Release v3.2.0

CITATION.cff

@@ -2,7 +2,7 @@ cff-version: 1.2.0
 message: "If you use VCF-RDFizer in your research, please cite it using the metadata below."
 title: "VCF-RDFizer"
 type: software
-version: "3.1.0"
+version: "3.2.0"
 authors:
   - name: "VCF-RDFizer maintainers"
 repository-code: "https://github.com/ecrum19/VCF-RDFizer"

README.md

@@ -17,6 +17,7 @@ VCF-RDFizer is a Docker-first CLI wrapper for:
 2. Optional RDF compression/decompression, into queryable HDT and COTTAS artifacts
 3. Semantic validation of a compressed RDF graph against its source VCF
 4. Data linking, which writes a provenance-tracked side-graph of external links
+5. Policy attachment, which applies ODRL policies to files, regions and variants and writes checked release views
 
 The conversion targets the **VCF Core vocabulary**, published at
 [https://w3id.org/vcf-core/vocab#](https://w3id.org/vcf-core/vocab#) (prefix
@@ -924,6 +925,26 @@ Links go into `sample.links.nt`; the base graph is unchanged. The
 See [Data linking](docs/datalinking.md) for all three worked examples, reference
 and network safeguards, provenance, and the remaining design limitations.
 
+### Policy attachment plug-in
+
+`vcf-rdfizer-policy` attaches ODRL policies to a converted graph and writes one
+release view per request, without Docker. A policy can target a file, a region
+or a variant, and withholding a record withholds everything it owns (its call,
+alleles and genotypes). Selectors are SPARQL declared in Turtle, so adding one
+needs no code. `check` confirms that a view withholds exactly what the policy
+says, optionally against the source VCF text:
+
+```bash
+vcf-rdfizer-policy evaluate --rdf converted/P00*.nt.gz --policy policy.ttl \
+  --assignee https://example.org/party/alz-consortium --purpose DUO:0000007 -o views/alz
+vcf-rdfizer-policy check --view views/alz --rdf converted/P00*.nt.gz \
+  --policy policy.ttl --vcf P00*.vcf
+```
+
+This is governed release, not anonymization: a released genotype still
+identifies the person it came from. See [Policy attachment](docs/policy-demonstrator.md)
+and the runnable cohort in [`examples/policy/`](examples/policy/README.md).
+
 ### Custom RML Mappings
 
 `--rules` accepts any RML mapping, so you can change what RDF the pipeline
@@ -1007,6 +1028,8 @@ launches Docker, and reads back the JSON/CSV reports each stage writes.
 | `vcf_rdfizer_rules.py` | `vcf-rdfizer-rules` CLI: scaffold, document, and validate custom RML mappings. |
 | `vcf_rdfizer_link.py`, `vcf_rdfizer_linking/` | Linker authoring CLI and shared token/interval/API runner. |
 | `vcf_rdfizer_data/linkers/` | Packaged examples of all three plug-in tiers. |
+| `vcf_rdfizer_policy.py`, `vcf_rdfizer_policies/` | `vcf-rdfizer-policy` CLI and its select → partition → decide engine. |
+| `vcf_rdfizer_data/policy/` | The VCF Core profile, a DUO subset and the `vcfp:` vocabulary. |
 | `vcf_rdfizer_gzip.py` | Uncompressed size of a gzip/BGZF VCF without decompressing it. Used by the host preflight estimate and, inside the image, by `run_conversion.sh`. |
 | `src/vcf_as_tsv.sh` | VCF -> per-input `records`/`header_lines`/`file_metadata` TSV, in one `awk` pass. |
 | `src/run_conversion.sh` | Runs RMLStreamer, normalizes Spark part files, merges them into one `.nt`/`.nt.gz` aggregate, records conversion metrics. |
@@ -1044,6 +1067,7 @@ how each part of the tool works, why, and where it stops working.
 | [Roadmap](docs/roadmap.md) | Planned work, known defects, and rejected options |
 | [Data linking](docs/datalinking.md) | Runnable examples of all three plug-in tiers, authoring, safeguards, and provenance |
 | [Data linking design](docs/datalinking-design.md) | Broader proposal and remaining work |
+| [Policy attachment](docs/policy-demonstrator.md) | Implemented v0.1.0: ODRL policies on files, regions and variants, release views, and checks |
 | [Privacy policy design](docs/privacy-policy-design.md) | Proposal: ODRL-based granular disclosure control over the graph |
 
