Merge pull request #181 from microbiomedata/conflict-resolved-backmerge

Conflict resolved backmerge

.github/workflows/main.yaml

@@ -4,15 +4,15 @@
 
 name: Build and test nmdc-schema
 
-on: [pull_request]
+on: [ pull_request ]
 
 jobs:
   test:
 
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9", "3.10"]
+        python-version: [ "3.9", "3.10" ]
 
     steps:
 
@@ -49,5 +49,5 @@ jobs:
       #              run test suite   
       #----------------------------------------------
       - name: Run tests
-        run: make test
+        run: make squeaky-clean all test
 

assets/my_emsl_prefix.ttl

@@ -0,0 +1 @@
+@prefix my_emsl: <https://release.my.emsl.pnnl.gov/released_data/> .

assets/yq-for-mixs_subset_modified.txt

@@ -213,3 +213,8 @@ make: *** [Makefile:102: gen-project] Error 1
 'del(.types)'
 
 '.imports += ["attribute_values"]'
+'.slots.elev.range |= "float"'
+'.slots.extreme_event.range |= "string"'
+'.slots.fire.range |= "string"'
+'.slots.flooding.range |= "string"'
+'.slots.water_content.range |= "string"'

assets/yq-for-nmdc_schema_accepting_legacy_ids.txt

@@ -1,38 +1,2 @@
-# probably should have made a list of classes and then looped over a parameterized version of this
-# could also assert that the range is string
-'(.classes[] | select(.name == "Biosample") | .slot_usage.id.pattern) = ".*"'
-'(.classes[] | select(.name == "Biosample") | .slot_usage.part_of.pattern) = ".*"'
-'(.classes[] | select(.name == "Biosample") | .slot_usage.id.structured_pattern.syntax) = ".*"'
-'(.classes[] | select(.name == "DataObject") | .slot_usage.id.pattern) = ".*"'
-'(.classes[] | select(.name == "DataObject") | .slot_usage.id.structured_pattern.syntax) = ".*"'
-'(.classes[] | select(.name == "MagsAnalysisActivity") | .slot_usage.id.pattern) = ".*"'
-'(.classes[] | select(.name == "MagsAnalysisActivity") | .slot_usage.id.structured_pattern.syntax) = ".*"'
-'(.classes[] | select(.name == "MetabolomicsAnalysisActivity") | .slot_usage.id.pattern) = ".*"'
-'(.classes[] | select(.name == "MetabolomicsAnalysisActivity") | .slot_usage.id.structured_pattern.syntax) = ".*"'
-'(.classes[] | select(.name == "MetagenomeAnnotationActivity") | .slot_usage.id.pattern) = ".*"'
-'(.classes[] | select(.name == "MetagenomeAnnotationActivity") | .slot_usage.id.structured_pattern.syntax) = ".*"'
-'(.classes[] | select(.name == "MetagenomeAssembly") | .slot_usage.id.pattern) = ".*"'
-'(.classes[] | select(.name == "MetagenomeAssembly") | .slot_usage.id.structured_pattern.syntax) = ".*"'
-'(.classes[] | select(.name == "MetagenomeSequencingActivity") | .slot_usage.id.pattern) = ".*"'
-'(.classes[] | select(.name == "MetagenomeSequencingActivity") | .slot_usage.id.structured_pattern.syntax) = ".*"'
-'(.classes[] | select(.name == "MetaproteomicsAnalysisActivity") | .slot_usage.id.pattern) = ".*"'
-'(.classes[] | select(.name == "MetaproteomicsAnalysisActivity") | .slot_usage.id.structured_pattern.syntax) = ".*"'
-'(.classes[] | select(.name == "MetatranscriptomeActivity") | .slot_usage.id.pattern) = ".*"'
-'(.classes[] | select(.name == "MetatranscriptomeActivity") | .slot_usage.id.structured_pattern.syntax) = ".*"'
-'(.classes[] | select(.name == "MetatranscriptomeAnnotationActivity") | .slot_usage.id.pattern) = ".*"'
-'(.classes[] | select(.name == "MetatranscriptomeAnnotationActivity") | .slot_usage.id.structured_pattern.syntax) = ".*"'
-'(.classes[] | select(.name == "MetatranscriptomeAssembly") | .slot_usage.id.pattern) = ".*"'
-'(.classes[] | select(.name == "MetatranscriptomeAssembly") | .slot_usage.id.structured_pattern.syntax) = ".*"'
-'(.classes[] | select(.name == "NomAnalysisActivity") | .slot_usage.id.pattern) = ".*"'
-'(.classes[] | select(.name == "NomAnalysisActivity") | .slot_usage.id.structured_pattern.syntax) = ".*"'
-'(.classes[] | select(.name == "OmicsProcessing") | .slot_usage.id.pattern) = ".*"'
-'(.classes[] | select(.name == "OmicsProcessing") | .slot_usage.part_of.pattern) = ".*"'
-'(.classes[] | select(.name == "OmicsProcessing") | .slot_usage.has_input.pattern) = ".*"'
-'(.classes[] | select(.name == "OmicsProcessing") | .slot_usage.has_output.pattern) = ".*"'
-'(.classes[] | select(.name == "OmicsProcessing") | .slot_usage.id.structured_pattern.syntax) = ".*"'
-'(.classes[] | select(.name == "ReadBasedTaxonomyAnalysisActivity") | .slot_usage.id.pattern) = ".*"'
-'(.classes[] | select(.name == "ReadBasedTaxonomyAnalysisActivity") | .slot_usage.id.structured_pattern.syntax) = ".*"'
-'(.classes[] | select(.name == "ReadQcAnalysisActivity") | .slot_usage.id.pattern) = ".*"'
-'(.classes[] | select(.name == "ReadQcAnalysisActivity") | .slot_usage.id.structured_pattern.syntax) = ".*"'
-'(.classes[] | select(.name == "Study") | .slot_usage.id.pattern) = ".*"'
-'(.classes[] | select(.name == "Study") | .slot_usage.id.structured_pattern.syntax) = ".*"'
+'(.classes.[].slot_usage.[] | select(has("pattern")).pattern) = ".*" '
+'(.classes.[].slot_usage.[] | select(has("structured_pattern")).structured_pattern.syntax) = ".*" '