nmdc-runtime 2.8.0__py3-none-any.whl → 2.10.0__py3-none-any.whl

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-2.8.0.dist-info/RECORD

@@ -1,84 +0,0 @@
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-nmdc_runtime/config.py,sha256=GKmovwYD3tIiUQX-mAOcHI8NMEMLhogjHDB9I8azA4c,195
-nmdc_runtime/containers.py,sha256=8m_S1wiFu8VOWvY7tyqzf-02X9gXY83YGc8FgjWzLGA,418
-nmdc_runtime/main.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-nmdc_runtime/mongo_util.py,sha256=7NRvqFE8W2CUcpcXAA4KElUACIdAkBehZ9TBG4k7zNE,3000
-nmdc_runtime/util.py,sha256=FfGNfcnHKS6Yzuwbdj0FtCcL-ks9HUjwWUfsPs1H2ao,33285
-nmdc_runtime/client/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-nmdc_runtime/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-nmdc_runtime/core/db/Database.py,sha256=WamgBUbq85A7-fr3p5B9Tk92U__yPdr9pBb4zyQok-4,377
-nmdc_runtime/core/db/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-nmdc_runtime/core/exceptions/__init__.py,sha256=s486odD0uhUuk9K7M5_NISOgRrUE5RNnDJSypA2Qe_I,520
-nmdc_runtime/core/exceptions/base.py,sha256=G5azYv0FJvbjrpQtK90BkM-KK2f534szdwrHj9N-SNo,1343
-nmdc_runtime/core/exceptions/token.py,sha256=7iTdfRQjfijDExd6-KJBjN7t0BGI_Kc1F6Lc-d0AsE8,293
-nmdc_runtime/domain/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-nmdc_runtime/domain/users/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-nmdc_runtime/domain/users/queriesInterface.py,sha256=0DjOehnsA5oKADmRKh8NTool2zoQZaejFigXHuUGoOg,476
-nmdc_runtime/domain/users/userSchema.py,sha256=eVpsB5aSbT89XjPh2_m7ao8XyyinEC94hpZQIouV4uk,758
-nmdc_runtime/domain/users/userService.py,sha256=b-HD7N-wWQyAux_iZsXMBFrz5_j9ygRc3qsJlm-vQGI,428
-nmdc_runtime/infrastructure/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-nmdc_runtime/infrastructure/database/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-nmdc_runtime/infrastructure/database/db.py,sha256=djdqVxXvvJWtJUj4yariINcOuYOkQ_OiAYI_jGqOtM8,32
-nmdc_runtime/infrastructure/database/models/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-nmdc_runtime/infrastructure/database/models/user.py,sha256=gOZVsQ9uZ_JlPKUcNOiJpj4_CQ9p2BpCaegcPiJQETs,188
-nmdc_runtime/lib/__init__.py,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
-nmdc_runtime/lib/extract_nmdc_data.py,sha256=xDFPoYsgkauN48R4v-tJIF0cP_p3J-sBjnyHd0InD9Y,1177
-nmdc_runtime/lib/load_nmdc_data.py,sha256=KO2cIqkY3cBCVcFIwsGokZNOKntOejZVG8ecq43NjFM,3934
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-nmdc_runtime/lib/nmdc_etl_class.py,sha256=tVh3rKVMkBHQE65_LhKeIjCsaCZQk_HJzbc9K4xUNCs,13522
-nmdc_runtime/lib/transform_nmdc_data.py,sha256=hij4lR3IMQRJQdL-rsP_I-m_WyFPsBMchV2MNFUkh0M,39906
-nmdc_runtime/minter/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-nmdc_runtime/minter/bootstrap.py,sha256=5Ej6pJVBRryRIi0ZwEloY78Zky7iE2okF6tPwRI2axM,822
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-nmdc_runtime/minter/adapters/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-nmdc_runtime/minter/adapters/repository.py,sha256=I-jmGP38-9kPhkogrwUht_Ir0CfHA9_5ZImw5I_wbcw,8323
-nmdc_runtime/minter/domain/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-nmdc_runtime/minter/domain/model.py,sha256=WMOuKub3dVzkOt_EZSRDLeTsJPqFbKx01SMQ53TOlDU,1416
-nmdc_runtime/minter/entrypoints/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-nmdc_runtime/minter/entrypoints/fastapi_app.py,sha256=JC4thvzfFwRc1mhWQ-kHy3yvs0SYxF6ktE7LXNCwqlI,4031
