GenBank/RefSeq Update Testing
There is currently no automated test suite for the GenBank update process.
Due to dependency on a large amount of external data, this is going to be a
bit tricky to implement. Currently a set of tools and procedures is used to
assist with testing.
Test programs and scripts
gbIndexTest
- Program to load and dump parts of the the
index files. Useful for testing the loading code and verifying the
contents of the index.
gbGetTestSubset
- Generate a subset download area for
testing. This requires a full download and a completed process step. This
extracts a small subset for testing the alignment and database loading
steps. List of extracted accessions can be saved for one release and then
used as extra access to extract from another release. This can then be
used for psl migration testing.
dump-test-tables
- Script to dump tables from a test
database in a form that can be diffed.
Testing methodology
- To aid in test incremental processing, update directories that are
not readable will be skipped. This allows changing view of what is
available for processing with
chmod
rather than moving
directories.