orfdata 0.41.0__tar.gz → 0.42.0__tar.gz

{orfdata-0.41.0/orfdata.egg-info → orfdata-0.42.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orfdata
-Version: 0.41.0
+Version: 0.42.0
 Summary: Reference proteomes with evidence-backed noncanonical ORFs on PyEnsembl genomes
 Author: OpenVax
 License-Expression: Apache-2.0
@@ -64,10 +64,18 @@ normalized sources do not need it.
 List every bundled, downloadable or buildable resource and what is installed:
 
 ```sh
-orfdata download list
-orfdata download status
+orfdata data list
+orfdata data status
+orfdata data info pfizer-atlas-dog-peptide-evidence
+orfdata data fetch pfizer-atlas-dog-peptide-evidence
+orfdata data path pfizer-atlas-dog-peptide-evidence
 ```
 
+`data fetch NAME` downloads a published artifact or builds from pinned sources
+when no artifact is distributed. The same command handles optional catalogues
+such as `openprot-mouse` and datasets such as `peptideatlas-dog-peptides`.
+`downloads` and `download` are aliases for `data`; `info` and `path` stay offline.
+
 `orfdata setup --species human` also installs `gdc-viruses`, the default
 200-reference GDC viral screen for human transcriptome analysis;
 `--collections none` skips it. Viral support is part of the base install, and

{orfdata-0.41.0 → orfdata-0.42.0}/README.md

@@ -32,10 +32,18 @@ normalized sources do not need it.
 List every bundled, downloadable or buildable resource and what is installed:
 
 ```sh
-orfdata download list
-orfdata download status
+orfdata data list
+orfdata data status
+orfdata data info pfizer-atlas-dog-peptide-evidence
+orfdata data fetch pfizer-atlas-dog-peptide-evidence
+orfdata data path pfizer-atlas-dog-peptide-evidence
 ```
 
+`data fetch NAME` downloads a published artifact or builds from pinned sources
+when no artifact is distributed. The same command handles optional catalogues
+such as `openprot-mouse` and datasets such as `peptideatlas-dog-peptides`.
+`downloads` and `download` are aliases for `data`; `info` and `path` stay offline.
+
 `orfdata setup --species human` also installs `gdc-viruses`, the default
 200-reference GDC viral screen for human transcriptome analysis;
 `--collections none` skips it. Viral support is part of the base install, and

