Remove external-reference smoke test

Remove only external_reference_smoke_20260727_v1 and its generated registry, manifest, catalog, summary, and target-specific path references. Leave the external source Dataset untouched.

data/community_contributions/external_reference_smoke_20260727_v1/source_reference.json

@@ -1,15 +0,0 @@
-{
-  "availability_status": "available_at_acceptance",
-  "contributor_affiliation": "ETH",
-  "contributor_name": "Daniel Tabares",
-  "embedding_id": "external_reference_smoke_20260727_v1",
-  "embeddings_sha256": "d53bbe7e6222f360f252ee2a63b16fe1e3dbc6b696f367625c456bb488307613",
-  "metadata_url": "https://huggingface.co/datasets/danieltslz/gene-embeddings-external-reference-smoke/blob/098258908de86982d2ced04e70f1353e46055d08/candidate_embedding/metadata.json",
-  "package_url": "https://huggingface.co/datasets/danieltslz/gene-embeddings-external-reference-smoke/tree/098258908de86982d2ced04e70f1353e46055d08/candidate_embedding",
-  "path": "candidate_embedding",
-  "repo_id": "danieltslz/gene-embeddings-external-reference-smoke",
-  "repo_type": "dataset",
-  "revision": "098258908de86982d2ced04e70f1353e46055d08",
-  "storage_mode": "external_reference",
-  "validation_outcome": "PASS"
-}

data/community_contributions/external_reference_smoke_20260727_v1/submission.yaml

@@ -1,40 +0,0 @@
-schema_version: 1
-embedding_id: external_reference_smoke_20260727_v1
-display_name: External Reference Smoke Test 2026-07-27
-candidate:
-  repo_id: danieltslz/gene-embeddings-external-reference-smoke
-  repo_type: dataset
-  revision: 098258908de86982d2ced04e70f1353e46055d08
-  path: candidate_embedding
-contributor:
-  name: Daniel Tabares
-  email: daniel.tabares645@gmail.com
-  affiliation: ETH
-scientific:
-  broad_modality: other
-  detailed_modality: synthetic external-reference pipeline smoke test
-  original_method: deterministic Gaussian fixture
-  model_checkpoint: not-applicable
-  source_publication: ''
-  description: Deterministic synthetic float32 vectors for 1,500 human Ensembl gene
-    IDs, created solely to verify the automatic contribution, validation, registration,
-    and external-reference publication workflow.
-provenance:
-  embedding_generated_by: project smoke-test generator
-  input_data_source: synthetic deterministic random values
-  input_data_release: '2026-07-27'
-  species: Homo sapiens
-  pooling_strategy: not-applicable
-  identifier_before_mapping: Ensembl gene ID
-  mapping_method: direct use of the first 1500 IDs in the project master gene universe
-licensing:
-  source_license: cc0-1.0
-  redistribution_allowed: true
-  terms_url: https://creativecommons.org/publicdomain/zero/1.0/
-attestations:
-  information_is_accurate: true
-  rights_to_redistribute: true
-  no_sensitive_human_data: true
-  no_patient_level_data: true
-  source_terms_reviewed: true
-  acceptance_of_automatic_checks: true

data/community_contributions/external_reference_smoke_20260727_v1/validation_report.json

