From 02180e06e85d5d732e5b3ac222eab6a41d8b181c Mon Sep 17 00:00:00 2001 From: Michael Terry Date: Fri, 17 Nov 2023 15:54:06 -0500 Subject: [PATCH] feat: add new DuckDB backend for reading ndjson directly This adds some new arguments: --db-type [athena,duckdb] (defaulting to athena) --load-ndjson-dir DIR (tells DuckDB where to find source ndjsons) A light abstraction layer has been added in databases.py to choose the correct backend based on the args. Mostly the SQL is the same. Some light tweaks for standardization, plus some compatibility user-defined functions injected into duckdb allow both backends to work on the same SQL. --- CONTRIBUTING.md | 12 + cumulus_library/__init__.py | 2 +- cumulus_library/base_table_builder.py | 7 +- cumulus_library/cli.py | 61 ++--- cumulus_library/cli_parser.py | 40 ++- cumulus_library/databases.py | 232 ++++++++++++++++++ .../studies/core/builder_encounter_coding.py | 2 +- .../studies/core/documentreference.sql | 4 +- cumulus_library/studies/core/patient.sql | 2 +- cumulus_library/study_parser.py | 33 ++- .../template_sql/column_datatype.sql.jinja | 2 +- cumulus_library/template_sql/count.sql.jinja | 2 +- .../template_sql/ctas_empty.sql.jinja | 4 +- .../template_sql/show_tables.sql.jinja | 7 +- .../template_sql/show_views.sql.jinja | 7 +- cumulus_library/template_sql/utils.py | 6 +- docs/creating-studies.md | 51 ++++ pyproject.toml | 5 +- tests/test_cli.py | 12 +- tests/test_data/duckdb_data/README.md | 4 + .../duckdb_data/condition/conditions.ndjson | 20 ++ .../duckdb_data/documentreference/docs.ndjson | 51 ++++ .../encounter/filenames.do.not.matter.ndjson | 50 ++++ .../core/core__count_condition_month.csv | 3 + .../core__count_documentreference_month.csv | 19 ++ .../core/core__count_encounter_month.csv | 65 +++++ .../core/core__count_encounter_type.csv | 9 + .../core/core__count_encounter_type_month.csv | 25 ++ .../core__count_medicationrequest_month.csv | 13 + .../core__count_observation_lab_month.csv | 15 ++ .../core/core__count_patient.csv | 13 + .../expected_export/core/core__meta_date.csv | 2 + .../core/core__meta_version.csv | 2 + .../duckdb_data/medicationrequest/meds.ndjson | 39 +++ .../duckdb_data/observation/obs.ndjson | 20 ++ .../patient/patient-remainder.ndjson | 49 ++++ .../duckdb_data/patient/patient1.ndjson | 1 + tests/test_duckdb.py | 44 ++++ tests/test_study_parser.py | 2 +- tests/test_template_utils.py | 59 ++--- tests/test_templates.py | 2 +- 41 files changed, 877 insertions(+), 121 deletions(-) create mode 100644 CONTRIBUTING.md create mode 100644 cumulus_library/databases.py create mode 100644 tests/test_data/duckdb_data/README.md create mode 100644 tests/test_data/duckdb_data/condition/conditions.ndjson create mode 100644 tests/test_data/duckdb_data/documentreference/docs.ndjson create mode 100644 tests/test_data/duckdb_data/encounter/filenames.do.not.matter.ndjson create mode 100644 tests/test_data/duckdb_data/expected_export/core/core__count_condition_month.csv create mode 100644 tests/test_data/duckdb_data/expected_export/core/core__count_documentreference_month.csv create mode 100644 tests/test_data/duckdb_data/expected_export/core/core__count_encounter_month.csv create mode 100644 tests/test_data/duckdb_data/expected_export/core/core__count_encounter_type.csv create mode 100644 tests/test_data/duckdb_data/expected_export/core/core__count_encounter_type_month.csv create mode 100644 tests/test_data/duckdb_data/expected_export/core/core__count_medicationrequest_month.csv create mode 100644 tests/test_data/duckdb_data/expected_export/core/core__count_observation_lab_month.csv create mode 100644 tests/test_data/duckdb_data/expected_export/core/core__count_patient.csv create mode 100644 tests/test_data/duckdb_data/expected_export/core/core__meta_date.csv create mode 100644 tests/test_data/duckdb_data/expected_export/core/core__meta_version.csv create mode 100644 tests/test_data/duckdb_data/medicationrequest/meds.ndjson create mode 100644 tests/test_data/duckdb_data/observation/obs.ndjson create mode 100644 tests/test_data/duckdb_data/patient/patient-remainder.ndjson create mode 100644 tests/test_data/duckdb_data/patient/patient1.ndjson create mode 100644 tests/test_duckdb.py diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 00000000..56452b54 --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,12 @@ +# Contributing to Cumulus Library + +## Set up your dev environment + +To use the same dev environment as us, you'll want to run these commands: +```sh +pip install .[dev] +pre-commit install +``` + +This will install dependencies & build tools, +as well as set up a `black` auto-formatter commit hook. diff --git a/cumulus_library/__init__.py b/cumulus_library/__init__.py index ec3d522c..db434d1a 100644 --- a/cumulus_library/__init__.py +++ b/cumulus_library/__init__.py @@ -1,2 +1,2 @@ """Package metadata""" -__version__ = "1.4.1" +__version__ = "1.5.0" diff --git a/cumulus_library/base_table_builder.py b/cumulus_library/base_table_builder.py index 4b6ab946..f8196578 100644 --- a/cumulus_library/base_table_builder.py +++ b/cumulus_library/base_table_builder.py @@ -4,6 +4,7 @@ from abc import ABC, abstractmethod from typing import final +from cumulus_library.databases import DatabaseCursor from cumulus_library.helper import get_progress_bar, query_console_output @@ -34,7 +35,11 @@ def prepare_queries(self, cursor: object, schema: str): @final def execute_queries( - self, cursor: object, schema: str, verbose: bool, drop_table: bool = False + self, + cursor: DatabaseCursor, + schema: str, + verbose: bool, + drop_table: bool = False, ): """Executes queries set up by a prepare_queries call diff --git a/cumulus_library/cli.py b/cumulus_library/cli.py index 9e9c0351..523f8e1d 100755 --- a/cumulus_library/cli.py +++ b/cumulus_library/cli.py @@ -9,14 +9,16 @@ from pathlib import Path, PosixPath from typing import Dict, List, Optional -import pyathena - -from pyathena.pandas.cursor import PandasCursor from rich.console import Console from rich.table import Table from cumulus_library import __version__ from cumulus_library.cli_parser import get_parser +from cumulus_library.databases import ( + AthenaDatabaseBackend, + DatabaseBackend, + create_db_backend, +) from cumulus_library.study_parser import StudyManifestParser from cumulus_library.upload import upload_files @@ -38,7 +40,10 @@ def __init__(self): def get_study_builder(self): """Convenience method for getting athena args from environment""" - return StudyBuilder(self.region, self.workgroup, self.profile, self.schema_name) + db = AthenaDatabaseBackend( + self.region, self.workgroup, self.profile, self.schema_name + ) + return StudyBuilder(db) class StudyBuilder: @@ -47,35 +52,10 @@ class StudyBuilder: verbose = False schema_name = None - def __init__( # pylint: disable=too-many-arguments - self, region: str, workgroup: str, profile: str, schema: str - ): - connect_kwargs = {} - for aws_env_name in [ - "AWS_ACCESS_KEY_ID", - "AWS_SECRET_ACCESS_KEY", - "AWS_SESSION_TOKEN", - ]: - if aws_env_val := os.environ.get(aws_env_name): - connect_kwargs[aws_env_name.lower()] = aws_env_val - # the profile may not be required, provided the above three AWS env vars - # are set. If both are present, the env vars take precedence - if profile is not None: - connect_kwargs["profile_name"] = profile - self.cursor = pyathena.connect( - region_name=region, - work_group=workgroup, - schema_name=schema, - **connect_kwargs, - ).cursor() - self.pandas_cursor = pyathena.connect( - region_name=region, - work_group=workgroup, - schema_name=schema, - cursor_class=PandasCursor, - **connect_kwargs, - ).cursor() - self.schema_name = schema + def __init__(self, db: DatabaseBackend): + self.db = db + self.cursor = db.cursor() + self.schema_name = db.schema_name def reset_data_path(self, study: PosixPath) -> None: """ @@ -163,7 +143,7 @@ def export_study(self, target: PosixPath, data_path: PosixPath) -> None: if data_path is None: sys.exit("Missing destination - please provide a path argument.") studyparser = StudyManifestParser(target) - studyparser.export_study(self.pandas_cursor, data_path) + studyparser.export_study(self.db, data_path) def export_all(self, study_dict: Dict, data_path: PosixPath): """Exports all defined count tables to disk""" @@ -248,15 +228,11 @@ def run_cli(args: Dict): # all other actions require connecting to AWS else: - builder = StudyBuilder( - args["region"], - args["workgroup"], - args["profile"], - args["schema_name"], - ) + db_backend = create_db_backend(args) + builder = StudyBuilder(db_backend) if args["verbose"]: builder.verbose = True - print("Testing connection to athena...") + print("Testing connection to database...") builder.cursor.execute("SHOW DATABASES") study_dict = get_study_dict(args["study_dir"]) @@ -297,6 +273,7 @@ def run_cli(args: Dict): for target in args["target"]: builder.export_study(study_dict[target], args["data_path"]) + db_backend.close() # returning the builder for ease of unit testing return builder @@ -319,12 +296,14 @@ def main(cli_args=None): break arg_env_pairs = ( + ("db_type", "CUMULUS_LIBRARY_DB_TYPE"), ("profile", "CUMULUS_LIBRARY_PROFILE"), ("schema_name", "CUMULUS_LIBRARY_DATABASE"), ("workgroup", "CUMULUS_LIBRARY_WORKGROUP"), ("region", "CUMULUS_LIBRARY_REGION"), ("study_dir", "CUMULUS_LIBRARY_STUDY_DIR"), ("data_path", "CUMULUS_LIBRARY_DATA_PATH"), + ("load_ndjson_dir", "CUMULUS_LIBRARY_LOAD_NDJSON_DIR"), ("user", "CUMULUS_AGGREGATOR_USER"), ("id", "CUMULUS_AGGREGATOR_ID"), ("url", "CUMULUS_AGGREGATOR_URL"), diff --git a/cumulus_library/cli_parser.py b/cumulus_library/cli_parser.py index f25005aa..5f951988 100644 --- a/cumulus_library/cli_parser.py +++ b/cumulus_library/cli_parser.py @@ -44,7 +44,7 @@ def add_data_path_argument(parser: argparse.ArgumentParser) -> None: nargs="?", help=( "The path to use for Athena counts data. " - "Can be povided via CUMULUS_LIBRARY_DATA_PATH environment variable." + "Can be provided via CUMULUS_LIBRARY_DATA_PATH environment variable." ), ) @@ -63,12 +63,6 @@ def add_aws_config(parser: argparse.ArgumentParser) -> None: """Adds arguments related to aws credentials to a subparser""" aws = parser.add_argument_group("AWS config") aws.add_argument("--profile", help="AWS profile", default="default") - aws.add_argument( - "--database", - # internally, we use PyAthena's terminology for this but the UX term is "database" - dest="schema_name", - help="Cumulus Athena database name", - ) aws.add_argument( "--workgroup", default="cumulus", @@ -81,6 +75,29 @@ def add_aws_config(parser: argparse.ArgumentParser) -> None: ) +def add_db_config(parser: argparse.ArgumentParser) -> None: + """Adds arguments related to database backends to a subparser""" + group = parser.add_argument_group("Database config") + group.add_argument( + "--db-type", + help="Which database backend to use (default athena)", + choices=["athena", "duckdb"], + default="athena", + ) + group.add_argument( + "--database", + # In Athena, we use this as the schema_name (which is also called a Database in their UX). + # In DuckDB, we use this as the path to the filename to store tables. + # Since we started as an Athena-centric codebase, we mostly keep referring to this as + # name "schema_name". But to the user, both uses are still conceptually a "database". + dest="schema_name", + help="Database name (for Athena) or file (for DuckDB)", + ) + + # Backend-specific config: + add_aws_config(parser) + + def get_parser() -> argparse.ArgumentParser: """Provides parser for handling CLI arguments""" parser = argparse.ArgumentParser( @@ -125,7 +142,7 @@ def get_parser() -> argparse.ArgumentParser: add_target_argument(clean) add_study_dir_argument(clean) add_verbose_argument(clean) - add_aws_config(clean) + add_db_config(clean) clean.add_argument( "--prefix", action="store_true", @@ -140,8 +157,11 @@ def get_parser() -> argparse.ArgumentParser: add_table_builder_argument(build) add_study_dir_argument(build) add_verbose_argument(build) - add_aws_config(build) + add_db_config(build) + build.add_argument( + "--load-ndjson-dir", help="Load ndjson files from this folder", metavar="DIR" + ) build.add_argument( "--continue", dest="continue_from", @@ -155,7 +175,7 @@ def get_parser() -> argparse.ArgumentParser: add_study_dir_argument(export) add_data_path_argument(export) add_verbose_argument(export) - add_aws_config(export) + add_db_config(export) upload = actions.add_parser( "upload", help="Bulk uploads data to Cumulus aggregator" diff --git a/cumulus_library/databases.py b/cumulus_library/databases.py new file mode 100644 index 00000000..0e8485eb --- /dev/null +++ b/cumulus_library/databases.py @@ -0,0 +1,232 @@ +"""Abstraction layers for supported database backends (e.g. AWS & DuckDB)""" + +import abc +import datetime +import json +import os +import sys +from pathlib import Path +from typing import Optional, Protocol, Union + +import cumulus_fhir_support +import duckdb +import pandas +import pyarrow +import pyathena +from pyathena.common import BaseCursor as AthenaCursor +from pyathena.pandas.cursor import PandasCursor as AthenaPandasCursor + + +class DatabaseCursor(Protocol): + """Protocol for a PEP-249 compatible cursor""" + + def execute(self, sql: str) -> None: + pass + + def fetchone(self) -> Optional[list]: + pass + + def fetchmany(self, size: Optional[int]) -> Optional[list[list]]: + pass + + def fetchall(self) -> Optional[list[list]]: + pass + + +class DatabaseBackend(abc.ABC): + """A generic database backend, supporting basic cursor operations""" + + def __init__(self, schema_name: str): + """Create connection to a database backend + + :param schema_name: the database name ('schema' is Athena-speak for a database) + """ + self.schema_name = schema_name + + @abc.abstractmethod + def cursor(self) -> DatabaseCursor: + """Returns a connection to the backing database""" + + @abc.abstractmethod + def execute_as_pandas(self, sql: str) -> pandas.DataFrame: + """Returns a pandas.DataFrame version of the results from the provided SQL""" + + def close(self) -> None: + """Clean up any resources necessary""" + + +class AthenaDatabaseBackend(DatabaseBackend): + """Database backend that can talk to AWS Athena""" + + def __init__(self, region: str, workgroup: str, profile: str, schema_name: str): + super().__init__(schema_name) + + connect_kwargs = {} + for aws_env_name in [ + "AWS_ACCESS_KEY_ID", + "AWS_SECRET_ACCESS_KEY", + "AWS_SESSION_TOKEN", + ]: + if aws_env_val := os.environ.get(aws_env_name): + connect_kwargs[aws_env_name.lower()] = aws_env_val + # the profile may not be required, provided the above three AWS env vars + # are set. If both are present, the env vars take precedence + if profile is not None: + connect_kwargs["profile_name"] = profile + + self.connection = pyathena.connect( + region_name=region, + work_group=workgroup, + schema_name=self.schema_name, + **connect_kwargs, + ) + self.pandas_cursor = self.connection.cursor(cursor=AthenaPandasCursor) + + def cursor(self) -> AthenaCursor: + return self.connection.cursor() + + def execute_as_pandas(self, sql: str) -> pandas.DataFrame: + return self.pandas_cursor.execute(sql).as_pandas() + + +class DuckDatabaseBackend(DatabaseBackend): + """Database backend that uses local files via duckdb""" + + def __init__(self, db_file: str): + super().__init__("main") + self.connection = duckdb.connect(db_file) + + # Paper over some syntax differences between Athena and DuckDB + self.connection.create_function( + # DuckDB's version is array_to_string -- seems there is no standard here. + "array_join", + self._compat_array_join, + ) + self.connection.create_function( + # We frequently use Athena's date() function because it's easier than + # the more widely-supported way of CAST(x AS DATE). + # Rather than convert all of our SQL to the longer version, + # we'll just make our own version of date(). + "date", + self._compat_date, + None, + duckdb.typing.DATE, + ) + self.connection.create_function( + "from_iso8601_timestamp", + self._compat_from_iso8601_timestamp, + None, + duckdb.typing.TIMESTAMP_TZ, + ) + + def insert_tables(self, tables: dict[str, pyarrow.Table]) -> None: + """Ingests all ndjson data from a folder tree (often the output folder of Cumulus ETL)""" + for name, table in tables.items(): + self.connection.register(name, table) + + @staticmethod + def _compat_array_join(value: list[str], delimiter: str) -> str: + return delimiter.join(value) + + @staticmethod + def _compat_date( + value: Union[str, datetime.datetime, datetime.date] + ) -> datetime.date: + if isinstance(value, str): + return datetime.date.fromisoformat(value) + elif isinstance(value, datetime.datetime): + return value.date() + elif isinstance(value, datetime.date): + return value + else: + raise ValueError("Unexpected date() argument:", type(value), value) + + @staticmethod + def _compat_from_iso8601_timestamp(value: str) -> datetime.datetime: + return datetime.datetime.fromisoformat(value) + + def cursor(self) -> duckdb.DuckDBPyConnection: + # Don't actually create a new connection, + # because then we'd have to re-register our json tables. + return self.connection + + def execute_as_pandas(self, sql: str) -> pandas.DataFrame: + return self.connection.execute(sql).df() + + def close(self) -> None: + self.connection.close() + + +def read_ndjson_dir(path: str) -> dict[str, pyarrow.Table]: + """Loads a directory tree of raw ndjson into schema-ful tables. + + :param path: a directory path + :returns: dictionary of table names (like 'documentreference') to table data (with schema) + """ + all_tables = {} + + # Manually specify the list of resources because we want to create each table even if the + # folder does not exist. + resources = [ + "AllergyIntolerance", + "Condition", + "Device", + "DiagnosticReport", + "DocumentReference", + "Encounter", + "Immunization", + "MedicationRequest", + "Observation", + "Patient", + "Procedure", + "ServiceRequest", + ] + for resource in resources: + table_name = resource.lower() + + # Grab filenames to load (ignoring .meta files and handling missing folders) + folder = Path(f"{path}/{table_name}") + filenames = [] + if folder.exists(): + filenames = sorted( + str(x) for x in folder.iterdir() if x.name.endswith(".ndjson") + ) + + # Read all ndjson directly into memory + rows = [] + for filename in filenames: + with open(filename, "r", encoding="utf8") as f: + for line in f: + rows.append(json.loads(line)) + + # Make a pyarrow table with full schema from the data + schema = cumulus_fhir_support.pyarrow_schema_from_rows(resource, rows) + all_tables[table_name] = pyarrow.Table.from_pylist(rows, schema) + + return all_tables + + +def create_db_backend(args: dict[str, str]) -> DatabaseBackend: + db_type = args["db_type"] + database = args["schema_name"] + load_ndjson_dir = args.get("load_ndjson_dir") + + if db_type == "duckdb": + backend = DuckDatabaseBackend(database) # `database` is path name in this case + if load_ndjson_dir: + backend.insert_tables(read_ndjson_dir(load_ndjson_dir)) + elif db_type == "athena": + backend = AthenaDatabaseBackend( + args["region"], + args["workgroup"], + args["profile"], + database, + ) + if load_ndjson_dir: + sys.exit( + "Loading an ndjson dir is not supported with --db-type=athena (try duckdb)" + ) + else: + raise ValueError(f"Unexpected --db-type value '{db_type}'") + + return backend diff --git a/cumulus_library/studies/core/builder_encounter_coding.py b/cumulus_library/studies/core/builder_encounter_coding.py index 0a3d30db..f6a9c7e9 100644 --- a/cumulus_library/studies/core/builder_encounter_coding.py +++ b/cumulus_library/studies/core/builder_encounter_coding.py @@ -43,7 +43,7 @@ def _check_data_in_fields(self, code_sources: list[dict], schema, cursor) -> dic with get_progress_bar(transient=True) as progress: task = progress.add_task( - "Detecting available encounter codaebleConcepts...", + "Detecting available encounter codeableConcepts...", # Each column in code_sources requires at most 3 queries to # detect valid data is in the DB total=len(code_sources), diff --git a/cumulus_library/studies/core/documentreference.sql b/cumulus_library/studies/core/documentreference.sql index 9a929869..337065b4 100644 --- a/cumulus_library/studies/core/documentreference.sql +++ b/cumulus_library/studies/core/documentreference.sql @@ -40,7 +40,7 @@ SELECT DISTINCT CASE WHEN type_coding.type_row.display IS NOT NULL - THEN replace(type_coding.type_row.display, ',') + THEN replace(type_coding.type_row.display, ',', '') ELSE type_row.code END AS doc_type_display, tdr.status, @@ -72,7 +72,7 @@ WITH powerset AS ( WHERE d.encounter_ref = e.encounter_ref AND d.status = 'current' - AND d.docstatus IN (NULL, 'final', 'amended') + AND (d.docstatus IS NULL OR d.docstatus IN ('final', 'amended')) GROUP BY cube(d.doc_type_display, d.author_month, e.enc_class_display) ) diff --git a/cumulus_library/studies/core/patient.sql b/cumulus_library/studies/core/patient.sql index 1e5e8410..529e917c 100644 --- a/cumulus_library/studies/core/patient.sql +++ b/cumulus_library/studies/core/patient.sql @@ -10,7 +10,7 @@ WITH temp_patient AS ( ee.ethnicity_display, p.address, p.id AS subject_id, - date(concat(p.birthdate, '-01-01')) AS birthdate, + date(concat(substr(p.birthdate, 1, 4), '-01-01')) AS birthdate, concat('Patient/', p.id) AS subject_ref FROM patient AS p diff --git a/cumulus_library/study_parser.py b/cumulus_library/study_parser.py index 6fab3e05..e2e0d112 100644 --- a/cumulus_library/study_parser.py +++ b/cumulus_library/study_parser.py @@ -11,6 +11,7 @@ from rich.progress import Progress, TaskID, track from cumulus_library.base_table_builder import BaseTableBuilder +from cumulus_library.databases import DatabaseBackend, DatabaseCursor from cumulus_library.errors import StudyManifestParsingError from cumulus_library.helper import ( query_console_output, @@ -146,7 +147,7 @@ def reset_export_dir(self) -> None: # SQL related functions def clean_study( self, - cursor: object, + cursor: DatabaseCursor, schema_name: str, verbose: bool = False, prefix: str = None, @@ -158,9 +159,6 @@ def clean_study( :verbose: toggle from progress bar to query output, optional :returns: list of dropped tables (for unit testing only) :prefix: override prefix discovery with the provided prefix - - TODO: If we need to support additional databases, we may need to investigate - additional ways to get a list of table prefixes """ if not schema_name: raise ValueError("No database provided") @@ -175,13 +173,13 @@ def clean_study( view_table_list = [] for query_and_type in [[view_sql, "VIEW"], [table_sql, "TABLE"]]: cursor.execute(query_and_type[0]) - for db_row_tuple in cursor: + for db_row_tuple in cursor.fetchall(): # this check handles athena reporting views as also being tables, # so we don't waste time dropping things that don't exist if query_and_type[1] == "TABLE": if not any( - db_row_tuple[0] in query_and_type - for query_and_type in view_table_list + db_row_tuple[0] in iter_q_and_t + for iter_q_and_t in view_table_list ): view_table_list.append([db_row_tuple[0], query_and_type[1]]) else: @@ -222,7 +220,7 @@ def clean_study( def _execute_drop_queries( self, - cursor: object, + cursor: DatabaseCursor, verbose: bool, view_table_list: List, progress: Progress, @@ -298,7 +296,7 @@ def _load_and_execute_builder( del table_builder_module def run_table_builder( - self, cursor: object, schema: str, verbose: bool = False + self, cursor: DatabaseCursor, schema: str, verbose: bool = False ) -> None: """Loads modules from a manifest and executes code via BaseTableBuilder @@ -310,7 +308,7 @@ def run_table_builder( self._load_and_execute_builder(file, cursor, schema, verbose) def run_counts_builder( - self, cursor: object, schema: str, verbose: bool = False + self, cursor: DatabaseCursor, schema: str, verbose: bool = False ) -> None: """Loads counts modules from a manifest and executes code via BaseTableBuilder @@ -322,7 +320,7 @@ def run_counts_builder( self._load_and_execute_builder(file, cursor, schema, verbose) def run_single_table_builder( - self, cursor: object, schema: str, name: str, verbose: bool = False + self, cursor: DatabaseCursor, schema: str, name: str, verbose: bool = False ): """targets a single table builder to run""" if not name.endswith(".py"): @@ -330,7 +328,7 @@ def run_single_table_builder( self._load_and_execute_builder(name, cursor, schema, verbose, drop_table=True) def build_study( - self, cursor: object, verbose: bool = False, continue_from: str = None + self, cursor: DatabaseCursor, verbose: bool = False, continue_from: str = None ) -> List: """Creates tables in the schema by iterating through the sql_config.file_names @@ -373,7 +371,7 @@ def _query_error(self, query_and_filename: List, exit_message: str) -> None: def _execute_build_queries( self, - cursor: object, + cursor: DatabaseCursor, verbose: bool, queries: list, progress: Progress, @@ -435,14 +433,11 @@ def _execute_build_queries( # Database exporting functions - def export_study(self, cursor: object, data_path: PosixPath) -> List: + def export_study(self, db: DatabaseBackend, data_path: PosixPath) -> List: """Exports csvs/parquet extracts of tables listed in export_list - :param cursor: A PEP-249 compatible cursor object + :param db: A database backend :returns: list of executed queries (for unit testing only) - - TODO: If we need to support additional databases, we may need to investigate - additional ways to convert the query to a pandas object """ self.reset_export_dir() queries = [] @@ -451,7 +446,7 @@ def export_study(self, cursor: object, data_path: PosixPath) -> List: description=f"Exporting {self.get_study_prefix()} counts...", ): query = f"select * from {table}" - dataframe = cursor.execute(query).as_pandas() + dataframe = db.execute_as_pandas(query) path = Path(f"{str(data_path)}/{self.get_study_prefix()}/") path.mkdir(parents=True, exist_ok=True) dataframe = dataframe.sort_values( diff --git a/cumulus_library/template_sql/column_datatype.sql.jinja b/cumulus_library/template_sql/column_datatype.sql.jinja index a75cfc6e..8c878a48 100644 --- a/cumulus_library/template_sql/column_datatype.sql.jinja +++ b/cumulus_library/template_sql/column_datatype.sql.jinja @@ -3,4 +3,4 @@ FROM information_schema.columns WHERE table_schema = '{{ schema_name }}' AND table_name = '{{ table_name }}' - AND column_name = '{{ column_name }}' + AND LOWER(column_name) = '{{ column_name }}' diff --git a/cumulus_library/template_sql/count.sql.jinja b/cumulus_library/template_sql/count.sql.jinja index ff18116c..0570fd05 100644 --- a/cumulus_library/template_sql/count.sql.jinja +++ b/cumulus_library/template_sql/count.sql.jinja @@ -27,7 +27,7 @@ CREATE TABLE {{ table_name }} AS ( FROM {{ source_table }} {%- if fhir_resource=='document' and filter_resource %} WHERE (status = 'current') - AND d.docStatus IN (null, 'final', 'amended') + AND (d.docStatus IS null OR d.docStatus IN ('final', 'amended')) {%- elif fhir_resource=='encounter' and filter_resource %} WHERE status = 'finished' {%- elif fhir_resource=='observation' and filter_resource %} diff --git a/cumulus_library/template_sql/ctas_empty.sql.jinja b/cumulus_library/template_sql/ctas_empty.sql.jinja index 6a8c3cbb..84d08d7a 100644 --- a/cumulus_library/template_sql/ctas_empty.sql.jinja +++ b/cumulus_library/template_sql/ctas_empty.sql.jinja @@ -1,14 +1,14 @@ CREATE TABLE "{{ schema_name }}"."