ga4gh-beacon · jrambla · Apr 12, 2023
diff --git a/docs/FAQ.md b/docs/FAQ.md
@@ -24,7 +24,7 @@
     ##### Example Boolean Response
 
     In this minimal response to the query above the beacon indicates that its default
-    response is Boolean and that it could interpreted it against the `genomicVariant` entity and in the context of the same Beacon version.
+    response is Boolean and that it could interpreted it against the `genomicVariant` entry type and in the context of the same Beacon version.
 
     In principle one could launch a Beacon instance using the example response document as a template
     in whatever server environment one has at hand. However, a proper Beacon v2
@@ -45,7 +45,7 @@
           "requestedGranularity": "boolean",
           "requestedSchemas": [
             {
-              "entityType": "genomicVariant",
+              "entryType": "genomicVariant",
               "schema": "https://progenetix.org/services/schemas/genomicVariant/"
             }
           ],
@@ -61,7 +61,7 @@
         "returnedGranularity": "boolean",
         "returnedSchemas": [
           {
-            "entityType": "genomicVariant",
+            "entryType": "genomicVariant",
             "schema": "https://progenetix.org/services/schemas/genomicVariant/"
           }
         ]

diff --git a/docs/formats-standards.md b/docs/formats-standards.md
@@ -6,7 +6,7 @@
 
 For historical reasons, in the names of entities, parameters and URLs we are following these conventions:
 
-* Entity names: `PascalCase` 
+* Entry Type names: `PascalCase` 
 * parameters: `camelCase` 
 * URI path elements: `snake_case` 
 

diff --git a/docs/implementations/org.progenetix.md b/docs/implementations/org.progenetix.md
@@ -13,10 +13,10 @@ of those to its supported responses and provide the results accordingly; it does
 if the endpoint was `/beacon/biosamples/` or `/beacon/variants/` etc.
 
 Below is an example for the standard test "small deletion CNVs in the CDKN2A locus, in gliomas"
-Progenetix test query, here responding with the matched variants. Exchanging the `entityType`
+Progenetix test query, here responding with the matched variants. Exchanging the `entryType`
 entry to
 
-* `{ "entityType": "biosample", "schema:": "https://progenetix.org/services/schemas/Biosample/"}`
+* `{ "entryType": "biosample", "schema:": "https://progenetix.org/services/schemas/Biosample/"}`
 
 would change this to a biosample response. The example ccan be tested by POSTing this as `application/json`
 to `http://progenetix.org/beacon/variants/` or `http://progenetix.org/beacon/biosamples/`.
@@ -28,7 +28,7 @@ to `http://progenetix.org/beacon/variants/` or `http://progenetix.org/beacon/bio
         "apiVersion": "2.0",
         "requestedSchemas": [
             {
-                "entityType": "genomicVariant",
+                "entryType": "genomicVariant",
                 "schema:": "https://progenetix.org/services/schemas/genomicVariant"
             }
         ]

diff --git a/docs/variant-queries.md b/docs/variant-queries.md
@@ -42,7 +42,7 @@ in the _EIF4A1_ eukaryotic translation initiation factor 4A1.
 	        "apiVersion": "2.0",
 	        "requestedSchemas": [
 	            {
-	                "entityType": "genomicVariation",
+	                "entryType": "genomicVariation",
 	                "schema:": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/models/json/beacon-v2-default-model/genomicVariations/defaultSchema.json"
 	            }
 	        ]
@@ -134,7 +134,7 @@ parameters.
 	        "apiVersion": "2.0",
 	        "requestedSchemas": [
 	            {
-	                "entityType": "genomicVariation",
+	                "entryType": "genomicVariation",
 	                "schema:": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/models/json/beacon-v2-default-model/genomicVariations/defaultSchema.json"
 	            }
 	        ]
@@ -246,7 +246,7 @@ larger than approx. 5Mb (operational definitions of focality vary between 1 and
 	        "apiVersion": "2.0",
 	        "requestedSchemas": [
 	            {
-	                "entityType": "genomicVariation",
+	                "entryType": "genomicVariation",
 	                "schema:": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/models/json/beacon-v2-default-model/genomicVariations/defaultSchema.json"
 	            }
 	        ]