@@ -1,382 +0,0 @@
-{
-  "checks": [
-    {
-      "check_id": "file.embeddings.npz",
-      "message": "embeddings.npz exists",
-      "status": "PASS",
-      "value": null
-    },
-    {
-      "check_id": "file.genes.tsv",
-      "message": "genes.tsv exists",
-      "status": "PASS",
-      "value": null
-    },
-    {
-      "check_id": "file.metadata.json",
-      "message": "metadata.json exists",
-      "status": "PASS",
-      "value": null
-    },
-    {
-      "check_id": "file.README.md",
-      "message": "README.md exists",
-      "status": "PASS",
-      "value": null
-    },
-    {
-      "check_id": "metadata.schema",
-      "message": "metadata.json matches the schema",
-      "status": "PASS",
-      "value": null
-    },
-    {
-      "check_id": "metadata.consistency.embedding_id",
-      "message": "metadata embedding_id matches submission",
-      "status": "PASS",
-      "value": {
-        "actual": "external_reference_smoke_20260727_v1",
-        "expected": "external_reference_smoke_20260727_v1"
-      }
-    },
-    {
-      "check_id": "metadata.consistency.display_name",
-      "message": "metadata display_name matches submission",
-      "status": "PASS",
-      "value": {
-        "actual": "External Reference Smoke Test 2026-07-27",
-        "expected": "External Reference Smoke Test 2026-07-27"
-      }
-    },
-    {
-      "check_id": "metadata.consistency.species",
-      "message": "metadata species matches submission",
-      "status": "PASS",
-      "value": {
-        "actual": "Homo sapiens",
-        "expected": "Homo sapiens"
-      }
-    },
-    {
-      "check_id": "metadata.consistency.original_method",
-      "message": "metadata original_method matches submission",
-      "status": "PASS",
-      "value": {
-        "actual": "deterministic Gaussian fixture",
-        "expected": "deterministic Gaussian fixture"
-      }
-    },
-    {
-      "check_id": "metadata.consistency.model_checkpoint",
-      "message": "metadata model_checkpoint matches submission",
-      "status": "PASS",
-      "value": {
-        "actual": "not-applicable",
-        "expected": "not-applicable"
-      }
-    },
-    {
-      "check_id": "metadata.consistency.embedding_generated_by",
-      "message": "metadata embedding_generated_by matches submission",
-      "status": "PASS",
-      "value": {
-        "actual": "project smoke-test generator",
-        "expected": "project smoke-test generator"
-      }
-    },
-    {
-      "check_id": "metadata.consistency.input_data_source",
-      "message": "metadata input_data_source matches submission",
-      "status": "PASS",
-      "value": {
-        "actual": "synthetic deterministic random values",
-        "expected": "synthetic deterministic random values"
-      }
-    },
-    {
-      "check_id": "metadata.consistency.input_data_release",
-      "message": "metadata input_data_release matches submission",
-      "status": "PASS",
-      "value": {
-        "actual": "2026-07-27",
-        "expected": "2026-07-27"
-      }
-    },
-    {
-      "check_id": "metadata.consistency.pooling_strategy",
-      "message": "metadata pooling_strategy matches submission",
-      "status": "PASS",
-      "value": {
-        "actual": "not-applicable",
-        "expected": "not-applicable"
-      }
-    },
-    {
-      "check_id": "metadata.consistency.original_identifier_type",
-      "message": "metadata original_identifier_type matches submission",
-      "status": "PASS",
-      "value": {
-        "actual": "Ensembl gene ID",
-        "expected": "Ensembl gene ID"
-      }
-    },
-    {
-      "check_id": "metadata.consistency.mapping_method",
-      "message": "metadata mapping_method matches submission",
-      "status": "PASS",
-      "value": {
-        "actual": "direct use of the first 1500 IDs in the project master gene universe",
-        "expected": "direct use of the first 1500 IDs in the project master gene universe"
-      }
-    },
-    {
-      "check_id": "metadata.consistency.source_license",
-      "message": "metadata source_license matches submission",
-      "status": "PASS",
-      "value": {
-        "actual": "cc0-1.0",
-        "expected": "cc0-1.0"
-      }
-    },
-    {
-      "check_id": "metadata.consistency.redistribution_allowed",
-      "message": "metadata redistribution_allowed matches submission",
-      "status": "PASS",
-      "value": {
-        "actual": true,
-        "expected": true
-      }
-    },
-    {
-      "check_id": "metadata.consistency.category",
-      "message": "metadata category matches submission",
-      "status": "PASS",
-      "value": {
-        "actual": "other",
-        "expected": "other"
-      }
-    },
-    {
-      "check_id": "metadata.consistency.modality",
-      "message": "metadata modality matches submission",
-      "status": "PASS",
-      "value": {
-        "actual": "synthetic external-reference pipeline smoke test",
-        "expected": "synthetic external-reference pipeline smoke test"
-      }
-    },
-    {
-      "check_id": "policy.species",
-      "message": "Species is allowed",
-      "status": "PASS",
-      "value": "Homo sapiens"
-    },
-    {
-      "check_id": "policy.category",
-      "message": "Category is a valid catalog category value",
-      "status": "PASS",
-      "value": "other"
-    },
-    {
