Bump setuptools from 67.7.2 to 70.0.0

.github/workflows/mk-bycon-docs.yaml

@@ -16,4 +16,6 @@ jobs:
       - run: pip install pymdown-extensions
       - run: pip install mkdocs-mermaid2-plugin
       - run: pip install mdx_gh_links
+      - run: pip install mkdocstrings-python
+      - run: pip install mkdocs-include-markdown-plugin
       - run: mkdocs gh-deploy --force

.gitignore

@@ -5,14 +5,24 @@ rsrc/remnants
 *.ods#
 *__pycache__*
 site
+logs
+logs/*
 build
 bycon.egg-info
 dist
 bycon/beaconServer/local/*
-.idea/bycon.iml
-.idea/misc.xml
-.idea/vcs.xml
-.idea/bycon.iml
-.idea/bycon.iml
-.idea/misc.xml
-.idea/vcs.xml
+.idea
+logs/inventory/progenetix_UBERON_existing_codes.tsv
+logs/inventory/progenetix_pgxcohort_existing_codes.tsv
+logs/inventory/progenetix_NCITtnm_existing_codes.tsv
+logs/inventory/progenetix_NCITstage_existing_codes.tsv
+logs/inventory/progenetix_NCITsex_existing_codes.tsv
+logs/inventory/progenetix_NCIT_existing_codes.tsv
+logs/inventory/progenetix_icdot_existing_codes.tsv
+logs/inventory/progenetix_icdom_existing_codes.tsv
+logs/inventory/progenetix_GEOseries_existing_codes.tsv
+logs/inventory/progenetix_GenomePlatforms_existing_codes.tsv
+logs/inventory/progenetix_EFOmaterial_existing_codes.tsv
+logs/inventory/progenetix_EDAMoperation_existing_codes.tsv
+logs/inventory/progenetix_cbioportal_existing_codes.tsv
+logs/inventory/progenetix_analysisPipeline_existing_codes.tsv

beaconServer/README.md

@@ -0,0 +1,4 @@
+## `bycon/beaconServer` directory
+
+This directory contains the Beacon app, calling the individual v2
+endpoints.

beaconServer/beacon.py

@@ -0,0 +1,48 @@
+#!/usr/bin/env python3
+
+from bycon import (
+    BYC,
+    BeaconDataResponse,
+    BeaconErrorResponse,
+    BeaconInfoResponse,
+    prdbug,
+    print_json_response
+)
+
+################################################################################
+
+def main():
+    """
+    The type of execution depends on the requested entity defined in the
+    `request_entity_path_id` (or aliases) in `entity_defaults`.
+    The entity is determined from different potential inputs and overwritten
+    by the next one in the order, if existing:
+
+    1. from the path (element after "beacon", e.g. `biosamples` from
+       `/beacon/biosamples/...`)
+    2. from a form value, e.g. `?requestEntityPathId=biosamples`
+    3. from a command line argument, e.g. `--requestEntityPathId biosamples`
+
+    Fallback is `/info` - so the 422 shouldn't be a thing...
+    """
+
+    b_r_c = BYC.get("bycon_response_class", "___none___")
+
+    r = None
+    if b_r_c == "BeaconInfoResponse":
+        r = BeaconInfoResponse().populatedInfoResponse()
+    elif b_r_c == "BeaconDataResponse":
+        r = BeaconDataResponse().dataResponseFromEntry()
+    BeaconErrorResponse().respond_if_errors()
+    if r:
+        print_json_response(r)
+
+    BYC["ERRORS"].append("No correct service path provided. Please refer to the documentation at http://docs.progenetix.org")
+    BeaconErrorResponse().respond_if_errors()
+
+
+################################################################################
+################################################################################
+
+if __name__ == '__main__':
+    main()

bycon/__init__.py

@@ -12,16 +12,14 @@
 
     from config import *
 
-    from args_parsing import *
     from beacon_auth import *
     from beacon_response_generation import *
     from bycon_helpers import *
-    from cgi_parsing import *
     from cytoband_parsing import *
     from dataset_parsing import *
     from genome_utils import *
     from handover_generation import *
-    from parse_filters_request import *
+    from parameter_parsing import *
     from query_execution import *
     from query_generation import *
     from read_specs import *
@@ -30,19 +28,20 @@
     from service_utils import *
     from variant_mapping import *
 
-    byc: object = {
-        "parsed_config_paths": []
-    }
+    # import byconServiceLibs
 
-    read_service_definition_files(byc)
-    # updates `entity_defaults`, `dataset_definitions` and `local_paths`
-    update_rootpars_from_local(LOC_PATH, byc)
-    set_entity_mappings()
-    set_beacon_defaults(byc)
-    parse_arguments(byc)
+    read_service_definition_files()
+    update_rootpars_from_local_or_HOST()
+    rest_path_elements()
+    set_beacon_defaults()
+    arguments_set_defaults()
+    parse_arguments()
+    set_entities()
+    initialize_bycon_service()
+    parse_filters()
 
 except Exception:
-    if not "local" in ENV:
+    if not "___shell___" in ENV:
         print('Content-Type: text/plain')
         print('status: 302')
         print()