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Merge pull request #216 from uc-cdis/fix/etl
Fix/etl
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,104 @@ | ||
| {{ if .Values.legacySupport }} | ||
| kind: Secret | ||
| apiVersion: v1 | ||
| metadata: | ||
| name: etl-secret | ||
| stringData: | ||
| settings.py: |- | ||
| import os | ||
| import tube.enums as enums | ||
| from cdislogging import get_logger | ||
| from tube.config_helper import find_paths, load_json | ||
| from .utils.general import get_resource_paths_from_yaml | ||
| logger = get_logger("__name__", log_level="warn") | ||
| LIST_TABLES_FILES = "tables.txt" | ||
| # | ||
| # Load db credentials from a creds.json file. | ||
| # See config_helper.py for paths searched for creds.json | ||
| # ex: export XDG_DATA_HOME="$HOME/.local/share" | ||
| # and setup $XDG_DATA_HOME/.local/share/gen3/tube/creds.json | ||
| # | ||
| conf_data = load_json("creds.json", "tube") | ||
| DB_HOST = os.getenv("DB_HOST") or conf_data.get("db_host", "localhost") | ||
| DB_PORT = os.getenv("DB_PORT") or conf_data.get("db_port", "5432") | ||
| DB_DATABASE = os.getenv("DB_DATABASE") or conf_data.get("db_database", "sheepdog") | ||
| DB_USERNAME = os.getenv("DB_USERNAME") or conf_data.get("db_username", "peregrine") | ||
| DB_PASSWORD = os.getenv("DB_PASSWORD") or conf_data.get("db_password", "unknown") | ||
| DB_USE_SSL = os.getenv("DB_USE_SSL") or conf_data.get( | ||
| "db_use_ssl", False | ||
| ) # optional property to db_use_ssl | ||
| JDBC = ( | ||
| "jdbc:postgresql://{}:{}/{}".format(DB_HOST, DB_PORT, DB_DATABASE) | ||
| if DB_USE_SSL is False | ||
| else "jdbc:postgresql://{}:{}/{}?sslmode=require".format( | ||
| DB_HOST, DB_PORT, DB_DATABASE | ||
| ) | ||
| ) | ||
| PYDBC = "postgresql://{}:{}@{}:{}/{}".format( | ||
| DB_USERNAME, DB_PASSWORD, DB_HOST, DB_PORT, DB_DATABASE | ||
| ) | ||
| DICTIONARY_URL = os.getenv( | ||
| "DICTIONARY_URL", | ||
| "https://s3.amazonaws.com/dictionary-artifacts/datadictionary/develop/schema.json", | ||
| ) | ||
| ES_URL = os.getenv("ES_URL", "esproxy-service") | ||
| HDFS_DIR = "/result" | ||
| # Three modes: Test, Dev, Prod | ||
| RUNNING_MODE = os.getenv("RUNNING_MODE", enums.RUNNING_MODE_DEV) # 'Prod' or 'Dev' | ||
| PARALLEL_JOBS = 1 | ||
| LOG_LEVEL = os.getenv("LOG_LEVEL", "INFO") | ||
| ES = { | ||
| "es.nodes": ES_URL, | ||
| "es.port": "9200", | ||
| "es.input.json": "yes", | ||
| "es.nodes.client.only": "false", | ||
| "es.nodes.discovery": "false", | ||
| "es.nodes.data.only": "false", | ||
| "es.nodes.wan.only": "true", | ||
| } | ||
| HADOOP_HOME = os.getenv("HADOOP_HOME", "/usr/local/Cellar/hadoop/3.1.0/libexec/") | ||
| JAVA_HOME = os.getenv( | ||
| "JAVA_HOME", "/Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/Home" | ||
| ) | ||
| HADOOP_URL = os.getenv("HADOOP_URL", "http://spark-service:9000") | ||
| ES_HADOOP_VERSION = os.getenv("ES_HADOOP_VERSION", "") | ||
| ES_HADOOP_HOME_BIN = "{}/elasticsearch-hadoop-{}".format( | ||
| os.getenv("ES_HADOOP_HOME", ""), os.getenv("ES_HADOOP_VERSION", "") | ||
| ) | ||
| HADOOP_HOST = os.getenv("HADOOP_HOST", "spark-service") | ||
| # Searches same folders as load_json above | ||
| try: | ||
| MAPPING_FILE = find_paths("etlMapping.yaml", "tube")[0] | ||
| except: | ||
| MAPPING_FILE = None | ||
| try: | ||
| USERYAML_FILE = find_paths("user.yaml", "tube")[0] | ||
| except IndexError: | ||
| USERYAML_FILE = None | ||
| PROJECT_TO_RESOURCE_PATH = get_resource_paths_from_yaml(USERYAML_FILE) | ||
| SPARK_MASTER = os.getenv("SPARK_MASTER", "local[1]") # 'spark-service' | ||
| SPARK_EXECUTOR_MEMORY = os.getenv("SPARK_EXECUTOR_MEMORY", "2g") | ||
| SPARK_DRIVER_MEMORY = os.getenv("SPARK_DRIVER_MEMORY", "512m") | ||
| APP_NAME = "Gen3 ETL" | ||
| os.environ[ | ||
| "PYSPARK_SUBMIT_ARGS" | ||
| ] = "--jars {}/dist/elasticsearch-spark-20_2.11-{}.jar pyspark-shell".format( | ||
| ES_HADOOP_HOME_BIN, ES_HADOOP_VERSION | ||
| ) | ||
| os.environ["HADOOP_CLIENT_OPTS"] = os.getenv("HADOOP_CLIENT_OPTS", "") | ||
| {{- end }} |
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