validation: make environment property mandatory in serial steps

Closes reanahub/reana-client#679.
giuseppe-steduto · Nov 13, 2023 · 269a6c5 · 269a6c5
1 parent 9c6e62e
commit 269a6c5
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diff --git a/CHANGES.rst b/CHANGES.rst
@@ -6,6 +6,7 @@ Version 0.9.4 (UNRELEASED)
 
 - Changes the REANA specification schema to use the ``draft 2020-12`` version of the JSON schema specification.
 - Changes validation of REANA specification to expose functions for loading workflow input parameters and workflow specifications.
+- Changes the validation schema of the REANA specification to make the ``environment`` property mandatory for the steps of serial workflows.
 - Fixes the mounting of CVMFS volumes for the REANA deployments that use non-default Kubernetes namespace.
 
 Version 0.9.3 (2023-09-26)

diff --git a/reana_commons/validation/schemas/reana_analysis_schema.json b/reana_commons/validation/schemas/reana_analysis_schema.json
@@ -1,6 +1,90 @@
 {
   "$schema": "https://json-schema.org/draft/2020-12/schema",
-  "definitions": {},
+  "$defs": {
+    "cwl_specification": {
+      "$id": "/properties/workflow/properties/specifications?type=cwl",
+      "type": "object",
+      "title": "CWL workflow specification.",
+      "description": "CWL workflow specification.",
+      "additionalProperties": false,
+      "properties": {
+        "cwlVersion": {
+          "type": "string",
+          "title": "CWL version.",
+          "description": "CWL version to which the workflow was written for.",
+          "enum": [
+            "v1.0"
+          ]
+        },
+        "class": {
+          "type": "string",
+          "title": "CWL class.",
+          "description": "CWL class which represents the type of the workflow.",
+          "enum": [
+            "Workflow"
+          ]
+        },
+        "inputs": {
+          "type": "array",
+          "title": "CWL workflow inputs.",
+          "description": "CWL workflow inputs."
+        }
+      }
+    },
+    "serial_specification": {
+      "$id": "/properties/workflow/properties/specifications?type=serial",
+      "type": "object",
+      "title": "Serial workflow specification.",
+      "description": "Serial workflow specification.",
+      "additionalProperties": false,
+      "properties": {
+        "steps": {
+          "type": "array",
+          "title": "Serial workflow steps.",
+          "description": "List of steps which represent the workflow.",
+          "items": {
+            "properties": {
+              "name": {
+                "type": "string",
+                "title": "Step name."
+              },
+              "environment": {
+                "type": "string",
+                "title": "Image to be used by the container in which the step should be run."
+              },
+              "kubernetes_memory_limit": {
+                "type": "string",
+                "title": "Memory limit for the step container (e.g. 256Mi)."
+              },
+              "commands": {
+                "type": "array",
+                "title": "Step commands.",
+                "description": "List of commands to be run in the step.",
+                "items": {
+                  "type": "string",
+                  "title": "Command to be run."
+                }
+              }
+            }
+          }
+        }
+      }
+    },
+    "snakemake_specification": {
+      "$id": "/properties/workflow/properties/specifications?type=snakemake",
+      "type": "object",
+      "title": "Snakemake workflow specification.",
+      "description": "Snakemake workflow specification.",
+      "additionalProperties": false
+    },
+    "yadage_specification": {
+      "$id": "/properties/workflow/properties/specifications?type=yadage",
+      "type": "object",
+      "title": "Yadage workflow specification.",
+      "description": "Yadage workflow specification.",
+      "additionalProperties": false
+    }
+  },
   "$id": "reana_spec",
   "type": "object",
   "title": "REANA analysis specification",
@@ -65,11 +149,6 @@
       "description": "Workflow which represents the steps that need to be run to reproduce an analysis.",
       "additionalProperties": false,
       "properties": {
-        "specification": {
-          "$id": "/properties/workflow/properties/specification",
-          "type": "object",
-          "title": "Workflow specification in yaml format."
-        },
         "file": {
           "$id": "/properties/workflow/properties/file",
           "type": "string",
@@ -108,6 +187,64 @@
           }
         }
       },
+      "oneOf": [
+        {
+          "properties": {
+            "type": {
+              "const": "serial"
+            },
+            "specification": {
+              "$ref": "#/properties/workflow/properties/specifications?type=serial"
+            }
+          },
+          "required": [
+            "type",
+            "specification"
+          ]
+        },
+        {
+          "properties": {
+            "type": {
+              "const": "cwl"
+            },
+            "specification": {
+              "$ref": "#/properties/workflow/properties/specifications?type=cwl"
+            }
+          },
+          "required": [
+            "type",
+            "specification"
+          ]
+        },
+        {
+          "properties": {
+            "type": {
+              "const": "snakemake"
+            },
+            "specification": {
+              "$ref": "#/properties/workflow/properties/specifications?type=snakemake"
+            }
+          },
+          "required": [
+            "type",
+            "specification"
+          ]
+        },
+        {
+          "properties": {
+            "type": {
+              "const": "yadage"
+            },
+            "specification": {
+              "$ref": "#/properties/workflow/properties/specifications?type=yadage"
+            }
+          },
+          "required": [
+            "type",
+            "specification"
+          ]
+        }
+      ],
       "anyOf": [
         {
           "required": [

diff --git a/reana_commons/validation/utils.py b/reana_commons/validation/utils.py
@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 #
 # This file is part of REANA.
-# Copyright (C) 2022 CERN.
+# Copyright (C) 2022, 2023 CERN.
 #
 # REANA is free software; you can redistribute it and/or modify it
 # under the terms of the MIT License; see LICENSE file for more details.
@@ -77,6 +77,8 @@ def validate_reana_yaml(reana_yaml: Dict) -> Dict:
     """Validate REANA specification file according to jsonschema.
 
     :param reana_yaml: Dictionary which represents REANA specification file.
+    :returns: Dictionary of non-critical warnings, in the form of
+    {warning_key: [warning_value1, warning_value2, ...]}.
     :raises ValidationError: Given REANA spec file does not validate against
         REANA specification schema.
     """

diff --git a/setup.py b/setup.py
@@ -62,7 +62,7 @@
     "checksumdir>=1.1.4,<1.2",
     "click>=7.0",
     "fs>=2.0",
-    "jsonschema[format]>=3.0.1,<4.0.0",
+    "jsonschema[format]>=4.0.1,<5.0.0",
     "kombu>=4.6",
     "mock>=3.0,<4",
     "PyYAML>=5.1,<7.0",