public class UpdateMarkerAndDNA_idxes
Once I have the datasets fixed, this class should not be needed. What it does: Initially the marker_idx and dnarun_idx columns of the dataset_marker and dataset_dnarun tables respectively were not populated. They are now needed and are populated. Kevin Palis created a couple scripts to handle populating these fields in tables when they were missing. These scripts live with the gobii_ifl_scripts on CBSU, and are called update_marker_idx.py and update_dnarun_idx.py. For GOBII, then are in the rpository at the same level as the gobii_ifl.py scrips. The file below creates an intermediate file that will be worked on by the preprocess_ifile.py script. You can also run the gobii_ifl.py script instead if you uncomment the "return" statement that occurs after the preprocess_ifile.py script has been called. Here is the order: 1. Run this class to create the needed files (DS_X.mh5i and DS_X.sh5i) 2. sftp these files to cbsudc01.tc.cornell into /workdir/lcj34/postgresFiles/update_idxes_files dir 3. Run the file through gobii_ifl.scripts (change the script to return after the preprocess_ifl.py step !!) python gobii_ifl.py -c postgresql://lcj34:@localhost:5432/gobii_maize2 -i /workdir/lcj34/postgresFiles/update_idxes_files/DS_5.sh5i -o /tmp/ -v 4. Run the /tmp/ppd_* file created in step 3 through the update_dnarun_idx.py or update_marker_idx.py script python update_dnarun_idx.py "postgresql://lcj34:@cbsudc01.tc.cornell.edu/gobii_maize2" /tmp/ppd_DS_5.sh5i 5 5. Verify the db has values for dataset_marker.marker_idx and dataset_dnarun.dnarun_idx for the specified dataset_id. 6. Change the gobii_ifl.py script to re-comment the "return" after the preprocess_ifl call