omnibenchmark · DanInci · Jun 21, 2024 · Jun 18, 2024
diff --git a/examples/Benchmark-001.yaml b/examples/Benchmark-001.yaml
diff --git a/examples/Benchmark_001.yaml b/examples/Benchmark_001.yaml
@@ -0,0 +1,130 @@
+---
+id: Benchmark_001
+description: simple benchmark, somewhat explicit, simple params
+version: 1.0
+benchmarker: "John Doe at Robinsons lab, [email protected]"
+storage: https://storage.github.com/
+storage_api: S3
+benchmark_yaml_spec: 0.01
+software_environments:
+  R:
+    description: "R 4.3.3 with gfbf-2023 toolchain"
+    easyconfig: R_4.3.3-gfbf-2023b.eb
+    envmodule: R/4.3.3-gfbf-2023b
+    conda: R_4.3.3_try.yaml # or perhaps not
+    apptainer: http://registry.ch/R_4.3.3-gfbf-2023b.sif
+  python:
+    description: "Ppython3.12.0 with gfbf-2023 toolchain"
+    easyconfig: python_vX-gfbf-2023b.eb
+    envmodule: python/vX-gfbf-2023b
+    conda: python_vX_test.yaml
+    apptainer: http://registry.ch/python_vX-gfbf-2023b.sif
+stages:
+  - id: data
+    modules:
+      - id: D1
+        name: "Dataset 1"
+        software_environment: "python"
+        repository:
+          url: https://github.com/omnibenchmark-example/data.git
+          commit: 061a981
+      - id: D2
+        name: "Dataset 2"
+        software_environment: "python"
+        repository:
+          url: https://github.com/omnibenchmark-example/data.git
+          commit: 061a981
+    outputs:
+      - id: data.counts
+        path: "{in}/{stage}/{module}/{params}/{dataset}.txt.gz"
+      - id: data.meta
+        path: "{in}/{stage}/{module}/{params}/{dataset}.meta.json"
+      - id: data.data_specific_params
+        path: "{in}/{stage}/{module}/{params}/{dataset}_params.txt"
+
+  - id: process
+    modules:
+      - id: P1
+        software_environment: "R"
+        parameters:
+          - values: ["-a 0", "-b 0.1"]
+          - values: ["-a 1", "-b 0.1"]
+        repository:
+          url: https://github.com/omnibenchmark-example/process.git
+          commit: 24579a8
+      - id: P2
+        software_environment: "R"
+        parameters:
+          - values: ["-a 0", "-c 0"]
+          - values: ["-a 1", "-c 0.1"]
+        repository:
+          url: https://github.com/omnibenchmark-example/process.git
+          commit: 24579a8
+    inputs:
+      - entries: [
+          data.counts,
+          data.meta
+        ]
+    outputs:
+      - id: process.filtered
+        path: "{in}/{stage}/{module}/{params}/{dataset}.txt.gz"
+
+  - id: methods
+    modules:
+      - id: M1
+        software_environment: "python"
+        exclude: [ D2 ]
+        repository:
+          url: https://github.com/omnibenchmark-example/method.git
+          commit: 709e114
+      - id: M2
+        software_environment: "python"
+        parameters:
+          - values: ["-d1", "-e 1"]
+          - values: ["-d1", "-e 2"]
+        exclude:
+          - D1
+        repository:
+          url: https://github.com/omnibenchmark-example/method.git
+          commit: 709e114
+    inputs:
+      - entries: [
+          data.counts,
+          data.meta,
+          data.data_specific_params
+        ]
+      - entries: [
+          process.filtered,
+          data.meta,
+          data.data_specific_params
+        ]
+    outputs:
+      - id: methods.mapping
+        path: "{in}/{stage}/{module}/{params}/{dataset}.model.out.gz"
+
+  - id: metrics
+    modules:
+      - id: m1
+        software_environment: "python"
+        repository:
+          url: [email protected]:omnibenchmark-example/metric.git
+          commit: ba781d7
+      - id: m2
+        software_environment: "python"
+        repository:
+          url: [email protected]:omnibenchmark-example/metric.git
+          commit: ba781d7
+      - id: m3
+        software_environment: "python"
+        repository:
+          url: [email protected]:omnibenchmark-example/metric.git
+          commit: ba781d7
+    inputs:
+      - entries: [
+          methods.mapping,
+          data.meta,
+          data.data_specific_params
+      ]
+    outputs:
+      - id: metrics.mapping
+        path: "{in}/{stage}/{module}/{params}/{dataset}.results.txt"
diff --git a/project/excel/omni_schema.xlsx b/project/excel/omni_schema.xlsx
diff --git a/project/graphql/omni_schema.graphql b/project/graphql/omni_schema.graphql
@@ -1,20 +1,21 @@
 type Benchmark
   {
     id: Uriorcurie!
-    name: String!
+    name: String
     description: String
     version: String!
-    platform: String!
+    benchmarker: String!
     storage: String!
-    orchestrator: Orchestrator!
-    validator: Validator!
-    steps: [Step]!
+    storageApi: StorageAPIEnum!
+    softwareEnvironments: [SoftwareEnvironment]!
+    benchmarkYamlSpec: String
+    stages: [Stage]!
   }
 
