From d01f9d628fcfc2a68d1ec5e6af4d32e4a67706f2 Mon Sep 17 00:00:00 2001 From: Marigold Date: Wed, 10 Jul 2024 10:33:27 +0200 Subject: [PATCH 1/6] :sparkles: use async when upserting to grapher --- apps/backport/datasync/data_metadata.py | 42 +- apps/backport/datasync/datasync.py | 24 + apps/chart_sync/admin_api.py | 60 +- etl/command.py | 10 +- etl/config.py | 4 - etl/db.py | 227 +- etl/grapher_helpers.py | 168 +- etl/grapher_import.py | 246 +- etl/grapher_model.py | 667 +- etl/steps/__init__.py | 16 +- .../biodiversity/2024-01-25/cherry_blossom.py | 3 + lib/catalog/owid/catalog/meta.py | 33 +- lib/catalog/owid/catalog/s3_utils.py | 14 +- lib/catalog/owid/catalog/utils.py | 10 + poetry.lock | 8870 +++++++++++++++++ pyproject.toml | 4 +- tests/test_grapher_helpers.py | 53 +- 17 files changed, 10159 insertions(+), 292 deletions(-) create mode 100644 poetry.lock diff --git a/apps/backport/datasync/data_metadata.py b/apps/backport/datasync/data_metadata.py index 1707164e42a..f2c674234d4 100644 --- a/apps/backport/datasync/data_metadata.py +++ b/apps/backport/datasync/data_metadata.py @@ -24,7 +24,7 @@ def variable_data(data_df: pd.DataFrame) -> Dict[str, Any]: return data # type: ignore -def _load_variable(session: Session, variable_id: int) -> Dict[str, Any]: +async def _load_variable(session: AsyncSession, variable_id: int) -> Dict[str, Any]: sql = """ SELECT variables.*, @@ -41,14 +41,14 @@ def _load_variable(session: Session, variable_id: int) -> Dict[str, Any]: """ # Using the session to execute raw SQL and fetching one row as a result - result = session.execute(text(sql), {"variable_id": variable_id}).fetchone() + result = (await session.execute(text(sql), {"variable_id": variable_id})).fetchone() # Ensure result exists and convert to dictionary assert result, f"variableId `{variable_id}` not found" return dict(result._mapping) -def _load_topic_tags(session: Session, variable_id: int) -> List[str]: +async def _load_topic_tags(session: AsyncSession, variable_id: int) -> List[str]: sql = """ SELECT tags.name @@ -59,13 +59,13 @@ def _load_topic_tags(session: Session, variable_id: int) -> List[str]: """ # Using the session to execute raw SQL - result = session.execute(text(sql), {"variable_id": variable_id}).fetchall() + result = (await session.execute(text(sql), {"variable_id": variable_id})).fetchall() # Extract tag names from the result and return as a list return [row[0] for row in result] -def _load_faqs(session: Session, variable_id: int) -> List[Dict[str, Any]]: +async def _load_faqs(session: AsyncSession, variable_id: int) -> List[Dict[str, Any]]: sql = """ SELECT gdocId, @@ -76,13 +76,13 @@ def _load_faqs(session: Session, variable_id: int) -> List[Dict[str, Any]]: """ # Using the session to execute raw SQL - result = session.execute(text(sql), {"variable_id": variable_id}).fetchall() + result = (await session.execute(text(sql), {"variable_id": variable_id})).fetchall() # Convert the result rows to a list of dictionaries return [dict(row._mapping) for row in result] -def _load_origins_df(session: Session, variable_id: int) -> pd.DataFrame: +async def _load_origins_df(session: AsyncSession, variable_id: int) -> pd.DataFrame: sql = """ SELECT origins.* @@ -93,7 +93,7 @@ def _load_origins_df(session: Session, variable_id: int) -> pd.DataFrame: """ # Use the session to execute the raw SQL - result_proxy = session.execute(text(sql), {"variable_id": variable_id}) + result_proxy = await session.execute(text(sql), {"variable_id": variable_id}) # Fetch the results into a DataFrame df = pd.DataFrame(result_proxy.fetchall(), columns=result_proxy.keys()) @@ -212,12 +212,17 @@ def _variable_metadata( return variableMetadata -def _move_population_origin_to_end(origins: List[Dict[str, Any]]) -> List[Dict[str, Any]]: +def _move_population_origin_to_end( + origins: List[Dict[str, Any]], +) -> List[Dict[str, Any]]: """Move population origin to the end of the list of origins. This way it gets displayed last on data page.""" new_origins = [] pop_origin = None for origin in origins: - if origin.get("title") == "Population" and origin.get("producer") == "Various sources": + if ( + origin.get("title") == "Population" + and origin.get("producer") == "Various sources" + ): pop_origin = origin else: new_origins.append(origin) @@ -226,17 +231,24 @@ def _move_population_origin_to_end(origins: List[Dict[str, Any]]) -> List[Dict[s return new_origins -def variable_metadata(session: Session, variable_id: int, variable_data: pd.DataFrame) -> Dict[str, Any]: +async def variable_metadata( + session: AsyncSession, variable_id: int, variable_data: pd.DataFrame +) -> Dict[str, Any]: """Fetch metadata for a single variable from database. This function was initially based on the one from owid-grapher repository and uses raw SQL commands. It'd be interesting to rewrite it using SQLAlchemy ORM in grapher_model.py. """ + task_variable = _load_variable(session, variable_id) + task_origins = _load_origins_df(session, variable_id) + task_topic_tags = _load_topic_tags(session, variable_id) + task_faqs = _load_faqs(session, variable_id) + return _variable_metadata( - db_variable_row=_load_variable(session, variable_id), + db_variable_row=await task_variable, variable_data=variable_data, - db_origins_df=_load_origins_df(session, variable_id), - db_topic_tags=_load_topic_tags(session, variable_id), - db_faqs=_load_faqs(session, variable_id), + db_origins_df=await task_origins, + db_topic_tags=await task_topic_tags, + db_faqs=await task_faqs, ) diff --git a/apps/backport/datasync/datasync.py b/apps/backport/datasync/datasync.py index a5c9a63c537..552203cab1b 100644 --- a/apps/backport/datasync/datasync.py +++ b/apps/backport/datasync/datasync.py @@ -1,3 +1,4 @@ +import asyncio import gzip import json from typing import Any, Dict @@ -17,6 +18,9 @@ config.enable_bugsnag() +R2_UPLOAD_SEMAPHORE = asyncio.Semaphore(10) + + def upload_gzip_dict(d: Dict[str, Any], s3_path: str, private: bool = False) -> None: return upload_gzip_string(json.dumps(d, default=str), s3_path=s3_path, private=private) @@ -46,3 +50,23 @@ def upload_gzip_string(s: str, s3_path: str, private: bool = False) -> None: ContentType="application/json", **extra_args, ) + + +async def upload_gzip_string_async(client: Any, s: str, s3_path: str, private: bool = False) -> None: + """Upload compressed dictionary to S3 and return its URL.""" + body_gzip = gzip.compress(s.encode()) + + bucket, key = s3_utils.s3_bucket_key(s3_path) + + assert not private, "r2 does not support private files yet" + extra_args = {} + + async with R2_UPLOAD_SEMAPHORE: + await client.put_object( + Bucket=bucket, + Body=body_gzip, + Key=key, + ContentEncoding="gzip", + ContentType="application/json", + **extra_args, + ) diff --git a/apps/chart_sync/admin_api.py b/apps/chart_sync/admin_api.py index 5dd3f73eefd..697ae962dbc 100644 --- a/apps/chart_sync/admin_api.py +++ b/apps/chart_sync/admin_api.py @@ -6,6 +6,7 @@ from functools import cache from typing import Any, Dict, List, Optional +import aiohttp import requests import structlog from requests.adapters import HTTPAdapter, Retry @@ -25,7 +26,9 @@ def is_502_error(exception): class AdminAPI(object): - def __init__(self, owid_env: OWIDEnv, grapher_user_id: Optional[int] = GRAPHER_USER_ID): + def __init__( + self, owid_env: OWIDEnv, grapher_user_id: Optional[int] = GRAPHER_USER_ID + ): self.owid_env = owid_env self.session_id = create_session_id(owid_env, grapher_user_id) @@ -64,7 +67,9 @@ def create_chart(self, chart_config: dict, user_id: Optional[int] = None) -> dic raise AdminAPIError({"error": js["error"], "chart_config": chart_config}) return js - def update_chart(self, chart_id: int, chart_config: dict, user_id: Optional[int] = None) -> dict: + def update_chart( + self, chart_id: int, chart_config: dict, user_id: Optional[int] = None + ) -> dict: resp = requests.put( f"{self.owid_env.admin_api}/charts/{chart_id}", cookies={"sessionid": self._get_session_id(user_id)}, @@ -75,7 +80,9 @@ def update_chart(self, chart_id: int, chart_config: dict, user_id: Optional[int] raise AdminAPIError({"error": js["error"], "chart_config": chart_config}) return js - def set_tags(self, chart_id: int, tags: List[Dict[str, Any]], user_id: Optional[int] = None) -> dict: + def set_tags( + self, chart_id: int, tags: List[Dict[str, Any]], user_id: Optional[int] = None + ) -> dict: resp = requests.post( f"{self.owid_env.admin_api}/charts/{chart_id}/setTags", cookies={"sessionid": self._get_session_id(user_id)}, @@ -86,7 +93,9 @@ def set_tags(self, chart_id: int, tags: List[Dict[str, Any]], user_id: Optional[ raise AdminAPIError({"error": js["error"], "tags": tags}) return js - def put_grapher_config(self, variable_id: int, grapher_config: Dict[str, Any]) -> dict: + def put_grapher_config( + self, variable_id: int, grapher_config: Dict[str, Any] + ) -> dict: # If schema is missing, use the default one grapher_config.setdefault("$schema", DEFAULT_GRAPHER_SCHEMA) @@ -98,9 +107,31 @@ def put_grapher_config(self, variable_id: int, grapher_config: Dict[str, Any]) - ) js = self._json_from_response(resp) if not js["success"]: - raise AdminAPIError({"error": js["error"], "variable_id": variable_id, "grapher_config": grapher_config}) + raise AdminAPIError( + { + "error": js["error"], + "variable_id": variable_id, + "grapher_config": grapher_config, + } + ) return js + async def put_grapher_config( + self, variable_id: int, grapher_config: Dict[str, Any] + ) -> dict: + async with aiohttp.ClientSession( + cookies={"sessionid": self.session_id} + ) as session: + async with session.put( + self.base_url + f"/admin/api/variables/{variable_id}/grapherConfigETL", + json=grapher_config, + ) as resp: + # TODO: make _json_from_response async + js = await resp.json() + assert js["success"] + return js + + # TODO: make it async def delete_grapher_config(self, variable_id: int) -> dict: resp = requests.delete( self.owid_env.admin_api + f"/variables/{variable_id}/grapherConfigETL", @@ -111,7 +142,9 @@ def delete_grapher_config(self, variable_id: int) -> dict: raise AdminAPIError({"error": js["error"], "variable_id": variable_id}) return js - def put_mdim_config(self, slug: str, mdim_config: dict, user_id: Optional[int] = None) -> dict: + def put_mdim_config( + self, slug: str, mdim_config: dict, user_id: Optional[int] = None + ) -> dict: # Retry in case we're restarting Admin on staging server resp = requests_with_retry().put( self.owid_env.admin_api + f"/multi-dim/{slug}", @@ -120,7 +153,9 @@ def put_mdim_config(self, slug: str, mdim_config: dict, user_id: Optional[int] = ) js = self._json_from_response(resp) if not js["success"]: - raise AdminAPIError({"error": js["error"], "slug": slug, "mdim_config": mdim_config}) + raise AdminAPIError( + {"error": js["error"], "slug": slug, "mdim_config": mdim_config} + ) return js @@ -153,7 +188,9 @@ def _generate_random_string(length=32) -> str: return result_str -def _create_user_session(session: Session, user_email: str, expiration_seconds=3600) -> str: +def _create_user_session( + session: Session, user_email: str, expiration_seconds=3600 +) -> str: """Create a new short-lived session for given user and return its session id.""" # Generate a random string session_key = _generate_random_string() @@ -161,7 +198,9 @@ def _create_user_session(session: Session, user_email: str, expiration_seconds=3 json_str = json.dumps({"user_email": user_email}) # Base64 encode - session_data = base64.b64encode(("prefix:" + json_str).encode("utf-8")).decode("utf-8") + session_data = base64.b64encode(("prefix:" + json_str).encode("utf-8")).decode( + "utf-8" + ) query = text( """ @@ -174,7 +213,8 @@ def _create_user_session(session: Session, user_email: str, expiration_seconds=3 params={ "session_key": session_key, "session_data": session_data, - "expire_date": dt.datetime.utcnow() + dt.timedelta(seconds=expiration_seconds), + "expire_date": dt.datetime.utcnow() + + dt.timedelta(seconds=expiration_seconds), }, ) diff --git a/etl/command.py b/etl/command.py index c70b8ec046c..ae9a99badd3 100644 --- a/etl/command.py +++ b/etl/command.py @@ -191,14 +191,9 @@ def main_cli( # make everything single threaded, useful for debugging if not use_threads: - config.GRAPHER_INSERT_WORKERS = 1 config.DIRTY_STEPS_WORKERS = 1 workers = 1 - # GRAPHER_INSERT_WORKERS should be split among workers - if workers > 1: - config.GRAPHER_INSERT_WORKERS = config.GRAPHER_INSERT_WORKERS // workers - kwargs = dict( steps=steps, dry_run=dry_run, @@ -223,7 +218,6 @@ def main_cli( for _ in runs: if ipdb: config.IPDB_ENABLED = True - config.GRAPHER_INSERT_WORKERS = 1 config.DIRTY_STEPS_WORKERS = 1 kwargs["workers"] = 1 with launch_ipdb_on_exception(): @@ -384,9 +378,7 @@ def run_dag( ) return exec_steps(steps, strict=strict) else: - print( - f"--- Running {len(steps)} steps with {workers} processes ({config.GRAPHER_INSERT_WORKERS} threads each):" - ) + print(f"--- Running {len(steps)} steps with {workers} processes:") return exec_steps_parallel(steps, workers, dag=dag, strict=strict) diff --git a/etl/config.py b/etl/config.py index 25d03772b24..d03b49faffc 100644 --- a/etl/config.py +++ b/etl/config.py @@ -178,10 +178,6 @@ def variable_metadata_url(variable_id): # because we're making a lot of HTTP requests DIRTY_STEPS_WORKERS = int(env.get("DIRTY_STEPS_WORKERS", 5)) -# number of workers for grapher inserts to DB, this is for all processes, so if -# --workers is higher than 1, this will be divided among them -GRAPHER_INSERT_WORKERS = int(env.get("GRAPHER_WORKERS", 40)) - # only upsert indicators matching this filter, this is useful for fast development # of data pages for a single indicator GRAPHER_FILTER = env.get("GRAPHER_FILTER", None) diff --git a/etl/db.py b/etl/db.py index a1b40706eb1..5a07cdf0506 100644 --- a/etl/db.py +++ b/etl/db.py @@ -10,6 +10,7 @@ from deprecated import deprecated from sqlalchemy import create_engine from sqlalchemy.engine import Engine +from sqlalchemy.ext.asyncio import AsyncEngine, create_async_engine from sqlalchemy.orm import Session from etl import config @@ -25,7 +26,9 @@ def can_connect(conf: Optional[Dict[str, Any]] = None) -> bool: return False -@deprecated("This function is deprecated. Instead, look at using etl.db.read_sql function.") +@deprecated( + "This function is deprecated. Instead, look at using etl.db.read_sql function." +) def get_connection(conf: Optional[Dict[str, Any]] = None) -> pymysql.Connection: "Connect to the Grapher database." cf: Any = dict_to_object(conf) if conf else config @@ -61,11 +64,219 @@ def get_engine(conf: Optional[Dict[str, Any]] = None) -> Engine: return _get_engine_cached(cf, pid) +def get_engine_async(conf: Optional[Dict[str, Any]] = None) -> AsyncEngine: + cf: Any = dict_to_object(conf) if conf else config + engine = create_async_engine( + f"mysql+aiomysql://{cf.DB_USER}:{quote(cf.DB_PASS)}@{cf.DB_HOST}:{cf.DB_PORT}/{cf.DB_NAME}", + pool_size=30, # Increase pool size + max_overflow=50, # Increase overflow limit + ) + return engine + + +def get_dataset_id( + dataset_name: str, + db_conn: Optional[pymysql.Connection] = None, + version: Optional[str] = None, +) -> Any: + """Get the dataset ID of a specific dataset name from database. + + If more than one dataset is found for the same name, or if no dataset is found, an error is raised. + + Parameters + ---------- + dataset_name : str + Dataset name. + db_conn : pymysql.Connection + Connection to database. Defaults to None, in which case a default connection is created (uses etl.config). + version : str + ETL version of the dataset. This is necessary when multiple datasets have the same title. In such a case, if + version is not given, the function will raise an error. + + Returns + ------- + dataset_id : int + Dataset ID. + + """ + if db_conn is None: + db_conn = get_connection() + + query = f""" + SELECT id + FROM datasets + WHERE name = '{dataset_name}' + """ + + if version: + query += f" AND version = '{version}'" + + with db_conn.cursor() as cursor: + cursor.execute(query) + result = cursor.fetchall() + + assert len(result) == 1, f"Ambiguous or unknown dataset name '{dataset_name}'" + dataset_id = result[0][0] + return dataset_id + + +def get_variables_in_dataset( + dataset_id: int, + only_used_in_charts: bool = False, + db_conn: Optional[pymysql.Connection] = None, +) -> Any: + """Get all variables data for a specific dataset ID from database. + + Parameters + ---------- + dataset_id : int + Dataset ID. + only_used_in_charts : bool + True to select variables only if they have been used in at least one chart. False to select all variables. + db_conn : pymysql.Connection + Connection to database. Defaults to None, in which case a default connection is created (uses etl.config). + + Returns + ------- + variables_data : pd.DataFrame + Variables data for considered dataset. + + """ + if db_conn is None: + db_conn = get_connection() + + query = f""" + SELECT * + FROM variables + WHERE datasetId = {dataset_id} + """ + if only_used_in_charts: + query += """ + AND id IN ( + SELECT DISTINCT variableId + FROM chart_dimensions + ) + """ + with warnings.catch_warnings(): + warnings.simplefilter("ignore", UserWarning) + variables_data = pd.read_sql(query, con=db_conn) + return variables_data + + +def _get_variables_data_with_filter( + field_name: Optional[str] = None, + field_values: Optional[List[Any]] = None, + db_conn: Optional[pymysql.Connection] = None, +) -> Any: + if db_conn is None: + db_conn = get_connection() + + if field_values is None: + field_values = [] + + # Construct the SQL query with a placeholder for each value in the list. + query = "SELECT * FROM variables" + + if (field_name is not None) and (len(field_values) > 0): + query += f"\nWHERE {field_name} IN ({', '.join(['%s'] * len(field_values))});" + + # Execute the query. + with warnings.catch_warnings(): + warnings.simplefilter("ignore", UserWarning) + variables_data = pd.read_sql(query, con=db_conn, params=field_values) + + assert set(variables_data[field_name]) <= set( + field_values + ), f"Unexpected values for {field_name}." + + # Warn about values that were not found. + missing_values = set(field_values) - set(variables_data[field_name]) + if len(missing_values) > 0: + log.warning(f"Values of {field_name} not found in database: {missing_values}") + + return variables_data + + +def get_variables_data( + filter: Optional[Dict[str, Any]] = None, + condition: Optional[str] = "OR", + db_conn: Optional[pymysql.Connection] = None, +) -> pd.DataFrame: + """Get data from variables table, given a certain condition. + + Parameters + ---------- + filter : Optional[Dict[str, Any]], optional + Filter to apply to the data, which must contain a field name and a list of field values, + e.g. {"id": [123456, 234567, 345678]}. + In principle, multiple filters can be given. + condition : Optional[str], optional + In case multiple filters are given, this parameter specifies whether the output filters should be the union + ("OR") or the intersection ("AND"). + db_conn : pymysql.Connection + Connection to database. Defaults to None, in which case a default connection is created (uses etl.config). + + Returns + ------- + df : pd.DataFrame + Variables data. + + """ + # NOTE: This function should be optimized. Instead of fetching data for each filter, their conditions should be + # combined with OR or AND before executing the query. + + # Initialize an empty dataframe. + if filter is not None: + df = pd.DataFrame({"id": []}).astype({"id": int}) + for field_name, field_values in filter.items(): + _df = _get_variables_data_with_filter( + field_name=field_name, field_values=field_values, db_conn=db_conn + ) + if condition == "OR": + df = pd.concat([df, _df], axis=0) + elif condition == "AND": + df = pd.merge(df, _df, on="id", how="inner") + else: + raise ValueError(f"Invalid condition: {condition}") + else: + # Fetch data for all variables. + df = _get_variables_data_with_filter(db_conn=db_conn) + + return df + + +def get_all_datasets( + archived: bool = True, db_conn: Optional[pymysql.Connection] = None +) -> pd.DataFrame: + """Get all datasets in database. + + Parameters + ---------- + db_conn : pymysql.connections.Connection + Connection to database. Defaults to None, in which case a default connection is created (uses etl.config). + + Returns + ------- + datasets : pd.DataFrame + All datasets in database. Table with three columns: dataset ID, dataset name, dataset namespace. + """ + if db_conn is None: + db_conn = get_connection() + + query = " SELECT namespace, name, id, updatedAt FROM datasets" + if not archived: + query += " WHERE isArchived = 0" + datasets = pd.read_sql(query, con=db_conn) + return datasets.sort_values(["name", "namespace"]) + + def dict_to_object(d): return type("DynamicObject", (object,), d)() -def read_sql(sql: str, engine: Optional[Engine | Session] = None, *args, **kwargs) -> pd.DataFrame: +def read_sql( + sql: str, engine: Optional[Engine | Session] = None, *args, **kwargs +) -> pd.DataFrame: """Wrapper around pd.read_sql that creates a connection and closes it after reading the data. This adds overhead, so if you need performance, reuse the same connection and cursor. """ @@ -81,7 +292,13 @@ def read_sql(sql: str, engine: Optional[Engine | Session] = None, *args, **kwarg raise ValueError(f"Unsupported engine type {type(engine)}") -def to_sql(df: pd.DataFrame, name: str, engine: Optional[Engine | Session] = None, *args, **kwargs): +def to_sql( + df: pd.DataFrame, + name: str, + engine: Optional[Engine | Session] = None, + *args, + **kwargs, +): """Wrapper around pd.to_sql that creates a connection and closes it after reading the data. This adds overhead, so if you need performance, reuse the same connection and cursor. """ @@ -104,5 +321,7 @@ def production_or_master_engine() -> Engine: elif config.ENV_FILE_PROD: return config.OWIDEnv.from_env_file(config.ENV_FILE_PROD).get_engine() else: - log.warning("ENV file doesn't connect to production DB, comparing against staging-site-master") + log.warning( + "ENV file doesn't connect to production DB, comparing against staging-site-master" + ) return config.OWIDEnv.from_staging("master").get_engine() diff --git a/etl/grapher_helpers.py b/etl/grapher_helpers.py index 926a1399f74..76533143915 100644 --- a/etl/grapher_helpers.py +++ b/etl/grapher_helpers.py @@ -17,6 +17,7 @@ from sqlalchemy.engine import Engine from sqlalchemy.orm import Session +from apps.backport.datasync import data_metadata as dm from etl.db import get_engine, read_sql from etl.files import yaml_dump from etl.grapher_io import add_entity_code_and_name, trim_long_variable_name @@ -45,7 +46,12 @@ def raise_helper(msg): # this might work too pd.api.types.is_integer_dtype(col) INT_TYPES = tuple( - {f"{n}{b}{p}" for n in ("int", "Int", "uint", "UInt") for b in ("8", "16", "32", "64") for p in ("", "[pyarrow]")} + { + f"{n}{b}{p}" + for n in ("int", "Int", "uint", "UInt") + for b in ("8", "16", "32", "64") + for p in ("", "[pyarrow]") + } ) @@ -65,7 +71,11 @@ def expand_dimensions(tb: catalog.Table) -> catalog.Table: This function is not very memory efficient as it returns a table that will be very sparse. """ # rename country to entity_id for the sake of `_yield_wide_table` - tb = tb.reset_index("country").rename(columns={"country": "entity_id"}).set_index("entity_id", append=True) + tb = ( + tb.reset_index("country") + .rename(columns={"country": "entity_id"}) + .set_index("entity_id", append=True) + ) tables = list(_yield_wide_table(tb, na_action="drop", warn_null_variables=False)) # join all tables @@ -109,11 +119,19 @@ def _yield_wide_table( for col in table.columns: if table[col].isna().any(): raise ValueError(f"Column `{col}` contains missing values") - cols_with_none_units = [col for col in table.columns if table[col].metadata.unit is None] + cols_with_none_units = [ + col for col in table.columns if table[col].metadata.unit is None + ] if cols_with_none_units: - raise Exception("Columns with missing units: " + ", ".join(cols_with_none_units)) + raise Exception( + "Columns with missing units: " + ", ".join(cols_with_none_units) + ) - dim_names = [k for k in table.primary_key if k not in ("year", "entityId", "entityCode", "entityName")] + dim_names = [ + k + for k in table.primary_key + if k not in ("year", "entityId", "entityCode", "entityName") + ] # Keep only entity_id and year in index table = table.reset_index(level=dim_names) @@ -121,7 +139,10 @@ def _yield_wide_table( if dim_names: # `dropna=False` makes sure we don't drop NaN values from index grouped = table.groupby( - dim_names if len(dim_names) > 1 else dim_names[0], as_index=False, observed=True, dropna=False + dim_names if len(dim_names) > 1 else dim_names[0], + as_index=False, + observed=True, + dropna=False, ) else: # a situation when there's only year and entity_id in index with no additional dimensions @@ -132,7 +153,9 @@ def _yield_wide_table( dim_values = (dim_values,) # Exclude dimensions - table_to_yield = table_to_yield[[c for c in table_to_yield.columns if c not in dim_names]] + table_to_yield = table_to_yield[ + [c for c in table_to_yield.columns if c not in dim_names] + ] # Filter NaN values from dimensions and return dictionary dim_dict = _create_dim_dict(dim_names, dim_values) # type: ignore @@ -143,7 +166,11 @@ def _yield_wide_table( # If all values are null, skip variable if table_to_yield[column].isnull().all(): if warn_null_variables: - log.warning("yield_wide_table.null_variable", column=column, dim_dict=dim_dict) + log.warning( + "yield_wide_table.null_variable", + column=column, + dim_dict=dim_dict, + ) continue # Safety check to see if the metadata is still intact @@ -172,12 +199,16 @@ def _yield_wide_table( tab.metadata.short_name = short_name tab.rename(columns={column: short_name}, inplace=True) - tab[short_name].metadata = _metadata_for_dimensions(tab[short_name].metadata, dim_dict, column) + tab[short_name].metadata = _metadata_for_dimensions( + tab[short_name].metadata, dim_dict, column + ) yield tab -def _metadata_for_dimensions(meta: catalog.VariableMeta, dim_dict: Dict[str, Any], column: str) -> catalog.VariableMeta: +def _metadata_for_dimensions( + meta: catalog.VariableMeta, dim_dict: Dict[str, Any], column: str +) -> catalog.VariableMeta: """Add dimensions to metadata and expand Jinja in metadata fields.""" # add info about dimensions to metadata if dim_dict: @@ -186,7 +217,8 @@ def _metadata_for_dimensions(meta: catalog.VariableMeta, dim_dict: Dict[str, Any "originalShortName": column, "originalName": meta.title, "filters": [ - {"name": dim_name, "value": sanitize_numpy(dim_value)} for dim_name, dim_value in dim_dict.items() + {"name": dim_name, "value": sanitize_numpy(dim_value)} + for dim_name, dim_value in dim_dict.items() ], } } @@ -247,7 +279,9 @@ def long_to_wide(long_tb: catalog.Table) -> catalog.Table: if short_name in short_names: duplicate_short_name_ix = short_names.index(short_name) # raise ValueError(f"Duplicate short name: {short_name} for column: {column} and dimensions: {dim_dict}") - duplicate_dim_dict = dict(zip(dim_names, wide_tb.columns[duplicate_short_name_ix][1:])) + duplicate_dim_dict = dict( + zip(dim_names, wide_tb.columns[duplicate_short_name_ix][1:]) + ) raise ValueError( f"Duplicate short name