Results export

gambit.results

Export query results in various formats.

gambit.results.base

class gambit.results.base.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 (str | PathLike | IO) – Open file-like object or file path to write to.
results (QueryResults) – Results to export.

class gambit.results.base.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 (str | PathLike | 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).

gambit.results.base.asdict_method(recurse=False, **kw): Create a to_json method which calls attrs.asdict() with the given options.

gambit.results.base.export_to_buffer(results, exporter)

Export query results to a StringIO buffer.

Parameters:: results (QueryResults) –
Return type:: StringIO

gambit.results.json

Export results to JSON.

class gambit.results.json.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(input)
to_json(gset)
to_json(taxon)
to_json(genome): Convert object to JSON-compatible format (need not work recursively).

gambit.results.csv

Export query results to CSV.

class gambit.results.csv.CSVResultsExporter

Bases: AbstractResultsExporter

Exports query results in CSV format.

format_opts

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

Type:: Dict[str, Any]

__init__(**format_opts)

export(file_or_path, results)

Write query results to file.

Parameters:

file_or_path (str | PathLike | 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

gambit.results.archive

Export results to JSON.

class gambit.results.archive.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 (str | PathLike | IO) – Readable file object or file path.
Return type:: QueryResults

class gambit.results.archive.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.

install_info

Add results of gambit.util.dev.install_info() to the QueryResults.extra dict.

Type:: bool

__init__(pretty=False, install_info=False)

Method generated by attrs for class ResultsArchiveWriter.

Parameters:

pretty (bool) –
install_info (bool) –

Return type:

None

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