Add smart on fhir and on prem accelerator deployment guides - #56
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📝 WalkthroughWalkthroughThis pull request expands healthcare API documentation with new guides for Key Manager configuration and FHIR API deployment in WSO2. The SMART on FHIR configuration guide is substantially rewritten to reflect a new flow using pre-built Ballerina services and pre-issue token actions. The overview guide is restructured with architectural diagrams and clearer security explanations. Manual installation documentation is updated to include Ballerina integration steps with certificate exchange. Navigation labels across sidebars and home page are renamed from "Secure Health APIs" to "SMART on FHIR" for consistency. Suggested reviewers
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Actionable comments posted: 9
🤖 Prompt for all review comments with AI agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
Inline comments:
In `@en/docs/install-and-setup/deploy-fhir-apis.md`:
- Line 77: The heading "## Step 4 - Verify the Deployment" is misnumbered (comes
after Step 2); update the header text to "## Step 3 - Verify the Deployment" and
scan the surrounding headings in this document (e.g., any other "Step X - ..."
headings) to ensure subsequent step numbers are consistent and renumber them if
necessary.
In `@en/docs/install-and-setup/manual.md`:
- Around line 30-36: The Markdown table in manual.md has a malformed separator
row missing the leading pipe which breaks rendering; update the separator line
so it starts with a pipe character (i.e., make the divider row align with the
header and body rows) so the table rows like "WSO2 Identity Server" /
`<WSO2_IS_HOME>`, "WSO2 API Manager" / `<WSO2_APIM_HOME>`, etc., render
correctly under the header and placeholder columns.
- Line 38: Remove the stray pilcrow characters ("¶") from the user-facing
headings/list items—specifically update the heading "## Getting WSO2 Updates¶"
to "## Getting WSO2 Updates" and remove the same stray "¶" characters found on
the other affected lines (around the content referenced at lines with markers 80
and 92) so no visible "¶" remains in headings or list items in manual.md.
- Around line 171-177: The command placeholders contain typos: in the export
command remove the stray trailing ">" from "<keystore path>>" and normalize to
"<keystore_path>", and in the import command correct "<trustore_path>" to
"<truststore_path>" (or consistently "<truststore_path>"); ensure both commands
use consistent placeholders like "<cert_alias>", "<certificate_path>",
"<keystore_path>", "<truststore_path>", and "<keystore_password>" so the keytool
-export and keytool -import lines are syntactically correct and consistent.
- Around line 82-84: The document uses two different accelerator placeholders;
replace all occurrences of <WSO2_HC_APIM_ACC_HOME> and <WSO2_HC_IS_ACC_HOME>
with the earlier-defined <WSO2_OH_APIM_ACC_HOME> and <WSO2_OH_IS_ACC_HOME>
respectively so the placeholder names are consistent across the manual
(including the merge script step and the later steps currently showing the HC
variants); update every instance of the HC placeholders to the OH placeholders
to avoid path confusion.
In `@en/docs/secure-health-apis/guides/configure-smart-on-fhir.md`:
- Around line 242-245: The discovery JSON and the token exchange example are
using different ports for the token endpoint (9443 vs 9453); update the
token_endpoint values in the discovery output (the "token_endpoint" and "issuer"
entries) and the token exchange example URLs in Step 6 so they match the same
port (choose either 9443 or 9453 consistently), and also update the duplicate
occurrences referenced around lines 269-272 to the same port so all token
endpoint references are aligned.
- Around line 174-176: Update the documentation so the config key names
referenced in the note match the documented schema: confirm whether the
`pre-issue-access-token-service-extension` uses `patientGroup` and
`practitionerGroup` in its Config.toml and then either (A) add those keys to the
configuration tables with their descriptions and example values, or (B) change
the note to reference the actual keys used by the extension; ensure the symbols
`Config.toml`, `pre-issue-access-token-service-extension`, `patientGroup`, and
`practitionerGroup` are used exactly as in code so readers can find and set the
correct keys.
- Around line 115-118: Remove the shell prompt symbols from the command examples
so they are plain commands (e.g., change "`$ bal build`" to "`bal build`") to
satisfy markdown lint rule MD014; update the three affected fenced code blocks
that currently include "$" (the block showing "bal build" and the blocks
referenced around lines 125-127 and 132-134) so all commands are presented
without the "$" prefix and without accompanying output.
In `@en/sidebars.ts`:
- Around line 123-125: The sidebar labels the doc id
'secure-health-apis/guides/smart-on-fhir-overview' as "SMART on FHIR" but the
site navbar in en/docusaurus.config.ts still uses "Secure Health APIs"; make
these consistent by updating the navbar item that references the doc id (the
navbar entry whose to/id points to
'secure-health-apis/guides/smart-on-fhir-overview' or the nav item with label
'Secure Health APIs') to use the label "SMART on FHIR" (or alternatively change
the sidebar label to "Secure Health APIs") so the link text matches across
navigation and sidebars.
