Models
Analyses
- class onecodex.models.analysis.Analyses(_resource=None, **kwargs)
Bases:
OneCodexBase- classmethod all(sort=None, limit=None)
Return all objects of this type. Alias for where() (without filter arguments).
See where for documentation on the sort and limit parameters.
- delete()
Delete this object from the One Codex server.
- classmethod get(uuid)
Retrieve a model record from the server by its UUID (unique 16-character id).
UUIDs are found in the web browser’s address bar while viewing analyses and other objects.
Parameters
- uuidstr
UUID of the object to retrieve.
Examples
All models implement the same method. To see a complete list of models which can be retrieved by ID, see the models page.
# Fetch a sample by ID >>> api.Sample.get('xxxxxxxxxxxxxxxx') <Sample xxxxxxxxxxxxxxxx> # Fetch a classification analysis by ID >>> api.Classifications.get('xxxxxxxxxxxxxxxx') <Classification xxxxxxxxxxxxxxxx> # Fetch a project by ID >>> api.Projects.get('xxxxxxxxxxxxxxxx') <Project xxxxxxxxxxxxxxxx>
Returns
- OneCodexBase or None
The object with that UUID or None if no object could be found.
- 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.
- save()
Either create or persist changes on this object back to the One Codex server.
- 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.
Alignments
- class onecodex.models.analysis.Alignments(_resource=None, **kwargs)
Bases:
Analyses- classmethod all(sort=None, limit=None)
Return all objects of this type. Alias for where() (without filter arguments).
See where for documentation on the sort and limit parameters.
- delete()
Delete this object from the One Codex server.
- classmethod get(uuid)
Retrieve a model record from the server by its UUID (unique 16-character id).
UUIDs are found in the web browser’s address bar while viewing analyses and other objects.
Parameters
- uuidstr
UUID of the object to retrieve.
Examples
All models implement the same method. To see a complete list of models which can be retrieved by ID, see the models page.
# Fetch a sample by ID >>> api.Sample.get('xxxxxxxxxxxxxxxx') <Sample xxxxxxxxxxxxxxxx> # Fetch a classification analysis by ID >>> api.Classifications.get('xxxxxxxxxxxxxxxx') <Classification xxxxxxxxxxxxxxxx> # Fetch a project by ID >>> api.Projects.get('xxxxxxxxxxxxxxxx') <Project xxxxxxxxxxxxxxxx>
Returns
- OneCodexBase or None
The object with that UUID or None if no object could be found.
- 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.
- save()
Either create or persist changes on this object back to the One Codex server.
- 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.
Classifications
- class onecodex.models.analysis.Classifications(_resource=None, **kwargs)
Bases:
Analyses- classmethod all(sort=None, limit=None)
Return all objects of this type. Alias for where() (without filter arguments).
See where for documentation on the sort and limit parameters.
- delete()
Delete this object from the One Codex server.
- classmethod get(uuid)
Retrieve a model record from the server by its UUID (unique 16-character id).
UUIDs are found in the web browser’s address bar while viewing analyses and other objects.
Parameters
- uuidstr
UUID of the object to retrieve.
Examples
All models implement the same method. To see a complete list of models which can be retrieved by ID, see the models page.
# Fetch a sample by ID >>> api.Sample.get('xxxxxxxxxxxxxxxx') <Sample xxxxxxxxxxxxxxxx> # Fetch a classification analysis by ID >>> api.Classifications.get('xxxxxxxxxxxxxxxx') <Classification xxxxxxxxxxxxxxxx> # Fetch a project by ID >>> api.Projects.get('xxxxxxxxxxxxxxxx') <Project xxxxxxxxxxxxxxxx>
Returns
- OneCodexBase or None
The object with that UUID or None if no object could be found.
- 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.
- save()
Either create or persist changes on this object back to the One Codex server.
- 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(_resource=None, **kwargs)
Bases:
Analyses- classmethod all(sort=None, limit=None)
Return all objects of this type. Alias for where() (without filter arguments).
See where for documentation on the sort and limit parameters.
- delete()
Delete this object from the One Codex server.
- classmethod get(uuid)
Retrieve a model record from the server by its UUID (unique 16-character id).
UUIDs are found in the web browser’s address bar while viewing analyses and other objects.
Parameters
- uuidstr
UUID of the object to retrieve.
Examples
All models implement the same method. To see a complete list of models which can be retrieved by ID, see the models page.
# Fetch a sample by ID >>> api.Sample.get('xxxxxxxxxxxxxxxx') <Sample xxxxxxxxxxxxxxxx> # Fetch a classification analysis by ID >>> api.Classifications.get('xxxxxxxxxxxxxxxx') <Classification xxxxxxxxxxxxxxxx> # Fetch a project by ID >>> api.Projects.get('xxxxxxxxxxxxxxxx') <Project xxxxxxxxxxxxxxxx>
Returns
- OneCodexBase or None
The object with that UUID or None if no object could be found.
