Source code for bioblend.galaxy.tool_data

"""
Contains possible interactions with the Galaxy Tool data tables
"""
from bioblend.galaxy.client import Client


[docs]class ToolDataClient(Client): def __init__(self, galaxy_instance): self.module = 'tool_data' super(ToolDataClient, self).__init__(galaxy_instance)
[docs] def get_data_tables(self): """ 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()
[docs] def show_data_table(self, data_table_id): """ 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)
[docs] def reload_data_table(self, data_table_id): """ 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 = "%s/tool_data/%s/reload" % (self.gi.url, data_table_id) return self._get(url=url)
[docs] def delete_data_table(self, data_table_id, values): """ 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 """ payload = {'values': values} return self._delete(payload=payload, id=data_table_id)