From 29c23ffb54ca2ce1da23bb43d15e658478ceee44 Mon Sep 17 00:00:00 2001 From: Patrick Kalita Date: Mon, 16 Oct 2023 10:14:54 -0700 Subject: [PATCH 1/6] Update submission portal translator to pass validation according to current nmdc-schema --- docker-compose.test.yml | 2 +- docker-compose.yml | 18 +- .../submission_portal_translator.py | 26 +- tests/test_data/conftest.py | 18 +- .../test_submission_portal_translator.py | 11 +- ...est_submission_portal_translator_data.yaml | 12516 +--------------- 6 files changed, 126 insertions(+), 12465 deletions(-) diff --git a/docker-compose.test.yml b/docker-compose.test.yml index c2a031c3..ee6d952a 100644 --- a/docker-compose.test.yml +++ b/docker-compose.test.yml @@ -65,7 +65,7 @@ services: dockerfile: nmdc_runtime/fastapi.Dockerfile container_name: fastapi ports: - - "8000:8000" + - "9000:9000" env_file: - .env.test depends_on: diff --git a/docker-compose.yml b/docker-compose.yml index 18cfdf5a..80045383 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -14,6 +14,8 @@ services: POSTGRES_USER: "postgres_user" POSTGRES_PASSWORD: "postgres_password" POSTGRES_DB: "postgres_db" + networks: + - nmdc-server_public # This service runs dagit. # Since our instance uses the QueuedRunCoordinator, any runs submitted from dagit will be put on @@ -38,6 +40,8 @@ services: - dagster-postgresql volumes: - ./:/opt/dagster/lib + networks: + - nmdc-server_public # This service runs the dagster-daemon process, which is responsible for taking runs # off of the queue and launching them, as well as creating runs from schedules or sensors. @@ -58,6 +62,8 @@ services: - dagster-postgresql volumes: - ./:/opt/dagster/lib + networks: + - nmdc-server_public fastapi: build: @@ -65,14 +71,16 @@ services: dockerfile: nmdc_runtime/fastapi.Dockerfile container_name: fastapi ports: - - "8000:8000" - command: ["uvicorn", "nmdc_runtime.api.main:app", "--reload", "--host", "0.0.0.0", "--port", "8000"] + - "9000:9000" + command: ["uvicorn", "nmdc_runtime.api.main:app", "--reload", "--host", "0.0.0.0", "--port", "9000"] env_file: - .env depends_on: - mongo volumes: - .:/code + networks: + - nmdc-server_public mongo: image: mongo:6.0.4 @@ -112,4 +120,8 @@ volumes: secrets: mongoKeyFile: - file: ./mongoKeyFile \ No newline at end of file + file: ./mongoKeyFile + +networks: + nmdc-server_public: + external: true diff --git a/nmdc_runtime/site/translation/submission_portal_translator.py b/nmdc_runtime/site/translation/submission_portal_translator.py index f9dbb7a8..60807b18 100644 --- a/nmdc_runtime/site/translation/submission_portal_translator.py +++ b/nmdc_runtime/site/translation/submission_portal_translator.py @@ -51,19 +51,17 @@ def _get_pi( orcid=study_form.get("piOrcid"), ) - def _get_doi( - self, metadata_submission: JSON_OBJECT - ) -> Union[nmdc.AttributeValue, None]: - """Construct an nmdc:AttributeValue object using information from the context form data + def _get_doi(self, metadata_submission: JSON_OBJECT) -> Union[List[str], None]: + """Get DOI information from the context form data :param metadata_submission: submission portal entry - :return: nmdc:AttributeValue + :return: string or None """ - doi = get_in(["contextForm", "datasetDoi"], metadata_submission) - if not doi: + dataset_doi = get_in(["contextForm", "datasetDoi"], metadata_submission) + if not dataset_doi: return None - return nmdc.AttributeValue(has_raw_value=doi) + return [dataset_doi] def _get_has_credit_associations( self, metadata_submission: JSON_OBJECT @@ -169,7 +167,7 @@ def _get_ontology_class( :param raw_value: string to parse :return: nmdc.OntologyClass """ - match = re.fullmatch("_*([^\[]+)(?:\[([^\]]+)\])", raw_value) + match = re.match("_*([^\[]+)(?:\[([^\]]+)\])", raw_value) if not match or not match.group(2): logging.warning( f'Could not infer OntologyClass id from value "{raw_value}"' @@ -315,13 +313,13 @@ def _translate_study( alternative_names=self._get_from( metadata_submission, ["multiOmicsForm", "alternativeNames"] ), + dataset_dois=self._get_doi(metadata_submission), description=self._get_from( metadata_submission, ["studyForm", "description"] ), - doi=self._get_doi(metadata_submission), - emsl_proposal_identifier=self._get_from( - metadata_submission, ["multiOmicsForm", "studyNumber"] - ), + # emsl_proposal_identifier=self._get_from( + # metadata_submission, ["multiOmicsForm", "studyNumber"] + # ), gold_study_identifiers=self._get_gold_study_identifiers( metadata_submission ), @@ -397,6 +395,8 @@ def _translate_biosample( transformed_value = None if slot.multivalued: + if isinstance(value, str): + value = [v.strip() for v in value.split("|")] transformed_value = [ self._transform_value_for_slot(item, slot) for item in value ] diff --git a/tests/test_data/conftest.py b/tests/test_data/conftest.py index 331183bd..04781788 100644 --- a/tests/test_data/conftest.py +++ b/tests/test_data/conftest.py @@ -1,17 +1,23 @@ +import string + import pytest -import uuid import random +from nmdc_runtime.minter.config import typecodes + @pytest.fixture def test_minter(): + typecode_list = typecodes() + def mint(type, how_many=1): + typecode = next(t for t in typecode_list if t["schema_class"] == type) return [ - "fake:" - + str( - uuid.UUID( - bytes=bytes(random.getrandbits(8) for _ in range(16)), version=4 - ) + "nmdc:" + + typecode["name"] + + "-00-" + + "".join( + random.choice(string.ascii_lowercase + string.digits) for _ in range(8) ) for _ in range(how_many) ] diff --git a/tests/test_data/test_submission_portal_translator.py b/tests/test_data/test_submission_portal_translator.py index ec9b7182..3ecd3c55 100644 --- a/tests/test_data/test_submission_portal_translator.py +++ b/tests/test_data/test_submission_portal_translator.py @@ -2,11 +2,16 @@ import random import yaml +from linkml_runtime.dumpers import json_dumper + from nmdc_runtime.site.translation.submission_portal_translator import ( SubmissionPortalTranslator, ) from nmdc_schema import nmdc +from nmdc_runtime.util import validate_json +from tests.conftest import get_mongo_test_db + def test_get_pi(): translator = SubmissionPortalTranslator() @@ -31,7 +36,7 @@ def test_get_doi(): translator = SubmissionPortalTranslator() doi = translator._get_doi({"contextForm": {"datasetDoi": "1234"}}) assert doi is not None - assert doi.has_raw_value == "1234" + assert doi == ["1234"] doi = translator._get_doi({"contextForm": {"datasetDoi": ""}}) assert doi is None @@ -235,6 +240,7 @@ def test_get_from(): def test_get_dataset(test_minter): + mongo_db = get_mongo_test_db() random.seed(0) with open( Path(__file__).parent / "test_submission_portal_translator_data.yaml" @@ -249,3 +255,6 @@ def test_get_dataset(test_minter): expected = nmdc.Database(**test_data["output"]) actual = translator.get_database() assert actual == expected + + validation_result = validate_json(json_dumper.to_dict(actual), mongo_db) + assert validation_result == {"result": "All Okay!"} diff --git a/tests/test_data/test_submission_portal_translator_data.yaml b/tests/test_data/test_submission_portal_translator_data.yaml index b7562096..12579faa 100644 --- a/tests/test_data/test_submission_portal_translator_data.yaml +++ b/tests/test_data/test_submission_portal_translator_data.yaml @@ -4,7 +4,7 @@ input: metadata_submission: packageName: plant-associated contextForm: - datasetDoi: 10.46936/10.25585/60000818 + datasetDoi: doi:10.46936/10.25585/60000818 dataGenerated: true facilityGenerated: true facilities: [] @@ -287,12396 +287,20 @@ input: ecosystem_subtype: Leaf ecosystem_category: Terrestrial specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R3_MAIN_09MAY2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:c54a1438-713a-4b6f-9e44-ecddbd27e974 - ecosystem_type: Plant-associated - collection_date: '2016-05-09' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R4_MAIN_09MAY2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:8e0225d6-f7a0-469b-a747-8f5f4d65dc69 - ecosystem_type: Plant-associated - collection_date: '2016-05-09' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R1_NF_09MAY2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:1d20602f-3a0a-4d58-96cf-16135467ba14 - ecosystem_type: Plant-associated - collection_date: '2016-05-09' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R2_NF_09MAY2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:f13b1234-886c-4f8f-9663-850f5daff8e1 - ecosystem_type: Plant-associated - collection_date: '2016-05-09' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R3_NF_09MAY2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:45c11d1c-4a00-4162-9cdb-1020966507c6 - ecosystem_type: Plant-associated - collection_date: '2016-05-09' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R4_NF_09MAY2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:76a6a11e-5e25-4270-8d0d-1701bd12517a - ecosystem_type: Plant-associated - collection_date: '2016-05-09' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R1_MAIN_31MAY2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:bac125d1-f295-4728-a7fd-e4911a985b44 - ecosystem_type: Plant-associated - collection_date: '2016-05-31' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R2_MAIN_31MAY2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:13d073fa-b45a-4e47-a570-71a8a5726ac7 - ecosystem_type: Plant-associated - collection_date: '2016-05-31' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R3_MAIN_31MAY2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:7a7c2686-18fc-4a3c-8c2c-e2a195cd0a28 - ecosystem_type: Plant-associated - collection_date: '2016-05-31' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R4_MAIN_31MAY2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:7325ce99-4347-4728-b5aa-dda21a760a07 - ecosystem_type: Plant-associated - collection_date: '2016-05-31' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R1_NF_31MAY2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:8a7956e3-0f51-4e60-8aa0-380285878c86 - ecosystem_type: Plant-associated - collection_date: '2016-05-31' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R2_NF_31MAY2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:df9a0e6b-28c6-490b-aae9-559126dcd31a - ecosystem_type: Plant-associated - collection_date: '2016-05-31' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R3_NF_31MAY2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:f1d3e678-eaa9-4e36-ae17-c8bed8133825 - ecosystem_type: Plant-associated - collection_date: '2016-05-31' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R4_NF_31MAY2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:d43c6831-cafe-4674-9e56-adf20da087f6 - ecosystem_type: Plant-associated - collection_date: '2016-05-31' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R1_MAIN_31MAY2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:a2e9ab67-4112-447e-82a1-2c674769ef3e - ecosystem_type: Plant-associated - collection_date: '2016-05-31' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R2_MAIN_31MAY2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:1083f373-69b8-4ca1-9f5e-406d34781d9d - ecosystem_type: Plant-associated - collection_date: '2016-05-31' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R3_MAIN_31MAY2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:20ec38cc-8e1d-4b16-a08a-5e75881701d5 - ecosystem_type: Plant-associated - collection_date: '2016-05-31' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R4_MAIN_31MAY2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:f408f2c4-5c6f-43b1-b1d5-dc264317f826 - ecosystem_type: Plant-associated - collection_date: '2016-05-31' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R1_NF_31MAY2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:78c5bfe7-2e39-4419-aae5-cc60ac5c6b80 - ecosystem_type: Plant-associated - collection_date: '2016-05-31' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R2_NF_31MAY2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:4bcd56e0-dc05-46f4-b93c-2c548ffd0f48 - ecosystem_type: Plant-associated - collection_date: '2016-05-31' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R3_NF_31MAY2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:090aa36b-b82e-4ff4-9c01-b3de17bd7720 - ecosystem_type: Plant-associated - collection_date: '2016-05-31' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R4_NF_31MAY2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:03aaf489-f1cc-43e4-b537-9cfd2d5fe7b6 - ecosystem_type: Plant-associated - collection_date: '2016-05-31' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R1_MAIN_20JUN2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:b16cb1c2-def5-45b3-aeee-1de1762fac8c - ecosystem_type: Plant-associated - collection_date: '2016-06-20' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R2_MAIN_20JUN2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:7635e9bf-db34-4211-abb3-53df9119fdfa - ecosystem_type: Plant-associated - collection_date: '2016-06-20' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R3_MAIN_20JUN2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:3558ef40-a322-4ea0-89c3-afb0cfba3199 - ecosystem_type: Plant-associated - collection_date: '2016-06-20' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R4_MAIN_20JUN2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:96c80952-f26a-4014-8ebc-72648e90e2bb - ecosystem_type: Plant-associated - collection_date: '2016-06-20' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R1_NF_20JUN2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:d0b85994-73f5-43f0-97c1-ef0ce27cae7f - ecosystem_type: Plant-associated - collection_date: '2016-06-20' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R2_NF_20JUN2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:0e8e63b0-b2ce-4f4a-af1f-a6242b44a205 - ecosystem_type: Plant-associated - collection_date: '2016-06-20' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R3_NF_20JUN2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:346b2bf3-3899-44b7-88b7-38cd157a78ac - ecosystem_type: Plant-associated - collection_date: '2016-06-20' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R4_NF_20JUN2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:0e337fca-5bdc-41b9-9c2c-9c043af02850 - ecosystem_type: Plant-associated - collection_date: '2016-06-20' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R1_MAIN_20JUN2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:d43031d6-4949-4af4-ab93-0d4a52ddc41b - ecosystem_type: Plant-associated - collection_date: '2016-06-20' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R2_MAIN_20JUN2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:247e0564-3ba0-4aed-bc73-237038d0f273 - ecosystem_type: Plant-associated - collection_date: '2016-06-20' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R3_MAIN_20JUN2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:99841196-4418-47c7-941a-475272baa537 - ecosystem_type: Plant-associated - collection_date: '2016-06-20' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R4_MAIN_20JUN2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:71ce7bb9-1267-4cfd-9437-42cac3175456 - ecosystem_type: Plant-associated - collection_date: '2016-06-20' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R1_NF_20JUN2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:7908e2ad-6c33-40ec-b00a-0b054560e5e3 - ecosystem_type: Plant-associated - collection_date: '2016-06-20' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R2_NF_20JUN2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:5efa5fcd-8ad5-488c-9684-91a2c5dfeb21 - ecosystem_type: Plant-associated - collection_date: '2016-06-20' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R3_NF_20JUN2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - 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specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R1_MAIN_12JUL2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:95f249ad-1b54-4c8f-900e-c2abf32e3836 - ecosystem_type: Plant-associated - collection_date: '2016-07-12' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R2_MAIN_12JUL2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:b7f2fece-413f-43ea-83f3-80c01fc218c1 - ecosystem_type: Plant-associated - collection_date: '2016-07-12' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R3_MAIN_12JUL2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:dae06229-433f-45fd-a2ef-d82712dcb14d - ecosystem_type: Plant-associated - collection_date: '2016-07-12' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R4_MAIN_12JUL2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:6a50b37a-10fc-4370-b2eb-c4ba33685a9e - ecosystem_type: Plant-associated - collection_date: '2016-07-12' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R1_NF_12JUL2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:99d5ad42-73d2-4eaa-a603-63e3e823ba8c - ecosystem_type: Plant-associated - collection_date: '2016-07-12' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R2_NF_12JUL2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:80fe230b-e255-4df6-875a-51dae2bfc222 - ecosystem_type: Plant-associated - collection_date: '2016-07-12' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R3_NF_12JUL2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:f1e2af4b-e345-4878-9cc9-b24e1007c85f - ecosystem_type: Plant-associated - collection_date: '2016-07-12' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R4_NF_12JUL2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:4a9a58de-6cb1-489d-95a6-86df4adffb23 - ecosystem_type: Plant-associated - collection_date: '2016-07-12' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R1_MAIN_12JUL2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:9f55830a-9871-4a8a-b872-f6b8d5513a65 - ecosystem_type: Plant-associated - collection_date: '2016-07-12' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R2_MAIN_12JUL2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:cecc6251-2151-49e2-9f55-fb5b9409cd4c - ecosystem_type: Plant-associated - collection_date: '2016-07-12' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R3_MAIN_12JUL2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:79d6bc42-19e6-4cbc-b394-26fff15492e5 - ecosystem_type: Plant-associated - collection_date: '2016-07-12' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R4_MAIN_12JUL2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:93486fde-e381-4aac-86eb-2387dd44f138 - ecosystem_type: Plant-associated - collection_date: '2016-07-12' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R1_NF_12JUL2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:7d9c0233-a597-407c-bdad-1c4f79a4cc6e - ecosystem_type: Plant-associated - collection_date: '2016-07-12' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R2_NF_12JUL2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:f8b5663d-3322-475b-880a-29377f37f346 - ecosystem_type: Plant-associated - collection_date: '2016-07-12' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R3_NF_12JUL2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:c07f456e-d797-437c-9b79-11e16494e90d - ecosystem_type: Plant-associated - collection_date: '2016-07-12' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R4_NF_12JUL2016" - env_medium: plant-associated biome [ENVO:01001001] - 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ecosystem: Environmental - samp_name: "G6R3_MAIN_01AUG2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:657ad6ac-4500-4f27-abc6-72deb60d1675 - ecosystem_type: Plant-associated - collection_date: '2016-08-01' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R4_MAIN_01AUG2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:b4ef37eb-319f-4e9a-aee7-a617a3ff1ce8 - ecosystem_type: Plant-associated - collection_date: '2016-08-01' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R1_NF_01AUG2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:c612cec1-0592-4304-98a8-58f8a925216c - ecosystem_type: Plant-associated - collection_date: '2016-08-01' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R2_NF_01AUG2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:602148a4-f4b9-40af-bfab-75228be3ae36 - ecosystem_type: Plant-associated - collection_date: '2016-08-01' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R3_NF_01AUG2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:94700929-aa94-4ef7-a6a9-0b295b54ddfa - ecosystem_type: Plant-associated - collection_date: '2016-08-01' - 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specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R4_MAIN_22AUG2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:b78cf581-f8e9-4194-aaa4-7062d35298d5 - ecosystem_type: Plant-associated - collection_date: '2016-08-22' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R1_NF_22AUG2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:53d7d022-896b-4803-b5fc-4003bc023af8 - ecosystem_type: Plant-associated - collection_date: '2016-08-22' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R2_NF_22AUG2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:63a6d110-3766-4e21-ac0b-62d613c36152 - ecosystem_type: Plant-associated - collection_date: '2016-08-22' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R3_NF_22AUG2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:ec6a2efb-da59-4b56-98bb-3705b73d3474 - ecosystem_type: Plant-associated - collection_date: '2016-08-22' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R4_NF_22AUG2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:f5faf681-beb8-4d82-b036-22ca261381b1 - ecosystem_type: Plant-associated - collection_date: '2016-08-22' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R1_MAIN_12SEP2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:0a7ccc91-f79d-4ef6-b625-20ee412ca032 - ecosystem_type: Plant-associated - collection_date: '2016-09-12' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R2_MAIN_12SEP2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:7ec7a3d2-60ac-4c43-829e-a2459351eaf8 - ecosystem_type: Plant-associated - collection_date: '2016-09-12' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R3_MAIN_12SEP2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:86598228-4d5d-44c1-8a20-c2b384b2d6d1 - ecosystem_type: Plant-associated - collection_date: '2016-09-12' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R4_MAIN_12SEP2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:f18cbbaa-2f56-492f-8b1e-ab79c76b4d83 - ecosystem_type: Plant-associated - collection_date: '2016-09-12' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R1_NF_12SEP2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:e2dcb077-16e1-4540-a7a3-261c9492e60c - ecosystem_type: Plant-associated - collection_date: '2016-09-12' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R2_NF_12SEP2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:1eadb7fb-7168-4b37-a018-8b7928316726 - ecosystem_type: Plant-associated - collection_date: '2016-09-12' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R3_NF_12SEP2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:17679294-55de-4b9b-86da-9fe3d9fdb890 - ecosystem_type: Plant-associated - collection_date: '2016-09-12' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R4_NF_12SEP2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:6aa94584-37ae-42cc-af29-31ccd73b56bd - ecosystem_type: Plant-associated - collection_date: '2016-09-12' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R1_MAIN_12SEP2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:e7b25f00-b6b2-4d22-8c4a-f608fd5474f7 - ecosystem_type: Plant-associated - collection_date: '2016-09-12' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R2_MAIN_12SEP2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:862a50b3-5d7a-4065-bf3d-6e423b055c99 - ecosystem_type: Plant-associated - collection_date: '2016-09-12' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R3_MAIN_12SEP2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:a4ad7b54-56fe-49dd-a09d-1a2b369b4f5f - ecosystem_type: Plant-associated - collection_date: '2016-09-12' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R4_MAIN_12SEP2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:f2e320bd-7868-453d-9850-234c47b72719 - ecosystem_type: Plant-associated - collection_date: '2016-09-12' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R1_NF_12SEP2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:f6ca2bc7-5573-4512-9bf5-fb389fcbb8ef - ecosystem_type: Plant-associated - collection_date: '2016-09-12' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R2_NF_12SEP2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:4954c20b-a444-4649-88f8-9e399143d3f5 - ecosystem_type: Plant-associated - collection_date: '2016-09-12' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R3_NF_12SEP2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:fa0e2a99-040d-4ec6-be7a-fe6d8ba90c5d - ecosystem_type: Plant-associated - collection_date: '2016-09-12' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R4_NF_12SEP2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:c8270368-e522-483f-8190-8c302bcaa140 - ecosystem_type: Plant-associated - collection_date: '2016-09-12' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R1_MAIN_03OCT2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:132e3aec-eb1a-438d-bcbc-ca4511fdf2a8 - ecosystem_type: Plant-associated - collection_date: '2016-10-03' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R2_MAIN_03OCT2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:ad43ccc5-c709-4dac-b598-be10a5bb4217 - ecosystem_type: Plant-associated - collection_date: '2016-10-03' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R3_MAIN_03OCT2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:a94c0efe-e560-4524-b5d7-8ac1d7a8a153 - ecosystem_type: Plant-associated - collection_date: '2016-10-03' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R4_MAIN_03OCT2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:c262276b-9011-4a02-8971-ec137979ebf7 - ecosystem_type: Plant-associated - collection_date: '2016-10-03' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R1_NF_03OCT2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:d53f3e07-9ad2-42a9-ae39-d920129112ac - ecosystem_type: Plant-associated - collection_date: '2016-10-03' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R2_NF_03OCT2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:f27f0840-4aff-4d94-93b5-e2b30b434927 - ecosystem_type: Plant-associated - collection_date: '2016-10-03' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R3_NF_03OCT2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:df66adfe-09fe-471c-a900-f3b208341da7 - ecosystem_type: Plant-associated - collection_date: '2016-10-03' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R4_NF_03OCT2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:b334ad62-f5dc-48d3-b7f0-b89788581244 - ecosystem_type: Plant-associated - collection_date: '2016-10-03' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R1_MAIN_03OCT2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:cbb88571-b9a9-4876-ad35-ba0b82b41c0d - ecosystem_type: Plant-associated - collection_date: '2016-10-03' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R2_MAIN_03OCT2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:ee7f1272-14ff-4c20-bed2-dc5528d4f39d - ecosystem_type: Plant-associated - collection_date: '2016-10-03' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R3_MAIN_03OCT2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:451aad09-d814-4e69-b384-c43aa45e480d - ecosystem_type: Plant-associated - collection_date: '2016-10-03' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R4_MAIN_03OCT2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:2c9efdf4-68c3-4085-98a4-2c9efc52d1ef - ecosystem_type: Plant-associated - collection_date: '2016-10-03' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R1_NF_03OCT2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:5f524de7-39f2-4573-b42d-e95c60038304 - ecosystem_type: Plant-associated - collection_date: '2016-10-03' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R2_NF_03OCT2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:49d025c5-94c3-483b-8004-de6a24a63e68 - ecosystem_type: Plant-associated - collection_date: '2016-10-03' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R3_NF_03OCT2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:bdf36513-e117-4b18-9847-1207e0b35fd5 - ecosystem_type: Plant-associated - collection_date: '2016-10-03' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R4_NF_03OCT2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:3af2c3f9-5822-4d57-8eea-4cf4f3144219 - ecosystem_type: Plant-associated - collection_date: '2016-10-03' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R1_MAIN_07NOV2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:d71ed350-917a-4a5b-9c4f-e491ad5df486 - ecosystem_type: Plant-associated - collection_date: '2016-11-07' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R2_MAIN_07NOV2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:b0226577-426e-47a0-a57a-14a4b8cb35b5 - ecosystem_type: Plant-associated - collection_date: '2016-11-07' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R3_MAIN_07NOV2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:5e45f92d-cb69-4059-be53-09074642e9ab - ecosystem_type: Plant-associated - collection_date: '2016-11-07' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R4_MAIN_07NOV2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:423d877e-f692-447f-852b-ca476101c2cd - ecosystem_type: Plant-associated - collection_date: '2016-11-07' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R1_NF_07NOV2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:bcdd3bb7-f1f3-4336-b7da-0d2153af08f2 - ecosystem_type: Plant-associated - collection_date: '2016-11-07' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R2_NF_07NOV2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:ce222def-a322-4cd0-9add-618f5abe4688 - ecosystem_type: Plant-associated - collection_date: '2016-11-07' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R3_NF_07NOV2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:b4a4262e-17fc-4d41-aa7c-c55727a74b25 - ecosystem_type: Plant-associated - collection_date: '2016-11-07' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G6R4_NF_07NOV2016" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:bd23a3e1-2fee-4023-834a-e4cb9a0571a1 - ecosystem_type: Plant-associated - collection_date: '2016-11-07' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R1_MAIN_15MAY2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:037b5f89-42e7-480a-82b9-4b3586890e28 - ecosystem_type: Plant-associated - collection_date: '2017-05-15' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R2_MAIN_15MAY2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:294adf08-906c-415c-a21e-372facfbda5a - ecosystem_type: Plant-associated - collection_date: '2017-05-15' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R3_MAIN_15MAY2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:ce94a886-65a2-4c9e-8c65-5a6711ec4551 - ecosystem_type: Plant-associated - collection_date: '2017-05-15' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R4_MAIN_15MAY2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:5ecc51f9-94a5-4b27-8ef9-27a59d6e8524 - ecosystem_type: Plant-associated - collection_date: '2017-05-15' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R1_NF_15MAY2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:1fa7ea40-2cf7-49ff-8478-f32239c95f70 - ecosystem_type: Plant-associated - collection_date: '2017-05-15' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R2_NF_15MAY2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:5cc6cfa9-7087-4c52-a11c-70e23b78f4aa - ecosystem_type: Plant-associated - collection_date: '2017-05-15' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R3_NF_15MAY2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:59981b52-c78c-465d-ac28-540d16892cc0 - ecosystem_type: Plant-associated - collection_date: '2017-05-15' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R4_NF_15MAY2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:c9ce3883-2df1-42dd-bee0-4f5edff4918d - ecosystem_type: Plant-associated - collection_date: '2017-05-15' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R1_MAIN_05JUN2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:c8ed3ef9-c883-423c-8f86-03a21ede6ad8 - ecosystem_type: Plant-associated - collection_date: '2017-06-05' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R2_MAIN_05JUN2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:cd66a0eb-dee0-4f6e-b58a-08f0b3d83516 - ecosystem_type: Plant-associated - collection_date: '2017-06-05' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R3_MAIN_05JUN2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:e865149e-3a15-4ad3-b167-c223dca36dd4 - ecosystem_type: Plant-associated - collection_date: '2017-06-05' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R4_MAIN_05JUN2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:84fd3d6d-6dd9-4a08-a775-794c3a674f5b - ecosystem_type: Plant-associated - collection_date: '2017-06-05' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R1_NF_05JUN2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:7a9060c2-4fc0-46e4-90d0-e22a188d7a85 - ecosystem_type: Plant-associated - collection_date: '2017-06-05' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R2_NF_05JUN2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - 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specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R4_NF_05JUN2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:14c783d2-e362-4714-b9c0-82d543416638 - ecosystem_type: Plant-associated - collection_date: '2017-06-05' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R1_MAIN_26JUN2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:9c3a480b-4fd0-4da8-823b-8b8a62481511 - ecosystem_type: Plant-associated - collection_date: '2017-06-26' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R2_MAIN_26JUN2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:a64ab1e2-b9f2-4fb6-8c7d-4b5804daf2c7 - ecosystem_type: Plant-associated - collection_date: '2017-06-26' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R3_MAIN_26JUN2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:c961d29c-9cbf-40ff-8e76-7d71b305e77a - ecosystem_type: Plant-associated - collection_date: '2017-06-26' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R4_MAIN_26JUN2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:bf9fdb1e-dc32-4ab0-a21e-dcdce379a46d - ecosystem_type: Plant-associated - collection_date: '2017-06-26' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R1_NF_26JUN2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:51b34532-a300-4936-a3a6-78a004833c10 - ecosystem_type: Plant-associated - collection_date: '2017-06-26' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R2_NF_26JUN2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:5e16e42e-fa44-4886-99a2-0327ee277102 - ecosystem_type: Plant-associated - collection_date: '2017-06-26' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R3_NF_26JUN2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:53d81d4e-31cf-40ae-afbc-7db4e5b6ec45 - ecosystem_type: Plant-associated - collection_date: '2017-06-26' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R4_NF_26JUN2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:aaababfe-dbd3-4df4-b5e8-c774025756e9 - ecosystem_type: Plant-associated - collection_date: '2017-06-26' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R1_MAIN_17JUL2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:70710e82-977d-4eb6-9ff9-824b48868741 - ecosystem_type: Plant-associated - collection_date: '2017-07-17' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R2_MAIN_17JUL2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:f5a9b5a6-7656-4e73-a5a0-c1260a456529 - ecosystem_type: Plant-associated - collection_date: '2017-07-17' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R3_MAIN_17JUL2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:0c78fda3-1424-4f6c-b4a9-9e07a84713f1 - ecosystem_type: Plant-associated - collection_date: '2017-07-17' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R4_MAIN_17JUL2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:74de6a27-6271-4338-a246-a51167fb6cd7 - ecosystem_type: Plant-associated - collection_date: '2017-07-17' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R1_NF_17JUL2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:fc666344-9d65-40f7-926e-d0f3e4056f69 - ecosystem_type: Plant-associated - collection_date: '2017-07-17' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R2_NF_17JUL2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:48f196f0-9267-42f7-b8ea-343b60b3b4c9 - ecosystem_type: Plant-associated - collection_date: '2017-07-17' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R3_NF_17JUL2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:4ede3f5e-419c-40e5-a38d-a525a212a918 - ecosystem_type: Plant-associated - collection_date: '2017-07-17' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R4_NF_17JUL2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:ef6c2246-3fd2-46ca-a744-00ca32d5287a - ecosystem_type: Plant-associated - collection_date: '2017-07-17' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R1_MAIN_07AUG2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:f2b2ff60-2cdd-4dba-9a3b-1d903a206ca8 - ecosystem_type: Plant-associated - collection_date: '2017-08-07' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R2_MAIN_07AUG2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:c0754834-384e-4282-a75c-39728ec343b8 - ecosystem_type: Plant-associated - collection_date: '2017-08-07' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R3_MAIN_07AUG2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:99757397-ff6e-4a92-b9ee-6b448a9a944d - ecosystem_type: Plant-associated - collection_date: '2017-08-07' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R4_MAIN_07AUG2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:9cc79dd8-95ef-4e8d-aade-6c9ac2216956 - ecosystem_type: Plant-associated - collection_date: '2017-08-07' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R1_NF_07AUG2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:d34b5892-b5a2-4392-83f5-53ea1abde7dd - ecosystem_type: Plant-associated - collection_date: '2017-08-07' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R2_NF_07AUG2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:41240494-f7e0-4f80-a417-93dfdc094a06 - ecosystem_type: Plant-associated - collection_date: '2017-08-07' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R3_NF_07AUG2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:d191dfe3-3845-455c-bfe1-665dbb7c5e8e - ecosystem_type: Plant-associated - collection_date: '2017-08-07' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R4_NF_07AUG2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:2ebb7684-ad20-41b0-b7be-ccf7c7210a13 - ecosystem_type: Plant-associated - collection_date: '2017-08-07' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R1_MAIN_28AUG2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:cb03f98b-1929-426a-b4e8-75c0b7f1208b - ecosystem_type: Plant-associated - collection_date: '2017-08-28' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R2_MAIN_28AUG2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:bee8b493-f526-4a8a-be59-f93e468a2618 - ecosystem_type: Plant-associated - collection_date: '2017-08-28' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R3_MAIN_28AUG2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:3e2bed09-0d41-4e67-bf73-008a6b3b1073 - ecosystem_type: Plant-associated - collection_date: '2017-08-28' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R4_MAIN_28AUG2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:451b29e2-f2b3-42f8-adfa-3d8e23ad8545 - ecosystem_type: Plant-associated - collection_date: '2017-08-28' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R1_NF_28AUG2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:8e985015-830a-4847-bc78-7723772a45d1 - ecosystem_type: Plant-associated - collection_date: '2017-08-28' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R2_NF_28AUG2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:8fb00ba7-a382-4df2-a1b7-eecd087e000a - ecosystem_type: Plant-associated - collection_date: '2017-08-28' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R3_NF_28AUG2017" - env_medium: plant-associated biome [ENVO:01001001] - env_package: soil - geo_loc_name: 'USA: Kellogg Biological Station, Michigan' - growth_facil: field - analysis_type: - - metagenomics - source_mat_id: UUID:dfee9c57-72a0-4a4d-8df3-743c1c8eb3e4 - ecosystem_type: Plant-associated - collection_date: '2017-08-28' - env_broad_scale: agricultural biome [ENVO:01001442] - env_local_scale: phyllosphere biome [ENVO:01001442] - samp_store_temp: "-80 Celsius" - ecosystem_subtype: Leaf - ecosystem_category: Terrestrial - specific_ecosystem: Phyllosphere - - elev: 286 - depth: '0' - lat_lon: 42.39 -85.37 - ecosystem: Environmental - samp_name: "G5R4_NF_28AUG2017" - env_medium: plant-associated biome [ENVO:01001001] - 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has_raw_value: '2017-08-07' - depth: - has_raw_value: '0' - has_numeric_value: 0.0 - elev: 286.0 - env_package: - has_raw_value: soil - geo_loc_name: - has_raw_value: 'USA: Kellogg Biological Station, Michigan' - lat_lon: - has_raw_value: 42.39 -85.37 - latitude: 42.39 - longitude: -85.37 - samp_store_temp: - has_raw_value: -80 Celsius - has_unit: Celsius - has_numeric_value: -80.0 - ecosystem: Environmental - ecosystem_category: Terrestrial - ecosystem_type: Plant-associated - ecosystem_subtype: Leaf - specific_ecosystem: Phyllosphere - growth_facil: - has_raw_value: field - source_mat_id: - has_raw_value: UUID:2ebb7684-ad20-41b0-b7be-ccf7c7210a13 - analysis_type: - - metagenomics - - id: fake:b5af6743-0596-42eb-a32b-e270900dea60 - part_of: - - fake:d862c2e3-6b0a-42f7-827c-67ebc8d44df7 - env_broad_scale: - has_raw_value: agricultural biome [ENVO:01001442] - term: - id: ENVO:01001442 - name: agricultural biome - env_local_scale: - has_raw_value: phyllosphere biome [ENVO:01001442] - term: - id: ENVO:01001442 - name: phyllosphere biome - env_medium: - has_raw_value: plant-associated biome [ENVO:01001001] - term: - id: ENVO:01001001 - name: plant-associated biome - samp_name: G5R1_MAIN_28AUG2017 - collection_date: - has_raw_value: '2017-08-28' - depth: - has_raw_value: '0' - has_numeric_value: 0.0 - elev: 286.0 - env_package: - has_raw_value: soil - geo_loc_name: - has_raw_value: 'USA: Kellogg Biological Station, Michigan' - lat_lon: - has_raw_value: 42.39 -85.37 - latitude: 42.39 - longitude: -85.37 - samp_store_temp: - has_raw_value: -80 Celsius - has_unit: Celsius - has_numeric_value: -80.0 - ecosystem: Environmental - ecosystem_category: Terrestrial - ecosystem_type: Plant-associated - ecosystem_subtype: Leaf - specific_ecosystem: Phyllosphere - growth_facil: - has_raw_value: field - source_mat_id: - has_raw_value: UUID:cb03f98b-1929-426a-b4e8-75c0b7f1208b - analysis_type: - - metagenomics - - id: fake:edcd16a4-9667-453b-81df-740a7a9e1a44 - part_of: - - fake:d862c2e3-6b0a-42f7-827c-67ebc8d44df7 - env_broad_scale: - has_raw_value: agricultural biome [ENVO:01001442] - term: - id: ENVO:01001442 - name: agricultural biome - env_local_scale: - has_raw_value: phyllosphere biome [ENVO:01001442] - term: - id: ENVO:01001442 - name: phyllosphere biome - env_medium: - has_raw_value: plant-associated biome [ENVO:01001001] - term: - id: ENVO:01001001 - name: plant-associated biome - samp_name: G5R2_MAIN_28AUG2017 - collection_date: - has_raw_value: '2017-08-28' - depth: - has_raw_value: '0' - has_numeric_value: 0.0 - elev: 286.0 - env_package: - has_raw_value: soil - geo_loc_name: - has_raw_value: 'USA: Kellogg Biological Station, Michigan' - lat_lon: - has_raw_value: 42.39 -85.37 - latitude: 42.39 - longitude: -85.37 - samp_store_temp: - has_raw_value: -80 Celsius - has_unit: Celsius - has_numeric_value: -80.0 - ecosystem: Environmental - ecosystem_category: Terrestrial - ecosystem_type: Plant-associated - ecosystem_subtype: Leaf - specific_ecosystem: Phyllosphere - growth_facil: - has_raw_value: field - source_mat_id: - has_raw_value: UUID:bee8b493-f526-4a8a-be59-f93e468a2618 - analysis_type: - - metagenomics - - id: fake:d5817d8d-a564-4943-ae3a-8a5d284dda9b - part_of: - - fake:d862c2e3-6b0a-42f7-827c-67ebc8d44df7 - env_broad_scale: - has_raw_value: agricultural biome [ENVO:01001442] - term: - id: ENVO:01001442 - name: agricultural biome - env_local_scale: - has_raw_value: phyllosphere biome [ENVO:01001442] - term: - id: ENVO:01001442 - name: phyllosphere biome - env_medium: - has_raw_value: plant-associated biome [ENVO:01001001] - term: - id: ENVO:01001001 - name: plant-associated biome - samp_name: G5R3_MAIN_28AUG2017 - collection_date: - has_raw_value: '2017-08-28' - depth: - has_raw_value: '0' - has_numeric_value: 0.0 - elev: 286.0 - env_package: - has_raw_value: soil - geo_loc_name: - has_raw_value: 'USA: Kellogg Biological Station, Michigan' - lat_lon: - has_raw_value: 42.39 -85.37 - latitude: 42.39 - longitude: -85.37 - samp_store_temp: - has_raw_value: -80 Celsius - has_unit: Celsius - has_numeric_value: -80.0 - ecosystem: Environmental - ecosystem_category: Terrestrial - ecosystem_type: Plant-associated - ecosystem_subtype: Leaf - specific_ecosystem: Phyllosphere - growth_facil: - has_raw_value: field - source_mat_id: - has_raw_value: UUID:3e2bed09-0d41-4e67-bf73-008a6b3b1073 - analysis_type: - - metagenomics - - id: fake:d4ea2474-11f6-417a-a490-f3688e17437b - part_of: - - fake:d862c2e3-6b0a-42f7-827c-67ebc8d44df7 - env_broad_scale: - has_raw_value: agricultural biome [ENVO:01001442] - term: - id: ENVO:01001442 - name: agricultural biome - env_local_scale: - has_raw_value: