nmdc-runtime 1.3.1__py3-none-any.whl → 2.12.0__py3-none-any.whl

nmdc_runtime/site/translation/emsl.py

@@ -1,42 +0,0 @@
-"""
-Translates EMSL data into JSON conformant with the NMDC JSON schema
-"""
-from dagster import op, graph
-
-from nmdc_runtime.lib.nmdc_etl_class import NMDC_ETL
-from nmdc_runtime.site.translation.util import (
-    load_nmdc_etl_class,
-    load_mongo_collection,
-    preset_prod,
-    preset_test,
-    schema_validate,
-)
-
-
-@op
-def transform_emsl_omics_processing(_context, nmdc_etl: NMDC_ETL) -> tuple:
-    return ("emsl.omics_processing_set", nmdc_etl.transform_emsl_omics_processing())
-
-
-@op
-def transform_emsl_data_object(_context, nmdc_etl: NMDC_ETL) -> tuple:
-    return ("emsl.data_object_set", nmdc_etl.transform_emsl_data_object())
-
-
-@graph
-def emsl():
-    # load_merged_data_source()
-    nmdc_etl = load_nmdc_etl_class()
-    emsl_omics_processing = transform_emsl_omics_processing(nmdc_etl)
-    emsl_omics_processing_validated = schema_validate(emsl_omics_processing)
-
-    emsl_data_object = transform_emsl_data_object(nmdc_etl)
-    emsl_data_object_validated = schema_validate(emsl_data_object)
-
-    # load data into mongo
-    load_mongo_collection(emsl_omics_processing_validated)
-    load_mongo_collection(emsl_data_object_validated)
-
-
-emsl_job = emsl.to_job(**preset_prod)
-test_emsl_job = emsl.to_job(name="test_emsl", **preset_test)

nmdc_runtime/site/translation/gold.py

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

nmdc_runtime/site/translation/jgi.py

@@ -1,31 +0,0 @@
-"""
-Translates EMSL data into JSON conformant with the NMDC JSON schema
-"""
-from dagster import op, graph
-
-from nmdc_runtime.lib.nmdc_etl_class import NMDC_ETL
-from nmdc_runtime.site.translation.util import (
-    load_nmdc_etl_class,
-    load_mongo_collection,
-    preset_prod,
-    preset_test,
-    schema_validate,
-)
-
-
-@op
-def transform_jgi_data_object(_context, nmdc_etl: NMDC_ETL) -> tuple:
-    # return "jgi.data_object_set", [{"foo": "bar"}]  # used for testing failure
-    return "jgi.data_object_set", nmdc_etl.transform_jgi_data_object()
-
-
-@graph
-def jgi():
-    nmdc_etl = load_nmdc_etl_class()
-    jgi_data_object = transform_jgi_data_object(nmdc_etl)
-    jgi_data_object_validated = schema_validate(jgi_data_object)
-    load_mongo_collection(jgi_data_object_validated)
-
-
-jgi_job = jgi.to_job(**preset_prod)
-test_jgi_job = jgi.to_job(name="test_jgi", **preset_test)

nmdc_runtime/site/translation/util.py

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

nmdc_runtime/site/validation/jgi.py

@@ -1,42 +0,0 @@
-"""
-Validates data in the JGI collection in the nmdc_etl_staging database.
-"""
-from dagster import op, graph
-
-from nmdc_runtime.site.ops import local_file_to_api_object
-from nmdc_runtime.site.validation.util import (
-    preset_prod,
-    preset_test,
-    validate_mongo_collection,
-    write_to_local_file,
-    announce_validation_report,
-)
-
-
-@op
-def jgi_data_object_set_collection_name():
-    return "jgi.data_object_set"
-
-
-@graph()
-def jgi():
-    report = validate_mongo_collection(jgi_data_object_set_collection_name())
-    # the below could also be a @graph and loaded as a "subgraph" by e.g. the jgi graph job.
-    local_path = write_to_local_file(report)
-    obj = local_file_to_api_object(local_path)
-    announce_validation_report(report, obj)
-
-
-# passing the collecton name via the config
-# problem: not sure if this best when multiple sets need to be validated
-# from toolz import assoc_in
-# config_ops = {
-#     "validate_mongo_collection": {"config": {"collection_name": "jgi.data_object_set"}}
-# }
-# validate_jgi_job = jgi.to_job(**assoc_in(preset_prod, ["config", "ops"], config_ops))
-# test_validate_jgi_job = jgi.to_job(
-#     **assoc_in(preset_test, ["config", "ops"], config_ops)
-# )
-
-validate_jgi_job = jgi.to_job(**preset_prod)
-test_validate_jgi_job = jgi.to_job(**preset_test)

