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. To load the data from raw data:
+
  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