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Update docs to generalize from DANDI Archive to DANDI instance #1548

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merged 6 commits into from
Dec 19, 2024
Merged

Update docs to generalize from DANDI Archive to DANDI instance #1548

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010cef9
Update to generalize docs from `DANDI Archive` to `DANDI instance`
kabilar Dec 10, 2024
19327dd
Fix syntax
kabilar Dec 10, 2024
7c25f82
Fix linting error
kabilar Dec 10, 2024
efb0b65
Fix linting error
kabilar Dec 10, 2024
bf04f1a
Update dandi/dandiapi.py
kabilar Dec 13, 2024
3d175a7
Update README.md
kabilar Dec 13, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/test.yml
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Expand Up @@ -110,7 +110,7 @@ jobs:
do python "$f"
done
- name: Run Dandi API tests only
- name: Run DANDI API tests only
if: matrix.mode == 'dandi-api'
run: |
export DANDI_TESTS_AUDIT_CSV=/tmp/audit.csv
Expand Down
14 changes: 7 additions & 7 deletions README.md
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Expand Up @@ -14,9 +14,9 @@ The [DANDI Python client](https://pypi.org/project/dandi/) allows you to:
* Validate data to locally conform to standards
* Organize your data locally before upload
* Upload `Dandisets`
* Interact with the DANDI archive's web API from Python
* Delete data in the DANDI archive
* Perform other auxiliary operations with data or the DANDI archive
* Interact with the DANDI instance's web API from Python
* Delete data in the DANDI instance
* Perform other auxiliary operations with data on the DANDI instance

**Note**: This project is under heavy development. See [the issues log](https://github.com/dandi/dandi-cli/issues) or
[Work-in-Progress (WiP)](https://github.com/dandi/dandi-cli/pulls).
Expand All @@ -37,14 +37,14 @@ or
## CLI Tool

This package provides a command line utility with a basic interface
to help you prepare and upload your data to, or obtain data from, the [DANDI archive](http://dandiarchive.org).
to help you prepare and upload your data to, or obtain data from, a DANDI instance such as the [DANDI Archive](http://dandiarchive.org).


```bash
$> dandi
Usage: dandi [OPTIONS] COMMAND [ARGS]...

A client to support interactions with DANDI archive
A client to support interactions with a DANDI instance, such as the DANDI Archive
(http://dandiarchive.org).

To see help for a specific command, run
Expand All @@ -65,7 +65,7 @@ Commands:
delete Delete dandisets and assets from the server.
digest Calculate file digests
download Download a file or entire folder from DANDI.
instances List known Dandi Archive instances that the CLI can...
instances List known DANDI instances that the CLI can interact
ls List .nwb files and dandisets metadata.
move Move or rename assets in a local Dandiset and/or on...
organize (Re)organize NWB files according to their metadata.
Expand All @@ -77,7 +77,7 @@ Run `dandi --help` or `dandi <subcommand> --help` (e.g. `dandi upload --help`) t

## Resources

* To learn how to interact with the DANDI archive and for examples on how to use the DANDI Client in various use cases,
* To learn how to interact with the DANDI Archive and for examples on how to use the DANDI Client in various use cases,
see [the handbook](https://www.dandiarchive.org/handbook/)
(specifically the sections on using the CLI to
[download](https://www.dandiarchive.org/handbook/12_download/) and
Expand Down
2 changes: 1 addition & 1 deletion dandi/cli/cmd_instances.py
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Expand Up @@ -11,7 +11,7 @@
@click.command()
@map_to_click_exceptions
def instances():
"""List known Dandi Archive instances that the CLI can interact with"""
"""List known DANDI instances that the CLI can interact with"""
yaml = ruamel.yaml.YAML(typ="safe")
yaml.default_flow_style = False
instances = {}
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3 changes: 2 additions & 1 deletion dandi/cli/command.py
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Expand Up @@ -70,7 +70,8 @@ def print_version(ctx, param, value):
@click.option("--pdb", help="Fall into pdb if errors out", is_flag=True)
@click.pass_context
def main(ctx, log_level, pdb=False):
"""A client to support interactions with DANDI archive (http://dandiarchive.org).
