some v2 naming/version use cleanup

mbaudis · mbaudis · commit 4d9e3069f206 · 2025-05-28T20:00:01.000+02:00
... and a line about contributions.
... and a bit of decluttering the index
... also introducing {{config.beacon_major_version}} at some places in the text
diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-# Unified repository for Beacon v2 Code & Documentation
+# Unified repository for Beacon Code & Documentation
 
 ## Description
 
diff --git a/bin/_jsonref2json.py b/bin/_jsonref2json.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 #
-#   Script to dereference JSON $ref in Beacon v2 Models schemas
+#   Script to dereference JSON $ref in Beacon Models schemas
 #
 #    ------------ DEPRECATED ------------
 #   *******************************************************
diff --git a/docs/beacon-flavours.md b/docs/beacon-flavours.md
@@ -1,7 +1,7 @@
 # Beacon "Flavours"
 
 !!! Note "About UI"
-    Most of the information that you will find here is related to the [Beacon v2 specification](/). For that reason, the examples are shown as REST API requests/responses in the form of [JSON](https://www.json.org/json-en.html). If you are only interested in using beacon with a **graphical interface** please visit the [implementations](implementations-options.md) page.
+    Most of the information that you will find here is related to the [Beacon {{config.beacon_major_version}} specification](/). For that reason, the examples are shown as REST API requests/responses in the form of [JSON](https://www.json.org/json-en.html). If you are only interested in using beacon with a **graphical interface** please visit the [implementations](implementations-options.md) page.
 
 While the original Beacon v1 only provided Boolean (_i.e._ **YES/NO**) responses
 on queries for the existence of specific genomic variants, Beacon v2 is a flexible
@@ -24,9 +24,10 @@ with a _true_ or _false_ value when queried for the existence of some data in a
 a _Count Response_ Beacon only returns aggregate information, _i.e._ the number of matched
 entries (e.g. genomic variants), a feature also part of the Beacon v1 protocol.
 
-However, in contrast to earlier versions, in Beacon v2 _in principle_ a beaconized resource
-may implement all types of query options (e.g. combinations of various filters and
-genomic query parameters) but still only offer a Boolean and optionally Count response.
+However, in contrast to earlier versions, in Beacon {{config.beacon_major_version}}
+_in principle_ a beaconized resource may implement all types of query options
+(e.g. combinations of various filters and genomic query parameters) but still
+only offer a Boolean and optionally Count response.
 
 Also, all Beacons _should_ implement the _Boolean Response_ format as fallback option and
 handle extended options depending on the user's authentication status.
@@ -84,6 +85,5 @@ Information about the different data delivery options can be found here:
 
 
 
-
 [^1]: Privacy protecting as in "reasonably protecting by design but not immune to complex
 re-identification attacks".
diff --git a/docs/changes-todo.md b/docs/changes-todo.md
@@ -119,7 +119,7 @@ to `beacon-v2`.
 
 * Reorganization of navigation
 * Deleted page `implement-and-deploy.md`
-* Added pages: [What is Beacon v2](what-is-beacon-v2.md) and [Implementation options](implementations-options.md)
+* Added pages: [What is Beacon](what-is-beacon-v2.md) and [Implementation options](implementations-options.md)
 * [Filters](filters.md) Page Updated
 
 ### 2022-03-18: Macros and Variables for Documentation pages
diff --git a/docs/contribute.md b/docs/contribute.md
@@ -5,4 +5,5 @@ and Health [**GA4GH**](https://ga4gh.org). Since 2016 Beacon development has bee
 organized through projects supported by ELIXIR with additional contributions from
 outside organizations and individual developers and implementers.
 
-==TBD==
+The easiest way to contribute to Beacon development - or to enquire about or 
+request additional features - is through the project's Github{{config.repo_icon}} [issues]({{config.repo_url}}/issues) and [discussions]({{config.repo_url}}/discussions).
diff --git a/docs/formats-standards.md b/docs/formats-standards.md
@@ -14,9 +14,9 @@ The only exception is: `service-info` which is a required GA4GH standard and has
 
 ### Schema Language and Conventions
 
-The **Beacon v2 API** follows [OpenAPI 3.0.2](https://spec.openapis.org/oas/v3.0.2) specification for the [endpoints](https://github.com/ga4gh-beacon/beacon-v2/blob/main/framework/src/endpoints.yaml), in conjuntion with JSON Schema ([2020-12]( https://json-schema.org/draft/2020-12/schema)) to define the [Framework](framework.md) {{config.repo_framework_icon}} and the [Models](models.md) {{config.repo_models_icon}} components. The specification uses JSON [references](https://json-spec.readthedocs.io/reference.html) (`$ref`) to reference internal (e.g., definitions) or external concepts/terms (e.g., [VRS](https://vrs.ga4gh.org/en/latest/terms_and_model.html)).
+The **Beacon API** follows [OpenAPI 3.0.2](https://spec.openapis.org/oas/v3.0.2) specification for the [endpoints](https://github.com/ga4gh-beacon/beacon-v2/blob/main/framework/src/endpoints.yaml), in conjuntion with JSON Schema ([2020-12]( https://json-schema.org/draft/2020-12/schema)) to define the [Framework](framework.md) {{config.repo_framework_icon}} and the [Models](models.md) {{config.repo_models_icon}} components. The specification uses JSON [references](https://json-spec.readthedocs.io/reference.html) (`$ref`) to reference internal (e.g., definitions) or external concepts/terms (e.g., [VRS](https://vrs.ga4gh.org/en/latest/terms_and_model.html)).
 
