#382 validation pattern for fire

Makefile

@@ -225,15 +225,17 @@ SCHEMA_TEST_EXAMPLES := \
 	nmdc_example_database \
 	samp_prep_db \
 	study_credit_test \
-	study_test
+	study_test \
+	minimal_valid_biosample_with_fire
 
 SCHEMA_TEST_EXAMPLES_INVALID := \
 	biosample_invalid_range \
 	biosample_mismatch_regex \
 	biosample_missing_required_field \
 	biosample_single_multi_value_mixup \
 	biosample_undeclared_slot \
-	study_credit_enum_mangle
+	study_credit_enum_mangle \
+	minimal_biosample_invalid_fire
 
 # 	functional_annotation_set_invalid has invalid ID pattern but regex tests aren't applied yet? MAM 2021-06-24
 

src/schema/nmdc.yaml

@@ -536,6 +536,7 @@ classes:
             tag: expected_value
             value: date string
         range: string
+        pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?(\s+to\s+[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?)?$
       flooding:
         annotations:
           expected_value:

test/data/invalid_data/minimal_biosample_invalid_fire.json

@@ -0,0 +1,29 @@
+{
+  "biosample_set": [
+    {
+      "id": "nmdc:bsm-99-dtTMNb",
+      "fire": "like a volcano",
+      "part_of": [
+        "gold:Gs0110115"
+      ],
+      "env_broad_scale": {
+        "has_raw_value": "ENVO:00002030",
+        "term": {
+          "id": "ENVO:00002030"
+        }
+      },
+      "env_local_scale": {
+        "has_raw_value": "ENVO:00002169",
+        "term": {
+          "id": "ENVO:00002169"
+        }
+      },
+      "env_medium": {
+        "has_raw_value": "ENVO:00005792",
+        "term": {
+          "id": "ENVO:00005792"
+        }
+      }
+    }
+  ]
+}

test/data/invalid_data/minimal_biosample_with_fire_test.json

@@ -0,0 +1,29 @@
+{
+  "biosample_set": [
+    {
+      "id": "nmdc:bsm-99-dtTMNb",
+      "fire": "1871-10-01 to 1871-10-31",
+      "part_of": [
+        "gold:Gs0110115"
+      ],
+      "env_broad_scale": {
+        "has_raw_value": "ENVO:00002030",
+        "term": {
+          "id": "ENVO:00002030"
+        }
+      },
+      "env_local_scale": {
+        "has_raw_value": "ENVO:00002169",
+        "term": {
+          "id": "ENVO:00002169"
+        }
+      },
+      "env_medium": {
+        "has_raw_value": "ENVO:00005792",
+        "term": {
+          "id": "ENVO:00005792"
+        }
+      }
+    }
+  ]
+}

test/data/minimal_valid_biosample_test.json

@@ -0,0 +1,32 @@
+// 20230124150223
+// https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/test/data/minimal_valid_biosample_test.json
+
+{
+  "biosample_set": [
+    {
+      "id": "nmdc:bsm-99-dtTMNb",
+      "fire": "1871-10-01 to 1871-10-31",
+      "part_of": [
+        "gold:Gs0110115"
+      ],
+      "env_broad_scale": {
+        "has_raw_value": "ENVO:00002030",
+        "term": {
+          "id": "ENVO:00002030"
+        }
+      },
+      "env_local_scale": {
+        "has_raw_value": "ENVO:00002169",
+        "term": {
+          "id": "ENVO:00002169"
+        }
+      },
+      "env_medium": {
+        "has_raw_value": "ENVO:00005792",
+        "term": {
+          "id": "ENVO:00005792"
+        }
+      }
+    }
+  ]
+}

test/data/minimal_valid_biosample_with_fire.json

@@ -0,0 +1,29 @@
+{
+  "biosample_set": [
+    {
+      "id": "nmdc:bsm-99-dtTMNb",
+      "fire": "1871-10-01 to 1871-10-31",
+      "part_of": [
+        "gold:Gs0110115"
+      ],
+      "env_broad_scale": {
+        "has_raw_value": "ENVO:00002030",
+        "term": {
+          "id": "ENVO:00002030"
+        }
+      },
+      "env_local_scale": {
+        "has_raw_value": "ENVO:00002169",
+        "term": {
+          "id": "ENVO:00002169"
+        }
+      },
+      "env_medium": {
+        "has_raw_value": "ENVO:00005792",
+        "term": {
+          "id": "ENVO:00005792"
+        }
+      }
+    }
+  ]
+}