Models
Analyses
- class onecodex.models.analysis.Analyses(*, field_uri: str, created_at: Annotated[datetime, PlainSerializer(func=rfc3339_encoder, return_type=str, when_used=always), BeforeValidator(func=rfc3339_decoder, json_schema_input_type=PydanticUndefined)], complete: bool = False, error_msg: str | None = None, job: Jobs | ApiRef, job_args: dict[str, Any] = {}, sample: Samples | ApiRef, success: bool = False, analysis_type: str)
Bases:
_AnalysesBase,AnalysisSchema- model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': False, 'extra': 'ignore', 'populate_by_alias': True}
Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].
- results(json=True)
Fetch the results of an Analyses resource.
Parameters
- jsonbool, optional
Return a JSON result (raw API result)? Default True.
Returns
Return type varies by Analyses resource sub-type. See, e.g., Classifications or Panels for documentation.
- classmethod where(*filters, **keyword_filters) List[OneCodexBase]
Filter model records of this type from the One Codex server.
This method works for all OneCodex model types including Samples, Classifications, Projects, and Panels.
Parameters
- filtersobject
Advanced filters to use (not implemented)
- sortstr or list, optional
Sort the results by this field (or list of fields). By default in descending order, but if any of the fields start with the special character ^, sort in ascending order. For example, sort=[‘size’, ‘^filename’] will sort by size from largest to smallest and filename from A-Z for items with the same size.
- limitint, optional
Number of records to return. For smaller searches, this can reduce the number of network requests made.
- keyword_filtersstr or object
Filter the results by specific keywords (or filter objects, in advanced usage)
Examples
You can filter objects that are returned locally using a lambda function
All models implement the same method. To see a complete list of models which can be retrieved by ID, see the models page.
# Filter samples by filename my_samples = Samples.where(filter=lambda s: s.filename.endswith('.gz')) # Filter classifications by completion status completed = Classifications.where(filter=lambda c: c.complete == True) # Filter projects by name my_projects = Projects.where(filter=lambda p: 'test' in p.name)
Returns
- list
A list of all objects matching these filters. If no filters are passed, this matches all objects.
Alignments
- class onecodex.models.analysis.Alignments(*, field_uri: str, created_at: Annotated[datetime, PlainSerializer(func=rfc3339_encoder, return_type=str, when_used=always), BeforeValidator(func=rfc3339_decoder, json_schema_input_type=PydanticUndefined)], complete: bool = False, error_msg: str | None = None, job: Jobs | ApiRef, job_args: dict[str, Any] = {}, sample: Samples | ApiRef, success: bool = False)
Bases:
_AnalysesBase,AlignmentSchema- model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': False, 'extra': 'ignore', 'populate_by_alias': True}
Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].
- results(json=True)
Fetch the results of an Analyses resource.
Parameters
- jsonbool, optional
Return a JSON result (raw API result)? Default True.
Returns
Return type varies by Analyses resource sub-type. See, e.g., Classifications or Panels for documentation.
- classmethod where(*filters, **keyword_filters) List[OneCodexBase]
Filter model records of this type from the One Codex server.
This method works for all OneCodex model types including Samples, Classifications, Projects, and Panels.
Parameters
- filtersobject
Advanced filters to use (not implemented)
- sortstr or list, optional
Sort the results by this field (or list of fields). By default in descending order, but if any of the fields start with the special character ^, sort in ascending order. For example, sort=[‘size’, ‘^filename’] will sort by size from largest to smallest and filename from A-Z for items with the same size.
- limitint, optional
Number of records to return. For smaller searches, this can reduce the number of network requests made.
- keyword_filtersstr or object
Filter the results by specific keywords (or filter objects, in advanced usage)
Examples
You can filter objects that are returned locally using a lambda function
All models implement the same method. To see a complete list of models which can be retrieved by ID, see the models page.
# Filter samples by filename my_samples = Samples.where(filter=lambda s: s.filename.endswith('.gz')) # Filter classifications by completion status completed = Classifications.where(filter=lambda c: c.complete == True) # Filter projects by name my_projects = Projects.where(filter=lambda p: 'test' in p.name)
Returns
- list
A list of all objects matching these filters. If no filters are passed, this matches all objects.
Classifications
- class onecodex.models.analysis.Classifications(*, field_uri: str, created_at: Annotated[datetime, PlainSerializer(func=rfc3339_encoder, return_type=str, when_used=always), BeforeValidator(func=rfc3339_decoder, json_schema_input_type=PydanticUndefined)], complete: bool = False, error_msg: str | None = None, job: Jobs | ApiRef, job_args: dict[str, Any] = {}, sample: Samples | ApiRef, success: bool = False)
Bases:
_AnalysesBase,ClassificationSchema- model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': False, 'extra': 'ignore', 'populate_by_alias': True}
Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].