- 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.
- save()
Either create or persist changes on this object back to the One Codex server.
- 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.
Assets
- class onecodex.models.misc.Assets(_resource=None, **kwargs)
Bases:
OneCodexBase,ResourceDownloadMixin- classmethod all(sort=None, limit=None)
Return all objects of this type. Alias for where() (without filter arguments).
See where for documentation on the sort and limit parameters.
- delete()
Delete this object from the One Codex server.
- download(path=None, file_obj=None, progressbar=False)
Download files from One Codex.
Parameters
- pathstring, optional
Full path to save the file to. If omitted, defaults to the original filename in the current working directory.
- file_objfile-like object, optional
Rather than save the file to a path, write it to this file-like object.
- progressbarbool
Display a progress bar using Click for the download?
Returns
- string
The path the file was downloaded to, if applicable. Otherwise, None.
Notes
If no arguments specified, defaults to download the file as the original filename in the current working directory. If file_obj given, will write data into the passed file-like object. If path given, will download the file to the path provided, but will not overwrite any existing files.
- classmethod get(uuid)
Retrieve a model record from the server by its UUID (unique 16-character id).
UUIDs are found in the web browser’s address bar while viewing analyses and other objects.
Parameters
- uuidstr
UUID of the object to retrieve.
Examples
All models implement the same method. To see a complete list of models which can be retrieved by ID, see the models page.
# Fetch a sample by ID >>> api.Sample.get('xxxxxxxxxxxxxxxx') <Sample xxxxxxxxxxxxxxxx> # Fetch a classification analysis by ID >>> api.Classifications.get('xxxxxxxxxxxxxxxx') <Classification xxxxxxxxxxxxxxxx> # Fetch a project by ID >>> api.Projects.get('xxxxxxxxxxxxxxxx') <Project xxxxxxxxxxxxxxxx>
Returns
- OneCodexBase or None
The object with that UUID or None if no object could be found.
- save()
Either create or persist changes on this object back to the One Codex server.
- classmethod upload(file_path, progressbar=None, name=None)
Upload a file to an asset.
Parameters
- file_pathstring
A path to a file on the system.
- progressbarclick.progressbar, optional
If passed, display a progress bar using Click.
- namestring, optional
If passed, name is sent with upload request and is associated with asset.
Returns
An Assets object upon successful upload. None if the upload failed.
- 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.
Documents
- class onecodex.models.misc.Documents(_resource=None, **kwargs)
Bases:
OneCodexBase,ResourceDownloadMixin- classmethod all(sort=None, limit=None)
Return all objects of this type. Alias for where() (without filter arguments).
See where for documentation on the sort and limit parameters.
- delete()
Delete this object from the One Codex server.
- download(path=None, file_obj=None, progressbar=False)
Download files from One Codex.
Parameters
- pathstring, optional
Full path to save the file to. If omitted, defaults to the original filename in the current working directory.
- file_objfile-like object, optional
Rather than save the file to a path, write it to this file-like object.
- progressbarbool
Display a progress bar using Click for the download?
Returns
- string
The path the file was downloaded to, if applicable. Otherwise, None.
Notes
If no arguments specified, defaults to download the file as the original filename in the current working directory. If file_obj given, will write data into the passed file-like object. If path given, will download the file to the path provided, but will not overwrite any existing files.
- classmethod get(uuid)
Retrieve a model record from the server by its UUID (unique 16-character id).
UUIDs are found in the web browser’s address bar while viewing analyses and other objects.
Parameters
- uuidstr
UUID of the object to retrieve.
Examples
All models implement the same method. To see a complete list of models which can be retrieved by ID, see the models page.
# Fetch a sample by ID >>> api.Sample.get('xxxxxxxxxxxxxxxx') <Sample xxxxxxxxxxxxxxxx> # Fetch a classification analysis by ID >>> api.Classifications.get('xxxxxxxxxxxxxxxx') <Classification xxxxxxxxxxxxxxxx> # Fetch a project by ID >>> api.Projects.get('xxxxxxxxxxxxxxxx') <Project xxxxxxxxxxxxxxxx>
Returns
- OneCodexBase or None
The object with that UUID or None if no object could be found.
- save()
Either create or persist changes on this object back to the One Codex server.
- 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)
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(_resource=None, **kwargs)
Bases:
OneCodexBase- classmethod all(sort=None, limit=None)
Return all objects of this type. Alias for where() (without filter arguments).
See where for documentation on the sort and limit parameters.
- delete()
Delete this object from the One Codex server.
- classmethod get(uuid)
Retrieve a model record from the server by its UUID (unique 16-character id).
UUIDs are found in the web browser’s address bar while viewing analyses and other objects.
Parameters
- uuidstr
UUID of the object to retrieve.
Examples
All models implement the same method. To see a complete list of models which can be retrieved by ID, see the models page.