orfdata-0.42.0/docs/dog-data-sources.md

@@ -0,0 +1,60 @@
+# Canine paired measurements and translation-evidence audit
+
+Source check: **28 October 2026**. This audit identifies importable measurement
+files and their limitations. It does not add a dataset to the registry.
+The [machine-readable audit](data/dog-source-audit-20261028.json) contains source
+URLs, hashes, counts, search queries and a candidate sample crosswalk.
+
+## Paired RNA and protein: a verified study
+
+[Amini et al., 2021](https://pmc.ncbi.nlm.nih.gov/articles/PMC8042244/)
+studied cancer-associated and normal stroma from archived canine mammary
+carcinomas. The authors explicitly reused the cases of their earlier RNA study.
+Original case 7 was excluded from proteomics because its paraffin block was
+unavailable. Measurements come from separate laser-capture preparations of
+the same tissue cases, not identical RNA/protein aliquots.
+
+| Source | Verified processed data | Download |
+| --- | --- | --- |
+| [GSE135183](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135183) | 18,582 genes × 30 RNA samples, 15 cases with two stromal compartments | [Raw counts, 606 KB compressed](https://ftp.ncbi.nlm.nih.gov/geo/series/GSE135nnn/GSE135183/suppl/GSE135183_raw_counts.csv.gz) |
+| [PXD023023](https://www.ebi.ac.uk/pride/archive/projects/PXD023023) | 1,583 native protein-group rows with 28 LFQ sample columns | [Protein groups, 2.8 MB](https://ftp.pride.ebi.ac.uk/pride/data/archive/2021/03/PXD023023/proteinGroups.txt) |
+| PXD023023 | 5,413 peptide rows with native quantitative fields | [Peptides, 4.5 MB](https://ftp.pride.ebi.ac.uk/pride/data/archive/2021/03/PXD023023/peptides.txt) |
+
+The downloaded protein and peptide files match PRIDE's deposited SHA-1 checksums;
+the audit also records SHA-256 for all three processed files. RNA values are
+nonnegative integer counts. Native protein-group counts include controls and
+contaminants and are not counts of confidently detected biological proteins.
+
+PRIDE filenames use case numbers 1–15; GEO uses case IDs such as 109 and 135.
+Matching the article's Table 1 to GEO by breed, age and histological subtype
+uniquely reconciles all 14 proteomics cases. The resulting 28 sample links are
+**metadata-derived**, not an author-supplied identifier crosswalk. Breed spelling
+normalizations are recorded. GEO case 127 is the unmatched RNA case.
+
+An importer must retain that pairing basis, separate stromal compartments,
+protein-group ambiguity, controls, missing quantities and native units. The
+deposited search used a dated canonical UniProt reference, but its FASTA is not
+among the 31 PRIDE files. Sequence/reference qualification remains necessary;
+these data do not establish ncORF translation. Author-derived contrasts in the
+supplementary workbooks must stay distinct from sample-level measurements.
+Import work remains tracked in [#20](https://github.com/openvax/orfdata/issues/20).
+
+## Dog Ribo-seq and ncORF translation
+
+The date-stamped dog-specific SRA, GEO and ENA queries in the audit returned no
+matching sequencing records. This is a bounded repository search, not proof
+that no unpublished or differently indexed experiment exists.
+
+[Pfeffer et al., 2015](https://www.nature.com/articles/ncomms9403)
+reports ribosome profiling and total RNA sequencing of canine pancreas rough-ER
+preparations aligned to CanFam3.1/Ensembl 77. Its accession section lists EMDB
+and PDB deposits, without a sequencing accession. No downloadable reads or
+processed ORF-level counts were verified in this audit. Even if recovered, the
+preparation would describe an enriched pancreatic compartment, not a broad
+normal-tissue canine translatome.
+
+Existing canine PeptideAtlas, Pfizer and DLA datasets retain their deposited
+canonical-search scope. The experimental dog ncORF search pipeline is a route
+to new analysis, not a released experimentally supported catalogue. Dog ncORF
+translation coverage therefore remains unavailable pending qualified data or
+a separately validated reanalysis. See [#12](https://github.com/openvax/orfdata/issues/12).

{orfdata-0.41.0 → orfdata-0.42.0}/docs/dog-peptides.md

@@ -5,6 +5,9 @@ spectrometry has observed. Neither searched for noncanonical ORFs, so they
 don't add ORFs to the dog proteome
 ([why dog has no ncORF catalogue](catalogs.md#dog)).
 
+For a verified paired RNA/protein study and the latest bounded search for dog
+Ribo-seq, see the [canine source audit](dog-data-sources.md).
+
 | Dataset | What it holds | How to get it |
 |---|---|---|
 | `kaabinejadian-dog-dla-ligands` | DLA class I ligands from four dog tumours and three DLA-88 monoallelic cell lines | `orfdata datasets download` (CC0, 25 MB) |