- results(json=True)
Return the complete results table for a classification.
Parameters
- jsonbool, optional
Return result as JSON? Default True.
Returns
- tabledict or pd.DataFrame
Return a JSON object with the classification results or a pd.DataFrame if json=False.
- table()
Return the complete results table for the classification.
Returns
- tablepd.DataFrame
A Pandas DataFrame of the classification results.
- classmethod where(*filters, **keyword_filters)
Filter model records of this type from the One Codex server.
This method works for all OneCodex model types including Samples, Classifications, Projects, and Panels.
Parameters
- filtersobject
Advanced filters to use (not implemented)
- sortstr or list, optional
Sort the results by this field (or list of fields). By default in descending order, but if any of the fields start with the special character ^, sort in ascending order. For example, sort=[‘size’, ‘^filename’] will sort by size from largest to smallest and filename from A-Z for items with the same size.
- limitint, optional
Number of records to return. For smaller searches, this can reduce the number of network requests made.
- keyword_filtersstr or object
Filter the results by specific keywords (or filter objects, in advanced usage)
Examples
You can filter objects that are returned locally using a lambda function
All models implement the same method. To see a complete list of models which can be retrieved by ID, see the models page.
# Filter samples by filename my_samples = Samples.where(filter=lambda s: s.filename.endswith('.gz')) # Filter classifications by completion status completed = Classifications.where(filter=lambda c: c.complete == True) # Filter projects by name my_projects = Projects.where(filter=lambda p: 'test' in p.name)
Returns
- list
A list of all objects matching these filters. If no filters are passed, this matches all objects.
FunctionalProfiles
Panels
- class onecodex.models.analysis.Panels(*, field_uri: str, created_at: Annotated[datetime, PlainSerializer(func=rfc3339_encoder, return_type=str, when_used=always), BeforeValidator(func=rfc3339_decoder, json_schema_input_type=PydanticUndefined)], complete: bool = False, error_msg: str | None = None, job: Jobs | ApiRef, job_args: dict[str, Any] = {}, sample: Samples | ApiRef, success: bool = False)
Bases:
_AnalysesBase,PanelSchema- model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': False, 'extra': 'ignore', 'populate_by_alias': True}
Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].
- results(json=True)
Fetch the results of an Analyses resource.
Parameters
- jsonbool, optional
Return a JSON result (raw API result)? Default True.
Returns
Return type varies by Analyses resource sub-type. See, e.g., Classifications or Panels for documentation.
- classmethod where(*filters, **keyword_filters) List[OneCodexBase]
Filter model records of this type from the One Codex server.
This method works for all OneCodex model types including Samples, Classifications, Projects, and Panels.
Parameters
- filtersobject
Advanced filters to use (not implemented)
- sortstr or list, optional
Sort the results by this field (or list of fields). By default in descending order, but if any of the fields start with the special character ^, sort in ascending order. For example, sort=[‘size’, ‘^filename’] will sort by size from largest to smallest and filename from A-Z for items with the same size.
- limitint, optional
Number of records to return. For smaller searches, this can reduce the number of network requests made.
- keyword_filtersstr or object
Filter the results by specific keywords (or filter objects, in advanced usage)
Examples
You can filter objects that are returned locally using a lambda function
All models implement the same method. To see a complete list of models which can be retrieved by ID, see the models page.
# Filter samples by filename my_samples = Samples.where(filter=lambda s: s.filename.endswith('.gz')) # Filter classifications by completion status completed = Classifications.where(filter=lambda c: c.complete == True) # Filter projects by name my_projects = Projects.where(filter=lambda p: 'test' in p.name)
Returns
- list
A list of all objects matching these filters. If no filters are passed, this matches all objects.
Assets
Documents
- class onecodex.models.misc.Documents(*, field_uri: str, created_at: Annotated[datetime, PlainSerializer(func=rfc3339_encoder, return_type=str, when_used=always), BeforeValidator(func=rfc3339_decoder, json_schema_input_type=PydanticUndefined)], filename: str, size: int | None = None, uploader: Users | ApiRef, downloaders: List[Users | ApiRef] = [])
Bases:
OneCodexBase,DocumentSchema,ResourceDownloadMixin- model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': False, 'extra': 'ignore', 'populate_by_alias': True}
Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].
- classmethod upload(file_path, progressbar=None)
Upload a series of files to the One Codex server.
Parameters
- file_pathstring
A path to a file on the system.
- progressbarclick.progressbar, optional
If passed, display a progress bar using Click.
Returns
A Documents object upon successful upload. None if the upload failed.