nmdc_runtime-1.3.1.dist-info/METADATA

@@ -1,181 +0,0 @@
-Metadata-Version: 2.1
-Name: nmdc_runtime
-Version: 1.3.1
-Summary: A runtime system for NMDC data management and orchestration
-Home-page: https://github.com/microbiomedata/nmdc-runtime
-Author: Donny Winston
-Author-email: donny@polyneme.xyz
-Classifier: Development Status :: 3 - Alpha
-Classifier: Programming Language :: Python :: 3
-Classifier: License :: OSI Approved :: Apache Software License
-Requires-Python: >=3.10
-Description-Content-Type: text/markdown
-License-File: LICENSE
-
-A runtime system for NMDC data management and orchestration.
-
-## Service Status
-
-http://nmdcstatus.polyneme.xyz/
-
-## How It Fits In
-
-* [issues](https://github.com/microbiomedata/issues)  
-tracks issues related to NMDC, which may necessitate work across multiple repos.
-  
-* [nmdc-schema](https://github.com/microbiomedata/nmdc-schema/)
-houses the LinkML schema specification, as well as generated artifacts (e.g. JSON Schema).
-
-* [nmdc-server](https://github.com/microbiomedata/nmdc-server)
-houses code specific to the data portal -- its database, back-end API, and front-end application.
-
-* [workflow_documentation](https://nmdc-workflow-documentation.readthedocs.io/en/latest/index.html)
-references workflow code spread across several repositories, that take source data and produce computed data.
-
-* This repo (nmdc-runtime)
-   * houses code that takes source data and computed data, and transforms it
-     to broadly accommodate downstream applications such as the data portal
-   * manages execution of the above (i.e., lightweight data transformations) and also
-     of computationally- and data-intensive workflows performed at other sites,
-     ensuring that claimed jobs have access to needed configuration and data resources.
-
-## Data exports
-
-The NMDC metadata as of 2021-10 is available here:
-
-https://drs.microbiomedata.org/ga4gh/drs/v1/objects/sys086d541
-
-The link returns a [GA4GH DRS API bundle object record](https://ga4gh.github.io/data-repository-service-schemas/preview/release/drs-1.0.0/docs/#_drs_datatypes), with the NMDC metadata collections (study_set, biosample_set, etc.) as contents, each a DRS API blob object.
-
-For example the blob for the study_set collection export, named "study_set.jsonl.gz", is listed with DRS API ID "sys0xsry70". Thus, it is retrievable via
-
-https://drs.microbiomedata.org/ga4gh/drs/v1/objects/sys0xsry70
-
-The returned blob object record lists https://nmdc-runtime.files.polyneme.xyz/nmdcdb-mongoexport/2021-10-14/study_set.jsonl.gz as the url for an access method.
-
-The 2021-10 exports are currently all accessible at `https://nmdc-runtime.files.polyneme.xyz/nmdcdb-mongoexport/2021-10-14/${COLLECTION_NAME}.jsonl.gz`, but the DRS API indirection allows these links to change in the future, for mirroring via other URLs, etc. So, the DRS API links should be the links you share.
-
-## Overview
-
-The runtime features:
-
-1. [Dagster](https://docs.dagster.io/concepts) orchestration:
-    - dagit - a web UI to monitor and manage the running system.
-    - dagster-daemon - a service that triggers pipeline runs based on time or external state.
-    - PostgresSQL database - for storing run history, event logs, and scheduler state.
-    - workspace code
-      - Code to run is loaded into a Dagster `workspace`. This code is loaded from
-         one or more dagster `repositories`. Each Dagster `repository` may be run with a different
-         Python virtual environment if need be, and may be loaded from a local Python file or
-         `pip install`ed from an external source. In our case, each Dagster `repository` is simply
-         loaded from a Python file local to the nmdc-runtime GitHub repository, and all code is
-         run in the same Python environment.
-      - A Dagster repository consists of `solids` and `pipelines`,