{orfdata-0.41.0 → orfdata-0.42.0}/docs/downloads.md

@@ -3,8 +3,48 @@
 ORFdata has one common entry point for data acquisition:
 
 ```sh
-orfdata download list
-orfdata download status
+orfdata data list
+orfdata data list --species dog
+orfdata data info pfizer-atlas-dog-peptide-evidence
+orfdata data fetch pfizer-atlas-dog-peptide-evidence
+orfdata data fetch peptideatlas-dog-peptides openprot-mouse
+orfdata data path pfizer-atlas-dog-peptide-evidence
+orfdata data status
+```
+
+`data`, `downloads` and `download` are aliases for the same command group.
+The `list/info/fetch/path` vocabulary follows other OpenVax download tools.
+`fetch` accepts one or more explicit resource names and chooses the registered
+acquisition route: download an artifact when available, otherwise build locally
+from checksum-pinned source files. All names and required terms are checked
+before the first acquisition. There is no implicit download-all operation.
+
+`info NAME` reports the version, source/coverage manifest and distribution
+metadata, including sizes and redistribution terms where declared. `path NAME`
+prints an installed file or directory for scripts; missing data is an error,
+and never triggers a download. Use `--verify` on reads to validate local bytes,
+`--cache-root DIR` to select a cache, and `--json` for machine output.
+`fetch --json` returns one result per distinct requested name.
+
+Use `--kind` to disambiguate colliding resource names. For one resource,
+`--version VERSION` selects a historical release and `--source-path ASSET=PATH`
+provides already downloaded catalogue/dataset sources or genome files. Source
+overrides remain checksum-checked. `--force` installs a fresh generation.
+Restricted chain downloads require `--accept-terms` after reviewing `info`.
+
+The same operations are available in Python:
+
+```python
+from orfdata import data_info, data_path, fetch_data
+
+details = data_info("openprot-mouse")  # Offline; shows the build route and terms.
+result = fetch_data("openprot-mouse")  # Explicit source download and processing.
+path = data_path("openprot-mouse")    # Offline file/directory lookup.
+```
+
+The focused forms remain available for additional resource-specific options:
+
+```sh
 orfdata download viral --species human
 orfdata download catalog NAME
 orfdata download dataset NAME
@@ -14,8 +54,7 @@ orfdata download chains --species human
 ```
 
 The operation comes first so the same discovery and installation model applies
-to every resource kind. `orfdata download viral` is therefore the primary
-command. Focused command groups such as `orfdata viral coverage` and
+to every resource kind. Focused command groups such as `orfdata viral coverage` and
 `orfdata viral summary` remain useful for domain-specific inspection.
 
 `list` shows every bundled, downloadable or locally buildable primary resource

{orfdata-0.41.0 → orfdata-0.42.0}/mkdocs.yml

@@ -44,6 +44,7 @@ nav:
       - Yeast protein and RNA: copy-yeast.md
       - Yeast RNA and ribosome occupancy: ingolia-yeast.md
       - Dog MHC ligands and PeptideAtlas: dog-peptides.md
+      - Dog paired-data and Ribo-seq source audit: dog-data-sources.md
   - Project:
       - Release notes: https://github.com/openvax/orfdata/blob/main/CHANGELOG.md
       - Data roadmap: https://github.com/openvax/orfdata/issues/3

{orfdata-0.41.0 → orfdata-0.42.0}/orfdata/__init__.py

@@ -17,6 +17,7 @@ from .catalog import (
 )
 from .catalog_manifest import CatalogManifest
 from .catalogs import CatalogRegistry, build_catalog
+from .data_resources import data_info, data_path, fetch_data
 from .dataset import QuantitativeDataset
 from .datasets import DatasetRegistry, build_dataset
 from .downloads import DataStatus, list_data
@@ -176,6 +177,9 @@ __all__ = [
     "build_dataset",
     "DataStatus",
     "list_data",
+    "data_info",
+    "data_path",
+    "fetch_data",
     "DatasetManifest",
     "SourceAsset",
     "Sample",

{orfdata-0.41.0 → orfdata-0.42.0}/orfdata/cli.py

@@ -30,10 +30,10 @@ def run(argv=None, prog=None, *, catalog_loader=load_catalog):
         from .proteome_cli import run as proteome_run
 
         return proteome_run(argv[1:], prog=(prog or "orfdata") + " proteome")
-    if argv and argv[0] == "download":
+    if argv and argv[0] in ("data", "download", "downloads"):
         from .download_cli import run as download_run
 