- classmethod where(*filters, **keyword_filters) List[OneCodexBase]
Filter model records of this type from the One Codex server.
This method works for all OneCodex model types including Samples, Classifications, Projects, and Panels.
Parameters
- filtersobject
Advanced filters to use (not implemented)
- sortstr or list, optional
Sort the results by this field (or list of fields). By default in descending order, but if any of the fields start with the special character ^, sort in ascending order. For example, sort=[‘size’, ‘^filename’] will sort by size from largest to smallest and filename from A-Z for items with the same size.
- limitint, optional
Number of records to return. For smaller searches, this can reduce the number of network requests made.
- keyword_filtersstr or object
Filter the results by specific keywords (or filter objects, in advanced usage)
Examples
You can filter objects that are returned locally using a lambda function
All models implement the same method. To see a complete list of models which can be retrieved by ID, see the models page.
# Filter samples by filename my_samples = Samples.where(filter=lambda s: s.filename.endswith('.gz')) # Filter classifications by completion status completed = Classifications.where(filter=lambda c: c.complete == True) # Filter projects by name my_projects = Projects.where(filter=lambda p: 'test' in p.name)
Returns
- list
A list of all objects matching these filters. If no filters are passed, this matches all objects.
Jobs
- class onecodex.models.misc.Jobs(*, field_uri: str, created_at: ~typing.Annotated[~datetime.datetime, ~pydantic.functional_serializers.PlainSerializer(func=~onecodex.models.schemas.types.rfc3339_encoder, return_type=str, when_used=always), ~pydantic.functional_validators.BeforeValidator(func=~onecodex.models.schemas.types.rfc3339_decoder, json_schema_input_type=PydanticUndefined)], name: str, job_args_schema: dict[str, ~typing.Any] = <factory>, analysis_type: str, public: bool)
Bases:
OneCodexBase,JobSchema- model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': False, 'extra': 'ignore', 'populate_by_alias': True}
Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].
- classmethod where(*filters, **keyword_filters) List[OneCodexBase]
Filter model records of this type from the One Codex server.
This method works for all OneCodex model types including Samples, Classifications, Projects, and Panels.
Parameters
- filtersobject
Advanced filters to use (not implemented)
- sortstr or list, optional
Sort the results by this field (or list of fields). By default in descending order, but if any of the fields start with the special character ^, sort in ascending order. For example, sort=[‘size’, ‘^filename’] will sort by size from largest to smallest and filename from A-Z for items with the same size.
- limitint, optional
Number of records to return. For smaller searches, this can reduce the number of network requests made.
- keyword_filtersstr or object
Filter the results by specific keywords (or filter objects, in advanced usage)
Examples
You can filter objects that are returned locally using a lambda function
All models implement the same method. To see a complete list of models which can be retrieved by ID, see the models page.
# Filter samples by filename my_samples = Samples.where(filter=lambda s: s.filename.endswith('.gz')) # Filter classifications by completion status completed = Classifications.where(filter=lambda c: c.complete == True) # Filter projects by name my_projects = Projects.where(filter=lambda p: 'test' in p.name)
Returns
- list
A list of all objects matching these filters. If no filters are passed, this matches all objects.
Projects
- class onecodex.models.misc.Projects(*, field_uri: str, description: str | None = None, external_id: str | None = None, name: str | None = None, owner: Users | ApiRef, permissions: list[str], project_name: Annotated[str | None, MinLen(min_length=3), MaxLen(max_length=15), _PydanticGeneralMetadata(pattern='^[a-zA-Z0-9_-]{3,15}$')], public: bool = False)
Bases:
OneCodexBase,ProjectSchema- model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': False, 'extra': 'ignore', 'populate_by_alias': True}
Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].
- classmethod where(*filters, **keyword_filters) List[OneCodexBase]
Filter model records of this type from the One Codex server.
This method works for all OneCodex model types including Samples, Classifications, Projects, and Panels.
Parameters
- filtersobject
Advanced filters to use (not implemented)
- sortstr or list, optional
Sort the results by this field (or list of fields). By default in descending order, but if any of the fields start with the special character ^, sort in ascending order. For example, sort=[‘size’, ‘^filename’] will sort by size from largest to smallest and filename from A-Z for items with the same size.
- limitint, optional
Number of records to return. For smaller searches, this can reduce the number of network requests made.
- keyword_filtersstr or object
Filter the results by specific keywords (or filter objects, in advanced usage)
Examples
You can filter objects that are returned locally using a lambda function
All models implement the same method. To see a complete list of models which can be retrieved by ID, see the models page.
# Filter samples by filename my_samples = Samples.where(filter=lambda s: s.filename.endswith('.gz')) # Filter classifications by completion status completed = Classifications.where(filter=lambda c: c.complete == True) # Filter projects by name my_projects = Projects.where(filter=lambda p: 'test' in p.name)
Returns
- list
A list of all objects matching these filters. If no filters are passed, this matches all objects.
