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Merge master into fhir-term-graph (#1828)
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* Enable OpenLiberty override the fhiropenapi functionality #1760

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Issue #1780 - add compartment search/search parameter config section

Signed-off-by: Mike Schroeder <mschroed@us.ibm.com>

* issue #1789 refresh-tenants does not handle Db2 multi-tenant/multi-schema scenarios

Signed-off-by: Robin Arnold <robin.arnold23@ibm.com>

* Invalid SQL object name `--pool-size` exception when running Docker
`fhir-persistence-schema` on PostgreSQL #1797

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Misleading error messages when using command line parameters and not
`persistence.json` for Docker `fhir-persistence-schema` #1796

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Schema defined for `fhir` in `persistence.json` not used correctly when
running Docker `fhir-persistence-schema`
#1795

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* doc: update must gather to include open shift details

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* use the fhiruser password from helm (set by overrides from KeyProtect)

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

* Fix the definition for List-identifier search

A workaround for https://jira.hl7.org/browse/FHIR-29937

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

* #1802

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* #1802

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Fix up the Must Gather

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* IBM FHIR Server audit does not log bundles correctly. #1803

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* update documentation for the mustgather

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* fix: per code review changed the compare, and added an additional ignore
for the metadata endpoints

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Update fhir-server/src/main/java/com/ibm/fhir/server/util/RestAuditLogger.java

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

Co-authored-by: Lee Surprenant <lmsurpre@us.ibm.com>

* doc: compilation errors are now fixed

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* doc: compilation errors are now fixed

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Add tests case and fixes for #1795

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Add tests case and fixes for #1795

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Add tests case and fixes for #1795

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Add tests case and fixes for #1796

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Add tests case and fixes for #1797

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Add tests for cp and #1802

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* fix: #1808

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Add tests for plain and base64 encoded environment variables

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* fix per comments in code review and issue

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Prevent unauthorized reads before they happen

This prevents us from leaking information about what patient resources
exist / don't exist on the system, which was deemed as useful in case an
implementer uses sensitive data for the Resource.id of the Patient
resources (which still isn't advised).

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

* Prevent unauthorized vread and history operations against Patient too

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

* doc: adding code of conduct md file to root of repository

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* doc: update to clarify the experimental use of the ibm-fhir-schematool

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* doc: update to clarify the experimental use of the ibm-fhir-schematool

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* doc: adding code of conduct md file to root of repository

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* add communication method

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

* Audit Refactoring #1542

- Refactor to separate Configuration, Mapping and AuditService
- Configuration to use EventStreams Binding by default
- Add a MapperFactory to split between cadf and auditevent types
	- AuditEventMapper - Wraps the AuditLogEntry into AuditEvent format
	- CADFMapper - Wraps the AuditLogEntry into CADF format
- Audit Service is now KafkaService, NoOpService separating the
Streaming framework from the mapping actions.
- Removed duplicate code for Event/EventStrams processing
- Add Test Coverage for Uncovered Classes

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Clean up spare printStackTrace

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* update the documentation for fhir-audit

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* updates per team code review

- Change NoOp to Nop Service
- Remove references to WHC/Disabled
- Changed and clarified package names
- Changed references to specific default places to generic/unknown
places (e.g. dallas to unknown)
- added examples for audit from config and audit from environment

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* issue #1818 reindex resource selection update slows down as reindex progresses

Signed-off-by: Robin Arnold <robin.arnold23@ibm.com>

* updates per team code review

- changed package names to remove logging.api and .model (reconciling it
to a flatter structure)

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* update docs

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* change formatting slightly on MapperFactory

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* fix: it tests were not running for drug formulary and c4bb

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* fix incorrect variable in minor startup log message

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

* Convert Strings to Constants for Kafka Key-Value in Properties objects

- Per Code Review with Robin Arnold

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Code Review for FHIR Audit

- CadfEvent doesn't write out target
- Addresses Written Twice in CadfResource

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Added Test for FHIR Audit so it doesn't have multiple address blocks

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* update docs

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Removed auditLogService <extension url="http://ibm.com/fhir/extension/auditLogProperties">

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* fix: referenced license was incorrect

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

Co-authored-by: Paul Bastide <pbastide@us.ibm.com>
Co-authored-by: Mike Schroeder <mschroed@us.ibm.com>
Co-authored-by: Robin Arnold <robin.arnold23@ibm.com>
Co-authored-by: Lee Surprenant <lmsurpre@us.ibm.com>
Co-authored-by: Michael W Schroeder <66479070+michaelwschroeder@users.noreply.github.com>
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6 people authored Dec 15, 2020
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134 changes: 134 additions & 0 deletions CODE_OF_CONDUCT.md
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# Contributor Covenant Code of Conduct

## Our Pledge

We as members, contributors, and leaders pledge to make participation in our
community a harassment-free experience for everyone, regardless of age, body
size, visible or invisible disability, ethnicity, sex characteristics, gender
identity and expression, level of experience, education, socio-economic status,
nationality, personal appearance, race, religion, or sexual identity
and orientation.

We pledge to act and interact in ways that contribute to an open, welcoming,
diverse, inclusive, and healthy community.

