test the Automation

To test the build, be sure to pre-set the environment variable `WORKSPACE` with `export WORKSPACE=$(pwd)`.
You must also start Docker, so the image is built that supports the IBM FHIR Server.
You must also start Docker, so the image is built that supports the LinuxForHealth FHIR Server.

If you have any questions, please reach out on Zulip.
4 changes: 2 additions & 2 deletions build/security/README.md
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Expand Up @@ -15,7 +15,7 @@ Events execute the `Application Security Testing` workflow are:

## AppScan on Cloud (asoc)

The [AppScan on Cloud](https://help.hcltechsw.com/appscan/ASoC/src_cli_linux_analysis.html#src_cli_linux_analysis__queue_analysis) enables the scanning of the IBM FHIR Server runtime bytecode. The automation wrapped around this analysis limits the surface area to IBM FHIR Server developed application code. The Implementation Guides are not scanned. The output is user generated, and the `irx` file is saved in the artifact output.
The [AppScan on Cloud](https://help.hcltechsw.com/appscan/ASoC/src_cli_linux_analysis.html#src_cli_linux_analysis__queue_analysis) enables the scanning of the LinuxForHealth FHIR Server runtime bytecode. The automation wrapped around this analysis limits the surface area to IBM FHIR Server developed application code. The Implementation Guides are not scanned. The output is user generated, and the `irx` file is saved in the artifact output.

### Generating the Latest Report (team members only)
The following steps under this section are designed to aid the team members in generating the security scan artifacts and reports. A link to the current application is at [scan](https://cloud.appscan.com/AsoCUI/serviceui/main/myapps/oneapp/c4658cf4-e742-4410-99d4-d1c4084b856e/scans)
Expand Down Expand Up @@ -76,7 +76,7 @@ The automation uses [Dockle](https://github.com/goodwithtech/dockle) to generate
<hr>

## Trivy
[Trivy](https://github.com/aquasecurity/trivy#embed-in-dockerfile) is used to check for vulnerabilities in the IBM FHIR Server container.
[Trivy](https://github.com/aquasecurity/trivy#embed-in-dockerfile) is used to check for vulnerabilities in the LinuxForHealth FHIR Server container.

<hr>

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2 changes: 1 addition & 1 deletion cql/fhir-cql-rest/README.md
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#fhir-cql-rest

This module provides an implementation of data and terminology providers for the open source CQL engine using an IBM FHIR Server REST client and model objects. This backend can be used by clients that want to run the CQL engine outside of the IBM FHIR server.
This module provides an implementation of data and terminology providers for the open source CQL engine using an IBM FHIR Server REST client and model objects. This backend can be used by clients that want to run the CQL engine outside of the LinuxForHealth FHIR Server.
2 changes: 1 addition & 1 deletion cql/fhir-cql-server/README.md
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#fhir-cql-server

This module provides an implementation of the open source CQL engine backend that runs directly on top of the the IBM FHIR Server persistence and terminology subsystems, bypassing the REST layer entirely. This backend could be used by in-server clients wishing to use the IBM FHIR Server itself as the processing engine for CQL evaluation or external clients wishing to reduce the extra processing required by the REST layer. In-server processing has the benefit of reducing data transfers that are necessary to perform the evaluation logic at the cost of using a FHIR server's resources for other operations such as routine data access.
This module provides an implementation of the open source CQL engine backend that runs directly on top of the the LinuxForHealth FHIR Server persistence and terminology subsystems, bypassing the REST layer entirely. This backend could be used by in-server clients wishing to use the LinuxForHealth FHIR Server itself as the processing engine for CQL evaluation or external clients wishing to reduce the extra processing required by the REST layer. In-server processing has the benefit of reducing data transfers that are necessary to perform the evaluation logic at the cost of using a FHIR server's resources for other operations such as routine data access.
2 changes: 1 addition & 1 deletion demo/README.md
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Expand Up @@ -23,7 +23,7 @@ To stop the services:
docker-compose down
```

### Using the IBM FHIR Server
### Using the LinuxForHealth FHIR Server
Once the server is running, navigate to http://localhost:9080/openapi/ui to explore the server endpoints.

### Adding implementation guides
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8 changes: 4 additions & 4 deletions docs/src/pages/blog/parquet.md
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Expand Up @@ -15,15 +15,15 @@ In IBM FHIR Server 4.4.0, we introduced experimental support for ["export to par
I planned to either split this into a separate component or use an external Spark service for this feature (or both!), but the demand for the feature has not warranted the investment that would require.
Thus, beginning with IBM FHIR Server 4.11.0, the "export to parquet" feature has been removed.

But fear not, the IBM FHIR Server still supports exporting to newline-delimited JSON (NDJSON) on Amazon S3 / IBM Cloud Object Storage and users with access to the bucket can use these same Spark features to convert from NDJSON to Parquet.
But fear not, the LinuxForHealth FHIR Server still supports exporting to newline-delimited JSON (NDJSON) on Amazon S3 / IBM Cloud Object Storage and users with access to the bucket can use these same Spark features to convert from NDJSON to Parquet.

# Bulk Export
Bulk export can be performed via HTTP GET or POST and the IBM FHIR Server supports three flavors:
Bulk export can be performed via HTTP GET or POST and the LinuxForHealth FHIR Server supports three flavors:
* System export: `[base]/$export`
* Patient export: `[base]/Patient/$export`
* Group export: `[base]/Group/[id]/$export`

The export operations are defined at https://hl7.org/fhir/uv/bulkdata/export.html and usage information can be found in the IBM FHIR Server [Bulk Data Guide](https://linuxforhealth.github.io/FHIR/guides/FHIRBulkOperations#export-operation-dollarexport).
The export operations are defined at https://hl7.org/fhir/uv/bulkdata/export.html and usage information can be found in the LinuxForHealth FHIR Server [Bulk Data Guide](https://linuxforhealth.github.io/FHIR/guides/FHIRBulkOperations#export-operation-dollarexport).

For example, to export all Patient and Condition resources from an IBM FHIR Server at example.com:
```
Expand All @@ -42,7 +42,7 @@ curl --request POST \
}'
```

By default, the IBM FHIR Server uses a psuedo-folder structure for the output files of each job. In the example above, it might produce output files like the following in the configured bucket:
By default, the LinuxForHealth FHIR Server uses a psuedo-folder structure for the output files of each job. In the example above, it might produce output files like the following in the configured bucket:
* long-job-id/Condition_1.ndjson
* long-job-id/Condition_2.ndjson
* long-job-id/Condition_3.ndjson
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