-nmdc_runtime/site/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-nmdc_runtime/site/graphs.py,sha256=cJfLCRYH6l3SW-0MYIOihORit6Fe_gziwQ6BJaph55c,17713
-nmdc_runtime/site/ops.py,sha256=m9p8dlfNVpdEyu0o06cT9jMLkjZh0GGFxEQxDuDPUaA,65917
-nmdc_runtime/site/repository.py,sha256=ZkIykDDaFTxB4QW1Eo_w-9IywQrXXTV7Ugogf8vQ604,47439
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-nmdc_runtime/site/util.py,sha256=h70UJCT9g-I63EJn0drZjv1iaQ8LHJTbG29R9kqJ04c,1821
-nmdc_runtime/site/backup/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-nmdc_runtime/site/backup/nmdcdb_mongodump.py,sha256=H5uosmEiXwLwklJrYJWrNhb_Nuf_ew8dBpZLl6_dYhs,2699
-nmdc_runtime/site/backup/nmdcdb_mongoexport.py,sha256=XIFI_AI3zl0dFr-ELOEmwvT41MyRKBGFaAT3RcamTNE,4166
-nmdc_runtime/site/backup/nmdcdb_mongoimport.py,sha256=k6w5yscMNYoMBVkaAA9soWS0Dj2CB0FRBSFlifRO3Ro,1739
-nmdc_runtime/site/changesheets/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-nmdc_runtime/site/changesheets/base.py,sha256=lZT6WCsEBl-FsTr7Ki8_ploT93uMiVyIWWKM36aOrRk,3171
-nmdc_runtime/site/drsobjects/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-nmdc_runtime/site/drsobjects/ingest.py,sha256=pcMP69WSzFHFqHB9JIL55ePFhilnCLRc2XHCQ97w1Ik,3107
-nmdc_runtime/site/drsobjects/registration.py,sha256=D1T3QUuxEOxqKZIvB5rkb_6ZxFZiA-U9SMPajyeWC2Y,3572
-nmdc_runtime/site/export/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-nmdc_runtime/site/export/ncbi_xml.py,sha256=iZQHBr3LL5Q32I2L_Xpfp9n4ZtgAz_MwrlxIF5do7Pw,29715
-nmdc_runtime/site/export/ncbi_xml_utils.py,sha256=RnoAW0HQwBG6JR63d9muI18RIC114wnX3iYPqOllw44,10700
-nmdc_runtime/site/export/study_metadata.py,sha256=yR5pXL6JG8d7cAtqcF-60Hp7bLD3dJ0Rut4AtYc0tXA,4844
-nmdc_runtime/site/normalization/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-nmdc_runtime/site/normalization/gold.py,sha256=iISDD4qs4d6uLhv631WYNeQVOzY5DO201ZpPtxHdkVk,1311
-nmdc_runtime/site/repair/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-nmdc_runtime/site/repair/database_updater.py,sha256=gRZ-NxZzXNd-vTIuygabEUqUSiF9eL4hL2rI9Qdf2WI,20764
-nmdc_runtime/site/translation/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-nmdc_runtime/site/translation/emsl.py,sha256=-aCTJTSCNaK-Koh8BE_4fTf5nyxP1KkquR6lloLEJl0,1245
-nmdc_runtime/site/translation/gold.py,sha256=R3W99sdQb7Pgu_esN7ruIC-tyREQD_idJ4xCzkqWuGw,1622
-nmdc_runtime/site/translation/gold_translator.py,sha256=HGbWeuxppqlVfU8F5oKTYIDoC6qaftugJeWFIALB9XE,32720
-nmdc_runtime/site/translation/jgi.py,sha256=qk878KhIw674TkrVfbl2x1QJrKi3zlvE0vesIpe9slM,876
-nmdc_runtime/site/translation/neon_benthic_translator.py,sha256=8_QF75Gf-dc2xVeO6jzTmdDrlGdh1-QrLJKG2SwUhCA,23797
-nmdc_runtime/site/translation/neon_soil_translator.py,sha256=IMeq4ABgWaSUbB_gmG8vBCMeynQSlbCUw9p2be6o8kE,38620
-nmdc_runtime/site/translation/neon_surface_water_translator.py,sha256=Js8_r6vHBW8b-_BpFySTUuYOFe7r51k8HwaNCQ7nAAg,30587
-nmdc_runtime/site/translation/neon_utils.py,sha256=d00o7duKKugpLHmsEifNbp4WjeC4GOqcgw0b5qlCg4I,5549
-nmdc_runtime/site/translation/submission_portal_translator.py,sha256=UEeqlkz_YGqcnx8vomFysetOlXxDu23q0Ryr93SZy78,41684
-nmdc_runtime/site/translation/translator.py,sha256=V6Aq0y03LoQ4LTL2iHDHxGTh_eMjOmDJJSwNHSrp2wo,837
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