phyllosphere biome [ENVO:01001442] - term: - id: ENVO:01001442 - name: phyllosphere biome - env_medium: - has_raw_value: plant-associated biome [ENVO:01001001] - term: - id: ENVO:01001001 - name: plant-associated biome - samp_name: G5R4_MAIN_28AUG2017 - collection_date: - has_raw_value: '2017-08-28' - depth: - has_raw_value: '0' - has_numeric_value: 0.0 - elev: 286.0 - env_package: - has_raw_value: soil - geo_loc_name: - has_raw_value: 'USA: Kellogg Biological Station, Michigan' - lat_lon: - has_raw_value: 42.39 -85.37 - latitude: 42.39 - longitude: -85.37 - samp_store_temp: - has_raw_value: -80 Celsius - has_unit: Celsius - has_numeric_value: -80.0 - ecosystem: Environmental - ecosystem_category: Terrestrial - ecosystem_type: Plant-associated - ecosystem_subtype: Leaf - specific_ecosystem: Phyllosphere - growth_facil: - has_raw_value: field - source_mat_id: - has_raw_value: UUID:451b29e2-f2b3-42f8-adfa-3d8e23ad8545 - analysis_type: - - metagenomics - - id: fake:3ad01c4b-245c-4f18-a3a8-dd0ed2aa2396 - part_of: - - fake:d862c2e3-6b0a-42f7-827c-67ebc8d44df7 - env_broad_scale: - has_raw_value: agricultural biome [ENVO:01001442] - term: - id: ENVO:01001442 - name: agricultural biome - env_local_scale: - has_raw_value: phyllosphere biome [ENVO:01001442] - term: - id: ENVO:01001442 - name: phyllosphere biome - env_medium: - has_raw_value: plant-associated biome [ENVO:01001001] - term: - id: ENVO:01001001 - name: plant-associated biome - samp_name: G5R1_NF_28AUG2017 - collection_date: - has_raw_value: '2017-08-28' - depth: - has_raw_value: '0' - has_numeric_value: 0.0 - elev: 286.0 - env_package: - has_raw_value: soil - geo_loc_name: - has_raw_value: 'USA: Kellogg Biological Station, Michigan' - lat_lon: - has_raw_value: 42.39 -85.37 - latitude: 42.39 - longitude: -85.37 - samp_store_temp: - has_raw_value: -80 Celsius - has_unit: Celsius - has_numeric_value: -80.0 - ecosystem: Environmental - ecosystem_category: Terrestrial - ecosystem_type: Plant-associated - ecosystem_subtype: Leaf - specific_ecosystem: Phyllosphere - growth_facil: - has_raw_value: field - source_mat_id: - has_raw_value: UUID:8e985015-830a-4847-bc78-7723772a45d1 - analysis_type: - - metagenomics - - id: fake:8f320108-dc67-4eb3-819a-7db6b01bee79 - part_of: - - fake:d862c2e3-6b0a-42f7-827c-67ebc8d44df7 - env_broad_scale: - has_raw_value: agricultural biome [ENVO:01001442] - term: - id: ENVO:01001442 - name: agricultural biome - env_local_scale: - has_raw_value: phyllosphere biome [ENVO:01001442] - term: - id: ENVO:01001442 - name: phyllosphere biome - env_medium: - has_raw_value: plant-associated biome [ENVO:01001001] - term: - id: ENVO:01001001 - name: plant-associated biome - samp_name: G5R2_NF_28AUG2017 - collection_date: - has_raw_value: '2017-08-28' - depth: - has_raw_value: '0' - has_numeric_value: 0.0 - elev: 286.0 - env_package: - has_raw_value: soil - geo_loc_name: - has_raw_value: 'USA: Kellogg Biological Station, Michigan' - lat_lon: - has_raw_value: 42.39 -85.37 - latitude: 42.39 - longitude: -85.37 - samp_store_temp: - has_raw_value: -80 Celsius - has_unit: Celsius - has_numeric_value: -80.0 - ecosystem: Environmental - ecosystem_category: Terrestrial - ecosystem_type: Plant-associated - ecosystem_subtype: Leaf - specific_ecosystem: Phyllosphere - growth_facil: - has_raw_value: field - source_mat_id: - has_raw_value: UUID:8fb00ba7-a382-4df2-a1b7-eecd087e000a - analysis_type: - - metagenomics - - id: fake:8f58dfc7-57df-48af-813d-3a7fd6fb4f46 + status: in-progress + id: d32b5eb6-71e8-4c98-8a57-3e64d05718b4 + author_orcid: 0000-0002-7705-343X + created: '2023-04-03T18:31:16.856377' + author: + id: 1bc43cf5-966e-4a44-8ab5-b61905210255 + orcid: 0000-0002-7705-343X + name: Adina Howe + is_admin: false +output: + biosample_set: + - id: nmdc:bsm-00-4wn6isig part_of: - - fake:d862c2e3-6b0a-42f7-827c-67ebc8d44df7 + - nmdc:sty-00-y0cq65zt env_broad_scale: has_raw_value: agricultural biome [ENVO:01001442] term: @@ -12692,9 +316,10 @@ output: term: id: ENVO:01001001 name: plant-associated biome - samp_name: G5R3_NF_28AUG2017 + samp_name: G5R1_MAIN_09MAY2016 + name: G5R1_MAIN_09MAY2016 collection_date: - has_raw_value: '2017-08-28' + has_raw_value: '2016-05-09' depth: has_raw_value: '0' has_numeric_value: 0.0 @@ -12719,12 +344,12 @@ output: growth_facil: has_raw_value: field source_mat_id: - has_raw_value: UUID:dfee9c57-72a0-4a4d-8df3-743c1c8eb3e4 + has_raw_value: UUID:e8ed34cc-32f4-4fc5-9b9f-c2699e43163c analysis_type: - metagenomics - - id: fake:39027e5a-f2f4-42ed-9717-134e926c39bd + - id: nmdc:bsm-00-q8jtgev4 part_of: - - fake:d862c2e3-6b0a-42f7-827c-67ebc8d44df7 + - nmdc:sty-00-y0cq65zt env_broad_scale: has_raw_value: agricultural biome [ENVO:01001442] term: @@ -12740,9 +365,10 @@ output: term: id: ENVO:01001001 name: plant-associated biome - samp_name: G5R4_NF_28AUG2017 + samp_name: G5R2_MAIN_09MAY2016 + name: G5R2_MAIN_09MAY2016 collection_date: - has_raw_value: '2017-08-28' + has_raw_value: '2016-05-09' depth: has_raw_value: '0' has_numeric_value: 0.0 @@ -12767,12 +393,12 @@ output: growth_facil: has_raw_value: field source_mat_id: - has_raw_value: UUID:bafedf91-1740-4efe-a542-40f259d68419 + has_raw_value: UUID:774bb4b9-5ebe-48d5-8236-1a60baa6af7a analysis_type: - metagenomics - - id: fake:5ef661dc-c225-4b49-af33-bec67ba8e1c8 + - id: nmdc:bsm-00-9gw1un94 part_of: - - fake:d862c2e3-6b0a-42f7-827c-67ebc8d44df7 + - nmdc:sty-00-y0cq65zt env_broad_scale: has_raw_value: agricultural biome [ENVO:01001442] term: @@ -12788,9 +414,10 @@ output: term: id: ENVO:01001001 name: plant-associated biome - samp_name: G5R1_MAIN_18SEP2017 + samp_name: G5R3_MAIN_09MAY2016 + name: G5R3_MAIN_09MAY2016 collection_date: - has_raw_value: '2017-09-18' + has_raw_value: '2016-05-09' depth: has_raw_value: '0' has_numeric_value: 0.0 @@ -12815,12 +442,12 @@ output: growth_facil: has_raw_value: field source_mat_id: - has_raw_value: UUID:d3f9dcb9-4f7a-4d7b-8ee7-2fa9447f210d + has_raw_value: UUID:c0bb595b-9992-4475-8019-775189b5250a analysis_type: - metagenomics - - id: fake:5b48629c-21d4-471e-a65a-80de783aa7b5 + - id: nmdc:bsm-00-27qd9afz part_of: - - fake:d862c2e3-6b0a-42f7-827c-67ebc8d44df7 + - nmdc:sty-00-y0cq65zt env_broad_scale: has_raw_value: agricultural biome [ENVO:01001442] term: @@ -12836,9 +463,10 @@ output: term: id: ENVO:01001001 name: plant-associated biome - samp_name: G5R2_MAIN_18SEP2017 + samp_name: G5R4_MAIN_09MAY2016 + name: G5R4_MAIN_09MAY2016 collection_date: - has_raw_value: '2017-09-18' + has_raw_value: '2016-05-09' depth: has_raw_value: '0' has_numeric_value: 0.0 @@ -12863,12 +491,12 @@ output: growth_facil: has_raw_value: field source_mat_id: - has_raw_value: UUID:a6cbb4e5-6482-4612-bccd-14778313c09b + has_raw_value: UUID:d74181a3-6fb9-406e-89f8-2d4861a4646c analysis_type: - metagenomics - - id: fake:5fa1ea5b-6e47-4bf9-a6c4-c4b6fe48dd1a + - id: nmdc:bsm-00-a5vpuemo part_of: - - fake:d862c2e3-6b0a-42f7-827c-67ebc8d44df7 + - nmdc:sty-00-y0cq65zt env_broad_scale: has_raw_value: agricultural biome [ENVO:01001442] term: @@ -12884,9 +512,10 @@ output: term: id: ENVO:01001001 name: plant-associated biome - samp_name: G5R3_MAIN_18SEP2017 + samp_name: G5R1_NF_09MAY2016 + name: G5R1_NF_09MAY2016 collection_date: - has_raw_value: '2017-09-18' + has_raw_value: '2016-05-09' depth: has_raw_value: '0' has_numeric_value: 0.0 @@ -12911,12 +540,12 @@ output: growth_facil: has_raw_value: field source_mat_id: - has_raw_value: UUID:fe48a1cc-4184-467b-ae68-5f599c00327b + has_raw_value: UUID:edfd5080-ccc2-495b-b17a-190ad6649291 analysis_type: - metagenomics - - id: fake:7ae74a1e-7227-48ee-bebe-2fedf4567f3a + - id: nmdc:bsm-00-pj82ffu6 part_of: - - fake:d862c2e3-6b0a-42f7-827c-67ebc8d44df7 + - nmdc:sty-00-y0cq65zt env_broad_scale: has_raw_value: agricultural biome [ENVO:01001442] term: @@ -12932,9 +561,10 @@ output: term: id: ENVO:01001001 name: plant-associated biome - samp_name: G5R4_MAIN_18SEP2017 + samp_name: G5R2_NF_09MAY2016 + name: G5R2_NF_09MAY2016 collection_date: - has_raw_value: '2017-09-18' + has_raw_value: '2016-05-09' depth: has_raw_value: '0' has_numeric_value: 0.0 @@ -12959,12 +589,12 @@ output: growth_facil: has_raw_value: field source_mat_id: - has_raw_value: UUID:ac03bdb2-f5b4-4131-9a9a-6d27e7100f55 + has_raw_value: UUID:483921c0-7fa9-4a31-b281-e09565a0d6f9 analysis_type: - metagenomics - - id: fake:1cae62f9-6376-4376-baef-faff90d49e38 + - id: nmdc:bsm-00-5gt9sh9v part_of: - - fake:d862c2e3-6b0a-42f7-827c-67ebc8d44df7 + - nmdc:sty-00-y0cq65zt env_broad_scale: has_raw_value: agricultural biome [ENVO:01001442] term: @@ -12980,9 +610,10 @@ output: term: id: ENVO:01001001 name: plant-associated biome - samp_name: G5R1_NF_18SEP2017 + samp_name: G5R3_NF_09MAY2016 + name: G5R3_NF_09MAY2016 collection_date: - has_raw_value: '2017-09-18' + has_raw_value: '2016-05-09' depth: has_raw_value: '0' has_numeric_value: 0.0 @@ -13007,12 +638,12 @@ output: growth_facil: has_raw_value: field source_mat_id: - has_raw_value: UUID:b2890880-d327-4cc3-91eb-5d06f3cad19d + has_raw_value: UUID:3b9aab19-0110-415b-8e29-849f0696de47 analysis_type: - metagenomics - - id: fake:ac66804f-7c3b-4084-af00-17785164e4f3 + - id: nmdc:bsm-00-8n9s2fyu part_of: - - fake:d862c2e3-6b0a-42f7-827c-67ebc8d44df7 + - nmdc:sty-00-y0cq65zt env_broad_scale: has_raw_value: agricultural biome [ENVO:01001442] term: @@ -13028,9 +659,10 @@ output: term: id: ENVO:01001001 name: plant-associated biome - samp_name: G5R2_NF_18SEP2017 + samp_name: G5R4_NF_09MAY2016 + name: G5R4_NF_09MAY2016 collection_date: - has_raw_value: '2017-09-18' + has_raw_value: '2016-05-09' depth: has_raw_value: '0' has_numeric_value: 0.0 @@ -13055,12 +687,12 @@ output: growth_facil: has_raw_value: field source_mat_id: - has_raw_value: UUID:202eb34b-4d7f-4157-a190-035a4dd907e0 + has_raw_value: UUID:579ec4b9-57c4-4431-8df9-432138233b0b analysis_type: - metagenomics - - id: fake:3ad2f76e-fb0c-43c5-8a68-174333b9532d + - id: nmdc:bsm-00-pslmlcq4 part_of: - - fake:d862c2e3-6b0a-42f7-827c-67ebc8d44df7 + - nmdc:sty-00-y0cq65zt env_broad_scale: has_raw_value: agricultural biome [ENVO:01001442] term: @@ -13076,9 +708,10 @@ output: term: id: ENVO:01001001 name: plant-associated biome - samp_name: G5R3_NF_18SEP2017 + samp_name: G6R1_MAIN_09MAY2016 + name: G6R1_MAIN_09MAY2016 collection_date: - has_raw_value: '2017-09-18' + has_raw_value: '2016-05-09' depth: has_raw_value: '0' has_numeric_value: 0.0 @@ -13103,12 +736,12 @@ output: growth_facil: has_raw_value: field source_mat_id: - has_raw_value: UUID:178856e7-f799-4f61-a356-d5d2bd098daa + has_raw_value: UUID:69dd84ff-d777-4d1e-ac22-9cdac87074f5 analysis_type: - metagenomics - - id: fake:1c2eccb2-5d07-4bf3-8b02-618801211dd2 + - id: nmdc:bsm-00-efijcf8z part_of: - - fake:d862c2e3-6b0a-42f7-827c-67ebc8d44df7 + - nmdc:sty-00-y0cq65zt env_broad_scale: has_raw_value: agricultural biome [ENVO:01001442] term: @@ -13124,9 +757,10 @@ output: term: id: ENVO:01001001 name: plant-associated biome - samp_name: G5R4_NF_18SEP2017 + samp_name: G6R2_MAIN_09MAY2016 + name: G6R2_MAIN_09MAY2016 collection_date: - has_raw_value: '2017-09-18' + has_raw_value: '2016-05-09' depth: has_raw_value: '0' has_numeric_value: 0.0 @@ -13151,11 +785,11 @@ output: growth_facil: has_raw_value: field source_mat_id: - has_raw_value: UUID:4720b174-508e-4b35-875f-373fe661a73a + has_raw_value: UUID:c0c4a2b5-0382-450a-8728-a176fa438efe analysis_type: - metagenomics study_set: - - id: fake:d862c2e3-6b0a-42f7-827c-67ebc8d44df7 + - id: nmdc:sty-00-y0cq65zt name: Seasonal activities of the phyllosphere microbiome