Clickhouse import process #59
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mandawilson
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Oct 18, 2024
scripts/clickhouse_import_support/copy_mysql_database_tables_to_clickhouse.sh
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| get_genetic_profile_id_list_query="SELECT genetic_profile_id FROM genetic_profile WHERE genetic_alteration_type NOT IN ('GENERIC_ASSAY', 'MUTATION_EXTENDED', 'STRUCTURAL_VARIANT')" | ||
| query_argument_template="--query={0}" | ||
| query_argument = query_argument_template.format(get_genetic_profile_id_list_query) | ||
| clickhouse_client_obtain_genetic_profile_id_list = ["clickhouse", "client", "--config-file=clickhouse_client_config_2024-10-14-09-03-02.yaml", query_argument] |
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Should the config-file always hardcoded to this?
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I see below you have a TODO to deal with that.
| @@ -0,0 +1,36 @@ | |||
| DROP TABLE IF EXISTS sample_to_gene_panel_derived; | |||
| DROP TABLE IF EXISTS gene_panel_to_gene_derived; | |||
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Aren't these commands stored somewhere else?
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Yes. This file was a placeholder. I need to add calls to the script which processes the .sql files from the github repo (clickhouse.sql and materialized_views.sql) and bursts them into individual sql statements (1 per file). Also, we need to detect and skip over the special cases (genetic_alteration_derived, generic_assay_data_derived).
So this file will be going away
| return 1 | ||
| fi | ||
| update_management_database_name="${my_properties['mysql_update_management_database']}" | ||
| ### TODO : fix this |
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I think this needs adding back.
| return 1 | ||
| fi | ||
| update_management_database_name="${my_properties['mysql_update_management_database']}" | ||
| ### TODO : fix this |
added 10 commits
November 11, 2024 08:53
also bugfixes added and TODO notes
…rloaded functions that clashed in mysql/sling/clickhouse shell scripts
…les_in_clickhouse_database_by_profile
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- focus on derived table construction and wrap up steps Co-authored-by: Manda Wilson <[email protected]> Co-authored-by: Robert Sheridan <[email protected]>
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Scripts, property files, and documentation for the blue-green deployment strategy to enable MySQL/Clickhouse database updates during cancer study import.