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Merge pull request #173 from microbiomedata/issue-154
Update GOLD ecosystem classification path terms
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@@ -137,3 +137,5 @@ dmypy.json | |
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| # Pyre type checker | ||
| .pyre/ | ||
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| /examples/output | ||
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@@ -207,8 +207,8 @@ local/nmdc.yaml | |
| --format yaml [email protected] > $@ | ||
| - $(RUN) linkml-lint $@ > local/with_modifications.lint_report.txt | ||
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| src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml: local/with_modifications.yaml | ||
| cp $< $@ | ||
| 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 $@ | ||
| # remove the multivalued true annotation from these gloabl slot definitions for the sake of linkml-convert | ||
| # esp to tsv? and dumping to SQLite? | ||
| # follow the .string_serialization=="{text};{float} {unit}" and .multivalued == true pattern? | ||
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@@ -310,6 +310,10 @@ project/json/nmdc_submission_schema.json: src/nmdc_submission_schema/schema/nmdc | |
| mkdir -p $(@D) | ||
| $(RUN) gen-linkml $< --format json --materialize-patterns --materialize-attributes > $@ | ||
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| project/thirdparty/GoldEcosystemTree.json: | ||
| mkdir -p $(@D) | ||
| wget https://gold.jgi.doe.gov/download?mode=biosampleEcosystemsJson -O $@ | ||
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| dh-dev: project/json/nmdc_submission_schema.json | ||
| cd data_harmonizer && npm run dev | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,76 @@ | ||
| import json | ||
| from collections import defaultdict | ||
| from enum import Enum | ||
| from pathlib import Path | ||
| from typing import Dict, Set, Iterable, Optional | ||
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| import click | ||
| from linkml_runtime import SchemaView | ||
| from linkml_runtime.dumpers import yaml_dumper | ||
| from linkml_runtime.linkml_model import EnumDefinition, PermissibleValue, SchemaDefinition | ||
| from linkml_runtime.loaders import yaml_loader | ||
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| class PathwayLevel(Enum): | ||
| ecosystem = 'Ecosystem' | ||
| ecosystem_category = 'EcosystemCategory' | ||
| ecosystem_type = 'EcosystemType' | ||
| ecosystem_subtype = 'EcosystemSubtype' | ||
| specific_ecosystem = 'SpecificEcosystem' | ||
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| class GoldTermSet: | ||
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| def __init__(self, *, schema_enum_suffix: str = '', include: Optional[Dict[PathwayLevel, Iterable[str]]] = None): | ||
| self.schema_enum_suffix: str = schema_enum_suffix | ||
| self.terms: Dict[PathwayLevel, Set[str]] = defaultdict(set) | ||
| self.include: Dict[PathwayLevel, Iterable[str]] = include if include is not None else {} | ||
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| def inject_gold_pathway_terms(gold_ecosystem_tree_path: Path, input_schema_path: SchemaDefinition) -> SchemaDefinition: | ||
| """Inject gold pathway terms into the schema.""" | ||
| with open(gold_ecosystem_tree_path) as f: | ||
| gold_ecosystem_tree = json.load(f) | ||
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| levels = list(PathwayLevel) | ||
| all_terms = GoldTermSet() | ||
| soil_terms = GoldTermSet(schema_enum_suffix='ForSoil', include={ | ||
| PathwayLevel.ecosystem: ['Environmental'], | ||
| PathwayLevel.ecosystem_category: ['Terrestrial'], | ||
| PathwayLevel.ecosystem_type: ['Soil'], | ||
| }) | ||
| term_sets = [all_terms, soil_terms] | ||
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| def _add_term(term_set, term, level_index): | ||
| level = levels[level_index] | ||
| if term_set.include.get(level) and term['name'] not in term_set.include[level]: | ||
| return | ||
| term_set.terms[level].add(term['name']) | ||
| for child in term.get('children', []): | ||
| _add_term(term_set, child, level_index + 1) | ||
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| for term_set in term_sets: | ||
| for ecosystem in gold_ecosystem_tree['children']: | ||
| _add_term(term_set, ecosystem, level_index=0) | ||
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| schemaview = SchemaView(input_schema_path) | ||
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| for term_set in term_sets: | ||
| for level in levels: | ||
| pvs = [PermissibleValue(text=term) for term in sorted(term_set.terms[level])] | ||
| schemaview.add_enum(EnumDefinition( | ||
| name=level.value + term_set.schema_enum_suffix + 'Enum', | ||
| permissible_values=pvs | ||
| )) | ||
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| return schemaview.schema | ||
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| @click.command() | ||
| @click.option('--gold-ecosystem-tree-path', '-g', type=click.Path(exists=True), | ||
| help='Path to the gold ecosystem tree.') | ||
| @click.option('--input-file', '-i', type=click.File('r'), default="-") | ||
| @click.option('--output-file', '-o', type=click.File('w'), default="-") | ||
| def main(gold_ecosystem_tree_path, input_file, output_file): | ||
| schema = yaml_loader.loads(input_file.read(), SchemaDefinition) | ||
| output = inject_gold_pathway_terms(Path(gold_ecosystem_tree_path), schema) | ||
| print(yaml_dumper.dumps(output), file=output_file) |