feat: add functions for project-dataset operations #82
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| function _close_dataset_version( | ||
| auth::Authentication, dataset_uuid::UUID, upload_config; local_path | ||
| )::_RESTResponse |
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| @@ -11,7 +11,7 @@ import SHA | |||
| import TimeZones | |||
| import TOML | |||
| import URIs | |||
| import UUIDs | |||
| using UUIDs: UUIDs, UUID | |||
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| function _close_dataset_version( | ||
| name, upload_config; local_path=nothing, auth::Authentication=__auth__() | ||
| auth::Authentication, name, upload_config; local_path=nothing | ||
| )::_RESTResponse |
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Always include a trailing comma when working with arrays, tuples or
functions arguments that span multiple lines. This allows future edits to
easily move around or add additional elements.
The trailing comma shouldn't be written when the collection is in a single line.
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| Presently, you can specify the project by directly passing the project UUID. | ||
| The UUID should be either a string (`<: AbstractString`) or an `UUIDs.UUID` object. | ||
| """ | ||
| const ProjectReference = Union{AbstractString, UUIDs.UUID} |
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| maxcount::Integer = $(_DEFAULT_authenticate_maxcount), | ||
| [project::Union{AbstractString, UUIDs.UUID, Nothing}], |
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When writing arrays that span multiple lines, the opening bracket should
not be on a separate line, and the indentation of the closing bracket
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| function _open_dataset_version( | ||
| auth::Authentication, dataset_uuid::UUID, project_uuid::UUID | ||
| )::_RESTResponse |
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functions arguments that span multiple lines. This allows future edits to
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| function _normalize_project( | ||
| project::Union{AbstractString, UUIDs.UUID, Nothing, Missing} | ||
| )::Union{UUID, Nothing} |
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functions arguments that span multiple lines. This allows future edits to
easily move around or add additional elements.
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src/datasets.jl
Outdated
| const _DOCS_nondynamic_datasets_object_warning = """ | ||
| !!! warning "Non-dynamic dataset objects" | ||
|
|
||
| [`Dataset`](@ref) objects represents the dataset metadata when the Julia object was created | ||
| (e.g. with [`dataset`](@ref)), and are not automatically kept up to date. To refresh the dataset | ||
| metadata, you can pass the existing [`Dataset`](@ref) to [`JuliaHub.dataset`](@ref). | ||
| [`Dataset`](@ref) and [`ProjectDataset`](@ref) objects represents the dataset metadata when the | ||
| Julia object was created (e.g. with [`dataset`](@ref)), and are not automatically kept up to date. | ||
| To refresh the dataset metadata, you can pass the existing [`Dataset`](@ref) to [`JuliaHub.dataset`](@ref), | ||
| or [`ProjectDataset`](@ref) to [`project_dataset`](@ref). | ||
| """ |
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|
Semgrep found 21
Avoid unnecessary whitespace padding inside brackets. Semgrep found 10
Block-form functions should explicity return a value. If no meaningful Semgrep found 8
Functions signatures with parameters that together exceed 92 characters should be Semgrep found 1 Functions signatures that span multiple lines should indent each parameter line by one level. Semgrep found 1 Global variables should be avoided whenever possible. When required, global variables should have an all uppercase name separated with underscores. |
mortenpi
changed the title
| function _parse_dataset_list( | ||
| datasets::Vector; | ||
| username::Union{AbstractString, Nothing}=nothing, | ||
| expected_project::Union{UUIDs.UUID, Nothing}=nothing, | ||
| )::Vector{Dataset} |
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Functions signatures with parameters that together exceed 92 characters should be
split so each parameter is in a separate line.
Why this might be safe to ignore:
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| InvalidRequestError( | ||
| "Local data type ($expected_dtype) does not match existing dataset dtype $(upload_config["dataset_type"])" |
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Avoid unnecessary whitespace padding inside brackets.
Why this might be safe to ignore:
The match is triggered by multi-line formatting in a legitimate function call rather than actual unnecessary padding; fixing it wouldn't meaningfully improve code quality.
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| function Base.show(io::IO, ::MIME"text/plain", d::Dataset) | ||
| printstyled(io, "Dataset:"; bold=true) | ||
| print(io, " ", d.name, " (", d.dtype, ")") |
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Semgrep identified an issue in your code:
Block-form functions should explicity return a value. If no meaningful
value is returned, explicity write return nothing instead.
