update db upload documentation

quanted · Jan 31, 2025 · 926fc29 · 926fc29
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diff --git a/database/DATA_INITIALIZATION.md b/database/DATA_INITIALIZATION.md
@@ -3,7 +3,7 @@ The four steps listed below are required to initialize the database and configur
 
 # Table Creation  
 The application is currently set up to work with a PostGreSQL database.  Run the DDL in _ms1_batch_search_table_ddl.sql_ 
-to create the table and properly index it.
+to create the table and properly index it. If the table already exists be sure to back it up somewhere.
 
     $ psql -h %host -p $port --dbname %databaseName --user %username < ms1_batch_search_table_ddl.sql 
 
@@ -17,10 +17,16 @@ associated with the %username input in the command.  If you would like the data
     $ mysql -h mysql-ip-m.epa.gov -u %username -p prod_dsstox <data_extraction.sql> ms1_data.tsv
 
 # Data Upload
-Login into PostGreSQL instance that will be used to service the nta_flask application.  Run the following command at
+Login into PostGreSQL instance that will be used to service the nta_flask application.  
+
+Run the following command at
 postgres command line prompt while in the database intended for use.
 
-    # \COPY ms1_batch_search (msr_dsstox_compound_id, msr_monoisotopic_mass,msr_smiles,msr_mol_formula, dsstox_substance_id,preferred_name,casrn,jchem_inchi_key,acd_iupac_name,mol_formula,monoisotopic_mass,total_median,expocast_comptox_link,nhanes_comptox_link,assay_count_active,assay_count_total) from '%path2File' with delimiter E'\t' null as 'NULL' csv header 
+    # \COPY ms1_batch_search (msr_dsstox_compound_id, msr_monoisotopic_mass,msr_smiles,msr_mol_formula, dsstox_substance_id,preferred_name,casrn,jchem_inchi_key,acd_iupac_name,mol_formula,monoisotopic_mass,total_median,expocast_comptox_link,nhanes_comptox_link,assay_count_active,assay_count_total,data_sources) from '%path2File' with delimiter E'\t' null as 'NA' csv header 
+
+Then grant the 'ntauser' read-only access to the new table.
+
+    GRANT SELECT ON ms1_batch_search to ntauser;
 
 
 

diff --git a/database/ms1_batch_search_table_ddl.sql b/database/ms1_batch_search_table_ddl.sql
@@ -7,7 +7,7 @@ CREATE TABLE ms1_batch_search (
   msr_smiles TEXT NULL,
   msr_mol_formula VARCHAR(255) NULL,
   dsstox_substance_id VARCHAR(45) NULL,
-  preferred_name VARCHAR(255) NULL,
+  preferred_name TEXT NULL,
   casrn VARCHAR(45) NULL,
   jchem_inchi_key VARCHAR(45) NULL,
   acd_iupac_name TEXT NULL,