Samples
- class onecodex.models.sample.Samples(*, field_uri: str, created_at: datetime, error_msg: str | None = None, filename: str | None = None, metadata: Metadata | ApiRef, owner: Users | ApiRef, primary_classification: Classifications | ApiRef | None = None, project: Projects | ApiRef | None = None, size: int | None = None, tags: List[Tags | ApiRef] = [], status: str, visibility: str, updated_at: datetime | None = None)
Bases:
OneCodexBase,_SampleSchema,ResourceDownloadMixin- model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': False, 'extra': 'ignore', 'populate_by_alias': True}
Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].
- classmethod preupload(metadata=None, tags=None, project=None)
Create a sample in a waiting state where the files will be sent later on.
Parameters
metadata : dict, optional tags : list, optional
A list of optional tags to create. Tags must be passed as dictionaries with a single key name and the tag name, e.g., {“name”: “my tag”}. New tags will be created on-the-fly as needed.
- projectstring, optional
UUID of project to associate this sample with.
- save()
Send changes on this Samples object to the One Codex server.
Changes to the metadata object and tags list are passed as well.
- classmethod upload(files, metadata=None, tags=None, project=None, coerce_ascii=False, progressbar=None, sample_id=None, external_sample_id=None)
Upload a series of files to the One Codex server.
Parameters
- filesstring or tuple
A single path to a file on the system, or a tuple containing a pairs of paths. Tuple values will be interleaved as paired-end reads and both files should contain the same number of records. Paths to single files will be uploaded as-is.
metadata : dict, optional tags : list, optional
A list of optional tags to create. Tags must be passed as dictionaries with a single key name and the tag name, e.g., {“name”: “my tag”}. New tags will be created on-the-fly as needed.
- projectstring, optional
UUID of project to associate this sample with.
- coerce_asciibool, optional
If true, rename unicode filenames to ASCII and issue warning.
- progressbarclick.progressbar, optional
If passed, display a progress bar using Click.
- sample_idstring, optional
If passed, will upload the file(s) to the sample with that id. Only works if the sample was pre-uploaded
- external_sample_idstring, optional
If passed, will upload the file(s) to the sample with that metadata external id. Only works if the sample was pre-uploaded
Returns
A Samples object upon successful upload. None if the upload failed.
- classmethod where(*filters, **keyword_filters)
Query and retrieve a set of samples.
Parameters
- limitint, optional
If set, retrieve a maximum of limit samples. Note a limit of 1000 samples is automatically enforced for queries of all public samples (public=True)
- organizationbool, optional
If True, search all samples within your organization (including your samples). May not be combined with public=True.
- publicbool, optional
If True, search all public samples (limited to 1000 results). May not be combined with organization=True.
- tagslist, optional
A list of optional Tags to filter by. Tags should be Tag objects retrieved with ocx.Tags.get() or ocx.Tags.where()
- projectProject, optional
Filter by a Project
- **keyword_filtersdict, optional
Pass any additional sample or metadata attribute to filter by that attribute. Metadata filtering is not currently supported for
Returns
A SampleCollection object with samples matching the query
Users
- class onecodex.models.misc.Users(*, field_uri: str, email: str | None)
Bases:
OneCodexBase,UserSchema- model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': False, 'extra': 'ignore', 'populate_by_alias': True}
Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].
- classmethod where(*filters, **keyword_filters) List[OneCodexBase]
Filter model records of this type from the One Codex server.
This method works for all OneCodex model types including Samples, Classifications, Projects, and Panels.
Parameters
- filtersobject
Advanced filters to use (not implemented)
- sortstr or list, optional
Sort the results by this field (or list of fields). By default in descending order, but if any of the fields start with the special character ^, sort in ascending order. For example, sort=[‘size’, ‘^filename’] will sort by size from largest to smallest and filename from A-Z for items with the same size.
- limitint, optional
Number of records to return. For smaller searches, this can reduce the number of network requests made.
- keyword_filtersstr or object
Filter the results by specific keywords (or filter objects, in advanced usage)
Examples
You can filter objects that are returned locally using a lambda function
All models implement the same method. To see a complete list of models which can be retrieved by ID, see the models page.
# Filter samples by filename my_samples = Samples.where(filter=lambda s: s.filename.endswith('.gz')) # Filter classifications by completion status completed = Classifications.where(filter=lambda c: c.complete == True) # Filter projects by name my_projects = Projects.where(filter=lambda p: 'test' in p.name)
Returns
- list
A list of all objects matching these filters. If no filters are passed, this matches all objects.