"""A client to support interactions with DANDI instances, such as the DANDI
Archive (http://dandiarchive.org).
To see help for a specific command, run
Expand Down
4 changes: 2 additions & 2 deletions dandi/cli/tests/data/update_dandiset_from_doi/biorxiv.json
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Expand Up @@ -13,13 +13,13 @@
],
"version": "draft",
"@context": "https://raw.githubusercontent.com/dandi/schema/master/releases/0.6.4/context.json",
"citation": "Aguillon-Rodriguez, Valeria; Angelaki, Dora E.; Bayer, Hannah M.; Bonacchi, Niccol\u00f2; Carandini, Matteo; Cazettes, Fanny; Chapuis, Gaelle A.; Churchland, Anne K.; Dan, Yang; Dewitt, Eric E. J.; Faulkner, Mayo; Forrest, Hamish; Haetzel, Laura M.; Hausser, Michael; Hofer, Sonja B.; Hu, Fei; Khanal, Anup; Krasniak, Christopher S.; Laranjeira, In\u00eas; Mainen, Zachary F.; Meijer, Guido T.; Miska, Nathaniel J.; Mrsic-Flogel, Thomas D.; Murakami, Masayoshi; Noel, Jean-Paul; Pan-Vazquez, Alejandro; Rossant, Cyrille; Sanders, Joshua I.; Socha, Karolina Z.; Terry, Rebecca; Urai, Anne E.; Vergara, Hernando M.; Wells, Miles J.; Wilson, Christian J.; Witten, Ilana B.; Wool, Lauren E.; Zador, Anthony (2023) Standardized and reproducible measurement of decision-making in mice (Version draft) [Data set]. DANDI archive. http://localhost:8085/dandiset/000001/draft",
"citation": "Aguillon-Rodriguez, Valeria; Angelaki, Dora E.; Bayer, Hannah M.; Bonacchi, Niccol\u00f2; Carandini, Matteo; Cazettes, Fanny; Chapuis, Gaelle A.; Churchland, Anne K.; Dan, Yang; Dewitt, Eric E. J.; Faulkner, Mayo; Forrest, Hamish; Haetzel, Laura M.; Hausser, Michael; Hofer, Sonja B.; Hu, Fei; Khanal, Anup; Krasniak, Christopher S.; Laranjeira, In\u00eas; Mainen, Zachary F.; Meijer, Guido T.; Miska, Nathaniel J.; Mrsic-Flogel, Thomas D.; Murakami, Masayoshi; Noel, Jean-Paul; Pan-Vazquez, Alejandro; Rossant, Cyrille; Sanders, Joshua I.; Socha, Karolina Z.; Terry, Rebecca; Urai, Anne E.; Vergara, Hernando M.; Wells, Miles J.; Wilson, Christian J.; Witten, Ilana B.; Wool, Lauren E.; Zador, Anthony (2023) Standardized and reproducible measurement of decision-making in mice (Version draft) [Data set]. DANDI Archive. http://localhost:8085/dandiset/000001/draft",
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those are coming from dandi-archive

❯ git grep 'DANDI archive'
dandiapi/api/models/version.py:        citation = f'{name} ({year}). (Version {version}) [Data set]. DANDI archive. {url}'
dandiapi/api/models/version.py:                    f'{cl} ({year}) {name} (Version {version}) [Data set]. DANDI archive. {url}'
...

there should be a "satellite" PR there to likely preceed these changes or we should improve testing here to allow for flexibility (didn't look ATM) but these are the cause of failing tests ATM e.g. https://github.com/dandi/dandi-cli/actions/runs/12262974763/job/34213512790?pr=1548#step:8:25905

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do you think you could remove those changes in the tests for now so we could not delay accepting major portion of the changes @kabilar to not breed conflicts etc?

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Hi @yarikoptic, I just created dandi/dandi-archive#2114.

