Bycon

This update is mostly addressing the further removal of methods specific for
"beyond Beacon" functionality (e.g. variant binning and calculations for CNVs, plotting ...).

Most of the "special outputs" code has been moved to byconaut -> services.
For legacy reasons (e.g. use by pgxRpi) the webserver configuration needed some
rewrites ... They only apply for the Progenetix use case and are not needed if
sticking to the Beacon formats or if following the use of the new apps like
`services/vcfvariants`). Our (temporary) mappings are:


RewriteEngine On

The following rules are for backward compatibilitty with pgxRpi before Oct 2023

RewriteCond %{QUERY_STRING} ^(.*?output=\w*?table.*?)$
RewriteRule "^/beacon/biosamples.*?$" /cgi-bin/bycon/services/sampletable.py?%1&responseEntityId=biosample [PT]

RewriteCond %{QUERY_STRING} ^(.*?output=\w*?table.*?)$
RewriteRule "^/beacon/individuals.*?$" /cgi-bin/bycon/services/sampletable.py?%1&responseEntityId=individual [PT]

RewriteCond %{QUERY_STRING} ^(.*?output=\w*?table.*?)$
RewriteRule "^/beacon/individuals.*?$" /cgi-bin/bycon/services/sampletable.py?%1&responseEntityId=individual [PT]

RewriteCond %{QUERY_STRING} ^(.*?output=\w*?matrix.*?)$
RewriteRule "^/beacon/analyses.*?$" /cgi-bin/bycon/services/samplematrix.py?%1&responseEntityId=analysis [PT]

RewriteCond %{QUERY_STRING} ^(.*?output=vcf.*?)$
RewriteRule "^/beacon/biosamples/([^/]+?)/g_variants.*?$" /cgi-bin/bycon/services/vcfvariants.py?%1&biosampleIds=$1 [PT]

RewriteCond %{QUERY_STRING} ^(.*?output=pgxseg.*?)$
RewriteRule "^/beacon/biosamples/([^/]+?)/g_variants.*?$" /cgi-bin/bycon/services/pgxsegvariants.py?%1&biosampleIds=$1 [PT]

This version removes the complete `bycon_plot` code (_i.e._ moves it to `byconaut`).
It still needs the further disentangling of the other alternative response options
(`.pgxseg`, `.pgxmatrix` ...) from the resultsets generation; this soon will follow
blueprint of the plot code removal.

**CAVE** Now all plotting options have been shifted to the `/services/collationplots`
and `/services/sampleplots` entry points.

This version provides another step in moving "non-standard" Beacon responses tp
the `byconeer` project.

* creatiing a `.../services/sampleplots/` entry point which will be used to handle
the sample (strips/clustered; histoplots from search results ...) web plotting
instead of adding the `output=histoplot` etyc. option to standard Beacon queries
- plot types can now be specified through `plotType=samplesplot` etc.
* some class (`ByconResultSets`) restructuring to allow plot outputs (this will be
changed further, probably moving the whole plot ... classes and methods to `byconeer`)

This is an extensive internal code update which

* moves service response generation to byconaut (implemented as `ByconServiceResponse`
class w/ its methods)
* removes many of the methods from `service_utils` since they have been implemented
in the beacon or services response classes and (mostly) limits the library to
general/initialization methods (still more to clean...)
* fixes some inconsistencies (e.g. snake vs. camel cases in paths where sometimes
non-standard versions were documented - now using the Beacon v2 defaults such as
`beacon/filtering_terms/` instead of `beacon/filteringTerms/`)
* similar for geo queries (e.g. `geoLatitude` as query parameter instead of `geolatitude`)
though this is "BeaconPlus" anyway

**CAVE**: These changes also affect the front-ends (`progenetix-web`, `beaconplus-web` etc.)
which need to be recompiled from the latest versions

* some defaults cleaning (e.g. removal of non-standard paths from built in `beacon_defaults`)