Merge pull request #260 from microbiomedata/env_triad

add PV terms from env triad to schema
microbiomedata · Nov 11, 2024 · 5067032 · 5067032
2 parents f156044 + 0be360a
commit 5067032
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Showing 17 changed files with 14,387 additions and 11,326 deletions.
diff --git a/Makefile b/Makefile
@@ -91,7 +91,7 @@ update-linkml:
 	poetry add -D linkml@latest
 
 all: site
-site: clean schema-clean src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml \
+site: clean schema-clean src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml ingest-triad \
 gen-project gendoc project/json/nmdc_submission_schema.json
 
 %.yaml: gen-project
@@ -124,7 +124,7 @@ test-schema:
 	$(RUN) gen-project ${GEN_PARGS} -d tmp $(SOURCE_SCHEMA_PATH)
 
 test-python:
-	$(RUN) python -m unittest discover
+	$(RUN) pytest
 
 lint:
 	$(RUN) linkml-lint $(SOURCE_SCHEMA_PATH)

diff --git a/.../post_google_sheets_soil_env_medium.ipynb → ...google_sheets_soil_env_medium_scale.ipynb b/.../post_google_sheets_soil_env_medium.ipynb → ...google_sheets_soil_env_medium_scale.ipynb
@@ -80,7 +80,7 @@
     }
    },
    "cell_type": "code",
-   "source": "output_file = \"post_google_sheets_soil_env_medium.tsv\"",
+   "source": "output_file = \"post_google_sheets_soil_env_medium_scale.tsv\"",
    "id": "4737c7dfdaa5400e",
    "outputs": [],
    "execution_count": 6

diff --git a/...um/post_google_sheets_soil_env_medium.tsv → ...t_google_sheets_soil_env_medium_scale.tsv b/...um/post_google_sheets_soil_env_medium.tsv → ...t_google_sheets_soil_env_medium_scale.tsv
diff --git a/...il_env_medium_retention_justification.tsv → ..._medium_scale_retention_justification.tsv b/...il_env_medium_retention_justification.tsv → ..._medium_scale_retention_justification.tsv
diff --git a/project.Makefile b/project.Makefile
@@ -181,6 +181,28 @@ local/nmdc.yaml
 		--format yaml [email protected] > $@
 	- $(RUN) linkml-lint $@ > local/with_modifications.lint_report.txt
 
+
+########### ENV Triad PV generation ##########
+# Specify that 'ingest-triad' is a phony target, meaning it doesn't correspond to an actual file
+.PHONY: ingest-triad
+WATCHED_DIR := notebooks/environmental_context_value_sets
+WATCHED_FILES := $(shell find $(WATCHED_DIR) -type f)
+
+# Define an intermediate target to prevent re-triggering
+.INTERMEDIATE: temp_target
+
+# Main target to run ingestion commands, depending on the intermediate target
+ingest-triad: temp_target
+
+# Intermediate target that has all dependencies
+temp_target: $(WATCHED_FILES) src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml
+	$(RUN) inject-env-triad-terms -f notebooks/environmental_context_value_sets/soil/env_local_scale/post_google_sheets_soil_env_local_scale.tsv -i src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml -o src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml
+	$(RUN) inject-env-triad-terms -f notebooks/environmental_context_value_sets/soil/env_medium/post_google_sheets_soil_env_medium_scale.tsv -i src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml -o src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml
+	$(RUN) inject-env-triad-terms -f notebooks/environmental_context_value_sets/soil/env_broad_scale/post_google_sheets_soil_env_broad_scale.tsv -i src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml -o src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml
+	touch temp_target
+
+################################################
+
 src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml: local/with_modifications.yaml project/thirdparty/GoldEcosystemTree.json
 	$(RUN) inject-gold-pathway-terms -g $(word 2,$^) -i $< -o $@
 	#cp $< $@