Mercurial > repos > tduigou > json_db_config_generating

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author tduigou
date Wed, 11 Jun 2025 16:00:37 +0000
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1 <tool id="json_db_config_generating" name="JSON DB_Config Generating" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
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2 <description>Genarate a JSON file used as DB config</description>
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3 <macros>
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4 <token name="@VERSION_SUFFIX@">2</token>
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5 <token name="@TOOL_VERSION@">0.1.0</token>
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6 </macros>
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7 <command detect_errors="exit_code"><![CDATA[
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8 python3 -c "import json; params = {
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9 'execution': '$db.execution',
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10 'JSON_db_uri': '$db.db_uri',
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11 'JSON_table': '$db.table_name',
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12 'JSON_fragment_column': '$db.fragment_column',
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13 'JSON_sequence_column': '$db.sequence_column',
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14 'JSON_annotation_column': '$db.annotation_column'
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15 }; f = open('$output_json', 'w'); json.dump(params, f, indent=4); f.close()" && echo DEBUG && cat '$output_json'
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16 ]]></command>
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17 <inputs>
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18 <section name="db" title="DB request" expanded="false">
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19 <conditional name="db_request">
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20 <param name="execution" type="boolean" label="Save To DB ?" checked ='false' help="If True the execution key in the json file will be true" />
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21 <when value='true'>
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22 <section name='db_config' title='DB config' expanded='true'>
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23 <param name="db_uri" type="text" label="DB Connection URI" optional="true" />
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24 <param name="table_name" type="text" label="DB Table Name" optional="true" />
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25 <param name="fragment_column" type="text" label="DB IDs Column Name" optional="true" />
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26 <param name="sequence_column" type="text" label="DB Column Contains Sequence For ganbank File" optional="true" />
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27 <param name="annotation_column" type="text" label="DB Column Contains Annotation For Ganbank File" optional="true" />
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28 </section>
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29 </when>
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30 <when value='false'>
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31 <section name='db_config' title='DB config' expanded='false'>
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32 <param name="db_uri" type="text" label="DB Connection URI" optional="true" />
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33 <param name="table_name" type="text" label="DB Table Name" optional="true" />
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34 <param name="fragment_column" type="text" label="DB IDs Column Name" optional="true" />
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35 <param name="sequence_column" type="text" label="DB Column Contains Sequence For ganbank File" optional="true" />
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36 <param name="annotation_column" type="text" label="DB Column Contains Annotation For Ganbank File" optional="true" />
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37 </section>
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38 </when>
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39 </conditional>
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40 </section>
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41 </inputs>
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42 <outputs>
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43 <data name="output_json" format="json" label="JSON Conf" />
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44 </outputs>
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45 <tests>
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46 <!--test execution is true -->
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47 <test>
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48 <conditional name="db_request">
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49 <param name="execution" value="true" />
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50 <param name="db_config|db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" />
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51 <param name="db_config|table_name" value="sample" />
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52 <param name="db_config|fragment_column" value="fragment" />
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53 <param name="db_config|sequence_column" value="sequence" />
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54 <param name="db_config|annotation_column" value="annotation" />
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55 </conditional>
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56 <output name="output_json">
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57 <assert_contents>
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58 <has_json_property_with_text property="execution" text="true" />
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59 <has_json_property_with_text property="JSON_db_uri" text="postgresql://postgres:RK17__at__localhost:5432/test_fragments_db" />
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60 <has_json_property_with_text property="JSON_table" text="sample" />
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61 <has_json_property_with_text property="JSON_fragment_column" text="fragment" />
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62 <has_json_property_with_text property="JSON_sequence_column" text="sequence" />
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63 <has_json_property_with_text property="JSON_annotation_column" text="annotation" />
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64 </assert_contents>
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65 </output>
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66 </test>
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67 <!--test execution is false -->
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68 <test>
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69 <conditional name="db_request">
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70 <param name="db|execution" value="false" />
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71 </conditional>
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72 <output name="output_json">
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73 <assert_contents>
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74 <has_json_property_with_text property="execution" text="false" />
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75 <has_json_property_with_text property="JSON_db_uri" text="" />
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76 <has_json_property_with_text property="JSON_table" text="" />
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77 <has_json_property_with_text property="JSON_fragment_column" text="" />
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78 <has_json_property_with_text property="JSON_sequence_column" text="" />
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79 <has_json_property_with_text property="JSON_annotation_column" text="" />
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80 </assert_contents>
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81 </output>
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82 </test>
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83 </tests>
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84
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85 <help><![CDATA[
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86 JSON DB_Config Generating
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87 =========================
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88
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89 Generate a JSON file to be used as a DB configuration. This JSON file can later be used to access the database via the specified URI, as well as the defined table and column names.
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90 This tool is primarily designed to control the execution of the save_to_db tool by enabling or disabling its execution and by providing the database configuration through a JSON file.
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91
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92 **Parameters**:
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93 ---------------
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94 * **execution key**: The value of execution key in the JSON (true or false)
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95 * **DB Table Name**: Name of the target table in the PostgreSQL database.
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96 * **DB Column Contains Sequence For ganbank File**: Column storing sequence data, expected to start with "ORIGIN".
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97 * **DB Column Contains Annotation For Ganbank File**: Column containing annotation data, to save al part before "ORIGIN" in the .gb file.
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98 * **DB IDs Column Name**: Column holding the unique fragment IDs.
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99 * **DB Connection URI**: URI used to connect to the database (e.g., postgresql://user:password@host:port/DB_name).
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100 * NOTE: This tool is designed to manage the execution of save_to_db within a workflow. If parameters are set directly in save_to_db via the user interface, the JSON file data will be ignored.
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101 ]]></help>
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102 <citations>
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103 <citation type="bibtex">
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104 @unpublished{json_db_config_generating
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105 author = {Ramiz Khaled},
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106 title = {{json_db_config_generating}},
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107 url = {https://github.com/brsynth/},
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108 }
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109 </citation>
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110 </citations>
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111 </tool>