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it was merged now, so we should be all set here. I will retrigger tests to see if all good (frankly I don't remember if we need release of archive first) and then we could proceed

"schemaKey": "Dandiset",
"identifier": "DANDI:000001",
"repository": "http://localhost:8085",
"contributor": [
{
"name": "Tests, Dandi-Cli",
"name": "Tests, DANDI-Cli",
"email": "[email protected]",
"roleName": [
"dcite:Author",
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4 changes: 2 additions & 2 deletions dandi/cli/tests/data/update_dandiset_from_doi/elife.json
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Expand Up @@ -13,13 +13,13 @@
],
"version": "draft",
"@context": "https://raw.githubusercontent.com/dandi/schema/master/releases/0.6.4/context.json",
"citation": "Chowdhury, Raeed H; Glaser, Joshua I; Miller, Lee E (2023) Area 2 of primary somatosensory cortex encodes kinematics of the whole arm (Version draft) [Data set]. DANDI archive. http://localhost:8085/dandiset/000004/draft",
"citation": "Chowdhury, Raeed H; Glaser, Joshua I; Miller, Lee E (2023) Area 2 of primary somatosensory cortex encodes kinematics of the whole arm (Version draft) [Data set]. DANDI Archive. http://localhost:8085/dandiset/000004/draft",
"schemaKey": "Dandiset",
"identifier": "DANDI:000004",
"repository": "http://localhost:8085",
"contributor": [
{
"name": "Tests, Dandi-Cli",
"name": "Tests, DANDI-Cli",
"email": "[email protected]",
"roleName": [
"dcite:Author",
Expand Down
4 changes: 2 additions & 2 deletions dandi/cli/tests/data/update_dandiset_from_doi/jneurosci.json
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Expand Up @@ -13,13 +13,13 @@
],
"version": "draft",
"@context": "https://raw.githubusercontent.com/dandi/schema/master/releases/0.6.4/context.json",
"citation": "Ito, Makoto; Doya, Kenji (2023) Validation of Decision-Making Models and Analysis of Decision Variables in the Rat Basal Ganglia (Version draft) [Data set]. DANDI archive. http://localhost:8085/dandiset/000002/draft",
"citation": "Ito, Makoto; Doya, Kenji (2023) Validation of Decision-Making Models and Analysis of Decision Variables in the Rat Basal Ganglia (Version draft) [Data set]. DANDI Archive. http://localhost:8085/dandiset/000002/draft",
"schemaKey": "Dandiset",
"identifier": "DANDI:000002",
"repository": "http://localhost:8085",
"contributor": [
{
"name": "Tests, Dandi-Cli",
"name": "Tests, DANDI-Cli",
"email": "[email protected]",
"roleName": [
"dcite:Author",
Expand Down
4 changes: 2 additions & 2 deletions dandi/cli/tests/data/update_dandiset_from_doi/nature.json
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Expand Up @@ -13,13 +13,13 @@
],
"version": "draft",
"@context": "https://raw.githubusercontent.com/dandi/schema/master/releases/0.6.4/context.json",
"citation": "Sit, Kevin K.; Goard, Michael J. (2023) Coregistration of heading to visual cues in retrosplenial cortex (Version draft) [Data set]. DANDI archive. http://localhost:8085/dandiset/000005/draft",
"citation": "Sit, Kevin K.; Goard, Michael J. (2023) Coregistration of heading to visual cues in retrosplenial cortex (Version draft) [Data set]. DANDI Archive. http://localhost:8085/dandiset/000005/draft",
"schemaKey": "Dandiset",
"identifier": "DANDI:000005",
"repository": "http://localhost:8085",
"contributor": [
{
"name": "Tests, Dandi-Cli",
"name": "Tests, DANDI-Cli",
"email": "[email protected]",
"roleName": [
"dcite:Author",
Expand Down
4 changes: 2 additions & 2 deletions dandi/cli/tests/data/update_dandiset_from_doi/neuron.json
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Expand Up @@ -13,13 +13,13 @@
],
"version": "draft",
"@context": "https://raw.githubusercontent.com/dandi/schema/master/releases/0.6.4/context.json",
"citation": "Tingley, David; Buzs\u00e1ki, Gy\u00f6rgy (2023) Routing of Hippocampal Ripples to Subcortical Structures via the Lateral Septum (Version draft) [Data set]. DANDI archive. http://localhost:8085/dandiset/000003/draft",
"citation": "Tingley, David; Buzs\u00e1ki, Gy\u00f6rgy (2023) Routing of Hippocampal Ripples to Subcortical Structures via the Lateral Septum (Version draft) [Data set]. DANDI Archive. http://localhost:8085/dandiset/000003/draft",
"schemaKey": "Dandiset",
"identifier": "DANDI:000003",
"repository": "http://localhost:8085",
"contributor": [
{
"name": "Tests, Dandi-Cli",