for column '{column}' with dim values:\n{duplicate_dim_dict}\n{dim_dict}" ) @@ -255,7 +289,9 @@ def long_to_wide(long_tb: catalog.Table) -> catalog.Table: short_names.append(short_name) # Create metadata for the column from dimensions - metadatas.append(_metadata_for_dimensions(long_tb[dims[0]].metadata.copy(), dim_dict, column)) + metadatas.append( + _metadata_for_dimensions(long_tb[dims[0]].metadata.copy(), dim_dict, column) + ) # Set column names to new short names and use proper metadata wide_tb.columns = short_names @@ -315,7 +351,9 @@ def _expand_jinja(obj: Any, dim_dict: Dict[str, str]) -> Any: return obj -def render_yaml_file(path: Union[str, Path], dim_dict: Dict[str, str]) -> Dict[str, Any]: +def render_yaml_file( + path: Union[str, Path], dim_dict: Dict[str, str] +) -> Dict[str, Any]: """Load YAML file and render Jinja in all fields. Return a dictionary. Usage: @@ -329,7 +367,9 @@ def render_yaml_file(path: Union[str, Path], dim_dict: Dict[str, str]) -> Dict[s return _expand_jinja(meta, dim_dict) -def render_variable_meta(meta: catalog.VariableMeta, dim_dict: Dict[str, str]) -> catalog.VariableMeta: +def render_variable_meta( + meta: catalog.VariableMeta, dim_dict: Dict[str, str] +) -> catalog.VariableMeta: """Render Jinja in all fields of VariableMeta. Return a new VariableMeta object. Usage: @@ -347,11 +387,16 @@ def _title_column_and_dimensions(title: str, dim_dict: Dict[str, Any]) -> str: For instance `Deaths`, ["age", "sex"], ["10-18", "male"] will be converted into Deaths - Age: 10-18 - Sex: male """ - dims = [f"{dim_name.replace('_', ' ').capitalize()}: {dim_value}" for dim_name, dim_value in dim_dict.items()] + dims = [ + f"{dim_name.replace('_', ' ').capitalize()}: {dim_value}" + for dim_name, dim_value in dim_dict.items() + ] return " - ".join([title] + dims) -def _underscore_column_and_dimensions(column: str, dim_dict: Dict[str, Any], trim_long_short_name: bool = True) -> str: +def _underscore_column_and_dimensions( + column: str, dim_dict: Dict[str, Any], trim_long_short_name: bool = True +) -> str: # add dimension names to dimensions dims = [f"{dim_name}_{dim_value}" for dim_name, dim_value in dim_dict.items()] @@ -370,7 +415,9 @@ def _underscore_column_and_dimensions(column: str, dim_dict: Dict[str, Any], tri dims=dim_dict, ) else: - raise AssertionError(f"short_name {short_name} is too long for MySQL variables.shortName column") + raise AssertionError( + f"short_name {short_name} is too long for MySQL variables.shortName column" + ) return short_name @@ -414,9 +461,9 @@ def long_to_wide_tables( # extract metadata from column and make sure it is identical for all rows meta = t.pop("meta") t.pop("variable") - assert set(meta.map(id)) == { - id(meta.iloc[0]) - }, f"Variable `{var_name}` must have same metadata objects in column `meta` for all rows" + assert ( + set(meta.map(id)) == {id(meta.iloc[0])} + ), f"Variable `{var_name}` must have same metadata objects in column `meta` for all rows" t[var_name].metadata = meta.iloc[0] # name table as variable name @@ -436,7 +483,9 @@ def _get_entities_from_db( return cast(Dict[str, int], df.set_index(by).entity_id.to_dict()) -def _get_and_create_entities_in_db(countries: Set[str], engine: Engine | None = None) -> Dict[str, int]: +def _get_and_create_entities_in_db( + countries: Set[str], engine: Engine | None = None +) -> Dict[str, int]: engine = engine or get_engine() with Session(engine) as session: log.info("Creating entities in DB", countries=countries) @@ -502,10 +551,16 @@ def country_to_entity_id( ix = entity_id.isnull() # cast to float to fix issues with categories entity_id[ix] = ( # type: ignore[reportCallIssue] - country[ix].map(_get_and_create_entities_in_db(set(country[ix].unique()), engine=engine)).astype(float) # type: ignore[reportCallIssue] + country[ix] + .map( + _get_and_create_entities_in_db(set(country[ix].unique()), engine=engine) + ) + .astype(float) # type: ignore[reportCallIssue] ) - assert not entity_id.isnull().any(), f"Some countries have not been mapped: {set(country[entity_id.isnull()])}" # type: ignore[reportCallIssue] + assert ( + not entity_id.isnull().any() + ), f"Some countries have not been mapped: {set(country[entity_id.isnull()])}" # type: ignore[reportCallIssue] return cast(pd.Series, entity_id.astype(int)) @@ -549,7 +604,13 @@ def combine_metadata_sources(sources: List[catalog.Source]) -> catalog.Source: # Combine sources' attributes into the first source (which is the only one that grapher will interpret). for attribute in attributes: # Gather non-empty values from each source for current attribute. - values = _unique([getattr(source, attribute) for source in sources if getattr(source, attribute) is not None]) + values = _unique( + [ + getattr(source, attribute) + for source in sources + if getattr(source, attribute) is not None + ] + ) if attribute == "description": # Descriptions are usually long, so it is better so put together descriptions from different sources in # separate lines. @@ -603,7 +664,9 @@ def _adapt_dataset_metadata_for_grapher( metadata.sources[0].description not in metadata.description and metadata.description not in metadata.sources[0].description ): - metadata.sources[0].description = metadata.description + "\n" + metadata.sources[0].description + metadata.sources[0].description = ( + metadata.description + "\n" + metadata.sources[0].description + ) else: metadata.sources[0].description = metadata.description @@ -637,7 +700,11 @@ def _adapt_table_for_grapher(table: catalog.Table, engine: Engine) -> catalog.Ta ), f"Variable titles are not unique:\n{variable_titles_counts[variable_titles_counts > 1].index}." # Remember original dimensions - dim_names = [n for n in table.index.names if n and n not in ("year", "date", "entity_id", "country")] + dim_names = [ + n + for n in table.index.names + if n and n not in ("year", "date", "entity_id", "country") + ] # Reset index unless we have default index if table.index.names != [None]: @@ -646,21 +713,30 @@ def _adapt_table_for_grapher(table: catalog.Table, engine: Engine) -> catalog.Ta # If a table contains `date` instead of `year`, adapt it for grapher if "date" in table.columns: # NOTE: this can be relaxed if we ever need it - assert "year" not in table.columns, "Table cannot have both `date` and `year` columns." + assert ( + "year" not in table.columns + ), "Table cannot have both `date` and `year` columns." table = adapt_table_with_dates_to_grapher(table) - assert {"year", "country"} <= set(table.columns), "Table must have columns country and year." + assert {"year", "country"} <= set( + table.columns + ), "Table must have columns country and year." assert "entity_id" not in table.columns, "Table must not have column entity_id." # Grapher needs a column entity id, that is constructed based on the unique entity names in the database. - table["entityId"] = country_to_entity_id(table["country"], create_entities=True, engine=engine) + table["entityId"] = country_to_entity_id( + table["country"], create_entities=True, engine=engine + ) table = table.drop(columns=["country"]) # Add entity code and name with Session(engine) as session: table = add_entity_code_and_name(session, table).copy_metadata(table) + # table = dm.add_entity_code_and_name(session, table).copy_metadata(table) - table = table.set_index(["entityId", "entityCode", "entityName", "year"] + dim_names) + table = table.set_index( + ["entityId", "entityCode", "entityName", "year"] + dim_names + ) # Ensure the default source of each column includes the description of the table (since that is the description that # will appear in grapher on the SOURCES tab). @@ -677,7 +753,9 @@ def _ensure_source_per_variable(table: catalog.Table) -> catalog.Table: # If neither variable and dataset has no sources, we're using origins instead. if len(variable_meta.sources) == 0 and len(dataset_meta.sources) == 0: - assert len(variable_meta.origins) > 0, f"Variable `{column}` has no sources or origins." + assert ( + len(variable_meta.origins) > 0 + ), f"Variable `{column}` has no sources or origins." continue if len(variable_meta.sources) == 0: @@ -690,7 +768,9 @@ def _ensure_source_per_variable(table: catalog.Table) -> catalog.Table: # Add the dataset description as if it was a source's description. if dataset_meta.description is not None: if source.description: - source.description = dataset_meta.description + "\n" + source.description + source.description = ( + dataset_meta.description + "\n" + source.description + ) else: source.description = dataset_meta.description else: @@ -824,7 +904,10 @@ def _rename_column(old_column_name: str, chart_slug: str) -> str: return f"{old_column_name}_chart_{underscore(chart_slug)}" # Create new columns. - new_columns = [_rename_column(old_column_name=column, chart_slug=chart_slug) for column in columns_in_chart] + new_columns = [ + _rename_column(old_column_name=column, chart_slug=chart_slug) + for column in columns_in_chart + ] table[new_columns] = table[columns_in_chart].copy() # Optionally fill some of the new columns with zeros. @@ -834,9 +917,12 @@ def _rename_column(old_column_name: str, chart_slug: str) -> str: assert set(columns_to_fill_with_zeros) <= set(columns_in_chart), error # Fill nans with zeros (in new columns). new_columns_to_fill_with_zeros = [ - _rename_column(old_column_name=column, chart_slug=chart_slug) for column in columns_to_fill_with_zeros + _rename_column(old_column_name=column, chart_slug=chart_slug) + for column in columns_to_fill_with_zeros ] - table[new_columns_to_fill_with_zeros] = table[new_columns_to_fill_with_zeros].fillna(0) + table[new_columns_to_fill_with_zeros] = table[ + new_columns_to_fill_with_zeros + ].fillna(0) # For each row, if any of the columns in the chart is nan, fill other columns in the same row with nan. table.loc[table[new_columns].isnull().any(axis=1), new_columns] = np.nan @@ -844,7 +930,9 @@ def _rename_column(old_column_name: str, chart_slug: str) -> str: # Handle metadata. for column in new_columns: # If the indicator did not have any display name, use the original title. - if ("name" not in table[column].display) or (table[column].metadata.display["name"] is None): + if ("name" not in table[column].display) or ( + table[column].metadata.display["name"] is None + ): table[column].metadata.display["name"] = table[column].metadata.title # To avoid having multiple indicators with the same title, add a suffix to the title. if suffix_for_titles is None: @@ -893,7 +981,11 @@ def adapt_table_with_dates_to_grapher( # If no columns are specified, list all columns in the table (except the country and date columns). if columns is None: - columns = [column for column in tb.columns if column not in [date_column, country_column]] + columns = [ + column + for column in tb.columns + if column not in [date_column, country_column] + ] for column in columns: # Find earliest date in the table. diff --git a/etl/grapher_import.py b/etl/grapher_import.py index e284b22eaf8..0ed1c8ce5c9 100644 --- a/etl/grapher_import.py +++ b/etl/grapher_import.py @@ -9,31 +9,35 @@ >>> import_dataset.main(dataset_dir, dataset_namespace) """ +import asyncio import datetime import json import os import warnings -from concurrent.futures import ThreadPoolExecutor from dataclasses import dataclass from threading import Lock from typing import Dict, List, Optional, cast import pandas as pd import structlog +from aiobotocore.session import get_session from owid import catalog from owid.catalog import Table, VariableMeta, utils +from owid.catalog import Table, VariableMeta, s3_utils, utils from owid.catalog.utils import hash_any from sqlalchemy import select, text, update from sqlalchemy.engine.base import Engine from sqlalchemy.exc import NoResultFound +from sqlalchemy.ext.asyncio import AsyncEngine, AsyncSession, async_sessionmaker from sqlalchemy.orm import Session from apps.backport.datasync import data_metadata as dm -from apps.backport.datasync.datasync import upload_gzip_string +from apps.backport.datasync.datasync import upload_gzip_string_async from apps.chart_sync.admin_api import AdminAPI from apps.wizard.app_pages.chart_diff.chart_diff import ChartDiffsLoader from etl import config from etl.db import get_engine, production_or_master_engine +from etl.db import get_engine, get_engine_async from . import grapher_helpers as gh from . import grapher_model as gm @@ -115,28 +119,29 @@ def upsert_dataset( assert source.name source_ids[hash(source)] = _upsert_source_to_db(session, source, ds.id) - session.commit() - return DatasetUpsertResult(ds.id, source_ids) -def _upsert_source_to_db(session: Session, source: catalog.Source, dataset_id: int) -> int: +async def _upsert_source_to_db(session: AsyncSession, source: catalog.Source, dataset_id: int) -> int: """Upsert source and return its id""" # NOTE: we need the lock because upserts can happen in multiple threads and `sources` table # has no unique constraint on `name`. It can be removed once we switch to variable views # and stop using threads with source_table_lock: - db_source = gm.Source.from_catalog_source(source, dataset_id).upsert(session) + db_source = await gm.Source.from_catalog_source(source, dataset_id).upsert(session) # commit within the lock to make sure other threads get the latest sources - session.commit() + await session.commit() assert db_source.id return db_source.id -def _add_or_update_source( - session: Session, variable_meta: catalog.VariableMeta, column_name: str, dataset_upsert_result: DatasetUpsertResult +async def _add_or_update_source( + session: AsyncSession, + variable_meta: catalog.VariableMeta, + column_name: str, + dataset_upsert_result: DatasetUpsertResult, ) -> Optional[int]: if not variable_meta.sources: assert variable_meta.origins, "Variable must have either sources or origins" @@ -163,11 +168,11 @@ def _add_or_update_source( return source_id -def _add_or_update_origins(session: Session, origins: list[catalog.Origin]) -> list[gm.Origin]: +async def _add_or_update_origins(session: AsyncSession, origins: list[catalog.Origin]) -> list[gm.Origin]: out = [] assert len(origins) == len(set(origins)), "origins must be unique" for origin in origins: - out.append(gm.Origin.from_origin(origin).upsert(session)) + out.append(await gm.Origin.from_origin(origin).upsert(session)) return out @@ -225,8 +230,12 @@ def _check_upserted_table(table: Table) -> None: assert not gh.contains_inf(table.iloc[:, 0]), f"Column `{table.columns[0]}` has inf values" -def upsert_table( - engine: Engine, +semaphore = asyncio.Semaphore(50) + + +async def upsert_table( + engine_async: AsyncEngine, + client, admin_api: AdminAPI, table: Table, dataset_upsert_result: DatasetUpsertResult, @@ -381,25 +390,167 @@ def upsert_metadata( ) session.add(db_variable) +""" + # All following functions assume that `value` is string + # NOTE: we could make the code more efficient if we didn't convert `value` to string + # TODO: can we avoid setting & resetting index back and forth? + df = table.reset_index().rename(columns={column_name: "value"}) + df["value"] = df["value"].astype("string") + + checksum_data = calculate_checksum_data(df) + checksum_metadata = calculate_checksum_metadata(variable_meta, df) + + # NOTE: this is useful for debugging, will be removed once it is stable + if os.environ.get("SKIP_CHECKSUMS"): + import random + + checksum_metadata = str(random.randint(0, 10000)) + checksum_data = str(random.randint(0, 10000)) + + async with semaphore: + log.info( + "upsert_dataset.upsert_table.start", + column_name=column_name, + ) + + async_session = async_sessionmaker(engine_async, expire_on_commit=False) + async with async_session() as session: + # compare checksums + try: + db_variable = await gm.Variable.load_from_catalog_path_async(session, catalog_path) + except NoResultFound: + db_variable = None + + upsert_metadata_kwargs = dict( + session=session, + df=df, + variable_meta=variable_meta, + column_name=column_name, + dataset_upsert_result=dataset_upsert_result, + catalog_path=catalog_path, + dimensions=dimensions, + admin_api=admin_api, + client=client, + ) + + # create variable if it doesn't exist + if not db_variable: + db_variable = await upsert_metadata(**upsert_metadata_kwargs) + await upsert_data(df, db_variable.s3_data_path(), client) + + # variable exists + else: + if db_variable.dataChecksum == checksum_data and db_variable.metadataChecksum == checksum_metadata: + if verbose: + log.info("upsert_table.skipped_no_changes", size=len(df), variable_id=db_variable.id) + return + + upsert_data_task = None + if db_variable.dataChecksum != checksum_data: + upsert_data_task = upsert_data(df, db_variable.s3_data_path(), client) + + if db_variable.metadataChecksum != checksum_metadata: + db_variable = await upsert_metadata(**upsert_metadata_kwargs) + + if upsert_data_task: + await upsert_data_task + + # Update checksums + db_variable.dataChecksum = checksum_data + db_variable.metadataChecksum = checksum_metadata + + # Commit new checksums + session.add(db_variable) + await session.commit() + + if verbose: + log.info("upsert_table.uploaded_to_s3", size=len(df), variable_id=db_variable.id) + + +async def upsert_data(df: pd.DataFrame, s3_data_path: str, client) -> None: + # upload data to R2 + var_data = dm.variable_data(df) + var_data_str = json.dumps(var_data, default=str) + await upload_gzip_string_async(client, var_data_str, s3_data_path) + + +async def upsert_metadata( + session: AsyncSession, + df: pd.DataFrame, + variable_meta: VariableMeta, + column_name: str, + dataset_upsert_result: DatasetUpsertResult, + catalog_path: str, + dimensions: Optional[gm.Dimensions], + admin_api: AdminAPI, + client, +) -> gm.Variable: + timespan = _get_timespan(df, variable_meta) + + source_id = await _add_or_update_source(session, variable_meta, column_name, dataset_upsert_result) + + # with origins_table_lock: + db_origins = await _add_or_update_origins(session, variable_meta.origins) + # commit within the lock to make sure other threads get the latest sources + await session.commit() + + # pop grapher_config from variable metadata, later we send it to Admin API + if variable_meta.presentation and variable_meta.presentation.grapher_config: + grapher_config = variable_meta.presentation.grapher_config + variable_meta.presentation.grapher_config = None + else: + grapher_config = None + + db_variable = await gm.Variable.from_variable_metadata( + variable_meta, + short_name=column_name, + timespan=timespan, + dataset_id=dataset_upsert_result.dataset_id, + source_id=source_id, + catalog_path=catalog_path, + dimensions=dimensions, + ).upsert(session) + db_variable_id = db_variable.id + assert db_variable_id + + # TODO: `type` is part of metadata, but not part of checksum! + if not db_variable.type: + db_variable.type = db_variable.infer_type(df["value"]) + session.add(db_variable) + + # update links, we need to do it after we commit deleted relationships above + update_links_task = db_variable.update_links( + session, + db_origins, + faqs=variable_meta.presentation.faqs if variable_meta.presentation else [], + tag_names=variable_meta.presentation.topic_tags if variable_meta.presentation else [], + ) +""" # we need to commit changes because `dm.variable_metadata` pulls all data from MySQL # and sends it to R2 # NOTE: we could optimize this by evading pulling from MySQL and instead constructing JSON files from objects # we have available - session.commit() + await session.commit() # grapher_config needs to be sent to Admin API because it has side effects + put_grapher_config_task = None if grapher_config: - admin_api.put_grapher_config(db_variable_id, grapher_config) + put_grapher_config_task = admin_api.put_grapher_config(db_variable_id, grapher_config) # grapher_config does not exist, but it's still in the database -> delete it elif not grapher_config and db_variable.grapherConfigIdETL: admin_api.delete_grapher_config(db_variable_id) # upload metadata to R2 - var_metadata = dm.variable_metadata(session, db_variable.id, df) + var_metadata = await dm.variable_metadata(session, db_variable.id, df) var_metadata_str = json.dumps(var_metadata, default=str) # upload them to R2 - upload_gzip_string(var_metadata_str, db_variable.s3_metadata_path()) + await upload_gzip_string_async(client, var_metadata_str, db_variable.s3_metadata_path()) + + # await all tasks + await update_links_task + if put_grapher_config_task: + await put_grapher_config_task return db_variable @@ -627,3 +778,64 @@ def _get_timespan(table: pd.DataFrame, variable_meta: VariableMeta) -> str: min_year = min(years) max_year = max(years) return f"{min_year}-{max_year}" + + +async def _upsert_tables_from_dataset_async(step_path, dataset, engine, admin_api, dataset_upsert_results): + i = 0 + catalog_paths = [] + tasks = [] + verbose = True + + engine_async = get_engine_async() + + async with get_session().create_client(**s3_utils.r2_config()) as client: + # NOTE: multiple tables will be saved under a single dataset, this could cause problems if someone + # is fetching the whole dataset from data-api as they would receive all tables merged in a single + # table. This won't be a problem after we introduce the concept of "tables" + for table in dataset: + assert not table.empty, f"table {table.metadata.short_name} is empty" + + # if GRAPHER_FILTER is set, only upsert matching columns + if config.GRAPHER_FILTER: + cols = table.filter(regex=config.GRAPHER_FILTER).columns.tolist() + if not cols: + continue + cols += [c for c in table.columns if c in {"year", "date", "country"} and c not in cols] + table = table.loc[:, cols] + + table = gh._adapt_table_for_grapher(table, engine) + + for t in gh._yield_wide_table(table, na_action="drop"): + i += 1 + assert len(t.columns) == 1 + catalog_path = f"{step_path}/{table.metadata.short_name}#{t.columns[0]}" + catalog_paths.append(catalog_path) + + # TODO: switch to asyncio or threads + # stop logging to stop cluttering logs + # if i > 20 and verbose: + # verbose = False + # thread_pool.submit( + # lambda: (time.sleep(10), log.info("upsert_dataset.continue_without_logging")) + # ) + + # generate table with entity_id, year and value for every column + task = upsert_table( + engine_async, + client, + admin_api, + t, + dataset_upsert_results, + catalog_path=catalog_path, + dimensions=(t.iloc[:, 0].metadata.additional_info or {}).get("dimensions"), + verbose=verbose, + ) + + tasks.append(task) + + await asyncio.gather(*tasks) + + await engine_async.dispose() + await client.close() + + return catalog_paths diff --git a/etl/grapher_model.py b/etl/grapher_model.py index 01d78d9c39a..ca9761d671e 100644 --- a/etl/grapher_model.py +++ b/etl/grapher_model.py @@ -45,6 +45,7 @@ SmallInteger, String, and_, + delete, func, or_, select, @@ -61,6 +62,7 @@ ) from sqlalchemy.engine import Engine from sqlalchemy.exc import NoResultFound +from sqlalchemy.ext.asyncio import AsyncSession from sqlalchemy.ext.hybrid import hybrid_property from sqlalchemy.orm import ( # type: ignore DeclarativeBase, @@ -113,7 +115,9 @@ def from_dict(cls, d: Dict[str, Any]) -> Self: return x @classmethod - def create_table(cls, engine: Engine, if_exists: Literal["fail", "replace", "skip"] = "fail") -> None: + def create_table( + cls, engine: Engine, if_exists: Literal["fail", "replace", "skip"] = "fail" + ) -> None: if if_exists == "replace": # Drop the table if it exists and create a new one cls.