-         and optionally `schedules` and `sensors`.
-         - `solids` represent individual units of computation
-         - `pipelines` are built up from solids
-         - `schedules` trigger recurring pipeline runs based on time
-         - `sensors` trigger pipeline runs based on external state
-      - Each `pipeline` can declare dependencies on any runtime `resources` or additional
-         configuration. There are TerminusDB and MongoDB `resources` defined, as well as `preset`
-         configuration definitions for both "dev" and "prod" `modes`. The `preset`s tell Dagster to
-         look to a set of known environment variables to load resources configurations, depending on
-         the `mode`.
-
-2. A [TerminusDB](https://terminusdb.com/) database supporting revision control of schema-validated
-data.
-   
-3. A MongoDB database supporting write-once, high-throughput internal
-data storage by the nmdc-runtime FastAPI instance.
-   
-4. A [FastAPI](https://fastapi.tiangolo.com/) service to interface with the orchestrator and
-database, as a hub for data management and workflow automation.
-
-## Local Development
-
-Ensure Docker (and Docker Compose) are installed; and the Docker engine is running.
-
-```shell
-docker --version
-docker compose version
-docker info
-```
-
-Ensure the permissions of `./mongoKeyFile` are such that only the file's owner can read or write the file.
-
-```shell
-chmod 600 ./mongoKeyFile
-```
-
-Ensure you have a `.env` file for the Docker services to source from. You may copy `.env.example` to
-`.env` (which is gitignore'd) to get started.
-
-```shell
-cp .env.example .env
-```
-
-Create environment variables in your shell session, based upon the contents of the `.env` file.
-
-```shell
-export $(grep -v '^#' .env | xargs)
-```
-
-If you are connecting to resources that require an SSH tunnel—for example, a MongoDB server that is only accessible on the NERSC network—set up the SSH tunnel.
-
-The following command could be useful to you, either directly or as a template (see `Makefile`).
-
-```shell
-make nersc-mongo-tunnels
-```
-
-Finally, spin up the Docker Compose stack.
-
-```bash
-make up-dev
-```
-
-Docker Compose is used to start local MongoDB and PostgresSQL (used by Dagster) instances, as well
-as a Dagster web server (dagit) and daemon (dagster-daemon).
-
-The Dagit web server is viewable at http://127.0.0.1:3000/. 
-
-The FastAPI service is viewable at http://127.0.0.1:8000/ -- e.g., rendered documentation at
-http://127.0.0.1:8000/redoc/.
-
-## Local Testing
-
-Tests can be found in `tests` and are run with the following commands:
-
-On an M1 Mac? May need to `export DOCKER_DEFAULT_PLATFORM=linux/amd64`.
-
-```bash
-make up-test
-make test
-```
-
-As you create Dagster solids and pipelines, add tests in `tests/` to check that your code behaves as
-desired and does not break over time.
-
-[For hints on how to write tests for solids and pipelines in Dagster, see their documentation
-tutorial on Testing](https://docs.dagster.io/tutorial/testable).
-
-## Publish to PyPI
-
-This repository contains a GitHub Actions workflow that publishes a Python package to [PyPI](https://pypi.org/project/nmdc-runtime/).
-
-You can also _manually_ publish the Python package to PyPI by issuing the following commands in the root directory of the repository:
-
-```
-rm -rf dist
-python -m build
-twine upload dist/*
-```
-
-## Links
-
-Here are links related to this repository:
-
-- Production API server: https://api.microbiomedata.org
-- PyPI package: https://pypi.org/project/nmdc-runtime
-- DockerHub image (API server): https://hub.docker.com/r/microbiomedata/nmdc-runtime-fastapi
-- DockerHub image (Dagster): https://hub.docker.com/r/microbiomedata/nmdc-runtime-dagster

nmdc_runtime-1.3.1.dist-info/RECORD

@@ -1,81 +0,0 @@
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@@ -1 +0,0 @@
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