Review PPI database-loading script

[dondi]

@ntran18 has run into some issues with the PPI loading code/documentation in beta (script doesn’t complete; tables do not get populated). We should compare this to what @nchun2 is seeing and in general troubleshoot what might be going on

This may include temporarily (or permanently) revising the scripts to produce better feedback while running so that the user can take note of any progress/issues

[ntran18]

Actually generate_protein_network.py would not populate any data into the database tables. It will create 5 different files that will later be used to populate data. Therefore, the tables don't contain any data.

After that, python3 loader.py | psql postgresql://localhost/postgres this script actually populates data into the database. It might stop because of duplicate protein Aad6p (might want to bold 1 from Aad16p to have a better distinguish between Aad6p and Aad16p.

After fixing the duplicate protein, if we run the script again, there might be some data already in the table. Thus, having more errors on duplicate keys. My solution was to add Truncate tables to remove existing data, and populate data again.

[dondi]

We need to look at the current deployed beta to make sure things are functional. @ntran18 and @nchun2 can re-run the scripts to test functionality on a pre-existing database; @ceciliazaragoza and @akaiap will be running these scripts for the for the first time as a part of #1078 and can also report back on functionality

[kdahlquist]

@ceciliazaragoza was able to get the PPI database running OK. But @akaiap wasn't. She'll see @dondi in office hours to troubleshoot, so we'll keep this open for a little while longer.

[dondi]

@akaiap and @dondi worked on this last Thursday and got the issues resolved