Command to migrate MariaDB database

[amyfromandi]

This branch contains migration code that enables a complete MariaDB to PostgreSQL database migration, as detailed in #60. The script in this pull request should make several key data evolutions:

• [x] Migrate the macrostrat MariaDB database to PostgreSQL, retaining all database tables, rows, etc.
• [x] Merge the resulting database (macrostrat_two, currently) into Macrostrat's PostgreSQL database/macrostrat schema, overwriting tables if needed
• [x] https://github.com/UW-Macrostrat/macrostrat/pull/73: Run PostgreSQL migrations to ensure all constraints/sequences/foreign keys are defined
• [x] https://github.com/UW-Macrostrat/macrostrat/issues/80: Regenerate foreign keys from other schemas (e.g., maps) as needed. This has been moved to future work, based on some complexities identified by @mwestphall.

A successful operation of this script will result in full integration of all data from MariaDB, allowing the Macrostrat API to operate off of a single PostgreSQL database (UW-Macrostrat/macrostrat-api#229)

Architecturally, this should be implemented within the macrostrat command-line application:

• [x] https://github.com/UW-Macrostrat/macrostrat/pull/74:
  • [x] Implement as a macrostrat subcommand, e.g., macrostrat migrate-mariadb (we can figure out the "right" name later)
  • [x] Use database credentials, etc. from macrostrat.toml rather than replicating them elsewhere
  • [x] Use the macrostrat.database module for running SQL commands
  • [x] As much as possible, we should use Docker for command-line processing
• [x] Once this is all validated, we can remove the macrostrat v1 schlep scripts that were the initial version of this process

Latest update:

• restored maria-migrate branch
• added .gitignore file
• refactored compare_data_counts() to compare any two databases passed through as parameters.

Next steps:

• Resolve all discrepancies between the PostgreSQL macrostrat_two database and the development/production macrostrat PostgreSQL database.

[davenquinn]

For data validation summary with these scripts (see #60), can we print row counts, etc. as tables to improve readability (maybe using the rich Python library)?

[amyfromandi]

Removed v1 schlep scripts and moved all index files here schlep-index. Kept schlep scripts for tables that are modified in the pre/post migration scripts in case they are needed for future references i.e. the process scripts. remaining schlep scripts

These changes are referenced from #81