{{ table_name }}" AS ( SELECT * FROM ( VALUES - (( + ( {%- for col in table_cols -%} cast(NULL AS varchar) {%- if not loop.last -%} , {%- endif -%} {%- endfor -%} - )) + ) ) AS t ( diff --git a/cumulus_library/template_sql/show_tables.sql.jinja b/cumulus_library/template_sql/show_tables.sql.jinja index 4d7480b7..a40dd66c 100644 --- a/cumulus_library/template_sql/show_tables.sql.jinja +++ b/cumulus_library/template_sql/show_tables.sql.jinja @@ -1 +1,6 @@ -SHOW TABLES IN `{{ schema_name }}` '{{ prefix }}*'; +SELECT table_name +FROM information_schema.tables +WHERE + table_schema = '{{ schema_name }}' + AND table_type = 'BASE TABLE' + AND table_name LIKE '{{ prefix }}%'; diff --git a/cumulus_library/template_sql/show_views.sql.jinja b/cumulus_library/template_sql/show_views.sql.jinja index 0861e7f9..2d4e5e48 100644 --- a/cumulus_library/template_sql/show_views.sql.jinja +++ b/cumulus_library/template_sql/show_views.sql.jinja @@ -1 +1,6 @@ -SHOW VIEWS IN "{{ schema_name }}" LIKE '{{ prefix }}*'; +SELECT table_name +FROM information_schema.tables +WHERE + table_schema = '{{ schema_name }}' + AND table_type = 'VIEW' + AND table_name LIKE '{{ prefix }}%'; diff --git a/cumulus_library/template_sql/utils.py b/cumulus_library/template_sql/utils.py index d206ed27..14e7f6a0 100644 --- a/cumulus_library/template_sql/utils.py +++ b/cumulus_library/template_sql/utils.py @@ -164,12 +164,12 @@ def _check_schema_if_exists( cursor.execute(query) schema_str = str(cursor.fetchone()[0]) required_fields = [coding_element] - if allow_partial: - required_fields + ["code", "system", "display"] + if not allow_partial: + required_fields += ["code", "system", "display"] if any(x not in schema_str for x in required_fields): return False return True - except: + except Exception: return False diff --git a/docs/creating-studies.md b/docs/creating-studies.md index 77f13c86..7b202ba2 100644 --- a/docs/creating-studies.md +++ b/docs/creating-studies.md @@ -165,6 +165,57 @@ styling. your study from scratch due to a change in your counts output. If this is not set, the version will implicitly be set to zero. +## Testing studies + +If you have a Cumulus database in Athena already, +you can easily point at that during study development. + +But it may also be faster or easier to work with local files, +where you can add edge cases. +Cumulus Library has an optional database backend driven by local ndjson just for that! + +### Set up your ndjson + +You can grab fake +[Synthea data](https://github.com/smart-on-fhir/sample-bulk-fhir-datasets), +or use the result of actual bulk-export results from your EHR. + +Once you have that, run Cumulus ETL on your source ndjson with the +`--output-format=ndjson` flag and pointing at some local directory. +For example: +```shell +docker compose run \ + --volume local_dir:/in \ + cumulus-etl \ + /in/ndjson \ + /in/output \ + /in/phi \ + --output-format=ndjson +``` + +This will generate a tree of processed & anonymized ndjson +(just like the ETL normally makes). + +### Run your study on the local ndjson + +Now you can run Cumulus Library but point it at the output files with the +`--db-type=duckdb` and `--load-ndjson-dir=DIR` flags. For example: +```shell +cumulus-library build \ + --db-type duckdb \ + --load-ndjson-dir local_dir/output \ + --database local_dir/duck.db \ + --target my_study +``` + +### Adding edge cases + +Not only is this faster than talking to Athena, +but you can edit the local ndjson to add interest edge cases that you want your +SQL to be able to handle. + +We use this feature in some of our studies to even add automated unit tests. + ## Sharing studies If you want to share your study as an official Cumulus study, please let us know diff --git a/pyproject.toml b/pyproject.toml index a383aeb4..fc218fed 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -3,6 +3,8 @@ name = "cumulus-library" requires-python = ">= 3.9" dependencies = [ "ctakesclient >= 1.3", + "cumulus-fhir-support >= 1", + "duckdb >= 0.9", "fhirclient >= 4.1", "Jinja2 > 3", "pandas <3, >=2.1.1", @@ -27,6 +29,7 @@ dynamic=["version"] [project.optional-dependencies] dev = [ "black", + "pre-commit", "pylint", ] test = [ @@ -37,7 +40,7 @@ test = [ [project.urls] Home = "https://smarthealthit.org/cumulus-a-universal-sidecar-for-a-smart-learning-healthcare-system/" Documentation = "https://docs.smarthealthit.org/cumulus/" -Source = "https://github.com/smart-on-fhir/cumulus-library-core" +Source = "https://github.com/smart-on-fhir/cumulus-library" [project.scripts] diff --git a/tests/test_cli.py b/tests/test_cli.py index cb5d87bf..c38550a7 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -201,10 +201,14 @@ def test_clean( ], ) def test_cli_executes_queries(mock_connect, args, cursor_calls, pandas_cursor_calls): - mock_connect.side_effect = [mock.MagicMock(), mock.MagicMock()] - builder = cli.main(cli_args=args) - assert builder.cursor.execute.call_count == cursor_calls - assert builder.pandas_cursor.execute.call_count == pandas_cursor_calls + mock_connection = mock.MagicMock() + normal_cursor = mock.MagicMock() + pandas_cursor = mock.MagicMock() + mock_connect.return_value = mock_connection + mock_connection.cursor.side_effect = [pandas_cursor, normal_cursor] + cli.main(cli_args=args) + assert normal_cursor.execute.call_count == cursor_calls + assert pandas_cursor.execute.call_count == pandas_cursor_calls @mock.patch("pathlib.PosixPath.mkdir") diff --git a/tests/test_data/duckdb_data/README.md b/tests/test_data/duckdb_data/README.md new file mode 100644 index 00000000..aa61256e --- /dev/null +++ b/tests/test_data/duckdb_data/README.md @@ -0,0 +1,4 @@ +This folder holds a small selection of results from Synthea. + +The selection is designed to be big enough to get past most of the 10-patient +bucketing cutoffs, while small enough to not overwhelm the repo with fake patient data. diff --git a/tests/test_data/duckdb_data/condition/conditions.ndjson b/tests/test_data/duckdb_data/condition/conditions.ndjson new file mode 100644 index 00000000..e5105f54 --- /dev/null +++ b/tests/test_data/duckdb_data/condition/conditions.ndjson @@ -0,0 +1,20 @@ +{"resourceType": "Condition", "id": "2902cab2-9b4c-0914-3770-375c1922b2be", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-condition-encounter-diagnosis"]}, "clinicalStatus": {"coding": [{"system": "http://terminology.hl7.org/CodeSystem/condition-clinical", "code": "resolved"}]}, "verificationStatus": {"coding": [{"system": "http://terminology.hl7.org/CodeSystem/condition-ver-status", "code": "confirmed"}]}, "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/condition-category", "code": "encounter-diagnosis", "display": "Encounter Diagnosis"}]}], "code": {"coding": [{"system": "http://snomed.info/sct", "code": "422650009", "display": "Social isolation (finding)"}], "text": "Social isolation (finding)"}, "subject": {"reference": "Patient/24906e2c-e556-71dc-23d9-3e1d5fb08986"}, "encounter": {"reference": "Encounter/1154d05c-8727-9373-4224-25b9fdba9ab3"}, "onsetDateTime": "2018-06-14T19:57:04-04:00", "abatementDateTime": "2019-06-20T19:53:30-04:00", "recordedDate": "2018-06-14T19:57:04-04:00"} +{"resourceType": "Condition", "id": "e42a4ee4-3751-0a77-2f0e-ef23efe809e4", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-condition-encounter-diagnosis"]}, "clinicalStatus": {"coding": [{"system": "http://terminology.hl7.org/CodeSystem/condition-clinical", "code": "resolved"}]}, "verificationStatus": {"coding": [{"system": "http://terminology.hl7.org/CodeSystem/condition-ver-status", "code": "confirmed"}]}, "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/condition-category", "code": "encounter-diagnosis", "display": "Encounter Diagnosis"}]}], "code": {"coding": [{"system": "http://snomed.info/sct", "code": "160903007", "display": "Full-time employment (finding)"}], "text": "Full-time employment (finding)"}, "subject": {"reference": "Patient/24906e2c-e556-71dc-23d9-3e1d5fb08986"}, "encounter": {"reference": "Encounter/1154d05c-8727-9373-4224-25b9fdba9ab3"}, "onsetDateTime": "2018-06-14T19:57:04-04:00", "abatementDateTime": "2019-06-20T19:53:30-04:00", "recordedDate": "2018-06-14T19:57:04-04:00"} +{"resourceType": "Condition", "id": "cd47a2f1-0790-a0bc-dc21-803a35b94f60", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-condition-encounter-diagnosis"]}, "clinicalStatus": {"coding": [{"system": "http://terminology.hl7.org/CodeSystem/condition-clinical", "code": "resolved"}]}, "verificationStatus": {"coding": [{"system": "http://terminology.hl7.org/CodeSystem/condition-ver-status", "code": "confirmed"}]}, "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/condition-category", "code": "encounter-diagnosis", "display": "Encounter Diagnosis"}]}], "code": {"coding": [{"system": "http://snomed.info/sct", "code": "10509002", "display": "Acute bronchitis (disorder)"}], "text": "Acute bronchitis (disorder)"}, "subject": {"reference": "Patient/7f941bcc-e7b2-99e1-585f-129d0ef1c13d"}, "encounter": {"reference": "Encounter/65f8fdca-a949-80a0-8072-094e9aaee474"}, "onsetDateTime": "2018-06-17T10:52:50-04:00", "abatementDateTime": "2018-06-28T11:16:28-04:00", "recordedDate": "2018-06-17T10:52:50-04:00"} +{"resourceType": "Condition", "id": "b6f8f751-fcdc-1cb8-a1e9-58b44e06e7f5", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-condition-encounter-diagnosis"]}, "clinicalStatus": {"coding": [{"system": "http://terminology.hl7.org/CodeSystem/condition-clinical", "code": "resolved"}]}, "verificationStatus": {"coding": [{"system": "http://terminology.hl7.org/CodeSystem/condition-ver-status", "code": "confirmed"}]}, "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/condition-category", "code": "encounter-diagnosis", "display": "Encounter Diagnosis"}]}], "code": {"coding": [{"system": "http://snomed.info/sct", "code": "73595000", "display": "Stress (finding)"}], "text": "Stress (finding)"}, "subject": {"reference": "Patient/8877ef1f-7cd7-3242-d7f0-73cf3f7165f4"}, "encounter": {"reference": "Encounter/299b6495-3fe7-8db3-c494-6e1ce8b7986d"}, "onsetDateTime": "2018-06-02T12:46:37-04:00", "abatementDateTime": "2018-06-30T12:41:01-04:00", "recordedDate": "2018-06-02T12:46:37-04:00"} +{"resourceType": "Condition", "id": "f1d8fe31-eafd-ab02-988c-5f9af674c005", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-condition-encounter-diagnosis"]}, "clinicalStatus": {"coding": [{"system": "http://terminology.hl7.org/CodeSystem/condition-clinical", "code": "resolved"}]}, "verificationStatus": {"coding": [{"system": "http://terminology.hl7.org/CodeSystem/condition-ver-status", "code": "confirmed"}]}, "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/condition-category", "code": "encounter-diagnosis", "display": "Encounter Diagnosis"}]}], "code": {"coding": [{"system": "http://snomed.info/sct", "code": "160903007", "display": "Full-time employment (finding)"}], "text": "Full-time employment (finding)"}, "subject": {"reference": "Patient/8877ef1f-7cd7-3242-d7f0-73cf3f7165f4"}, "encounter": {"reference": "Encounter/299b6495-3fe7-8db3-c494-6e1ce8b7986d"}, "onsetDateTime": "2018-06-02T12:46:37-04:00", "abatementDateTime": "2018-06-30T12:41:01-04:00", "recordedDate": "2018-06-02T12:46:37-04:00"} +{"resourceType": "Condition", "id": "37d6e6ce-f2fe-47be-5d9b-d071ad17d6d9", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-condition-encounter-diagnosis"]}, "clinicalStatus": {"coding": [{"system": "http://terminology.hl7.org/CodeSystem/condition-clinical", "code": "resolved"}]}, "verificationStatus": {"coding": [{"system": "http://terminology.hl7.org/CodeSystem/condition-ver-status", "code": "confirmed"}]}, "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/condition-category", "code": "encounter-diagnosis", "display": "Encounter Diagnosis"}]}], "code": {"coding": [{"system": "http://snomed.info/sct", "code": "195662009", "display": "Acute viral pharyngitis (disorder)"}], "text": "Acute viral pharyngitis (disorder)"}, "subject": {"reference": "Patient/19158de4-66a2-f70f-e3bf-4396b312c8f1"}, "encounter": {"reference": "Encounter/ed151e04-3dd6-8cb7-a3e5-777c8a8667f1"}, "onsetDateTime": "2018-06-05T22:02:28-04:00", "abatementDateTime": "2018-06-13T06:02:28-04:00", "recordedDate": "2018-06-05T22:02:28-04:00"} +{"resourceType": "Condition", "id": "16862137-0796-d625-f46a-3d0c6a04ab21", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-condition-encounter-diagnosis"]}, "clinicalStatus": {"coding": [{"system": "http://terminology.hl7.org/CodeSystem/condition-clinical", "code": "resolved"}]}, "verificationStatus": {"coding": [{"system": "http://terminology.hl7.org/CodeSystem/condition-ver-status", "code": "confirmed"}]}, "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/condition-category", "code": "encounter-diagnosis", "display": "Encounter Diagnosis"}]}], "code": {"coding": [{"system": "http://snomed.info/sct", "code": "160903007", "display": "Full-time employment (finding)"}], "text": "Full-time employment (finding)"}, "subject": {"reference": "Patient/c1bfec36-dc2c-afc8-c767-3d35ed2bf6f0"}, "encounter": {"reference": "Encounter/8ff1dc01-5a28-b2d8-3b42-4b7a7d539970"}, "onsetDateTime": "2018-07-15T13:22:50-04:00", "abatementDateTime": "2018-07-29T13:38:25-04:00", "recordedDate": "2018-07-15T13:22:50-04:00"} +{"resourceType": "Condition", "id": "9da05ddf-80b1-649e-84a0-716fadbc3a18", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-condition-encounter-diagnosis"]}, "clinicalStatus": {"coding": [{"system": "http://terminology.hl7.org/CodeSystem/condition-clinical", "code": "resolved"}]}, "verificationStatus": {"coding": [{"system": "http://terminology.hl7.org/CodeSystem/condition-ver-status", "code": "confirmed"}]}, "category": [{"coding": 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b/tests/test_data/duckdb_data/expected_export/core/core__count_documentreference_month.csv new file mode 100644 index 00000000..c50613f4 --- /dev/null +++ b/tests/test_data/duckdb_data/expected_export/core/core__count_documentreference_month.csv @@ -0,0 +1,19 @@ +cnt,author_month,enc_class_display,doc_type_display +50,,, +50,,,Evaluation + Plan note +50,,,Emergency department note +46,,ambulatory, +46,,ambulatory,Evaluation + Plan note +46,,ambulatory,Emergency department note +26,2018-07-01,, +26,2018-07-01,,Evaluation + Plan note +26,2018-07-01,,Emergency department note +24,2018-07-01,ambulatory, +24,2018-07-01,ambulatory,Evaluation + Plan note +24,2018-07-01,ambulatory,Emergency department note +24,2018-06-01,, +24,2018-06-01,,Evaluation + Plan note +24,2018-06-01,,Emergency department note +22,2018-06-01,ambulatory, +22,2018-06-01,ambulatory,Evaluation + Plan note +22,2018-06-01,ambulatory,Emergency department note \ No newline at end of file diff --git a/tests/test_data/duckdb_data/expected_export/core/core__count_encounter_month.csv b/tests/test_data/duckdb_data/expected_export/core/core__count_encounter_month.csv new file mode 100644 index 00000000..6242c76f --- /dev/null +++ b/tests/test_data/duckdb_data/expected_export/core/core__count_encounter_month.csv @@ -0,0 +1,65 @@ +cnt,start_month,enc_class_display,age_at_visit,gender,race_display,ethnicity_display +50,,,,,, +47,,,,,white, +46,,ambulatory,,,, +45,,,,,,not hispanic or latino +43,,,,,white,not hispanic or latino +43,,ambulatory,,,white, +42,,ambulatory,,,,not hispanic or latino +40,,ambulatory,,,white,not hispanic or latino +29,,,,female,, +28,,,,female,white, +27,,,,female,,not hispanic or latino +27,,ambulatory,,female,, +26,,,,female,white,not hispanic or latino +26,,ambulatory,,female,white, +26,2018-07-01,,,,, +26,2018-07-01,,,,white, +25,,ambulatory,,female,,not hispanic or latino +24,,ambulatory,,female,white,not hispanic or latino +24,2018-07-01,,,,,not hispanic or latino +24,2018-07-01,,,,white,not hispanic or latino +24,2018-07-01,ambulatory,,,, +24,2018-07-01,ambulatory,,,white, +24,2018-06-01,,,,, +23,2018-07-01,ambulatory,,,,not hispanic or latino +23,2018-07-01,ambulatory,,,white,not hispanic or latino +22,2018-06-01,ambulatory,,,, +21,,,,male,, +21,2018-06-01,,,,,not hispanic or latino +21,2018-06-01,,,,white, +19,,,,male,white, +19,,ambulatory,,male,, +19,2018-06-01,,,,white,not hispanic or latino +19,2018-06-01,ambulatory,,,,not hispanic or latino +19,2018-06-01,ambulatory,,,white, +18,,,,male,,not hispanic or latino +17,,,,male,white,not hispanic or latino +17,,ambulatory,,male,,not hispanic or latino +17,,ambulatory,,male,white, +17,2018-06-01,ambulatory,,,white,not hispanic or latino +16,,ambulatory,,male,white,not hispanic or latino +15,2018-06-01,,,female,, +14,2018-07-01,,,female,, +14,2018-07-01,,,female,,not hispanic or latino +14,2018-07-01,,,female,white, +14,2018-07-01,,,female,white,not hispanic or latino +14,2018-06-01,,,female,white, +14,2018-06-01,ambulatory,,female,, +13,2018-07-01,ambulatory,,female,, +13,2018-07-01,ambulatory,,female,,not hispanic or latino +13,2018-07-01,ambulatory,,female,white, +13,2018-07-01,ambulatory,,female,white,not hispanic or latino +13,2018-06-01,,,female,,not hispanic or latino +13,2018-06-01,ambulatory,,female,white, +12,2018-07-01,,,male,, +12,2018-07-01,,,male,white, +12,2018-06-01,,,female,white,not hispanic or latino +12,2018-06-01,ambulatory,,female,,not hispanic or latino +11,2018-07-01,ambulatory,,male,, +11,2018-07-01,ambulatory,,male,white, +11,2018-06-01,ambulatory,,female,white,not hispanic or latino +10,2018-07-01,,,male,,not hispanic or latino +10,2018-07-01,,,male,white,not hispanic or latino +10,2018-07-01,ambulatory,,male,,not hispanic or latino +10,2018-07-01,ambulatory,,male,white,not hispanic or latino \ No newline at end of file diff --git a/tests/test_data/duckdb_data/expected_export/core/core__count_encounter_type.csv b/tests/test_data/duckdb_data/expected_export/core/core__count_encounter_type.csv new file mode 100644 index 00000000..d5a1b912 --- /dev/null +++ b/tests/test_data/duckdb_data/expected_export/core/core__count_encounter_type.csv @@ -0,0 +1,9 @@ +cnt,enc_class_display,enc_type_display,enc_service_display,enc_priority_display +50,,,, +50,,,,None +50,,,None, +50,,,None,None +46,ambulatory,,, +46,ambulatory,,,None +46,ambulatory,,None, +46,ambulatory,,None,None \ No newline at end of file diff --git a/tests/test_data/duckdb_data/expected_export/core/core__count_encounter_type_month.csv b/tests/test_data/duckdb_data/expected_export/core/core__count_encounter_type_month.csv new file mode 100644 index 00000000..62079c0d --- /dev/null +++ b/tests/test_data/duckdb_data/expected_export/core/core__count_encounter_type_month.csv @@ -0,0 +1,25 @@ +cnt,enc_class_display,enc_type_display,enc_service_display,enc_priority_display,start_month +50,,,,, +50,,,,None, +50,,,None,, +50,,,None,None, +46,ambulatory,,,, +46,ambulatory,,,None, +46,ambulatory,,None,, +46,ambulatory,,None,None, +26,,,,,2018-07-01 +26,,,,None,2018-07-01 +26,,,None,,2018-07-01 +26,,,None,None,2018-07-01 +24,,,,,2018-06-01 +24,,,,None,2018-06-01 +24,,,None,,2018-06-01 +24,,,None,None,2018-06-01 +24,ambulatory,,,,2018-07-01 +24,ambulatory,,,None,2018-07-01 +24,ambulatory,,None,,2018-07-01 +24,ambulatory,,None,None,2018-07-01 +22,ambulatory,,,,2018-06-01 +22,ambulatory,,,None,2018-06-01 +22,ambulatory,,None,,2018-06-01 +22,ambulatory,,None,None,2018-06-01 \ No newline at end of file diff --git a/tests/test_data/duckdb_data/expected_export/core/core__count_medicationrequest_month.csv b/tests/test_data/duckdb_data/expected_export/core/core__count_medicationrequest_month.csv new file mode 100644 index 00000000..51a49fef --- /dev/null +++ b/tests/test_data/duckdb_data/expected_export/core/core__count_medicationrequest_month.csv @@ -0,0 +1,13 @@ +cnt,status,intent,authoredon_month,display +27,,,, +27,,order,, +26,stopped,,, +26,stopped,order,, +15,,,2018-07-01, +15,,order,2018-07-01, +15,stopped,,2018-07-01, +15,stopped,order,2018-07-01, +12,,,2018-06-01, +12,,order,2018-06-01, +11,stopped,,2018-06-01, +11,stopped,order,2018-06-01, \ No newline at end of file diff --git a/tests/test_data/duckdb_data/expected_export/core/core__count_observation_lab_month.csv b/tests/test_data/duckdb_data/expected_export/core/core__count_observation_lab_month.csv new file mode 100644 index 00000000..c23acb61 --- /dev/null +++ b/tests/test_data/duckdb_data/expected_export/core/core__count_observation_lab_month.csv @@ -0,0 +1,15 @@ +cnt,lab_month,lab_code,lab_result_display,enc_class_code +20,,,, +20,,,,AMB +10,,,Urine smell ammoniacal (finding), +10,,,Urine smell ammoniacal (finding),AMB +10,,,Brown color (qualifier value), +10,,,Brown color (qualifier value),AMB +10,,5778-6,, +10,,5778-6,,AMB +10,,5778-6,Brown color (qualifier value), +10,,5778-6,Brown color (qualifier value),AMB +10,,34533-0,, +10,,34533-0,,AMB +10,,34533-0,Urine smell ammoniacal (finding), +10,,34533-0,Urine smell ammoniacal (finding),AMB \ No newline at end of file diff --git a/tests/test_data/duckdb_data/expected_export/core/core__count_patient.csv b/tests/test_data/duckdb_data/expected_export/core/core__count_patient.csv new file mode 100644 index 00000000..580ed24b --- /dev/null +++ b/tests/test_data/duckdb_data/expected_export/core/core__count_patient.csv @@ -0,0 +1,13 @@ +cnt,age,gender,race_display,ethnicity_display +50,,,, +47,,,white, +45,,,,not hispanic or latino +43,,,white,not hispanic or latino +29,,female,, +28,,female,white, +27,,female,,not hispanic or latino +26,,female,white,not hispanic or latino +21,,male,, +19,,male,white, +18,,male,,not hispanic or latino +17,,male,white,not hispanic or latino \ No newline at end of file diff --git a/tests/test_data/duckdb_data/expected_export/core/core__meta_date.csv b/tests/test_data/duckdb_data/expected_export/core/core__meta_date.csv new file mode 100644 index 00000000..b54a75ca --- /dev/null +++ b/tests/test_data/duckdb_data/expected_export/core/core__meta_date.csv @@ -0,0 +1,2 @@ +min_date,max_date +2018-06-01,2018-07-31 \ No newline at end of file diff --git a/tests/test_data/duckdb_data/expected_export/core/core__meta_version.csv b/tests/test_data/duckdb_data/expected_export/core/core__meta_version.csv new file mode 100644 index 00000000..49bfa56c --- /dev/null +++ b/tests/test_data/duckdb_data/expected_export/core/core__meta_version.csv @@ -0,0 +1,2 @@ +data_package_version +2 diff --git a/tests/test_data/duckdb_data/medicationrequest/meds.ndjson b/tests/test_data/duckdb_data/medicationrequest/meds.ndjson new file mode 100644 index 00000000..34ecee1c --- /dev/null +++ b/tests/test_data/duckdb_data/medicationrequest/meds.ndjson @@ -0,0 +1,39 @@ +{"resourceType": "MedicationRequest", "id": "1066a8ec-d791-0f90-18ed-46e9db5c230a", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-medicationrequest"]}, "status": "stopped", "intent": "order", "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/medicationrequest-category", "code": "community", "display": "Community"}], "text": "Community"}], "medicationCodeableConcept": {"coding": [{"system": "http://www.nlm.nih.gov/research/umls/rxnorm", "code": "106892", "display": "insulin isophane, human 70 UNT/ML / insulin, regular, human 30 UNT/ML Injectable Suspension [Humulin]"}], "text": "insulin isophane, human 70 UNT/ML / insulin, regular, human 30 UNT/ML Injectable Suspension [Humulin]"}, "subject": {"reference": "Patient/9eaa056b-1efc-0cc8-70ff-62c8f704cc13"}, "encounter": {"reference": "Encounter/5c994000-aa78-2be5-e6cf-99f230d50c2f"}, "authoredOn": "2018-07-13T13:30:43-04:00", "requester": {"reference": "Practitioner?identifier=http://hl7.org/fhir/sid/us-npi|9999970798", "display": "Dr. Tamra871 Kerluke267"}, "reasonReference": [{"reference": "Condition/ffaab9ea-9839-a750-a1ed-9c3a472831e0", "display": "Prediabetes"}]} +{"resourceType": "MedicationRequest", "id": "3dd7628f-309e-48aa-f9c3-ef4ca336d7d0", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-medicationrequest"]}, "status": "stopped", "intent": "order", "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/medicationrequest-category", "code": "community", "display": "Community"}], "text": "Community"}], "medicationCodeableConcept": {"coding": [{"system": "http://www.nlm.nih.gov/research/umls/rxnorm", "code": "308136", "display": "amLODIPine 2.5 MG Oral Tablet"}], "text": "amLODIPine 2.5 MG Oral Tablet"}, "subject": {"reference": "Patient/9eaa056b-1efc-0cc8-70ff-62c8f704cc13"}, "encounter": {"reference": "Encounter/5c994000-aa78-2be5-e6cf-99f230d50c2f"}, "authoredOn": "2018-07-13T13:30:43-04:00", "requester": {"reference": "Practitioner?identifier=http://hl7.org/fhir/sid/us-npi|9999970798", "display": "Dr. Tamra871 Kerluke267"}, "reasonReference": [{"reference": "Condition/4b38f042-4e91-335d-7488-15fa989c8ac4", "display": "Essential hypertension (disorder)"}], "dosageInstruction": [{"sequence": 1, "timing": {"repeat": {"frequency": 1, "period": 1.0, "periodUnit": "d"}}, "asNeededBoolean": false, "doseAndRate": [{"type": {"coding": [{"system": "http://terminology.hl7.org/CodeSystem/dose-rate-type", "code": "ordered", "display": "Ordered"}]}, "doseQuantity": {"value": 1.0}}]}]} +{"resourceType": "MedicationRequest", "id": "3f33044e-7035-a01d-c5f9-030a7c027888", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-medicationrequest"]}, "status": "stopped", "intent": "order", "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/medicationrequest-category", "code": "community", "display": "Community"}], "text": "Community"}], "medicationCodeableConcept": {"coding": [{"system": "http://www.nlm.nih.gov/research/umls/rxnorm", "code": "314076", "display": "lisinopril 10 MG Oral Tablet"}], "text": "lisinopril 10 MG Oral Tablet"}, "subject": {"reference": "Patient/24906e2c-e556-71dc-23d9-3e1d5fb08986"}, "encounter": {"reference": "Encounter/1154d05c-8727-9373-4224-25b9fdba9ab3"}, "authoredOn": "2018-06-14T19:21:26-04:00", "requester": {"reference": "Practitioner?identifier=http://hl7.org/fhir/sid/us-npi|9999949198", "display": "Dr. Florance664 Leannon79"}, "reasonReference": [{"reference": "Condition/de0b2487-6095-f38e-ce77-da1093f4e67c", "display": "Essential hypertension (disorder)"}], "dosageInstruction": [{"sequence": 1, "timing": {"repeat": {"frequency": 1, "period": 1.0, "periodUnit": "d"}}, "asNeededBoolean": false, "doseAndRate": [{"type": {"coding": [{"system": "http://terminology.hl7.org/CodeSystem/dose-rate-type", "code": "ordered", "display": "Ordered"}]}, "doseQuantity": {"value": 1.0}}]}]} +{"resourceType": "MedicationRequest", "id": "48f27039-a404-e01f-1b25-0c747637a524", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-medicationrequest"]}, "status": "stopped", "intent": "order", "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/medicationrequest-category", "code": "community", "display": "Community"}], "text": "Community"}], "medicationCodeableConcept": {"coding": [{"system": "http://www.nlm.nih.gov/research/umls/rxnorm", "code": "308136", "display": "amLODIPine 2.5 MG Oral Tablet"}], "text": "amLODIPine 2.5 MG Oral Tablet"}, "subject": {"reference": "Patient/24906e2c-e556-71dc-23d9-3e1d5fb08986"}, "encounter": {"reference": "Encounter/1154d05c-8727-9373-4224-25b9fdba9ab3"}, "authoredOn": "2018-06-14T19:21:26-04:00", "requester": {"reference": "Practitioner?identifier=http://hl7.org/fhir/sid/us-npi|9999949198", "display": "Dr. Florance664 Leannon79"}, "reasonReference": [{"reference": "Condition/de0b2487-6095-f38e-ce77-da1093f4e67c", "display": "Essential hypertension (disorder)"}], "dosageInstruction": [{"sequence": 