__table__.drop(engine, checkfirst=True) # type: ignore @@ -130,17 +134,24 @@ def create_table(cls, engine: Engine, if_exists: Literal["fail", "replace", "ski class Entity(Base): __tablename__ = "entities" - __table_args__ = (Index("code", "code", unique=True), Index("name", "name", unique=True)) + __table_args__ = ( + Index("code", "code", unique=True), + Index("name", "name", unique=True), + ) id: Mapped[int] = mapped_column(Integer, primary_key=True, init=False) name: Mapped[str] = mapped_column(VARCHAR(255)) validated: Mapped[int] = mapped_column(TINYINT(1)) - createdAt: Mapped[datetime] = mapped_column(DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False) + createdAt: Mapped[datetime] = mapped_column( + DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False + ) code: Mapped[Optional[str]] = mapped_column(VARCHAR(255)) updatedAt: Mapped[Optional[datetime]] = mapped_column(DateTime, init=False) @classmethod - def load_entity_mapping(cls, session: Session, entity_ids: Optional[List[int]] = None) -> Dict[int, str]: + def load_entity_mapping( + cls, session: Session, entity_ids: Optional[List[int]] = None + ) -> Dict[int, str]: q = text( """ select @@ -183,8 +194,12 @@ class Namespace(Base): id: Mapped[int] = mapped_column(Integer, primary_key=True, init=False) name: Mapped[str] = mapped_column(VARCHAR(255)) - isArchived: Mapped[int] = mapped_column(TINYINT(1), server_default=text("'0'"), default=0) - createdAt: Mapped[datetime] = mapped_column(DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False) + isArchived: Mapped[int] = mapped_column( + TINYINT(1), server_default=text("'0'"), default=0 + ) + createdAt: Mapped[datetime] = mapped_column( + DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False + ) description: Mapped[Optional[str]] = mapped_column(VARCHAR(255), default=None) updatedAt: Mapped[Optional[datetime]] = mapped_column(DateTime, init=False) @@ -212,15 +227,28 @@ def upsert(self, session: Session) -> "Namespace": class Tag(Base): __tablename__ = "tags" __table_args__ = ( - ForeignKeyConstraint(["parentId"], ["tags.id"], ondelete="RESTRICT", onupdate="RESTRICT", name="tags_ibfk_1"), - Index("dataset_subcategories_name_fk_dst_cat_id_6ce1cc36_uniq", "name", "parentId", unique=True), + ForeignKeyConstraint( + ["parentId"], + ["tags.id"], + ondelete="RESTRICT", + onupdate="RESTRICT", + name="tags_ibfk_1", + ), + Index( + "dataset_subcategories_name_fk_dst_cat_id_6ce1cc36_uniq", + "name", + "parentId", + unique=True, + ), Index("parentId", "parentId"), Index("slug", "slug", unique=True), ) id: Mapped[int] = mapped_column(Integer, primary_key=True, init=False) name: Mapped[str] = mapped_column(VARCHAR(255)) - createdAt: Mapped[datetime] = mapped_column(DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False) + createdAt: Mapped[datetime] = mapped_column( + DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False + ) updatedAt: Mapped[Optional[datetime]] = mapped_column(DateTime, init=False) parentId: Mapped[Optional[int]] = mapped_column(Integer) specialType: Mapped[Optional[str]] = mapped_column(VARCHAR(255)) @@ -231,9 +259,11 @@ def load_tags(cls, session: Session) -> List["Tag"]: return list(session.scalars(select(cls).where(cls.slug.isnot(None))).all()) @classmethod - def load_tags_by_names(cls, session: Session, tag_names: List[str]) -> List["Tag"]: + async def load_tags_by_names( + cls, session: AsyncSession, tag_names: List[str] + ) -> List["Tag"]: """Load topic tags by their names in the order given in `tag_names`.""" - tags = session.scalars(select(Tag).where(Tag.name.in_(tag_names))).all() + tags = (await session.scalars(select(Tag).where(Tag.name.in_(tag_names)))).all() if len(tags) != len(tag_names): found_tags = [tag.name for tag in tags] @@ -241,7 +271,10 @@ def load_tags_by_names(cls, session: Session, tag_names: List[str]) -> List["Tag tag_names = found_tags log.warning("create_links.missing_tags", tags=missing_tags) - tags = [next(tag for tag in tags if tag.name == ordered_name) for ordered_name in tag_names] + tags = [ + next(tag for tag in tags if tag.name == ordered_name) + for ordered_name in tag_names + ] return tags @@ -252,7 +285,9 @@ class User(Base): id: Mapped[int] = mapped_column(Integer, primary_key=True, init=False) isSuperuser: Mapped[int] = mapped_column(TINYINT(1), server_default=text("'0'")) email: Mapped[str] = mapped_column(VARCHAR(255)) - createdAt: Mapped[datetime] = mapped_column(DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False) + createdAt: Mapped[datetime] = mapped_column( + DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False + ) isActive: Mapped[int] = mapped_column(TINYINT(1), server_default=text("'1'")) fullName: Mapped[str] = mapped_column(VARCHAR(255)) githubUsername: Mapped[str] = mapped_column(VARCHAR(255)) @@ -263,21 +298,29 @@ class User(Base): @classmethod def load_user(cls, session: Session, github_username: str) -> Optional["User"]: - return session.scalars(select(cls).where(cls.githubUsername == github_username)).one_or_none() + return session.scalars( + select(cls).where(cls.githubUsername == github_username) + ).one_or_none() class ChartRevisions(Base): __tablename__ = "chart_revisions" __table_args__ = ( ForeignKeyConstraint( - ["userId"], ["users.id"], ondelete="RESTRICT", onupdate="RESTRICT", name="chart_revisions_userId" + ["userId"], + ["users.id"], + ondelete="RESTRICT", + onupdate="RESTRICT", + name="chart_revisions_userId", ), Index("chartId", "chartId"), Index("chart_revisions_userId", "userId"), ) id: Mapped[int] = mapped_column(BigInteger, primary_key=True) - createdAt: Mapped[datetime] = mapped_column(DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False) + createdAt: Mapped[datetime] = mapped_column( + DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False + ) chartId: Mapped[Optional[int]] = mapped_column(Integer) userId: Mapped[Optional[int]] = mapped_column(Integer) config: Mapped[Optional[dict]] = mapped_column(JSON) @@ -291,9 +334,12 @@ class ChartConfig(Base): id: Mapped[bytes] = mapped_column(CHAR(36), primary_key=True) patch: Mapped[dict] = mapped_column(JSON, nullable=False) full: Mapped[dict] = mapped_column(JSON, nullable=False) - fullMd5: Mapped[str] = mapped_column(CHAR(24), Computed("(to_base64(unhex(md5(full))))", persisted=True)) + fullMd5: Mapped[str] = mapped_column( + CHAR(24), Computed("(to_base64(unhex(md5(full))))", persisted=True) + ) slug: Mapped[Optional[str]] = mapped_column( - String(255), Computed("(json_unquote(json_extract(`full`, '$.slug')))", persisted=True) + String(255), + Computed("(json_unquote(json_extract(`full`, '$.slug')))", persisted=True), ) chartType: Mapped[Optional[str]] = mapped_column( String(255), @@ -302,17 +348,27 @@ class ChartConfig(Base): persisted=True, ), ) - createdAt: Mapped[datetime] = mapped_column(DateTime, server_default=text("CURRENT_TIMESTAMP"), nullable=False) - updatedAt: Mapped[Optional[datetime]] = mapped_column(DateTime, onupdate=func.current_timestamp()) + createdAt: Mapped[datetime] = mapped_column( + DateTime, server_default=text("CURRENT_TIMESTAMP"), nullable=False + ) + updatedAt: Mapped[Optional[datetime]] = mapped_column( + DateTime, onupdate=func.current_timestamp() + ) - chartss: Mapped[List["Chart"]] = relationship("Chart", back_populates="chart_config") + chartss: Mapped[List["Chart"]] = relationship( + "Chart", back_populates="chart_config" + ) class Chart(Base): __tablename__ = "charts" __table_args__ = ( ForeignKeyConstraint( - ["configId"], ["chart_configs.id"], ondelete="RESTRICT", onupdate="RESTRICT", name="charts_configId" + ["configId"], + ["chart_configs.id"], + ondelete="RESTRICT", + onupdate="RESTRICT", + name="charts_configId", ), ForeignKeyConstraint( ["lastEditedByUserId"], @@ -335,7 +391,9 @@ class Chart(Base): id: Mapped[int] = mapped_column(Integer, primary_key=True, init=False) configId: Mapped[bytes] = mapped_column(CHAR(36)) - createdAt: Mapped[datetime] = mapped_column(DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False) + createdAt: Mapped[datetime] = mapped_column( + DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False + ) lastEditedAt: Mapped[datetime] = mapped_column(DateTime) lastEditedByUserId: Mapped[int] = mapped_column(Integer) isIndexable: Mapped[int] = mapped_column(TINYINT(1), server_default=text("'0'")) @@ -343,7 +401,9 @@ class Chart(Base): publishedAt: Mapped[Optional[datetime]] = mapped_column(DateTime) publishedByUserId: Mapped[Optional[int]] = mapped_column(Integer) - chart_config: Mapped["ChartConfig"] = relationship("ChartConfig", back_populates="chartss", lazy="joined") + chart_config: Mapped["ChartConfig"] = relationship( + "ChartConfig", back_populates="chartss", lazy="joined" + ) @hybrid_property def updatedAt(self) -> datetime: # type: ignore @@ -360,7 +420,11 @@ def config(self) -> dict[str, Any]: # type: ignore @config.expression def config(cls): - return select(ChartConfig.full).where(ChartConfig.id == cls.configId).scalar_subquery() + return ( + select(ChartConfig.full) + .where(ChartConfig.id == cls.configId) + .scalar_subquery() + ) @hybrid_property def slug(self) -> Optional[str]: # type: ignore @@ -368,10 +432,19 @@ def slug(self) -> Optional[str]: # type: ignore @slug.expression def slug(cls): - return select(ChartConfig.slug).where(ChartConfig.id == cls.configId).scalar_subquery() + return ( + select(ChartConfig.slug) + .where(ChartConfig.id == cls.configId) + .scalar_subquery() + ) @classmethod - def load_chart(cls, session: Session, chart_id: Optional[int] = None, slug: Optional[str] = None) -> "Chart": + def load_chart( + cls, + session: Session, + chart_id: Optional[int] = None, + slug: Optional[str] = None, + ) -> "Chart": """Load chart with id `chart_id`.""" if chart_id: cond = cls.id == chart_id @@ -401,11 +474,17 @@ def load_charts(cls, session: Session, chart_ids: List[int]) -> List["Chart"]: return list(charts) @classmethod - def load_charts_using_variables(cls, session: Session, variable_ids: List[int]) -> List["Chart"]: + def load_charts_using_variables( + cls, session: Session, variable_ids: List[int] + ) -> List["Chart"]: """Load charts that use any of the given variables in `variable_ids`.""" # Find IDs of charts chart_ids = ( - session.scalars(select(ChartDimensions.chartId).where(ChartDimensions.variableId.in_(variable_ids))) + session.scalars( + select(ChartDimensions.chartId).where( + ChartDimensions.variableId.in_(variable_ids) + ) + ) .unique() .all() ) @@ -439,7 +518,9 @@ def load_chart_variables(self, session: Session) -> Dict[int, "Variable"]: return variables @classmethod - def load_variables_checksums(cls, session: Session, chart_ids: List[int]) -> pd.DataFrame: + def load_variables_checksums( + cls, session: Session, chart_ids: List[int] + ) -> pd.DataFrame: """Load checksums for all variables from the chart and return them as a list of dicts.""" q = """ select @@ -451,7 +532,9 @@ def load_variables_checksums(cls, session: Session, chart_ids: List[int]) -> pd. join variables as v on v.id = cd.variableId where cd.chartId in %(chart_id)s """ - return read_sql(q, session, params={"chart_id": chart_ids}).set_index(["chartId", "catalogPath"]) + return read_sql(q, session, params={"chart_id": chart_ids}).set_index( + ["chartId", "catalogPath"] + ) def load_variable_checksums(self, session: Session) -> pd.DataFrame: """Load checksums for all variables from the chart and return them as a list of dicts.""" @@ -464,9 +547,13 @@ def load_variable_checksums(self, session: Session) -> pd.DataFrame: join variables as v on v.id = cd.variableId where cd.chartId = %(chart_id)s """ - return read_sql(q, session, params={"chart_id": self.id}).set_index("catalogPath") + return read_sql(q, session, params={"chart_id": self.id}).set_index( + "catalogPath" + ) - def migrate_config(self, source_session: Session, target_session: Session) -> Dict[str, Any]: + def migrate_config( + self, source_session: Session, target_session: Session + ) -> Dict[str, Any]: """Remap variable ids from source to target session. Variable in source is uniquely identified by its catalogPath if available, or by name and datasetId otherwise. It is looked up by this identifier in the target session to get the new variable id. @@ -481,15 +568,20 @@ def migrate_config(self, source_session: Session, target_session: Session) -> Di for source_var_id, source_var in source_variables.items(): if source_var.catalogPath: try: - target_var = Variable.from_catalog_path(target_session, source_var.catalogPath) + target_var = Variable.from_catalog_path( + target_session, source_var.catalogPath + ) except NoResultFound: - raise ValueError(f"variables.catalogPath not found in target: {source_var.catalogPath}") + raise ValueError( + f"variables.catalogPath not found in target: {source_var.catalogPath}" + ) # old style variable, match it on name and dataset id else: try: target_var = target_session.scalars( select(Variable).where( - Variable.name == source_var.name, Variable.datasetId == source_var.datasetId + Variable.name == source_var.name, + Variable.datasetId == source_var.datasetId, ) ).one() @@ -509,7 +601,9 @@ def migrate_config(self, source_session: Session, target_session: Session) -> Di # This should not be happening - it means that there's a chart with a variable that doesn't exist in # chart_dimensions and possibly not even in variables table. It's possible that you see it admin, but # only because it is cached. - raise ValueError(f"Issue with chart {self.id} - variable id not found in chart_dimensions table: {e}") + raise ValueError( + f"Issue with chart {self.id} - variable id not found in chart_dimensions table: {e}" + ) return config @@ -572,7 +666,11 @@ class Dataset(Base): __tablename__ = "datasets" __table_args__ = ( ForeignKeyConstraint( - ["createdByUserId"], ["users.id"], ondelete="RESTRICT", onupdate="RESTRICT", name="datasets_createdByUserId" + ["createdByUserId"], + ["users.id"], + ondelete="RESTRICT", + onupdate="RESTRICT", + name="datasets_createdByUserId", ), ForeignKeyConstraint( ["dataEditedByUserId"], @@ -597,20 +695,30 @@ class Dataset(Base): id: Mapped[int] = mapped_column(Integer, primary_key=True, init=False) name: Mapped[str] = mapped_column(VARCHAR(512)) description: Mapped[str] = mapped_column(LONGTEXT) - createdAt: Mapped[datetime] = mapped_column(DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False) + createdAt: Mapped[datetime] = mapped_column( + DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False + ) namespace: Mapped[str] = mapped_column(VARCHAR(255)) isPrivate: Mapped[int] = mapped_column(TINYINT(1), server_default=text("'0'")) createdByUserId: Mapped[int] = mapped_column(Integer) metadataEditedByUserId: Mapped[int] = mapped_column(Integer) dataEditedByUserId: Mapped[int] = mapped_column(Integer) - nonRedistributable: Mapped[int] = mapped_column(TINYINT(1), server_default=text("'0'")) + nonRedistributable: Mapped[int] = mapped_column( + TINYINT(1), server_default=text("'0'") + ) updatedAt: Mapped[Optional[datetime]] = mapped_column(DateTime, init=False) shortName: Mapped[Optional[str]] = mapped_column(VARCHAR(255)) version: Mapped[Optional[str]] = mapped_column(VARCHAR(255)) updatePeriodDays: Mapped[Optional[int]] = mapped_column(Integer) - dataEditedAt: Mapped[datetime] = mapped_column(DateTime, default=func.utc_timestamp()) - metadataEditedAt: Mapped[datetime] = mapped_column(DateTime, default=func.utc_timestamp()) - isArchived: Mapped[Optional[int]] = mapped_column(TINYINT(1), server_default=text("'0'"), default=0) + dataEditedAt: Mapped[datetime] = mapped_column( + DateTime, default=func.utc_timestamp() + ) + metadataEditedAt: Mapped[datetime] = mapped_column( + DateTime, default=func.utc_timestamp() + ) + isArchived: Mapped[Optional[int]] = mapped_column( + TINYINT(1), server_default=text("'0'"), default=0 + ) sourceChecksum: Mapped[Optional[str]] = mapped_column(VARCHAR(64), default=None) catalogPath: Mapped[Optional[str]] = mapped_column(VARCHAR(767), default=None) tables: Mapped[Optional[list]] = mapped_column(JSON, default=None) @@ -647,7 +755,11 @@ def upsert(self, session: Session) -> "Dataset": @classmethod def from_dataset_metadata( - cls, metadata: catalog.DatasetMeta, namespace: str, user_id: int, table_names: List[str] + cls, + metadata: catalog.DatasetMeta, + namespace: str, + user_id: int, + table_names: List[str], ) -> "Dataset": assert metadata.title return cls( @@ -671,14 +783,24 @@ def load_dataset(cls, session: Session, dataset_id: int) -> "Dataset": return session.scalars(select(cls).where(cls.id == dataset_id)).one() @classmethod - def load_with_path(cls, session: Session, namespace: str, short_name: str, version: str) -> "Dataset": + def load_with_path( + cls, session: Session, namespace: str, short_name: str, version: str + ) -> "Dataset": return session.scalars( - select(cls).where(cls.namespace == namespace, cls.shortName == short_name, cls.version == version) + select(cls).where( + cls.namespace == namespace, + cls.shortName == short_name, + cls.version == version, + ) ).one() @classmethod - def load_variables_for_dataset(cls, session: Session, dataset_id: int) -> list["Variable"]: - vars = session.scalars(select(Variable).where(Variable.datasetId == dataset_id)).all() + def load_variables_for_dataset( + cls, session: Session, dataset_id: int + ) -> list["Variable"]: + vars = session.scalars( + select(Variable).where(Variable.datasetId == dataset_id) + ).all() assert vars, f"Dataset {dataset_id} has no variables" return list(vars) @@ -737,14 +859,20 @@ class Source(Base): __tablename__ = "sources" __table_args__ = ( ForeignKeyConstraint( - ["datasetId"], ["datasets.id"], ondelete="RESTRICT", onupdate="RESTRICT", name="sources_datasetId" + ["datasetId"], + ["datasets.id"], + ondelete="RESTRICT", + onupdate="RESTRICT", + name="sources_datasetId", ), Index("sources_datasetId", "datasetId"), ) id: Mapped[int] = mapped_column(Integer, primary_key=True, init=False) description: Mapped[SourceDescription] = mapped_column(JSON) - createdAt: Mapped[datetime] = mapped_column(DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False) + createdAt: Mapped[datetime] = mapped_column( + DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False + ) name: Mapped[Optional[str]] = mapped_column(VARCHAR(512), default=None) updatedAt: Mapped[Optional[datetime]] = mapped_column(DateTime, init=False) datasetId: Mapped[Optional[int]] = mapped_column(Integer, default=None) @@ -757,13 +885,21 @@ def _upsert_select(self) -> Select: conds = [ cls.name == self.name, cls.datasetId == self.datasetId, - _json_is(cls.description, "additionalInfo", self.description.get("additionalInfo")), - _json_is(cls.description, "dataPublishedBy", self.description.get("dataPublishedBy")), + _json_is( + cls.description, + "additionalInfo", + self.description.get("additionalInfo"), + ), + _json_is( + cls.description, + "dataPublishedBy", + self.description.get("dataPublishedBy"), + ), ] return select(cls).where(*conds) - def upsert(self, session: Session) -> "Source": - ds = session.scalars(self._upsert_select).one_or_none() + async def upsert(self, session: AsyncSession) -> "Source": + ds = (await session.scalars(self._upsert_select)).one_or_none() if not ds: ds = self @@ -772,7 +908,9 @@ def upsert(self, session: Session) -> "Source": ds.description = self.description session.add(ds) - session.flush() # Ensure the object is written to the database and its ID is generated + await ( + session.flush() + ) # Ensure the object is written to the database and its ID is generated return ds @classmethod @@ -853,16 +991,24 @@ class Dimensions(TypedDict): class PostsGdocs(Base): __tablename__ = "posts_gdocs" - __table_args__ = (Index("idx_posts_gdocs_type", "type"), Index("idx_updatedAt", "updatedAt")) + __table_args__ = ( + Index("idx_posts_gdocs_type", "type"), + Index("idx_updatedAt", "updatedAt"), + ) id: Mapped[str] = mapped_column(VARCHAR(255), primary_key=True) slug: Mapped[str] = mapped_column(VARCHAR(255)) content: Mapped[dict] = mapped_column(JSON) published: Mapped[int] = mapped_column(TINYINT) createdAt: Mapped[datetime] = mapped_column(DateTime, init=False) - publicationContext: Mapped[str] = mapped_column(ENUM("unlisted", "listed"), server_default=text("'unlisted'")) + publicationContext: Mapped[str] = mapped_column( + ENUM("unlisted", "listed"), server_default=text("'unlisted'") + ) type: Mapped[Optional[str]] = mapped_column( - VARCHAR(255), Computed("(json_unquote(json_extract(`content`,_utf8mb4'$.type')))", persisted=False) + VARCHAR(255), + Computed( + "(json_unquote(json_extract(`content`,_utf8mb4'$.type')))", persisted=False + ), ) publishedAt: Mapped[Optional[datetime]] = mapped_column(DateTime) updatedAt: Mapped[Optional[datetime]] = mapped_column(DateTime, init=False) @@ -874,22 +1020,38 @@ class PostsGdocs(Base): class OriginsVariablesLink(Base): __tablename__ = "origins_variables" __table_args__ = ( - ForeignKeyConstraint(["originId"], ["origins.id"], name="origins_variables_ibfk_1"), - ForeignKeyConstraint(["variableId"], ["variables.id"], name="origins_variables_ibfk_2"), + ForeignKeyConstraint( + ["originId"], ["origins.id"], name="origins_variables_ibfk_1" + ), + ForeignKeyConstraint( + ["variableId"], ["variables.id"], name="origins_variables_ibfk_2" + ), Index("variableId", "variableId"), ) - originId: Mapped[int] = mapped_column(Integer, ForeignKey("users.id"), primary_key=True) - variableId: Mapped[int] = mapped_column(Integer, ForeignKey("variables.id"), primary_key=True) + originId: Mapped[int] = mapped_column( + Integer, ForeignKey("users.id"), primary_key=True + ) + variableId: Mapped[int] = mapped_column( + Integer, ForeignKey("variables.id"), primary_key=True + ) displayOrder: Mapped[int] = mapped_column(SmallInteger, server_default=text("'0'")) @classmethod - def link_with_variable(cls, session: Session, variable_id: int, new_origin_ids: List[int]) -> None: + async def link_with_variable( + cls, session: AsyncSession, variable_id: int, new_origin_ids: List[int] + ) -> None: """Link the given Variable ID with the given Origin IDs.""" # Fetch current linked Origins for the given Variable ID - existing_links = session.query(cls.originId, cls.displayOrder).filter(cls.variableId == variable_id).all() + existing_links = ( + await session.execute( + select(cls.originId, cls.displayOrder).filter_by(variableId=variable_id) + ) + ).all() - existing_origins = {(link.originId, link.displayOrder) for link in existing_links} + existing_origins = { + (link.originId, link.displayOrder) for link in existing_links + } new_origins = {(origin_id, i) for i, origin_id in enumerate(new_origin_ids)} # Find the Origin IDs to delete and the IDs to add @@ -898,17 +1060,29 @@ def link_with_variable(cls, session: Session, variable_id: int, new_origin_ids: # Delete the obsolete Origin-Variable links for origin_id, display_order in to_delete: - session.query(cls).filter( + # TODO: test that it works + stmt = delete(cls).where( cls.variableId == variable_id, cls.originId == origin_id, cls.displayOrder == display_order, - ).delete(synchronize_session="fetch") + ) + await session.execute(stmt) + + # session.query(cls).filter( + # cls.variableId == variable_id, + # cls.originId == origin_id, + # cls.displayOrder == display_order, + # ).delete(synchronize_session="fetch") # Add the new Origin-Variable links if to_add: session.add_all( [ - cls(originId=origin_id, variableId=variable_id, displayOrder=display_order) + cls( + originId=origin_id, + variableId=variable_id, + displayOrder=display_order, + ) for origin_id, display_order in to_add ] ) @@ -917,8 +1091,12 @@ def link_with_variable(cls, session: Session, variable_id: int, new_origin_ids: class PostsGdocsVariablesFaqsLink(Base): __tablename__ = "posts_gdocs_variables_faqs" __table_args__ = ( - ForeignKeyConstraint(["gdocId"], ["posts_gdocs.id"], name="posts_gdocs_variables_faqs_ibfk_1"), - ForeignKeyConstraint(["variableId"], ["variables.id"], name="posts_gdocs_variables_faqs_ibfk_2"), + ForeignKeyConstraint( + ["gdocId"], ["posts_gdocs.id"], name="posts_gdocs_variables_faqs_ibfk_1" + ), + ForeignKeyConstraint( + ["variableId"], ["variables.id"], name="posts_gdocs_variables_faqs_ibfk_2" + ), Index("variableId", "variableId"), ) @@ -928,32 +1106,55 @@ class PostsGdocsVariablesFaqsLink(Base): displayOrder: Mapped[int] = mapped_column(SmallInteger, server_default=text("'0'")) @classmethod - def link_with_variable(cls, session: Session, variable_id: int, new_faqs: List[catalog.FaqLink]) -> None: + async def link_with_variable( + cls, session: AsyncSession, variable_id: int, new_faqs: List[catalog.FaqLink] + ) -> None: """Link the given Variable ID with Faqs""" # Fetch current linked Faqs for the given Variable ID - existing_faqs = session.query(cls).filter(cls.variableId == variable_id).all() + existing_faqs = ( + (await session.execute(select(cls).filter_by(variableId=variable_id))) + .scalars() + .all() + ) # Work with tuples instead - existing_gdoc_fragment = {(f.gdocId, f.fragmentId, f.displayOrder) for f in existing_faqs} - new_gdoc_fragment = {(f.gdoc_id, f.fragment_id, i) for i, f in enumerate(new_faqs)} + existing_gdoc_fragment = { + (f.gdocId, f.fragmentId, f.displayOrder) for f in existing_faqs + } + new_gdoc_fragment = { + (f.gdoc_id, f.fragment_id, i) for i, f in enumerate(new_faqs) + } to_delete = existing_gdoc_fragment - new_gdoc_fragment to_add = new_gdoc_fragment - existing_gdoc_fragment # Delete the obsolete links for gdoc_id, fragment_id, display_order in to_delete: - session.query(cls).filter( + stmt = delete(cls).where( cls.variableId == variable_id, cls.gdocId == gdoc_id, cls.fragmentId == fragment_id, cls.displayOrder == display_order, - ).delete(synchronize_session="fetch") + ) + await session.execute(stmt) + + # session.query(cls).filter( + # cls.variableId == variable_id, + # cls.gdocId == gdoc_id, + # cls.fragmentId == fragment_id, + # cls.displayOrder == display_order, + # ).delete(synchronize_session="fetch") # Add the new links if to_add: session.add_all( [ - cls(gdocId=gdoc_id, fragmentId=fragment_id, displayOrder=display_order, variableId=variable_id) + cls( + gdocId=gdoc_id, + fragmentId=fragment_id, + displayOrder=display_order, + variableId=variable_id, + ) for gdoc_id, fragment_id, display_order in to_add ] ) @@ -962,8 +1163,12 @@ def link_with_variable(cls, session: Session, variable_id: int, new_faqs: List[c class TagsVariablesTopicTagsLink(Base): __tablename__ = "tags_variables_topic_tags" __table_args__ = ( - ForeignKeyConstraint(["tagId"], ["tags.id"], name="tags_variables_topic_tags_ibfk_1"), - ForeignKeyConstraint(["variableId"], ["variables.id"], name="tags_variables_topic_tags_ibfk_2"), + ForeignKeyConstraint( + ["tagId"], ["tags.id"], name="tags_variables_topic_tags_ibfk_1" + ), + ForeignKeyConstraint( + ["variableId"], ["variables.id"], name="tags_variables_topic_tags_ibfk_2" + ), Index("variableId", "variableId"), ) @@ -972,12 +1177,18 @@ class TagsVariablesTopicTagsLink(Base): displayOrder: Mapped[int] = mapped_column(SmallInteger, server_default=text("'0'")) @classmethod - def link_with_variable(cls, session: Session, variable_id: int, new_tag_ids: List[int]) -> None: + async def link_with_variable( + cls, session: AsyncSession, variable_id: int, new_tag_ids: List[int] + ) -> None: """Link the given Variable ID with the given Tag IDs.""" assert len(new_tag_ids) == len(set(new_tag_ids)), "Tag IDs must be unique" # Fetch current linked tags for the given Variable ID - existing_links = session.query(cls.tagId, cls.displayOrder).filter(cls.variableId == variable_id).all() + existing_links = ( + await session.execute( + select(cls.tagId, cls.displayOrder).filter_by(variableId=variable_id) + ) + ).all() existing_tags = {(link.tagId, link.displayOrder) for link in existing_links} new_tags = {(tag_id, i) for i, tag_id in enumerate(new_tag_ids)} @@ -988,17 +1199,25 @@ def link_with_variable(cls, session: Session, variable_id: int, new_tag_ids: Lis # Delete the obsolete links for tag_id, display_order in to_delete: - session.query(cls).filter( + stmt = delete(cls).where( cls.variableId == variable_id, cls.tagId == tag_id, cls.displayOrder == display_order, - ).delete(synchronize_session="fetch") + ) + await session.execute(stmt) + # session.query(cls).filter( + # cls.variableId == variable_id, + # cls.tagId == tag_id, + # cls.displayOrder == display_order, + # ).delete(synchronize_session="fetch") # Add the new links if to_add: session.add_all( [ - cls(tagId=tag_id, variableId=variable_id, displayOrder=display_order) + cls( + tagId=tag_id, variableId=variable_id, displayOrder=display_order + ) for tag_id, display_order in to_add ] ) @@ -1043,22 +1262,32 @@ class Variable(Base): ), Index("idx_catalogPath", "catalogPath", unique=True), Index("unique_short_name_per_dataset", "shortName", "datasetId", unique=True), - Index("variables_code_fk_dst_id_7bde8c2a_uniq", "code", "datasetId", unique=True), + Index( + "variables_code_fk_dst_id_7bde8c2a_uniq", "code", "datasetId", unique=True + ), Index("variables_datasetId_50a98bfd_fk_datasets_id", "datasetId"), - Index("variables_name_fk_dst_id_f7453c33_uniq", "name", "datasetId", unique=True), + Index( + "variables_name_fk_dst_id_f7453c33_uniq", "name", "datasetId", unique=True + ), Index("variables_sourceId_31fce80a_fk_sources_id", "sourceId"), ) id: Mapped[int] = mapped_column(Integer, primary_key=True, init=False) description: Mapped[Optional[str]] = mapped_column(LONGTEXT) unit: Mapped[str] = mapped_column(VARCHAR(255)) - createdAt: Mapped[datetime] = mapped_column(DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False) + createdAt: Mapped[datetime] = mapped_column( + DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False + ) coverage: Mapped[str] = mapped_column(VARCHAR(255)) timespan: Mapped[str] = mapped_column(VARCHAR(255)) datasetId: Mapped[int] = mapped_column(Integer) display: Mapped[dict] = mapped_column(JSON) - columnOrder: Mapped[int] = mapped_column(Integer, server_default=text("'0'"), default=0) - schemaVersion: Mapped[int] = mapped_column(Integer, server_default=text("'1'"), default=1) + columnOrder: Mapped[int] = mapped_column( + Integer, server_default=text("'0'"), default=0 + ) + schemaVersion: Mapped[int] = mapped_column( + Integer, server_default=text("'1'"), default=1 + ) name: Mapped[Optional[str]] = mapped_column(VARCHAR(750), default=None) updatedAt: Mapped[Optional[datetime]] = mapped_column(DateTime, init=False) code: Mapped[Optional[str]] = mapped_column(VARCHAR(255), default=None) @@ -1068,7 +1297,9 @@ class Variable(Base): shortName: Mapped[Optional[str]] = mapped_column(VARCHAR(255), default=None) catalogPath: Mapped[Optional[str]] = mapped_column(VARCHAR(767), default=None) dimensions: Mapped[Optional[Dimensions]] = mapped_column(JSON, default=None) - processingLevel: Mapped[Optional[catalog.meta.PROCESSING_LEVELS]] = mapped_column(VARCHAR(30), default=None) + processingLevel: Mapped[Optional[catalog.meta.PROCESSING_LEVELS]] = mapped_column( + VARCHAR(30), default=None + ) processingLog: Mapped[Optional[dict]] = mapped_column(JSON, default=None) titlePublic: Mapped[Optional[str]] = mapped_column(VARCHAR(512), default=None) titleVariant: Mapped[Optional[str]] = mapped_column(VARCHAR(255), default=None) @@ -1082,14 +1313,18 @@ class Variable(Base): licenses: Mapped[Optional[list[dict]]] = mapped_column(JSON, default=None) # NOTE: License should be the resulting license, given all licenses of the indicator’s origins and given the indicator’s processing level. license: Mapped[Optional[dict]] = mapped_column(JSON, default=None) - type: Mapped[Optional[VARIABLE_TYPE]] = mapped_column(ENUM(*get_args(VARIABLE_TYPE)), default=None) + type: Mapped[Optional[VARIABLE_TYPE]] = mapped_column( + ENUM(*get_args(VARIABLE_TYPE)), default=None + ) sort: Mapped[Optional[list[str]]] = mapped_column(JSON, default=None) - grapherConfigIdAdmin: Mapped[Optional[str]] = mapped_column(VARCHAR(32), default=None) + grapherConfigIdAdmin: Mapped[Optional[str]] = mapped_column( + VARCHAR(32), default=None + ) grapherConfigIdETL: Mapped[Optional[bytes]] = mapped_column(CHAR(32), default=None) dataChecksum: Mapped[Optional[str]] = mapped_column(VARCHAR(64), default=None) metadataChecksum: Mapped[Optional[str]] = mapped_column(VARCHAR(64), default=None) - def upsert(self, session: Session) -> "Variable": + async def upsert(self, session: AsyncSession) -> "Variable": assert self.catalogPath assert self.shortName @@ -1106,24 +1341,10 @@ def upsert(self, session: Session) -> "Variable": # try matching on shortName first q = select(cls).where( - or_( - cls.shortName == self.shortName, - # NOTE: we used to slugify shortName which replaced double underscore by a single underscore - # this was a bug, we should have kept the double underscore - # match even those variables and correct their shortName - cls.shortName == self.shortName.replace("__", "_"), - ), + cls.catalogPath == self.catalogPath, cls.datasetId == self.datasetId, ) - ds = session.scalars(q).one_or_none() - - # try matching on name if there was no match on shortName - if not ds: - q = select(cls).where( - cls.name == self.name, - cls.datasetId == self.datasetId, - ) - ds = session.scalars(q).one_or_none() + ds = (await session.scalars(q)).one_or_none() # there's a unique index on `name` which can cause conflict if we swap names of two variables # in that case, we append "(conflict)" to the name of the conflicting variable (it will be cleaned @@ -1136,12 +1357,12 @@ def upsert(self, session: Session) -> "Variable": cls.shortName != self.shortName, cls.datasetId == self.datasetId, ) - conflict = session.scalars(q).one_or_none() + conflict = (await session.scalars(q)).one_or_none() if conflict: # modify the conflicting variable name, it'll be cleaned up later conflict.name = f"{conflict.name} (conflict {random.randint(0, 1000)})" session.add(conflict) - session.commit() + await session.commit() if not ds: ds = self @@ -1183,7 +1404,9 @@ def upsert(self, session: Session) -> "Variable": ds.sort = self.sort session.add(ds) - session.flush() # Ensure the object is written to the database and its ID is generated + await ( + session.flush() + ) # Ensure the object is written to the database and its ID is generated return ds @classmethod @@ -1212,7 +1435,9 @@ def from_variable_metadata( presentation_dict.pop("faqs", None) if metadata.description_key: - assert isinstance(metadata.description_key, list), "descriptionKey should be a list of bullet points" + assert isinstance( + metadata.description_key, list + ), "descriptionKey should be a list of bullet points" return cls( shortName=short_name, @@ -1233,7 +1458,9 @@ def from_variable_metadata( descriptionFromProducer=metadata.description_from_producer, descriptionKey=metadata.description_key, descriptionProcessing=metadata.description_processing, - licenses=[license.to_dict() for license in metadata.licenses] if metadata.licenses else None, + licenses=[license.to_dict() for license in metadata.licenses] + if metadata.licenses + else None, license=metadata.license.to_dict() if metadata.license else None, type=metadata.type, sort=metadata.sort, @@ -1265,19 +1492,27 @@ def load_variable(cls, session: Session, variable_id: int) -> "Variable": @classmethod @deprecated("Use from_id_or_path instead") - def load_variables(cls, session: Session, variables_id: List[int]) -> List["Variable"]: + def load_variables( + cls, session: Session, variables_id: List[int] + ) -> List["Variable"]: return session.scalars(select(cls).where(cls.id.in_(variables_id))).all() # type: ignore @overload @classmethod def from_id_or_path( - cls, session: Session, id_or_path: str | int, columns: Optional[List[str]] = None + cls, + session: Session, + id_or_path: str | int, + columns: Optional[List[str]] = None, ) -> "Variable": ... @overload @classmethod def from_id_or_path( - cls, session: Session, id_or_path: List[str | int], columns: Optional[List[str]] = None + cls, + session: Session, + id_or_path: List[str | int], + columns: Optional[List[str]] = None, ) -> List["Variable"]: ... @classmethod @@ -1293,7 +1528,9 @@ def from_id_or_path( return cls.from_id(session=session, variable_id=id_or_path, columns=columns) # Single path elif isinstance(id_or_path, str): - return cls.from_catalog_path(session=session, catalog_path=id_or_path, columns=columns) + return cls.from_catalog_path( + session=session, catalog_path=id_or_path, columns=columns + ) # Multiple path or id elif isinstance(id_or_path, list): @@ -1302,10 +1539,14 @@ def from_id_or_path( str_ids = [i for i in id_or_path if isinstance(i, str)] # Multiple IDs if len(int_ids) == len(id_or_path): - return cls.from_id(session=session, variable_id=int_ids, columns=columns) + return cls.from_id( + session=session, variable_id=int_ids, columns=columns + ) # Multiple paths elif len(str_ids) == len(id_or_path): - return cls.from_catalog_path(session=session, catalog_path=str_ids, columns=columns) + return cls.from_catalog_path( + session=session, catalog_path=str_ids, columns=columns + ) else: raise TypeError("All elements in the list must be integers") @@ -1329,42 +1570,75 @@ def from_catalog_path( @overload @classmethod def from_catalog_path( - cls, session: Session, catalog_path: List[str], columns: Optional[List[str]] = None + cls, + session: Session, + catalog_path: List[str], + columns: Optional[List[str]] = None, ) -> List["Variable"]: ... @classmethod def from_catalog_path( - cls, session: Session, catalog_path: str | List[str], columns: Optional[List[str]] = None + cls, + session: Session, + catalog_path: str | List[str], + columns: Optional[List[str]] = None, ) -> "Variable" | List["Variable"]: """Load a variable from the DB by its catalog path.""" assert "#" in catalog_path, "catalog_path should end with #indicator_short_name" if isinstance(catalog_path, str): - return session.scalars(_select_columns(cls, columns).where(cls.catalogPath == catalog_path)).one() + return session.scalars( + _select_columns(cls, columns).where(cls.catalogPath == catalog_path) + ).one() elif isinstance(catalog_path, list): - return session.scalars(_select_columns(cls, columns).where(cls.catalogPath.in_(catalog_path))).all() # type: ignore + return session.scalars( + _select_columns(cls, columns).where(cls.catalogPath.in_(catalog_path)) + ).all() # type: ignore @overload @classmethod - def from_id(cls, session: Session, variable_id: int, columns: Optional[List[str]] = None) -> "Variable": ... + def from_id( + cls, session: Session, variable_id: int, columns: Optional[List[str]] = None + ) -> "Variable": ... @overload @classmethod def from_id( - cls, session: Session, variable_id: List[int], columns: Optional[List[str]] = None + cls, + session: Session, + variable_id: List[int], + columns: Optional[List[str]] = None, ) -> List["Variable"]: ... @classmethod def from_id( - cls, session: Session, variable_id: int | List[int], columns: Optional[List[str]] = None + cls, + session: Session, + variable_id: int | List[int], + columns: Optional[List[str]] = None, ) -> "Variable" | List["Variable"]: """Load a variable (or list of variables) from the DB by its ID path.""" if isinstance(variable_id, int): - return session.scalars(_select_columns(cls, columns).where(cls.id == variable_id)).one() + return session.scalars( + _select_columns(cls, columns).where(cls.id == variable_id) + ).one() elif isinstance(variable_id, list): - return session.scalars(_select_columns(cls, columns).where(cls.id.in_(variable_id))).all() # type: ignore + return session.scalars( + _select_columns(cls, columns).where(cls.id.in_(variable_id)) + ).all() # type: ignore + + @classmethod + async def load_from_catalog_path_async( + cls, session: AsyncSession, catalog_path: str + ) -> "Variable": + assert "#" in catalog_path, "catalog_path should end with #indicator_short_name" + return ( + await session.scalars(select(cls).where(cls.catalogPath == catalog_path)) + ).one() @classmethod - def catalog_paths_to_variable_ids(cls, session: Session, catalog_paths: List[str]) -> Dict[str, int]: + def catalog_paths_to_variable_ids( + cls, session: Session, catalog_paths: List[str] + ) -> Dict[str, int]: """Return a mapping from catalog paths to variable IDs.""" query = select(Variable).where(Variable.catalogPath.in_(catalog_paths)) return {var.catalogPath: var.id for var in session.scalars(query).all()} # type: ignore @@ -1374,33 +1648,49 @@ def infer_type(cls, values: pd.Series) -> VARIABLE_TYPE: """Set type and sort fields based on indicator values.""" return _infer_variable_type(values) - def update_links( - self, session: Session, db_origins: List["Origin"], faqs: List[catalog.FaqLink], tag_names: List[str] + async def _link_faqs( + self, session: AsyncSession, faqs: List[catalog.FaqLink] ) -> None: - """ - Establishes relationships between the current variable and a list of origins and a list of posts. - """ - assert self.id - - # establish relationships between variables and origins - OriginsVariablesLink.link_with_variable(session, self.id, [origin.id for origin in db_origins]) - # establish relationships between variables and posts required_gdoc_ids = {faq.gdoc_id for faq in faqs} query = select(PostsGdocs).where(PostsGdocs.id.in_(required_gdoc_ids)) - gdoc_posts = session.scalars(query).all() + gdoc_posts = (await session.scalars(query)).all() existing_gdoc_ids = {gdoc_post.id for gdoc_post in gdoc_posts} missing_gdoc_ids = required_gdoc_ids - existing_gdoc_ids if missing_gdoc_ids: log.warning("create_links.missing_faqs", missing_gdoc_ids=missing_gdoc_ids) - PostsGdocsVariablesFaqsLink.link_with_variable( + await PostsGdocsVariablesFaqsLink.link_with_variable( session, self.id, [faq for faq in faqs if faq.gdoc_id in existing_gdoc_ids] ) + async def update_links( + self, + session: AsyncSession, + db_origins: List["Origin"], + faqs: List[catalog.FaqLink], + tag_names: List[str], + ) -> None: + """ + Establishes relationships between the current variable and a list of origins and a list of posts. + """ + assert self.id + + # establish relationships between variables and origins + origins_variables_task = OriginsVariablesLink.link_with_variable( + session, self.id, [origin.id for origin in db_origins] + ) + + link_faqs_task = self._link_faqs(session, faqs) + # establish relationships between variables and tags - tags = Tag.load_tags_by_names(session, tag_names) + tags = await Tag.load_tags_by_names(session, tag_names) + + await TagsVariablesTopicTagsLink.link_with_variable( + session, self.id, [tag.id for tag in tags] + ) - TagsVariablesTopicTagsLink.link_with_variable(session, self.id, [tag.id for tag in tags]) + await origins_variables_task + await link_faqs_task def s3_data_path(self, typ: S3_PATH_TYP = "s3") -> str: """Path to S3 with data in JSON format for Grapher. Typically @@ -1433,7 +1723,9 @@ def table_name(self) -> str: def step_path(self) -> Path: """Return path to indicator step file.""" assert self.catalogPath - base_path = paths.STEP_DIR / "data" / self.catalogPath.split("#")[0].rsplit("/", 1)[0] + base_path = ( + paths.STEP_DIR / "data" / self.catalogPath.split("#")[0].rsplit("/", 1)[0] + ) return base_path.with_suffix(".py") @property @@ -1450,7 +1742,9 @@ def get_data(self, session: Optional[Session] = None) -> pd.DataFrame: df = pd.DataFrame(data) if session is not None: - df = add_entity_name(session=session, df=df, col_id="entities", col_name="entity") + df = add_entity_name( + session=session, df=df, col_id="entities", col_name="entity" + ) return df @@ -1486,7 +1780,9 @@ class ChartDimensions(Base): property: Mapped[str] = mapped_column(VARCHAR(255)) chartId: Mapped[int] = mapped_column(Integer) variableId: Mapped[int] = mapped_column(Integer) - createdAt: Mapped[datetime] = mapped_column(DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False) + createdAt: Mapped[datetime] = mapped_column( + DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False + ) updatedAt: Mapped[Optional[datetime]] = mapped_column(DateTime, init=False) @@ -1561,7 +1857,7 @@ def _upsert_select(self) -> Select: cls.dateAccessed == self.dateAccessed, ) - def upsert(self, session: Session) -> "Origin": + async def upsert(self, session: AsyncSession) -> "Origin": """ # NOTE: this would be an ideal solution if we only stored unique rows in # origins table, but there are weird race conditions and we cannot have @@ -1581,8 +1877,7 @@ def upsert(self, session: Session) -> "Origin": # select added object to get its id return session.scalars(self._upsert_select).one() """ - - origins = session.scalars(self._upsert_select).all() + origins = (await session.scalars(self._upsert_select)).all() if not origins: # create new origin origin = self @@ -1612,7 +1907,11 @@ class ChartDiffApprovals(Base): __tablename__ = "chart_diff_approvals" __table_args__ = ( ForeignKeyConstraint( - ["chartId"], ["charts.id"], ondelete="CASCADE", onupdate="CASCADE", name="chart_diff_approvals_ibfk_1" + ["chartId"], + ["charts.id"], + ondelete="CASCADE", + onupdate="CASCADE", + name="chart_diff_approvals_ibfk_1", ), Index("chartId", "chartId"), ) @@ -1626,7 +1925,11 @@ class ChartDiffApprovals(Base): @classmethod def latest_chart_approval_batch( - cls, session: Session, chart_ids: list[int], source_updated_ats: list, target_updated_ats: list + cls, + session: Session, + chart_ids: list[int], + source_updated_ats: list, + target_updated_ats: list, ) -> List[Optional["ChartDiffApprovals"]]: """Load the latest approval of the charts. @@ -1670,7 +1973,9 @@ def latest_chart_approval_batch( approval = results[chart_id] approvals.append(approval) - assert len(chart_ids) == len(approvals), "Length of chart_ids and approvals must be the same." + assert len(chart_ids) == len( + approvals + ), "Length of chart_ids and approvals must be the same." return approvals @@ -1691,7 +1996,11 @@ class ChartDiffConflicts(Base): __tablename__ = "chart_diff_conflicts" __table_args__ = ( ForeignKeyConstraint( - ["chartId"], ["charts.id"], ondelete="CASCADE", onupdate="CASCADE", name="chart_diff_conflicts_ibfk_1" + ["chartId"], + ["charts.id"], + ondelete="CASCADE", + onupdate="CASCADE", + name="chart_diff_conflicts_ibfk_1", ), Index("chartId", "chartId"), ) @@ -1747,7 +2056,9 @@ def get_conflict_batch( conflict = results[chart_id] conflicts.append(conflict) - assert len(chart_ids) == len(conflicts), "Length of chart_ids and conflicts must be the same." + assert len(chart_ids) == len( + conflicts + ), "Length of chart_ids and conflicts must be the same." return conflicts @@ -1757,15 +2068,23 @@ class MultiDimDataPage(Base): slug: Mapped[str] = mapped_column(VARCHAR(255), primary_key=True) config: Mapped[dict] = mapped_column(JSON) - published: Mapped[int] = mapped_column(TINYINT, server_default=text("'0'"), init=False) - createdAt: Mapped[datetime] = mapped_column(DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False) + published: Mapped[int] = mapped_column( + TINYINT, server_default=text("'0'"), init=False + ) + createdAt: Mapped[datetime] = mapped_column( + DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False + ) updatedAt: Mapped[datetime] = mapped_column( - DateTime, server_default=text("CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP"), init=False + DateTime, + server_default=text("CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP"), + init=False, ) def upsert(self, session: Session) -> "MultiDimDataPage": cls = self.__class__ - existing = session.scalars(select(cls).where(cls.slug == self.slug)).one_or_none() + existing = session.scalars( + select(cls).where(cls.slug == self.slug) + ).one_or_none() if existing: existing.config = self.config return existing @@ -1779,16 +2098,24 @@ class Anomaly(Base): # __table_args__ = (Index("catalogPath", "catalogPath"),) id: Mapped[int] = mapped_column(Integer, primary_key=True, init=False) - createdAt: Mapped[datetime] = mapped_column(DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False) + createdAt: Mapped[datetime] = mapped_column( + DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False + ) updatedAt: Mapped[datetime] = mapped_column( - DateTime, server_default=text("CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP"), init=False + DateTime, + server_default=text("CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP"), + init=False, ) datasetId: Mapped[int] = mapped_column(Integer) - datasetSourceChecksum: Mapped[Optional[str]] = mapped_column(VARCHAR(64), default=None) + datasetSourceChecksum: Mapped[Optional[str]] = mapped_column( + VARCHAR(64), default=None + ) anomalyType: Mapped[str] = mapped_column(VARCHAR(255), default=str) path_file: Mapped[Optional[str]] = mapped_column(VARCHAR(255), default=None) _dfScore: Mapped[Optional[bytes]] = mapped_column("dfScore", LONGBLOB, default=None) - _dfReduced: Mapped[Optional[bytes]] = mapped_column("dfReduced", LONGBLOB, default=None) + _dfReduced: Mapped[Optional[bytes]] = mapped_column( + "dfReduced", LONGBLOB, default=None + ) # catalogPath: Mapped[str] = mapped_column(VARCHAR(255), default=None) # NOTE: why do we need indicatorChecksum? # Answer: This can be useful to assign an anomaly to a specific snapshot of the indicator. Unclear if we need it atm, but maybe in the future... @@ -1807,7 +2134,11 @@ def __repr__(self) -> str: @classmethod def load(cls, session: Session, dataset_id: int, anomaly_type: str) -> "Anomaly": - return session.scalars(select(cls).where(cls.datasetId == dataset_id, cls.anomalyType == anomaly_type)).one() + return session.scalars( + select(cls).where( + cls.datasetId == dataset_id, cls.anomalyType == anomaly_type + ) + ).one() @hybrid_property def dfScore(self) -> Optional[pd.DataFrame]: # type: ignore @@ -1856,7 +2187,9 @@ def _json_is(json_field: Any, key: str, val: Any) -> Any: return json_field[key] == val -def _remap_variable_ids(config: Union[List, Dict[str, Any], Any], remap_ids: Dict[int, int]) -> Any: +def _remap_variable_ids( + config: Union[List, Dict[str, Any], Any], remap_ids: Dict[int, int] +) -> Any: """Replace variableIds from chart config using `remap_ids` mapping.""" if isinstance(config, dict): out = {} @@ -1932,7 +2265,9 @@ def add_entity_name( # Get entity names unique_entities = df[col_id].unique() - entities = _fetch_entities(session, list(unique_entities), col_id, col_name, col_code) + entities = _fetch_entities( + session, list(unique_entities), col_id, col_name, col_code + ) # Sanity check if set(unique_entities) - set(entities[col_id]): diff --git a/etl/steps/__init__.py b/etl/steps/__init__.py index de7649cf9b2..f6f48f89a4f 100644 --- a/etl/steps/__init__.py +++ b/etl/steps/__init__.py @@ -2,6 +2,7 @@ # __init__.py # steps # +import asyncio import graphlib import hashlib import json @@ -41,6 +42,7 @@ from etl import grapher_helpers as gh from etl import grapher_model as gm from etl.config import OWID_ENV, TLS_VERIFY +from etl.config import TLS_VERIFY from etl.db import get_engine from etl.snapshot import Snapshot @@ -897,12 +899,10 @@ def run(self) -> None: futures = [] verbose = True i = 0 + # import yappi - # NOTE: multiple tables will be saved under a single dataset, this could cause problems if someone - # is fetching the whole dataset from data-api as they would receive all tables merged in a single - # table. This won't be a problem after we introduce the concept of "tables" - for table in dataset: - assert not table.empty, f"table {table.metadata.short_name} is empty" + # yappi.set_clock_type("wall") # Use "cpu" for CPU time profiling + # yappi.start() # if GRAPHER_FILTER is set, only upsert matching columns if config.GRAPHER_FILTER: @@ -911,8 +911,12 @@ def run(self) -> None: continue cols += [c for c in table.columns if c in {"year", "date", "country"} and c not in cols] table = table.loc[:, cols] + catalog_paths = asyncio.run( + gi._upsert_tables_from_dataset_async(self.path, dataset, engine, admin_api, dataset_upsert_results) + ) - table = gh._adapt_table_for_grapher(table, engine) + # # Stop profiling + # yappi.stop() for t in gh._yield_wide_table(table, na_action="drop"): i += 1 diff --git a/etl/steps/data/grapher/biodiversity/2024-01-25/cherry_blossom.py b/etl/steps/data/grapher/biodiversity/2024-01-25/cherry_blossom.py index dc8556eab7c..f53020bd836 100644 --- a/etl/steps/data/grapher/biodiversity/2024-01-25/cherry_blossom.py +++ b/etl/steps/data/grapher/biodiversity/2024-01-25/cherry_blossom.py @@ -15,6 +15,9 @@ def run(dest_dir: str) -> None: # Read table from garden dataset. tb = ds_garden["cherry_blossom"] + + # tb = tb[["full_flowering_date"]] + # # Save outputs. # diff --git a/lib/catalog/owid/catalog/meta.py b/lib/catalog/owid/catalog/meta.py index 3913ec1fda6..594200b2b28 100644 --- a/lib/catalog/owid/catalog/meta.py +++ b/lib/catalog/owid/catalog/meta.py @@ -149,8 +149,12 @@ def __post_init__(self): if isinstance(self.date_published, (dt.date, int)): self.date_published = YearDateLatest(str(self.date_published)) - if self.date_published != "latest" and not is_year_or_date(self.date_published): - raise ValueError("date_published should be either a year or a date or latest") + if self.date_published != "latest" and not is_year_or_date( + self.date_published + ): + raise ValueError( + "date_published should be either a year or a date or latest" + ) # Minor is for cases where we only harmonized the countries or similar @@ -223,14 +227,18 @@ class VariableMeta(MetaBase): description_from_producer: Optional[str] = None # List of bullet points for the description key (can use markdown formatting) description_key: List[str] = field(default_factory=list) - origins: List[Origin] = field(default_factory=list) # Origins is the new replacement for sources + origins: List[Origin] = field( + default_factory=list + ) # Origins is the new replacement for sources # Use of `licenses` is discouraged, they should be captured in origins. licenses: List[License] = field(default_factory=list) unit: Optional[str] = None short_unit: Optional[str] = None # We keep display for the time being as the "less powerful sibling" of grapherConfig below display: Optional[Dict[str, Any]] = None - additional_info: Optional[Dict[str, Any]] = None # Only used for internal bookkeeping + additional_info: Optional[Dict[str, Any]] = ( + None # Only used for internal bookkeeping + ) # How much processing did we do to this data? processing_level: Optional[PROCESSING_LEVELS] = None @@ -420,7 +428,9 @@ def to_html(record: Any) -> Optional[str]: k, v_str ) ) - return '{}
'.format("".join(rows)) + return '{}
'.format( + "".join(rows) + ) elif isinstance(record, list): record = list(filter(None, record)) @@ -430,7 +440,9 @@ def to_html(record: Any) -> Optional[str]: rows = [] for item in record: rows.append("
  • {}
