Merge bugfix4.2 branch - #819

Bugfix in hmmer web service

…coding region on the forward strand

…e position on mRNA for the genes leaving on the forward strand

…for the genes leaving on the forward strand

…eceding the coding region

Updating to latest RCSB URLs for 4.2.x

Cherry-pick the c5fa135 commit

…sses

Fix rcsb/symmetry#92: NullPointerException

log slow downloads upon start

The main change hasn't been implemented, so we want tests to fail.
However, the tests exposed some NPE and IO exceptions. These are now
fixed, so the tests fail in the expected manner.

- Use ATP ligand, which is not covered by the ReducedChemCompProvider
- Use the ReducedChemCompProvider as a fallback consistently, preventing
  null chemComp
- Defensive parsing in SimpleMMcifConsumer
- Robust test, doesn't require internet!

Files less than 40 bytes are deleted to allow for gzip headers.

This addresses biojava#703

This is necessary when changing the cache path.

See comments on biojava#774

Use GlobalsHelper.pushState()/restoreState() before and after tests
to ensure that state isn't carried between tests.

This is applied to the AtomCacheTest to fix test regressions
while simplifying the code.

Maven runs tests with a clean environment, so we can't restore PDB_DIR

4LNC was updated to remove the X-Ray experimental method.
This switches the test to 6F2Q, which uses both Neutron & Xray.

Parsing such a file again throws a NumberFormatException.
Further work/discussion of this issue is on biojava#775, but it was blocking
the merging of biojava#774.

Fix biojava#703: Recover from empty structure files in PDB_CACHE_DIR

Uniprot now redirects to https. This fixes the URL, as well as adds
code to do the redirect