Merge pull request #545 from microbiomedata/issue-374_update-extreme-…

…events

Issue 374 update extreme events

pyproject.toml

@@ -44,25 +44,26 @@ migrate_3_2_to_7 = "nmdc_schema.migrate_3_2_to_7:cli"
 
 [tool.poetry.dependencies]
 python = "^3.9"
-linkml-runtime ="^1.3.0"
+linkml-runtime = "^1.3.0"
 
 [tool.poetry.dev-dependencies]
 black = "^22.10.0"
 build = "^0.9.0"
+check-jsonschema = "^0.19.2"
 click-log = "^0.4.0"
+deepdiff = "^6.2.1"
+docutils = "^0.19"
 jq = "^1.3.0"
+jupyter = "^1.0.0"
+linkml = "^1.3.15"
 mkdocs = "^1.4.2"
 mkdocs-material = "^8.5.7"
 mkdocs-mermaid2-plugin = "^0.6.0"
-twine = "^4.0.1"
-check-jsonschema = "^0.19.2"
-docutils = "^0.19"
-jupyter = "^1.0.0"
-linkml = "^1.3.15"
 pandas = "^1.5.1"
 pendulum = "^2.1.2"
 pymongo = "^4.3.3"
 python-dotenv = "^0.21.0"
+twine = "^4.0.1"
 
 [build-system]
 requires = ["poetry-core>=1.0.0"]

src/schema/nmdc.yaml

@@ -496,6 +496,7 @@ classes:
           syntax: "{id_nmdc_prefix}:{id_typecode_biosample}-{id_shoulder}-{id_blade}{id_version}{id_locus}"
           interpolated: true
           partial_match: false
+
       gold_biosample_identifiers:
         description: Unique identifier for a biosample submitted to GOLD that matches the NMDC submitted biosample
         comments: This is the ID provided by GOLD that starts with 'GB'
@@ -507,6 +508,7 @@ classes:
       alternative_identifiers:
         description: Unique identifier for a biosample submitted to additional resources. Matches the entity that has been submitted to NMDC
         required: false
+
       lat_lon:
         required: false
         description: This is currently a required field but it's not clear if this
@@ -522,6 +524,16 @@ classes:
         required: false
       part_of:
         required: true
+
+      extreme_event:
+        examples:
+          - value: 1980-05-18, volcanic eruption
+        annotations:
+          expected_value:
+            tag: expected_value
+            value: date, string
+        range: string
+
     id_prefixes:
       - GOLD
     exact_mappings:

util/compare_new_usage.py

@@ -0,0 +1,39 @@
+import pprint
+
+from linkml_runtime import SchemaView
+from linkml_runtime.dumpers import yaml_dumper
+
+import ruamel.yaml
+
+from deepdiff import DeepDiff \
+# print_diff
+
+schema_file = "../src/schema/nmdc.yaml"
+slots_added_in_induction = ['owner','domain_of']
+schema_view = SchemaView(schema_file)
+
+global_extreme_event = schema_view.get_slot("extreme_event")
+biosample_extreme_event = schema_view.induced_slot("extreme_event", "Biosample")
+
+# refactor
+# or better yet, direct element -> text dict conversion
+# and vice versa
+gee_yaml = yaml_dumper.dumps(global_extreme_event)
+gee_dict = ruamel.yaml.load(gee_yaml, Loader=ruamel.yaml.RoundTripLoader)
+
+bee_yaml = yaml_dumper.dumps(biosample_extreme_event)
+bee_dict = ruamel.yaml.load(bee_yaml, Loader=ruamel.yaml.RoundTripLoader)
+for i in slots_added_in_induction:
+    del bee_dict[i]
+
+print("Global extreme event")
+pprint.pprint(gee_dict)
+
+print("\n")
+print("Biosample extreme event")
+pprint.pprint(bee_dict)
+
+diff = DeepDiff(gee_dict, bee_dict)
+
+print("\n")
+pprint.pprint(diff)