[DC-3729] Generate derived tables #1854
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nishanthpp93
requested changes
Feb 13, 2024
data_steward/cdr_cleaner/cleaning_rules/generate_derived_tables.py
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data_steward/cdr_cleaner/cleaning_rules/generate_derived_tables.py
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| POPULATE_OBS_PRD = JINJA_ENV.from_string(""" | ||
| INSERT INTO `{{project_id}}.{{dataset_id}}.{{storage_table_name}}` | ||
| SELECT person_id, |
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Suggested change
| SELECT person_id, | |
| SELECT ROW_NUMBER() OVER (ORDER BY person_id) AS observation_period_id, | |
| person_id, |
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Let me know when you add this
nishanthpp93
requested changes
Feb 29, 2024
| """ | ||
| :return: a list of SQL strings to run | ||
| """ | ||
| create_sandbox_table_list = [] |
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Rename for clarity
Suggested change
| create_sandbox_table_list = [] | |
| create_derived_table_list = [] |
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| POPULATE_OBS_PRD = JINJA_ENV.from_string(""" | ||
| INSERT INTO `{{project_id}}.{{dataset_id}}.{{storage_table_name}}` | ||
| SELECT person_id, |
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Let me know when you add this
| """) | ||
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| POPULATE_OBS_PRD = JINJA_ENV.from_string(""" | ||
| INSERT INTO `{{project_id}}.{{dataset_id}}.{{storage_table_name}}` |
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Add cols for all 3 queries
Suggested change
| INSERT INTO `{{project_id}}.{{dataset_id}}.{{storage_table_name}}` | |
| INSERT INTO `{{project_id}}.{{dataset_id}}.{{storage_table_name}}` {{cols}} |
| dataset_id=self.dataset_id, | ||
| sandbox_dataset_id=self.sandbox_dataset_id, | ||
| ehr_cutoff_date=self.ehr_cutoff_date, | ||
| storage_table_name=OBSERVATION_PERIOD) |
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Add cols, and fields can be retrieved from the schema json
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| storage_table_name=OBSERVATION_PERIOD) | |
| storage_table_name=OBSERVATION_PERIOD, | |
| cols=f"({','.join(fields_list)})") |
nishanthpp93
reviewed
Mar 4, 2024
| FROM `{{project_id}}.{{dataset_id}}.person` AS pt | ||
| JOIN `{{project_id}}.{{dataset_id}}.visit_occurrence` AS vt ON pt.person_id = vt.person_id | ||
| JOIN `{{project_id}}.{{dataset_id}}.visit_occurrence_ext` AS e ON vt.visit_occurrence_id = e.visit_occurrence_id | ||
| WHERE src_id LIKE '%EHR%' |
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We can remove this EHR restrictions from all the tables.
| FROM `{{project_id}}.{{dataset_id}}.person` AS pt | ||
| JOIN `{{project_id}}.{{dataset_id}}.visit_occurrence` AS vt ON pt.person_id = vt.person_id | ||
| JOIN `{{project_id}}.{{dataset_id}}.visit_occurrence_ext` AS e ON vt.visit_occurrence_id = e.visit_occurrence_id | ||
| AND EXTRACT(YEAR FROM vt.visit_start_date) >= 1985 |
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These can be updated to "WHERE"
Suggested change
| AND EXTRACT(YEAR FROM vt.visit_start_date) >= 1985 | |
| WHERE EXTRACT(YEAR FROM vt.visit_start_date) >= 1985 |
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generate derived table on deid step cleaning rule.