-        return download_run(argv[1:], prog=(prog or "orfdata") + " download")
+        return download_run(argv[1:], prog=f"{prog or 'orfdata'} {argv[0]}")
     if argv and argv[0] == "viral":
         from .viral_cli import run as viral_run
 
@@ -56,7 +56,7 @@ def run(argv=None, prog=None, *, catalog_loader=load_catalog):
                "catalogues with 'orfdata catalogs --help'; lift a catalogue to another assembly with "
                "'orfdata lift --help' and 'orfdata chains --help'; annotations PyEnsembl lacks, such as "
                "T2T-CHM13, with 'orfdata genomes --help'; discover and acquire data with "
-               "'orfdata download --help'; viral coverage, subsets and installed layers with "
+               "'orfdata data --help' (also 'downloads' or 'download'); viral coverage, subsets and installed layers with "
                "'orfdata viral --help'.")
     _add_query_arguments(parser)
     args = parser.parse_args(argv)

orfdata-0.42.0/orfdata/data_resources.py

@@ -0,0 +1,140 @@
+"""Named access to optional data, independent of source and species."""
+
+from dataclasses import replace
+from pathlib import Path
+
+from .downloads import _fetch_command, list_data
+
+
+def _registry(kind, cache_root):
+    from .catalogs import CatalogRegistry
+    from .datasets import DatasetRegistry
+
+    return {"catalog": CatalogRegistry, "dataset": DatasetRegistry}[kind](cache_root=cache_root)
+
+
+def _resolve(name, kind, version, cache_root, verify_files):
+    rows = [r for r in list_data(kind=kind, cache_root=cache_root, verify_files=False)
+            if r.name == name]
+    if not rows:
+        raise ValueError(f"Unknown data resource {name!r}; see 'orfdata data list'")
+    if len({r.kind for r in rows}) != 1:
+        raise ValueError(f"Ambiguous data resource {name!r}; select --kind")
+    row = rows[0]
+    if row.kind in ("dataset", "catalog") and row.acquire is not None:
+        registry = _registry(row.kind, cache_root)
+        manifest = registry.info(name, version)
+        inspection = registry.inspect(name, manifest.version, verify_files=verify_files)
+        acquire = "download" if registry.published(name, manifest.version) else "build"
+        row = replace(row, version=manifest.version, title=manifest.title,
+                      status=inspection.status, path=str(inspection.path), acquire=acquire,
+                      origin=acquire if inspection.status == "available" else None)
+    elif row.kind == "reference":
+        from .datasets import DatasetRegistry
+
+        registry = DatasetRegistry(cache_root=cache_root)
+        dataset, asset = name.split(":", 1)
+        manifest = registry.info(dataset, version)
+        inspection = registry.inspect_reference(dataset, manifest.version, asset_id=asset,
+                                                verify_files=verify_files)
+        row = replace(row, version=manifest.version, status=inspection.status,
+                      path=str(inspection.path),
+                      origin="download" if inspection.status == "available" else None)
+    else:
+        if version is not None and version != row.version:
+            raise ValueError(f"{name!r} has version {row.version!r}, not {version!r}")
+        if verify_files:
+            row = next(r for r in list_data(kind=row.kind, cache_root=cache_root, verify_files=True)
+                       if r.name == name and r.version == row.version)
+    return replace(row, command=_fetch_command(row))
+
+
+def data_info(name, *, kind=None, version=None, cache_root=None, verify_files=False):
+    """Describe a named resource, its pins and acquisition route, entirely offline."""
+    row = _resolve(name, kind, version, cache_root, verify_files)
+    result = row.to_dict()
+    if row.kind in ("catalog", "dataset") and row.acquire is not None:
+        registry = _registry(row.kind, cache_root)
+        result["manifest"] = registry.info(name, row.version).to_dict()
+        result.update(registry.download_metadata(name, row.version))
+    elif row.kind == "reference":
+        from .datasets import DatasetRegistry
+
+        dataset, asset = name.split(":", 1)