-The Beacon v2 specification is written in [YAML](https://yaml.org). The original files are located under `src` directory (see below). For technical purposes, we also provide a **copy** of the original YAML in JSON format (see `json` directory below). Changes in the specification must be performed in the YAML version and are then rewritten to the JSON version.
+The Beacon specification is written in [YAML](https://yaml.org). The original files are located under `src` directory (see below). For technical purposes, we also provide a **copy** of the original YAML in JSON format (see `json` directory below). Changes in the specification must be performed in the YAML version and are then rewritten to the JSON version.
 
 === "Framework"
 
@@ -96,8 +96,7 @@ The Beacon v2 specification is written in [YAML](https://yaml.org). The original
 <a href="https://xkcd.com/1179/" target="_blank"><img src="https://imgs.xkcd.com/comics/iso_8601.png"  align="right" style="margin 20px 0px 30px 20px; width: 200px; clear:none;" /></a>
 
 Date and time formats are specified as [ISO8601](https://www.w3.org/TR/NOTE-datetime)
-compatible strings, both for time points as well as for durations. Some of the ISO8601
-compatible formats have not (yet) been used in the Beacon v2 default model.
+compatible strings, both for time points as well as for durations.
 
 #### Examples
 
@@ -109,11 +108,11 @@ compatible formats have not (yet) been used in the Beacon v2 default model.
     - *P43Y08M*
 
 ##### LINK: W3C [ISO8601](https://www.w3.org/TR/NOTE-datetime)
-##### LINK: ISO8601 documentation at [GA4GH SchemaBlocks](https://schemablocks.org/standards/dates-times.html)
+##### LINK: ISO8601 documentation at [GA4GH SchemaBlocks](https://genomestandards.org/standards/dates-times.html)
 
 ## Integration with External Standards
 
-The development of the Beacon v2 framework and default model closely follows
+The development of the Beacon framework and default model closely follows
 and widely adopts concepts and schemas from approved GA4GH products such as
 Phenopackets and the Variant Representation Standard (VRS).
 
@@ -125,7 +124,7 @@ has been approved and covers a set of use cases and requirements, especially wit
 to genomic (including cytogenetic or feature based) locations. However, it is not yet
 suitable for a number of practical use cases, especially the representation of some structural variations.
 
-The Beacon v2 default model for `GenomicVariation` makes use of the VRS standard to represent
+The Beacon default model for `GenomicVariation` makes use of the VRS standard to represent
 the `variation` part, _i.e._ the location and sequence or copy number changes of the
 genomic variation. While a "legacy" alternative is still allowed this one too has been adjusted
 to make use of the VRS `Location` format.
@@ -237,7 +236,7 @@ The examples are for different forma of the `location` property inside a `genomi
 
 ### Phenopackets
 
-In the Beacon v2 default data model, many schemas are either directly compatible to
+In the Beacon default data model, many schemas are either directly compatible to
 [Phenopackets v2 building blocks](https://phenopacket-schema.readthedocs.io/en/latest/building-blocks.html)
 or at least reflect them but with some adjustments. While the Beacon v2 default model's schemas do not _per se_ have to reflect
 PXF schemas, we target an as-close-as-possible alignment to promote/leverage GA4GH-wide
diff --git a/docs/framework.md b/docs/framework.md
@@ -1,4 +1,4 @@
-# Beacon v2 Framework
+# Beacon Framework
 
 ## Introduction
 
diff --git a/docs/implementations-options.md b/docs/implementations-options.md
@@ -1,9 +1,9 @@
 !!! Important
-    As previously described, **Beacon v2 is an specification** for sharing/discovery of data. Thus, _a priori_, it has nothing to do with any particular software, database or computer language.
+    As previously described, **Beacon is an specification** for sharing/discovery of data. Thus, _a priori_, it has nothing to do with any particular software, database or computer language.
 