 interface IdentifiableEntity
   {
     id: Uriorcurie!
-    name: String!
+    name: String
     description: String
   }
 
@@ -26,49 +27,51 @@ type InputCollection
 type IOFile
   {
     id: Uriorcurie!
-    name: String!
+    name: String
     description: String
     path: String
   }
 
 type Module
   {
     id: Uriorcurie!
-    name: String!
+    name: String
     description: String
-    repo: String!
+    softwareEnvironment: SoftwareEnvironment!
+    repository: Repository!
     exclude: [Module]
     parameters: [Parameter]
   }
 
-type Orchestrator
+type Parameter
   {
-    name: String!
-    url: String!
+    values: [String]
   }
 
-type Parameter
+type Repository
   {
-    values: [String]
+    url: String!
+    commit: String!
   }
 
-type Step
+type SoftwareEnvironment
   {
     id: Uriorcurie!
-    name: String!
+    name: String
     description: String
-    initial: Boolean
-    terminal: Boolean
-    after: [Step]
-    members: [Module]!
-    inputs: [InputCollection]
-    outputs: [IOFile]
+    easyconfig: String
+    envmodule: String
+    conda: String
+    apptainer: String
   }
 
-type Validator
+type Stage
   {
-    name: String!
-    url: String!
-    schemaUrl: String!
+    id: Uriorcurie!
+    name: String
+    description: String
+    modules: [Module]!
+    inputs: [InputCollection]
+    outputs: [IOFile]
   }
 
diff --git a/project/jsonld/omni_schema.context.jsonld b/project/jsonld/omni_schema.context.jsonld
@@ -1,18 +1,16 @@
 {
    "comments": {
       "description": "Auto generated by LinkML jsonld context generator",
-      "generation_date": "2024-03-08T14:09:12",
+      "generation_date": "2024-06-18T18:10:53",
       "source": "omni_schema.yaml"
    },
    "@context": {
       "example": "https://example.org/",
       "linkml": "https://w3id.org/linkml/",
       "omni_schema": "https://w3id.org/omnibenchmark/omni-schema/",
       "schema": "http://schema.org/",
+      "skos": "http://www.w3.org/2004/02/skos/core#",
       "@vocab": "https://w3id.org/omnibenchmark/omni-schema/",
-      "after": {
-         "@type": "@id"
-      },
       "description": {
          "@id": "schema:description"
       },
@@ -23,36 +21,41 @@
          "@type": "@id"
       },
       "id": "@id",
-      "initial": {
-         "@type": "xsd:boolean"
-      },
       "inputs": {
          "@type": "@id"
       },
-      "members": {
+      "modules": {
          "@type": "@id"
       },
       "name": {
          "@id": "schema:name"
       },
-      "orchestrator": {
-         "@type": "@id"
-      },
       "outputs": {
          "@type": "@id"
       },
       "parameters": {
          "@type": "@id"
       },
-      "steps": {
+      "repository": {
          "@type": "@id"
       },
-      "terminal": {
-         "@type": "xsd:boolean"
+      "software_environment": {
+         "@type": "@id"
+      },
+      "software_environments": {
+         "@type": "@id"
       },
-      "validator": {
+      "stages": {
          "@type": "@id"
       },
+      "storage_api": {
+         "@context": {
+            "@vocab": "@null",
+            "text": "skos:notation",
+            "description": "skos:prefLabel",
+            "meaning": "@id"
+         }
+      },
       "IdentifiableEntity": {
          "@id": "schema:Thing"
       }