The pre-job is meant to exit quietly if the prerequisite data is not
available yet. However, the epi pre-job check was raising an error
if AlternativeSuccessFileTemplate was missing from the config for
either Deposition or Environment. This is now handled quietly too.
CAUTION: This means the epi component will never raise an error
for missing input data, i.e., no email will ever say epi has failed to
run.

The WRSIS download KEY column is an intger which made a problem in the survey data remove subprocess. The solution is to read the KEY column always as a string.

Date formating is necessery for the WRSIS API.

1) There is now a python alternative to the R-based wheat-source-
generation, called source_gen. The functionality to call source_gen
has been added (see ProcessorSurveys.pyL939 and L1032-1040), but not
yet switched on while we await testing of
output at the Met Office.

2) ProcessorComponents was huge (2100 lines!) and the structure was
not apparent. Each component's supporting functions are now in a
separate directory. There is also a ProcessorServer.py relating to
file down/up-loads. ProcessorComponents is now essentially a directory
 to import all the functions. This might inspire a more systematic
 (object-oriented?) structure for each component within coordinator
 in the future.

9-use-mo-nc-files-rather-than-name

See merge request gilligan-epid/wheat-rusts/ews-coordinator!4

reading NAME.nc files rather than NAME.txt files (#19)

simplifying the import required to a single statement by putting generate_all_jobs within the job_runner file

reverting code to run in the standard way (running with overwrite as false, etc). Removing redundant code from EnvSuitPipeline.py

There are now three different functions used to download surveys from
three different server types: ODK, kobotoolbox and WRSIS. All three
functions can use past downloads if there is no connection currently, but
they have different hard-coded settings. This fix makes them
consistent and configurable with the config parameter
['Survey']['AcceptableDowntimeDays'].

import and shell script changes to use new plotting and met_extractor (now met_processing) package structures

An input argument config['Epidemiology']['Deposition']['VariableNames']
is expected as a list, so that a different variable name can be loaded
 for each listed disease. The list parsing has a bug, and is picked up
only now because the config file now provides a list of variable names.