Skip to content

Remove complicated PI tag from example #2

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
OliverWoolland merged 6 commits into from
Aug 3, 2026
Merged

Remove complicated PI tag from example #2

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
de03efc
Remove complicated PI tag from example
OliverWoolland Jul 31, 2026
0954cb8
Base built schema is needed
OliverWoolland Jul 31, 2026
ce6252a
Bump generated schema
OliverWoolland Jul 31, 2026
f0e048d
Update README
OliverWoolland Jul 31, 2026
e2c55db
Missed a code tag
OliverWoolland Jul 31, 2026
9aaafb8
Update example
OliverWoolland Jul 31, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
29 changes: 29 additions & 0 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,4 +13,33 @@ The initial use-case is capture of provenance on HPC systems (SLURM), for adding
4. A creation tool will be provided for these files. This will guide users in populating the appropriate files, and will validate the files against the LINK-ML schema.
5. SLURM plugin will scan PFFPATH locations as job runs. *.pff files found will be validated against the schema, then metadata ingested.

## Schemas

- `schema.yaml` — entry schema (imports the fragments below)
- `user.schema.yaml` / `project.schema.yaml` / `system.schema.yaml` — definitions

## Development

Setup (requires [uv](https://docs.astral.sh/uv/)):

```bash
uv sync --group dev
```

## Regenerating the compiled schema

`schema.json` is the compiled output of `schema.yaml`. After changing any schema, regenerate it and commit:

```bash
uv run linkml generate json-schema schema.yaml > schema.json
```

CI fails if `schema.json` is out of date.

## Validating the example

```bash
uv run linkml validate -s schema.yaml -C PFF examples/example.yaml
```


4 changes: 0 additions & 4 deletions examples/example.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,10 +8,6 @@ project:
description: >
Fictional research programme in psychoceramics, the supposed study of
cracked pots. Professor Carberry is said to still teach at Brown University.
PI:
id: jcarberry
full_name: Josiah Stinkney Carberry
orcid: https://orcid.org/0000-0002-1825-0097
start_date: "1929-04-01"
system:
hardware:
Expand Down
2 changes: 0 additions & 2 deletions project.schema.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6,8 +6,6 @@ classes:
id:
title:
description:
PI:
range: User
start_date:
range: date
end_date:
Expand Down
241 changes: 241 additions & 0 deletions schema.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,241 @@
{
"$defs": {
"CPU": {
"additionalProperties": false,
"description": "",
"properties": {
"cores": {
"type": [
"integer",
"null"
]
},
"name": {
"type": [
"string",
"null"
]
},
"threads": {
"type": [
"integer",
"null"
]
},
"vendor": {
"type": [
"string",
"null"
]
}
},
"title": "CPU",
"type": "object"
},
"OS": {
"additionalProperties": false,
"description": "",
"properties": {
"name": {
"type": [
"string",
"null"
]
},
"version": {
"type": [
"string",
"null"
]
}
},
"title": "OS",
"type": "object"
},
"PFF": {
"additionalProperties": false,
"description": "",
"properties": {
"project": {
"anyOf": [
{
"$ref": "#/$defs/Project"
},
{
"type": "null"
}
]
},
"system": {
"anyOf": [
{
"$ref": "#/$defs/System"
},
{
"type": "null"
}
]
},
"user": {
"anyOf": [
{
"$ref": "#/$defs/User"
},
{
"type": "null"
}
]
}
},
"title": "PFF",
"type": "object"
},
"Project": {
"additionalProperties": false,
"description": "",
"properties": {
"description": {
"type": [
"string",
"null"
]
},
"end_date": {
"format": "date",
"type": [
"string",
"null"
]
},
"id": {
"type": [
"string",
"null"
]
},
"start_date": {
"format": "date",
"type": [
"string",
"null"
]
},
"title": {
"type": [
"string",
"null"
]
}
},
"title": "Project",
"type": "object"
},
"System": {
"additionalProperties": false,
"description": "",
"properties": {
"hardware": {
"anyOf": [
{
"$ref": "#/$defs/CPU"
},
{
"type": "null"
}
]
},
"hostname": {
"type": [
"string",
"null"
]
},
"software": {
"anyOf": [
{
"$ref": "#/$defs/OS"
},
{
"type": "null"
}
]
}
},
"title": "System",
"type": "object"
},
"User": {
"additionalProperties": false,
"description": "",
"properties": {
"email": {
"type": [
"string",
"null"
]
},
"full_name": {
"type": [
"string",
"null"
]
},
"id": {
"type": [
"string",
"null"
]
},
"orcid": {
"type": [
"string",
"null"
]
}
},
"title": "User",
"type": "object"
}
},
"$id": "provenance-file-format",
"$schema": "https://json-schema.org/draft/2019-09/schema",
"additionalProperties": true,
"description": "",
"metamodel_version": "1.11.0",
"properties": {
"project": {
"anyOf": [
{
"$ref": "#/$defs/Project"
},
{
"type": "null"
}
]
},
"system": {
"anyOf": [
{
"$ref": "#/$defs/System"
},
{
"type": "null"
}
]
},
"user": {
"anyOf": [
{
"$ref": "#/$defs/User"
},
{
"type": "null"
}
]
}
},
"title": "provenance-file-format",
"type": "object",
"version": null
}

Loading