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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)[source]

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[source]
data: List[List[str]]
configure_and_load(config_element, tool_data_path, from_shed_config=False, url_timeout=10)[source]

Configure and load table from an XML element.

parse_column_spec(config_element)[source]

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__')[source]

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

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

class galaxy.tools.data.TabularToolDataField(data: Dict)[source]

Bases: Dictifiable

dict_collection_visible_keys: List[str] = []
__init__(data: Dict)[source]
get_base_path()[source]
get_base_dir()[source]
clean_base_dir(path)[source]
get_files()[source]
get_filesize_map(rm_base_dir=False)[source]
get_fingerprint()[source]
to_dict(view: str = 'collection', value_mapper: Optional[Dict[str, Callable]] = None) Dict[str, Any][source]

Return item dictionary.

class galaxy.tools.data.TabularToolDataTable(config_element: _Element, tool_data_path: Optional[Union[str, PathLike]], tool_data_path_files: ToolDataPathFiles, from_shed_config: bool = False, filename: Optional[Union[str, PathLike]] = None, other_config_dict: Optional[Union[GalaxyAppConfiguration, Dict[str, Any]]] = None)[source]

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: Optional[Union[str, PathLike]], tool_data_path_files: ToolDataPathFiles, from_shed_config: bool = False, filename: Optional[Union[str, PathLike]] = None, other_config_dict: Optional[Union[GalaxyAppConfiguration, Dict[str, Any]]] = None) None[source]
data: List[List[str]]
configure_and_load(config_element: _Element, tool_data_path: Optional[Union[str, PathLike]], from_shed_config: bool = False, url_timeout: float = 10) None[source]

Configure and load table from an XML element.

merge_tool_data_table(other_table, allow_duplicates=True, persist=False, entry_source=None, **kwd)[source]
handle_found_index_file(filename)[source]
get_fields() List[List[str]][source]
get_field(value)[source]
get_named_fields_list() List[Dict[Union[str, int], str]][source]
get_version_fields()[source]
parse_column_spec(config_element: _Element) None[source]

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

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[Optional[str]][source]
get_entry(query_attr: str, query_val: str, return_attr: str, default: None = None)[source]

Returns table entry associated with a col/val pair.

get_entries(query_attr: str, query_val: str, return_attr: str, limit=None) List[source]

Returns table entries associated with a col/val pair.

get_filename_for_source(source: Optional[Union[Dict, DataManager]], default: Optional[str] = None) Optional[str][source]
filter_file_fields(loc_file, values)[source]

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: Optional[Dict[str, Callable]] = None) Dict[str, Any][source]

Return item dictionary.

class galaxy.tools.data.ToolDataTable(config_element: _Element, tool_data_path: Optional[Union[str, PathLike]], tool_data_path_files: ToolDataPathFiles, from_shed_config: bool = False, filename: Optional[Union[str, PathLike]] = None, other_config_dict: Optional[Union[GalaxyAppConfiguration, Dict[str, Any]]] = None)[source]

Bases: Dictifiable

type_key: str
data: List[List[str]]
classmethod from_dict(d)[source]
__init__(config_element: _Element, tool_data_path: Optional[Union[str, PathLike]], tool_data_path_files: ToolDataPathFiles, from_shed_config: bool = False, filename: Optional[Union[str, PathLike]] = None, other_config_dict: Optional[Union[GalaxyAppConfiguration, Dict[str, Any]]] = None) None[source]
get_empty_field_by_name(name)[source]
add_entry(entry: Union[List[str], Dict[str, str]], allow_duplicates: bool = True, persist: bool = False, entry_source=None, **kwd) int[source]
add_entries(entries: List[List[str]], allow_duplicates: bool = True, persist: bool = False, entry_source=None, **kwd) int[source]
remove_entry(values)[source]
is_current_version(other_version)[source]
merge_tool_data_table(other_table: ToolDataTable, allow_duplicates: bool = True, persist: bool = False, entry_source=None, **kwd) int[source]
reload_from_files() int[source]
class galaxy.tools.data.ToolDataTableManager(tool_data_path: str, config_filename: Optional[Union[str, PathLike, List[Union[str, PathLike]]]] = None, tool_data_table_config_path_set=None, other_config_dict: Optional[Union[GalaxyAppConfiguration, Dict[str, Any]]] = None)[source]

Bases: ToolDataTableManager

tool_data_table_types = {'refgenie': <class 'galaxy.tools.data.RefgenieToolDataTable'>, 'tabular': <class 'galaxy.tool_util.data.TabularToolDataTable'>}
data_tables: Dict[str, ToolDataTable]