Merge pull request #10 from GenomicsStandardsConsortium/first-any_of-…

…range first-any_of-range
GenomicsStandardsConsortium · Sep 13, 2024 · 9953119 · 9953119
2 parents 2649d3c + 69c9abf
commit 9953119
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Showing 8 changed files with 55 additions and 2 deletions.
diff --git a/assets/MimsSoil-collection_date-absent-report.txt b/assets/MimsSoil-collection_date-absent-report.txt
@@ -0,0 +1 @@
+[ERROR] [src/data/examples/invalid/MimsSoil-collection_date-absent.yaml/0] 'collection_date' is a required property in /
diff --git a/assets/MimsSoil-collection_date-from_enum-report.txt b/assets/MimsSoil-collection_date-from_enum-report.txt
@@ -0,0 +1 @@
+No issues found
diff --git a/assets/MixsCompliantData-001-report.txt b/assets/MixsCompliantData-001-report.txt
@@ -0,0 +1 @@
+No issues found
diff --git a/project.Makefile b/project.Makefile
@@ -1,13 +1,27 @@
 RUN=poetry run
 
-src/data/valid/MixsCompliantData-001-report.txt: src/data/examples/valid \
+assets/MixsCompliantData-001-report.txt: src/data/examples/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/examples/valid \
+assets/MimsSoil-collection_date-absent-report.txt: src/data/examples/invalid/MimsSoil-collection_date-absent.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) \
+		$(word 1,$^) > $@
+
+assets/MimsSoil-collection_date-from_enum-report.txt: src/data/examples/valid/MimsSoil-collection_date-from_enum.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) \
+		$(word 1,$^) > $@
+
+assets/MixsCompliantData-001.tsv: src/data/examples/valid/MixsCompliantData-001.yaml \
 src/mixs_missing_value_sandbox/schema/mixs_missing_value_sandbox.yaml
 	$(RUN) linkml-convert --schema $(word 2,$^) \
 		--output $@ \

diff --git a/src/data/examples/invalid/MimsSoil-collection_date-absent.yaml b/src/data/examples/invalid/MimsSoil-collection_date-absent.yaml
@@ -0,0 +1,12 @@
+depth: "123"
+elev: "123"
+project_name: abc
+samp_name: abc
+
+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
diff --git a/...les/invalid/Soil-missing_sample_name.yaml → ...ples/invalid/Soil-sample_name-absent.yaml b/...les/invalid/Soil-missing_sample_name.yaml → ...ples/invalid/Soil-sample_name-absent.yaml
diff --git a/src/data/examples/valid/MimsSoil-collection_date-from_enum.yaml b/src/data/examples/valid/MimsSoil-collection_date-from_enum.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
diff --git a/src/mixs_missing_value_sandbox/schema/mixs_missing_value_sandbox.yaml b/src/mixs_missing_value_sandbox/schema/mixs_missing_value_sandbox.yaml
@@ -72,6 +72,11 @@ classes:
     mixins:
       - Mims
     class_uri: MIXS:0010007_0016012
+    slot_usage:
+      collection_date:
+        any_of:
+          - range: datetime
+          - range: MixsMissingValueEnum
   Mims:
     description: Metagenome or Environmental
     title: MIMS
@@ -1882,6 +1887,12 @@ slots:
       partial_match: true
 
 enums:
+  MixsMissingValueEnum:
+    permissible_values:
+      missing1: { }
+      missing2: { }
+      missing3: { }
+
   DrainageClassEnum:
     permissible_values:
       excessively drained: