Difference between revisions of "Clinical Trials Loading"
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2. SQL queries to create a new clinical trial schema and table are located in zinc code: | 2. SQL queries to create a new clinical trial schema and table are located in zinc code: | ||
| − | SQL_statement/clinical_trial | + | zinc/SQL_statement/clinical_trial.sql |
| − | 3. | + | 3. Load raw data to the database tables: |
| + | If you want to delete all the existing data, then use --wipe | ||
| + | Otherwise it will load data incrementally to the existing data. | ||
| + | |||
| + | source /nfs/soft/www/apps/zinc15/envs/dev/bin/activate | ||
| + | python /nfs/soft/www/apps/zinc15/envs/dev/bin/zinc-manage utils clinical-trials load_ct /nfs/db/trials/important/studies.txt | ||
| + | python /nfs/soft/www/apps/zinc15/envs/dev/bin/zinc-manage utils clinical-trials load_condition /nfs/db/trials/important/browse_conditions.txt | ||
| + | python /nfs/soft/www/apps/zinc15/envs/dev/bin/zinc-manage utils clinical-trials load_intervention /nfs/db/trials/important/interventions.txt | ||
Revision as of 19:58, 24 August 2017
1. Relevant Files: /nfs/db/trials/important --> clinical trials raw data /nfs/home/teague/work/Projects/trials/extract.py --> script to clean the raw data http://wiki.docking.org/index.php/Creating_clinical_name_mappings --> how to create name_mappings
2. SQL queries to create a new clinical trial schema and table are located in zinc code:
zinc/SQL_statement/clinical_trial.sql
3. Load raw data to the database tables: If you want to delete all the existing data, then use --wipe Otherwise it will load data incrementally to the existing data.
source /nfs/soft/www/apps/zinc15/envs/dev/bin/activate python /nfs/soft/www/apps/zinc15/envs/dev/bin/zinc-manage utils clinical-trials load_ct /nfs/db/trials/important/studies.txt python /nfs/soft/www/apps/zinc15/envs/dev/bin/zinc-manage utils clinical-trials load_condition /nfs/db/trials/important/browse_conditions.txt python /nfs/soft/www/apps/zinc15/envs/dev/bin/zinc-manage utils clinical-trials load_intervention /nfs/db/trials/important/interventions.txt