integrated mixs_env_triad_field but with build errors

Author: turbomam

assets/other_mixs_yaml_files/mixs_env_triad_field_slot.yaml

@@ -0,0 +1,28 @@
+id: http:/example.com/mixs_env_triad_field_schema
+name: mixs_env_triad_field_schema
+slots:
+  name: mixs_env_triad_field
+  annotations:
+    tooltip:
+      tag: tooltip
+      value: >-
+        The MIxS environmental triad provides context about where a sample was collected and what it consists of.
+    annotations:
+      source:
+        tag: source
+        value: https://link.springer.com/protocol/10.1007/978-1-0716-3838-5_20
+  description: >-
+    The MIxS environmental triad provides context about where a sample was collected and what it consists of.
+    Its component slots capture the biome that the sample was found in, nearby geographical features that
+    might influence the organisms in the sample, 
+    and the substance that was displaced in the process of collecting the sample.
+    Careful population of these slots makes it easier for data users to find samples that are similar,
+    not just in terms of textual values, but through ontological relationships.
+    Furthermore, NMDC requires that its three component slots are populated because the INSDC Biosample databases
+    require that they are populated because the MIxS standard from the GSC requires that they are populated.
+  abstract: true
+  range: ControlledIdentifiedTermValue
+  see_also:
+    - https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS
+
+

assets/yq-for-mixs_subset_modified.txt

@@ -1,3 +1,7 @@
+'.slots.env_broad_scale.is_a |= "TextValue"'
+'.slots.env_local_scale.is_a |= "TextValue"'
+'.slots.env_medium.is_a |= "TextValue"'
+
 '.slots.agrochem_addition.range |= "TextValue"'
 '.slots.air_temp_regm.range |= "TextValue"'
 '.slots.antibiotic_regm.range |= "TextValue"'

project.Makefile

@@ -36,7 +36,7 @@ shuttle-clean:
 	touch local/mixs_regen/.gitkeep
 
 
-src/schema/mixs.yaml: shuttle-clean local/mixs_regen/mixs_subset_modified_inj_env_medium_alt_description.yaml
+src/schema/mixs.yaml: shuttle-clean local/mixs_regen/mixs_subset_modified_inj_mixs_env_triad_field_slot.yaml
 	mv $(word 2,$^) $@
 	rm -rf local/mixs_regen/mixs_subset_modified.yaml.bak
 
@@ -92,6 +92,13 @@ assets/other_mixs_yaml_files/nmdc_mixs_env_triad_tooltips.yaml
 		'select(fileIndex==0).slots.env_medium.annotations.tooltip = select(fileIndex==1).slots.env_medium.annotations.tooltip | select(fileIndex==0)' \
 		$^ | cat > $@
 
+
+local/mixs_regen/mixs_subset_modified_inj_mixs_env_triad_field_slot.yaml: local/mixs_regen/mixs_subset_modified_inj_env_medium_alt_description.yaml \
+assets/other_mixs_yaml_files/mixs_env_triad_field_slot.yaml
+	yq eval-all \
+		'select(fileIndex==0).slots.mixs_env_triad_field = select(fileIndex==1).slots.mixs_env_triad_field | select(fileIndex==0)' \
+		$^ | cat > $@
+
 examples/output: nmdc_schema/nmdc_materialized_patterns.yaml
 	mkdir -p $@
 	$(RUN) linkml-run-examples \