nmdc-runtime 2.9.0__py3-none-any.whl → 2.10.0__py3-none-any.whl

nmdc_runtime-2.10.0.dist-info/RECORD

@@ -0,0 +1,138 @@
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nmdc_runtime/site/translation/emsl.py

@@ -1,43 +0,0 @@
-"""
-Translates EMSL data into JSON conformant with the NMDC JSON schema
-"""
-
-from dagster import op, graph
-
-from nmdc_runtime.lib.nmdc_etl_class import NMDC_ETL
-from nmdc_runtime.site.translation.util import (
-    load_nmdc_etl_class,
-    load_mongo_collection,
-    preset_prod,
-    preset_test,
-    schema_validate,
-)
-
-
-@op
-def transform_emsl_omics_processing(_context, nmdc_etl: NMDC_ETL) -> tuple:
-    return ("emsl.omics_processing_set", nmdc_etl.transform_emsl_omics_processing())
-
-
-@op
-def transform_emsl_data_object(_context, nmdc_etl: NMDC_ETL) -> tuple:
-    return ("emsl.data_object_set", nmdc_etl.transform_emsl_data_object())
-
-
-@graph
-def emsl():
-    # load_merged_data_source()
-    nmdc_etl = load_nmdc_etl_class()
-    emsl_omics_processing = transform_emsl_omics_processing(nmdc_etl)
-    emsl_omics_processing_validated = schema_validate(emsl_omics_processing)
-
-    emsl_data_object = transform_emsl_data_object(nmdc_etl)
-    emsl_data_object_validated = schema_validate(emsl_data_object)
-
-    # load data into mongo
-    load_mongo_collection(emsl_omics_processing_validated)
-    load_mongo_collection(emsl_data_object_validated)
-
-
-emsl_job = emsl.to_job(**preset_prod)
-test_emsl_job = emsl.to_job(name="test_emsl", **preset_test)

nmdc_runtime/site/translation/gold.py

@@ -1,53 +0,0 @@
-"""
-Translate an export of the JGI GOLD [1] study, project, and biosample data into JSON conformant with the NMDC JSON schema.
-[1] Genomes OnLine Database (GOLD) <https://gold.jgi.doe.gov/>.
-"""
-
-from dagster import op, graph
-
-from nmdc_runtime.lib.nmdc_etl_class import NMDC_ETL
-from nmdc_runtime.site.translation.util import (
-    load_nmdc_etl_class,
-    load_mongo_collection,
-    preset_prod,
-    preset_test,
-    schema_validate,
-)
-
-
-@op
-def transform_study(_context, nmdc_etl: NMDC_ETL) -> tuple:
-    # return {"study_set": nmdc_etl.transform_study()}
-    return ("gold.study_set", nmdc_etl.transform_study())
-
-
-@op
-def transform_gold_omics_processing(_context, nmdc_etl: NMDC_ETL) -> tuple:
-    return ("gold.omics_processing_set", nmdc_etl.transform_omics_processing())
-
-
-@op
-def transform_biosample(_context, nmdc_etl: NMDC_ETL) -> tuple:
-    return ("gold.biosample_set", nmdc_etl.transform_biosample())
-
-
-@graph
-def gold():
-    nmdc_etl = load_nmdc_etl_class()
-    gold_study = transform_study(nmdc_etl)
-    gold_study_validated = schema_validate(gold_study)
-
-    gold_omics_processing = transform_gold_omics_processing(nmdc_etl)
-    gold_omics_processing_validated = schema_validate(gold_omics_processing)
-
-    gold_biosample = transform_biosample(nmdc_etl)
-    gold_biosample_validated = schema_validate(gold_biosample)
-
-    # load data into mongo
-    load_mongo_collection(gold_study_validated)
-    load_mongo_collection(gold_omics_processing_validated)
-    load_mongo_collection(gold_biosample_validated)
-
-
-gold_job = gold.to_job(**preset_prod)
-test_gold_job = gold.to_job(name="test_gold", **preset_test)

nmdc_runtime/site/translation/jgi.py

@@ -1,32 +0,0 @@
-"""
-Translates EMSL data into JSON conformant with the NMDC JSON schema
-"""
-
-from dagster import op, graph
-
-from nmdc_runtime.lib.nmdc_etl_class import NMDC_ETL
-from nmdc_runtime.site.translation.util import (
-    load_nmdc_etl_class,
-    load_mongo_collection,
-    preset_prod,
-    preset_test,
-    schema_validate,
-)
-
-
-@op
-def transform_jgi_data_object(_context, nmdc_etl: NMDC_ETL) -> tuple:
-    # return "jgi.data_object_set", [{"foo": "bar"}]  # used for testing failure
-    return "jgi.data_object_set", nmdc_etl.transform_jgi_data_object()
-
-
-@graph
-def jgi():
-    nmdc_etl = load_nmdc_etl_class()
-    jgi_data_object = transform_jgi_data_object(nmdc_etl)
-    jgi_data_object_validated = schema_validate(jgi_data_object)
-    load_mongo_collection(jgi_data_object_validated)
-
-
-jgi_job = jgi.to_job(**preset_prod)
-test_jgi_job = jgi.to_job(name="test_jgi", **preset_test)