of perennial crops description: Understanding the interactions between plants and microorganisms can inform microbiome management to enhance crop productivity and resilience to stress. @@ -13176,8 +810,8 @@ output: orcid: 0000-0002-7189-3067 email: shade.ashley@gmail.com name: Ashley Shade - doi: - has_raw_value: 10.46936/10.25585/60000818 + dataset_dois: + - doi:10.46936/10.25585/60000818 title: Seasonal activities of the phyllosphere microbiome of perennial crops websites: - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9950430/ From 395842ab2bcfaf1ff7d802867ba39c148dc65a91 Mon Sep 17 00:00:00 2001 From: Patrick Kalita Date: Mon, 16 Oct 2023 11:27:29 -0700 Subject: [PATCH 2/6] Add op for getting CSV data from arbitrary URL --- nmdc_runtime/site/ops.py | 11 +++++++ tests/test_ops/test_get_csv_file_from_url.py | 30 ++++++++++++++++++++ 2 files changed, 41 insertions(+) create mode 100644 tests/test_ops/test_get_csv_file_from_url.py diff --git a/nmdc_runtime/site/ops.py b/nmdc_runtime/site/ops.py index 0f2fc2c3..cd1166c4 100644 --- a/nmdc_runtime/site/ops.py +++ b/nmdc_runtime/site/ops.py @@ -1,3 +1,4 @@ +import csv import json import mimetypes import os @@ -8,6 +9,7 @@ from io import BytesIO from zipfile import ZipFile import pandas as pd +import requests from bson import ObjectId, json_util from dagster import ( @@ -773,3 +775,12 @@ def id_minter(*args, **kwargs): @op def nmdc_schema_database_export_filename_neon() -> str: return "database_from_neon_metadata.json" + + +@op +def get_csv_file_from_url(url: str) -> List[Dict]: + response = requests.get(url) + response.raise_for_status() + + reader = csv.DictReader(response.text.splitlines()) + return [row for row in reader] diff --git a/tests/test_ops/test_get_csv_file_from_url.py b/tests/test_ops/test_get_csv_file_from_url.py new file mode 100644 index 00000000..a60e468d --- /dev/null +++ b/tests/test_ops/test_get_csv_file_from_url.py @@ -0,0 +1,30 @@ +import pytest +import requests +import requests_mock +from dagster import build_op_context + +from nmdc_runtime.site.ops import get_csv_file_from_url + + +def test_valid_data(): + context = build_op_context() + with requests_mock.mock() as mock: + mock.get( + "http://www.example.com/data.csv", + text='a,b,c\n1,hello,"apple, banana"\n2,wow,great', + ) + + result = get_csv_file_from_url(context, "http://www.example.com/data.csv") + assert result == [ + {"a": "1", "b": "hello", "c": "apple, banana"}, + {"a": "2", "b": "wow", "c": "great"}, + ] + + +def test_not_found(): + context = build_op_context() + with requests_mock.mock() as mock: + mock.get("http://www.example.com/data.csv", status_code=404) + + with pytest.raises(requests.HTTPError): + get_csv_file_from_url(context, "http://www.example.com/data.csv") From 292650836b1dc37d242e2c2e397fa791f09b5ee2 Mon Sep 17 00:00:00 2001 From: Patrick Kalita Date: Wed, 18 Oct 2023 10:33:52 -0700 Subject: [PATCH 3/6] Update submission portal graphs to accept a CSV mapping file to produce OmicsProcessing and DataObject records --- nmdc_runtime/site/graphs.py | 32 +++- nmdc_runtime/site/ops.py | 46 ++++- nmdc_runtime/site/repository.py | 16 +- .../submission_portal_translator.py | 159 +++++++++++++++--- .../test_submission_portal_translator.py | 20 ++- ...est_submission_portal_translator_data.yaml | 154 +++++++++++++++++ .../test_submission_portal_graphs.py | 6 +- tests/test_ops/test_data_api_ops.py | 5 +- 8 files changed, 394 insertions(+), 44 deletions(-) diff --git a/nmdc_runtime/site/graphs.py b/nmdc_runtime/site/graphs.py index 503e6e8c..d5e3156f 100644 --- a/nmdc_runtime/site/graphs.py +++ b/nmdc_runtime/site/graphs.py @@ -40,6 +40,8 @@ nmdc_schema_database_export_filename_neon, get_neon_pipeline_mms_data_product, get_neon_pipeline_sls_data_product, + get_submission_portal_pipeline_inputs, + get_csv_file_from_url, ) @@ -134,8 +136,19 @@ def gold_study_to_database(): @graph def translate_metadata_submission_to_nmdc_schema_database(): - metadata_submission = fetch_nmdc_portal_submission_by_id() - database = translate_portal_submission_to_nmdc_schema_database(metadata_submission) + ( + submission_id, + omics_processing_mapping_file_url, + data_object_mapping_file_url, + ) = get_submission_portal_pipeline_inputs() + + metadata_submission = fetch_nmdc_portal_submission_by_id(submission_id) + omics_processing_mapping = get_csv_file_from_url(omics_processing_mapping_file_url) + data_object_mapping = get_csv_file_from_url(data_object_mapping_file_url) + + database = translate_portal_submission_to_nmdc_schema_database( + metadata_submission, omics_processing_mapping, data_object_mapping + ) validate_metadata(database) @@ -147,8 +160,19 @@ def translate_metadata_submission_to_nmdc_schema_database(): @graph def ingest_metadata_submission(): - metadata_submission = fetch_nmdc_portal_submission_by_id() - database = translate_portal_submission_to_nmdc_schema_database(metadata_submission) + ( + submission_id, + omics_processing_mapping_file_url, + data_object_mapping_file_url, + ) = get_submission_portal_pipeline_inputs() + + metadata_submission = fetch_nmdc_portal_submission_by_id(submission_id) + omics_processing_mapping = get_csv_file_from_url(omics_processing_mapping_file_url) + data_object_mapping = get_csv_file_from_url(data_object_mapping_file_url) + + database = translate_portal_submission_to_nmdc_schema_database( + metadata_submission, omics_processing_mapping, data_object_mapping + ) run_id = submit_metadata_to_db(database) poll_for_run_completion(run_id) diff --git a/nmdc_runtime/site/ops.py b/nmdc_runtime/site/ops.py index cd1166c4..83c27763 100644 --- a/nmdc_runtime/site/ops.py +++ b/nmdc_runtime/site/ops.py @@ -7,6 +7,7 @@ from collections import defaultdict from datetime import datetime, timezone from io import BytesIO +from typing import Tuple from zipfile import ZipFile import pandas as pd import requests @@ -27,6 +28,7 @@ RetryRequested, String, op, + Optional, ) from gridfs import GridFS from linkml_runtime.dumpers import json_dumper @@ -79,7 +81,7 @@ from pymongo.database import Database as MongoDatabase from starlette import status from terminusdb_client.woqlquery import WOQLQuery as WQ -from toolz import assoc, dissoc, get_in +from toolz import assoc, dissoc, get_in, valfilter, identity @op @@ -640,12 +642,34 @@ def id_minter(*args, **kwargs): return database +@op( + config_schema={ + "submission_id": str, + "omics_processing_mapping_file_url": str, + "data_object_mapping_file_url": str, + }, + out={ + "submission_id": Out(), + "omics_processing_mapping_file_url": Out(), + "data_object_mapping_file_url": Out(), + }, +) +def get_submission_portal_pipeline_inputs( + context: OpExecutionContext, +) -> Tuple[str, str, str]: + return ( + context.op_config["submission_id"], + context.op_config["omics_processing_mapping_file_url"], + context.op_config["data_object_mapping_file_url"], + ) + + @op( required_resource_keys={"nmdc_portal_api_client"}, - config_schema={"submission_id": str}, ) -def fetch_nmdc_portal_submission_by_id(context: OpExecutionContext) -> Dict[str, Any]: - submission_id = context.op_config["submission_id"] +def fetch_nmdc_portal_submission_by_id( + context: OpExecutionContext, submission_id: str +) -> Dict[str, Any]: client: NmdcPortalApiClient = context.resources.nmdc_portal_api_client return client.fetch_metadata_submission(submission_id) @@ -654,6 +678,8 @@ def fetch_nmdc_portal_submission_by_id(context: OpExecutionContext) -> Dict[str, def translate_portal_submission_to_nmdc_schema_database( context: OpExecutionContext, metadata_submission: Dict[str, Any], + omics_processing_mapping: List, + data_object_mapping: List, ) -> nmdc.Database: client: RuntimeApiSiteClient = context.resources.runtime_api_site_client @@ -661,7 +687,12 @@ def id_minter(*args, **kwargs): response = client.mint_id(*args, **kwargs) return response.json() - translator = SubmissionPortalTranslator(metadata_submission, id_minter=id_minter) + translator = SubmissionPortalTranslator( + metadata_submission, + omics_processing_mapping, + data_object_mapping, + id_minter=id_minter, + ) database = translator.get_database() return database @@ -779,8 +810,11 @@ def nmdc_schema_database_export_filename_neon() -> str: @op def get_csv_file_from_url(url: str) -> List[Dict]: + if not url: + return [] + response = requests.get(url) response.raise_for_status() reader = csv.DictReader(response.text.splitlines()) - return [row for row in reader] + return [valfilter(identity, row) for row in reader] diff --git a/nmdc_runtime/site/repository.py b/nmdc_runtime/site/repository.py index 50a91be9..44270249 100644 --- a/nmdc_runtime/site/repository.py +++ b/nmdc_runtime/site/repository.py @@ -518,8 +518,12 @@ def biosample_submission_ingest(): ), "ops": { "export_json_to_drs": {"config": {"username": "..."}}, - "fetch_nmdc_portal_submission_by_id": { - "config": {"submission_id": "..."} + "get_submission_portal_pipeline_inputs": { + "config": { + "submission_id": "", + "omics_processing_mapping_file_url": "", + "data_object_mapping_file_url": "", + } }, }, }, @@ -542,8 +546,12 @@ def biosample_submission_ingest(): }, ), "ops": { - "fetch_nmdc_portal_submission_by_id": { - "config": {"submission_id": "..."} + "get_submission_portal_pipeline_inputs": { + "config": { + "submission_id": "", + "omics_processing_mapping_file_url": "", + "data_object_mapping_file_url": "", + } }, }, }, diff --git a/nmdc_runtime/site/translation/submission_portal_translator.py b/nmdc_runtime/site/translation/submission_portal_translator.py index 60807b18..ad821557 100644 --- a/nmdc_runtime/site/translation/submission_portal_translator.py +++ b/nmdc_runtime/site/translation/submission_portal_translator.py @@ -1,13 +1,16 @@ import logging import re -from typing import Any, List, Optional, Union -from nmdc_runtime.site.translation.translator import JSON_OBJECT, Translator -from nmdc_schema import nmdc -from toolz import get_in, groupby, concat +from datetime import datetime +from functools import lru_cache from importlib import resources +from typing import Any, List, Optional, Union + from linkml_runtime import SchemaView from linkml_runtime.linkml_model import SlotDefinition -from functools import lru_cache +from nmdc_schema import nmdc +from toolz import get_in, groupby, concat, valmap, dissoc + +from nmdc_runtime.site.translation.translator import JSON_OBJECT, Translator @lru_cache @@ -27,10 +30,19 @@ class SubmissionPortalTranslator(Translator): the nmdc:Biosample class (via a SchemaView instance) """ - def __init__(self, metadata_submission: JSON_OBJECT = {}, *args, **kwargs) -> None: + def __init__( + self, + metadata_submission: JSON_OBJECT = {}, + omics_processing_mapping: Optional[list] = None, + data_object_mapping: Optional[list] = None, + *args, + **kwargs, + ) -> None: super().