Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/bioblend/galaxy/tool_data/__init__.py @ 0:4f3585e2f14b draft default tip
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author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 """ |
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2 Contains possible interactions with the Galaxy Tool data tables |
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3 """ |
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4 from bioblend.galaxy.client import Client |
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5 |
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6 |
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7 class ToolDataClient(Client): |
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8 |
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9 def __init__(self, galaxy_instance): |
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10 self.module = 'tool_data' |
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11 super().__init__(galaxy_instance) |
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12 |
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13 def get_data_tables(self): |
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14 """ |
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15 Get the list of all data tables. |
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16 |
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17 :rtype: list |
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18 :return: A list of dicts with details on individual data tables. |
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19 For example:: |
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20 |
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21 [{"model_class": "TabularToolDataTable", "name": "fasta_indexes"}, |
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22 {"model_class": "TabularToolDataTable", "name": "bwa_indexes"}] |
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23 """ |
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24 return self._get() |
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25 |
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26 def show_data_table(self, data_table_id): |
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27 """ |
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28 Get details of a given data table. |
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29 |
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30 :type data_table_id: str |
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31 :param data_table_id: ID of the data table |
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32 |
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33 :rtype: dict |
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34 :return: A description of the given data table and its content. |
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35 For example:: |
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36 |
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37 {'columns': ['value', 'dbkey', 'name', 'path'], |
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38 'fields': [['test id', |
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39 'test', |
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40 'test name', |
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41 '/opt/galaxy-dist/tool-data/test/seq/test id.fa']], |
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42 'model_class': 'TabularToolDataTable', |
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43 'name': 'all_fasta'} |
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44 |
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45 """ |
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46 return self._get(id=data_table_id) |
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47 |
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48 def reload_data_table(self, data_table_id): |
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49 """ |
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50 Reload a data table. |
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51 |
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52 :type data_table_id: str |
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53 :param data_table_id: ID of the data table |
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54 |
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55 :rtype: dict |
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56 :return: A description of the given data table and its content. |
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57 For example:: |
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58 |
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59 {'columns': ['value', 'dbkey', 'name', 'path'], |
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60 'fields': [['test id', |
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61 'test', |
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62 'test name', |
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63 '/opt/galaxy-dist/tool-data/test/seq/test id.fa']], |
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64 'model_class': 'TabularToolDataTable', |
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65 'name': 'all_fasta'} |
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66 """ |
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67 url = self._make_url(data_table_id) + '/reload' |
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68 return self._get(url=url) |
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69 |
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70 def delete_data_table(self, data_table_id, values): |
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71 """ |
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72 Delete an item from a data table. |
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73 |
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74 :type data_table_id: str |
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75 :param data_table_id: ID of the data table |
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76 |
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77 :type values: str |
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78 :param values: a "|" separated list of column contents, there must be a |
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79 value for all the columns of the data table |
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80 |
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81 :rtype: dict |
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82 :return: Remaining contents of the given data table |
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83 """ |
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84 payload = {'values': values} |
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85 return self._delete(payload=payload, id=data_table_id) |