To resolve this comment:
✨ Commit Assistant fix suggestion
| function Base.show(io::IO, ::MIME"text/plain", d::Dataset) | |
| printstyled(io, "Dataset:"; bold=true) | |
| print(io, " ", d.name, " (", d.dtype, ")") | |
| function Base.show(io::IO, ::MIME"text/plain", d::Dataset) | |
| printstyled(io, "Dataset:"; bold=true) | |
| print(io, " ", d.name, " (", d.dtype, ")") | |
| print(io, "\n owner: ", d.owner) | |
| print(io, "\n description: ", d.description) | |
| print(io, "\n versions: ", length(d.versions)) | |
| print(io, "\n size: ", d.size, " bytes") | |
| isempty(d.tags) || print(io, "\n tags: ", join(d.tags, ", ")) | |
| if !isnothing(d.project) | |
| print( | |
| io, | |
| "\n project: ", d.project.uuid, " ", | |
| d.project.is_writable ? "(writable)" : "(not writable)", | |
| ) | |
| end | |
| return nothing # Explicitly indicate no meaningful value is returned | |
| end |
View step-by-step instructions
- Locate the
Base.showfunction definition forMIME"text/plain"in your code. - Add a
return nothingstatement at the end of the function to explicitly indicate that the function does not return a meaningful value. This should be placed after the lastprintstatement.
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| _get_json(project_json, "project_id", String; msg=".project") | ||
| ) |
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Semgrep identified an issue in your code:
Avoid unnecessary whitespace padding inside brackets.
To resolve this comment:
✨ Commit Assistant fix suggestion
| _get_json(project_json, "project_id", String; msg=".project") | |
| ) | |
| project_json_uuid = UUIDs.UUID(_get_json(project_json, "project_id", String; msg=".project")) |
View step-by-step instructions
- Remove the unnecessary whitespace inside the brackets in the code line
project_json_uuid = UUIDs.UUID( _get_json(project_json, "project_id", String; msg=".project") ). - Update the line to
project_json_uuid = UUIDs.UUID(_get_json(project_json, "project_id", String; msg=".project")).
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| function Base.show(io::IO, d::Dataset) | ||
| print(io, "JuliaHub.dataset((\"", d.owner, "\", \"", d.name, "\"))") | ||
| dsref = string("(\"", d.owner, "\", \"", d.name, "\")") | ||
| if isnothing(d.project) | ||
| print(io, "JuliaHub.dataset(", dsref, ")") | ||
| else | ||
| print(io, "JuliaHub.project_dataset(", dsref, "; project=", d.project.uuid, ")") |
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Semgrep identified an issue in your code:
Block-form functions should explicity return a value. If no meaningful
value is returned, explicity write return nothing instead.
To resolve this comment:
✨ Commit Assistant fix suggestion
| function Base.show(io::IO, d::Dataset) | |
| print(io, "JuliaHub.dataset((\"", d.owner, "\", \"", d.name, "\"))") | |
| dsref = string("(\"", d.owner, "\", \"", d.name, "\")") | |
| if isnothing(d.project) | |
| print(io, "JuliaHub.dataset(", dsref, ")") | |
| else | |
| print(io, "JuliaHub.project_dataset(", dsref, "; project=", d.project.uuid, ")") | |
| function Base.show(io::IO, d::Dataset) | |
| dsref = string("(\"", d.owner, "\", \"", d.name, "\")") | |
| if isnothing(d.project) | |
| print(io, "JuliaHub.dataset(", dsref, ")") | |
| else | |
| print(io, "JuliaHub.project_dataset(", dsref, "; project=", d.project.uuid, ")") | |
| end | |
| return nothing | |
| end |
View step-by-step instructions
- Add an explicit return statement at the end of the
Base.showfunction. - Since the function does not return any meaningful value, use
return nothingto indicate this.