__init__(*args, **kwargs) self.metadata_submission = metadata_submission + self.omics_processing_mapping = omics_processing_mapping + self.data_object_mapping = data_object_mapping self.schema_view: SchemaView = _get_schema_view() def _get_pi( @@ -362,6 +374,38 @@ def _transform_value_for_slot(self, value: Any, slot: SlotDefinition): return transformed_value + def _transform_dict_for_class(self, raw_values: dict, class_name: str) -> dict: + """Transform a dict of values according to class slots. + + raw_values is a dict where the keys are slot names and the values are plain strings. + Each of the items in this dict will be transformed by the _transform_value_for_slot + method. If the slot is multivalued each individual value will be transformed. If the + slot is multivalued and the value is a string it will be split in pipe characters + before transforming. + """ + slot_names = self.schema_view.class_slots(class_name) + transformed_values = {} + for column, value in raw_values.items(): + if column not in slot_names: + logging.warning(f"No slot '{column}' on class '{class_name}'") + continue + + slot_definition = self.schema_view.induced_slot(column, class_name) + if slot_definition.multivalued: + if isinstance(value, str): + value = [v.strip() for v in value.split("|")] + transformed_value = [ + self._transform_value_for_slot(item, slot_definition) + for item in value + ] + else: + transformed_value = self._transform_value_for_slot( + value, slot_definition + ) + + transformed_values[column] = transformed_value + return transformed_values + def _translate_biosample( self, sample_data: List[JSON_OBJECT], nmdc_biosample_id: str, nmdc_study_id: str ) -> nmdc.Biosample: @@ -385,25 +429,9 @@ def _translate_biosample( "part_of": nmdc_study_id, "name": sample_data[0].get("samp_name"), } - biosample_slot_names = self.schema_view.class_slots("Biosample") for tab in sample_data: - for column, value in tab.items(): - if column not in biosample_slot_names: - logging.warning(f"No slot {column} on nmdc:Biosample") - continue - slot = self.schema_view.induced_slot(column, "Biosample") - - transformed_value = None - if slot.multivalued: - if isinstance(value, str): - value = [v.strip() for v in value.split("|")] - transformed_value = [ - self._transform_value_for_slot(item, slot) for item in value - ] - else: - transformed_value = self._transform_value_for_slot(value, slot) - - slots[column] = transformed_value + transformed_tab = self._transform_dict_for_class(tab, "Biosample") + slots.update(transformed_tab) return nmdc.Biosample(**slots) @@ -444,4 +472,87 @@ def get_database(self) -> nmdc.Database: if sample_data ] + if self.omics_processing_mapping: + # If there is data from an OmicsProcessing mapping file, process it now. This part + # assumes that there is a column in that file with the header __biosample_source_mat_id + # that can be used to join with the sample data from the submission portal. The + # biosample identified by that `source_mat_id` will be referenced in the `has_input` + # slot of the OmicsProcessing object. If a DataObject mapping file was also provided, + # those objects will also be generated and referenced in the `has_output` slot of the + # OmicsProcessing object. By keying off of the `source_mat_id` slot of the submission's + # sample data there is an implicit 1:1 relationship between Biosample objects and + # OmicsProcessing objects generated here. + join_key = "__biosample_source_mat_id" + database.omics_processing_set = [] + database.data_object_set = [] + data_objects_by_sample_data_id = {} + today = datetime.now().strftime("%Y-%m-%d") + + if self.data_object_mapping: + # If DataObject mapping data was provided, group it by the sample ID key and then + # strip that key out of the resulting grouped data. + grouped = groupby(join_key, self.data_object_mapping) + data_objects_by_sample_data_id = valmap( + lambda data_objects: [ + dissoc(data_object, join_key) for data_object in data_objects + ], + grouped, + ) + + for omics_processing_row in self.omics_processing_mapping: + # For each row in the OmicsProcessing mapping file, first grab the minted Biosample + # id that corresponds to the sample ID from the submission + sample_data_id = omics_processing_row.pop(join_key) + if ( + not sample_data_id + or sample_data_id not in sample_data_to_nmdc_biosample_ids + ): + logging.warning( + f"Unrecognized biosample source_mat_id: {sample_data_id}" + ) + continue + nmdc_biosample_id = sample_data_to_nmdc_biosample_ids[sample_data_id] + + # Transform the raw row data according to the OmicsProcessing class's slots, and + # generate an instance. A few key slots do not come from the mapping file, but + # instead are defined here. + omics_processing_slots = { + "id": self._id_minter("nmdc:OmicsProcessing", 1)[0], + "has_input": [nmdc_biosample_id], + "has_output": [], + "part_of": nmdc_study_id, + "add_date": today, + "mod_date": today, + "type": "nmdc:OmicsProcessing", + } + omics_processing_slots.update( + self._transform_dict_for_class( + omics_processing_row, "OmicsProcessing" + ) + ) + omics_processing = nmdc.OmicsProcessing(**omics_processing_slots) + + for data_object_row in data_objects_by_sample_data_id.get( + sample_data_id, [] + ): + # For each row in the DataObject mapping file that correspond to the sample ID, + # transform the raw row data according to the DataObject class's slots, generate + # an instance, and connect that instance's minted ID to the OmicsProcessing + # instance + data_object_id = self._id_minter("nmdc:DataObject", 1)[0] + data_object_slots = { + "id": data_object_id, + "type": "nmdc:DataObject", + } + data_object_slots.update( + self._transform_dict_for_class(data_object_row, "DataObject") + ) + data_object = nmdc.DataObject(**data_object_slots) + + omics_processing.has_output.append(data_object_id) + + database.data_object_set.append(data_object) + + database.omics_processing_set.append(omics_processing) + return database diff --git a/tests/test_data/test_submission_portal_translator.py b/tests/test_data/test_submission_portal_translator.py index 3ecd3c55..0cf76b4a 100644 --- a/tests/test_data/test_submission_portal_translator.py +++ b/tests/test_data/test_submission_portal_translator.py @@ -1,3 +1,4 @@ +import datetime from pathlib import Path import random @@ -239,15 +240,30 @@ def test_get_from(): assert translator._get_from(metadata, ["one", "some_empty"]) == ["one", "three"] -def test_get_dataset(test_minter): +def test_get_dataset(test_minter, monkeypatch): + # OmicsProcess objects have an add_date and a mod_date slot that are populated with the + # current date. In order to compare with a static expected output we need to patch + # the datetime.now() call to return a predefined date. + the_time = datetime.datetime(2023, 10, 17, 9, 0, 0) + + class FrozenDatetime(datetime.datetime): + @classmethod + def now(cls, **kwargs): + return the_time + + monkeypatch.setattr( + "nmdc_runtime.site.translation.submission_portal_translator.datetime", + FrozenDatetime, + ) + mongo_db = get_mongo_test_db() - random.seed(0) with open( Path(__file__).parent / "test_submission_portal_translator_data.yaml" ) as f: test_datasets = yaml.safe_load_all(f) for test_data in test_datasets: + random.seed(0) translator = SubmissionPortalTranslator( **test_data["input"], id_minter=test_minter ) diff --git a/tests/test_data/test_submission_portal_translator_data.yaml b/tests/test_data/test_submission_portal_translator_data.yaml index 12579faa..779a9d46 100644 --- a/tests/test_data/test_submission_portal_translator_data.yaml +++ b/tests/test_data/test_submission_portal_translator_data.yaml @@ -835,3 +835,157 @@ output: - Software - Principal Investigator - Funding acquisition +--- +input: + metadata_submission: + id: 00000000-0000-0000-0000-000000000000, + metadata_submission: + contextForm: + datasetDoi: doi:10.12345/10.12345/00000000 + packageName: plant-associated + sampleData: + plant_associated_data: + - analysis_type: + - metagenomics + collection_date: '2016-05-09' + depth: '0' + ecosystem: Environmental + ecosystem_category: Terrestrial + ecosystem_subtype: Leaf + ecosystem_type: Plant-associated + elev: '286' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + lat_lon: 42.39 -85.37 + samp_name: G5R1_MAIN_09MAY2016 + samp_store_temp: -80 Celsius + source_mat_id: UUID:e8ed34cc-32f4-4fc5-9b9f-c2699e43163c + specific_ecosystem: Phyllosphere + studyForm: + contributors: + - name: Test Testerson + orcid: 0000-0000-0000-0000 + roles: + - Principal Investigator + description: This is a test submission + linkOutWebpage: + - http://www.example.com/submission-test + multiOmicsForm: + GOLDStudyId: '' + JGIStudyId: '' + NCBIBioProjectId: '' + alternativeNames: [ ] + studyNumber: '' + piEmail: test.testerson@example.com + piName: Test Testerson + piOrcid: 0000-0000-0000-0000 + studyName: A test submission + templates: + - plant-associated + omics_processing_mapping: + - __biosample_source_mat_id: UUID:e8ed34cc-32f4-4fc5-9b9f-c2699e43163c + processing_institution: JGI + instrument_name: Some fancy expensive thing + omics_type: Metagenome + data_object_mapping: + - __biosample_source_mat_id: UUID:e8ed34cc-32f4-4fc5-9b9f-c2699e43163c + data_object_type: Metagenome Raw Reads + url: http://example.com/data.fastq.gz + name: Metagenome Raw Reads + description: Metagenome Raw Reads +output: + biosample_set: + - id: nmdc:bsm-00-4wn6isig + name: G5R1_MAIN_09MAY2016 + part_of: + - nmdc:sty-00-y0cq65zt + env_broad_scale: + has_raw_value: agricultural biome [ENVO:01001442] + term: + id: ENVO:01001442 + name: agricultural biome + env_local_scale: + has_raw_value: phyllosphere biome [ENVO:01001442] + term: + id: ENVO:01001442 + name: phyllosphere biome + env_medium: + has_raw_value: plant-associated biome [ENVO:01001001] + term: + id: ENVO:01001001 + name: plant-associated biome + samp_name: G5R1_MAIN_09MAY2016 + collection_date: + has_raw_value: '2016-05-09' + depth: + has_raw_value: '0' + has_numeric_value: 0.0 + ecosystem: Environmental + ecosystem_category: Terrestrial + ecosystem_subtype: Leaf + ecosystem_type: Plant-associated + elev: 286.0 + env_package: + has_raw_value: soil + geo_loc_name: + has_raw_value: 'USA: Kellogg Biological Station, Michigan' + growth_facil: + has_raw_value: field + lat_lon: + has_raw_value: 42.39 -85.37 + latitude: 42.39 + longitude: -85.37 + samp_store_temp: + has_raw_value: -80 Celsius + has_unit: Celsius + has_numeric_value: -80.0 + source_mat_id: + has_raw_value: UUID:e8ed34cc-32f4-4fc5-9b9f-c2699e43163c + specific_ecosystem: Phyllosphere + analysis_type: + - metagenomics + data_object_set: + - id: nmdc:dobj-00-9gw1un94 + name: Metagenome Raw Reads + description: Metagenome Raw Reads + data_object_type: Metagenome Raw Reads + url: http://example.com/data.fastq.gz + type: nmdc:DataObject + omics_processing_set: + - id: nmdc:omprc-00-q8jtgev4 + has_input: + - nmdc:bsm-00-4wn6isig + add_date: '2023-10-17' + has_output: + - nmdc:dobj-00-9gw1un94 + instrument_name: Some fancy expensive thing + mod_date: '2023-10-17' + omics_type: + has_raw_value: Metagenome + part_of: + - nmdc:sty-00-y0cq65zt + processing_institution: JGI + type: nmdc:OmicsProcessing + study_set: + - id: nmdc:sty-00-y0cq65zt + name: A test submission + description: This is a test submission + dataset_dois: + - doi:10.12345/10.12345/00000000 + has_credit_associations: + - applies_to_person: + orcid: 0000-0000-0000-0000 + name: Test Testerson + applied_roles: + - Principal Investigator + principal_investigator: + orcid: 0000-0000-0000-0000 + email: test.testerson@example.com + name: Test Testerson + title: A test submission + websites: + - http://www.example.com/submission-test diff --git a/tests/test_graphs/test_submission_portal_graphs.py b/tests/test_graphs/test_submission_portal_graphs.py index f7972a3c..d6057f89 100644 --- a/tests/test_graphs/test_submission_portal_graphs.py +++ b/tests/test_graphs/test_submission_portal_graphs.py @@ -12,7 +12,7 @@ "id": MOCK_PORTAL_SUBMISSION_ID, "metadata_submission": { "packageName": "plant-associated", - "contextForm": {"datasetDoi": "10.12345/10.12345/00000000"}, + "contextForm": {"datasetDoi": "doi:10.12345/10.12345/00000000"}, "templates": ["plant-associated"], "studyForm": { "studyName": "A