+        registry = DatasetRegistry(cache_root=cache_root)
+        result["sources"] = [s.source.to_dict() for s in registry.search_references(dataset, row.version)
+                             if s.source.asset_id == asset]
+    elif row.kind == "chain":
+        from dataclasses import asdict
+
+        from .liftover import pinned_chains
+
+        result["source"] = asdict(next(c for c in pinned_chains() if c.name == name))
+    elif row.kind == "genome":
+        from dataclasses import asdict
+
+        from .genomes import pinned_genomes
+
+        result["source"] = asdict(next(g for g in pinned_genomes() if g.name == name))
+    return result
+
+
+def data_path(name, *, kind=None, version=None, cache_root=None, verify_files=False):
+    """Return an installed file/directory; missing data never triggers acquisition."""
+    info = data_info(name, kind=kind, version=version, cache_root=cache_root,
+                     verify_files=verify_files)
+    if not info["installed"] or info["path"] is None:
+        raise ValueError(f"{name!r} is {info['status']}; install it with {info['command']}")
+    return Path(info["path"])
+
+
+def fetch_data(name, *, kind=None, version=None, cache_root=None, force=False,
+               source_paths=None, timeout=60, show_progress=True, accept_terms=False):
+    """Install one resource and return its status, downloading or building as declared.
+
+    Downloads retain their checksum validation. Builds use the same pinned source
+    adapters as the focused commands. Existing valid files are reused; discovery
+    and ordinary queries never invoke this function implicitly.
+    """
+    row = _resolve(name, kind, version, cache_root, True)
+    if source_paths is not None and row.kind not in ("catalog", "dataset", "genome"):
+        raise ValueError("Source overrides here require a catalogue, dataset or genome; use the focused command for other kinds")
+    if row.restricted and not accept_terms:
+        raise ValueError(f"{name!r} requires --accept-terms; see 'orfdata data info {name}'")
+    if row.acquire is None or (row.installed and not force):
+        return dict(row.to_dict(), acquired="already installed")
+    if row.kind in ("catalog", "dataset"):
+        registry = _registry(row.kind, cache_root)
+        options = dict(timeout=timeout, show_progress=show_progress)
+        if row.acquire == "download":
+            registry.download(name, row.version, force=force, source_paths=source_paths, **options)
+        else:
+            registry.build(name, row.version, force=force, source_paths=source_paths,
+                           download_options=options)
+    elif row.kind == "reference":
+        from .datasets import DatasetRegistry
+
+        dataset, asset = name.split(":", 1)
+        DatasetRegistry(cache_root=cache_root).download_reference(
+            dataset, row.version, asset_id=asset, force=force, timeout=timeout,
+            show_progress=show_progress)
+    elif row.kind == "genome":
+        from .genomes import install_genome
+
+        install_genome(name, cache_root=cache_root, force=force, source_paths=source_paths,
+                       download_options=dict(timeout=timeout, show_progress=show_progress))
+    elif row.kind == "chain":
+        from .liftover import download_chain, pinned_chains
+
+        chain = next(c for c in pinned_chains() if c.name == name)
+        download_chain(chain.source_build, chain.target_build, species=chain.species,
+                       cache_root=cache_root, force=force, accept_terms=accept_terms,
+                       download_options=dict(timeout=timeout, show_progress=show_progress))
+    elif row.kind == "viral":
+        from .downloads import install_collection
+
+        install_collection(name, cache_root=cache_root, force=force, timeout=timeout)
+    result = _resolve(name, row.kind, row.version, cache_root, False)
+    if not result.installed:
+        raise RuntimeError(f"{name!r} installation finished with status {result.status}")
+    return dict(result.to_dict(), acquired="downloaded" if row.acquire == "download" else "built")