diff --git a/framework/json/common/beaconCommonComponents.json b/framework/json/common/beaconCommonComponents.json
@@ -162,7 +162,7 @@
         "ListOfSchemas": {
             "description": "Set of schemas to be used in the response to a request.",
             "items": {
-                "$ref": "#/definitions/SchemasPerEntity"
+                "$ref": "#/definitions/SchemasPerEntryType"
             },
             "type": "array"
         },
@@ -208,10 +208,10 @@
             },
             "type": "object"
         },
-        "SchemasPerEntity": {
+        "SchemasPerEntryType": {
             "description": "Schema to be used for the requested entry type in the response.",
             "properties": {
-                "entityType": {
+                "entryType": {
                     "$comment": "TO REVIEW: Should that refer to a concept definition? Or would that include an undesired dependency to the configuration?",
                     "example": "Individual",
                     "type": "string"

diff --git a/framework/json/common/examples/beaconCommonComponents-example.json b/framework/json/common/examples/beaconCommonComponents-example.json
@@ -45,11 +45,11 @@
     ],
     "listOfSchemas": [
         {
-            "entityType": "EntryTypeA",
+            "entryType": "EntryTypeA",
             "schema": "entry-typeA-schema-v0.1"
         },
         {
-            "entityType": "EntryTypeB",
+            "entryType": "EntryTypeB",
             "schema": "entry-typeB-schema-v1.0"
         }
     ],
@@ -58,8 +58,8 @@
         "limit": 10,
         "skip": 0
     },
-    "schemasPerEntity": {
-        "entityType": "Individual",
+    "schemasPerEntryType": {
+        "entryType": "Individual",
         "schema": "ga4gh-phenopacket-individual-v0.1"
     }
 }
diff --git a/framework/json/common/validation/beaconCommonComponents.json b/framework/json/common/validation/beaconCommonComponents.json
@@ -45,8 +45,8 @@
         "pagination": {
             "$ref": "../beaconCommonComponents.json#/definitions/Pagination"
         },
-        "schemasPerEntity": {
-            "$ref": "../beaconCommonComponents.json#/definitions/SchemasPerEntity"
+        "SchemasPerEntryType": {
+            "$ref": "../beaconCommonComponents.json#/definitions/SchemasPerEntryType"
         }
     },
     "title": "Schema for validating Beacon Common Components examples",

diff --git a/framework/json/requests/examples-fullDocuments/beaconRequestBody-MAX-example.json b/framework/json/requests/examples-fullDocuments/beaconRequestBody-MAX-example.json
@@ -4,7 +4,7 @@
         "apiVersion": "2.0",
         "requestedSchemas": [
             {
-                "entityType": "EntryTypeA",
+                "entryType": "EntryTypeA",
                 "schema": "entry-typeA-schema-v0.1"
             }
         ]

diff --git a/framework/json/requests/examples-sections/beaconRequestMeta-example.json b/framework/json/requests/examples-sections/beaconRequestMeta-example.json
@@ -3,7 +3,7 @@
     "apiVersion": "2.0",
     "requestedSchemas": [
         {
-            "entityType": "EntryTypeA",
+            "entryType": "EntryTypeA",
             "schema": "entry-typeA-schema-v0.1"
         }
     ]

diff --git a/framework/json/requests/requestParameters.json b/framework/json/requests/requestParameters.json
@@ -3,7 +3,7 @@
     "additionalProperties": {
         "type": "object"
     },
-    "description": "The schema below is a placeholder for a dictionary 'key':'object'. The individual definitions depend on the model (e.g. beacon-v2-default-model) and entity (e.g. `genomicVariant`).",
+    "description": "The schema below is a placeholder for a dictionary 'key':'object'. The individual definitions depend on the model (e.g. beacon-v2-default-model) and entry type (e.g. `genomicVariant`).",
     "properties": {
         "$schema": {
             "description": "Added here to allow proper validation of the documents w/o providing specific values.",

diff --git a/framework/json/responses/examples-fullDocuments/beaconBooleanResponse-example.json b/framework/json/responses/examples-fullDocuments/beaconBooleanResponse-example.json
@@ -11,14 +11,14 @@
             },
             "requestedSchemas": [
                 {
-                    "entityType": "EntryTypeB",
+                    "entryType": "EntryTypeB",
                     "schema": "entry-typeB-schema-v1.0"
                 }
             ]
         },
         "returnedSchemas": [
             {
-                "entityType": "EntryTypeB",
+                "entryType": "EntryTypeB",
                 "schema": "entry-typeB-schema-v1.0"
             }
         ]

diff --git a/framework/json/responses/examples-fullDocuments/beaconCollectionsResponse-MID-example.json b/framework/json/responses/examples-fullDocuments/beaconCollectionsResponse-MID-example.json
@@ -11,14 +11,14 @@
             },
             "requestedSchemas": [
                 {
-                    "entityType": "dataset",
+                    "entryType": "dataset",
                     "schema": "dataset-schema-v1.0"
                 }
             ]
         },
         "returnedSchemas": [
             {
-                "entityType": "dataset",
+                "entryType": "dataset",
                 "schema": "dataset-schema-v1.0"
             }
         ]

