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galaxy.tools.data package

extend base tool data table implementations with special implementations requiring full Galaxy dependencies (specifically the refgenie configuration client currently).

class galaxy.tools.data.RefgenieToolDataTable(config_element, tool_data_path, tool_data_path_files, from_shed_config=False, filename=None, other_config_dict=None)

Bases: TabularToolDataTable

Data stored in refgenie

<table name="all_fasta" type="refgenie" asset="fasta" >
    <file path="refgenie.yml" />
    <field name="value" template="true">${__REFGENIE_UUID__}</field>
    <field name="dbkey" template="true">${__REFGENIE_GENOME__}</field>
    <field name="name" template="true">${__REFGENIE_DISPLAY_NAME__}</field>
    <field name="path" template="true">${__REFGENIE_ASSET__}</field>
</table>

dict_collection_visible_keys = ['name']

dict_element_visible_keys = ['name', 'fields']

dict_export_visible_keys = ['name', 'data', 'rg_asset', 'largest_index', 'columns', 'missing_index_file']

type_key: str = 'refgenie'

__init__(config_element, tool_data_path, tool_data_path_files, from_shed_config=False, filename=None, other_config_dict=None) → None

data: List[List[str]]

configure_and_load(config_element, tool_data_path, from_shed_config=False, url_timeout=10)

Configure and load table from an XML element.

parse_column_spec(config_element)

Parse column definitions, which can either be a set of ‘column’ elements with a name and index (as in dynamic options config), or a shorthand comma separated list of names in order as the text of a ‘column_names’ element.

A column named ‘value’ is required.

parse_file_fields(filename, errors=None, here='__HERE__')

Parse separated lines from file and return a list of tuples.

TODO: Allow named access to fields using the column names.

empty_field_value: str

empty_field_values: Dict[str | None, str]

filenames: Dict[str, FileNameInfoT]

class galaxy.tools.data.TabularToolDataField(data: Dict)

Bases: Dictifiable

dict_collection_visible_keys: List[str] = []

__init__(data: Dict)

get_base_path()

get_base_dir()

clean_base_dir(path)

get_files()

get_filesize_map(rm_base_dir=False)

get_fingerprint()

to_dict(view: str = 'collection', value_mapper: Dict[str, Callable] | None = None) → Dict[str, Any]

Return item dictionary.

class galaxy.tools.data.TabularToolDataTable(config_element: Element, tool_data_path: str | PathLike | None, tool_data_path_files: ToolDataPathFiles, from_shed_config: bool = False, filename: str | PathLike | None = None, other_config_dict: StoresConfigFilePaths | None = None)

Bases: ToolDataTable

Data stored in a tabular / separated value format on disk, allows multiple files to be merged but all must have the same column definitions:

<table type="tabular" name="test">
    <column name='...' index = '...' />
    <file path="..." />
    <file path="..." />
</table>

dict_collection_visible_keys = ['name']

dict_element_visible_keys = ['name', 'fields']

dict_export_visible_keys = ['name', 'data', 'largest_index', 'columns', 'missing_index_file']

type_key: str = 'tabular'

__init__(config_element: Element, tool_data_path: str | PathLike | None, tool_data_path_files: ToolDataPathFiles, from_shed_config: bool = False, filename: str | PathLike | None = None, other_config_dict: StoresConfigFilePaths | None = None) → None

data: List[List[str]]

configure_and_load(config_element: Element, tool_data_path: str | PathLike | None, from_shed_config: bool = False, url_timeout: float = 10) → None

Configure and load table from an XML element.

merge_tool_data_table(other_table, allow_duplicates=True, persist=False, **kwd)

handle_found_index_file(filename)

get_fields() → List[List[str]]

get_field(value)

get_named_fields_list() → List[Dict[str | int, str]]

get_version_fields()

parse_column_spec(config_element: Element) → None

Parse column definitions, which can either be a set of ‘column’ elements with a name and index (as in dynamic options config), or a shorthand comma separated list of names in order as the text of a ‘column_names’ element.

A column named ‘value’ is required.

extend_data_with(filename: str, errors: List[str] | None = None) → None

parse_file_fields(filename: str, errors: List[str] | None = None, here: str = '__HERE__') → List[List[str]]

Parse separated lines from file and return a list of tuples.

TODO: Allow named access to fields using the column names.

get_column_name_list() → List[str | None]

get_entry(query_attr: str, query_val: str, return_attr: str, default: None = None)

Returns table entry associated with a col/val pair.

get_entries(query_attr: str, query_val: str, return_attr: str, limit=None) → List

Returns table entries associated with a col/val pair.

get_filename_for_source(source: dict | RepoInfo | DataManager | None, default: str | None = None) → str | None

filter_file_fields(loc_file, values)

Reads separated lines from file and print back only the lines that pass a filter.

property xml_string

to_dict(view: str = 'collection', value_mapper: Dict[str, Callable] | None = None) → Dict[str, Any]

Return item dictionary.

empty_field_value: str

empty_field_values: Dict[str | None, str]

filenames: Dict[str, FileNameInfoT]

class galaxy.tools.data.ToolDataTable(config_element: Element, tool_data_path: str | PathLike | None, tool_data_path_files: ToolDataPathFiles, from_shed_config: bool = False, filename: str | PathLike | None = None, other_config_dict: StoresConfigFilePaths | None = None)

Bases: Dictifiable

type_key: str

data: List[List[str]]

classmethod from_dict(d)

__init__(config_element: Element, tool_data_path: str | PathLike | None, tool_data_path_files: ToolDataPathFiles, from_shed_config: bool = False, filename: str | PathLike | None = None, other_config_dict: StoresConfigFilePaths | None = None) → None

empty_field_value: str

empty_field_values: Dict[str | None, str]

filenames: Dict[str, FileNameInfoT]

get_empty_field_by_name(name: str | None) → str

add_entry(entry: List[str] | Dict[str, str], allow_duplicates: bool = True, persist: bool = False, entry_source: dict | RepoInfo | DataManager | None = None, tool_data_file_path: str | None = None, use_first_file_path: bool = False, **kwd) → int

add_entries(entries: List[List[str]], allow_duplicates: bool = True, persist: bool = False, entry_source: dict | RepoInfo | DataManager | None = None, **kwd) → int

remove_entry(values)

is_current_version(other_version)

merge_tool_data_table(other_table: ToolDataTable, allow_duplicates: bool = True, persist: bool = False, **kwd) → int

reload_from_files() → int

class galaxy.tools.data.ToolDataTableManager(tool_data_path: str, config_filename: str | PathLike | List[str | PathLike] | None = None, tool_data_table_config_path_set=None, other_config_dict: StoresConfigFilePaths | None = None)

Bases: ToolDataTableManager

tool_data_table_types = {'refgenie': <class 'galaxy.tools.data.RefgenieToolDataTable'>, 'tabular': <class 'galaxy.tool_util.data.TabularToolDataTable'>}

data_tables: Dict[str, ToolDataTable]