Mercurial > repos > shellac > sam_consensus_v3
comparison 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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-1:000000000000 | 0:4f3585e2f14b |
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1 """ | |
2 Contains possible interactions with the Galaxy Tool data tables | |
3 """ | |
4 from bioblend.galaxy.client import Client | |
5 | |
6 | |
7 class ToolDataClient(Client): | |
8 | |
9 def __init__(self, galaxy_instance): | |
10 self.module = 'tool_data' | |
11 super().__init__(galaxy_instance) | |
12 | |
13 def get_data_tables(self): | |
14 """ | |
15 Get the list of all data tables. | |
16 | |
17 :rtype: list | |
18 :return: A list of dicts with details on individual data tables. | |
19 For example:: | |
20 | |
21 [{"model_class": "TabularToolDataTable", "name": "fasta_indexes"}, | |
22 {"model_class": "TabularToolDataTable", "name": "bwa_indexes"}] | |
23 """ | |
24 return self._get() | |
25 | |
26 def show_data_table(self, data_table_id): | |
27 """ | |
28 Get details of a given data table. | |
29 | |
30 :type data_table_id: str | |
31 :param data_table_id: ID of the data table | |
32 | |
33 :rtype: dict | |
34 :return: A description of the given data table and its content. | |
35 For example:: | |
36 | |
37 {'columns': ['value', 'dbkey', 'name', 'path'], | |
38 'fields': [['test id', | |
39 'test', | |
40 'test name', | |
41 '/opt/galaxy-dist/tool-data/test/seq/test id.fa']], | |
42 'model_class': 'TabularToolDataTable', | |
43 'name': 'all_fasta'} | |
44 | |
45 """ | |
46 return self._get(id=data_table_id) | |
47 | |
48 def reload_data_table(self, data_table_id): | |
49 """ | |
50 Reload a data table. | |
51 | |
52 :type data_table_id: str | |
53 :param data_table_id: ID of the data table | |
54 | |
55 :rtype: dict | |
56 :return: A description of the given data table and its content. | |
57 For example:: | |
58 | |
59 {'columns': ['value', 'dbkey', 'name', 'path'], | |
60 'fields': [['test id', | |
61 'test', | |
62 'test name', | |
63 '/opt/galaxy-dist/tool-data/test/seq/test id.fa']], | |
64 'model_class': 'TabularToolDataTable', | |
65 'name': 'all_fasta'} | |
66 """ | |
67 url = self._make_url(data_table_id) + '/reload' | |
68 return self._get(url=url) | |
69 | |
70 def delete_data_table(self, data_table_id, values): | |
71 """ | |
72 Delete an item from a data table. | |
73 | |
74 :type data_table_id: str | |
75 :param data_table_id: ID of the data table | |
76 | |
77 :type values: str | |
78 :param values: a "|" separated list of column contents, there must be a | |
79 value for all the columns of the data table | |
80 | |
81 :rtype: dict | |
82 :return: Remaining contents of the given data table | |
83 """ | |
84 payload = {'values': values} | |
85 return self._delete(payload=payload, id=data_table_id) |