{orfdata-0.41.0 → orfdata-0.42.0}/orfdata/download_cli.py

@@ -1,6 +1,8 @@
 """Discover and acquire ORFdata resources through one command."""
 
 import argparse
+import sys
+from contextlib import redirect_stdout
 
 from .cli_output import print_fields, print_json, print_table
 from .downloads import list_data
@@ -88,6 +90,23 @@ def run(argv=None, prog="orfdata download"):
     status = commands.add_parser("status", help="Show resources already available locally")
     _add_discovery(status, status=True)
 
+    for verb, description in (("info", "Describe a resource's source pins and download/build route"),
+                              ("path", "Print the installed path without downloading"),
+                              ("fetch", "Install named resources, downloading or building as needed")):
+        command = commands.add_parser(verb, help=description)
+        command.add_argument("names", metavar="NAME", nargs="+" if verb == "fetch" else None)
+        command.add_argument("--kind", choices=("viral", "catalog", "dataset", "reference", "genome", "chain"))
+        command.add_argument("--version", help="Exact resource version; defaults to its registered version")
+        _add_cache(command)
+        _add_json(command)
+        if verb == "fetch":
+            _add_force_timeout(command)
+            command.add_argument("--source-path", action="append", default=[], metavar="ASSET=PATH")
+            command.add_argument("--quiet", action="store_true")
+            command.add_argument("--accept-terms", action="store_true")
+        else:
+            command.add_argument("--verify", action="store_true", help="Hash and validate installed files")
+
     viral = commands.add_parser(
         "viral", help="Download the current human-targeted viral collection and paired FASTAs")
     viral.add_argument("--species", default="human",
@@ -167,6 +186,36 @@ def run(argv=None, prog="orfdata download"):
 
     args = parser.parse_args(argv)
     try:
+        if args.command in ("info", "path", "fetch"):
+            from .data_resources import data_info, data_path, fetch_data
+
+            options = dict(kind=args.kind, version=args.version, cache_root=args.cache_root)
+            if args.command == "info":
+                _show_result(data_info(args.names, verify_files=args.verify, **options), args.json)
+            elif args.command == "path":
+                path = str(data_path(args.names, verify_files=args.verify, **options))
+                print_json(dict(path=path)) if args.json else print(path)
+            else:
+                names = list(dict.fromkeys(args.names))
+                if len(names) > 1 and (args.source_path or args.version):
+                    raise ValueError("--source-path and --version require exactly one resource")
+                # Resolve every name and terms requirement before starting any downloads.
+                for name in names:
+                    info = data_info(name, **options)
+                    if info["restricted"] and not args.accept_terms:
+                        raise ValueError(f"{name!r} requires --accept-terms; see 'orfdata data info {name}'")
+                paths = _source_paths(args.source_path, "Source overrides")
+                # Source processors may print progress; keep stdout machine-readable.
+                with redirect_stdout(sys.stderr):
+                    output = [fetch_data(name, **options, force=args.force, source_paths=paths,
+                                         timeout=args.timeout, show_progress=not args.quiet and not args.json,
+                                         accept_terms=args.accept_terms) for name in names]
+                if args.json:
+                    print_json(output)
+                else:
+                    for result in output:
+                        print_fields(result)
+            return
         if args.command in ("list", "status"):
             rows = list_data(
                 kind=args.kind, species=args.species, contexts=args.context,

{orfdata-0.41.0 → orfdata-0.42.0}/orfdata/downloads.py

@@ -1,8 +1,9 @@
 """Discover ORFdata resources and their local installation state."""
 
 from collections.abc import Iterable
-from dataclasses import asdict, dataclass
+from dataclasses import asdict, dataclass, replace
 from os import PathLike
+from shlex import join
 from typing import Optional
 
 from .reference import canonical_species, species_taxon
@@ -48,6 +49,17 @@ def default_collections(species: str | int) -> tuple[str, ...]:
     return tuple(collection.name for collection in viral_collections(species=species))
 
