Fix CI: download publisher.jar before running _build.sh build by bvdh · Pull Request #4 · IHE/RAD.MADO

bvdh · 2026-05-29T15:01:11Z

The FHIR IG Docker Build CI job was failing because _build.sh build requires publisher.jar to exist in input-cache/, but nothing in the workflow downloaded it beforehand. When the JAR is missing, _build.sh logs "IG Publisher NOT FOUND … Aborting…" and exits 0 without producing any output, causing the subsequent test -f output/qa.json verification step to fail with exit code 1.

Root Cause

_build.sh build checks for publisher.jar in input-cache/ or a parent folder. Since neither location had the JAR in the CI environment, the build was silently aborted.

Fix

Added a "Download FHIR IG Publisher" step to .github/workflows/ig-docker-build.yml (before the Docker _build.sh step) that:

Creates input-cache/ in the workspace.
Downloads the latest publisher.jar from the HL7 GitHub releases (https://github.com/HL7/fhir-ig-publisher/releases/latest/download/publisher.jar).

Because the workspace is mounted into the Docker container as /home/publisher/ig, the JAR is immediately available at the path _build.sh expects ($(pwd)/input-cache/publisher.jar), and the build proceeds normally.

…the only expression.

Copilot

Pull request overview

This PR transitions the MADO FHIR Imaging Study Manifest from a collection Bundle to a FHIR document Bundle, introducing a new MadoComposition profile (and supporting MadoNarrativeNotEmpty ValueSet) as the required first Bundle entry. Provenance is removed (commented out) from the bundle profile, examples, and generated outputs. The PR also performs terminology cleanup — standardizing on "FHIR Imaging Study Manifest", migrating documentation links from {{...}} Liquid aliases to IG Publisher [[[...]]] syntax (removing now-unused profiles.md/fhir-resources.md include files), refreshing examples/generated resources, and fixing spelling/grammar.

Changes:

Switch MadoFhirBundle to a document Bundle and add a required MadoComposition slice (and new profile/intro/ValueSet); regenerate example bundles accordingly.
Comment out MadoProvenance profile, bundle slice, and example.
Standardize naming/links: "FHIR Imaging Study Manifest" across pages/profiles, replace {{...}} aliases with [[[...]]], drop the corresponding include files, and apply spelling/grammar fixes.

Reviewed changes

Copilot reviewed 43 out of 48 changed files in this pull request and generated 9 comments.

Show a summary per file

File	Description
sushi-config.yaml	Enable `show-inherited-invariants`.
input/fsh/profiles/Bundle-Mado.fsh	Switch to document Bundle, add composition slice, comment out provenance slice.
input/fsh/profiles/Composition-Mado.fsh	New `MadoComposition` profile with required narrative, author slices, event detail, and section structure.
input/fsh/profiles/Provenance.fsh	Entire `MadoProvenance` profile commented out.
input/fsh/profiles/ImagingStudy-MADO.fsh	Minor comment rewording.
input/fsh/profiles/Endpoint-wado-rs.fsh	Bump data-absent-reason cross-version extension to 5.3.0.
input/fsh/profiles/Extension-AnatomicalRegion.fsh	Lower maturity status from trial-use to draft.
input/fsh/profiles/Device-MadoCreator.fsh	Description wording update (introduces "an FHIR").
input/fsh/mhd/MHD-documentreference.fsh	Update title/short text to "FHIR Imaging Study Manifest".
input/fsh/terminology/narrative-status.fsh	New ValueSet for non-empty narrative statuses.
input/fsh/terminology/anatomical-region.fsh, imaging-procedures.fsh	Drop explicit `Id` declarations.
input/fsh/example-two-content/*.fsh	Rename instances, add Composition example, comment out provenance, update bundle.
input/fsh/example-two-content-with-transform/* and example-one-content/*	Update references to renamed `ExamplePatient` and title wording.
input/fsh/actors/consumer.fsh	Fix "subgorups" typo.
input/resources/*.json	Regenerated examples: document Bundle, Composition, removed Provenance, updated patient identifier use, new timestamps.
input/pagecontent/fhir-imaging-manifest.md, manifest-envelope.md, mapping.md, issues.md	Narrative rewording, switch to `[[[...]]]` links, spelling/grammar fixes.
input/intro-notes/StructureDefinition-MadoComposition-intro.md	New intro describing required Composition narrative content.
input/includes/aliases.md, profiles.md, fhir-resources.md	Remove unused Liquid alias include files.
input/images/*.drawio.svg	Update overview diagram for document Bundle and Composition, fix "attachement" typo.
input/ignoreWarnings.txt	Fix "polute" → "pollute".
.gitignore	Ignore `/tmp` and codespell venv.