diff --git a/framework/json/responses/examples-fullDocuments/beaconCollectionsResponse-MIN-example.json b/framework/json/responses/examples-fullDocuments/beaconCollectionsResponse-MIN-example.json
@@ -11,14 +11,14 @@
             },
             "requestedSchemas": [
                 {
-                    "entityType": "dataset",
+                    "entryType": "dataset",
                     "schema": "dataset-schema-v1.0"
                 }
             ]
         },
         "returnedSchemas": [
             {
-                "entityType": "dataset",
+                "entryType": "dataset",
                 "schema": "dataset-schema-v1.0"
             }
         ]

diff --git a/framework/json/responses/examples-fullDocuments/beaconConfigurationResponse-example.json b/framework/json/responses/examples-fullDocuments/beaconConfigurationResponse-example.json
@@ -6,7 +6,7 @@
         "beaconId": "string",
         "returnedSchemas": [
             {
-                "entityType": "info",
+                "entryType": "info",
                 "schema": "beacon-map-v2.0.0"
             }
         ]

diff --git a/framework/json/responses/examples-fullDocuments/beaconCountResponse-example.json b/framework/json/responses/examples-fullDocuments/beaconCountResponse-example.json
@@ -32,14 +32,14 @@
             },
             "requestedSchemas": [
                 {
-                    "entityType": "EntryTypeB",
+                    "entryType": "EntryTypeB",
                     "schema": "entry-typeB-schema-v1.0"
                 }
             ]
         },
         "returnedSchemas": [
             {
-                "entityType": "EntryTypeB",
+                "entryType": "EntryTypeB",
                 "schema": "entry-typeB-schema-v1.0"
             }
         ]

diff --git a/framework/json/responses/examples-fullDocuments/beaconEntryTypesResponse-example.json b/framework/json/responses/examples-fullDocuments/beaconEntryTypesResponse-example.json
@@ -6,7 +6,7 @@
         "beaconId": "string",
         "returnedSchemas": [
             {
-                "entityType": "info",
+                "entryType": "info",
                 "schema": "beacon-map-v2.0.0"
             }
         ]

diff --git a/framework/json/responses/examples-fullDocuments/beaconErrorResponse_example.json b/framework/json/responses/examples-fullDocuments/beaconErrorResponse_example.json
@@ -19,7 +19,7 @@
             },
             "requestParameters": [
                 {
-                    "entity": "individual",
+                    "entryType": "individual",
                     "parameters": [
                         {
                             "id": "123"
@@ -32,7 +32,7 @@
             ],
             "requestedSchemas": [
                 {
-                    "entityType": "Individual",
+                    "entryType": "Individual",
                     "schema": "ga4gh-phenopacket-individual-v0.1"
                 }
             ]

diff --git a/framework/json/responses/examples-fullDocuments/beaconInfo-MAX-example.json b/framework/json/responses/examples-fullDocuments/beaconInfo-MAX-example.json
@@ -6,7 +6,7 @@
         "beaconId": "string",
         "returnedSchemas": [
             {
-                "entityType": "info",
+                "entryType": "info",
                 "schema": "beacon-info-v2.0.0"
             }
         ]

diff --git a/framework/json/responses/examples-fullDocuments/beaconInfo-MIN-example.json b/framework/json/responses/examples-fullDocuments/beaconInfo-MIN-example.json
@@ -5,7 +5,7 @@
         "beaconId": "string",
         "returnedSchemas": [
             {
-                "entityType": "info",
+                "entryType": "info",
                 "schema": "beacon-info-v2.0.0"
             }
         ]

diff --git a/framework/json/responses/examples-fullDocuments/beaconMapResponse-example.json b/framework/json/responses/examples-fullDocuments/beaconMapResponse-example.json
@@ -6,7 +6,7 @@
         "beaconId": "string",
         "returnedSchemas": [
             {
-                "entityType": "info",
+                "entryType": "info",
                 "schema": "beacon-map-v2.0.0"
             }
         ]