The updated function should look like this:
function Base.show(io::IO, d::Dataset)
dsref = string("(\"", d.owner, "\", \"", d.name, "\")")
if isnothing(d.project)
print(io, "JuliaHub.dataset(", dsref, ")")
else
print(io, "JuliaHub.project_dataset(", dsref, "; project=", d.project.uuid, ")")
end
return nothing
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| function Dataset(d::Dict; expected_project::Union{UUIDs.UUID, Nothing}=nothing) | ||
| owner = d["owner"]["username"] | ||
| name = d["name"] | ||
| versions_json = _get_json_or(d, "versions", Vector, []) | ||
| versions = sort([DatasetVersion(json; owner, name) for json in versions_json]; by=dsv -> dsv.id) | ||
| project = if !isnothing(expected_project) | ||
| project_json = _get_json(d, "project", Dict) | ||
| project_json_uuid = UUIDs.UUID( | ||
| _get_json(project_json, "project_id", String; msg=".project") | ||
| ) | ||
| if project_json_uuid != expected_project | ||
| msg = "Project UUID mismatch in dataset response: $(project_json_uuid), requested $(project)" | ||
| throw(JuliaHubError(msg)) | ||
| end | ||
| is_writable = _get_json( | ||
| project_json, | ||
| "is_writable", | ||
| Bool; | ||
| msg="Unable to parse .project in /datasets?project response", | ||
| ) | ||
| DatasetProjectLink(project_json_uuid, is_writable) | ||
| else | ||
| nothing | ||
| end | ||
| Dataset(; | ||
| uuid=UUIDs.UUID(d["id"]), | ||
| name, owner, versions, | ||
| dtype=d["type"], | ||
| description=d["description"], | ||
| size=d["size"], | ||
| tags=d["tags"], | ||
| project=project, | ||
| _downloadURL=d["downloadURL"], | ||
| _last_modified=_nothing_or(d["lastModified"]) do last_modified | ||
| datetime_utc = Dates.DateTime( |
There was a problem hiding this comment.
Semgrep identified an issue in your code:
Block-form functions should explicity return a value. If no meaningful
value is returned, explicity write return nothing instead.
To resolve this comment:
✨ Commit Assistant fix suggestion
| function Dataset(d::Dict; expected_project::Union{UUIDs.UUID, Nothing}=nothing) | |
| owner = d["owner"]["username"] | |
| name = d["name"] | |
| versions_json = _get_json_or(d, "versions", Vector, []) | |
| versions = sort([DatasetVersion(json; owner, name) for json in versions_json]; by=dsv -> dsv.id) | |
| project = if !isnothing(expected_project) | |
| project_json = _get_json(d, "project", Dict) | |
| project_json_uuid = UUIDs.UUID( | |
| _get_json(project_json, "project_id", String; msg=".project") | |
| ) | |
| if project_json_uuid != expected_project | |
| msg = "Project UUID mismatch in dataset response: $(project_json_uuid), requested $(project)" | |
| throw(JuliaHubError(msg)) | |
| end | |
| is_writable = _get_json( | |
| project_json, | |
| "is_writable", | |
| Bool; | |
| msg="Unable to parse .project in /datasets?project response", | |
| ) | |
| DatasetProjectLink(project_json_uuid, is_writable) | |
| else | |
| nothing | |
| end | |
| Dataset(; | |
| uuid=UUIDs.UUID(d["id"]), | |
| name, owner, versions, | |
| dtype=d["type"], | |
| description=d["description"], | |
| size=d["size"], | |
| tags=d["tags"], | |
| project=project, | |
| _downloadURL=d["downloadURL"], | |
| _last_modified=_nothing_or(d["lastModified"]) do last_modified | |
| datetime_utc = Dates.DateTime( | |
| function Dataset(d::Dict; expected_project::Union{UUIDs.UUID, Nothing}=nothing) | |
| owner = d["owner"]["username"] | |
| name = d["name"] | |
| versions_json = _get_json_or(d, "versions", Vector, []) | |
| versions = sort([DatasetVersion(json; owner, name) for json in versions_json]; by=dsv -> dsv.id) | |
| project = if !isnothing(expected_project) | |
| project_json = _get_json(d, "project", Dict) | |
| project_json_uuid = UUIDs.UUID( | |
| _get_json(project_json, "project_id", String; msg=".project") | |
| ) | |
| if project_json_uuid != expected_project | |
| msg = "Project UUID mismatch in dataset response: $(project_json_uuid), requested $(project)" | |
| throw(JuliaHubError(msg)) | |
| end | |
| is_writable = _get_json( | |
| project_json, | |
| "is_writable", | |
| Bool; | |
| msg="Unable to parse .project in /datasets?project response", | |
| ) | |
| DatasetProjectLink(project_json_uuid, is_writable) | |