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+* type
+  * coding[+] = $loinc#18748-4 "Diagnostic Imaging Study"
+* subject = Reference(ExamplePatient)
+* author[source-device] = Reference( MadoCreatorDeviceExample )
+* author[source-organization] = Reference( MadoCreatorOrganizationExample )
+* identifier
+  * system = "urn:dicom:uid"
+  * value = "1.2.392.200140.2.1.1.1.2.799008771.2076.1519721309.448"
+* type = $loinc#18748-4 "Diagnostic imaging study"
+* category = $loinc#18748-4 "Diagnostic imaging study"


+
+Optionally, each section in the Composition may provide information on each series.
+
+Besides the author information, all information in is a derivative of and should not be used as the definitive source of information.


+### FHIR Imaging Study Manifest overview

-The figure below presents an overview of the data that is part of the imaging-manifest. In order to keep the diagram readable, not all references are included.
+The FHIR Imaging Study Manifest is a FHIR document [[[Bundle]]]. The figure below presents an overview of the Bundle and the imaging manifest data that included in it. In order to keep the diagram readable, not all references are included.


-  * A FHIR manifest is represented as a FHIR json encoded FHIR {{Bundle}} following the profile {{MadoFhirBundle}}. This Bundle contains the {{ImagingStudy}} resource as well other resources such as the {{Patient}} and various {{Endpoint}}s.
-  * The FHIR DocumentReference SHALL include the identifier of the {{MadoFhirBundle}} as `masterIdentifier`.
+* FHIR Imaging Study Manifest:
+  * An FHIR Imaging Study Manifest is represented as a FHIR json encoded FHIR [[[Bundle]]] following the profile [[[MadoFhirBundle]]]. This Bundle contains the [[[ImagingStudy]]] resource as well other resources such as the [[[Patient]]] and various [[[Endpoint]]]s.


 InstanceOf: MadoFhirBundle
 Title: "Bundle: MADO FHIR document"
-Description: "An example of a MADO FHIR manifest."
+Description: "An example of an FHIR Imaging Study Manifest."


-Title: "DocumentReference Example for FHIR manifests with transform"
-Description: "DocumentReference Example for FHIR manifests with transform service called to transform the KOS manifest into a FHIR manifest"
+Title: "DocumentReference Example for FHIR Imaging Study Manifest with transform"
+Description: "DocumentReference Example for FHIR Imaging Study Manifest with transform service called to transform the KOS manifest into an FHIR Imaging Study Manifest"


 Parent: Device
 Title: "MADO Creator"
-Description: """A profile for the Device resource that represents the creator of an imaging study manifest. The primary goal is to communicate the fields:
+Description: """A profile for the Device resource that represents the creator of an FHIR Imaging Study Manifest. The primary goal is to communicate the fields:


+// Profile: MadoProvenance
+// Parent: Provenance
+// Title: "MADO Provenance"
+// Description: """
+// The purpose of this resource is to indicate information about the system that created the manifest. Additionally, it can be used to sign the content of the Bundle.

-In DICOM KOS this information (and the referred MadoCreator) corresponds to the Institution Name, Institution Id, Manufacturer Name in the General Equipment module.
-"""
-* insert SetFmmAndStatusRule( 1, draft )
+// In DICOM KOS this information (and the referred MadoCreator) corresponds to the Institution Name, Institution Id, Manufacturer Name in the General Equipment module.
+// """
+// * insert SetFmmAndStatusRule( 1, draft )

-* target MS
-  * ^short = "SHALL contain a list with all resources in the Bundle."
-* recorded
-  * ^short = "When the bundle/provenance was created."
-* agent
-  * insert SliceElement( #value, type )
-* agent contains mado-creator 1..1 MS 
-* agent[mado-creator]
-  * type = http://terminology.hl7.org/CodeSystem/provenance-participant-type#assembler
-  * who only Reference( MadoCreator )
-  * onBehalfOf 1..1 MS
-  * onBehalfOf only Reference( MadoCreatorOrganization )
-    * ^short = "The owner of the MadoCreator device."
+// * target MS
+//   * ^short = "SHALL contain a list with all resources in the Bundle."
+// * recorded
+//   * ^short = "When the bundle/provenance was created."
+// * agent
+//   * insert SliceElement( #value, type )
+// * agent contains mado-creator 1..1 MS 
+// * agent[mado-creator]
+//   * type = http://terminology.hl7.org/CodeSystem/provenance-participant-type#assembler
+//   * who only Reference( MadoCreator )
+//   * onBehalfOf 1..1 MS
+//   * onBehalfOf only Reference( MadoCreatorOrganization )
+//     * ^short = "The owner of the MadoCreator device."