"name": "Tests, DANDI-Cli",
"email": "[email protected]",
"roleName": [
"dcite:Author",
Expand Down
2 changes: 1 addition & 1 deletion dandi/conftest.py
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Expand Up @@ -10,7 +10,7 @@ def pytest_addoption(parser: Parser) -> None:
"--dandi-api",
action="store_true",
default=False,
help="Only run tests of the new Django Dandi API",
help="Only run tests of the new Django DANDI API",
)
parser.addoption(
"--scheduled",
Expand Down
18 changes: 9 additions & 9 deletions dandi/dandiapi.py
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Expand Up @@ -397,7 +397,7 @@ def get_page(pageno: int) -> list:


class DandiAPIClient(RESTFullAPIClient):
"""A client for interacting with a Dandi Archive server"""
"""A client for interacting with a DANDI API server"""

def __init__(
self,
Expand All @@ -406,7 +406,7 @@ def __init__(
dandi_instance: DandiInstance | None = None,
) -> None:
"""
Construct a client instance for the given API URL or Dandi instance
Construct a client instance for the given API URL or DANDI instance
(mutually exclusive options). If no URL or instance is supplied, the
instance specified by the :envvar:`DANDI_INSTANCE` environment variable
(default value: ``"dandi"``) is used.
Expand Down Expand Up @@ -442,7 +442,7 @@ def for_dandi_instance(
) -> DandiAPIClient:
"""
Construct a client instance for the server identified by ``instance``
(either the name of a registered Dandi Archive instance or a
(either the name of a registered DANDI instance or a
`DandiInstance` instance) and an optional authentication token/API key.
If no token is supplied and ``authenticate`` is true,
`dandi_authenticate()` is called on the instance before returning it.
Expand Down Expand Up @@ -638,7 +638,7 @@ def create_dandiset(

def check_schema_version(self, schema_version: str | None = None) -> None:
"""
Confirms that the server is using the same version of the Dandi schema
Confirms that the server is using the same version of the DANDI schema
as the client. If it is not, a `SchemaVersionError` is raised.

:param schema_version: the schema version to confirm that the server
Expand Down Expand Up @@ -889,7 +889,7 @@ def draft_version(self) -> Version:
@property
def api_path(self) -> str:
"""
The path (relative to the base endpoint for a Dandi Archive API) at
The path (relative to the base endpoint for the DANDI API) at
which API requests for interacting with the Dandiset itself are made
"""
return f"/dandisets/{self.identifier}/"
Expand All @@ -905,7 +905,7 @@ def api_url(self) -> str:
@property
def version_api_path(self) -> str:
"""
The path (relative to the base endpoint for a Dandi Archive API) at
The path (relative to the base endpoint for the DANDI API) at
which API requests for interacting with the version in question of the
Dandiset are made
"""
Expand Down Expand Up @@ -1429,7 +1429,7 @@ def from_base_data(
@property
def api_path(self) -> str:
"""
The path (relative to the base endpoint for a Dandi Archive API) at
The path (relative to the base endpoint for the DANDI API) at
which API requests for interacting with the asset itself are made
"""
return f"/assets/{self.identifier}/"
Expand Down Expand Up @@ -1639,7 +1639,7 @@ def digest_type(self) -> models.DigestType:
"""
.. versionadded:: 0.36.0

The primary digest algorithm used by Dandi Archive for the asset,
The primary digest algorithm used by DANDI for the asset,
determined based on its underlying data: dandi-etag for blob resources,
dandi-zarr-checksum for Zarr resources
"""
Expand Down Expand Up @@ -1825,7 +1825,7 @@ def from_data(
@property
def api_path(self) -> str:
"""
The path (relative to the base endpoint for a Dandi Archive API) at
The path (relative to the base endpoint for the DANDI API) at
which API requests for interacting with the asset itself are made
"""
return f"/dandisets/{self.dandiset_id}/versions/{self.version_id}/assets/{self.identifier}/"
Expand Down
12 changes: 6 additions & 6 deletions dandi/dandiarchive.py
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@@ -1,6 +1,6 @@
"""
This module provides functionality for parsing URLs and other resource
identifiers for Dandisets & assets on Dandi Archive servers and for fetching
identifiers for Dandisets & assets on DANDI instances and for fetching
the objects to which the URLs refer. See :ref:`resource_ids` for a list of
accepted URL formats.