    • ".format(to_html(item))) - return ''.format("".join(rows)) + return ''.format( + "".join(rows) + ) else: return mistune.html(str(record)) # type: ignore @@ -460,7 +472,14 @@ def _deepcopy_dataclass(dc) -> Any: lis = type(v)(lis) setattr(dc, k, lis) elif isinstance(v, dict): - setattr(dc, k, {x: _deepcopy_dataclass(y) if is_dataclass(y) else y for x, y in v.items()}) + setattr( + dc, + k, + { + x: _deepcopy_dataclass(y) if is_dataclass(y) else y + for x, y in v.items() + }, + ) else: pass return dc diff --git a/lib/catalog/owid/catalog/s3_utils.py b/lib/catalog/owid/catalog/s3_utils.py index 564306ed695..dbeb97e7a87 100644 --- a/lib/catalog/owid/catalog/s3_utils.py +++ b/lib/catalog/owid/catalog/s3_utils.py @@ -144,10 +144,7 @@ def _read_owid_rclone_config() -> Dict[str, str]: return dict(config["owid-r2"].items()) -def connect_r2() -> BaseClient: - "Return a connection to Cloudflare's R2." - import boto3 - +def r2_config(): # first, get the R2 credentials from dotenv R2_ACCESS_KEY = env.get("R2_ACCESS_KEY") R2_SECRET_KEY = env.get("R2_SECRET_KEY") @@ -165,7 +162,7 @@ def connect_r2() -> BaseClient: except KeyError: pass - client = boto3.client( + return dict( service_name="s3", aws_access_key_id=R2_ACCESS_KEY, aws_secret_access_key=R2_SECRET_KEY, @@ -173,7 +170,12 @@ def connect_r2() -> BaseClient: region_name=R2_REGION_NAME or "auto", ) - return client + +def connect_r2() -> BaseClient: + "Return a connection to Cloudflare's R2." + import boto3 + + return boto3.client(**r2_config()) @lru_cache(maxsize=None) diff --git a/lib/catalog/owid/catalog/utils.py b/lib/catalog/owid/catalog/utils.py index c0dd0a65c71..fc2ec27e949 100644 --- a/lib/catalog/owid/catalog/utils.py +++ b/lib/catalog/owid/catalog/utils.py @@ -327,3 +327,13 @@ def dataclass_from_dict(cls: Optional[Type[T]], d: Dict[str, Any]) -> T: init_args[field_name] = v return cls(**init_args) + return hash(tuple([hash_any(y) for y in x])) + elif isinstance(x, dict): + return 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+content-hash = "d042113e7fdec8c807549a5b069b8c376f3e7d8592b0a31b4d767440c182181f" diff --git a/pyproject.toml b/pyproject.toml index 16272913362..e725208df62 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -52,7 +52,7 @@ dependencies = [ "html2text>=2020.1.16", "pygithub>=2.3.0", "pandas==2.2.3", - "sqlalchemy>=2.0.30", + sqlalchemy = {extras = ["asyncio"], version = "^2.0.34"} "pymysql>=1.1.1", "tiktoken>=0.7.0", "earthengine-api>=0.1.411", @@ -68,6 +68,8 @@ dependencies = [ "geopy>=2.4.1", "py7zr>=0.22.0", "pyreadr>=0.5.2", + aiobotocore = "^2.14.0" + aiomysql = "^0.2.0" ] [tool.uv.sources] diff --git a/tests/test_grapher_helpers.py b/tests/test_grapher_helpers.py index 661afe0b633..d4261c29c9b 100644 --- a/tests/test_grapher_helpers.py +++ b/tests/test_grapher_helpers.py @@ -120,7 +120,8 @@ def test_ensure_source_per_variable_multiple_sources(): ) ) table.metadata.dataset = DatasetMeta( - description="Dataset description", sources=[Source(name="s3", description="s3 description")] + description="Dataset description", + sources=[Source(name="s3", description="s3 description")], ) table.metadata.description = "Table description" @@ -177,15 +178,19 @@ def _sample_table() -> Table: ) ) table.metadata.dataset = DatasetMeta( - description="Dataset description", sources=[Source(name="s3", description="s3 description")] + description="Dataset description", + sources=[Source(name="s3", description="s3 description")], ) table.metadata.description = "Table description" return table def test_adapt_table_for_grapher_multiindex(): - with mock.patch("etl.grapher_helpers._get_entities_from_db") as mock_get_entities_from_db: + with mock.patch( + "etl.grapher_helpers._get_entities_from_db" + ) as mock_get_entities_from_db: with mock.patch("etl.grapher_io._fetch_entities") as mock_fetch_entities: + # with mock.patch("apps.backport.datasync.data_metadata._fetch_entities") as mock_fetch_entities: mock_get_entities_from_db.return_value = {"Poland": 1, "France": 2} mock_fetch_entities.return_value = pd.DataFrame( { @@ -199,17 +204,34 @@ def test_adapt_table_for_grapher_multiindex(): table = _sample_table() out_table = gh._adapt_table_for_grapher(table, engine) - assert out_table.index.names == ["entityId", "entityCode", "entityName", "year"] + assert out_table.index.names == [ + "entityId", + "entityCode", + "entityName", + "year", + ] assert out_table.columns.tolist() == ["deaths", "sex"] table = _sample_table().set_index(["country", "year", "sex"]) out_table = gh._adapt_table_for_grapher(table, engine) - assert out_table.index.names == ["entityId", "entityCode", "entityName", "year", "sex"] + assert out_table.index.names == [ + "entityId", + "entityCode", + "entityName", + "year", + "sex", + ] assert out_table.columns.tolist() == ["deaths"] table = _sample_table().set_index(["sex"]) out_table = gh._adapt_table_for_grapher(table, engine) - assert out_table.index.names == ["entityId", "entityCode", "entityName", "year", "sex"] + assert out_table.index.names == [ + "entityId", + "entityCode", + "entityName", + "year", + "sex", + ] assert out_table.columns.tolist() == ["deaths"] @@ -239,12 +261,20 @@ def test_underscore_column_and_dimensions(): short_name = "a" * 200 dims = {"age": "1" * 100} expected = short_name + "__age_1111111111111111_4e8d3bae4e8b9786396245429a8430af" - assert gh._underscore_column_and_dimensions(short_name, dims, trim_long_short_name=True) == expected + assert ( + gh._underscore_column_and_dimensions( + short_name, dims, trim_long_short_name=True + ) + == expected + ) def test_title_column_and_dimensions(): assert gh._title_column_and_dimensions("A", {"age": "1"}) == "A - Age: 1" - assert gh._title_column_and_dimensions("A", {"age_group": "15-18"}) == "A - Age group: 15-18" + assert ( + gh._title_column_and_dimensions("A", {"age_group": "15-18"}) + == "A - Age group: 15-18" + ) def test_long_to_wide(): @@ -262,7 +292,12 @@ def test_long_to_wide(): wide = gh.long_to_wide(table) - assert list(wide.columns) == ["deaths", "deaths__age_10_18", "deaths__age_19_25", "deaths__age_26_30"] + assert list(wide.columns) == [ + "deaths", + "deaths__age_10_18", + "deaths__age_19_25", + "deaths__age_26_30", + ] assert wide["deaths"].m.title == "Deaths" assert wide["deaths__age_10_18"].m.title == "Deaths - Age: 10-18" From a24ce286a733c92bc726d50ad7e4205a85b9cd31 Mon Sep 17 00:00:00 2001 From: Marigold Date: Thu, 19 Dec 2024 11:23:10 +0100 Subject: [PATCH 2/6] wip --- apps/backport/datasync/data_metadata.py | 11 +- apps/chart_sync/admin_api.py | 43 +- etl/db.py | 24 +- etl/grapher_helpers.py | 155 +- etl/grapher_import.py | 144 +- etl/grapher_model.py | 399 +- etl/steps/__init__.py | 52 - .../biodiversity/2024-01-25/cherry_blossom.py | 3 - poetry.lock | 8870 ----------------- pyproject.toml | 6 +- tests/test_grapher_helpers.py | 16 +- uv.lock | 84 +- 12 files changed, 234 insertions(+), 9573 deletions(-) delete mode 100644 poetry.lock diff --git a/apps/backport/datasync/data_metadata.py b/apps/backport/datasync/data_metadata.py index f2c674234d4..fa972f7e4a4 100644 --- a/apps/backport/datasync/data_metadata.py +++ b/apps/backport/datasync/data_metadata.py @@ -5,7 +5,7 @@ import numpy as np import pandas as pd from sqlalchemy import text -from sqlalchemy.orm import Session +from sqlalchemy.ext.asyncio import AsyncSession from structlog import get_logger log = get_logger() @@ -219,10 +219,7 @@ def _move_population_origin_to_end( new_origins = [] pop_origin = None for origin in origins: - if ( - origin.get("title") == "Population" - and origin.get("producer") == "Various sources" - ): + if origin.get("title") == "Population" and origin.get("producer") == "Various sources": pop_origin = origin else: new_origins.append(origin) @@ -231,9 +228,7 @@ def _move_population_origin_to_end( return new_origins -async def variable_metadata( - session: AsyncSession, variable_id: int, variable_data: pd.DataFrame -) -> Dict[str, Any]: +async def variable_metadata(session: AsyncSession, variable_id: int, variable_data: pd.DataFrame) -> Dict[str, Any]: """Fetch metadata for a single variable from database. This function was initially based on the one from owid-grapher repository and uses raw SQL commands. It'd be interesting to rewrite it using SQLAlchemy ORM in grapher_model.py. diff --git a/apps/chart_sync/admin_api.py b/apps/chart_sync/admin_api.py index 697ae962dbc..8cdd5ed52d5 100644 --- a/apps/chart_sync/admin_api.py +++ b/apps/chart_sync/admin_api.py @@ -26,9 +26,7 @@ def is_502_error(exception): class AdminAPI(object): - def __init__( - self, owid_env: OWIDEnv, grapher_user_id: Optional[int] = GRAPHER_USER_ID - ): + def __init__(self, owid_env: OWIDEnv, grapher_user_id: Optional[int] = GRAPHER_USER_ID): self.owid_env = owid_env self.session_id = create_session_id(owid_env, grapher_user_id) @@ -67,9 +65,7 @@ def create_chart(self, chart_config: dict, user_id: Optional[int] = None) -> dic raise AdminAPIError({"error": js["error"], "chart_config": chart_config}) return js - def update_chart( - self, chart_id: int, chart_config: dict, user_id: Optional[int] = None - ) -> dict: + def update_chart(self, chart_id: int, chart_config: dict, user_id: Optional[int] = None) -> dict: resp = requests.put( f"{self.owid_env.admin_api}/charts/{chart_id}", cookies={"sessionid": self._get_session_id(user_id)}, @@ -80,9 +76,7 @@ def update_chart( raise AdminAPIError({"error": js["error"], "chart_config": chart_config}) return js - def set_tags( - self, chart_id: int, tags: List[Dict[str, Any]], user_id: Optional[int] = None - ) -> dict: + def set_tags(self, chart_id: int, tags: List[Dict[str, Any]], user_id: Optional[int] = None) -> dict: resp = requests.post( f"{self.owid_env.admin_api}/charts/{chart_id}/setTags", cookies={"sessionid": self._get_session_id(user_id)}, @@ -93,9 +87,7 @@ def set_tags( raise AdminAPIError({"error": js["error"], "tags": tags}) return js - def put_grapher_config( - self, variable_id: int, grapher_config: Dict[str, Any] - ) -> dict: + def put_grapher_config(self, variable_id: int, grapher_config: Dict[str, Any]) -> dict: # If schema is missing, use the default one grapher_config.setdefault("$schema", DEFAULT_GRAPHER_SCHEMA) @@ -116,12 +108,8 @@ def put_grapher_config( ) return js - async def put_grapher_config( - self, variable_id: int, grapher_config: Dict[str, Any] - ) -> dict: - async with aiohttp.ClientSession( - cookies={"sessionid": self.session_id} - ) as session: + async def put_grapher_config(self, variable_id: int, grapher_config: Dict[str, Any]) -> dict: + async with aiohttp.ClientSession(cookies={"sessionid": self.session_id}) as session: async with session.put( self.base_url + f"/admin/api/variables/{variable_id}/grapherConfigETL", json=grapher_config, @@ -142,9 +130,7 @@ def delete_grapher_config(self, variable_id: int) -> dict: raise AdminAPIError({"error": js["error"], "variable_id": variable_id}) return js - def put_mdim_config( - self, slug: str, mdim_config: dict, user_id: Optional[int] = None - ) -> dict: + def put_mdim_config(self, slug: str, mdim_config: dict, user_id: Optional[int] = None) -> dict: # Retry in case we're restarting Admin on staging server resp = requests_with_retry().put( self.owid_env.admin_api + f"/multi-dim/{slug}", @@ -153,9 +139,7 @@ def put_mdim_config( ) js = self._json_from_response(resp) if not js["success"]: - raise AdminAPIError( - {"error": js["error"], "slug": slug, "mdim_config": mdim_config} - ) + raise AdminAPIError({"error": js["error"], "slug": slug, "mdim_config": mdim_config}) return js @@ -188,9 +172,7 @@ def _generate_random_string(length=32) -> str: return result_str -def _create_user_session( - session: Session, user_email: str, expiration_seconds=3600 -) -> str: +def _create_user_session(session: Session, user_email: str, expiration_seconds=3600) -> str: """Create a new short-lived session for given user and return its session id.""" # Generate a random string session_key = _generate_random_string() @@ -198,9 +180,7 @@ def _create_user_session( json_str = json.dumps({"user_email": user_email}) # Base64 encode - session_data = base64.b64encode(("prefix:" + json_str).encode("utf-8")).decode( - "utf-8" - ) + session_data = base64.b64encode(("prefix:" + json_str).encode("utf-8")).decode("utf-8") query = text( """ @@ -213,8 +193,7 @@ def _create_user_session( params={ "session_key": session_key, "session_data": session_data, - "expire_date": dt.datetime.utcnow() - + dt.timedelta(seconds=expiration_seconds), + "expire_date": dt.datetime.utcnow() + dt.timedelta(seconds=expiration_seconds), }, ) diff --git a/etl/db.py b/etl/db.py index 5a07cdf0506..673d6a23f2a 100644 --- a/etl/db.py +++ b/etl/db.py @@ -26,9 +26,7 @@ def can_connect(conf: Optional[Dict[str, Any]] = None) -> bool: return False -@deprecated( - "This function is deprecated. Instead, look at using etl.db.read_sql function." -) +@deprecated("This function is deprecated. Instead, look at using etl.db.read_sql function.") def get_connection(conf: Optional[Dict[str, Any]] = None) -> pymysql.Connection: "Connect to the Grapher database." cf: Any = dict_to_object(conf) if conf else config @@ -185,9 +183,7 @@ def _get_variables_data_with_filter( warnings.simplefilter("ignore", UserWarning) variables_data = pd.read_sql(query, con=db_conn, params=field_values) - assert set(variables_data[field_name]) <= set( - field_values - ), f"Unexpected values for {field_name}." + assert set(variables_data[field_name]) <= set(field_values), f"Unexpected values for {field_name}." # Warn about values that were not found. missing_values = set(field_values) - set(variables_data[field_name]) @@ -229,9 +225,7 @@ def get_variables_data( if filter is not None: df = pd.DataFrame({"id": []}).astype({"id": int}) for field_name, field_values in filter.items(): - _df = _get_variables_data_with_filter( - field_name=field_name, field_values=field_values, db_conn=db_conn - ) + _df = _get_variables_data_with_filter(field_name=field_name, field_values=field_values, db_conn=db_conn) if condition == "OR": df = pd.concat([df, _df], axis=0) elif condition == "AND": @@ -245,9 +239,7 @@ def get_variables_data( return df -def get_all_datasets( - archived: bool = True, db_conn: Optional[pymysql.Connection] = None -) -> pd.DataFrame: +def get_all_datasets(archived: bool = True, db_conn: Optional[pymysql.Connection] = None) -> pd.DataFrame: """Get all datasets in database. Parameters @@ -274,9 +266,7 @@ def dict_to_object(d): return type("DynamicObject", (object,), d)() -def read_sql( - sql: str, engine: Optional[Engine | Session] = None, *args, **kwargs -) -> pd.DataFrame: +def read_sql(sql: str, engine: Optional[Engine | Session] = None, *args, **kwargs) -> pd.DataFrame: """Wrapper around pd.read_sql that creates a connection and closes it after reading the data. This adds overhead, so if you need performance, reuse the same connection and cursor. """ @@ -321,7 +311,5 @@ def production_or_master_engine() -> Engine: elif config.ENV_FILE_PROD: return config.OWIDEnv.from_env_file(config.ENV_FILE_PROD).get_engine() else: - log.warning( - "ENV file doesn't connect to production DB, comparing against staging-site-master" - ) + log.warning("ENV file doesn't connect to production DB, comparing against staging-site-master") return config.OWIDEnv.from_staging("master").get_engine() diff --git a/etl/grapher_helpers.py b/etl/grapher_helpers.py index 76533143915..156e326ad26 100644 --- a/etl/grapher_helpers.py +++ b/etl/grapher_helpers.py @@ -46,12 +46,7 @@ def raise_helper(msg): # this might work too pd.api.types.is_integer_dtype(col) INT_TYPES = tuple( - { - f"{n}{b}{p}" - for n in ("int", "Int", "uint", "UInt") - for b in ("8", "16", "32", "64") - for p in ("", "[pyarrow]") - } + {f"{n}{b}{p}" for n in ("int", "Int", "uint", "UInt") for b in ("8", "16", "32", "64") for p in ("", "[pyarrow]")} ) @@ -71,11 +66,7 @@ def expand_dimensions(tb: catalog.Table) -> catalog.Table: This function is not very memory efficient as it returns a table that will be very sparse. """ # rename country to entity_id for the sake of `_yield_wide_table` - tb = ( - tb.reset_index("country") - .rename(columns={"country": "entity_id"}) - .set_index("entity_id", append=True) - ) + tb = tb.reset_index("country").rename(columns={"country": "entity_id"}).set_index("entity_id", append=True) tables = list(_yield_wide_table(tb, na_action="drop", warn_null_variables=False)) # join all tables @@ -119,19 +110,11 @@ def _yield_wide_table( for col in table.columns: if table[col].isna().any(): raise ValueError(f"Column `{col}` contains missing values") - cols_with_none_units = [ - col for col in table.columns if table[col].metadata.unit is None - ] + cols_with_none_units = [col for col in table.columns if table[col].metadata.unit is None] if cols_with_none_units: - raise Exception( - "Columns with missing units: " + ", ".join(cols_with_none_units) - ) + raise Exception("Columns with missing units: " + ", ".join(cols_with_none_units)) - dim_names = [ - k - for k in table.primary_key - if k not in ("year", "entityId", "entityCode", "entityName") - ] + dim_names = [k for k in table.primary_key if k not in ("year", "entityId", "entityCode", "entityName")] # Keep only entity_id and year in index table = table.reset_index(level=dim_names) @@ -153,9 +136,7 @@ def _yield_wide_table( dim_values = (dim_values,) # Exclude dimensions - table_to_yield = table_to_yield[ - [c for c in table_to_yield.columns if c not in dim_names] - ] + table_to_yield = table_to_yield[[c for c in table_to_yield.columns if c not in dim_names]] # Filter NaN values from dimensions and return dictionary dim_dict = _create_dim_dict(dim_names, dim_values) # type: ignore @@ -199,16 +180,12 @@ def _yield_wide_table( tab.metadata.short_name = short_name tab.rename(columns={column: short_name}, inplace=True) - tab[short_name].metadata = _metadata_for_dimensions( - tab[short_name].metadata, dim_dict, column - ) + tab[short_name].metadata = _metadata_for_dimensions(tab[short_name].metadata, dim_dict, column) yield tab -def _metadata_for_dimensions( - meta: catalog.VariableMeta, dim_dict: Dict[str, Any], column: str -) -> catalog.VariableMeta: +def _metadata_for_dimensions(meta: catalog.VariableMeta, dim_dict: Dict[str, Any], column: str) -> catalog.VariableMeta: """Add dimensions to metadata and expand Jinja in metadata fields.""" # add info about dimensions to metadata if dim_dict: @@ -217,8 +194,7 @@ def _metadata_for_dimensions( "originalShortName": column, "originalName": meta.title, "filters": [ - {"name": dim_name, "value": sanitize_numpy(dim_value)} - for dim_name, dim_value in dim_dict.items() + {"name": dim_name, "value": sanitize_numpy(dim_value)} for dim_name, dim_value in dim_dict.items() ], } } @@ -279,9 +255,7 @@ def long_to_wide(long_tb: catalog.Table) -> catalog.Table: if short_name in short_names: duplicate_short_name_ix = short_names.index(short_name) # raise ValueError(f"Duplicate short name: {short_name} for column: {column} and dimensions: {dim_dict}") - duplicate_dim_dict = dict( - zip(dim_names, wide_tb.columns[duplicate_short_name_ix][1:]) - ) + duplicate_dim_dict = dict(zip(dim_names, wide_tb.columns[duplicate_short_name_ix][1:])) raise ValueError( f"Duplicate short name for column '{column}' with dim values:\n{duplicate_dim_dict}\n{dim_dict}" ) @@ -289,9 +263,7 @@ def long_to_wide(long_tb: catalog.Table) -> catalog.Table: short_names.append(short_name) # Create metadata for the column from dimensions - metadatas.append( - _metadata_for_dimensions(long_tb[dims[0]].metadata.copy(), dim_dict, column) - ) + metadatas.append(_metadata_for_dimensions(long_tb[dims[0]].metadata.copy(), dim_dict, column)) # Set column names to new short names and use proper metadata wide_tb.columns = short_names @@ -351,9 +323,7 @@ def _expand_jinja(obj: Any, dim_dict: Dict[str, str]) -> Any: return obj -def render_yaml_file( - path: Union[str, Path], dim_dict: Dict[str, str] -) -> Dict[str, Any]: +def render_yaml_file(path: Union[str, Path], dim_dict: Dict[str, str]) -> Dict[str, Any]: """Load YAML file and render Jinja in all fields. Return a dictionary. Usage: @@ -367,9 +337,7 @@ def render_yaml_file( return _expand_jinja(meta, dim_dict) -def render_variable_meta( - meta: catalog.VariableMeta, dim_dict: Dict[str, str] -) -> catalog.VariableMeta: +def render_variable_meta(meta: catalog.VariableMeta, dim_dict: Dict[str, str]) -> catalog.VariableMeta: """Render Jinja in all fields of VariableMeta. Return a new VariableMeta object. Usage: @@ -387,16 +355,11 @@ def _title_column_and_dimensions(title: str, dim_dict: Dict[str, Any]) -> str: For instance `Deaths`, ["age", "sex"], ["10-18", "male"] will be converted into Deaths - Age: 10-18 - Sex: male """ - dims = [ - f"{dim_name.replace('_', ' ').capitalize()}: {dim_value}" - for dim_name, dim_value in dim_dict.items() - ] + dims = [f"{dim_name.replace('_', ' ').capitalize()}: {dim_value}" for dim_name, dim_value in dim_dict.items()] return " - ".join([title] + dims) -def _underscore_column_and_dimensions( - column: str, dim_dict: Dict[str, Any], trim_long_short_name: bool = True -) -> str: +def _underscore_column_and_dimensions(column: str, dim_dict: Dict[str, Any], trim_long_short_name: bool = True) -> str: # add dimension names to dimensions dims = [f"{dim_name}_{dim_value}" for dim_name, dim_value in dim_dict.items()] @@ -415,9 +378,7 @@ def _underscore_column_and_dimensions( dims=dim_dict, ) else: - raise AssertionError( - f"short_name {short_name} is too long for MySQL variables.shortName column" - ) + raise AssertionError(f"short_name {short_name} is too long for MySQL variables.shortName column") return short_name @@ -461,9 +422,9 @@ def long_to_wide_tables( # extract metadata from column and make sure it is identical for all rows meta = t.pop("meta") t.pop("variable") - assert ( - set(meta.map(id)) == {id(meta.iloc[0])} - ), f"Variable `{var_name}` must have same metadata objects in column `meta` for all rows" + assert set(meta.map(id)) == { + id(meta.iloc[0]) + }, f"Variable `{var_name}` must have same metadata objects in column `meta` for all rows" t[var_name].metadata = meta.iloc[0] # name table as variable name @@ -483,9 +444,7 @@ def _get_entities_from_db( return cast(Dict[str, int], df.set_index(by).entity_id.to_dict()) -def _get_and_create_entities_in_db( - countries: Set[str], engine: Engine | None = None -) -> Dict[str, int]: +def _get_and_create_entities_in_db(countries: Set[str], engine: Engine | None = None) -> Dict[str, int]: engine = engine or get_engine() with Session(engine) as session: log.info("Creating entities in DB", countries=countries) @@ -551,16 +510,10 @@ def country_to_entity_id( ix = entity_id.isnull() # cast to float to fix issues with categories entity_id[ix] = ( # type: ignore[reportCallIssue] - country[ix] - .map( - _get_and_create_entities_in_db(set(country[ix].unique()), engine=engine) - ) - .astype(float) # type: ignore[reportCallIssue] + country[ix].map(_get_and_create_entities_in_db(set(country[ix].unique()), engine=engine)).astype(float) # type: ignore[reportCallIssue] ) - assert ( - not entity_id.isnull().any() - ), f"Some countries have not been mapped: {set(country[entity_id.isnull()])}" # type: ignore[reportCallIssue] + assert not entity_id.isnull().any(), f"Some countries have not been mapped: {set(country[entity_id.isnull()])}" # type: ignore[reportCallIssue] return cast(pd.Series, entity_id.astype(int)) @@ -604,13 +557,7 @@ def combine_metadata_sources(sources: List[catalog.Source]) -> catalog.Source: # Combine sources' attributes into the first source (which is the only one that grapher will interpret). for attribute in attributes: # Gather non-empty values from each source for current attribute. - values = _unique( - [ - getattr(source, attribute) - for source in sources - if getattr(source, attribute) is not None - ] - ) + values = _unique([getattr(source, attribute) for source in sources if getattr(source, attribute) is not None]) if attribute == "description": # Descriptions are usually long, so it is better so put together descriptions from different sources in # separate lines. @@ -664,9 +611,7 @@ def _adapt_dataset_metadata_for_grapher( metadata.sources[0].description not in metadata.description and metadata.description not in metadata.sources[0].description ): - metadata.sources[0].description = ( - metadata.description + "\n" + metadata.sources[0].description - ) + metadata.sources[0].description = metadata.description + "\n" + metadata.sources[0].description else: metadata.sources[0].description = metadata.description @@ -700,11 +645,7 @@ def _adapt_table_for_grapher(table: catalog.Table, engine: Engine) -> catalog.Ta ), f"Variable titles are not unique:\n{variable_titles_counts[variable_titles_counts > 1].index}." # Remember original dimensions - dim_names = [ - n - for n in table.index.names - if n and n not in ("year", "date", "entity_id", "country") - ] + dim_names = [n for n in table.index.names if n and n not in ("year", "date", "entity_id", "country")] # Reset index unless we have default index if table.index.names != [None]: @@ -713,20 +654,14 @@ def _adapt_table_for_grapher(table: catalog.Table, engine: Engine) -> catalog.Ta # If a table contains `date` instead of `year`, adapt it for grapher if "date" in table.columns: # NOTE: this can be relaxed if we ever need it - assert ( - "year" not in table.columns - ), "Table cannot have both `date` and `year` columns." + assert "year" not in table.columns, "Table cannot have both `date` and `year` columns." table = adapt_table_with_dates_to_grapher(table) - assert {"year", "country"} <= set( - table.columns - ), "Table must have columns country and year." + assert {"year", "country"} <= set(table.columns), "Table must have columns country and year." assert "entity_id" not in table.columns, "Table must not have column entity_id." # Grapher needs a column entity id, that is constructed based on the unique entity names in the database. - table["entityId"] = country_to_entity_id( - table["country"], create_entities=True, engine=engine - ) + table["entityId"] = country_to_entity_id(table["country"], create_entities=True, engine=engine) table = table.drop(columns=["country"]) # Add entity code and name @@ -734,9 +669,7 @@ def _adapt_table_for_grapher(table: catalog.Table, engine: Engine) -> catalog.Ta table = add_entity_code_and_name(session, table).copy_metadata(table) # table = dm.add_entity_code_and_name(session, table).copy_metadata(table) - table = table.set_index( - ["entityId", "entityCode", "entityName", "year"] + dim_names - ) + table = table.set_index(["entityId", "entityCode", "entityName", "year"] + dim_names) # Ensure the default source of each column includes the description of the table (since that is the description that # will appear in grapher on the SOURCES tab). @@ -753,9 +686,7 @@ def _ensure_source_per_variable(table: catalog.Table) -> catalog.Table: # If neither variable and dataset has no sources, we're using origins instead. if len(variable_meta.sources) == 0 and len(dataset_meta.sources) == 0: - assert ( - len(variable_meta.origins) > 0 - ), f"Variable `{column}` has no sources or origins." + assert len(variable_meta.origins) > 0, f"Variable `{column}` has no sources or origins." continue if len(variable_meta.sources) == 0: @@ -768,9 +699,7 @@ def _ensure_source_per_variable(table: catalog.Table) -> catalog.Table: # Add the dataset description as if it was a source's description. if dataset_meta.description is not None: if source.description: - source.description = ( - dataset_meta.description + "\n" + source.description - ) + source.description = dataset_meta.description + "\n" + source.description else: source.description = dataset_meta.description else: @@ -904,10 +833,7 @@ def _rename_column(old_column_name: str, chart_slug: str) -> str: return f"{old_column_name}_chart_{underscore(chart_slug)}" # Create new columns. - new_columns = [ - _rename_column(old_column_name=column, chart_slug=chart_slug) - for column in columns_in_chart - ] + new_columns = [_rename_column(old_column_name=column, chart_slug=chart_slug) for column in columns_in_chart] table[new_columns] = table[columns_in_chart].copy() # Optionally fill some of the new columns with zeros. @@ -917,12 +843,9 @@ def _rename_column(old_column_name: str, chart_slug: str) -> str: assert set(columns_to_fill_with_zeros) <= set(columns_in_chart), error # Fill nans with zeros (in new columns). new_columns_to_fill_with_zeros = [ - _rename_column(old_column_name=column, chart_slug=chart_slug) - for column in columns_to_fill_with_zeros + _rename_column(old_column_name=column, chart_slug=chart_slug) for column in columns_to_fill_with_zeros ] - table[new_columns_to_fill_with_zeros] = table[ - new_columns_to_fill_with_zeros - ].fillna(0) + table[new_columns_to_fill_with_zeros] = table[new_columns_to_fill_with_zeros].fillna(0) # For each row, if any of the columns in the chart is nan, fill other columns in the same row with nan. table.loc[table[new_columns].isnull().any(axis=1), new_columns] = np.nan @@ -930,9 +853,7 @@ def _rename_column(old_column_name: str, chart_slug: str) -> str: # Handle metadata. for column in new_columns: # If the indicator did not have any display name, use the original title. - if ("name" not in table[column].display) or ( - table[column].metadata.display["name"] is None - ): + if ("name" not in table[column].display) or (table[column].metadata.display["name"] is None): table[column].metadata.display["name"] = table[column].metadata.title # To avoid having multiple indicators with the same title, add a suffix to the title. if suffix_for_titles is None: @@ -981,11 +902,7 @@ def adapt_table_with_dates_to_grapher( # If no columns are specified, list all columns in the table (except the country and date columns). if columns is None: - columns = [ - column - for column in tb.columns - if column not in [date_column, country_column] - ] + columns = [column for column in tb.columns if column not in [date_column, country_column]] for column in columns: # Find earliest date in the table. diff --git a/etl/grapher_import.py b/etl/grapher_import.py index 0ed1c8ce5c9..dde690e35b2 100644 --- a/etl/grapher_import.py +++ b/etl/grapher_import.py @@ -22,7 +22,6 @@ import structlog from aiobotocore.session import get_session from owid import catalog -from owid.catalog import Table, VariableMeta, utils from owid.catalog import Table, VariableMeta, s3_utils, utils from owid.catalog.utils import hash_any from sqlalchemy import select, text, update @@ -36,8 +35,7 @@ from apps.chart_sync.admin_api import AdminAPI from apps.wizard.app_pages.chart_diff.chart_diff import ChartDiffsLoader from etl import config -from etl.db import get_engine, production_or_master_engine -from etl.db import get_engine, get_engine_async +from etl.db import get_engine, get_engine_async, production_or_master_engine from . import grapher_helpers