test submission", @@ -80,9 +80,11 @@ def test_translate_metadata_submission_to_nmdc_schema_database(): "export_json_to_drs": { "config": {"username": "test"}, }, - "fetch_nmdc_portal_submission_by_id": { + "get_submission_portal_pipeline_inputs": { "config": { "submission_id": MOCK_PORTAL_SUBMISSION_ID, + "omics_processing_mapping_file_url": "", + "data_object_mapping_file_url": "", } }, }, diff --git a/tests/test_ops/test_data_api_ops.py b/tests/test_ops/test_data_api_ops.py index 91a97413..b5b301dd 100644 --- a/tests/test_ops/test_data_api_ops.py +++ b/tests/test_ops/test_data_api_ops.py @@ -20,7 +20,6 @@ def op_context(client_config): client_config ) }, - op_config={"submission_id": "353d751f-cff0-4558-9051-25a87ba00d3f"}, ) @@ -31,6 +30,8 @@ def test_metadata_submission(op_context): json={"id": "353d751f-cff0-4558-9051-25a87ba00d3f"}, ) - fetch_nmdc_portal_submission_by_id(op_context) + fetch_nmdc_portal_submission_by_id( + op_context, "353d751f-cff0-4558-9051-25a87ba00d3f" + ) assert len(mock.request_history) == 1 From 0f7d4cada7daa13f7107628b2f4295f913a48ba7 Mon Sep 17 00:00:00 2001 From: Patrick Kalita Date: Wed, 18 Oct 2023 10:42:00 -0700 Subject: [PATCH 4/6] Revert docker compose test changes --- docker-compose.test.yml | 2 +- docker-compose.yml | 20 +++++--------------- 2 files changed, 6 insertions(+), 16 deletions(-) diff --git a/docker-compose.test.yml b/docker-compose.test.yml index ee6d952a..c2a031c3 100644 --- a/docker-compose.test.yml +++ b/docker-compose.test.yml @@ -65,7 +65,7 @@ services: dockerfile: nmdc_runtime/fastapi.Dockerfile container_name: fastapi ports: - - "9000:9000" + - "8000:8000" env_file: - .env.test depends_on: diff --git a/docker-compose.yml b/docker-compose.yml index 80045383..64518988 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -14,8 +14,6 @@ services: POSTGRES_USER: "postgres_user" POSTGRES_PASSWORD: "postgres_password" POSTGRES_DB: "postgres_db" - networks: - - nmdc-server_public # This service runs dagit. # Since our instance uses the QueuedRunCoordinator, any runs submitted from dagit will be put on @@ -40,8 +38,6 @@ services: - dagster-postgresql volumes: - ./:/opt/dagster/lib - networks: - - nmdc-server_public # This service runs the dagster-daemon process, which is responsible for taking runs # off of the queue and launching them, as well as creating runs from schedules or sensors. @@ -62,8 +58,6 @@ services: - dagster-postgresql volumes: - ./:/opt/dagster/lib - networks: - - nmdc-server_public fastapi: build: @@ -71,16 +65,14 @@ services: dockerfile: nmdc_runtime/fastapi.Dockerfile container_name: fastapi ports: - - "9000:9000" - command: ["uvicorn", "nmdc_runtime.api.main:app", "--reload", "--host", "0.0.0.0", "--port", "9000"] + - "8000:8000" + command: ["uvicorn", "nmdc_runtime.api.main:app", "--reload", "--host", "0.0.0.0", "--port", "8000"] env_file: - .env depends_on: - mongo volumes: - .:/code - networks: - - nmdc-server_public mongo: image: mongo:6.0.4 @@ -94,6 +86,8 @@ services: environment: MONGO_INITDB_ROOT_USERNAME: admin MONGO_INITDB_ROOT_PASSWORD: root + networks: + - nmdc-server_public terminus: image: terminusdb/terminusdb-server:v11.0.6 @@ -120,8 +114,4 @@ volumes: secrets: mongoKeyFile: - file: ./mongoKeyFile - -networks: - nmdc-server_public: - external: true + file: ./mongoKeyFile \ No newline at end of file From ca5c7806ca02a2741b262e2f417365ceb099bb1d Mon Sep 17 00:00:00 2001 From: Patrick Kalita Date: Wed, 18 Oct 2023 10:42:46 -0700 Subject: [PATCH 5/6] Revert docker compose test change --- docker-compose.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/docker-compose.yml b/docker-compose.yml index 64518988..18cfdf5a 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -86,8 +86,6 @@ services: environment: MONGO_INITDB_ROOT_USERNAME: admin MONGO_INITDB_ROOT_PASSWORD: root - networks: - - nmdc-server_public terminus: image: terminusdb/terminusdb-server:v11.0.6 From b88bb77027bc2feece73ac0d31d00517e4176f08 Mon Sep 17 00:00:00 2001 From: Patrick Kalita Date: Thu, 19 Oct 2023 10:33:26 -0700 Subject: [PATCH 6/6] Add additional comments and improve variable names --- nmdc_runtime/site/graphs.py | 10 +++++----- nmdc_runtime/site/ops.py | 14 +++++++++++++- .../translation/submission_portal_translator.py | 11 ++++++----- .../test_data/test_submission_portal_translator.py | 2 ++ ...e_from_url.py => test_get_csv_rows_from_url.py} | 6 +++--- 5 files changed, 29 insertions(+), 14 deletions(-) rename tests/test_ops/{test_get_csv_file_from_url.py => test_get_csv_rows_from_url.py} (79%) diff --git a/nmdc_runtime/site/graphs.py b/nmdc_runtime/site/graphs.py index d5e3156f..6c8cb4b9 100644 --- a/nmdc_runtime/site/graphs.py +++ b/nmdc_runtime/site/graphs.py @@ -41,7 +41,7 @@ get_neon_pipeline_mms_data_product, get_neon_pipeline_sls_data_product, get_submission_portal_pipeline_inputs, - get_csv_file_from_url, + get_csv_rows_from_url, ) @@ -143,8 +143,8 @@ def translate_metadata_submission_to_nmdc_schema_database(): ) = get_submission_portal_pipeline_inputs() metadata_submission = fetch_nmdc_portal_submission_by_id(submission_id) - omics_processing_mapping = get_csv_file_from_url(omics_processing_mapping_file_url) - data_object_mapping = get_csv_file_from_url(data_object_mapping_file_url) + omics_processing_mapping = get_csv_rows_from_url(omics_processing_mapping_file_url) + data_object_mapping = get_csv_rows_from_url(data_object_mapping_file_url) database = translate_portal_submission_to_nmdc_schema_database( metadata_submission, omics_processing_mapping, data_object_mapping @@ -167,8 +167,8 @@ def ingest_metadata_submission(): ) = get_submission_portal_pipeline_inputs() metadata_submission = fetch_nmdc_portal_submission_by_id(submission_id) - omics_processing_mapping = get_csv_file_from_url(omics_processing_mapping_file_url) - data_object_mapping = get_csv_file_from_url(data_object_mapping_file_url) + omics_processing_mapping = get_csv_rows_from_url(omics_processing_mapping_file_url) + data_object_mapping = get_csv_rows_from_url(data_object_mapping_file_url) database = translate_portal_submission_to_nmdc_schema_database( metadata_submission, omics_processing_mapping, data_object_mapping diff --git a/nmdc_runtime/site/ops.py b/nmdc_runtime/site/ops.py index 83c27763..828fe4e8 100644 --- a/nmdc_runtime/site/ops.py +++ b/nmdc_runtime/site/ops.py @@ -809,7 +809,17 @@ def nmdc_schema_database_export_filename_neon() -> str: @op -def get_csv_file_from_url(url: str) -> List[Dict]: +def get_csv_rows_from_url(url: str) -> List[Dict]: + """Download and parse a CSV file from a remote URL. + + This method fetches data from the given URL and parses that data as CSV. The parsed data + is returned as a list (each element corresponds to a row) of dicts (each key is a column + name and the value is the corresponding cell value). The dict will *not* contain keys + for columns where the cell was empty. + + :param url: Url to fetch and parse + :return: List[Dict] + """ if not url: return [] @@ -817,4 +827,6 @@ def get_csv_file_from_url(url: str) -> List[Dict]: response.raise_for_status() reader = csv.DictReader(response.text.splitlines()) + # Collect all the rows into a list of dicts while stripping out (valfilter) cells where the + # value is an empty string (identity returns a Falsy value). return [valfilter(identity, row) for row in reader] diff --git a/nmdc_runtime/site/translation/submission_portal_translator.py b/nmdc_runtime/site/translation/submission_portal_translator.py index ad821557..c3050166 100644 --- a/nmdc_runtime/site/translation/submission_portal_translator.py +++ b/nmdc_runtime/site/translation/submission_portal_translator.py @@ -67,7 +67,7 @@ def _get_doi(self, metadata_submission: JSON_OBJECT) -> Union[List[str], None]: """Get DOI information from the context form data :param metadata_submission: submission portal entry - :return: string or None + :return: list of strings or None """ dataset_doi = get_in(["contextForm", "datasetDoi"], metadata_submission) if not dataset_doi: @@ -380,7 +380,7 @@ def _transform_dict_for_class(self, raw_values: dict, class_name: str) -> dict: raw_values is a dict where the keys are slot names and the values are plain strings. Each of the items in this dict will be transformed by the _transform_value_for_slot method. If the slot is multivalued each individual value will be transformed. If the - slot is multivalued and the value is a string it will be split in pipe characters + slot is multivalued and the value is a string it will be split at pipe characters before transforming. """ slot_names = self.schema_view.class_slots(class_name) @@ -392,11 +392,12 @@ def _transform_dict_for_class(self, raw_values: dict, class_name: str) -> dict: slot_definition = self.schema_view.induced_slot(column, class_name) if slot_definition.multivalued: + value_list = value if isinstance(value, str): - value = [v.strip() for v in value.split("|")] + value_list = [v.strip() for v in value.split("|")] transformed_value = [ self._transform_value_for_slot(item, slot_definition) - for item in value + for item in value_list ] else: transformed_value = self._transform_value_for_slot( @@ -535,7 +536,7 @@ def get_database(self) -> nmdc.Database: for data_object_row in data_objects_by_sample_data_id.get( sample_data_id, [] ): - # For each row in the DataObject mapping file that correspond to the sample ID, + # For each row in the DataObject mapping file that corresponds to the sample ID, # transform the raw row data according to the DataObject class's slots, generate # an instance, and connect that instance's minted ID to the OmicsProcessing # instance diff --git a/tests/test_data/test_submission_portal_translator.py b/tests/test_data/test_submission_portal_translator.py index 0cf76b4a..533455e7 100644 --- a/tests/test_data/test_submission_portal_translator.py +++ b/tests/test_data/test_submission_portal_translator.py @@ -263,6 +263,8 @@ def now(cls, **kwargs): test_datasets = yaml.safe_load_all(f) for test_data in test_datasets: + # Reset the random number seed here so that fake IDs generated by the `test_minter` + # fixture are stable across test runs random.seed(0) translator = SubmissionPortalTranslator( **test_data["input"], id_minter=test_minter diff --git a/tests/test_ops/test_get_csv_file_from_url.py b/tests/test_ops/test_get_csv_rows_from_url.py similarity index 79% rename from tests/test_ops/test_get_csv_file_from_url.py rename to tests/test_ops/test_get_csv_rows_from_url.py index a60e468d..087a953f 100644 --- a/tests/test_ops/test_get_csv_file_from_url.py +++ b/tests/test_ops/test_get_csv_rows_from_url.py @@ -3,7 +3,7 @@ import requests_mock from dagster import build_op_context -from nmdc_runtime.site.ops import get_csv_file_from_url +from nmdc_runtime.site.ops import get_csv_rows_from_url def test_valid_data(): @@ -14,7 +14,7 @@ def test_valid_data(): text='a,b,c\n1,hello,"apple, banana"\n2,wow,great', ) - result = get_csv_file_from_url(context, "http://www.example.com/data.csv") + result = get_csv_rows_from_url(context, "http://www.example.com/data.csv") assert result == [ {"a": "1", "b": "hello", "c": "apple, banana"}, {"a": "2", "b": "wow", "c": "great"}, @@ -27,4 +27,4 @@ def test_not_found(): mock.get("http://www.example.com/data.csv", status_code=404) with pytest.raises(requests.HTTPError): - get_csv_file_from_url(context, "http://www.example.com/data.csv") + get_csv_rows_from_url(context, "http://www.example.com/data.csv")