nmdc_runtime/site/translation/util.py

@@ -1,132 +0,0 @@
-from pathlib import Path
-
-from dagster import op, Failure, AssetMaterialization
-from dagster.core.definitions.events import AssetKey, Output
-from fastjsonschema import JsonSchemaValueException
-
-from nmdc_runtime.lib.nmdc_etl_class import NMDC_ETL
-from nmdc_runtime.site.resources import mongo_resource
-from nmdc_runtime.util import nmdc_jsonschema_validator
-
-mode_prod = {"resource_defs": {"mongo": mongo_resource}}
-mode_dev = {
-    "resource_defs": {"mongo": mongo_resource}
-}  # Connect to a real MongoDB instance for development.
-mode_test = {
-    "resource_defs": {"mongo": mongo_resource}
-}  # Connect to a real MongoDB instance for testing.
-
-config_prod = {
-    "resources": {
-        "mongo": {
-            "config": {
-                "host": {"env": "MONGO_HOST"},
-                "username": {"env": "MONGO_USERNAME"},
-                "password": {"env": "MONGO_PASSWORD"},
-                "dbname": "nmdc_etl_staging",
-            },
-        }
-    },
-    "ops": {
-        "load_nmdc_etl_class": {
-            "config": {
-                "data_file": str(
-                    Path(__file__).parent.parent.parent.parent.joinpath(
-                        "metadata-translation/src/data/nmdc_merged_data.tsv.zip"
-                    )
-                ),
-                "sssom_map_file": "",
-                "spec_file": str(
-                    Path(__file__).parent.parent.parent.parent.joinpath(
-                        "nmdc_runtime/lib/nmdc_data_source.yaml"
-                    )
-                ),
-            }
-        }
-    },
-}
-
-config_test = {
-    "resources": {
-        "mongo": {
-            "config": {
-                # local docker container via docker-compose.yml
-                "host": "mongo",
-                "username": "admin",
-                "password": "root",
-                "dbname": "nmdc_etl_staging",
-            },
-        }
-    },
-    "ops": {
-        "load_nmdc_etl_class": {
-            "config": {
-                "data_file": str(
-                    Path(__file__).parent.parent.parent.parent.joinpath(
-                        "metadata-translation/src/data/nmdc_merged_data.tsv.zip"
-                    )
-                ),
-                "sssom_map_file": "",
-                "spec_file": str(
-                    Path(__file__).parent.parent.parent.parent.joinpath(
-                        "nmdc_runtime/lib/nmdc_data_source.yaml"
-                    )
-                ),
-            }
-        }
-    },
-}
-
-preset_prod = dict(**mode_prod, config=config_prod)
-preset_test = dict(**mode_test, config=config_test)
-
-
-@op
-def load_nmdc_etl_class(context) -> NMDC_ETL:
-    # build instance of NMDC_ETL class
-    etl = NMDC_ETL(
-        merged_data_file=context.op_config["data_file"],
-        data_source_spec_file=context.op_config["spec_file"],
-        sssom_file="",
-    )
-    return etl
-
-
-@op(required_resource_keys={"mongo"})
-def load_mongo_collection(context, data: tuple):
-    mongo_db = context.resources.mongo.db
-    collection_name, documents = data
-    collection = mongo_db[collection_name]  # get mongo collection
-
-    # drop collection if exists
-    collection.drop()
-
-    # insert data
-    collection.insert(documents)
-    context.log.info(f"inserted {len(documents)} documents into {collection.name}")
-    return collection_name
-
-
-@op()
-def schema_validate(context, data: tuple):
-    def schema_validate_asset(collection_name, status, errors):
-        return AssetMaterialization(
-            asset_key=AssetKey(["translation", f"{collection_name}_translation"]),
-            description=f"{collection_name} translation validation",
-            metadata={"status": status, "errors": errors},
-        )
-
-    collection_name, documents = data
-    _, schema_collection_name = collection_name.split(".")
-    try:
-        nmdc_jsonschema_validator({schema_collection_name: documents})
-        context.log.info(f"data for {collection_name} is valid")
-        yield schema_validate_asset(collection_name, "valid", "none")
-        return data  # do I need a return statement and an Output?
-    except JsonSchemaValueException as e:
-        context.log.error(f"validation failed for {schema_collection_name} " + str(e))
-        context.log.error(f"documents: {documents}")
-        yield schema_validate_asset(collection_name, "not valid", str(e))
-        raise Failure(str(e))
-    finally:
-        yield Output(data)

nmdc_runtime/site/validation/jgi.py

@@ -1,43 +0,0 @@
-"""
-Validates data in the JGI collection in the nmdc_etl_staging database.
-"""
-
-from dagster import op, graph
-
-from nmdc_runtime.site.ops import local_file_to_api_object
-from nmdc_runtime.site.validation.util import (
-    preset_prod,
-    preset_test,
-    validate_mongo_collection,
-    write_to_local_file,
-    announce_validation_report,
-)
-
-
-@op
-def jgi_data_object_set_collection_name():
-    return "jgi.data_object_set"
-
-
-@graph()
-def jgi():
-    report = validate_mongo_collection(jgi_data_object_set_collection_name())
-    # the below could also be a @graph and loaded as a "subgraph" by e.g. the jgi graph job.
-    local_path = write_to_local_file(report)
-    obj = local_file_to_api_object(local_path)
-    announce_validation_report(report, obj)
-
-
-# passing the collecton name via the config
-# problem: not sure if this best when multiple sets need to be validated
-# from toolz import assoc_in
-# config_ops = {
-#     "validate_mongo_collection": {"config": {"collection_name": "jgi.data_object_set"}}
-# }
-# validate_jgi_job = jgi.to_job(**assoc_in(preset_prod, ["config", "ops"], config_ops))
-# test_validate_jgi_job = jgi.to_job(
-#     **assoc_in(preset_test, ["config", "ops"], config_ops)
-# )
-
-validate_jgi_job = jgi.to_job(**preset_prod)
-test_validate_jgi_job = jgi.to_job(**preset_test)

nmdc_runtime-2.9.0.dist-info/RECORD

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