-      "check_id": "policy.modality",
-      "message": "Modality is a valid free-text description",
-      "status": "PASS",
-      "value": "synthetic external-reference pipeline smoke test"
-    },
-    {
-      "check_id": "policy.license",
-      "message": "License is on the automatic allowlist",
-      "status": "PASS",
-      "value": "cc0-1.0"
-    },
-    {
-      "check_id": "genes.nonempty",
-      "message": "All gene identifiers are non-empty",
-      "status": "PASS",
-      "value": null
-    },
-    {
-      "check_id": "genes.unique",
-      "message": "Gene identifiers are unique",
-      "status": "PASS",
-      "value": 0
-    },
-    {
-      "check_id": "genes.format",
-      "message": "All identifiers are unversioned Ensembl gene IDs",
-      "status": "PASS",
-      "value": 0
-    },
-    {
-      "check_id": "genes.unknown_fraction",
-      "message": "Unknown identifier fraction is within policy",
-      "status": "PASS",
-      "value": 0.0
-    },
-    {
-      "check_id": "genes.master_coverage",
-      "message": "Master-universe coverage is within policy",
-      "status": "PASS",
-      "value": 0.07463800567248843
-    },
-    {
-      "check_id": "genes.count",
-      "message": "Gene count is within policy",
-      "status": "PASS",
-      "value": 1500
-    },
-    {
-      "check_id": "npz.uncompressed_size",
-      "message": "NPZ uncompressed size is within policy",
-      "status": "PASS",
-      "value": 96128
-    },
-    {
-      "check_id": "npz.not_encrypted",
-      "message": "NPZ archive is not encrypted",
-      "status": "PASS",
-      "value": null
-    },
-    {
-      "check_id": "matrix.single_key",
-      "message": "NPZ contains exactly the 'embeddings' array",
-      "status": "PASS",
-      "value": [
-        "embeddings"
-      ]
-    },
-    {
-      "check_id": "matrix.ndim",
-      "message": "Embedding matrix is two-dimensional",
-      "status": "PASS",
-      "value": 2
-    },
-    {
-      "check_id": "matrix.rows",
-      "message": "Matrix row count equals genes.tsv row count",
-      "status": "PASS",
-      "value": {
-        "gene_rows": 1500,
-        "matrix_rows": 1500
-      }
-    },
-    {
-      "check_id": "matrix.dimensions",
-      "message": "Embedding dimensionality is within policy",
-      "status": "PASS",
-      "value": 16
-    },
-    {
-      "check_id": "matrix.dtype",
-      "message": "Matrix dtype is float32",
-      "status": "PASS",
-      "value": "float32"
-    },
-    {
-      "check_id": "matrix.numeric",
-      "message": "Matrix has a floating numeric dtype",
-      "status": "PASS",
-      "value": "float32"
-    },
-    {
-      "check_id": "matrix.finite",
-      "message": "Matrix contains no NaN or infinite values",
-      "status": "PASS",
-      "value": 0
-    },
-    {
-      "check_id": "matrix.zero_vectors",
-      "message": "Matrix contains no zero vectors",
-      "status": "PASS",
-      "value": 0
-    },
-    {
-      "check_id": "matrix.constant_columns",
-      "message": "Matrix contains no constant columns",
-      "status": "PASS",
-      "value": 0
-    },
-    {
-      "check_id": "matrix.duplicate_vectors",
-      "message": "Matrix contains no exact duplicate vectors",
-      "status": "PASS",
-      "value": 0
-    },
-    {
-      "check_id": "readme.nonempty",
-      "message": "README.md contains substantive documentation",
-      "status": "PASS",
-      "value": 500
-    }
-  ],
-  "outcome": "PASS",
-  "provenance": {
-    "source_license": "cc0-1.0",
-    "validator_environment": {
-      "numpy": "2.4.6",
-      "pandas": "2.3.3",
-      "python": "3.11.15"
-    }
-  },
-  "summary": {
-    "checksums_sha256": {
-      "README.md": "4b6e398313289b2ecdd1066f4de97c7eafc5923dba1f1d1993b7b2059e391e6f",
-      "embeddings.npz": "d53bbe7e6222f360f252ee2a63b16fe1e3dbc6b696f367625c456bb488307613",
-      "genes.tsv": "306d56cb7e5e8b3b9263290ff761ed33f67c94cdfd4fc5b130c5f23325de6812",
-      "metadata.json": "46d6fe915fc7ea8dd01a2e4a0a841bc5892dbba4ef5736bb67834bc74231ec48"
-    },
-    "constant_columns": 0,
-    "display_name": "External Reference Smoke Test 2026-07-27",
-    "dtype": "float32",
-    "duplicate_vectors": 0,
-    "embedding_id": "external_reference_smoke_20260727_v1",
-    "master_coverage_fraction": 0.07463800567248843,
-    "master_genes_matched": 1500,
-    "n_dimensions": 16,
-    "n_genes": 1500,
-    "norm_max": 6.339675426483154,
-    "norm_median": 3.9106478691101074,
-    "norm_min": 1.9258896112442017,
-    "submitted_category": "other",
-    "submitted_modality": "synthetic external-reference pipeline smoke test",
-    "trace": [
-      0.424897,
-      0.0,
-      1.0,
-      0.044766,
-      0.719459,
-      0.813992,
-      0.319309,
-      0.473156,
-      0.761471,
-      0.535774,
-      0.274129,
-      0.555382,
-      0.573005,
-      0.786742,
-      0.576876,
-      0.088022,
-      0.569755,
-      0.569755,
-      0.569755,
-      0.569755,
-      0.569755,
-      0.569755,
-      0.569755,
-      0.569755,
-      0.569755,
-      0.569755,
-      0.569755,
-      0.569755,
-      0.569755,
-      0.569755,
-      0.569755,
-      0.569755
-    ],
-    "trace_gene": "ENSG00000000003",
-    "unknown_identifier_fraction": 0.0,
-    "value_max": 3.543017864227295,
-    "value_min": -4.0558576583862305,
-    "zero_vectors": 0
-  }
-}

