Mercurial > repos > shellac > sam_consensus_v3
diff env/lib/python3.9/site-packages/bioblend/galaxy/tool_data/__init__.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/env/lib/python3.9/site-packages/bioblend/galaxy/tool_data/__init__.py Mon Mar 22 18:12:50 2021 +0000 @@ -0,0 +1,85 @@ +""" +Contains possible interactions with the Galaxy Tool data tables +""" +from bioblend.galaxy.client import Client + + +class ToolDataClient(Client): + + def __init__(self, galaxy_instance): + self.module = 'tool_data' + super().__init__(galaxy_instance) + + 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() + + 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) + + 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 = self._make_url(data_table_id) + '/reload' + return self._get(url=url) + + 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 + + :rtype: dict + :return: Remaining contents of the given data table + """ + payload = {'values': values} + return self._delete(payload=payload, id=data_table_id)