FHIR Bundle Assembler

What it does

When your agent uses it

• Combining several Condition, Observation and MedicationStatement resources into one Bundle
• Preparing resources to POST to an EHR or FHIR server
• Making Bundle output byte-identical for golden tests

Example prompts

• “Take these exported Condition and Observation resources and assemble one transaction Bundle for our FHIR server.”
• “Build the Bundle with deterministic fullUrls so we can use it in a golden test.”

Requirements

• Python with the OpenMed package
• FHIR R4 resources already exported by the exporting-to-fhir skill

Workflow steps

3 steps, taken from the first numbered list in SKILL.md.

1. 1Deterministic fullUrl. Each resource gets a urn:uuid seeded by
2. 2Reference rewriting. Any {"reference": "ResourceType/id"} whose target
3. 3Request blocks. For transaction/batch bundles each entry gets a

What it can do on your machine

Read from SKILL.md and the folder at commit 34d7b8c. It shows what the files ask for, not the result of running them.

• Tool permissions

  Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

  From allowed-tools in the SKILL.md frontmatter.

• Runs code

  No scripts in the folder and no shell commands in SKILL.md (its code samples are python and json).

  From the folder's file list and the shell code blocks in SKILL.md.

• Network

  Hosts in commands or code, which the agent is likely to contact:

  • terminology.hl7.org

  Also links to:

  • hl7.org

  From URLs in SKILL.md, links to its own repository left out.

• Credentials

  Names no API keys, tokens, secrets or passwords.

  From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

FHIR Bundle Assembler loads about 2.2k tokens when it runs. Until then it costs about 162 tokens; SKILL.md has 690 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it

~162

When it runs · the whole SKILL.md, loaded when a task matches

~2.2k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from maziyarpanahi/openmed at commit 34d7b8c, republished under its Apache-2.0 licence (© maziyarpanahi). 690 words, ~2,194 tokens.

name

assembling-fhir-bundles

description

Package multiple FHIR R4 resources produced from OpenMed output into a single valid transaction Bundle ready to POST to an EHR, using OpenMed's verified bundle assembler openmed.clinical.exporters.fhir.to_bundle. Covers deterministic urn:uuid fullUrls, automatic in-Bundle reference rewriting, request blocks (method/url) for transaction vs batch, and conditional create. Use after exporting-to-fhir when the user has several Condition/Observation/MedicationStatement resources and wants one transaction Bundle, mentions Bundle, transaction, references, or posting to a FHIR server. Builds on exporting-to-fhir; pairs after.

license

Apache-2.0

metadata.project

OpenMed

metadata.category

fhir-interop

metadata.pairs

after

metadata.version

1.0

from openmed.clinical.exporters.fhir import to_bundle, deterministic_fullurl

bundle = to_bundle(
    resources,                       # Sequence[Mapping] each with a resourceType
    doc_id="note-2024-03-02-001",    # seeds stable urn:uuid fullUrls
    bundle_type="transaction",       # "transaction" | "batch" | "collection" | ...
)

from openmed.clinical.exporters.fhir import to_bundle
from openmed.clinical.exporters.codeable_concept_simple import coding, codeable_concept

condition = {
    "resourceType": "Condition", "id": "cond-1",
    "clinicalStatus": {"coding": [{
        "system": "http://terminology.hl7.org/CodeSystem/condition-clinical",
        "code": "active"}]},
    "code": codeable_concept(
        [coding("snomed", "44054006", "Diabetes mellitus type 2")],
        text="type 2 diabetes"),
    "subject": {"reference": "Patient/patient-1"},   # internal ref, rewritten
}
medication = {
    "resourceType": "MedicationStatement", "id": "med-1", "status": "active",
    "medicationCodeableConcept": codeable_concept(
        [coding("rxnorm", "860975", "metformin 500 MG Oral Tablet")],
        text="metformin 500 mg"),
    "subject": {"reference": "Patient/patient-1"},
}
patient = {
    "resourceType": "Patient", "id": "patient-1",
    "gender": "unknown",                              # de-identified, synthetic
}

bundle = to_bundle([patient, condition, medication],
                   doc_id="demo-note", bundle_type="transaction")

{
  "resourceType": "Bundle",
  "type": "transaction",
  "entry": [
    {
      "fullUrl": "urn:uuid:6f1c...e2",
      "resource": { "resourceType": "Patient", "id": "patient-1", "gender": "unknown" },
      "request": { "method": "POST", "url": "Patient" }
    },
    {
      "fullUrl": "urn:uuid:9a3b...77",
      "resource": {
        "resourceType": "Condition", "id": "cond-1",
        "subject": { "reference": "urn:uuid:6f1c...e2" }
      },
      "request": { "method": "POST", "url": "Condition" }
    },
    {
      "fullUrl": "urn:uuid:c0d4...19",
      "resource": {
        "resourceType": "MedicationStatement", "id": "med-1",
        "subject": { "reference": "urn:uuid:6f1c...e2" }
      },
      "request": { "method": "POST", "url": "MedicationStatement" }
    }
  ]
}

for entry in bundle["entry"]:
    if entry["resource"]["resourceType"] == "Patient":
        entry["request"]["ifNoneExist"] = "identifier=http://hospital.example|MRN-REDACTED"

© maziyarpanahi, Apache-2.0. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

Just SKILL.md in skills/assembling-fhir-bundles of maziyarpanahi/openmed.

Open the folder on GitHubat commit 34d7b8c