# Fetch a sample by ID >>> api.Sample.get('xxxxxxxxxxxxxxxx') <Sample xxxxxxxxxxxxxxxx> # Fetch a classification analysis by ID >>> api.Classifications.get('xxxxxxxxxxxxxxxx') <Classification xxxxxxxxxxxxxxxx> # Fetch a project by ID >>> api.Projects.get('xxxxxxxxxxxxxxxx') <Project xxxxxxxxxxxxxxxx>
Returns
- OneCodexBase or None
The object with that UUID or None if no object could be found.
- save()
Either create or persist changes on this object back to the One Codex server.
- 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.
Projects
- class onecodex.models.misc.Projects(_resource=None, **kwargs)
Bases:
OneCodexBase- classmethod all(sort=None, limit=None)
Return all objects of this type. Alias for where() (without filter arguments).
See where for documentation on the sort and limit parameters.
- delete()
Delete this object from the One Codex server.
- classmethod get(uuid)
Retrieve a model record from the server by its UUID (unique 16-character id).
UUIDs are found in the web browser’s address bar while viewing analyses and other objects.
Parameters
- uuidstr
UUID of the object to retrieve.
Examples
All models implement the same method. To see a complete list of models which can be retrieved by ID, see the models page.
# Fetch a sample by ID >>> api.Sample.get('xxxxxxxxxxxxxxxx') <Sample xxxxxxxxxxxxxxxx> # Fetch a classification analysis by ID >>> api.Classifications.get('xxxxxxxxxxxxxxxx') <Classification xxxxxxxxxxxxxxxx> # Fetch a project by ID >>> api.Projects.get('xxxxxxxxxxxxxxxx') <Project xxxxxxxxxxxxxxxx>
Returns
- OneCodexBase or None
The object with that UUID or None if no object could be found.
- save()
Either create or persist changes on this object back to the One Codex server.
- 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.
Samples
- class onecodex.models.sample.Samples(_resource=None, **kwargs)
Bases:
OneCodexBase,ResourceDownloadMixin- classmethod all(sort=None, limit=None)
Return all objects of this type. Alias for where() (without filter arguments).
See where for documentation on the sort and limit parameters.
- delete()
Delete this object from the One Codex server.
- download(path=None, file_obj=None, progressbar=False)
Download files from One Codex.
Parameters
- pathstring, optional
Full path to save the file to. If omitted, defaults to the original filename in the current working directory.
- file_objfile-like object, optional
Rather than save the file to a path, write it to this file-like object.
- progressbarbool
Display a progress bar using Click for the download?
Returns
- string
The path the file was downloaded to, if applicable. Otherwise, None.
Notes
If no arguments specified, defaults to download the file as the original filename in the current working directory. If file_obj given, will write data into the passed file-like object. If path given, will download the file to the path provided, but will not overwrite any existing files.
- classmethod get(uuid)
Retrieve a model record from the server by its UUID (unique 16-character id).
UUIDs are found in the web browser’s address bar while viewing analyses and other objects.
Parameters
- uuidstr
UUID of the object to retrieve.
Examples
All models implement the same method. To see a complete list of models which can be retrieved by ID, see the models page.
# Fetch a sample by ID >>> api.Sample.get('xxxxxxxxxxxxxxxx') <Sample xxxxxxxxxxxxxxxx> # Fetch a classification analysis by ID >>> api.Classifications.get('xxxxxxxxxxxxxxxx') <Classification xxxxxxxxxxxxxxxx> # Fetch a project by ID >>> api.Projects.get('xxxxxxxxxxxxxxxx') <Project xxxxxxxxxxxxxxxx>
Returns
- OneCodexBase or None
The object with that UUID or None if no object could be found.
- 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(_resource=None, **kwargs)
Bases:
OneCodexBase- classmethod all(sort=None, limit=None)
Return all objects of this type. Alias for where() (without filter arguments).
See where for documentation on the sort and limit parameters.
- delete()
Delete this object from the One Codex server.
- classmethod get(uuid)
Retrieve a model record from the server by its UUID (unique 16-character id).
UUIDs are found in the web browser’s address bar while viewing analyses and other objects.
Parameters
- uuidstr
UUID of the object to retrieve.
Examples
All models implement the same method. To see a complete list of models which can be retrieved by ID, see the models page.
# Fetch a sample by ID >>> api.Sample.get('xxxxxxxxxxxxxxxx') <Sample xxxxxxxxxxxxxxxx> # Fetch a classification analysis by ID >>> api.Classifications.get('xxxxxxxxxxxxxxxx') <Classification xxxxxxxxxxxxxxxx> # Fetch a project by ID >>> api.Projects.get('xxxxxxxxxxxxxxxx') <Project xxxxxxxxxxxxxxxx>
Returns
- OneCodexBase or None
The object with that UUID or None if no object could be found.
- save()
Either create or persist changes on this object back to the One Codex server.
- 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.