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"a34e6e99-2cf9-6f0b-8f1f-1af5742e9a99", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-medicationrequest"]}, "status": "stopped", "intent": "order", "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/medicationrequest-category", "code": "community", "display": "Community"}], "text": "Community"}], "medicationCodeableConcept": {"coding": [{"system": "http://www.nlm.nih.gov/research/umls/rxnorm", "code": "313782", "display": "Acetaminophen 325 MG Oral Tablet"}], "text": "Acetaminophen 325 MG Oral Tablet"}, "subject": {"reference": "Patient/7f941bcc-e7b2-99e1-585f-129d0ef1c13d"}, "encounter": {"reference": "Encounter/65f8fdca-a949-80a0-8072-094e9aaee474"}, "authoredOn": "2018-06-17T11:16:28-04:00", "requester": {"reference": "Practitioner?identifier=http://hl7.org/fhir/sid/us-npi|9999993691", "display": "Dr. Jacques50 Quigley282"}, "reasonReference": [{"reference": "Condition/5f7d91ec-026c-5bbe-4cbc-4f476d0b79be", "display": "Acute bronchitis (disorder)"}]} +{"resourceType": "MedicationRequest", "id": "a7a6a67e-de2a-44b5-97f2-a18f642a686b", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-medicationrequest"]}, "status": "stopped", "intent": "order", "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/medicationrequest-category", "code": "community", "display": "Community"}], "text": "Community"}], "medicationCodeableConcept": {"coding": [{"system": "http://www.nlm.nih.gov/research/umls/rxnorm", "code": "1000126", "display": "1 ML medroxyPROGESTERone acetate 150 MG/ML Injection"}], "text": "1 ML medroxyPROGESTERone acetate 150 MG/ML Injection"}, "subject": {"reference": "Patient/c20e5afd-30df-ac3d-6684-cc29438a9bc4"}, "encounter": {"reference": "Encounter/b864bcd8-14e0-8bec-b7cc-f8629d91470e"}, "authoredOn": "2018-06-28T02:22:49-04:00", "requester": {"reference": "Practitioner?identifier=http://hl7.org/fhir/sid/us-npi|9999997593", "display": "Dr. Felix524 Rogahn59"}} +{"resourceType": "MedicationRequest", "id": "e9d53e1d-3a31-4b3a-cb64-6382e74b5c09", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-medicationrequest"]}, "status": "stopped", "intent": "order", "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/medicationrequest-category", "code": "community", "display": "Community"}], "text": "Community"}], "medicationCodeableConcept": {"coding": [{"system": "http://www.nlm.nih.gov/research/umls/rxnorm", "code": "108515", "display": "1 ML tacrolimus 5 MG/ML Injection"}], "text": "1 ML tacrolimus 5 MG/ML Injection"}, "subject": {"reference": "Patient/9c8d8539-0b1e-73e2-b64f-83f1ea601fa4"}, "encounter": {"reference": "Encounter/f2752dd7-1bf1-739d-dd8c-40122d0b63bc"}, "authoredOn": "2018-06-01T20:27:06-04:00", "requester": {"reference": "Practitioner?identifier=http://hl7.org/fhir/sid/us-npi|9999987099", "display": "Dr. Trinidad33 King743"}, "reasonReference": [{"reference": 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"}, "extension": [{"url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race", "extension": [{"url": "ombCategory", "valueCoding": {"system": "urn:oid:2.16.840.1.113883.6.238", "code": "2054-5", "display": "Black or African American"}}, {"url": "text", "valueString": "Black or African American"}]}, {"url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity", "extension": [{"url": "ombCategory", "valueCoding": {"system": "urn:oid:2.16.840.1.113883.6.238", "code": "2186-5", "display": "Not Hispanic or Latino"}}, {"url": "text", "valueString": "Not Hispanic or Latino"}]}, {"url": "http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName", "valueString": "Maybelle917 Deckow585"}, {"url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex", "valueCode": "F"}, {"url": "http://hl7.org/fhir/StructureDefinition/patient-birthPlace", "valueAddress": {"city": "Kansas City", "state": "Kansas", "country": "US"}}, {"url": "http://synthetichealth.github.io/synthea/disability-adjusted-life-years", "valueDecimal": 0.0}, {"url": "http://synthetichealth.github.io/synthea/quality-adjusted-life-years", "valueDecimal": 19.0}], "identifier": [{"system": "https://github.com/synthetichealth/synthea", "value": "e80dda2c-a260-dbf7-3167-bf0945f3a91d"}, {"type": {"coding": [{"system": "http://terminology.hl7.org/CodeSystem/v2-0203", "code": "MR", "display": "Medical Record Number"}], "text": "Medical Record Number"}, "system": "http://hospital.smarthealthit.org", "value": "e80dda2c-a260-dbf7-3167-bf0945f3a91d"}, {"type": {"coding": [{"system": "http://terminology.hl7.org/CodeSystem/v2-0203", "code": "SS", "display": "Social Security Number"}], "text": "Social Security Number"}, "system": "http://hl7.org/fhir/sid/us-ssn", "value": "999-82-9398"}, {"type": {"coding": [{"system": "http://terminology.hl7.org/CodeSystem/v2-0203", "code": "DL", "display": "Driver's license number"}], "text": "Driver's license number"}, "system": "urn:oid:2.16.840.1.113883.4.3.25", "value": "S99957047"}], "name": [{"use": "official", "family": "Dicki44", "given": ["Cameron381", "Stacee229"], "prefix": ["Ms."]}], "telecom": [{"system": "phone", "value": "555-988-4378", "use": "home"}], "gender": "female", "birthDate": "2003-05-15", "address": [{"extension": [{"url": "http://hl7.org/fhir/StructureDefinition/geolocation", "extension": [{"url": "latitude", "valueDecimal": 37.59966545319182}, {"url": "longitude", "valueDecimal": -97.46092511479074}]}], "line": ["899 Rowe Boulevard"], "city": "Wichita", "state": "KS", "postalCode": "67219", "country": "US"}], "maritalStatus": {"coding": [{"system": "http://terminology.hl7.org/CodeSystem/v3-MaritalStatus", "code": "S", "display": "Never Married"}], "text": "Never Married"}, "multipleBirthBoolean": false, "communication": [{"language": {"coding": [{"system": "urn:ietf:bcp:47", "code": "en-US", "display": "English (United States)"}], "text": "English (United States)"}}]} +{"resourceType": "Patient", "id": "f9399f0d-5401-09f3-d4ff-89b1aa51b9c8", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient"]}, "text": {"status": "generated", "div": "
Generated by Synthea.Version identifier: dd1e3be\n . Person seed: 4182744072739949499 Population seed: 54321
"}, "extension": [{"url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race", "extension": [{"url": "ombCategory", "valueCoding": {"system": "urn:oid:2.16.840.1.113883.6.238", "code": "2106-3", "display": "White"}}, {"url": "text", "valueString": "White"}]}, {"url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity", "extension": [{"url": "ombCategory", "valueCoding": {"system": "urn:oid:2.16.840.1.113883.6.238", "code": "2186-5", "display": "Not Hispanic or Latino"}}, {"url": "text", "valueString": "Not Hispanic or Latino"}]}, {"url": "http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName", "valueString": "Twanna669 Murazik203"}, {"url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex", "valueCode": "M"}, {"url": "http://hl7.org/fhir/StructureDefinition/patient-birthPlace", "valueAddress": {"city": "Hays", "state": "Kansas", "country": "US"}}, {"url": "http://synthetichealth.github.io/synthea/disability-adjusted-life-years", "valueDecimal": 0.07035170871210875}, {"url": "http://synthetichealth.github.io/synthea/quality-adjusted-life-years", "valueDecimal": 19.92964829128789}], "identifier": [{"system": "https://github.com/synthetichealth/synthea", "value": "f9399f0d-5401-09f3-d4ff-89b1aa51b9c8"}, {"type": {"coding": [{"system": "http://terminology.hl7.org/CodeSystem/v2-0203", "code": "MR", "display": "Medical Record Number"}], "text": "Medical Record Number"}, "system": "http://hospital.smarthealthit.org", "value": "f9399f0d-5401-09f3-d4ff-89b1aa51b9c8"}, {"type": {"coding": [{"system": "http://terminology.hl7.org/CodeSystem/v2-0203", "code": "SS", "display": "Social Security Number"}], "text": "Social Security Number"}, "system": "http://hl7.org/fhir/sid/us-ssn", "value": "999-13-6002"}, {"type": {"coding": [{"system": "http://terminology.hl7.org/CodeSystem/v2-0203", "code": "DL", "display": "Driver's license number"}], "text": "Driver's license number"}, "system": "urn:oid:2.16.840.1.113883.4.3.25", "value": "S99970173"}, {"type": {"coding": [{"system": "http://terminology.hl7.org/CodeSystem/v2-0203", "code": "PPN", "display": "Passport Number"}], "text": "Passport Number"}, "system": "http://standardhealthrecord.org/fhir/StructureDefinition/passportNumber", "value": "X33028658X"}], "name": [{"use": "official", "family": "Kirlin939", "given": ["Brain142", "Lonny638"], "prefix": ["Mr."]}], "telecom": [{"system": "phone", "value": "555-601-3353", "use": "home"}], "gender": "male", "birthDate": "2002-03-08", "address": [{"extension": [{"url": "http://hl7.org/fhir/StructureDefinition/geolocation", "extension": [{"url": "latitude", "valueDecimal": 38.80044476921883}, {"url": "longitude", "valueDecimal": -97.61718325232847}]}], "line": ["106 Kilback Village Suite 72"], "city": "Salina", "state": "KS", "postalCode": "67401", "country": "US"}], "maritalStatus": {"coding": [{"system": "http://terminology.hl7.org/CodeSystem/v3-MaritalStatus", "code": "S", "display": "Never Married"}], "text": "Never Married"}, "multipleBirthInteger": 1, "communication": [{"language": {"coding": [{"system": "urn:ietf:bcp:47", "code": "en-US", "display": "English (United States)"}], "text": "English (United States)"}}]} diff --git a/tests/test_data/duckdb_data/patient/patient1.ndjson b/tests/test_data/duckdb_data/patient/patient1.ndjson new file mode 100644 index 00000000..394a68be --- /dev/null +++ b/tests/test_data/duckdb_data/patient/patient1.ndjson @@ -0,0 +1 @@ +{"resourceType": "Patient", "id": "0734762a-9db6-22fc-b595-c3e472bb2a9a", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient"]}, "text": {"status": "generated", "div": "
