Created
September 30, 2019 13:33
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Export OnDemand Job Composer Database to CSV
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| #!/usr/bin/env python | |
| import csv | |
| import json | |
| import os.path | |
| import sqlite3 | |
| def flatten_results(row): | |
| result = dict(**row) | |
| result.update(json.loads(row['job_cache'])) | |
| return result | |
| def main(): | |
| path = os.path.expanduser('~/ondemand/data/sys/myjobs/production.sqlite3') | |
| db = sqlite3.connect(path) | |
| db.row_factory = sqlite3.Row | |
| conn = db.cursor() | |
| with open(os.path.expanduser('job_composer_export.csv'), 'w') as output_file: | |
| headers = ('pbsid', 'cluster', 'created', 'host', 'name', 'status', 'script') | |
| query = ''' | |
| SELECT | |
| j.created_at as created, w.name as name, | |
| j.job_cache as job_cache, w.batch_host as cluster, | |
| j.status as status | |
| FROM jobs AS j | |
| LEFT JOIN workflows AS w ON j.workflow_id = w.id; | |
| ''' | |
| writer = csv.DictWriter(output_file, headers) | |
| writer.writeheader() | |
| writer.writerows([ | |
| dict( (k, v) for k, v in row.items() if k in headers ) | |
| for row in map( | |
| flatten_results, | |
| conn.execute(query).fetchall() | |
| ) | |
| ]) | |
| if __name__ == '__main__': | |
| main() |
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