2.0.9

Mostly work on schemas and generated documentation:

* removing examples etc. from the schemas since they're not tracked and don't represent anything bycon specific
* adjusting $ref pointers to use progenetix instead of the beacon-v2 Github files (which is an odd design anyway)
* starting to improve top-level "description"s in schemas, which are then parsed using `markdowner.py`

bycon/config/entity_defaults.yaml

@@ -1,76 +1,59 @@
-info:
-  description: >-
-    The `info` endpoint provides information about the Beacon, such as its name,
-    the organization responsible for the Beacon, a contact email,
-    and the API version. It is based on the GA4GH `service-info` standard.
-  request_entity_path_id: info
-  request_entity_path_aliases:
-    - "/"
-    - "service-info"
-    - "service_info"
-  response_entity_id: info
-  response_schema: beaconInfoResponse
-  bycon_response_class: BeaconInfoResponse
-  beacon_schema:
-    entity_type: configuration
-    schema: https://progenetix.org/services/schemas/beaconInfoResults/
-  is_beacon_entity: true
-  content: {}
-
-################################################################################
-
-beaconMap:
-  description: >-
-    The `beaconMap` object provides a map of the Beacon's REST endpoints.
-  request_entity_path_id: map
-  response_entity_id: beaconMap
-  collection: Null
-  response_schema: beaconMapResponse
-  bycon_response_class: BeaconInfoResponse
-  beacon_schema:
-    entity_type: map
-    schema: https://progenetix.org/services/schemas/beaconMapSchema/
-  is_beacon_entity: true
-
-################################################################################
-
-configuration:
-  request_entity_path_id: configuration
-  response_entity_id: configuration
+dataset:
+  request_entity_path_id: datasets
+  response_entity_id: dataset
   collection: Null
-  response_schema: beaconConfigurationResponse
-  bycon_response_class: BeaconInfoResponse
+  response_schema: beaconCollectionsResponse
+  bycon_response_class: BeaconDataResponse
   beacon_schema:
-    entity_type: configuration
-    schema: https://progenetix.org/services/schemas/beaconConfigurationSchema/
+    entity_type: dataset
+    schema: https://progenetix.org/services/schemas/dataset/
+  pagination:
+    skip: 0
+    limit: 10
   is_beacon_entity: true
+  path_id_value_bycon_parameter: dataset_ids
+  examples:
+    - /progenetix
 
-################################################################################
+##############################################################################
 
-entryType:
-  request_entity_path_id: entry_types
-  response_entity_id: entryType
-  collection: Null
-  response_schema: beaconEntryTypesResponse
-  bycon_response_class: BeaconInfoResponse
+cohort:
+  request_entity_path_id: cohorts
+  response_entity_id: cohort
+  collection: collations
+  response_schema: beaconCollectionsResponse
+  bycon_response_class: BeaconDataResponse
   beacon_schema:
-    entity_type: entryType
-    schema: https://progenetix.org/services/schemas/entryTypesSchema/
+    entity_type: cohort
+    schema: https://progenetix.org/services/schemas/cohort/
+  pagination:
+    skip: 0
+    limit: 10
   is_beacon_entity: true
+  path_id_value_bycon_parameter: filters
 
 ################################################################################
 
-filteringTerm:
-  request_entity_path_id: filtering_terms
-  response_entity_id: filteringTerm
-  collection: collations
-  response_schema: beaconFilteringTermsResponse
+genomicVariant:
+  request_entity_path_id: g_variants
+  request_entity_path_aliases:
+    - genomicVariations
+    - variants
+  response_entity_id: genomicVariant
+  collection: variants
+  response_schema: beaconResultsetsResponse
   bycon_response_class: BeaconDataResponse
   beacon_schema:
-    entity_type: filteringTerm
-    schema: https://progenetix.org/services/schemas/filteringTermsSchema/
+    entity_type: genomicVariant
+    schema: https://progenetix.org/services/schemas/genomicVariant/
+  h->o_access_key: variants.id
   is_beacon_entity: true
-  path_id_value_bycon_parameter: filters
+  path_id_value_bycon_parameter: variant_ids
+  examples:
+    - /pgxvar-5bab576a727983b2e00b8d32
+    - /pgxvar-5bab576a727983b2e00b8d32/individuals
+    - ?geneId=CDKN2A&variantMaxSize=100000&limit=5
+    - ?referenceName=NC_000017.11&start=7577120&referenceBases=G&alternateBases=A
 
 ################################################################################
 
@@ -87,6 +70,21 @@ analysis:
   is_beacon_entity: true
   path_id_value_bycon_parameter: analysis_ids
 
+##############################################################################
+
+run:
+  request_entity_path_id: runs
+  response_entity_id: run
+  collection: analyses  
+  response_schema: beaconResultsetsResponse
+  bycon_response_class: BeaconDataResponse
+  beacon_schema:
+    entity_type: run
+    schema: https://progenetix.org/services/schemas/run/
+  h->o_access_key: analyses.id
+  is_beacon_entity: true
+  path_id_value_bycon_parameter: run_ids
+
 ################################################################################
 
 biosample:
@@ -103,28 +101,10 @@ biosample:
   h->o_access_key: biosamples.id
   is_beacon_entity: true
   path_id_value_bycon_parameter: biosample_ids
-  tests:
+  examples:
     - ?filters=NCIT:C4017&limit=3
+    - ?referenceName=refseq:NC_000009.12&variantType=EFO:0030067&start=21000000,21975098&end=21967753,23000000&filters=NCIT:C3058&limit=10
 