| else | |
| nothing | |
| end | |
| return Dataset(; | |
| uuid=UUIDs.UUID(d["id"]), | |
| name, owner, versions, | |
| dtype=d["type"], | |
| description=d["description"], | |
| size=d["size"], | |
| tags=d["tags"], | |
| project=project, | |
| _downloadURL=d["downloadURL"], | |
| _last_modified=_nothing_or(d["lastModified"]) do last_modified | |
| datetime_utc = Dates.DateTime( | |
| last_modified, Dates.dateformat"YYYY-mm-ddTHH:MM:SS.ss" | |
| ) | |
| _utc2localtz(datetime_utc) | |
| end, | |
| _storage=_DatasetStorage(; | |
| credentials_url=d["credentials_url"], | |
| region=d["storage"]["bucket_region"], | |
| bucket=d["storage"]["bucket"], | |
| prefix=d["storage"]["prefix"], | |
| ), | |
| _json=d, | |
| ) | |
| end |
View step-by-step instructions
- Add a
returnstatement at the end of theDatasetfunction to explicitly return the constructedDatasetobject. - Modify the last line of the function to
return Dataset(...);to ensure the function explicitly returns a value.
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| d.project.is_writable ? "(writable)" : "(not writable)", | ||
| ) |
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Semgrep identified an issue, but thinks it may be safe to ignore.
Avoid unnecessary whitespace padding inside brackets.
Why this might be safe to ignore:
The rule aims to fix extra whitespace padding in code syntax, not inside string literals. This instance, being a string intended for output, is a false positive and fixing it wouldn’t improve code quality.
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| project_json_uuid = UUIDs.UUID( | ||
| _get_json(project_json, "project_id", String; msg=".project") |
There was a problem hiding this comment.
Semgrep identified an issue, but thinks it may be safe to ignore.
Avoid unnecessary whitespace padding inside brackets.
Why this might be safe to ignore:
The whitespace is due to multiline formatting and proper indentation rather than unnecessary inline padding, so fixing it wouldn't improve code quality.
To resolve this comment:
🔧 No guidance has been designated for this issue. Fix according to your organization's approved methods.
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/fp <comment>for false positive/ar <comment>for acceptable risk/other <comment>for all other reasons
Alternatively, triage in [Semgrep AppSec Platform](https://semgrep.dev/orgs/JuliaHub, Inc/findings/154643365) to ignore the finding created by no-whitespace-padding.
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| "Local data type ($expected_dtype) does not match existing dataset dtype $(upload_config["dataset_type"])" | ||
| ), |
There was a problem hiding this comment.
Semgrep identified an issue, but thinks it may be safe to ignore.
Avoid unnecessary whitespace padding inside brackets.
Why this might be safe to ignore:
The matched code is part of a string literal used for error messages, and the whitespace inside it does not affect functionality or readability, so it doesn't need fixing.
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/fp <comment>for false positive/ar <comment>for acceptable risk/other <comment>for all other reasons
Alternatively, triage in [Semgrep AppSec Platform](https://semgrep.dev/orgs/JuliaHub, Inc/findings/154643361) to ignore the finding created by no-whitespace-padding.
You can view more details about [this finding](https://semgrep.dev/orgs/JuliaHub, Inc/findings/154643361) in the Semgrep AppSec Platform.
This adds:
JuliaHub.project_dataset(s)to get dataset(s) that are attached to a projectJuliaHub.upload_project_datasetto upload a new version of a dataset that attached to a project (if you have write access).To make things easier for the user,
JuliaHub.authenticatewill automatically pick up the project UUID from theJULIAHUB_PROJECT_UUIDenvironment variable, in which case you don't need to pass the project UUID to any of the project-dataset function. You can also manually set it by passingprojecttoJuliaHub.authenticate.The project-dataset function will still return
Datasetobjects, but it now can also contain a.projectfield which can contain the project-dataset link metadata (e.g. writability).Close #15.