Generated by Synthea.Version identifier: dd1e3be\n . Person seed: 6849163071282260453 Population seed: 54321
"}, "extension": [{"url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race", "extension": [{"url": "ombCategory", "valueCoding": {"system": "urn:oid:2.16.840.1.113883.6.238", "code": "2106-3", "display": "White"}}, {"url": "text", "valueString": "White"}]}, {"url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity", "extension": [{"url": "ombCategory", "valueCoding": {"system": "urn:oid:2.16.840.1.113883.6.238", "code": "2186-5", "display": "Not Hispanic or Latino"}}, {"url": "text", "valueString": "Not Hispanic or Latino"}]}, {"url": "http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName", "valueString": "Willodean275 Predovic534"}, {"url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex", "valueCode": "F"}, {"url": "http://hl7.org/fhir/StructureDefinition/patient-birthPlace", "valueAddress": {"city": "Lawrence", "state": "Kansas", "country": "US"}}, {"url": "http://synthetichealth.github.io/synthea/disability-adjusted-life-years", "valueDecimal": 0.3108091009970718}, {"url": "http://synthetichealth.github.io/synthea/quality-adjusted-life-years", "valueDecimal": 19.689190899002927}], "identifier": [{"system": "https://github.com/synthetichealth/synthea", "value": "0734762a-9db6-22fc-b595-c3e472bb2a9a"}, {"type": {"coding": [{"system": "http://terminology.hl7.org/CodeSystem/v2-0203", "code": "MR", "display": "Medical Record Number"}], "text": "Medical Record Number"}, "system": "http://hospital.smarthealthit.org", "value": "0734762a-9db6-22fc-b595-c3e472bb2a9a"}, {"type": {"coding": [{"system": "http://terminology.hl7.org/CodeSystem/v2-0203", "code": "SS", "display": "Social Security Number"}], "text": "Social Security Number"}, "system": "http://hl7.org/fhir/sid/us-ssn", "value": "999-89-4169"}, {"type": {"coding": [{"system": "http://terminology.hl7.org/CodeSystem/v2-0203", "code": "DL", "display": "Driver's license number"}], "text": "Driver's license number"}, "system": "urn:oid:2.16.840.1.113883.4.3.25", "value": "S99986210"}, {"type": {"coding": [{"system": "http://terminology.hl7.org/CodeSystem/v2-0203", "code": "PPN", "display": "Passport Number"}], "text": "Passport Number"}, "system": "http://standardhealthrecord.org/fhir/StructureDefinition/passportNumber", "value": "X16797661X"}], "name": [{"use": "official", "family": "Kerluke267", "given": ["Marni913", "Scarlett814"], "prefix": ["Ms."]}], "telecom": [{"system": "phone", "value": "555-100-2596", "use": "home"}], "gender": "female", "birthDate": "2002-12-21", "address": [{"extension": [{"url": "http://hl7.org/fhir/StructureDefinition/geolocation", "extension": [{"url": "latitude", "valueDecimal": 37.62901746670738}, {"url": "longitude", "valueDecimal": -97.55651294281942}]}], "line": ["342 Wilderman Gateway"], "city": "Wichita", "state": "KS", "postalCode": "67226", "country": "US"}], "maritalStatus": {"coding": [{"system": "http://terminology.hl7.org/CodeSystem/v3-MaritalStatus", "code": "S", "display": "Never Married"}], "text": "Never Married"}, "multipleBirthBoolean": false, "communication": [{"language": {"coding": [{"system": "urn:ietf:bcp:47", "code": "en-US", "display": "English (United States)"}], "text": "English (United States)"}}]} diff --git a/tests/test_duckdb.py b/tests/test_duckdb.py new file mode 100644 index 00000000..477f54d2 --- /dev/null +++ b/tests/test_duckdb.py @@ -0,0 +1,44 @@ +""" tests for duckdb backend support """ + +import glob +import os +import tempfile +from pathlib import Path + +from cumulus_library import cli + + +def test_duckdb_core_build_and_export(): + data_dir = f"{Path(__file__).parent}/test_data/duckdb_data" + + with tempfile.TemporaryDirectory() as tmpdir: + cli.main( + [ + "build", + "--target=core", + "--db-type=duckdb", + f"--database={tmpdir}/duck.db", + f"--load-ndjson-dir={data_dir}", + ] + ) + cli.main( + [ + "export", + "--target=core", + "--db-type=duckdb", + f"--database={tmpdir}/duck.db", + f"{tmpdir}/counts", + ] + ) + + # Now check each csv file - we'll assume the parquest are alright + csv_files = glob.glob(f"{tmpdir}/counts/core/*.csv") + for csv_file in csv_files: + basename = Path(csv_file).name + with open(csv_file, encoding="utf8") as f: + generated = f.read().strip() + with open( + f"{data_dir}/expected_export/core/{basename}", encoding="utf8" + ) as f: + expected = f.read().strip() + assert generated == expected, basename diff --git a/tests/test_study_parser.py b/tests/test_study_parser.py index 9d16dcbb..dc7c3643 100644 --- a/tests/test_study_parser.py +++ b/tests/test_study_parser.py @@ -94,7 +94,7 @@ def test_clean_study(mock_output, schema, verbose, prefix, confirm, query_res, r with raises: with mock.patch.object(builtins, "input", lambda _: confirm): mock_cursor = mock.MagicMock() - mock_cursor.__iter__.return_value = [[query_res]] + mock_cursor.fetchall.return_value = [[query_res]] parser = StudyManifestParser("./tests/test_data/study_valid/") tables = parser.clean_study(mock_cursor, schema, verbose, prefix=prefix) diff --git a/tests/test_template_utils.py b/tests/test_template_utils.py index b23129b8..3e312805 100644 --- a/tests/test_template_utils.py +++ b/tests/test_template_utils.py @@ -1,13 +1,14 @@ """ tests for the cli interface to studies """ from unittest import mock -from rich.progress import Progress import pyathena import pytest -from cumulus_library.helper import get_progress_bar -from cumulus_library.template_sql.utils import is_codeable_concept_populated +from cumulus_library.template_sql.utils import ( + is_codeable_concept_array_populated, + is_codeable_concept_populated, +) REGION = "us-east-1" WORKGROUP = "test_wg" @@ -16,53 +17,53 @@ @mock.patch("pyathena.connect") @pytest.mark.parametrize( - "query_results,expected", + "query_results,allow_partial,expected", [ - ((("foo"), (["coding"]), ("baz")), True), - ((("foo"), (["coding"]), None), False), - ((("foo"), (["varchar"]), None), False), - ((None, (["varchar"]), None), False), + ((("foo"), (["coding"]), ("baz")), True, True), + ((("foo"), (["coding"]), ("baz")), False, False), + ((("foo"), (["coding, code, system, display"]), ("baz")), False, True), + ((("foo"), (["coding"]), None), True, False), + ((("foo"), (["varchar"]), None), True, False), + ((None, (["varchar"]), None), True, False), ], ) -def test_is_codeable_concept_populated(mock_pyathena, query_results, expected): +def test_is_codeable_concept_populated( + _mock_pyathena, query_results, allow_partial, expected +): cursor = pyathena.connect( region_name=REGION, work_group=WORKGROUP, schema_name=SCHEMA, ).cursor() cursor.fetchone.side_effect = query_results - progress = Progress() - with get_progress_bar(transient=True) as progress: - task = progress.add_task( - "test_task", - total=3, - ) - res = is_codeable_concept_populated(SCHEMA, "table", "base_col", cursor) + res = is_codeable_concept_populated( + SCHEMA, "table", "base_col", cursor, allow_partial=allow_partial + ) assert res == expected @mock.patch("pyathena.connect") @pytest.mark.parametrize( - "query_results,expected", + "query_results,allow_partial,expected", [ - ((("foo"), (["coding"]), ("baz")), True), - ((("foo"), (["coding"]), None), False), - ((("foo"), (["varchar"]), None), False), - ((None, (["varchar"]), None), False), + ((("foo"), (["coding"]), ("baz")), True, True), + ((("foo"), (["coding"]), ("baz")), False, False), + ((("foo"), (["coding, code, system, display"]), ("baz")), False, True), + ((("foo"), (["coding"]), None), True, False), + ((("foo"), (["varchar"]), None), True, False), + ((None, (["varchar"]), None), True, False), ], ) -def test_is_codeable_concept_array_populated(mock_pyathena, query_results, expected): +def test_is_codeable_concept_array_populated( + _mock_pyathena, query_results, allow_partial, expected +): cursor = pyathena.connect( region_name=REGION, work_group=WORKGROUP, schema_name=SCHEMA, ).cursor() cursor.fetchone.side_effect = query_results - progress = Progress() - with get_progress_bar(transient=True) as progress: - task = progress.add_task( - "test_task", - total=3, - ) - res = is_codeable_concept_populated(SCHEMA, "table", "base_col", cursor) + res = is_codeable_concept_array_populated( + SCHEMA, "table", "base_col", cursor, allow_partial=allow_partial + ) assert res == expected diff --git a/tests/test_templates.py b/tests/test_templates.py index 3552c46e..2370b1f1 100644 --- a/tests/test_templates.py +++ b/tests/test_templates.py @@ -158,7 +158,7 @@ def test_get_column_datatype_query(): WHERE table_schema = 'schema_name' AND table_name = 'table_name' - AND column_name = 'column_name'""" + AND LOWER(column_name) = 'column_name'""" query = get_column_datatype_query( schema_name="schema_name",