as gh from . import grapher_model as gm @@ -119,6 +117,8 @@ def upsert_dataset( assert source.name source_ids[hash(source)] = _upsert_source_to_db(session, source, ds.id) + await session.commit() + return DatasetUpsertResult(ds.id, source_ids) @@ -332,141 +332,6 @@ async def upsert_table( log.info("upsert_table.uploaded_to_s3", size=len(df), variable_id=db_variable.id) -def upsert_data(df: pd.DataFrame, s3_data_path: str): - # upload data to R2 - var_data = dm.variable_data(df) - var_data_str = json.dumps(var_data, default=str) - upload_gzip_string(var_data_str, s3_data_path) - - -def upsert_metadata( - session: Session, - df: pd.DataFrame, - variable_meta: VariableMeta, - column_name: str, - dataset_upsert_result: DatasetUpsertResult, - catalog_path: str, - dimensions: Optional[gm.Dimensions], - admin_api: AdminAPI, -) -> gm.Variable: - timespan = _get_timespan(df, variable_meta) - - source_id = _add_or_update_source(session, variable_meta, column_name, dataset_upsert_result) - - with origins_table_lock: - db_origins = _add_or_update_origins(session, variable_meta.origins) - # commit within the lock to make sure other threads get the latest sources - session.commit() - - # pop grapher_config from variable metadata, later we send it to Admin API - if variable_meta.presentation and variable_meta.presentation.grapher_config: - grapher_config = variable_meta.presentation.grapher_config - variable_meta.presentation.grapher_config = None - else: - grapher_config = None - - db_variable = gm.Variable.from_variable_metadata( - variable_meta, - short_name=column_name, - timespan=timespan, - dataset_id=dataset_upsert_result.dataset_id, - source_id=source_id, - catalog_path=catalog_path, - dimensions=dimensions, - ).upsert(session) - db_variable_id = db_variable.id - assert db_variable_id - - # TODO: `type` is part of metadata, but not part of checksum! - if not db_variable.type: - db_variable.type = db_variable.infer_type(df["value"]) - - # update links, we need to do it after we commit deleted relationships above - db_variable.update_links( - session, - db_origins, - faqs=variable_meta.presentation.faqs if variable_meta.presentation else [], - tag_names=variable_meta.presentation.topic_tags if variable_meta.presentation else [], - ) - session.add(db_variable) - -""" - # All following functions assume that `value` is string - # NOTE: we could make the code more efficient if we didn't convert `value` to string - # TODO: can we avoid setting & resetting index back and forth? - df = table.reset_index().rename(columns={column_name: "value"}) - df["value"] = df["value"].astype("string") - - checksum_data = calculate_checksum_data(df) - checksum_metadata = calculate_checksum_metadata(variable_meta, df) - - # NOTE: this is useful for debugging, will be removed once it is stable - if os.environ.get("SKIP_CHECKSUMS"): - import random - - checksum_metadata = str(random.randint(0, 10000)) - checksum_data = str(random.randint(0, 10000)) - - async with semaphore: - log.info( - "upsert_dataset.upsert_table.start", - column_name=column_name, - ) - - async_session = async_sessionmaker(engine_async, expire_on_commit=False) - async with async_session() as session: - # compare checksums - try: - db_variable = await gm.Variable.load_from_catalog_path_async(session, catalog_path) - except NoResultFound: - db_variable = None - - upsert_metadata_kwargs = dict( - session=session, - df=df, - variable_meta=variable_meta, - column_name=column_name, - dataset_upsert_result=dataset_upsert_result, - catalog_path=catalog_path, - dimensions=dimensions, - admin_api=admin_api, - client=client, - ) - - # create variable if it doesn't exist - if not db_variable: - db_variable = await upsert_metadata(**upsert_metadata_kwargs) - await upsert_data(df, db_variable.s3_data_path(), client) - - # variable exists - else: - if db_variable.dataChecksum == checksum_data and db_variable.metadataChecksum == checksum_metadata: - if verbose: - log.info("upsert_table.skipped_no_changes", size=len(df), variable_id=db_variable.id) - return - - upsert_data_task = None - if db_variable.dataChecksum != checksum_data: - upsert_data_task = upsert_data(df, db_variable.s3_data_path(), client) - - if db_variable.metadataChecksum != checksum_metadata: - db_variable = await upsert_metadata(**upsert_metadata_kwargs) - - if upsert_data_task: - await upsert_data_task - - # Update checksums - db_variable.dataChecksum = checksum_data - db_variable.metadataChecksum = checksum_metadata - - # Commit new checksums - session.add(db_variable) - await session.commit() - - if verbose: - log.info("upsert_table.uploaded_to_s3", size=len(df), variable_id=db_variable.id) - - async def upsert_data(df: pd.DataFrame, s3_data_path: str, client) -> None: # upload data to R2 var_data = dm.variable_data(df) @@ -516,7 +381,6 @@ async def upsert_metadata( # TODO: `type` is part of metadata, but not part of checksum! if not db_variable.type: db_variable.type = db_variable.infer_type(df["value"]) - session.add(db_variable) # update links, we need to do it after we commit deleted relationships above update_links_task = db_variable.update_links( @@ -525,7 +389,7 @@ async def upsert_metadata( faqs=variable_meta.presentation.faqs if variable_meta.presentation else [], tag_names=variable_meta.presentation.topic_tags if variable_meta.presentation else [], ) -""" + # we need to commit changes because `dm.variable_metadata` pulls all data from MySQL # and sends it to R2 # NOTE: we could optimize this by evading pulling from MySQL and instead constructing JSON files from objects diff --git a/etl/grapher_model.py b/etl/grapher_model.py index ca9761d671e..a07ac849027 100644 --- a/etl/grapher_model.py +++ b/etl/grapher_model.py @@ -115,9 +115,7 @@ def from_dict(cls, d: Dict[str, Any]) -> Self: return x @classmethod - def create_table( - cls, engine: Engine, if_exists: Literal["fail", "replace", "skip"] = "fail" - ) -> None: + def create_table(cls, engine: Engine, if_exists: Literal["fail", "replace", "skip"] = "fail") -> None: if if_exists == "replace": # Drop the table if it exists and create a new one cls.__table__.drop(engine, checkfirst=True) # type: ignore @@ -142,16 +140,12 @@ class Entity(Base): id: Mapped[int] = mapped_column(Integer, primary_key=True, init=False) name: Mapped[str] = mapped_column(VARCHAR(255)) validated: Mapped[int] = mapped_column(TINYINT(1)) - createdAt: Mapped[datetime] = mapped_column( - DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False - ) + createdAt: Mapped[datetime] = mapped_column(DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False) code: Mapped[Optional[str]] = mapped_column(VARCHAR(255)) updatedAt: Mapped[Optional[datetime]] = mapped_column(DateTime, init=False) @classmethod - def load_entity_mapping( - cls, session: Session, entity_ids: Optional[List[int]] = None - ) -> Dict[int, str]: + def load_entity_mapping(cls, session: Session, entity_ids: Optional[List[int]] = None) -> Dict[int, str]: q = text( """ select @@ -194,12 +188,8 @@ class Namespace(Base): id: Mapped[int] = mapped_column(Integer, primary_key=True, init=False) name: Mapped[str] = mapped_column(VARCHAR(255)) - isArchived: Mapped[int] = mapped_column( - TINYINT(1), server_default=text("'0'"), default=0 - ) - createdAt: Mapped[datetime] = mapped_column( - DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False - ) + isArchived: Mapped[int] = mapped_column(TINYINT(1), server_default=text("'0'"), default=0) + createdAt: Mapped[datetime] = mapped_column(DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False) description: Mapped[Optional[str]] = mapped_column(VARCHAR(255), default=None) updatedAt: Mapped[Optional[datetime]] = mapped_column(DateTime, init=False) @@ -246,9 +236,7 @@ class Tag(Base): id: Mapped[int] = mapped_column(Integer, primary_key=True, init=False) name: Mapped[str] = mapped_column(VARCHAR(255)) - createdAt: Mapped[datetime] = mapped_column( - DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False - ) + createdAt: Mapped[datetime] = mapped_column(DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False) updatedAt: Mapped[Optional[datetime]] = mapped_column(DateTime, init=False) parentId: Mapped[Optional[int]] = mapped_column(Integer) specialType: Mapped[Optional[str]] = mapped_column(VARCHAR(255)) @@ -259,9 +247,7 @@ def load_tags(cls, session: Session) -> List["Tag"]: return list(session.scalars(select(cls).where(cls.slug.isnot(None))).all()) @classmethod - async def load_tags_by_names( - cls, session: AsyncSession, tag_names: List[str] - ) -> List["Tag"]: + async def load_tags_by_names(cls, session: AsyncSession, tag_names: List[str]) -> List["Tag"]: """Load topic tags by their names in the order given in `tag_names`.""" tags = (await session.scalars(select(Tag).where(Tag.name.in_(tag_names)))).all() @@ -271,10 +257,7 @@ async def load_tags_by_names( tag_names = found_tags log.warning("create_links.missing_tags", tags=missing_tags) - tags = [ - next(tag for tag in tags if tag.name == ordered_name) - for ordered_name in tag_names - ] + tags = [next(tag for tag in tags if tag.name == ordered_name) for ordered_name in tag_names] return tags @@ -285,9 +268,7 @@ class User(Base): id: Mapped[int] = mapped_column(Integer, primary_key=True, init=False) isSuperuser: Mapped[int] = mapped_column(TINYINT(1), server_default=text("'0'")) email: Mapped[str] = mapped_column(VARCHAR(255)) - createdAt: Mapped[datetime] = mapped_column( - DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False - ) + createdAt: Mapped[datetime] = mapped_column(DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False) isActive: Mapped[int] = mapped_column(TINYINT(1), server_default=text("'1'")) fullName: Mapped[str] = mapped_column(VARCHAR(255)) githubUsername: Mapped[str] = mapped_column(VARCHAR(255)) @@ -298,9 +279,7 @@ class User(Base): @classmethod def load_user(cls, session: Session, github_username: str) -> Optional["User"]: - return session.scalars( - select(cls).where(cls.githubUsername == github_username) - ).one_or_none() + return session.scalars(select(cls).where(cls.githubUsername == github_username)).one_or_none() class ChartRevisions(Base): @@ -318,9 +297,7 @@ class ChartRevisions(Base): ) id: Mapped[int] = mapped_column(BigInteger, primary_key=True) - createdAt: Mapped[datetime] = mapped_column( - DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False - ) + createdAt: Mapped[datetime] = mapped_column(DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False) chartId: Mapped[Optional[int]] = mapped_column(Integer) userId: Mapped[Optional[int]] = mapped_column(Integer) config: Mapped[Optional[dict]] = mapped_column(JSON) @@ -334,9 +311,7 @@ class ChartConfig(Base): id: Mapped[bytes] = mapped_column(CHAR(36), primary_key=True) patch: Mapped[dict] = mapped_column(JSON, nullable=False) full: Mapped[dict] = mapped_column(JSON, nullable=False) - fullMd5: Mapped[str] = mapped_column( - CHAR(24), Computed("(to_base64(unhex(md5(full))))", persisted=True) - ) + fullMd5: Mapped[str] = mapped_column(CHAR(24), Computed("(to_base64(unhex(md5(full))))", persisted=True)) slug: Mapped[Optional[str]] = mapped_column( String(255), Computed("(json_unquote(json_extract(`full`, '$.slug')))", persisted=True), @@ -348,16 +323,10 @@ class ChartConfig(Base): persisted=True, ), ) - createdAt: Mapped[datetime] = mapped_column( - DateTime, server_default=text("CURRENT_TIMESTAMP"), nullable=False - ) - updatedAt: Mapped[Optional[datetime]] = mapped_column( - DateTime, onupdate=func.current_timestamp() - ) + createdAt: Mapped[datetime] = mapped_column(DateTime, server_default=text("CURRENT_TIMESTAMP"), nullable=False) + updatedAt: Mapped[Optional[datetime]] = mapped_column(DateTime, onupdate=func.current_timestamp()) - chartss: Mapped[List["Chart"]] = relationship( - "Chart", back_populates="chart_config" - ) + chartss: Mapped[List["Chart"]] = relationship("Chart", back_populates="chart_config") class Chart(Base): @@ -391,9 +360,7 @@ class Chart(Base): id: Mapped[int] = mapped_column(Integer, primary_key=True, init=False) configId: Mapped[bytes] = mapped_column(CHAR(36)) - createdAt: Mapped[datetime] = mapped_column( - DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False - ) + createdAt: Mapped[datetime] = mapped_column(DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False) lastEditedAt: Mapped[datetime] = mapped_column(DateTime) lastEditedByUserId: Mapped[int] = mapped_column(Integer) isIndexable: Mapped[int] = mapped_column(TINYINT(1), server_default=text("'0'")) @@ -401,9 +368,7 @@ class Chart(Base): publishedAt: Mapped[Optional[datetime]] = mapped_column(DateTime) publishedByUserId: Mapped[Optional[int]] = mapped_column(Integer) - chart_config: Mapped["ChartConfig"] = relationship( - "ChartConfig", back_populates="chartss", lazy="joined" - ) + chart_config: Mapped["ChartConfig"] = relationship("ChartConfig", back_populates="chartss", lazy="joined") @hybrid_property def updatedAt(self) -> datetime: # type: ignore @@ -420,11 +385,7 @@ def config(self) -> dict[str, Any]: # type: ignore @config.expression def config(cls): - return ( - select(ChartConfig.full) - .where(ChartConfig.id == cls.configId) - .scalar_subquery() - ) + return select(ChartConfig.full).where(ChartConfig.id == cls.configId).scalar_subquery() @hybrid_property def slug(self) -> Optional[str]: # type: ignore @@ -432,11 +393,7 @@ def slug(self) -> Optional[str]: # type: ignore @slug.expression def slug(cls): - return ( - select(ChartConfig.slug) - .where(ChartConfig.id == cls.configId) - .scalar_subquery() - ) + return select(ChartConfig.slug).where(ChartConfig.id == cls.configId).scalar_subquery() @classmethod def load_chart( @@ -474,17 +431,11 @@ def load_charts(cls, session: Session, chart_ids: List[int]) -> List["Chart"]: return list(charts) @classmethod - def load_charts_using_variables( - cls, session: Session, variable_ids: List[int] - ) -> List["Chart"]: + def load_charts_using_variables(cls, session: Session, variable_ids: List[int]) -> List["Chart"]: """Load charts that use any of the given variables in `variable_ids`.""" # Find IDs of charts chart_ids = ( - session.scalars( - select(ChartDimensions.chartId).where( - ChartDimensions.variableId.in_(variable_ids) - ) - ) + session.scalars(select(ChartDimensions.chartId).where(ChartDimensions.variableId.in_(variable_ids))) .unique() .all() ) @@ -518,9 +469,7 @@ def load_chart_variables(self, session: Session) -> Dict[int, "Variable"]: return variables @classmethod - def load_variables_checksums( - cls, session: Session, chart_ids: List[int] - ) -> pd.DataFrame: + def load_variables_checksums(cls, session: Session, chart_ids: List[int]) -> pd.DataFrame: """Load checksums for all variables from the chart and return them as a list of dicts.""" q = """ select @@ -532,9 +481,7 @@ def load_variables_checksums( join variables as v on v.id = cd.variableId where cd.chartId in %(chart_id)s """ - return read_sql(q, session, params={"chart_id": chart_ids}).set_index( - ["chartId", "catalogPath"] - ) + return read_sql(q, session, params={"chart_id": chart_ids}).set_index(["chartId", "catalogPath"]) def load_variable_checksums(self, session: Session) -> pd.DataFrame: """Load checksums for all variables from the chart and return them as a list of dicts.""" @@ -547,13 +494,9 @@ def load_variable_checksums(self, session: Session) -> pd.DataFrame: join variables as v on v.id = cd.variableId where cd.chartId = %(chart_id)s """ - return read_sql(q, session, params={"chart_id": self.id}).set_index( - "catalogPath" - ) + return read_sql(q, session, params={"chart_id": self.id}).set_index("catalogPath") - def migrate_config( - self, source_session: Session, target_session: Session - ) -> Dict[str, Any]: + def migrate_config(self, source_session: Session, target_session: Session) -> Dict[str, Any]: """Remap variable ids from source to target session. Variable in source is uniquely identified by its catalogPath if available, or by name and datasetId otherwise. It is looked up by this identifier in the target session to get the new variable id. @@ -568,13 +511,9 @@ def migrate_config( for source_var_id, source_var in source_variables.items(): if source_var.catalogPath: try: - target_var = Variable.from_catalog_path( - target_session, source_var.catalogPath - ) + target_var = Variable.from_catalog_path(target_session, source_var.catalogPath) except NoResultFound: - raise ValueError( - f"variables.catalogPath not found in target: {source_var.catalogPath}" - ) + raise ValueError(f"variables.catalogPath not found in target: {source_var.catalogPath}") # old style variable, match it on name and dataset id else: try: @@ -601,9 +540,7 @@ def migrate_config( # This should not be happening - it means that there's a chart with a variable that doesn't exist in # chart_dimensions and possibly not even in variables table. It's possible that you see it admin, but # only because it is cached. - raise ValueError( - f"Issue with chart {self.id} - variable id not found in chart_dimensions table: {e}" - ) + raise ValueError(f"Issue with chart {self.id} - variable id not found in chart_dimensions table: {e}") return config @@ -695,30 +632,20 @@ class Dataset(Base): id: Mapped[int] = mapped_column(Integer, primary_key=True, init=False) name: Mapped[str] = mapped_column(VARCHAR(512)) description: Mapped[str] = mapped_column(LONGTEXT) - createdAt: Mapped[datetime] = mapped_column( - DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False - ) + createdAt: Mapped[datetime] = mapped_column(DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False) namespace: Mapped[str] = mapped_column(VARCHAR(255)) isPrivate: Mapped[int] = mapped_column(TINYINT(1), server_default=text("'0'")) createdByUserId: Mapped[int] = mapped_column(Integer) metadataEditedByUserId: Mapped[int] = mapped_column(Integer) dataEditedByUserId: Mapped[int] = mapped_column(Integer) - nonRedistributable: Mapped[int] = mapped_column( - TINYINT(1), server_default=text("'0'") - ) + nonRedistributable: Mapped[int] = mapped_column(TINYINT(1), server_default=text("'0'")) updatedAt: Mapped[Optional[datetime]] = mapped_column(DateTime, init=False) shortName: Mapped[Optional[str]] = mapped_column(VARCHAR(255)) version: Mapped[Optional[str]] = mapped_column(VARCHAR(255)) updatePeriodDays: Mapped[Optional[int]] = mapped_column(Integer) - dataEditedAt: Mapped[datetime] = mapped_column( - DateTime, default=func.utc_timestamp() - ) - metadataEditedAt: Mapped[datetime] = mapped_column( - DateTime, default=func.utc_timestamp() - ) - isArchived: Mapped[Optional[int]] = mapped_column( - TINYINT(1), server_default=text("'0'"), default=0 - ) + dataEditedAt: Mapped[datetime] = mapped_column(DateTime, default=func.utc_timestamp()) + metadataEditedAt: Mapped[datetime] = mapped_column(DateTime, default=func.utc_timestamp()) + isArchived: Mapped[Optional[int]] = mapped_column(TINYINT(1), server_default=text("'0'"), default=0) sourceChecksum: Mapped[Optional[str]] = mapped_column(VARCHAR(64), default=None) catalogPath: Mapped[Optional[str]] = mapped_column(VARCHAR(767), default=None) tables: Mapped[Optional[list]] = mapped_column(JSON, default=None) @@ -783,9 +710,7 @@ def load_dataset(cls, session: Session, dataset_id: int) -> "Dataset": return session.scalars(select(cls).where(cls.id == dataset_id)).one() @classmethod - def load_with_path( - cls, session: Session, namespace: str, short_name: str, version: str - ) -> "Dataset": + def load_with_path(cls, session: Session, namespace: str, short_name: str, version: str) -> "Dataset": return session.scalars( select(cls).where( cls.namespace == namespace, @@ -795,12 +720,8 @@ def load_with_path( ).one() @classmethod - def load_variables_for_dataset( - cls, session: Session, dataset_id: int - ) -> list["Variable"]: - vars = session.scalars( - select(Variable).where(Variable.datasetId == dataset_id) - ).all() + def load_variables_for_dataset(cls, session: Session, dataset_id: int) -> list["Variable"]: + vars = session.scalars(select(Variable).where(Variable.datasetId == dataset_id)).all() assert vars, f"Dataset {dataset_id} has no variables" return list(vars) @@ -870,9 +791,7 @@ class Source(Base): id: Mapped[int] = mapped_column(Integer, primary_key=True, init=False) description: Mapped[SourceDescription] = mapped_column(JSON) - createdAt: Mapped[datetime] = mapped_column( - DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False - ) + createdAt: Mapped[datetime] = mapped_column(DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False) name: Mapped[Optional[str]] = mapped_column(VARCHAR(512), default=None) updatedAt: Mapped[Optional[datetime]] = mapped_column(DateTime, init=False) datasetId: Mapped[Optional[int]] = mapped_column(Integer, default=None) @@ -908,9 +827,7 @@ async def upsert(self, session: AsyncSession) -> "Source": ds.description = self.description session.add(ds) - await ( - session.flush() - ) # Ensure the object is written to the database and its ID is generated + await session.flush() # Ensure the object is written to the database and its ID is generated return ds @classmethod @@ -1001,14 +918,10 @@ class PostsGdocs(Base): content: Mapped[dict] = mapped_column(JSON) published: Mapped[int] = mapped_column(TINYINT) createdAt: Mapped[datetime] = mapped_column(DateTime, init=False) - publicationContext: Mapped[str] = mapped_column( - ENUM("unlisted", "listed"), server_default=text("'unlisted'") - ) + publicationContext: Mapped[str] = mapped_column(ENUM("unlisted", "listed"), server_default=text("'unlisted'")) type: Mapped[Optional[str]] = mapped_column( VARCHAR(255), - Computed( - "(json_unquote(json_extract(`content`,_utf8mb4'$.type')))", persisted=False - ), + Computed("(json_unquote(json_extract(`content`,_utf8mb4'$.type')))", persisted=False), ) publishedAt: Mapped[Optional[datetime]] = mapped_column(DateTime) updatedAt: Mapped[Optional[datetime]] = mapped_column(DateTime, init=False) @@ -1020,38 +933,24 @@ class PostsGdocs(Base): class OriginsVariablesLink(Base): __tablename__ = "origins_variables" __table_args__ = ( - ForeignKeyConstraint( - ["originId"], ["origins.id"], name="origins_variables_ibfk_1" - ), - ForeignKeyConstraint( - ["variableId"], ["variables.id"], name="origins_variables_ibfk_2" - ), + ForeignKeyConstraint(["originId"], ["origins.id"], name="origins_variables_ibfk_1"), + ForeignKeyConstraint(["variableId"], ["variables.id"], name="origins_variables_ibfk_2"), Index("variableId", "variableId"), ) - originId: Mapped[int] = mapped_column( - Integer, ForeignKey("users.id"), primary_key=True - ) - variableId: Mapped[int] = mapped_column( - Integer, ForeignKey("variables.id"), primary_key=True - ) + originId: Mapped[int] = mapped_column(Integer, ForeignKey("users.id"), primary_key=True) + variableId: Mapped[int] = mapped_column(Integer, ForeignKey("variables.id"), primary_key=True) displayOrder: Mapped[int] = mapped_column(SmallInteger, server_default=text("'0'")) @classmethod - async def link_with_variable( - cls, session: AsyncSession, variable_id: int, new_origin_ids: List[int] - ) -> None: + async def link_with_variable(cls, session: AsyncSession, variable_id: int, new_origin_ids: List[int]) -> None: """Link the given Variable ID with the given Origin IDs.""" # Fetch current linked Origins for the given Variable ID existing_links = ( - await session.execute( - select(cls.originId, cls.displayOrder).filter_by(variableId=variable_id) - ) + await session.execute(select(cls.originId, cls.displayOrder).filter_by(variableId=variable_id)) ).all() - existing_origins = { - (link.originId, link.displayOrder) for link in existing_links - } + existing_origins = {(link.originId, link.displayOrder) for link in existing_links} new_origins = {(origin_id, i) for i, origin_id in enumerate(new_origin_ids)} # Find the Origin IDs to delete and the IDs to add @@ -1091,12 +990,8 @@ async def link_with_variable( class PostsGdocsVariablesFaqsLink(Base): __tablename__ = "posts_gdocs_variables_faqs" __table_args__ = ( - ForeignKeyConstraint( - ["gdocId"], ["posts_gdocs.id"], name="posts_gdocs_variables_faqs_ibfk_1" - ), - ForeignKeyConstraint( - ["variableId"], ["variables.id"], name="posts_gdocs_variables_faqs_ibfk_2" - ), + ForeignKeyConstraint(["gdocId"], ["posts_gdocs.id"], name="posts_gdocs_variables_faqs_ibfk_1"), + ForeignKeyConstraint(["variableId"], ["variables.id"], name="posts_gdocs_variables_faqs_ibfk_2"), Index("variableId", "variableId"), ) @@ -1106,24 +1001,14 @@ class PostsGdocsVariablesFaqsLink(Base): displayOrder: Mapped[int] = mapped_column(SmallInteger, server_default=text("'0'")) @classmethod - async def link_with_variable( - cls, session: AsyncSession, variable_id: int, new_faqs: List[catalog.FaqLink] - ) -> None: + async def link_with_variable(cls, session: AsyncSession, variable_id: int, new_faqs: List[catalog.FaqLink]) -> None: """Link the given Variable ID with Faqs""" # Fetch current linked Faqs for the given Variable ID - existing_faqs = ( - (await session.execute(select(cls).filter_by(variableId=variable_id))) - .scalars() - .all() - ) + existing_faqs = (await session.execute(select(cls).filter_by(variableId=variable_id))).scalars().all() # Work with tuples instead - existing_gdoc_fragment = { - (f.gdocId, f.fragmentId, f.displayOrder) for f in existing_faqs - } - new_gdoc_fragment = { - (f.gdoc_id, f.fragment_id, i) for i, f in enumerate(new_faqs) - } + existing_gdoc_fragment = {(f.gdocId, f.fragmentId, f.displayOrder) for f in existing_faqs} + new_gdoc_fragment = {(f.gdoc_id, f.fragment_id, i) for i, f in enumerate(new_faqs)} to_delete = existing_gdoc_fragment - new_gdoc_fragment to_add = new_gdoc_fragment - existing_gdoc_fragment @@ -1163,12 +1048,8 @@ async def link_with_variable( class TagsVariablesTopicTagsLink(Base): __tablename__ = "tags_variables_topic_tags" __table_args__ = ( - ForeignKeyConstraint( - ["tagId"], ["tags.id"], name="tags_variables_topic_tags_ibfk_1" - ), - ForeignKeyConstraint( - ["variableId"], ["variables.id"], name="tags_variables_topic_tags_ibfk_2" - ), + ForeignKeyConstraint(["tagId"], ["tags.id"], name="tags_variables_topic_tags_ibfk_1"), + ForeignKeyConstraint(["variableId"], ["variables.id"], name="tags_variables_topic_tags_ibfk_2"), Index("variableId", "variableId"), ) @@ -1177,17 +1058,13 @@ class TagsVariablesTopicTagsLink(Base): displayOrder: Mapped[int] = mapped_column(SmallInteger, server_default=text("'0'")) @classmethod - async def link_with_variable( - cls, session: AsyncSession, variable_id: int, new_tag_ids: List[int] - ) -> None: + async def link_with_variable(cls, session: AsyncSession, variable_id: int, new_tag_ids: List[int]) -> None: """Link the given Variable ID with the given Tag IDs.""" assert len(new_tag_ids) == len(set(new_tag_ids)), "Tag IDs must be unique" # Fetch current linked tags for the given Variable ID existing_links = ( - await session.execute( - select(cls.tagId, cls.displayOrder).filter_by(variableId=variable_id) - ) + await session.execute(select(cls.tagId, cls.displayOrder).filter_by(variableId=variable_id)) ).all() existing_tags = {(link.tagId, link.displayOrder) for link in existing_links} @@ -1215,9 +1092,7 @@ async def link_with_variable( if to_add: session.add_all( [ - cls( - tagId=tag_id, variableId=variable_id, displayOrder=display_order - ) + cls(tagId=tag_id, variableId=variable_id, displayOrder=display_order) for tag_id, display_order in to_add ] ) @@ -1262,32 +1137,22 @@ class Variable(Base): ), Index("idx_catalogPath", "catalogPath", unique=True), Index("unique_short_name_per_dataset", "shortName", "datasetId", unique=True), - Index( - "variables_code_fk_dst_id_7bde8c2a_uniq", "code", "datasetId", unique=True - ), + Index("variables_code_fk_dst_id_7bde8c2a_uniq", "code", "datasetId", unique=True), Index("variables_datasetId_50a98bfd_fk_datasets_id", "datasetId"), - Index( - "variables_name_fk_dst_id_f7453c33_uniq", "name", "datasetId", unique=True - ), + Index("variables_name_fk_dst_id_f7453c33_uniq", "name", "datasetId", unique=True), Index("variables_sourceId_31fce80a_fk_sources_id", "sourceId"), ) id: Mapped[int] = mapped_column(Integer, primary_key=True, init=False) description: Mapped[Optional[str]] = mapped_column(LONGTEXT) unit: Mapped[str] = mapped_column(VARCHAR(255)) - createdAt: Mapped[datetime] = mapped_column( - DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False - ) + createdAt: Mapped[datetime] = mapped_column(DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False) coverage: Mapped[str] = mapped_column(VARCHAR(255)) timespan: Mapped[str] = mapped_column(VARCHAR(255)) datasetId: Mapped[int] = mapped_column(Integer) display: Mapped[dict] = mapped_column(JSON) - columnOrder: Mapped[int] = mapped_column( - Integer, server_default=text("'0'"), default=0 - ) - schemaVersion: Mapped[int] = mapped_column( - Integer, server_default=text("'1'"), default=1 - ) + columnOrder: Mapped[int] = mapped_column(Integer, server_default=text("'0'"), default=0) + schemaVersion: Mapped[int] = mapped_column(Integer, server_default=text("'1'"), default=1) name: Mapped[Optional[str]] = mapped_column(VARCHAR(750), default=None) updatedAt: Mapped[Optional[datetime]] = mapped_column(DateTime, init=False) code: Mapped[Optional[str]] = mapped_column(VARCHAR(255), default=None) @@ -1297,9 +1162,7 @@ class Variable(Base): shortName: Mapped[Optional[str]] = mapped_column(VARCHAR(255), default=None) catalogPath: Mapped[Optional[str]] = mapped_column(VARCHAR(767), default=None) dimensions: Mapped[Optional[Dimensions]] = mapped_column(JSON, default=None) - processingLevel: Mapped[Optional[catalog.meta.PROCESSING_LEVELS]] = mapped_column( - VARCHAR(30), default=None - ) + processingLevel: Mapped[Optional[catalog.meta.PROCESSING_LEVELS]] = mapped_column(VARCHAR(30), default=None) processingLog: Mapped[Optional[dict]] = mapped_column(JSON, default=None) titlePublic: Mapped[Optional[str]] = mapped_column(VARCHAR(512), default=None) titleVariant: Mapped[Optional[str]] = mapped_column(VARCHAR(255), default=None) @@ -1313,13 +1176,9 @@ class Variable(Base): licenses: Mapped[Optional[list[dict]]] = mapped_column(JSON, default=None) # NOTE: License should be the resulting license, given all licenses of the indicator’s origins and given the indicator’s processing level. license: Mapped[Optional[dict]] = mapped_column(JSON, default=None) - type: Mapped[Optional[VARIABLE_TYPE]] = mapped_column( - ENUM(*get_args(VARIABLE_TYPE)), default=None - ) + type: Mapped[Optional[VARIABLE_TYPE]] = mapped_column(ENUM(*get_args(VARIABLE_TYPE)), default=None) sort: Mapped[Optional[list[str]]] = mapped_column(JSON, default=None) - grapherConfigIdAdmin: Mapped[Optional[str]] = mapped_column( - VARCHAR(32), default=None - ) + grapherConfigIdAdmin: Mapped[Optional[str]] = mapped_column(VARCHAR(32), default=None) grapherConfigIdETL: Mapped[Optional[bytes]] = mapped_column(CHAR(32), default=None) dataChecksum: Mapped[Optional[str]] = mapped_column(VARCHAR(64), default=None) metadataChecksum: Mapped[Optional[str]] = mapped_column(VARCHAR(64), default=None) @@ -1404,9 +1263,7 @@ async def upsert(self, session: AsyncSession) -> "Variable": ds.sort = self.sort session.add(ds) - await ( - session.flush() - ) # Ensure the object is written to the database and its ID is generated + await session.flush() # Ensure the object is written to the database and its ID is generated return ds @classmethod @@ -1435,9 +1292,7 @@ def from_variable_metadata( presentation_dict.pop("faqs", None) if metadata.description_key: - assert isinstance( - metadata.description_key, list - ), "descriptionKey should be a list of bullet points" + assert isinstance(metadata.description_key, list), "descriptionKey should be a list of bullet points" return cls( shortName=short_name, @@ -1458,9 +1313,7 @@ def from_variable_metadata( descriptionFromProducer=metadata.description_from_producer, descriptionKey=metadata.description_key, descriptionProcessing=metadata.description_processing, - licenses=[license.to_dict() for license in metadata.licenses] - if metadata.licenses - else None, + licenses=[license.to_dict() for license in metadata.licenses] if metadata.licenses else None, license=metadata.license.to_dict() if metadata.license else None, type=metadata.type, sort=metadata.sort, @@ -1492,9 +1345,7 @@ def load_variable(cls, session: Session, variable_id: int) -> "Variable": @classmethod @deprecated("Use from_id_or_path instead") - def load_variables( - cls, session: Session, variables_id: List[int] - ) -> List["Variable"]: + def load_variables(cls, session: Session, variables_id: List[int]) -> List["Variable"]: return session.scalars(select(cls).where(cls.id.in_(variables_id))).all() # type: ignore @overload @@ -1528,9 +1379,7 @@ def from_id_or_path( return cls.from_id(session=session, variable_id=id_or_path, columns=columns) # Single path elif isinstance(id_or_path, str): - return cls.from_catalog_path( - session=session, catalog_path=id_or_path, columns=columns - ) + return cls.from_catalog_path(session=session, catalog_path=id_or_path, columns=columns) # Multiple path or id elif isinstance(id_or_path, list): @@ -1539,14 +1388,10 @@ def from_id_or_path( str_ids = [i for i in id_or_path if isinstance(i, str)] # Multiple IDs if len(int_ids) == len(id_or_path): - return cls.from_id( - session=session, variable_id=int_ids, columns=columns - ) + return cls.from_id(session=session, variable_id=int_ids, columns=columns) # Multiple paths elif len(str_ids) == len(id_or_path): - return cls.from_catalog_path( - session=session, catalog_path=str_ids, columns=columns - ) + return cls.from_catalog_path(session=session, catalog_path=str_ids, columns=columns) else: raise TypeError("All elements in the list must be integers") @@ -1586,19 +1431,13 @@ def from_catalog_path( """Load a variable from the DB by its catalog path.""" assert "#" in catalog_path, "catalog_path should end with #indicator_short_name" if isinstance(catalog_path, str): - return session.scalars( - _select_columns(cls, columns).where(cls.catalogPath == catalog_path) - ).one() + return session.scalars(_select_columns(cls, columns).where(cls.catalogPath == catalog_path)).one() elif isinstance(catalog_path, list): - return session.scalars( - _select_columns(cls, columns).where(cls.catalogPath.in_(catalog_path)) - ).all() # type: ignore + return session.scalars(_select_columns(cls, columns).where(cls.catalogPath.in_(catalog_path))).all() # type: ignore @overload @classmethod - def from_id( - cls, session: Session, variable_id: int, columns: Optional[List[str]] = None - ) -> "Variable": ... + def from_id(cls, session: Session, variable_id: int, columns: Optional[List[str]] = None) -> "Variable": ... @overload @classmethod @@ -1618,27 +1457,17 @@ def from_id( ) -> "Variable" | List["Variable"]: """Load a variable (or list of variables) from the DB by its ID path.""" if isinstance(variable_id, int): - return session.scalars( - _select_columns(cls, columns).where(cls.id == variable_id) - ).one() + return session.scalars(_select_columns(cls, columns).where(cls.id == variable_id)).one() elif isinstance(variable_id, list): - return session.scalars( - _select_columns(cls, columns).where(cls.id.in_(variable_id)) - ).all() # type: ignore + return session.scalars(_select_columns(cls, columns).where(cls.id.in_(variable_id))).all() # type: ignore @classmethod - async def load_from_catalog_path_async( - cls, session: AsyncSession, catalog_path: str - ) -> "Variable": + async def load_from_catalog_path_async(cls, session: AsyncSession, catalog_path: str) -> "Variable": assert "#" in catalog_path, "catalog_path should end with #indicator_short_name" - return ( - await session.scalars(select(cls).where(cls.catalogPath == catalog_path)) - ).one() + return (await session.scalars(select(cls).where(cls.catalogPath == catalog_path))).one() @classmethod - def catalog_paths_to_variable_ids( - cls, session: Session, catalog_paths: List[str] - ) -> Dict[str, int]: + def catalog_paths_to_variable_ids(cls, session: Session, catalog_paths: List[str]) -> Dict[str, int]: """Return a mapping from catalog paths to variable IDs.""" query = select(Variable).where(Variable.catalogPath.in_(catalog_paths)) return {var.catalogPath: var.id for var in session.scalars(query).all()} # type: ignore @@ -1648,9 +1477,7 @@ def infer_type(cls, values: pd.Series) -> VARIABLE_TYPE: """Set type and sort fields based on indicator values.""" return _infer_variable_type(values) - async def _link_faqs( - self, session: AsyncSession, faqs: List[catalog.FaqLink] - ) -> None: + async def _link_faqs(self, session: AsyncSession, faqs: List[catalog.FaqLink]) -> None: # establish relationships between variables and posts required_gdoc_ids = {faq.gdoc_id for faq in faqs} query = select(PostsGdocs).where(PostsGdocs.id.in_(required_gdoc_ids)) @@ -1685,9 +1512,7 @@ async def update_links( # establish relationships between variables and tags tags = await Tag.load_tags_by_names(session, tag_names) - await TagsVariablesTopicTagsLink.link_with_variable( - session, self.id, [tag.id for tag in tags] - ) + await TagsVariablesTopicTagsLink.link_with_variable(session, self.id, [tag.id for tag in tags]) await origins_variables_task await link_faqs_task @@ -1723,9 +1548,7 @@ def table_name(self) -> str: def step_path(self) -> Path: """Return path to indicator step file.""" assert self.catalogPath - base_path = ( - paths.STEP_DIR / "data" / self.catalogPath.split("#")[0].rsplit("/", 1)[0] - ) + base_path = paths.STEP_DIR / "data" / self.catalogPath.split("#")[0].rsplit("/", 1)[0] return base_path.with_suffix(".py") @property @@ -1742,9 +1565,7 @@ def get_data(self, session: Optional[Session] = None) -> pd.DataFrame: df = pd.DataFrame(data) if session is not None: - df = add_entity_name( - session=session, df=df, col_id="entities", col_name="entity" - ) + df = add_entity_name(session=session, df=df, col_id="entities", col_name="entity") return df @@ -1780,9 +1601,7 @@ class ChartDimensions(Base): property: Mapped[str] = mapped_column(VARCHAR(255)) chartId: Mapped[int] = mapped_column(Integer) variableId: Mapped[int] = mapped_column(Integer) - createdAt: Mapped[datetime] = mapped_column( - DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False - ) + createdAt: Mapped[datetime] = mapped_column(DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False) updatedAt: Mapped[Optional[datetime]] = mapped_column(DateTime, init=False) @@ -1973,9 +1792,7 @@ def latest_chart_approval_batch( approval = results[chart_id] approvals.append(approval) - assert len(chart_ids) == len( - approvals - ), "Length of chart_ids and approvals must be the same." + assert len(chart_ids) == len(approvals), "Length of chart_ids and approvals must be the same." return approvals @@ -2056,9 +1873,7 @@ def get_conflict_batch( conflict = results[chart_id] conflicts.append(conflict) - assert len(chart_ids) == len( - conflicts - ), "Length of chart_ids and conflicts must be the same." + assert len(chart_ids) == len(conflicts), "Length of chart_ids and conflicts must be the same." return conflicts @@ -2068,12 +1883,8 @@ class MultiDimDataPage(Base): slug: Mapped[str] = mapped_column(VARCHAR(255), primary_key=True) config: Mapped[dict] = mapped_column(JSON) - published: Mapped[int] = mapped_column( - TINYINT, server_default=text("'0'"), init=False - ) - createdAt: Mapped[datetime] = mapped_column( - DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False - ) + published: Mapped[int] = mapped_column(TINYINT, server_default=text("'0'"), init=False) + createdAt: Mapped[datetime] = mapped_column(DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False) updatedAt: Mapped[datetime] = mapped_column( DateTime, server_default=text("CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP"), @@ -2082,9 +1893,7 @@ class MultiDimDataPage(Base): def upsert(self, session: Session) -> "MultiDimDataPage": cls = self.__class__ - existing = session.scalars( - select(cls).where(cls.slug == self.slug) - ).one_or_none() + existing = session.scalars(select(cls).where(cls.slug == self.slug)).one_or_none() if existing: existing.config = self.config return existing @@ -2098,24 +1907,18 @@ class Anomaly(Base): # __table_args__ = (Index("catalogPath", "catalogPath"),) id: Mapped[int] = mapped_column(Integer, primary_key=True, init=False) - createdAt: Mapped[datetime] = mapped_column( - DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False - ) + createdAt: Mapped[datetime] = mapped_column(DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False) updatedAt: Mapped[datetime] = mapped_column( DateTime, server_default=text("CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP"), init=False, ) datasetId: Mapped[int] = mapped_column(Integer) - datasetSourceChecksum: Mapped[Optional[str]] = mapped_column( - VARCHAR(64), default=None - ) + datasetSourceChecksum: Mapped[Optional[str]] = mapped_column(VARCHAR(64), default=None) anomalyType: Mapped[str] = mapped_column(VARCHAR(255), default=str) path_file: Mapped[Optional[str]] = mapped_column(VARCHAR(255), default=None) _dfScore: Mapped[Optional[bytes]] = mapped_column("dfScore", LONGBLOB, default=None) - _dfReduced: Mapped[Optional[bytes]] = mapped_column( - "dfReduced", LONGBLOB, default=None - ) + _dfReduced: Mapped[Optional[bytes]] = mapped_column("dfReduced", LONGBLOB, default=None) # catalogPath: Mapped[str] = mapped_column(VARCHAR(255), default=None) # NOTE: why do we need indicatorChecksum? # Answer: This can be useful to assign an anomaly to a specific snapshot of the indicator. Unclear if we need it atm, but maybe in the future... @@ -2134,11 +1937,7 @@ def __repr__(self) -> str: @classmethod def load(cls, session: Session, dataset_id: int, anomaly_type: str) -> "Anomaly": - return session.scalars( - select(cls).where( - cls.datasetId == dataset_id, cls.anomalyType == anomaly_type - ) - ).one() + return session.scalars(select(cls).where(cls.datasetId == dataset_id, cls.anomalyType == anomaly_type)).one() @hybrid_property def dfScore(self) -> Optional[pd.DataFrame]: # type: ignore @@ -2187,9 +1986,7 @@ def _json_is(json_field: Any, key: str, val: Any) -> Any: return json_field[key] == val -def _remap_variable_ids( - config: Union[List, Dict[str, Any], Any], remap_ids: Dict[int, int] -) -> Any: +def _remap_variable_ids(config: Union[List, Dict[str, Any], Any], remap_ids: Dict[int, int]) -> Any: """Replace variableIds from chart config using `remap_ids` mapping.""" if isinstance(config, dict): out = {} @@ -2265,9 +2062,7 @@ def add_entity_name( # Get entity names unique_entities = df[col_id].unique() - entities = _fetch_entities( - session, list(unique_entities), col_id, col_name, col_code - ) + entities = _fetch_entities(session, list(unique_entities), col_id, col_name, col_code) # Sanity check if set(unique_entities) - set(entities[col_id]): diff --git a/etl/steps/__init__.py b/etl/steps/__init__.py index f6f48f89a4f..f5d9b0f2211 100644 --- a/etl/steps/__init__.py +++ b/etl/steps/__init__.py @@ -42,7 +42,6 @@ from etl import grapher_helpers as gh from etl import grapher_model as gm from etl.config import OWID_ENV, TLS_VERIFY -from etl.config import TLS_VERIFY from etl.db import get_engine from etl.snapshot import Snapshot @@ -893,61 +892,10 @@ def run(self) -> None: # Passing a BlockManager to Table is deprecated and will raise in a future version. Use public APIs instead. warnings.filterwarnings("ignore", category=DeprecationWarning) - catalog_paths = [] - - with ThreadPoolExecutor(max_workers=config.GRAPHER_INSERT_WORKERS) as thread_pool: - futures = [] - verbose = True - i = 0 - # import yappi - - # yappi.set_clock_type("wall") # Use "cpu" for CPU time profiling - # yappi.start() - - # if GRAPHER_FILTER is set, only upsert matching columns - if config.GRAPHER_FILTER: - cols = table.filter(regex=config.GRAPHER_FILTER).columns.tolist() - if not cols: - continue - cols += [c for c in table.columns if c in {"year", "date", "country"} and c not in cols] - table = table.loc[:, cols] catalog_paths = asyncio.run( gi._upsert_tables_from_dataset_async(self.path, dataset, engine, admin_api, dataset_upsert_results) ) - # # Stop profiling - # yappi.stop() - - for t in gh._yield_wide_table(table, na_action="drop"): - i += 1 - assert len(t.columns) == 1 - catalog_path = f"{self.path}/{table.metadata.short_name}#{t.columns[0]}" - catalog_paths.append(catalog_path) - - # stop logging to stop cluttering logs - if i > 20 and verbose: - verbose = False - thread_pool.submit( - lambda: (time.sleep(10), log.info("upsert_dataset.continue_without_logging")) - ) - - # generate table with entity_id, year and value for every column - futures.append( - thread_pool.submit( - gi.upsert_table, - engine, - admin_api, - t, - dataset_upsert_results, - catalog_path=catalog_path, - dimensions=(t.iloc[:, 0].metadata.additional_info or {}).get("dimensions"), - verbose=verbose, - ) - ) - - # wait for all tables to be inserted - [future.result() for future in as_completed(futures)] - if not config.GRAPHER_FILTER and not config.SUBSET: # cleaning up ghost resources could be unsuccessful if someone renamed short_name of a variable # and remapped it in chart-sync. 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sqlalchemy = {extras = ["asyncio"], version = "^2.0.34"} + "sqlalchemy[asyncio]>=2.0.34", "pymysql>=1.1.1", "tiktoken>=0.7.0", "earthengine-api>=0.1.411", @@ -68,8 +68,8 @@ dependencies = [ "geopy>=2.4.1", "py7zr>=0.22.0", "pyreadr>=0.5.2", - aiobotocore = "^2.14.0" - aiomysql = "^0.2.0" + "aiobotocore>=2.14.0", + "aiomysql>=0.2.0" ] [tool.uv.sources] diff --git a/tests/test_grapher_helpers.py b/tests/test_grapher_helpers.py index d4261c29c9b..7fa69703d02 100644 --- a/tests/test_grapher_helpers.py +++ b/tests/test_grapher_helpers.py @@ -186,9 +186,7 @@ def _sample_table() -> Table: def test_adapt_table_for_grapher_multiindex(): - with mock.patch( - "etl.grapher_helpers._get_entities_from_db" - ) as mock_get_entities_from_db: + with mock.patch("etl.grapher_helpers._get_entities_from_db") as mock_get_entities_from_db: with mock.patch("etl.grapher_io._fetch_entities") as mock_fetch_entities: # with mock.patch("apps.backport.datasync.data_metadata._fetch_entities") as mock_fetch_entities: mock_get_entities_from_db.return_value = {"Poland": 1, "France": 2} @@ -261,20 +259,12 @@ def test_underscore_column_and_dimensions(): short_name = "a" * 200 dims = {"age": "1" * 100} expected = short_name + "__age_1111111111111111_4e8d3bae4e8b9786396245429a8430af" - 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{ name = "sqlalchemy" }, + { name = "sqlalchemy", extra = ["asyncio"] }, { name = "structlog" }, { name = "tenacity" }, { name = "tiktoken" }, @@ -1117,6 +1165,8 @@ dev = [ [package.metadata] requires-dist = [ + { name = "aiobotocore", specifier = ">=2.14.0" }, + { name = "aiomysql", specifier = ">=0.2.0" }, { name = "bugsnag", specifier = ">=4.2.1" }, { name = "cdsapi", specifier = ">=0.7.0" }, { name = "click", specifier = ">=8.0.1" }, @@ -1174,7 +1224,7 @@ requires-dist = [ { name = "simplejson", specifier = ">=3.17.6" }, { name = "slack-sdk", marker = "extra == 'api'", specifier = ">=3.26.2" }, { name = "sparqlwrapper", specifier = ">=1.8.5" }, - { name = "sqlalchemy", specifier = ">=2.0.30" }, + { name = "sqlalchemy", extras = ["asyncio"], specifier = ">=2.0.34" }, { name = "statsmodels", marker = "extra == 'wizard'", specifier = ">=0.14.4" }, { name = "streamlit", marker = "extra == 'wizard'", specifier = ">=1.41.0" }, { name = "streamlit-ace", marker = "extra == 'wizard'", specifier = ">=0.1.1" }, @@ -3267,6 +3317,9 @@ wheels = [ name = "multidict" version = "6.1.0" source = { registry = "https://pypi.org/simple" } +dependencies = [ + { name = "typing-extensions", marker = "python_full_version < '3.11'" }, +] sdist = { url = "https://files.pythonhosted.org/packages/d6/be/504b89a5e9ca731cd47487e91c469064f8ae5af93b7259758dcfc2b9c848/multidict-6.1.0.tar.gz", hash = "sha256:22ae2ebf9b0c69d206c003e2f6a914ea33f0a932d4aa16f236afc049d9958f4a", size = 64002 } wheels = [ { url = "https://files.pythonhosted.org/packages/29/68/259dee7fd14cf56a17c554125e534f6274c2860159692a414d0b402b9a6d/multidict-6.1.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:3380252550e372e8511d49481bd836264c009adb826b23fefcc5dd3c69692f60", size = 48628 }, @@ -6208,6 +6261,11 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/b8/49/21633706dd6feb14cd3f7935fc00b60870ea057686035e1a99ae6d9d9d53/SQLAlchemy-2.0.36-py3-none-any.whl", hash = "sha256:fddbe92b4760c6f5d48162aef14824add991aeda8ddadb3c31d56eb15ca69f8e", size = 1883787 }, ] +[package.optional-dependencies] +asyncio = [ + { name = "greenlet" }, +] + [[package]] name = "st-annotated-text" version = "4.0.1" @@ -7473,9 +7531,9 @@ name = "yarl" version = "1.18.3" source = { registry = "https://pypi.org/simple" } dependencies = [ - { name = "idna", marker = "python_full_version >= '3.12'" }, - { name = "multidict", marker = "python_full_version >= '3.12'" }, - { name = "propcache", marker = "python_full_version >= '3.12'" }, + { name = "idna" }, + { name = "multidict" }, + { name = "propcache" }, ] sdist = { url = "https://files.pythonhosted.org/packages/b7/9d/4b94a8e6d2b51b599516a5cb88e5bc99b4d8d4583e468057eaa29d5f0918/yarl-1.18.3.tar.gz", hash = "sha256:ac1801c45cbf77b6c99242eeff4fffb5e4e73a800b5c4ad4fc0be5def634d2e1", size = 181062 } wheels = [ From cb83cfb21d748415f361a0599181803f17a690a1 Mon Sep 17 00:00:00 2001 From: Marigold Date: Thu, 19 Dec 2024 11:30:09 +0100 Subject: [PATCH 3/6] wip --- etl/db.py | 190 ------------------------------ etl/grapher_helpers.py | 1 - etl/grapher_io.py | 10 +- lib/catalog/owid/catalog/utils.py | 10 -- 4 files changed, 7 insertions(+), 204 deletions(-) diff --git a/etl/db.py b/etl/db.py index 673d6a23f2a..8f936df98f5 100644 --- a/etl/db.py +++ b/etl/db.py @@ -72,196 +72,6 @@ def get_engine_async(conf: Optional[Dict[str, Any]] = None) -> AsyncEngine: return engine -def get_dataset_id( - dataset_name: str, - db_conn: Optional[pymysql.Connection] = None, - version: Optional[str] = None, -) -> Any: - """Get the dataset ID of a specific dataset name from database. - - If more than one dataset is found for the same name, or if no dataset is found, an error is raised. - - Parameters - ---------- - dataset_name : str - Dataset name. - db_conn : pymysql.Connection - Connection to database. Defaults to None, in which case a default connection is created (uses etl.config). - version : str - ETL version of the dataset. This is necessary when multiple datasets have the same title. In such a case, if - version is not given, the function will raise an error. - - Returns - ------- - dataset_id : int - Dataset ID. - - """ - if db_conn is None: - db_conn = get_connection() - - query = f""" - SELECT id - FROM datasets - WHERE name = '{dataset_name}' - """ - - if version: - query += f" AND version = '{version}'" - - with db_conn.cursor() as cursor: - cursor.execute(query) - result = cursor.fetchall() - - assert len(result) == 1, f"Ambiguous or unknown dataset name '{dataset_name}'" - dataset_id = result[0][0] - return dataset_id - - -def get_variables_in_dataset( - dataset_id: int, - only_used_in_charts: bool = False, - db_conn: Optional[pymysql.Connection] = None, -) -> Any: - """Get all variables data for a specific dataset ID from database. - - Parameters - ---------- - dataset_id : int - Dataset ID. - only_used_in_charts : bool - True to select variables only if they have been used in at least one chart. False to select all variables. - db_conn : pymysql.Connection - Connection to database. Defaults to None, in which case a default connection is created (uses etl.config). - - Returns - ------- - variables_data : pd.DataFrame - Variables data for considered dataset. - - """ - if db_conn is None: - db_conn = get_connection() - - query = f""" - SELECT * - FROM variables - WHERE datasetId = {dataset_id} - """ - if only_used_in_charts: - query += """ - AND id IN ( - SELECT DISTINCT variableId - FROM chart_dimensions - ) - """ - with warnings.catch_warnings(): - warnings.simplefilter("ignore", UserWarning) - variables_data = pd.read_sql(query, con=db_conn) - return variables_data - - -def _get_variables_data_with_filter( - field_name: Optional[str] = None, - field_values: Optional[List[Any]] = None, - db_conn: Optional[pymysql.Connection] = None, -) -> Any: - if db_conn is None: - db_conn = get_connection() - - if field_values is None: - field_values = [] - - # Construct the SQL query with a placeholder for each value in the list. - query = "SELECT * FROM variables" - - if (field_name is not None) and (len(field_values) > 0): - query += f"\nWHERE {field_name} IN ({', '.join(['%s'] * len(field_values))});" - - # Execute the query. - with warnings.catch_warnings(): - warnings.simplefilter("ignore", UserWarning) - variables_data = pd.read_sql(query, con=db_conn, params=field_values) - - assert set(variables_data[field_name]) <= set(field_values), f"Unexpected values for {field_name}." - - # Warn about values that were not found. - missing_values = set(field_values) - set(variables_data[field_name]) - if len(missing_values) > 0: - log.warning(f"Values of {field_name} not found in database: {missing_values}") - - return variables_data - - -def get_variables_data( - filter: Optional[Dict[str, Any]] = None, - condition: Optional[str] = "OR", - db_conn: Optional[pymysql.Connection] = None, -) -> pd.DataFrame: - """Get data from variables table, given a certain condition. - - Parameters - ---------- - filter : Optional[Dict[str, Any]], optional - Filter to apply to the data, which must contain a field name and a list of field values, - e.g. {"id": [123456, 234567, 345678]}. - In principle, multiple filters can be given. - condition : Optional[str], optional - In case multiple filters are given, this parameter specifies whether the output filters should be the union - ("OR") or the intersection ("AND"). - db_conn : pymysql.Connection - Connection to database. Defaults to None, in which case a default connection is created (uses etl.config). - - Returns - ------- - df : pd.DataFrame - Variables data. - - """ - # NOTE: This function should be optimized. Instead of fetching data for each filter, their conditions should be - # combined with OR or AND before executing the query. - - # Initialize an empty dataframe. - if filter is not None: - df = pd.DataFrame({"id": []}).astype({"id": int}) - for field_name, field_values in filter.items(): - _df = _get_variables_data_with_filter(field_name=field_name, field_values=field_values, db_conn=db_conn) - if