 - [`ACKNOWLEDGEMENTS.md`](ACKNOWLEDGEMENTS.md) - funding and attribution
@@ -1098,7 +1122,7 @@ Safe termination:
 
 If you use VCF-RDFizer in a publication, please cite:
 
-VCF-RDFizer maintainers. (2026). *VCF-RDFizer* (Version 3.1.0) [Computer software]. GitHub. https://github.com/ecrum19/VCF-RDFizer
+VCF-RDFizer maintainers. (2026). *VCF-RDFizer* (Version 3.2.0) [Computer software]. GitHub. https://github.com/ecrum19/VCF-RDFizer
 
 BibTeX:
 
@@ -1107,7 +1131,7 @@ BibTeX:
   author  = {{VCF-RDFizer maintainers}},
   title   = {VCF-RDFizer},
   year    = {2026},
-  version = {3.1.0},
+  version = {3.2.0},
   url     = {https://github.com/ecrum19/VCF-RDFizer},
   note    = {Computer software}
 }

conda-recipe/README.md

@@ -7,11 +7,11 @@ do not submit this package to `staged-recipes`.
 
 ## Before submitting to conda-forge
 
-1. Commit the version bump, then create and push a Git tag (for example `v3.1.0`).
+1. Commit the version bump, then create and push a Git tag (for example `v3.2.0`).
 2. Download the source tarball and compute sha256:
    ```bash
    curl -L -o vcf-rdfizer.tar.gz \
-     https://github.com/ecrum19/VCF-RDFizer/archive/refs/tags/v3.1.0.tar.gz
+     https://github.com/ecrum19/VCF-RDFizer/archive/refs/tags/v3.2.0.tar.gz
    shasum -a 256 vcf-rdfizer.tar.gz
    ```
 3. Replace `version` and `sha256` in the feedstock's `recipe/meta.yaml`.

conda-recipe/meta.yaml

@@ -1,13 +1,13 @@
 {% set name = "vcf-rdfizer" %}
-{% set version = "3.1.0" %}
+{% set version = "3.2.0" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
   url: https://github.com/ecrum19/VCF-RDFizer/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 0fa8dfd1e4d35c39594a5183a7c36569cee5857974f69b6db746dd705fae03ca
+  sha256: REPLACE_WITH_GITHUB_TARBALL_SHA256
 
 build:
   noarch: python

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "vcf-rdfizer"
-version = "3.1.0"
+version = "3.2.0"
 description = "Docker-first VCF to RDF conversion targeting the VCF Core vocabulary, with compressed queryable representations (HDT, COTTAS), semantic validation, and data linking"
 readme = "README.md"
 requires-python = ">=3.10"

vcf_rdfizer_data/VOCABULARY_PROVENANCE.json

@@ -1,9 +1,9 @@
 {
   "source_repository": "https://github.com/ecrum19/vcf-rdfizer-vocabulary",
-  "source_commit": "5bfd19d3c8fc377cd7eda689f3f8cad0d8d9bf8b",
+  "source_commit": "8a5f23ae552f519f1a14a9370e6d9d3f14934027",
   "note": "Vendored so SHACL validation works from an installed package, with no vocabulary checkout. test_shacl_default_unit.py re-checks these digests against a sibling checkout when one is present.",
   "files": {
-    "ontology/vcf-core-vocabulary.bundle.ttl": "20fd2d8820eb3c8d2796175a6e89212bc5ce04f607ab092addc631e4eff2489c",
+    "ontology/vcf-core-vocabulary.bundle.ttl": "b645b363a395dcd7e4bec990aab655814b589f21af6db4dff171299aaf2aa16e",
     "shacl/vcf-4.1.shacl.ttl": "5eafc441f2bae5c3b19d80dfc34eff0c2c6cefd61b569eadd38900f4343721f9",
     "shacl/vcf-4.2.shacl.ttl": "186131c85a483eaec457b545a9e1d310b6eccc2c9fadc95aaa37b34946d7e226",
     "shacl/vcf-4.3.shacl.ttl": "026105bb56660348239e3ada633e5d00a82f74df28b98798e0db2d1906b63470",

