Merge pull request #194 from microbiomedata/microbiomedata-main

merge in v10.5.3
microbiomedata · Jun 5, 2024 · 110777a · 110777a
2 parents a613c4f + c998f6a
commit 110777a
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diff --git a/nmdc_schema/gold-to-mixs.sssom.tsv b/nmdc_schema/gold-to-mixs.sssom.tsv
diff --git a/nmdc_schema/nmdc.py b/nmdc_schema/nmdc.py
diff --git a/nmdc_schema/nmdc.schema.json b/nmdc_schema/nmdc.schema.json
diff --git a/nmdc_schema/nmdc_materialized_patterns.schema.json b/nmdc_schema/nmdc_materialized_patterns.schema.json
diff --git a/nmdc_schema/nmdc_materialized_patterns.yaml b/nmdc_schema/nmdc_materialized_patterns.yaml
diff --git a/nmdc_schema/nmdc_schema_accepting_legacy_ids.py b/nmdc_schema/nmdc_schema_accepting_legacy_ids.py
diff --git a/nmdc_schema/nmdc_schema_accepting_legacy_ids.schema.json b/nmdc_schema/nmdc_schema_accepting_legacy_ids.schema.json
diff --git a/nmdc_schema/nmdc_schema_accepting_legacy_ids.yaml b/nmdc_schema/nmdc_schema_accepting_legacy_ids.yaml
diff --git a/nmdc_schema/nmdc_schema_merged.yaml b/nmdc_schema/nmdc_schema_merged.yaml
diff --git a/poetry.lock b/poetry.lock
diff --git a/project.Makefile b/project.Makefile
@@ -215,6 +215,8 @@ local/mongo_as_unvalidated_nmdc_database.yaml:
 		--selected-collections metagenome_annotation_activity_set \
 		--selected-collections metagenome_annotation_set \
 		--selected-collections metagenome_assembly_set \
+		--selected-collections metagenome_sequencing_activity_set \
+		--selected-collections metagenome_sequencing_set \
 		--selected-collections metap_gene_function_aggregation \
 		--selected-collections metatranscriptome_activity_set \
 		--selected-collections metatranscriptome_analysis_set \

diff --git a/src/data/invalid/MetagenomeSequencing-bad_id.yaml b/src/data/invalid/MetagenomeSequencing-bad_id.yaml
@@ -1,9 +1,10 @@
 id: nmdc:bad_id
 has_input:
-  - 'nmdc:unvalidated_placeholder'
+  - nmdc:procsm-99-123456
 # legacy part_of id? validator won't catch pattern violations
 #   or referential integrity violations
-part_of: nmdc:mga0vx38
+part_of:
+  - nmdc:wfch-99-123456
 git_url: 'https://github.com/microbiomedata/RawSequencingData'
 execution_resource: JGI
 version: v1.0.0

diff --git a/src/schema/workflow_execution_activity.yaml b/src/schema/workflow_execution_activity.yaml
@@ -183,16 +183,10 @@ classes:
         structured_pattern:
           syntax: "{id_nmdc_prefix}:wfmsa-{id_shoulder}-{id_blade}{id_version}$"
           interpolated: true
-  #      has_input:
-  #        comments:
-  #          - the value is always expected to be the string "None", but that isn't a valid prefixed CURIe
-  #      has_output:
-  #        structured_pattern:
-  #          syntax: "{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$"
-  #        structured_pattern:
-  #          syntax: ".*" # todo this accounts for an extreme edge case and should nto be repeated anywhere
-  #          interpolated: true
-
+      has_input:
+        structured_pattern:
+          syntax: "{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$"
+          interpolated: true
 
   ReadQcAnalysis:
     class_uri: nmdc:ReadQcAnalysis