Expand All @@ -9,7 +9,7 @@
Dandiset and/or assets specified in the URL. Call an instance's
`~ParsedDandiURL.get_dandiset()` and/or `~ParsedDandiURL.get_assets()` to get
the assets, passing in a `~dandi.dandiapi.DandiAPIClient` for the appropriate
Dandi Archive API instance; an unauthenticated client pointing to the correct
DANDI API instance; an unauthenticated client pointing to the correct
instance can be acquired via the `~ParsedDandiURL.get_client()` method. As a
convenience, one can acquire a client, the Dandiset, and an iterator of all
assets by using the `~ParsedDandiAPI.navigate()` context manager like so:
Expand Down Expand Up @@ -59,7 +59,7 @@
@dataclass
class ParsedDandiURL(ABC):
"""
Parsed representation of a URL pointing to a Dandi Archive resource
Parsed representation of a URL pointing to a DANDI resource
(Dandiset or asset(s)). Subclasses must implement `get_assets()`.

Most methods take a ``client: DandiAPIClient`` argument, which must be a
Expand All @@ -69,7 +69,7 @@ class ParsedDandiURL(ABC):
passed instead.
"""

#: The Dandi Archive instance that the URL points to
#: The DANDI instance that the URL points to
instance: DandiInstance
#: The ID of the Dandiset given in the URL
dandiset_id: str | None
Expand All @@ -80,7 +80,7 @@ class ParsedDandiURL(ABC):

@property
def api_url(self) -> AnyHttpUrl:
"""The base URL of the Dandi API service, without a trailing slash"""
"""The base URL of the DANDI API service, without a trailing slash"""
# Kept for backwards compatibility
adapter = TypeAdapter(AnyHttpUrl)
return adapter.validate_python(self.instance.api.rstrip("/"))
Expand Down Expand Up @@ -717,7 +717,7 @@ def parse(
cls, url: str, *, map_instance: bool = True, glob: bool = False
) -> ParsedDandiURL:
"""
Parse a Dandi Archive URL and return a `ParsedDandiURL` instance. See
Parse a DANDI instance URL and return a `ParsedDandiURL` instance. See
:ref:`resource_ids` for the supported URL formats.

.. versionadded:: 0.54.0
Expand Down
2 changes: 1 addition & 1 deletion dandi/delete.py
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Expand Up @@ -126,7 +126,7 @@ def register_url(self, url: str) -> None:
if isinstance(parsed_url, DandisetURL):
if parsed_url.version_id is not None:
raise NotImplementedError(
"Dandi API server does not support deletion of individual"
"DANDI API server does not support deletion of individual"
" versions of a dandiset"
)
assert parsed_url.dandiset_id is not None
Expand Down
2 changes: 1 addition & 1 deletion dandi/download.py
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Expand Up @@ -262,7 +262,7 @@ def download_generator(self) -> Iterator[dict]:

This function is a generator which yields records on ongoing
activities. Activities include traversal of the remote resource (DANDI
archive), download of individual assets while yielding records (TODO:
Archive), download of individual assets while yielding records (TODO:
schema) while validating their checksums "on the fly", etc.