diff --git a/framework/json/responses/examples-fullDocuments/beaconResultsetResponse-MIN-example.json b/framework/json/responses/examples-fullDocuments/beaconResultsetResponse-MIN-example.json
@@ -11,14 +11,14 @@
             },
             "requestedSchemas": [
                 {
-                    "entityType": "EntryTypeB",
+                    "entryType": "EntryTypeB",
                     "schema": "entry-typeB-schema-v1.0"
                 }
             ]
         },
         "returnedSchemas": [
             {
-                "entityType": "EntryTypeB",
+                "entryType": "EntryTypeB",
                 "schema": "entry-typeB-schema-v1.0"
             }
         ]

diff --git a/framework/json/responses/examples-sections/beaconReceivedRequestSummary-MAX-example.json b/framework/json/responses/examples-sections/beaconReceivedRequestSummary-MAX-example.json
@@ -22,7 +22,7 @@
     "requestedGranularity": "count",
     "requestedSchemas": [
         {
-            "entityType": "Individual",
+            "entryType": "Individual",
             "schema": "ga4gh-phenopacket-individual-v0.1"
         }
     ],

diff --git a/framework/json/responses/examples-sections/beaconResponseMeta-example.json b/framework/json/responses/examples-sections/beaconResponseMeta-example.json
@@ -11,7 +11,7 @@
         "requestedGranularity": "count",
         "requestedSchemas": [
             {
-                "entityType": "EntryTypeB",
+                "entryType": "EntryTypeB",
                 "schema": "entry-typeB-schema-v1.0"
             }
         ],
@@ -20,7 +20,7 @@
     "returnedGranularity": "count",
     "returnedSchemas": [
         {
-            "entityType": "EntryTypeB",
+            "entryType": "EntryTypeB",
             "schema": "entry-typeB-schema-v1.0"
         }
     ]

diff --git a/framework/json/responses/sections/beaconResponseMeta.json b/framework/json/responses/sections/beaconResponseMeta.json
@@ -17,7 +17,7 @@
         },
         "returnedSchemas": {
             "$ref": "../../common/beaconCommonComponents.json#/definitions/ListOfSchemas",
-            "description": "The `returnedSchemas` parameter indicates that the request has been interpreted for the indicated entity. This helps to disambiguate between negative responses due to e.g. no hit on a well understood request and failures to interpret or answer the request due to a missing entity. "
+            "description": "The `returnedSchemas` parameter indicates that the request has been interpreted for the indicated entry type. This helps to disambiguate between negative responses due to e.g. no hit on a well understood request and failures to interpret or answer the request due to a missing entry type. "
         },
         "testMode": {
             "$ref": "../../common/beaconCommonComponents.json#/definitions/TestMode"

diff --git a/framework/src/common/beaconCommonComponents.yaml b/framework/src/common/beaconCommonComponents.yaml
@@ -67,13 +67,13 @@ definitions:
       Set of schemas to be used in the response to a request.
     type: array
     items:
-      $ref: '#/definitions/SchemasPerEntity'
-  SchemasPerEntity:
+      $ref: '#/definitions/SchemasPerEntryType'
+  SchemasPerEntryType:
     description: >-
       Schema to be used for the requested entry type in the response.
     type: object
     properties:
-      entityType:
+      entryType:
         type: string
         example: Individual
         $comment: >-

diff --git a/framework/src/common/examples/beaconCommonComponents-example.yaml b/framework/src/common/examples/beaconCommonComponents-example.yaml
@@ -5,12 +5,12 @@ beaconError:
   errorCode: 404
   errorMessage: the provided parameters are incomplete. 'xyz' is missing.
 listOfSchemas:
-  - entityType: EntryTypeA
+  - entryType: EntryTypeA
     schema: entry-typeA-schema-v0.1
-  - entityType: EntryTypeB
+  - entryType: EntryTypeB
     schema: entry-typeB-schema-v1.0
-schemasPerEntity:
-  entityType: Individual
+SchemasPerEntryType:
+  entryType: Individual
   schema: ga4gh-phenopacket-individual-v0.1
 pagination:
   skip: 0

diff --git a/framework/src/common/validation/beaconCommonComponents.yaml b/framework/src/common/validation/beaconCommonComponents.yaml
@@ -14,8 +14,8 @@ properties:
     $ref: ../beaconCommonComponents.yaml#/definitions/BeaconError
   listOfSchemas:
     $ref: ../beaconCommonComponents.yaml#/definitions/ListOfSchemas
-  schemasPerEntity:
-    $ref: ../beaconCommonComponents.yaml#/definitions/SchemasPerEntity
+  SchemasPerEntryType:
+    $ref: ../beaconCommonComponents.yaml#/definitions/SchemasPerEntryType
   pagination:
     $ref: ../beaconCommonComponents.yaml#/definitions/Pagination
   includeResultsetResponses: