2.0.2 (start inline doc deparsing)

bycon/__init__.py

@@ -36,6 +36,7 @@
     update_rootpars_from_local_or_HOST()
     rest_path_elements()
     set_beacon_defaults()
+    arguments_set_defaults()
     parse_arguments()
     set_entities()
     initialize_bycon_service()

bycon/byconServiceLibs/bycon_plot.py

@@ -27,7 +27,6 @@
 ################################################################################
 
 class ByconPlotPars:
-
     def __init__(self):
         self.plot_type = BYC_PARS.get("plot_type", "histoplot")
         self.plot_defaults = BYC.get("plot_defaults", {})

bycon/byconServiceLibs/datatable_utils.py

@@ -83,8 +83,8 @@ def import_datatable_dict_line(parent, fieldnames, lineobj, primary_scope="biosa
 ################################################################################
 
 def create_table_header(io_params):
-    """podmd
-    podmd"""
+    """
+    """
     header_labs = [ ]
     for par, par_defs in io_params.items():
         pres = par_defs.get("prefix_split", {})

bycon/byconServiceLibs/export_file_generation.py

@@ -139,7 +139,7 @@ def export_pgxseg_download(datasets_results, ds_id):
 ################################################################################
 
 def write_variants_bedfile(datasets_results, ds_id):
-    """podmd
+    """
     ##### Accepts
 
     * a Bycon `h_o` handover object with its `target_values` representing `_id` 
@@ -157,7 +157,7 @@ def write_variants_bedfile(datasets_results, ds_id):
     +separate configuration entry and subroutine.
     * evaluate to use "bedDetails" format
 
-    podmd"""
+    """
     if not (local_paths := BYC.get("local_paths")):
         return False
     tmp_path = path.join( *local_paths[ "server_tmp_dir_loc" ])

bycon/byconServiceLibs/ontology_utils.py

@@ -15,6 +15,14 @@
 )
 
 class OntologyMaps:
+    """
+    The `OntologyMaps` class is used to create, retrieve and store ontology maps,
+    i.e. the corresponding terms for codes from different ontologies or controlled
+    vocabularies. In the context of the Progenetix Beacon as a data-rich `bycon`
+    deployment, a particlular use is the mapping of codes from different cancer
+    related diagnostic codes, specifically from ICD-O 3 histology/topography doublets
+    with NCIt cancer codes.
+    """
     def __init__(self):
         self.query = {}
         self.term_groups = []

bycon/config/plot_defaults.yaml

@@ -6,7 +6,7 @@
 # `bycon` package.
 
 plot_type_defs:
-
+  
   histoplot:
     description: >-
       The default option, used to plot histograms of the CNV frequencies per
@@ -63,7 +63,6 @@ plot_type_defs:
 #------------------------------------------------------------------------------#
 
 plot_parameters:
-
   # To limit the amount of pre-defined parameters accepted through the `bycon`
   # interface we are using a special syntax for plot parameters. Plot parameters
   # (see below for all pre-defined ones) are provided as a single string to `plotPars`

bycon/config/services_entity_defaults.yaml

@@ -40,7 +40,7 @@ cytomapper:
   beacon_schema:
     entity_type: cytobandMapping
     schema: https://progenetix.org/services/schemas/CytobandMapping/
-  path_id_value_bycon_parameter: cytoBands
+  path_id_value_bycon_parameter: cyto_bands
 
 endpoints:
   request_entity_path_id: endpoints
@@ -78,6 +78,7 @@ geoLocation:
 
 ids:
   request_entity_path_id: ids
+  path_id_value_bycon_parameter: id
 
 intervalFrequencies:
   request_entity_path_id: intervalFrequencies
@@ -155,8 +156,10 @@ sampleplots:
     schema: NA
   path_id_value_bycon_parameter: biosample_ids
 
-schemas:
-  request_entity_path_id: schemas
+byconschemas:
+  request_entity_path_aliases:
+    - schemas
+  request_entity_path_id: byconschemas
   path_id_value_bycon_parameter: id
 
 uploader:

bycon/lib/cgi_parsing.py

@@ -8,14 +8,27 @@
 
 ################################################################################
 
-def parse_arguments():
+class ByconParameters:
+    def __init__(self):
+        self.arg_defs = BYC.get("argument_definitions", {})
+        self.byc_pars = {}
+
+
+################################################################################
+
+def arguments_set_defaults():
     a_defs = BYC.get("argument_definitions", {})
     for a, d in a_defs.items():
         if "default" in d:
             BYC_PARS.update({a: d["default"]})
-    if "local" in ENV:
-        if "local" in d:
+        if "local" in d and "local" in ENV:
             BYC_PARS.update({a: d["local"]})
+
+
+################################################################################
+
+def parse_arguments():
+    if "local" in ENV:
         args_update_form()
     else:
         r_m = environ.get('REQUEST_METHOD', '')