data/community_contributions/external_reference_smoke_20260727_v1/validation_summary.md

@@ -1,61 +0,0 @@
-# Candidate validation: PASS
-
-## Summary
-
-- Embedding: `external_reference_smoke_20260727_v1`
-- Category: `other`
-- Modality: `synthetic external-reference pipeline smoke test`
-- Genes: 1500
-- Dimensions: 16
-- Dtype: float32
-- Master coverage: 7.46%
-
-## Checks
-
-| Check | Status | Message |
-|---|---:|---|
-| `file.embeddings.npz` | **PASS** | embeddings.npz exists |
-| `file.genes.tsv` | **PASS** | genes.tsv exists |
-| `file.metadata.json` | **PASS** | metadata.json exists |
-| `file.README.md` | **PASS** | README.md exists |
-| `metadata.schema` | **PASS** | metadata.json matches the schema |
-| `metadata.consistency.embedding_id` | **PASS** | metadata embedding_id matches submission |
-| `metadata.consistency.display_name` | **PASS** | metadata display_name matches submission |
-| `metadata.consistency.species` | **PASS** | metadata species matches submission |
-| `metadata.consistency.original_method` | **PASS** | metadata original_method matches submission |
-| `metadata.consistency.model_checkpoint` | **PASS** | metadata model_checkpoint matches submission |
-| `metadata.consistency.embedding_generated_by` | **PASS** | metadata embedding_generated_by matches submission |
-| `metadata.consistency.input_data_source` | **PASS** | metadata input_data_source matches submission |
-| `metadata.consistency.input_data_release` | **PASS** | metadata input_data_release matches submission |
-| `metadata.consistency.pooling_strategy` | **PASS** | metadata pooling_strategy matches submission |
-| `metadata.consistency.original_identifier_type` | **PASS** | metadata original_identifier_type matches submission |
-| `metadata.consistency.mapping_method` | **PASS** | metadata mapping_method matches submission |
-| `metadata.consistency.source_license` | **PASS** | metadata source_license matches submission |
-| `metadata.consistency.redistribution_allowed` | **PASS** | metadata redistribution_allowed matches submission |
-| `metadata.consistency.category` | **PASS** | metadata category matches submission |
-| `metadata.consistency.modality` | **PASS** | metadata modality matches submission |
-| `policy.species` | **PASS** | Species is allowed |
-| `policy.category` | **PASS** | Category is a valid catalog category value |
-| `policy.modality` | **PASS** | Modality is a valid free-text description |
-| `policy.license` | **PASS** | License is on the automatic allowlist |
-| `genes.nonempty` | **PASS** | All gene identifiers are non-empty |
-| `genes.unique` | **PASS** | Gene identifiers are unique |
-| `genes.format` | **PASS** | All identifiers are unversioned Ensembl gene IDs |
-| `genes.unknown_fraction` | **PASS** | Unknown identifier fraction is within policy |
-| `genes.master_coverage` | **PASS** | Master-universe coverage is within policy |
-| `genes.count` | **PASS** | Gene count is within policy |
-| `npz.uncompressed_size` | **PASS** | NPZ uncompressed size is within policy |
-| `npz.not_encrypted` | **PASS** | NPZ archive is not encrypted |
-| `matrix.single_key` | **PASS** | NPZ contains exactly the 'embeddings' array |
-| `matrix.ndim` | **PASS** | Embedding matrix is two-dimensional |
-| `matrix.rows` | **PASS** | Matrix row count equals genes.tsv row count |
-| `matrix.dimensions` | **PASS** | Embedding dimensionality is within policy |
-| `matrix.dtype` | **PASS** | Matrix dtype is float32 |
-| `matrix.numeric` | **PASS** | Matrix has a floating numeric dtype |
-| `matrix.finite` | **PASS** | Matrix contains no NaN or infinite values |
-| `matrix.zero_vectors` | **PASS** | Matrix contains no zero vectors |
-| `matrix.constant_columns` | **PASS** | Matrix contains no constant columns |
-| `matrix.duplicate_vectors` | **PASS** | Matrix contains no exact duplicate vectors |
-| `readme.nonempty` | **PASS** | README.md contains substantive documentation |
-
-> Automatic inclusion confirms compliance with the configured technical policy. It is not independent scientific or legal verification.