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"""
Contains possible interactions with the Galaxy Tool data tables
"""
from typing import (
Any,
Dict,
List,
TYPE_CHECKING,
)
from bioblend.galaxy.client import Client
if TYPE_CHECKING:
from bioblend.galaxy import GalaxyInstance
class ToolDataClient(Client):
module = "tool_data"
def __init__(self, galaxy_instance: "GalaxyInstance") -> None:
super().__init__(galaxy_instance)
def get_data_tables(self) -> List[Dict[str, Any]]:
"""
Get the list of all data tables.
:rtype: list
:return: A list of dicts with details on individual data tables.
For example::
[{"model_class": "TabularToolDataTable", "name": "fasta_indexes"},
{"model_class": "TabularToolDataTable", "name": "bwa_indexes"}]
"""
return self._get()
def show_data_table(self, data_table_id: str) -> Dict[str, Any]:
"""
Get details of a given data table.
:type data_table_id: str
:param data_table_id: ID of the data table
:rtype: dict
:return: A description of the given data table and its content.
For example::
{'columns': ['value', 'dbkey', 'name', 'path'],
'fields': [['test id',
'test',
'test name',
'/opt/galaxy-dist/tool-data/test/seq/test id.fa']],
'model_class': 'TabularToolDataTable',
'name': 'all_fasta'}
"""
return self._get(id=data_table_id)
def reload_data_table(self, data_table_id: str) -> Dict[str, Any]:
"""
Reload a data table.
:type data_table_id: str
:param data_table_id: ID of the data table
:rtype: dict
:return: A description of the given data table and its content.
For example::
{'columns': ['value', 'dbkey', 'name', 'path'],
'fields': [['test id',
'test',
'test name',
'/opt/galaxy-dist/tool-data/test/seq/test id.fa']],
'model_class': 'TabularToolDataTable',
'name': 'all_fasta'}
"""
url = self._make_url(data_table_id) + "/reload"
return self._get(url=url)
def delete_data_table(self, data_table_id: str, values: str) -> Dict[str, Any]:
"""
Delete an item from a data table.
:type data_table_id: str
:param data_table_id: ID of the data table
:type values: str
:param values: a "|" separated list of column contents, there must be a
value for all the columns of the data table
:rtype: dict
:return: Remaining contents of the given data table
"""
payload = {"values": values}
return self._delete(payload=payload, id=data_table_id)
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