-##############################################################################
-
-genomicVariant:
-  request_entity_path_id: g_variants
-  request_entity_path_aliases:
-    - genomicVariations
-    - variants
-  response_entity_id: genomicVariant
-  collection: variants
-  response_schema: beaconResultsetsResponse
-  bycon_response_class: BeaconDataResponse
-  beacon_schema:
-    entity_type: genomicVariant
-    schema: https://progenetix.org/services/schemas/genomicVariant/
-  h->o_access_key: variants.id
-  is_beacon_entity: true
-  path_id_value_bycon_parameter: variant_ids
-  tests:
-    - ?geneId=CDKN2A&variantMaxSize=100000&limit=5
 
 ##############################################################################
 
@@ -140,55 +120,84 @@ individual:
   h->o_access_key: individuals.id
   is_beacon_entity: true
   path_id_value_bycon_parameter: individual_ids
-  tests:
+  examples:
     - ?filters=EFO:0030049&limit=5
 
-##############################################################################
 
-run:
-  request_entity_path_id: runs
-  response_entity_id: run
-  collection: analyses  
-  response_schema: beaconResultsetsResponse
+################################################################################
+
+filteringTerm:
+  request_entity_path_id: filtering_terms
+  response_entity_id: filteringTerm
+  collection: collations
+  response_schema: beaconFilteringTermsResponse
   bycon_response_class: BeaconDataResponse
   beacon_schema:
-    entity_type: run
-    schema: https://progenetix.org/services/schemas/run/
-  h->o_access_key: analyses.id
+    entity_type: filteringTerm
+    schema: https://progenetix.org/services/schemas/filteringTermsSchema/
   is_beacon_entity: true
-  path_id_value_bycon_parameter: run_ids
+  path_id_value_bycon_parameter: filters
+
 
 ################################################################################
 
-cohort:
-  request_entity_path_id: cohorts
-  response_entity_id: cohort
-  collection: collations
-  response_schema: beaconCollectionsResponse
-  bycon_response_class: BeaconDataResponse
+info:
+  description: >-
+    The `info` endpoint provides information about the Beacon, such as its name,
+    the organization responsible for the Beacon, a contact email,
+    and the API version. It is based on the GA4GH `service-info` standard.
+  request_entity_path_id: info
+  request_entity_path_aliases:
+    - "/"
+    - "service-info"
+    - "service_info"
+  response_entity_id: info
+  response_schema: beaconInfoResponse
+  bycon_response_class: BeaconInfoResponse
   beacon_schema:
-    entity_type: cohort
-    schema: https://progenetix.org/services/schemas/cohort/
-  pagination:
-    skip: 0
-    limit: 10
+    entity_type: configuration
+    schema: https://progenetix.org/services/schemas/beaconInfoResults/
   is_beacon_entity: true
-  path_id_value_bycon_parameter: filters
+  content: {}
 
-##############################################################################
+################################################################################
 
-dataset:
-  request_entity_path_id: datasets
-  response_entity_id: dataset
+beaconMap:
+  description: >-
+    The `beaconMap` object provides a map of the Beacon's REST endpoints.
+  request_entity_path_id: map
+  response_entity_id: beaconMap
   collection: Null
-  response_schema: beaconCollectionsResponse
-  bycon_response_class: BeaconDataResponse
+  response_schema: beaconMapResponse
+  bycon_response_class: BeaconInfoResponse
   beacon_schema:
-    entity_type: dataset
-    schema: https://progenetix.org/services/schemas/dataset/
-  pagination:
-    skip: 0
-    limit: 10
+    entity_type: map
+    schema: https://progenetix.org/services/schemas/beaconMapSchema/
+  is_beacon_entity: true
+
+################################################################################
+
+configuration:
+  request_entity_path_id: configuration
+  response_entity_id: configuration
+  collection: Null
+  response_schema: beaconConfigurationResponse
+  bycon_response_class: BeaconInfoResponse
+  beacon_schema:
+    entity_type: configuration
+    schema: https://progenetix.org/services/schemas/beaconConfigurationSchema/
+  is_beacon_entity: true
+
+################################################################################
+
+entryType:
+  request_entity_path_id: entry_types
+  response_entity_id: entryType
+  collection: Null
+  response_schema: beaconEntryTypesResponse
+  bycon_response_class: BeaconInfoResponse
+  beacon_schema:
+    entity_type: entryType
+    schema: https://progenetix.org/services/schemas/entryTypesSchema/
   is_beacon_entity: true
-  path_id_value_bycon_parameter: dataset_ids
 

bycon/lib/schema_parsing.py

@@ -20,6 +20,7 @@ def read_schema_file(schema_name, item, ext="json"):
             schema_name = r_p_id
 
     s_f_p = get_default_schema_file_path(schema_name, "defaultSchema", ext)
+    # prdbug(f'...read_schema_file {schema_name}: {s_f_p}')
     if s_f_p is False:  # in case the name had been used as request_entity_path_id
         s_f_p = get_schema_file_path(schema_name, ext)