updated CCS DOI, other tweaks

added PCL mappings, as hinted by Evan (plus other updates)

Todor Kondic authored 4 years ago and Emma Schymanski committed 4 years ago

The input and build scripts have so far been tightly coupled. For
example, the filter list input had to have a specific order and each
time it was necessary to add another category of pubchem to pubchemlite,
it was needed to create a matching condition in rest_grab_props.pl.

This unnecessarily inflexible approach was replaced by two different
inputs -- a mapping file which creates a relationship between the
pubchem table of contents and the metfrag columns and a manifest file in
a human-readable YAML format which allows user to direct build in a
convenient fashion.

Logging and error interception was further improved.

The most important changes are reflected in the top-level driver
script pb-driver-lite.sh and rest_grab_props.pl . The new file
read_manifest.pl is generating the filter bits and the legend file used
by rest_grab_props.pl to set up MetFrag column headers.