Bycon

* simplification of internal parameter processing
* `bycon` / `byconaut` - new method "variantsbedfile"
- takes over for the previous bedfile/UCSC variants handover generation (removed
from `handover_generation`)
- defaults to bedfile download from variant query
- `output=ucsclink` creates the UCSC link with added bedfile payload
* `byconaut` - refactoring of `frequencymapsCreator.py` to use the standard collation
bundle generation instead of custom queries
* `byconaut` - change of collation retrieval to work now with `collationTypes`
parameter
- this allows to e.g. get all clustered CNV plots for a classification tree:
* `/services/collationplots/?collationTypes=NCIT&minNumber=200`
* bug fix: broken server address in handovers
* bug fix: `id` specific query for collations was broken (delivered all)
* bug fix: mapping of basic chromosome ids (`9`) to refseqs was broken

* new `instance_definitions.yaml` config document in `local`
- this allows to override Beacon instance parameters based on
the URL the service is running under, enabling multiple Beacon
instances per server
* new `analysis_operation` in `analyses` (_i.e._ "pgxAnalysis" in Progenetix
database model) allows now the filtering of analyses based on the type of
genomic profiling performed with its (so far) values:
- `"analysis_operation.id":"EDAM:operation_3961",
"analysis_operation.label":"Copy number variation detection"`
- `"analysis_operation.id":"EDAM:operation_3227",
"analysis_operation.label":"Variant Calling"`

* `BYC_PARS` now as a global parameter, not passed around in methods (formerly
`byc["form_data"]`)
* byconaut: fix of parsing of plot variables (which can be shown through
`&showHelp=true`)
* hot fix: added "protected" status for `external_references` in general empty
field clean-up since the object is required by the front-end (even if empty list)

* refactoring global configs into `bycon/config.py` to slowly get rid of some of
the `byc` -> ... imports (e.g. global DB parameters, collecting warnings...)
* removal of `service_config` parameter & generator code from `bycon`, nof handled
explicitely in the different byconaut services
* fixed `geneVariantRequest` to be selected as type when a `geneId` parameter is
provided
* fixed handovers for non-default datasets by adding the `datasetIds` parameter
to the handover
- bug was based on older design retrieving the dataset id directly from the
handover in the temp storage ...
* moved (partially so far) `external_references` to `references` in biosamples
- reference objects are now standard `id`, `label` term objects
- `references` is an object, i.e. the items are keyed `{"pubmed": {"id": "PMID:1234567", ...`
- regeneration of the reference structure from Beacon/Phenopackets is done at export time
* `byconaut` with new `/services/samplemap/` endpoint for plotting geolocations
of sample data after standard Beacon query
* `filter_definitions`
- fix for arrayexpress series processing (now `AEseries`)
- changed `collatiionType` `PMID` => `pubmed`
* fixed `uploader` fail due to missing import

* more consolidation of argument/cgi parsing libraries
* filter flag parameters now properly defined in `argument_definitions.yaml`
* use of a common `db_config` object for database configuration parameters
* piecemeal move of placeholder parameters from `config.yaml` (either
through removal & fallbacks in methods, or through definition in
`argument_definitions`)
* working on error responses...
* removed generic pre-processing methods for error & general responses
* fixed a bug which allowed non-matching filters to pass
* fixed examples in `tests`
* fixed `POST` processing (wrong `filters` nesting as in examples ...)
* fixed the OpenAPI "endpoints" info for the entry types
- The `openAPIEndpointsDefinition` parameter in http://progenetix.org/beacon/map/
should now point to working definitions per entity, e.g.
https://progenetix.org/services/endpoints/biosamples

* new `ChroNames` class for accessing chromosome and refseq ID mappings (still utilising
`byc["refseq_chromosomes"]` as input, read during init from `rsrc/.../refseq_chromosomes.yaml`)
* `byconaut`: Added a new `plotType=histosparklines` plotting option. It basically modifies
`plot_defaults` parameters for minimal histoplots (no border, no background, small
and narrow), e.g. for use in mouse-overs or in tables
- one can still override those parameters, e.g. with `&plotPars=plotDendrogramWidth=50::plotAreaHeight=32`
* `byconaut`: added option to use sequence id values for plotPars.plot_chros, e.g. `plotPars=plot_width=980::plotChros=NC_000023.11`
* fix: a `g_variants` endpoint w/o any parameter led to a query error
* removal of some `byconaut` code remnants
* some internal reshuffling; e.g. move of export/print helpers to from `cgi_parsing`
to `beacon_response_generation` and `bycon_helpers`