 
+def _fetch_command(row):
+    if row.acquire is None:
+        return None
+    args = ["orfdata", "data", "fetch", row.name, "--kind", row.kind]
+    if row.version is not None:
+        args.extend(["--version", row.version])
+    if row.restricted:
+        args.append("--accept-terms")
+    return join(args)
+
+
 def collection_state(
     name: str,
     *,
@@ -121,13 +133,15 @@ def _viral(cache_root, verify_files):
             path=str(_bundle_path(cache_root, species, collection)),
             origin="download" if status == "available" else None,
             acquire="download",
-            command=f"orfdata download viral --collection {collection.name}",
+            command=None,
         ))
     return tuple(rows)
 
 
 def _catalogs(cache_root, verify_files):
-    from .catalog import catalog_status
+    from importlib.resources import files
+
+    from .catalog import _BUNDLED, catalog_status
     from .catalogs import CatalogRegistry
 
     registry = CatalogRegistry(cache_root=cache_root)
@@ -139,9 +153,6 @@ def _catalogs(cache_root, verify_files):
         else:
             inspection = registry.inspect(item.name, item.version, verify_files=verify_files)
             status = inspection.status
-        command = None
-        if item.acquire is not None:
-            command = f"orfdata download catalog {item.name} --version {item.version}"
         rows.append(DataStatus(
             kind="catalog",
             name=item.name,
@@ -151,10 +162,11 @@ def _catalogs(cache_root, verify_files):
             taxon_ids=(species_taxon(item.species),),
             contexts=(),
             status=status,
-            path=str(inspection.path) if inspection is not None else None,
+            path=(str(inspection.path) if inspection is not None else
+                  str(files("orfdata").joinpath(f"data/{_BUNDLED[item.species, item.genome_build]}/catalog.json.gz"))),
             origin=item.installed if status == "available" else None,
             acquire=item.acquire,
-            command=command,
+            command=None,
         ))
     return tuple(rows)
 
@@ -184,7 +196,7 @@ def _datasets(cache_root, verify_files):
             path=str(inspection.path),
             origin=("download" if published else "build") if inspection.status == "available" else None,
             acquire=acquire,
-            command=f"orfdata download dataset {name} --version {version}",
+            command=None,
         ))
     return tuple(rows)
 
@@ -211,8 +223,7 @@ def _references(cache_root, verify_files):
                 path=str(inspection.path),
                 origin="download" if inspection.status == "available" else None,
                 acquire="download",
-                command=(f"orfdata download reference {manifest.dataset_id} --version {manifest.version} "
-                         f"--reference {spec.reference.key} --asset {spec.source.asset_id}"),
+                command=None,
             ))
     return tuple(rows)
 
@@ -236,7 +247,7 @@ def _genomes(cache_root, verify_files):
             path=str(inspection.path),
             origin="download" if inspection.status == "available" else None,
             acquire="download",
-            command=f"orfdata download genome {genome.name}",
+            command=None,
         ))
     return tuple(rows)
 
@@ -248,7 +259,6 @@ def _chains(cache_root, verify_files):
     for chain in pinned_chains():
         inspection = _chain_registry(chain, cache_root).inspect(
             chain.name, "1", verify_files=verify_files)
-        accept = " --accept-terms" if chain.restricted else ""
         rows.append(DataStatus(
             kind="chain",
             name=chain.name,
@@ -261,8 +271,7 @@ def _chains(cache_root, verify_files):
             path=str(inspection.path),
             origin="download" if inspection.status == "available" else None,
             acquire="download",
-            command=(f"orfdata download chains {chain.source_build} {chain.target_build} "
-                     f"--species {chain.species}{accept}"),
+            command=None,
             restricted=chain.restricted,
         ))
     return tuple(rows)
@@ -327,4 +336,5 @@ def list_data(
                 if predicate(context in row.contexts for context in selected_contexts)]
     if installed is not None:
         rows = [row for row in rows if row.installed is installed]
-    return tuple(sorted(rows, key=lambda row: (row.kind, row.name, row.version or "")))
+    return tuple(replace(row, command=_fetch_command(row)) for row in
+                 sorted(rows, key=lambda row: (row.kind, row.name, row.version or "")))