CwCvW · 2026-06-11T10:56:15Z

-| Study series.description                          | MadoImagingStudy.series.description                                         | SR: EV(111028,DCM,"Image Library") -> EV(126200,DCM,"Image Library Group") -> EV (MADOTEMP002, 99IHE, “Series Description”)                                                                                            | Temp Code |
-| Study series.started                              | MadoImagingStudy.series.started                                             | SR: EV(111028,DCM,"Image Library") -> EV(126200,DCM,"Image Library Group") -> EV (MADOTEMP003, 99IHE, “Series Date”) & EV (MADOTEMP004, DCM, “Series Time”)                                                            | Temp Code |
-| Study series.numberOfInstances                    | MadoImagingStudy.series.numberOfInstances                                   | SR: EV(111028,DCM,"Image Library") -> EV(126200,DCM,"Image Library Group") -> EV (MADOTEMP007, 99IHE, “Number of Series Related Instances”)                                                                            | Temp Code |
+| Study series.description                          | MadoImagingStudy.series.description                                         | SR: EV(111028,DCM,"Image Library") -> EV(126200,DCM,"Image Library Group") -> EV (131563, DCM, “Series Description”)                                                                                            | Temp Code |


Do these lines still need the term "Temp Code" at the end, would expect you can remove this as it are now the final codes.

bvdh added 7 commits May 29, 2026 11:43

Updated the profiles and examples

f6565bb

Update titles and descriptions to use FHIR Imaging Study Manifest as …

d98da76

…the only expression.

replaced aliases for profiles with [[[profile]]]

186ce6f

Text updates to reflect the change to a document bundle

bad9fd3

replace {{{resource}}} with [[[resource]]]

82d4b1c

Spelling corrections

618a019

Updated the examples. Added imagingstudy in Composition.event.detail

1275fa6

bvdh requested a review from Copilot May 29, 2026 15:01

Copilot started reviewing on behalf of bvdh May 29, 2026 15:01 View session

bvdh requested a review from CwCvW May 29, 2026 15:01

Copilot AI reviewed May 29, 2026

View reviewed changes

bvdh added 4 commits June 9, 2026 16:42

Refine description in Composition.text field

795874a

Changes approved at the IHE.RAD call of 2026-6-10.

011ed56

Updated 99IHE codes with the new DCM values from CP2595

4669147

Update MADO examples

f1375c0

CwCvW reviewed Jun 11, 2026

View reviewed changes

bvdh added 3 commits June 11, 2026 13:04

Add FHIR IG Docker Build workflow configuration

e480da6

Update IG docker workflow to run _build.sh

d19d3c3

Run _build.sh non-interactively in IG docker workflow

1c6b246

Copilot started work on behalf of bvdh June 11, 2026 11:19 View session

Fix CI: download publisher.jar before running _build.sh build

6dd5282

Copilot AI changed the title ~~Update FHIR manifest bundle to document~~ Fix CI: download publisher.jar before running _build.sh build Jun 11, 2026

Copilot finished work on behalf of bvdh June 11, 2026 11:23

Copilot started work on behalf of bvdh June 11, 2026 11:25 View session

Fix CI: ensure Java is installed in publisher container build step

21e1c5c

Copilot finished work on behalf of bvdh June 11, 2026 11:30

bvdh added 2 commits June 11, 2026 14:27

change to validate template.

c87b806

fix in validate

3f35cb2

Copilot started work on behalf of bvdh June 11, 2026 12:28 View session

fix: add Jekyll installation step to validate workflow

f777d4d

Copilot finished work on behalf of bvdh June 11, 2026 12:32

bvdh merged commit 7f76426 into master Jun 11, 2026
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Fix CI: download publisher.jar before running _build.sh build - #4

Fix CI: download publisher.jar before running _build.sh build#4
bvdh merged 19 commits into
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		Optionally, each section in the Composition may provide information on each series.

		Besides the author information, all information in is a derivative of and should not be used as the definitive source of information. No newline at end of file

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bvdh commented May 29, 2026 •

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