Bycon

This update targets the example database:

* `housekeepers/recordsSampler.py` now provides a method to create an example database (currently hard coded to `examplez`)
based on a query towards a target database e.g. such as
bash
./housekeepers/recordsSampler.py -d progenetix --filters "pgx:icdom-81703,pgx:icdom-94003" --filterLogic OR --limit 222

* the project's `rsrc/mongodump/` directory contains now
- the resulting `examplez` database dump (database contents might change over time)
- a dump of the `_byconServicesDB` to be installed alongside for query support

The [documentation](https://bycon.progenetix.org/installation/#loading-and-maintaining-data) has been updated accordingly.

* fixed new `/ids` services bug
* fixed new `/publication` services bug
* modifications to table definitions
- add `individuals.ethnicity`
- added variants table generation for most frequent parameters

* bringing the documentaion into `bycon`
- seriously using Python heredocs, starting with embedding the main information
about their functionality into the service caller functions
- project root `markdowner.py` now parses services (and some preference
files) into `.md` sources for website generation
* see e.g. <http://bycon.progenetix.org/generated/services/>
- data import documentation at <http://bycon.progenetix.org/importers/>
* revision of `importTablesGenerator.py`

* added a `ontologymapsReplacer.py` service app to (re-) create the `_byconServicesDB.ontologymaps` collection
- this uses the now extended `OntologyMaps` class
* fixed the `schemas` service (recently broken during path parsing refactoring)

* bug fix for query generation for `/datasets` endpoint where `testMode=true`
pragma wasn't interpolated towards alternative response entities
- test with <https://progenetix.org/beacon/datasets/progenetix/biosamples/?testMode=true>
* clean up of location and handling of configuration files, both for the package
and local installs
- renamed `bycon/definitions` back to `bycon/config` since no other local
configs in the package anymore
- removed the previous duplication of local configs since now consistent
hierarchy both for local scripts in the project directory as well as in the
web server context (_i.e._ the `local` directory is at the same level so
local references work)
- removed `install.yaml` and point to `local/local_paths.yaml` during installations
so that no double definition of local paths is needed

2024-10-10 (v2.0.0 "Taito City")

General Summary

The 2.0.0 version of `bycon` represents a milestone release where a general
updated project structure and code base has been established. The main changes involve:

* re-integration of utility functionality into the project
- `byconServices`, `housekeepers`, `importers`, `rsrc` have been (re-)integrated
from `byconaut`
- similarly, `byconServiceLibs` are now part of the `bycon` libraries
* re-structuring of the `beaconServer` apps and calling
- all general Beacon functions in `bycon` are now invoked from a few
classes which correspond to the Beacon response types
* (ongoing) deprecation of non-standard parameters and functions

Recent Additions

* rewrote path parsing and entity selection
- added `path_id_value_bycon_parameter` to map the REST path `{id}`
to a parameter name (e.g. `biosampleId` or `filters` for some services); this removes the separate processing of `request_entity_path_id_value`
later on
* moved more service functions into dedicated modules; most of the service "apps"
now just call the response modules/functions
- this might led to a future removal of the separate apps/module files
and adding the calls directly to `services.py` in the near future...

* general refactoring of the calling from the `beacon.py` app
- remval of all the dedicated caller modules (e.g. `datasets.py`, `filtering_terms.py` ...)
which are now just called by there response functions
* more code streamlining for `byconServices` apps
- mostly removal of executable status
- more removal of functions from main modules (e.g. `ontologymaps` now uses a
separate `OntologyMaps` class in a library module)