## Our Standards

Examples of behavior that contributes to a positive environment for our
community include:

* Demonstrating empathy and kindness toward other people
* Being respectful of differing opinions, viewpoints, and experiences
* Giving and gracefully accepting constructive feedback
* Accepting responsibility and apologizing to those affected by our mistakes,
and learning from the experience
* Focusing on what is best not just for us as individuals, but for the
overall community

Examples of unacceptable behavior include:

* The use of sexualized language or imagery, and sexual attention or
advances of any kind
* Trolling, insulting or derogatory comments, and personal or political attacks
* Public or private harassment
* Publishing others' private information, such as a physical or email
address, without their explicit permission
* Other conduct which could reasonably be considered inappropriate in a
professional setting

## Enforcement Responsibilities

Community leaders are responsible for clarifying and enforcing our standards of
acceptable behavior and will take appropriate and fair corrective action in
response to any behavior that they deem inappropriate, threatening, offensive,
or harmful.

Community leaders have the right and responsibility to remove, edit, or reject
comments, commits, code, wiki edits, issues, and other contributions that are
not aligned to this Code of Conduct, and will communicate reasons for moderation
decisions when appropriate.

## Scope

This Code of Conduct applies within all community spaces, and also applies when
an individual is officially representing the community in public spaces.
Examples of representing our community include using an official e-mail address,
posting via an official social media account, or acting as an appointed
representative at an online or offline event.

## Enforcement

Instances of abusive, harassing, or otherwise unacceptable behavior may be
reported to the community leaders responsible for enforcement via a private
message at https://chat.fhir.org/.
All complaints will be reviewed and investigated promptly and fairly.

All community leaders are obligated to respect the privacy and security of the
reporter of any incident.

## Enforcement Guidelines

Community leaders will follow these Community Impact Guidelines in determining
the consequences for any action they deem in violation of this Code of Conduct:

### 1. Correction

**Community Impact**: Use of inappropriate language or other behavior deemed
unprofessional or unwelcome in the community.

**Consequence**: A private, written warning from community leaders, providing
clarity around the nature of the violation and an explanation of why the
behavior was inappropriate. A public apology may be requested.

### 2. Warning

**Community Impact**: A violation through a single incident or series
of actions.

**Consequence**: A warning with consequences for continued behavior. No
interaction with the people involved, including unsolicited interaction with
those enforcing the Code of Conduct, for a specified period of time. This
includes avoiding interactions in community spaces as well as external channels
like social media. Violating these terms may lead to a temporary or
permanent ban.

### 3. Temporary Ban

**Community Impact**: A serious violation of community standards, including
sustained inappropriate behavior.

**Consequence**: A temporary ban from any sort of interaction or public
communication with the community for a specified period of time. No public or
private interaction with the people involved, including unsolicited interaction
with those enforcing the Code of Conduct, is allowed during this period.
Violating these terms may lead to a permanent ban.

### 4. Permanent Ban

**Community Impact**: Demonstrating a pattern of violation of community
standards, including sustained inappropriate behavior, harassment of an
individual, or aggression toward or disparagement of classes of individuals.

**Consequence**: A permanent ban from any sort of public interaction within
the community.

## Attribution

This Code of Conduct is adapted from the [Contributor Covenant][homepage],
version 2.0, available at
[https://www.contributor-covenant.org/version/2/0/code_of_conduct.html][v2.0].

Community Impact Guidelines were inspired by
[Mozilla's code of conduct enforcement ladder][Mozilla CoC].

For answers to common questions about this code of conduct, see the FAQ at
[https://www.contributor-covenant.org/faq][FAQ]. Translations are available
at [https://www.contributor-covenant.org/translations][translations].

[homepage]: https://www.contributor-covenant.org
[v2.0]: https://www.contributor-covenant.org/version/2/0/code_of_conduct.html
[Mozilla CoC]: https://github.com/mozilla/diversity
[FAQ]: https://www.contributor-covenant.org/faq
[translations]: https://www.contributor-covenant.org/translations

4 changes: 4 additions & 0 deletions README.md
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### Running the IBM FHIR Server
The IBM FHIR Server is available from the [Releases tab](https://github.com/IBM/FHIR/releases) as a zip file with installation scripts for Mac/Linux and Windows or as a docker image at https://hub.docker.com/r/ibmcom/ibm-fhir-server.

Note: The Docker image [ibmcom/ibm-fhir-schematool](https://hub.docker.com/r/ibmcom/ibm-fhir-schematool) is an early technology preview and is experimental.

More information on installing and running the server is available in the User Guide at https://ibm.github.io/FHIR/guides/FHIRServerUsersGuide.

### Building on top of the IBM FHIR Server Modules
Expand Down Expand Up @@ -123,6 +125,8 @@ See [Setting up for development](https://github.com/IBM/FHIR/wiki/Setting-up-for
See [CONTRIBUTING.md](CONTRIBUTING.md) for contributing your changes back to the project.
See [CODE_OF_CONDUCT.md](CODE_OF_CONDUCT.md) for code of conduct.
### License
The IBM FHIR Server is licensed under the Apache 2.0 license. Full license text is
available at [LICENSE](LICENSE).
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4 changes: 3 additions & 1 deletion conformance/fhir-ig-davinci-pdex-formulary/CHANGELOG.md
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30 NOV 2020 - Initial Load
- remove invalid <br/> tags from between <li> tags in CapabilityStatement-usdf-server.json (see ResourceProcessor.java)
- removed invalid ImplementationGuide parameters `copyrightyear`, `releaselabel`, and more
- removed invalid ImplementationGuide parameters `copyrightyear`, `releaselabel`, and more
- added missing / to the CapabilityStatement.url (https://jira.hl7.org/browse/FHIR-29936)
- update the searchParam.definition for List-identifier to properly reference a core spec parameter (https://jira.hl7.org/browse/FHIR-29937)
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