SQL On Fhir

What it does

When your agent uses it

• The user asks to create ViewDefinitions
• Flatten FHIR resources into tables
• Write FHIRPath expressions for data extraction
• Implement forEach/forEachOrNull/repeat patterns for unnesting

Example prompts

• “ViewDefinition”
• “SQL on FHIR”
• “flatten FHIR”
• “/sql-on-fhir”

Workflow steps

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

1. 1Starts at the resource root
2. 2Evaluates each path in the repeat array
3. 3For each result, recursively applies the same paths
4. 4Continues until no more matches exist
5. 5Unions all results from all levels

What it can do on your machine

Read from SKILL.md and the folder at commit 56a3b4a. 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 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:

  • 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

SQL On Fhir loads about 2.3k tokens when it runs, and up to ~12k if it reads all its reference files. Until then it costs about 202 tokens; SKILL.md has 568 words of instructions outside code blocks.

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

~202

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

~2.3k

With references · SKILL.md plus every file in references/, read only if the agent opens them

~12k

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 aehrc/pathling at commit 56a3b4a, republished under its Apache-2.0 licence (© aehrc). 568 words, ~2,338 tokens.

name

sql-on-fhir

description

Expert guidance for implementing SQL on FHIR v2 ViewDefinitions and operations to create portable, tabular projections of FHIR data. Use this skill when the user asks to create ViewDefinitions, flatten FHIR resources into tables, write FHIRPath expressions for data extraction, implement forEach/forEachOrNull/repeat patterns for unnesting, create where clauses for filtering, use constants in view definitions, combine data with unionAll, execute ViewDefinitions with $run or $export operations, or implement SQL on FHIR server capabilities. Trigger keywords include "ViewDefinition", "SQL on FHIR", "flatten FHIR", "tabular FHIR", "FHIR to SQL", "FHIR analytics", "FHIRPath columns", "unnest FHIR", "$viewdefinition-run", "$export", "view runner", "repeat", "recursive", "QuestionnaireResponse".

{
    "resourceType": "ViewDefinition",
    "resource": "Patient",
    "status": "active",
    "select": [
        {
            "column": [
                { "name": "id", "path": "id" },
                { "name": "gender", "path": "gender" },
                { "name": "birth_date", "path": "birthDate" }
            ]
        }
    ]
}

{
    "column": [
        {
            "name": "family_name",
            "path": "name.first().family",
            "type": "string",
            "description": "Patient's primary family name"
        }
    ]
}

{
    "resource": "Patient",
    "select": [
        { "column": [{ "name": "id", "path": "id" }] },
        {
            "forEach": "name",
            "column": [
                { "name": "family", "path": "family" },
                { "name": "given", "path": "given.first()" }
            ]
        }
    ]
}

{
    "forEach": "contact",
    "select": [
        {
            "column": [
                {
                    "name": "contact_phone",
                    "path": "telecom.where(system='phone').value"
                }
            ]
        },
        {
            "forEach": "name.given",
            "column": [{ "name": "given_name", "path": "$this" }]
        }
    ]
}

{
    "resource": "QuestionnaireResponse",
    "select": [
        { "column": [{ "name": "response_id", "path": "id" }] },
        {
            "repeat": ["item", "answer.item"],
            "column": [
                { "name": "link_id", "path": "linkId" },
                {
                    "name": "answer_text",
                    "path": "answer.value.ofType(string).first()"
                }
            ]
        }
    ]
}

{
  "resource": "Patient",
  "where": [
    {"path": "active = true"},
    {"path": "name.exists()"}
  ],
  "select": [...]
}

{
    "constant": [{ "name": "use_type", "valueString": "official" }],
    "select": [
        {
            "forEach": "name.where(use = %use_type)",
            "column": [{ "name": "official_name", "path": "family" }]
        }
    ]
}

{
    "select": [
        { "column": [{ "name": "id", "path": "id" }] },
        {
            "unionAll": [
                {
                    "forEach": "telecom",
                    "column": [
                        { "name": "contact", "path": "value" },
                        { "name": "system", "path": "system" }
                    ]
                },
                {
                    "forEach": "contact.telecom",
                    "column": [
                        { "name": "contact", "path": "value" },
                        { "name": "system", "path": "system" }
                    ]
                }
            ]
        }
    ]
}

{
    "column": [
        {
            "name": "birth_sex",
            "path": "extension('http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex').value.ofType(code).first()"
        }
    ]
}

{
    "path": "extension('http://hl7.org/fhir/us/core/StructureDefinition/us-core-race').extension('ombCategory').value.ofType(Coding).code.first()"
}

GET  [base]/ViewDefinition/[id]/$run?_format=csv
POST [base]/ViewDefinition/$run

POST [base]/ViewDefinition/$export

© aehrc, 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

SKILL.md and 4 other files (references) in .claude/skills/sql-on-fhir of aehrc/pathling.

• SKILL.md
• references/examples.md
• references/fhirpath-subset.md
• references/operations.md
• references/view-definition-structure.md

Open the folder on GitHubat commit 56a3b4a