minimal MimsSoil schema with examples

.gitignore

@@ -1,3 +1,5 @@
+.idea/
+
 /docs/
 /project/docs/
 /tmp/

project.Makefile

@@ -1 +1,14 @@
-## Add your own custom Makefile targets here
+RUN=poetry run
+
+src/data/valid/MixsCompliantData-001-report.txt: src/data/valid/MixsCompliantData-001.yaml \
+src/mixs_missing_value_sandbox/schema/mixs_missing_value_sandbox.yaml
+	$(RUN) linkml-validate \
+		--schema $(word 2,$^) \
+		--target-class $(shell echo $(basename $(notdir $(word 1,$^))) | cut -d'-' -f1) \
+		$(word 1,$^) > $@
+
+src/data/valid/MixsCompliantData-001.tsv: src/data/valid/MixsCompliantData-001.yaml \
+src/mixs_missing_value_sandbox/schema/mixs_missing_value_sandbox.yaml
+	$(RUN) linkml-convert --schema $(word 2,$^) \
+		--output $@ \
+		--index-slot mims_soil_data $(word 1,$^)

src/data/valid/MimsSoil-data-001.yaml

@@ -0,0 +1,13 @@
+depth: "123"
+elev: "123"
+project_name: abc
+samp_name: abc
+
+collection_date: '2013-03-25T12:42:31+01:00'
+env_broad_scale: unicorn [example:999]
+env_local_scale: unicorn [example:999]
+env_medium: unicorn [example:999]
+geo_loc_name: "unicorn: unicorn, unicorn"
+lat_lon: 45.67 45.67
+samp_taxon_id: unicorn [NCBITaxon:999]
+seq_meth: xxx

src/data/valid/MixsCompliantData-001-report.txt

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+No issues found

src/data/valid/MixsCompliantData-001.tsv

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+depth	elev	project_name	samp_name	collection_date	env_broad_scale	env_local_scale	env_medium	geo_loc_name	lat_lon	samp_taxon_id	seq_meth
+123	123	abc	abc	2013-03-25T12:42:31+01:00	unicorn [example:999]	unicorn [example:999]	unicorn [example:999]	unicorn: unicorn, unicorn	45.67 45.67	unicorn [NCBITaxon:999]	xxx
+123	123	abc	abc	2013-03-25T12:42:31+01:00	unicorn [example:999]	unicorn [example:999]	unicorn [example:999]	unicorn: unicorn, unicorn	45.67 45.67	unicorn [NCBITaxon:999]	xxx

src/data/valid/MixsCompliantData-001.yaml

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+mims_soil_data:
+  - depth: "123"
+    elev: "123"
+    project_name: abc
+    samp_name: abc
+    collection_date: '2013-03-25T12:42:31+01:00'
+    env_broad_scale: unicorn [example:999]
+    env_local_scale: unicorn [example:999]
+    env_medium: unicorn [example:999]
+    geo_loc_name: "unicorn: unicorn, unicorn"
+    lat_lon: 45.67 45.67
+    samp_taxon_id: unicorn [NCBITaxon:999]
+    seq_meth: xxx
+  - depth: "123"
+    elev: "123"
+    project_name: abc # no primary id?
+    samp_name: abc
+    collection_date: '2013-03-25T12:42:31+01:00'
+    env_broad_scale: unicorn [example:999]
+    env_local_scale: unicorn [example:999]
+    env_medium: unicorn [example:999]
+    geo_loc_name: "unicorn: unicorn, unicorn"
+    lat_lon: 45.67 45.67
+    samp_taxon_id: unicorn [NCBITaxon:999]
+    seq_meth: xxx

src/data/valid/Soil-data-001.yaml

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+depth: "123"
+elev: "123"
+project_name: abc
+samp_name: abc
+