"""

Expand Down
2 changes: 1 addition & 1 deletion dandi/exceptions.py
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Expand Up @@ -14,7 +14,7 @@ class OrganizeImpossibleError(ValueError):


class UnknownURLError(ValueError):
"""Given url is not known to correspond to DANDI archive schema(s)"""
"""Given url is not known to correspond to DANDI schema(s)"""

pass

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2 changes: 1 addition & 1 deletion dandi/files/__init__.py
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Expand Up @@ -183,7 +183,7 @@
dandiset_path = Path(dandiset_path)
path = filepath.relative_to(dandiset_path).as_posix()
if path == ".":
raise ValueError("Dandi file path cannot equal Dandiset path")
raise ValueError("DANDI file path cannot equal Dandiset path")

Check warning on line 186 in dandi/files/__init__.py

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dandi/files/__init__.py#L186 

Added line #L186 was not covered by tests
else:
path = filepath.name
if filepath.is_file() and path == dandiset_metadata_file:
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4 changes: 2 additions & 2 deletions dandi/files/bases.py
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Expand Up @@ -71,7 +71,7 @@ def get_metadata(
digest: Digest | None = None,
ignore_errors: bool = True,
) -> CommonModel:
"""Return the Dandi metadata for the file"""
"""Return the DANDI metadata for the file"""
...

@abstractmethod
Expand Down Expand Up @@ -165,7 +165,7 @@ def get_metadata(
digest: Digest | None = None,
ignore_errors: bool = True,
) -> BareAsset:
"""Return the Dandi metadata for the asset"""
"""Return the DANDI metadata for the asset"""
...

# TODO: @validate_cache.memoize_path
Expand Down
4 changes: 2 additions & 2 deletions dandi/files/zarr.py
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Expand Up @@ -95,7 +95,7 @@ def iterdir(self) -> Iterator[LocalZarrEntry]:
def get_digest(self) -> Digest:
"""
Calculate the DANDI etag digest for the entry. If the entry is a
directory, the algorithm will be the Dandi Zarr checksum algorithm; if
directory, the algorithm will be the DANDI Zarr checksum algorithm; if
it is a file, it will be MD5.
"""
# Avoid heavy import by importing within function:
Expand Down Expand Up @@ -132,7 +132,7 @@ class ZarrStat:

#: The total size of the asset
size: int
#: The Dandi Zarr checksum of the asset
#: The DANDI Zarr checksum of the asset
digest: Digest
#: A list of all files in the asset in unspecified order
files: list[LocalZarrEntry]
Expand Down
2 changes: 1 addition & 1 deletion dandi/organize.py
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Expand Up @@ -1123,7 +1123,7 @@ def validate_organized_path(
severity=Severity.ERROR,
scope=Scope.FILE,
path=filepath,
message="Filename does not conform to Dandi standard",
message="Filename does not conform to DANDI standard",
path_regex=ORGANIZED_FILENAME_REGEX,
dandiset_path=dandiset_path,
)
Expand Down
2 changes: 1 addition & 1 deletion dandi/tests/fixtures.py
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Expand Up @@ -585,7 +585,7 @@ def mkdandiset(self, name: str, embargo: bool = False) -> SampleDandiset:
"contributor": [
{
"schemaKey": "Person",
"name": "Tests, Dandi-Cli",
"name": "Tests, DANDI-Cli",
"email": "[email protected]",
"roleName": ["dcite:Author", "dcite:ContactPerson"],
}
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2 changes: 1 addition & 1 deletion dandi/tests/test_delete.py
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Expand Up @@ -398,7 +398,7 @@ def test_delete_version(
force=True,
)
assert str(excinfo.value) == (
"Dandi API server does not support deletion of individual versions of a"
"DANDI API server does not support deletion of individual versions of a"
" dandiset"
)
delete_spy.assert_not_called()
Expand Down
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