{orfdata-0.41.0 → orfdata-0.42.0}/orfdata/genomes.py

@@ -65,7 +65,7 @@ def _registry(genome, cache_root):
         store_path=lambda name, version: get_data_dir(cache_root) / "genomes" / name / _digest(assets))
 
 
-def install_genome(name, *, force=False, source_paths=None, cache_root=None):
+def install_genome(name, *, force=False, source_paths=None, cache_root=None, download_options=None):
     """Download a pinned annotation, check each file's size and SHA-256, and index it for PyEnsembl.
 
     ``source_paths`` maps ``"gtf"``, ``"transcripts"`` or ``"proteins"`` to
@@ -79,7 +79,8 @@ def install_genome(name, *, force=False, source_paths=None, cache_root=None):
         if unknown:
             raise ValueError(f"Unknown genome files {sorted(unknown)}; use {', '.join(_ROLES)}")
         paths = {_files(genome)[role]: str(path) for role, path in source_paths.items()}
-    _registry(genome, cache_root).download(genome.name, "1", force=force, source_paths=paths)
+    _registry(genome, cache_root).download(genome.name, "1", force=force, source_paths=paths,
+                                         **(download_options or {}))
     return _open(genome, cache_root, rebuild=force)
 
 

orfdata-0.42.0/orfdata/version.py

@@ -0,0 +1 @@
+__version__ = "0.42.0"

{orfdata-0.41.0 → orfdata-0.42.0/orfdata.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orfdata
-Version: 0.41.0
+Version: 0.42.0
 Summary: Reference proteomes with evidence-backed noncanonical ORFs on PyEnsembl genomes
 Author: OpenVax
 License-Expression: Apache-2.0
@@ -64,10 +64,18 @@ normalized sources do not need it.
 List every bundled, downloadable or buildable resource and what is installed:
 
 ```sh
-orfdata download list
-orfdata download status
+orfdata data list
+orfdata data status
+orfdata data info pfizer-atlas-dog-peptide-evidence
+orfdata data fetch pfizer-atlas-dog-peptide-evidence
+orfdata data path pfizer-atlas-dog-peptide-evidence
 ```
 
+`data fetch NAME` downloads a published artifact or builds from pinned sources
+when no artifact is distributed. The same command handles optional catalogues
+such as `openprot-mouse` and datasets such as `peptideatlas-dog-peptides`.
+`downloads` and `download` are aliases for `data`; `info` and `path` stay offline.
+
 `orfdata setup --species human` also installs `gdc-viruses`, the default
 200-reference GDC viral screen for human transcriptome analysis;
 `--collections none` skips it. Viral support is part of the base install, and

{orfdata-0.41.0 → orfdata-0.42.0}/orfdata.egg-info/SOURCES.txt

@@ -10,6 +10,7 @@ test.sh
 docs/catalogs.md
 docs/copy-yeast.md
 docs/coverage.md
+docs/dog-data-sources.md
 docs/dog-peptides.md
 docs/downloads.md
 docs/downstream.md
@@ -41,6 +42,7 @@ orfdata/catalog_manifest.py
 orfdata/catalogs.py
 orfdata/cli.py
 orfdata/cli_output.py
+orfdata/data_resources.py
 orfdata/dataset.py
 orfdata/dataset_cli.py
 orfdata/datasets.py
@@ -130,6 +132,7 @@ tests/test_artifact_archives.py
 tests/test_catalog_registry.py
 tests/test_copy.py
 tests/test_cross_reference_pairing.py
+tests/test_data_resources.py
 tests/test_dog_export_read_ahead.py
 tests/test_dog_ncorf_search.py
 tests/test_dog_peptides.py