Results export

gambit.results

Export query results in various formats.

class gambit.results.AbstractResultsExporter

Bases: ABC

Base for classes that export formatted query results.

Subclasses must implement export().

abstract export(file_or_path, results)

Write query results to file.

Parameters:

file_or_path (FilePath | IO) – Open file-like object or file path to write to.
results (QueryResults) – Results to export.

class gambit.results.BaseJSONResultsExporter

Bases: AbstractResultsExporter

Base class for JSON exporters.

Subclasses need to implement the to_json method.

pretty

Write in more human-readable but less compact format. Defaults to False.

Type:: bool

__init__(pretty=False)

Method generated by attrs for class BaseJSONResultsExporter.

Parameters:: pretty (bool)
Return type:: None

export(file_or_path, results)

Write query results to file.

Parameters:

file_or_path (FilePath | TextIO) – Open file-like object or file path to write to.
results (QueryResults) – Results to export.

to_json(obj): Convert object to JSON-compatible format (need not work recursively).

class gambit.results.CSVResultsExporter

Bases: AbstractResultsExporter

Exports query results in CSV format.

format_opts

Dialect and other formatting arguments passed to csv.writer().

Type:: dict[str, Any]

__init__(**format_opts)

export(file_or_path, results)

Write query results to file.

Parameters:

file_or_path (FilePath | TextIO) – Open file-like object or file path to write to.
results (QueryResults) – Results to export.

get_header()

Get values for header row.

Return type:: list[str]

get_row(item)

Get row values for single result item.

Parameters:: item (QueryResultItem)
Return type:: list

class gambit.results.JSONResultsExporter

Bases: BaseJSONResultsExporter

Exports query results in basic JSON format.

Currently it assumes that the query was run with classify_strict=False, so the only relevant information from ClassifierResult is the closest genome match.

__init__(pretty=False)

Method generated by attrs for class JSONResultsExporter.

Parameters:: pretty (bool)
Return type:: None

to_json(obj)
to_json(results)
to_json(item)
to_json(gset)
to_json(taxon)
to_json(genome): Convert object to JSON-compatible format (need not work recursively).

class gambit.results.ResultsArchiveReader

Bases: object

Loads query results from file created by ResultsArchiveWriter.

session

SQLAlchemy session used to load database objects.

Type:: sqlalchemy.orm.session.Session

__init__(session)

read(file_or_path)

Read query results from JSON file.

Parameters:: file_or_path (FilePath | IO) – Readable file object or file path.
Return type:: QueryResults

results_from_json(data)

Recreate results object from loaded JSON data.

Parameters:: data (dict[str, Any])
Return type:: QueryResults

class gambit.results.ResultsArchiveWriter

Bases: BaseJSONResultsExporter

Exports query results to “archive” format which captures all stored data.

This format is not intended to be read by users of the application. The exported data can be read and converted back into an identical QueryResults object using ResultsArchiveReader.

Only the ID attributes of database models are saved, when loading the saved results the models are recreated by database queries.

to_json(obj)
to_json(gset)
to_json(taxon)
to_json(genome): Convert object to JSON-compatible format (need not work recursively).