vcf_rdfizer_data/ontology/vcf-core-vocabulary.bundle.ttl

@@ -33,8 +33,8 @@ vcfc: a owl:Ontology ;
   dct:description "Vocabulary for representing the logical VCF 4.5 model in RDF: files, headers, records, alleles, values, genotype data, and VCF-specific structural-variant syntax. It supports both expanded per-sample and condensed, sample-ordered representations, and delegates broader variation semantics through FALDO, VRS, SO, GENO, and ChEBI alignments. BCF 2.2 byte layout is out of scope."@en ;
   dct:license <https://creativecommons.org/licenses/by/4.0/> ;
   dct:creator "Elias Crum" ;
-  owl:versionIRI <https://w3id.org/vcf-core/vocab/2.1.2> ;
-  owl:versionInfo "2.1.2" ;
+  owl:versionIRI <https://w3id.org/vcf-core/vocab/2.1.3> ;
+  owl:versionInfo "2.1.3" ;
   dct:modified "2026-09-08"^^xsd:date ;
   owl:priorVersion <https://w3id.org/vcf-core/vocab/2.0.0> ;
   dct:replaces <https://w3id.org/vcf-rdfizer/vocab> ;
@@ -846,7 +846,7 @@ vcfc:VCF45File a owl:Class ; rdfs:subClassOf vcfc:VCFFile ; rdfs:label "VCF 4.5
   rdfs:label "VCF Core allele and value-indexing module"@en ;
   dct:description "VCF-specific allele carriers and indexed values for Number=A/R/G/LA/LR/LG/P/M fields."@en ;
   owl:imports <https://w3id.org/vcf-core/vocab> ;
-  owl:versionInfo "2.1.2" .
+  owl:versionInfo "2.1.3" .
 
 vcfc:Allele a owl:Class ;
   rdfs:label "VCF allele"@en ;
@@ -1011,7 +1011,7 @@ vcfc:paddingAnchorPosition a owl:DatatypeProperty ;
   rdfs:label "VCF Core genotype module"@en ;
   dct:description "Parsed GT, phasing, phase-set, local-allele, and sample-filter carriers for VCF 4.5."@en ;
   owl:imports <https://w3id.org/vcf-core/vocab>, <https://w3id.org/vcf-core/alleles> ;
-  owl:versionInfo "2.1.2" .
+  owl:versionInfo "2.1.3" .
 
 vcfc:Genotype a owl:Class ;
   rdfs:label "VCF genotype"@en ;
@@ -1115,7 +1115,7 @@ vcfc:allelePhaseSet a owl:ObjectProperty ; rdfs:label "allele phase set"@en ;
   owl:imports <https://w3id.org/vcf-core/vocab>,
               <https://w3id.org/vcf-core/alleles>,
               <https://w3id.org/vcf-core/genotypes> ;
-  owl:versionInfo "2.1.2" .
+  owl:versionInfo "2.1.3" .
 
 vcfc:SymbolicAlleleType a owl:Class ;
   rdfs:label "symbolic allele type"@en ;
@@ -1295,7 +1295,7 @@ vcfc:blockAllele a owl:ObjectProperty ; rdfs:label "block allele"@en ; rdfs:doma
   rdfs:label "VCF Core reserved-key registry for VCF 4.5"@en ;
   dct:source <https://raw.githubusercontent.com/samtools/hts-specs/master/VCFv4.5.tex> ;
   owl:imports <https://w3id.org/vcf-core/vocab> ;
-  owl:versionInfo "2.1.2" ;
+  owl:versionInfo "2.1.3" ;
   vcfc:specificationVersion "VCFv4.5" .
 
 vcfc:specificationVersion a owl:AnnotationProperty ;