Merge pull request #4722 from galaxyproject/hyena-kelvin

Add API for individual tools mapped to servers
galaxyproject · Feb 13, 2024 · bc76b41 · bc76b41
2 parents a06e767 + a71e0dc
commit bc76b41
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diff --git a/_includes/instance-dropdown.html b/_includes/instance-dropdown.html
@@ -19,7 +19,7 @@
     {% for inst in usegalaxy_exact %}
 	<li>
 		<a class="dropdown-item" href="{{ inst.url }}" title="{{ inst[0] }}">
-			{{ inst.name }} <abbr title="This instance supports the precise tool versions used in this tutorial">✅</abbr> ⭐️
+			{{ inst.name }} <abbr title="This instance supports the precise tool versions used in this tutorial">✅</abbr> <abbr title="This is a UseGalaxy.* server which meets minimum requirements for a public Galaxy">⭐️</abbr>
 		</a>
 	</li>
     {% endfor %}

diff --git a/_plugins/api.rb b/_plugins/api.rb
@@ -375,6 +375,26 @@ def generate(site)
 Jekyll::Hooks.register :site, :post_write do |site|
   dir = File.join(site.dest, 'api', 'workflows')
 
+  # Public tool listing: reorganised
+  if site.data['public-server-tools'] and site.data['public-server-tools']['tools']
+    site.data['public-server-tools']['tools'].each do |tool, version_data|
+      path = File.join(site.dest, 'api', 'psl', "#{tool}.json")
+      dir = File.dirname(path)
+      FileUtils.mkdir_p(dir) unless File.directory?(dir)
+
+      d = version_data.dup
+      d.keys.each do |k|
+        # Replace the indexes with the server URLs from site['public-server-tools']['servers']
+        d[k] = d[k].map { |v| site.data['public-server-tools']['servers'][v] }
+      end
+
+      File.write(path, JSON.generate(d))
+    end
+    Jekyll.logger.debug "[GTN/API/PSL] PSL written"
+  else
+    Jekyll.logger.debug "[GTN/API/PSL] PSL Dataset not available, are you in a CI environment?"
+  end
+
   # ro-crate-metadata.json
   TopicFilter.list_all_materials(site).select { |m| m['workflows'] }.each do |material|
     material['workflows'].each do |workflow|

diff --git a/api/swagger.json b/api/swagger.json
@@ -345,6 +345,58 @@
           }
         }
       }
+    },
+    "/psl.json": {
+      "get": {
+        "tags": [
+          "tools"
+        ],
+        "summary": "Get the GTN's public server tool listing. It lists all known public servers that are reachable at the time of the GTN's deployment, and which tool versions are installed on each of those servers.",
+        "responses": {
+          "200": {
+            "description": "successful operation",
+            "content": {
+              "application/json": {
+                "schema": {
+                  "$ref": "#/components/schemas/Psl"
+                }
+              }
+            }
+          }
+        }
+      }
+    },
+    "/psl/{toolId}.json": {
+      "get": {
+        "tags": [
+          "tools"
+        ],
+        "parameters": [
+          {
+            "name": "toolId",
+            "in": "path",
+            "example": "toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate",
+            "description": "Tool ID WITHOUT the version component!!",
+            "required": true,
+            "schema": {
+              "type": "string"
+            }
+          }
+        ],
+        "summary": "Get the GTN's public server tool listing for a specific tool ID. It lists all known public servers that are reachable at the time of the GTN's deployment, and which versions of this tool are available. It's very important that you strip the version component!",
+        "responses": {
+          "200": {
+            "description": "successful operation",
+            "content": {
+              "application/json": {
+                "schema": {
+                  "$ref": "#/components/schemas/PslIndividual"
+                }
+              }
+            }
+          }
+        }
+      }
     }
   },
   "components": {
@@ -571,6 +623,53 @@
             }
           }
         }
+      },
+      "Psl": {
+        "type": "object",
+        "properties": {
+          "servers": {
+            "$ref": "#/components/schemas/ArrayOfServers"
+          },
+          "tools": {
+            "$ref": "#/components/schemas/ArrayOfToolVersions"
+          }
+        }
+      },
+      "PslIndividual": {
+        "$ref": "#/components/schemas/ToolVersionClear"
+      },
+      "ArrayOfServers": {
+        "type": "array",
+        "items": {
+          "$ref": "#/components/schemas/Server"
+        }
+      },
+      "Server": {
+        "type": "object",
+        "properties": {
+          "url": {
+            "type": "string",
+            "description": "A url for the server"
+          },
+          "name": {
+            "type": "string",
+            "description": "A human readable description"
+          }
+        }
+      },
+      "ArrayOfToolVersions": {
+        "type": "array",
+        "items": {
+          "$ref": "#/components/schemas/ToolVersionOpaque"
+        }
+      },
+      "ToolVersionOpaque": {
+        "type": "object",
+        "description": "A hash/dict where the top level keys are the known versions of that tool (or '_' for built in tools), and then the servers that have that tool. Note that the servers are actually a list of integers which refer to the Server listing field."
+      },
+      "ToolVersionClear": {
+        "type": "object",
+        "description": "A hash/dict where the top level keys are the known versions of that tool (or '_' for built in tools), and then the servers that have that tool."
       }
     }
   }

diff --git a/metadata/swagger.yaml b/metadata/swagger.yaml
@@ -225,6 +225,40 @@ paths:
         200:
           description: successful operation
 
+  /psl.json:
+    get:
+      tags:
+      - tools
+      summary: Get the GTN's public server tool listing. It lists all known public servers that are reachable at the time of the GTN's deployment, and which tool versions are installed on each of those servers.
+      responses:
+        200:
+          description: successful operation
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/Psl'
+
+  /psl/{toolId}.json:
+    get:
+      tags:
+      - tools
+      parameters:
+      - name: toolId
+        in: path
+        example: toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate
+        description: Tool ID WITHOUT the version component!! Also when you call it properly you do NOT need to encode the /.
+        required: true
+        schema:
+          type: string
+      summary: Get the GTN's public server tool listing for a specific tool ID. It lists all known public servers that are reachable at the time of the GTN's deployment, and which versions of this tool are available. It's very important that you strip the version component!
+      responses:
+        200:
+          description: successful operation
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/PslIndividual'
+
 components:
   schemas:
     TrainingMaterial:
@@ -389,3 +423,35 @@ components:
           type: array
           items:
             $ref: '#/components/schemas/TrainingMaterial'
+    Psl:
+      type: object
+      properties:
+        servers:
+          $ref: '#/components/schemas/ArrayOfServers'
+        tools:
+          $ref: '#/components/schemas/ArrayOfToolVersions'
+    PslIndividual:
+      $ref: '#/components/schemas/ToolVersionClear'
+    ArrayOfServers:
+      type: array
+      items:
+        $ref: "#/components/schemas/Server"
+    Server:
+      type: object
+      properties:
+        url:
+          type: string
+          description: A url for the server
+        name:
+          type: string
+          description: A human readable description
+    ArrayOfToolVersions:
+      type: array
+      items:
+        $ref: "#/components/schemas/ToolVersionOpaque"
+    ToolVersionOpaque:
+      type: object
+      description: A hash/dict where the top level keys are the known versions of that tool (or '_' for built in tools), and then the servers that have that tool. Note that the servers are actually a list of integers which refer to the Server listing field.
+    ToolVersionClear:
+      type: object
+      description: A hash/dict where the top level keys are the known versions of that tool (or '_' for built in tools), and then the servers that have that tool.