 # Which are the implementation options?
 
-Two elements are needed to implement (or "light") a Beacon v2: 
+Two elements are needed to implement (or "light") a Beacon: 
 
 1. An internal **database** (where the biological data are stored).
 2. A **REST API** that provides a standardized way to send queries and receive responses (containing yes/no, counts or data).
@@ -14,11 +14,11 @@ In this section we are going to present three implementation options, going from
 
 ![Option A](img/option-A.png)
 
-Let's say that you have your data organized and structured in a database (e.g. [SQL](https://en.wikipedia.org/wiki/SQL) or [NoSQL](https://en.wikipedia.org/wiki/NoSQL) which may or may not have an internal layer to get access to it). Let's also say that you have the resources (and knowledge) to read the "instructions" (i.e., Beacon v2 specification) to build an API on top of your existing solution. If that's your case, then this is the option for you. You are one of what we call **Beacon v2 API implementers**. We have a few of them already in the [Beacon v2 Service Registry](https://ga4gh-approval-service-registry-demo.ega-archive.org):
+Let's say that you have your data organized and structured in a database (e.g. [SQL](https://en.wikipedia.org/wiki/SQL) or [NoSQL](https://en.wikipedia.org/wiki/NoSQL) which may or may not have an internal layer to get access to it). Let's also say that you have the resources (and knowledge) to read the "instructions" (i.e., Beacon specification) to build an API on top of your existing solution. If that's your case, then this is the option for you. You are one of what we call **Beacon API implementers**. We have a few of them already in the [Beacon Service Registry](https://ga4gh-approval-service-registry-demo.ega-archive.org):
 
  * [European Genome-Phenome Archive Beacon](https://ga4gh-approval-beacon.ega-archive.org/api/info)
+ * [`bycon` Python stack](https://bycon.progenetix.org) driving full featured v2.n under the [Progenetix](https://progenetix.org), [cancercelllines.org](https://cancercelllines.org) and [refCNV](https://refcnv.org) genomics resources
  * [Cafe Variome](https://beaconv2.cafevariome.org/form)
- * [`bycon` Python stack](https://bycon.progenetix.org) driving full featured v2 under the [Progenetix](https://progenetix.org) resource
  * [Fundacion Progreso y Salud Beacon v2 API](https://csvs-beacon.clinbioinfosspa.es/csvs/ga4ghbeacon/v2/api/)
  * [CNAG Beacon v2 API](https://playground.rd-connect.eu/beacon2/api)
 
@@ -39,4 +39,4 @@ Let's say that you have your data _somewhat_ structured (you may have Excel file
 You want to "beaconize" your data to be part of a larger ecosystem, but you're unsure where to start, and/or don't want to invest a lot of resources because you are still unsure if the whole thing will pay off. Well, you're a not alone! Most centers are in this situation. For that reason at [CRG](https://www.crg.eu) we developed the [**Beacon v2 Reference Implementation**](https://b2ri-documentation.readthedocs.io).
 
 !!! Important
-    People that download and install _B2RI_ or another pre-packaged solution are named **Beacon v2 deployers**.
+    People that download and install _B2RI_ or another pre-packaged solution are named **Beacon deployers**.
diff --git a/docs/implementations/org.progenetix.md b/docs/implementations/org.progenetix.md
@@ -2,8 +2,8 @@
 <h2>Progenetix & Beacon<span style="color: red; font-weight: 800;"><sup>+</sup></span></h2>
 
 The Beacon+ implementation - developed in the Python & MongoDB based [`bycon` project](https://github.com/progenetix/bycon/) -
-implements an expanding set of Beacon v2 paths for the [Progenetix](https://progenetix.org)
-resource :flag_ch:.
+implements an expanding set of Beacon {{config.beacon_major_version}} paths for the [Progenetix](https://progenetix.org)
+and other resource :flag_ch:.
 
 ### Scoped responses from query object
 
@@ -25,7 +25,7 @@ to `https://progenetix.org/beacon/variants/` or `https://progenetix.org/beacon/b
 {
     "$schema":"beaconRequestBody.json",
     "meta": {
-        "apiVersion": "2.0",
+        "apiVersion": "2.1",
         "requestedSchemas": [
             {
                 "entityType": "genomicVariant",
diff --git a/docs/index.md b/docs/index.md
diff --git a/docs/models.md b/docs/models.md
diff --git a/docs/networks.md b/docs/networks.md
diff --git a/mkdocs.yaml b/mkdocs.yaml

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-# Unified repository for Beacon v2 Code & Documentation`
	`1`	`+# Unified repository for Beacon Code & Documentation`
`2`	`2`
`3`	`3`	`## Description`
`4`	`4`
Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,6 @@`
`1`	`1`	`#!/usr/bin/env python3`
`2`	`2`	`#`
`3`		`-# Script to dereference JSON $ref in Beacon v2 Models schemas`
	`3`	`+# Script to dereference JSON $ref in Beacon Models schemas`
`4`	`4`	`#`
`5`	`5`	`# ------------ DEPRECATED ------------`
`6`	`6`	`# *******************************************************`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-# Beacon v2 Framework`
	`1`	`+# Beacon Framework`
`2`	`2`
`3`	`3`	`## Introduction`
`4`	`4`