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Fix all unresolved CodeRabbit comments on this PR:
- Push a commit to this branch (recommended)
- Create a new PR with the fixes
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en/docs/assets/img/get-started/add-key-manager.pngis excluded by!**/*.pngen/docs/assets/img/learn/smart-on-fhir/IS_actions.pngis excluded by!**/*.pngen/docs/assets/img/learn/smart-on-fhir/IS_add_attribute.pngis excluded by!**/*.pngen/docs/assets/img/learn/smart-on-fhir/IS_app_type.pngis excluded by!**/*.pngen/docs/assets/img/learn/smart-on-fhir/IS_attribute-configuraions.pngis excluded by!**/*.pngen/docs/assets/img/learn/smart-on-fhir/IS_attributes.pngis excluded by!**/*.pngen/docs/assets/img/learn/smart-on-fhir/IS_protocols.pngis excluded by!**/*.pngen/docs/assets/img/learn/smart-on-fhir/IS_user_groups.pngis excluded by!**/*.pngen/docs/assets/img/learn/smart-on-fhir/authenticate.pngis excluded by!**/*.pngen/docs/assets/img/learn/smart-on-fhir/consent.pngis excluded by!**/*.pngen/docs/assets/img/learn/smart-on-fhir/key-generation.pngis excluded by!**/*.pngen/docs/assets/img/learn/smart-on-fhir/patient-picker.pngis excluded by!**/*.pngen/docs/assets/img/learn/smart-on-fhir/smart_on_fhir.svgis excluded by!**/*.svg
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en/docs/install-and-setup/configure-km.mden/docs/install-and-setup/deploy-fhir-apis.mden/docs/install-and-setup/manual.mden/docs/secure-health-apis/guides/configure-smart-on-fhir.mden/docs/secure-health-apis/guides/smart-on-fhir-overview.mden/mkdocs.ymlen/sidebars.jsen/sidebars.tsen/src/pages/index.tsx
Contributor
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Shall we add the Inferno conformance test results as a note |
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Actionable comments posted: 2
♻️ Duplicate comments (1)
en/docs/install-and-setup/manual.md (1)
171-171:⚠️ Potential issue | 🟡 Minor | ⚡ Quick winNormalize placeholder format in keytool command.
Use underscore-style placeholder names without spaces for consistency and clarity.
Suggested fix
- keytool -export -alias <cert_alias> -file <certificate_path> -keystore <keystore path> + keytool -export -alias <cert_alias> -file <certificate_path> -keystore <keystore_path>🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the rest with a brief reason, keep changes minimal, and validate. In `@en/docs/install-and-setup/manual.md` at line 171, Update the keytool command's placeholders to use underscore-style names with no spaces: locate the line starting with "keytool -export -alias" and change any placeholders (e.g., "<keystore path>") to use underscores (e.g., "<keystore_path>") so all placeholders like "<cert_alias>", "<certificate_path>", "<keystore_path>" are consistent and contain no spaces.
🤖 Prompt for all review comments with AI agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
Inline comments:
In `@en/docs/install-and-setup/fhir-artifacts.md`:
- Around line 19-165: The download links in
en/docs/install-and-setup/fhir-artifacts.md use the wrong relative URL pattern
"../../assets/specs/oas/*.yaml" which resolves to a non-existent en/assets/...
location and breaks all "Download" links; update each link in the FHIR artifacts
tables to point to the correct assets location (or the canonical repo asset
URLs) by replacing the "../../assets/specs/oas/*.yaml" references with the
actual assets path where the YAMLs live (or add/move the YAML files to match the
existing links), then verify every table entry (e.g., PatientAPI.yaml,
ObservationAPI.yaml, MedicationAPI.yaml, CapabilityStatementAPI.yaml) resolves
correctly.
In `@en/docs/install-and-setup/manual.md`:
- Line 84: The documentation uses concatenated placeholders like
<WSO2_APIM_HOME>/<WSO2_OH_APIM_ACC_HOME>/bin for the merge script path; change
these to use the accelerator-home placeholder directly (i.e.,
<WSO2_OH_APIM_ACC_HOME>/bin) wherever the merge/merge-script path is shown (same
fix for the corresponding OpenHub IS accelerator placeholder
<WSO2_OH_IS_ACC_HOME> instances), so update the path strings in the merge script
instructions to reference only the accelerator-home placeholder.
---
Duplicate comments:
In `@en/docs/install-and-setup/manual.md`:
- Line 171: Update the keytool command's placeholders to use underscore-style
names with no spaces: locate the line starting with "keytool -export -alias" and
change any placeholders (e.g., "<keystore path>") to use underscores (e.g.,
"<keystore_path>") so all placeholders like "<cert_alias>",
"<certificate_path>", "<keystore_path>" are consistent and contain no spaces.
🪄 Autofix (Beta)
Fix all unresolved CodeRabbit comments on this PR:
- Push a commit to this branch (recommended)
- Create a new PR with the fixes
ℹ️ Review info
⚙️ Run configuration
Configuration used: Organization UI
Review profile: CHILL
Plan: Pro
Run ID: 08c489a2-082a-4016-9ef9-eef32c4d46d8
📒 Files selected for processing (5)
en/docs/install-and-setup/deploy-fhir-apis.mden/docs/install-and-setup/fhir-artifacts.mden/docs/install-and-setup/manual.mden/docs/secure-health-apis/guides/configure-smart-on-fhir.mden/docusaurus.config.ts
✅ Files skipped from review due to trivial changes (2)
- en/docusaurus.config.ts
- en/docs/install-and-setup/deploy-fhir-apis.md
🚧 Files skipped from review as they are similar to previous changes (1)
- en/docs/secure-health-apis/guides/configure-smart-on-fhir.md
sameeragunarathne
approved these changes
Jun 2, 2026
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Summary
bullet points, added "See Also" section, and fixed frontmatter
with collapsible details and Config.toml reference tables, pre-issue extension setup, user/group management, OpenFGC consent system, application registration, authorization code flow with PKCE, and FHIR API
access