condition == "OR": - df = pd.concat([df, _df], axis=0) - elif condition == "AND": - df = pd.merge(df, _df, on="id", how="inner") - else: - raise ValueError(f"Invalid condition: {condition}") - else: - # Fetch data for all variables. - df = _get_variables_data_with_filter(db_conn=db_conn) - - return df - - -def get_all_datasets(archived: bool = True, db_conn: Optional[pymysql.Connection] = None) -> pd.DataFrame: - """Get all datasets in database. - - Parameters - ---------- - db_conn : pymysql.connections.Connection - Connection to database. Defaults to None, in which case a default connection is created (uses etl.config). - - Returns - ------- - datasets : pd.DataFrame - All datasets in database. Table with three columns: dataset ID, dataset name, dataset namespace. - """ - if db_conn is None: - db_conn = get_connection() - - query = " SELECT namespace, name, id, updatedAt FROM datasets" - if not archived: - query += " WHERE isArchived = 0" - datasets = pd.read_sql(query, con=db_conn) - return datasets.sort_values(["name", "namespace"]) - - def dict_to_object(d): return type("DynamicObject", (object,), d)() diff --git a/etl/grapher_helpers.py b/etl/grapher_helpers.py index 156e326ad26..e87092e934c 100644 --- a/etl/grapher_helpers.py +++ b/etl/grapher_helpers.py @@ -667,7 +667,6 @@ def _adapt_table_for_grapher(table: catalog.Table, engine: Engine) -> catalog.Ta # Add entity code and name with Session(engine) as session: table = add_entity_code_and_name(session, table).copy_metadata(table) - # table = dm.add_entity_code_and_name(session, table).copy_metadata(table) table = table.set_index(["entityId", "entityCode", "entityName", "year"] + dim_names) diff --git a/etl/grapher_io.py b/etl/grapher_io.py index 53becf2c020..1667ae915a0 100644 --- a/etl/grapher_io.py +++ b/etl/grapher_io.py @@ -559,7 +559,9 @@ def variable_data_table_from_catalog( def get_dataset_id( - dataset_name: str, db_conn: Optional[pymysql.Connection] = None, version: Optional[str] = None + dataset_name: str, + db_conn: Optional[pymysql.Connection] = None, + version: Optional[str] = None, ) -> Any: """Get the dataset ID of a specific dataset name from database. @@ -604,7 +606,9 @@ def get_dataset_id( @deprecated("This function is deprecated. Its logic will be soon moved to etl.grapher_model.Dataset.") def get_variables_in_dataset( - dataset_id: int, only_used_in_charts: bool = False, db_conn: Optional[pymysql.Connection] = None + dataset_id: int, + only_used_in_charts: bool = False, + db_conn: Optional[pymysql.Connection] = None, ) -> Any: """Get all variables data for a specific dataset ID from database. @@ -660,7 +664,7 @@ def get_all_datasets(archived: bool = True, db_conn: Optional[pymysql.Connection if db_conn is None: db_conn = get_connection() - query = " SELECT namespace, name, id, updatedAt, isArchived FROM datasets" + query = " SELECT namespace, name, id, updatedAt FROM datasets" if not archived: query += " WHERE isArchived = 0" datasets = pd.read_sql(query, con=db_conn) diff --git a/lib/catalog/owid/catalog/utils.py b/lib/catalog/owid/catalog/utils.py index fc2ec27e949..c0dd0a65c71 100644 --- a/lib/catalog/owid/catalog/utils.py +++ b/lib/catalog/owid/catalog/utils.py @@ -327,13 +327,3 @@ def dataclass_from_dict(cls: Optional[Type[T]], d: Dict[str, Any]) -> T: init_args[field_name] = v return cls(**init_args) - return hash(tuple([hash_any(y) for y in x])) - elif isinstance(x, dict): - return hash(tuple([(hash_any(k), hash_any(v)) for k, v in sorted(x.items())])) - elif isinstance(x, str): - # get md5 of the string and truncate to 64 bits - return int(hashlib.md5(x.encode()).hexdigest(), 16) & ((1 << 64) - 1) - elif x is None: - return 0 - else: - return hash(x) From 95176735ceca5601f84d071247d80cfcd130f7bd Mon Sep 17 00:00:00 2001 From: Marigold Date: Thu, 19 Dec 2024 11:30:54 +0100 Subject: [PATCH 4/6] wip --- etl/grapher_helpers.py | 1 - etl/grapher_import.py | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/etl/grapher_helpers.py b/etl/grapher_helpers.py index e87092e934c..3f621e90687 100644 --- a/etl/grapher_helpers.py +++ b/etl/grapher_helpers.py @@ -17,7 +17,6 @@ from sqlalchemy.engine import Engine from sqlalchemy.orm import Session -from apps.backport.datasync import data_metadata as dm from etl.db import get_engine, read_sql from etl.files import yaml_dump from etl.grapher_io import add_entity_code_and_name, trim_long_variable_name diff --git a/etl/grapher_import.py b/etl/grapher_import.py index dde690e35b2..9b8efb11c64 100644 --- a/etl/grapher_import.py +++ b/etl/grapher_import.py @@ -27,7 +27,7 @@ from sqlalchemy import select, text, update from sqlalchemy.engine.base import Engine from sqlalchemy.exc import NoResultFound -from sqlalchemy.ext.asyncio import AsyncEngine, AsyncSession, async_sessionmaker +from sqlalchemy.ext.asyncio import AsyncEngine, AsyncSession from sqlalchemy.orm import Session from apps.backport.datasync import data_metadata as dm From 4e90fe583e38cf5e872137671e9601cbc1043101 Mon Sep 17 00:00:00 2001 From: Marigold Date: Thu, 19 Dec 2024 11:43:10 +0100 Subject: [PATCH 5/6] wip --- apps/backport/datasync/data_metadata.py | 4 +- apps/chart_sync/admin_api.py | 27 +--- etl/db.py | 8 +- etl/grapher_helpers.py | 11 +- etl/grapher_import.py | 104 ++++++++-------- etl/grapher_io.py | 10 +- etl/grapher_model.py | 158 +++++------------------- etl/steps/__init__.py | 3 +- lib/catalog/owid/catalog/meta.py | 33 ++--- tests/test_grapher_helpers.py | 36 +----- 10 files changed, 110 insertions(+), 284 deletions(-) diff --git a/apps/backport/datasync/data_metadata.py b/apps/backport/datasync/data_metadata.py index fa972f7e4a4..db46843b1e6 100644 --- a/apps/backport/datasync/data_metadata.py +++ b/apps/backport/datasync/data_metadata.py @@ -212,9 +212,7 @@ def _variable_metadata( return variableMetadata -def _move_population_origin_to_end( - origins: List[Dict[str, Any]], -) -> List[Dict[str, Any]]: +def _move_population_origin_to_end(origins: List[Dict[str, Any]]) -> List[Dict[str, Any]]: """Move population origin to the end of the list of origins. This way it gets displayed last on data page.""" new_origins = [] pop_origin = None diff --git a/apps/chart_sync/admin_api.py b/apps/chart_sync/admin_api.py index 8cdd5ed52d5..2979e69caa5 100644 --- a/apps/chart_sync/admin_api.py +++ b/apps/chart_sync/admin_api.py @@ -87,36 +87,21 @@ def set_tags(self, chart_id: int, tags: List[Dict[str, Any]], user_id: Optional[ raise AdminAPIError({"error": js["error"], "tags": tags}) return js - def put_grapher_config(self, variable_id: int, grapher_config: Dict[str, Any]) -> dict: + async def put_grapher_config(self, variable_id: int, grapher_config: Dict[str, Any]) -> dict: # If schema is missing, use the default one grapher_config.setdefault("$schema", DEFAULT_GRAPHER_SCHEMA) - # Retry in case we're restarting Admin on staging server - resp = requests_with_retry().put( - self.owid_env.admin_api + f"/variables/{variable_id}/grapherConfigETL", - cookies={"sessionid": self.session_id}, - json=grapher_config, - ) - js = self._json_from_response(resp) - if not js["success"]: - raise AdminAPIError( - { - "error": js["error"], - "variable_id": variable_id, - "grapher_config": grapher_config, - } - ) - return js - - async def put_grapher_config(self, variable_id: int, grapher_config: Dict[str, Any]) -> dict: async with aiohttp.ClientSession(cookies={"sessionid": self.session_id}) as session: async with session.put( - self.base_url + f"/admin/api/variables/{variable_id}/grapherConfigETL", + self.owid_env.admin_api + f"/variables/{variable_id}/grapherConfigETL", json=grapher_config, ) as resp: # TODO: make _json_from_response async js = await resp.json() - assert js["success"] + if not js["success"]: + raise AdminAPIError( + {"error": js["error"], "variable_id": variable_id, "grapher_config": grapher_config} + ) return js # TODO: make it async diff --git a/etl/db.py b/etl/db.py index 8f936df98f5..95539243056 100644 --- a/etl/db.py +++ b/etl/db.py @@ -92,13 +92,7 @@ def read_sql(sql: str, engine: Optional[Engine | Session] = None, *args, **kwarg raise ValueError(f"Unsupported engine type {type(engine)}") -def to_sql( - df: pd.DataFrame, - name: str, - engine: Optional[Engine | Session] = None, - *args, - **kwargs, -): +def to_sql(df: pd.DataFrame, name: str, engine: Optional[Engine | Session] = None, *args, **kwargs): """Wrapper around pd.to_sql that creates a connection and closes it after reading the data. This adds overhead, so if you need performance, reuse the same connection and cursor. """ diff --git a/etl/grapher_helpers.py b/etl/grapher_helpers.py index 3f621e90687..926a1399f74 100644 --- a/etl/grapher_helpers.py +++ b/etl/grapher_helpers.py @@ -121,10 +121,7 @@ def _yield_wide_table( if dim_names: # `dropna=False` makes sure we don't drop NaN values from index grouped = table.groupby( - dim_names if len(dim_names) > 1 else dim_names[0], - as_index=False, - observed=True, - dropna=False, + dim_names if len(dim_names) > 1 else dim_names[0], as_index=False, observed=True, dropna=False ) else: # a situation when there's only year and entity_id in index with no additional dimensions @@ -146,11 +143,7 @@ def _yield_wide_table( # If all values are null, skip variable if table_to_yield[column].isnull().all(): if warn_null_variables: - log.warning( - "yield_wide_table.null_variable", - column=column, - dim_dict=dim_dict, - ) + log.warning("yield_wide_table.null_variable", column=column, dim_dict=dim_dict) continue # Safety check to see if the metadata is still intact diff --git a/etl/grapher_import.py b/etl/grapher_import.py index 9b8efb11c64..51d41f757ad 100644 --- a/etl/grapher_import.py +++ b/etl/grapher_import.py @@ -269,67 +269,71 @@ async def upsert_table( checksum_data = calculate_checksum_data(df) checksum_metadata = calculate_checksum_metadata(variable_meta, df) - with Session(engine) as session: - # compare checksums - try: - db_variable = gm.Variable.from_catalog_path(session, catalog_path) - except NoResultFound: - db_variable = None - - upsert_metadata_kwargs = dict( - session=session, - df=df, - variable_meta=variable_meta, + # NOTE: this is useful for debugging, will be removed once it is stable + if os.environ.get("SKIP_CHECKSUMS"): + import random + + checksum_metadata = str(random.randint(0, 10000)) + checksum_data = str(random.randint(0, 10000)) + + async with semaphore: + log.info( + "upsert_dataset.upsert_table.start", column_name=column_name, - dataset_upsert_result=dataset_upsert_result, - catalog_path=catalog_path, - dimensions=dimensions, - admin_api=admin_api, ) - # create variable if it doesn't exist - if not db_variable: - db_variable = upsert_metadata(**upsert_metadata_kwargs) - upsert_data(df, db_variable.s3_data_path()) + async_session = async_sessionmaker(engine_async, expire_on_commit=False) + async with async_session() as session: + # compare checksums + try: + db_variable = await gm.Variable.load_from_catalog_path_async(session, catalog_path) + except NoResultFound: + db_variable = None + + upsert_metadata_kwargs = dict( + session=session, + df=df, + variable_meta=variable_meta, + column_name=column_name, + dataset_upsert_result=dataset_upsert_result, + catalog_path=catalog_path, + dimensions=dimensions, + admin_api=admin_api, + client=client, + ) + + # create variable if it doesn't exist + if not db_variable: + db_variable = await upsert_metadata(**upsert_metadata_kwargs) + await upsert_data(df, db_variable.s3_data_path(), client) - # variable exists - else: - if db_variable.dataChecksum == checksum_data and db_variable.metadataChecksum == checksum_metadata: - if verbose: - log.info("upsert_table.skipped_no_changes", size=len(df), variable_id=db_variable.id) - return - - # NOTE: sequantial upserts are slower than parallel, but they will be useful once we switch to asyncio - # if db_variable.dataChecksum != checksum_data: - # upsert_data(df, db_variable.s3_data_path()) - # if db_variable.metadataChecksum != checksum_metadata: - # db_variable = upsert_metadata(**upsert_metadata_kwargs) - - futures = {} - with ThreadPoolExecutor() as executor: + # variable exists + else: + if db_variable.dataChecksum == checksum_data and db_variable.metadataChecksum == checksum_metadata: + if verbose: + log.info("upsert_table.skipped_no_changes", size=len(df), variable_id=db_variable.id) + return + + upsert_data_task = None if db_variable.dataChecksum != checksum_data: - futures["data"] = executor.submit(upsert_data, df, db_variable.s3_data_path()) + upsert_data_task = upsert_data(df, db_variable.s3_data_path(), client) if db_variable.metadataChecksum != checksum_metadata: - futures["metadata"] = executor.submit(upsert_metadata, **upsert_metadata_kwargs) + db_variable = await upsert_metadata(**upsert_metadata_kwargs) - if futures: - # Wait for futures to complete in case exceptions are raised - if "data" in futures: - futures["data"].result() - if "metadata" in futures: - db_variable = futures["metadata"].result() + if upsert_data_task: + await upsert_data_task - # Update checksums - db_variable.dataChecksum = checksum_data - db_variable.metadataChecksum = checksum_metadata + # Update checksums + db_variable.dataChecksum = checksum_data + db_variable.metadataChecksum = checksum_metadata - # Commit new checksums - session.add(db_variable) - session.commit() + # Commit new checksums + session.add(db_variable) + await session.commit() - if verbose: - log.info("upsert_table.uploaded_to_s3", size=len(df), variable_id=db_variable.id) + if verbose: + log.info("upsert_table.uploaded_to_s3", size=len(df), variable_id=db_variable.id) async def upsert_data(df: pd.DataFrame, s3_data_path: str, client) -> None: diff --git a/etl/grapher_io.py b/etl/grapher_io.py index 1667ae915a0..53becf2c020 100644 --- a/etl/grapher_io.py +++ b/etl/grapher_io.py @@ -559,9 +559,7 @@ def variable_data_table_from_catalog( def get_dataset_id( - dataset_name: str, - db_conn: Optional[pymysql.Connection] = None, - version: Optional[str] = None, + dataset_name: str, db_conn: Optional[pymysql.Connection] = None, version: Optional[str] = None ) -> Any: """Get the dataset ID of a specific dataset name from database. @@ -606,9 +604,7 @@ def get_dataset_id( @deprecated("This function is deprecated. Its logic will be soon moved to etl.grapher_model.Dataset.") def get_variables_in_dataset( - dataset_id: int, - only_used_in_charts: bool = False, - db_conn: Optional[pymysql.Connection] = None, + dataset_id: int, only_used_in_charts: bool = False, db_conn: Optional[pymysql.Connection] = None ) -> Any: """Get all variables data for a specific dataset ID from database. @@ -664,7 +660,7 @@ def get_all_datasets(archived: bool = True, db_conn: Optional[pymysql.Connection if db_conn is None: db_conn = get_connection() - query = " SELECT namespace, name, id, updatedAt FROM datasets" + query = " SELECT namespace, name, id, updatedAt, isArchived FROM datasets" if not archived: query += " WHERE isArchived = 0" datasets = pd.read_sql(query, con=db_conn) diff --git a/etl/grapher_model.py b/etl/grapher_model.py index a07ac849027..a05355685f7 100644 --- a/etl/grapher_model.py +++ b/etl/grapher_model.py @@ -132,10 +132,7 @@ def create_table(cls, engine: Engine, if_exists: Literal["fail", "replace", "ski class Entity(Base): __tablename__ = "entities" - __table_args__ = ( - Index("code", "code", unique=True), - Index("name", "name", unique=True), - ) + __table_args__ = (Index("code", "code", unique=True), Index("name", "name", unique=True)) id: Mapped[int] = mapped_column(Integer, primary_key=True, init=False) name: Mapped[str] = mapped_column(VARCHAR(255)) @@ -217,19 +214,8 @@ def upsert(self, session: Session) -> "Namespace": class Tag(Base): __tablename__ = "tags" __table_args__ = ( - ForeignKeyConstraint( - ["parentId"], - ["tags.id"], - ondelete="RESTRICT", - onupdate="RESTRICT", - name="tags_ibfk_1", - ), - Index( - "dataset_subcategories_name_fk_dst_cat_id_6ce1cc36_uniq", - "name", - "parentId", - unique=True, - ), + ForeignKeyConstraint(["parentId"], ["tags.id"], ondelete="RESTRICT", onupdate="RESTRICT", name="tags_ibfk_1"), + Index("dataset_subcategories_name_fk_dst_cat_id_6ce1cc36_uniq", "name", "parentId", unique=True), Index("parentId", "parentId"), Index("slug", "slug", unique=True), ) @@ -286,11 +272,7 @@ class ChartRevisions(Base): __tablename__ = "chart_revisions" __table_args__ = ( ForeignKeyConstraint( - ["userId"], - ["users.id"], - ondelete="RESTRICT", - onupdate="RESTRICT", - name="chart_revisions_userId", + ["userId"], ["users.id"], ondelete="RESTRICT", onupdate="RESTRICT", name="chart_revisions_userId" ), Index("chartId", "chartId"), Index("chart_revisions_userId", "userId"), @@ -313,8 +295,7 @@ class ChartConfig(Base): full: Mapped[dict] = mapped_column(JSON, nullable=False) fullMd5: Mapped[str] = mapped_column(CHAR(24), Computed("(to_base64(unhex(md5(full))))", persisted=True)) slug: Mapped[Optional[str]] = mapped_column( - String(255), - Computed("(json_unquote(json_extract(`full`, '$.slug')))", persisted=True), + String(255), Computed("(json_unquote(json_extract(`full`, '$.slug')))", persisted=True) ) chartType: Mapped[Optional[str]] = mapped_column( String(255), @@ -333,11 +314,7 @@ class Chart(Base): __tablename__ = "charts" __table_args__ = ( ForeignKeyConstraint( - ["configId"], - ["chart_configs.id"], - ondelete="RESTRICT", - onupdate="RESTRICT", - name="charts_configId", + ["configId"], ["chart_configs.id"], ondelete="RESTRICT", onupdate="RESTRICT", name="charts_configId" ), ForeignKeyConstraint( ["lastEditedByUserId"], @@ -396,12 +373,7 @@ def slug(cls): return select(ChartConfig.slug).where(ChartConfig.id == cls.configId).scalar_subquery() @classmethod - def load_chart( - cls, - session: Session, - chart_id: Optional[int] = None, - slug: Optional[str] = None, - ) -> "Chart": + def load_chart(cls, session: Session, chart_id: Optional[int] = None, slug: Optional[str] = None) -> "Chart": """Load chart with id `chart_id`.""" if chart_id: cond = cls.id == chart_id @@ -519,8 +491,7 @@ def migrate_config(self, source_session: Session, target_session: Session) -> Di try: target_var = target_session.scalars( select(Variable).where( - Variable.name == source_var.name, - Variable.datasetId == source_var.datasetId, + Variable.name == source_var.name, Variable.datasetId == source_var.datasetId ) ).one() @@ -603,11 +574,7 @@ class Dataset(Base): __tablename__ = "datasets" __table_args__ = ( ForeignKeyConstraint( - ["createdByUserId"], - ["users.id"], - ondelete="RESTRICT", - onupdate="RESTRICT", - name="datasets_createdByUserId", + ["createdByUserId"], ["users.id"], ondelete="RESTRICT", onupdate="RESTRICT", name="datasets_createdByUserId" ), ForeignKeyConstraint( ["dataEditedByUserId"], @@ -682,11 +649,7 @@ def upsert(self, session: Session) -> "Dataset": @classmethod def from_dataset_metadata( - cls, - metadata: catalog.DatasetMeta, - namespace: str, - user_id: int, - table_names: List[str], + cls, metadata: catalog.DatasetMeta, namespace: str, user_id: int, table_names: List[str] ) -> "Dataset": assert metadata.title return cls( @@ -712,11 +675,7 @@ def load_dataset(cls, session: Session, dataset_id: int) -> "Dataset": @classmethod def load_with_path(cls, session: Session, namespace: str, short_name: str, version: str) -> "Dataset": return session.scalars( - select(cls).where( - cls.namespace == namespace, - cls.shortName == short_name, - cls.version == version, - ) + select(cls).where(cls.namespace == namespace, cls.shortName == short_name, cls.version == version) ).one() @classmethod @@ -780,11 +739,7 @@ class Source(Base): __tablename__ = "sources" __table_args__ = ( ForeignKeyConstraint( - ["datasetId"], - ["datasets.id"], - ondelete="RESTRICT", - onupdate="RESTRICT", - name="sources_datasetId", + ["datasetId"], ["datasets.id"], ondelete="RESTRICT", onupdate="RESTRICT", name="sources_datasetId" ), Index("sources_datasetId", "datasetId"), ) @@ -804,16 +759,8 @@ def _upsert_select(self) -> Select: conds = [ cls.name == self.name, cls.datasetId == self.datasetId, - _json_is( - cls.description, - "additionalInfo", - self.description.get("additionalInfo"), - ), - _json_is( - cls.description, - "dataPublishedBy", - self.description.get("dataPublishedBy"), - ), + _json_is(cls.description, "additionalInfo", self.description.get("additionalInfo")), + _json_is(cls.description, "dataPublishedBy", self.description.get("dataPublishedBy")), ] return select(cls).where(*conds) @@ -908,10 +855,7 @@ class Dimensions(TypedDict): class PostsGdocs(Base): __tablename__ = "posts_gdocs" - __table_args__ = ( - Index("idx_posts_gdocs_type", "type"), - Index("idx_updatedAt", "updatedAt"), - ) + __table_args__ = (Index("idx_posts_gdocs_type", "type"), Index("idx_updatedAt", "updatedAt")) id: Mapped[str] = mapped_column(VARCHAR(255), primary_key=True) slug: Mapped[str] = mapped_column(VARCHAR(255)) @@ -920,8 +864,7 @@ class PostsGdocs(Base): createdAt: Mapped[datetime] = mapped_column(DateTime, init=False) publicationContext: Mapped[str] = mapped_column(ENUM("unlisted", "listed"), server_default=text("'unlisted'")) type: Mapped[Optional[str]] = mapped_column( - VARCHAR(255), - Computed("(json_unquote(json_extract(`content`,_utf8mb4'$.type')))", persisted=False), + VARCHAR(255), Computed("(json_unquote(json_extract(`content`,_utf8mb4'$.type')))", persisted=False) ) publishedAt: Mapped[Optional[datetime]] = mapped_column(DateTime) updatedAt: Mapped[Optional[datetime]] = mapped_column(DateTime, init=False) @@ -977,11 +920,7 @@ async def link_with_variable(cls, session: AsyncSession, variable_id: int, new_o if to_add: session.add_all( [ - cls( - originId=origin_id, - variableId=variable_id, - displayOrder=display_order, - ) + cls(originId=origin_id, variableId=variable_id, displayOrder=display_order) for origin_id, display_order in to_add ] ) @@ -1034,12 +973,7 @@ async def link_with_variable(cls, session: AsyncSession, variable_id: int, new_f if to_add: session.add_all( [ - cls( - gdocId=gdoc_id, - fragmentId=fragment_id, - displayOrder=display_order, - variableId=variable_id, - ) + cls(gdocId=gdoc_id, fragmentId=fragment_id, displayOrder=display_order, variableId=variable_id) for gdoc_id, fragment_id, display_order in to_add ] ) @@ -1351,19 +1285,13 @@ def load_variables(cls, session: Session, variables_id: List[int]) -> List["Vari @overload @classmethod def from_id_or_path( - cls, - session: Session, - id_or_path: str | int, - columns: Optional[List[str]] = None, + cls, session: Session, id_or_path: str | int, columns: Optional[List[str]] = None ) -> "Variable": ... @overload @classmethod def from_id_or_path( - cls, - session: Session, - id_or_path: List[str | int], - columns: Optional[List[str]] = None, + cls, session: Session, id_or_path: List[str | int], columns: Optional[List[str]] = None ) -> List["Variable"]: ... @classmethod @@ -1415,18 +1343,12 @@ def from_catalog_path( @overload @classmethod def from_catalog_path( - cls, - session: Session, - catalog_path: List[str], - columns: Optional[List[str]] = None, + cls, session: Session, catalog_path: List[str], columns: Optional[List[str]] = None ) -> List["Variable"]: ... @classmethod def from_catalog_path( - cls, - session: Session, - catalog_path: str | List[str], - columns: Optional[List[str]] = None, + cls, session: Session, catalog_path: str | List[str], columns: Optional[List[str]] = None ) -> "Variable" | List["Variable"]: """Load a variable from the DB by its catalog path.""" assert "#" in catalog_path, "catalog_path should end with #indicator_short_name" @@ -1442,18 +1364,12 @@ def from_id(cls, session: Session, variable_id: int, columns: Optional[List[str] @overload @classmethod def from_id( - cls, - session: Session, - variable_id: List[int], - columns: Optional[List[str]] = None, + cls, session: Session, variable_id: List[int], columns: Optional[List[str]] = None ) -> List["Variable"]: ... @classmethod def from_id( - cls, - session: Session, - variable_id: int | List[int], - columns: Optional[List[str]] = None, + cls, session: Session, variable_id: int | List[int], columns: Optional[List[str]] = None ) -> "Variable" | List["Variable"]: """Load a variable (or list of variables) from the DB by its ID path.""" if isinstance(variable_id, int): @@ -1726,11 +1642,7 @@ class ChartDiffApprovals(Base): __tablename__ = "chart_diff_approvals" __table_args__ = ( ForeignKeyConstraint( - ["chartId"], - ["charts.id"], - ondelete="CASCADE", - onupdate="CASCADE", - name="chart_diff_approvals_ibfk_1", + ["chartId"], ["charts.id"], ondelete="CASCADE", onupdate="CASCADE", name="chart_diff_approvals_ibfk_1" ), Index("chartId", "chartId"), ) @@ -1744,11 +1656,7 @@ class ChartDiffApprovals(Base): @classmethod def latest_chart_approval_batch( - cls, - session: Session, - chart_ids: list[int], - source_updated_ats: list, - target_updated_ats: list, + cls, session: Session, chart_ids: list[int], source_updated_ats: list, target_updated_ats: list ) -> List[Optional["ChartDiffApprovals"]]: """Load the latest approval of the charts. @@ -1813,11 +1721,7 @@ class ChartDiffConflicts(Base): __tablename__ = "chart_diff_conflicts" __table_args__ = ( ForeignKeyConstraint( - ["chartId"], - ["charts.id"], - ondelete="CASCADE", - onupdate="CASCADE", - name="chart_diff_conflicts_ibfk_1", + ["chartId"], ["charts.id"], ondelete="CASCADE", onupdate="CASCADE", name="chart_diff_conflicts_ibfk_1" ), Index("chartId", "chartId"), ) @@ -1886,9 +1790,7 @@ class MultiDimDataPage(Base): published: Mapped[int] = mapped_column(TINYINT, server_default=text("'0'"), init=False) createdAt: Mapped[datetime] = mapped_column(DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False) updatedAt: Mapped[datetime] = mapped_column( - DateTime, - server_default=text("CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP"), - init=False, + DateTime, server_default=text("CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP"), init=False ) def upsert(self, session: Session) -> "MultiDimDataPage": @@ -1909,9 +1811,7 @@ class Anomaly(Base): id: Mapped[int] = mapped_column(Integer, primary_key=True, init=False) createdAt: Mapped[datetime] = mapped_column(DateTime, server_default=text("CURRENT_TIMESTAMP"), init=False) updatedAt: Mapped[datetime] = mapped_column( - DateTime, - server_default=text("CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP"), - init=False, + DateTime, server_default=text("CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP"), init=False ) datasetId: Mapped[int] = mapped_column(Integer) datasetSourceChecksum: Mapped[Optional[str]] = mapped_column(VARCHAR(64), default=None) diff --git a/etl/steps/__init__.py b/etl/steps/__init__.py index f5d9b0f2211..4ad05d8d85f 100644 --- a/etl/steps/__init__.py +++ b/etl/steps/__init__.py @@ -11,10 +11,9 @@ import subprocess import sys import tempfile -import time import warnings from collections import defaultdict -from concurrent.futures import ThreadPoolExecutor, as_completed +from concurrent.futures import ThreadPoolExecutor from dataclasses import dataclass, field from glob import glob from importlib import import_module diff --git a/lib/catalog/owid/catalog/meta.py b/lib/catalog/owid/catalog/meta.py index 594200b2b28..3913ec1fda6 100644 --- a/lib/catalog/owid/catalog/meta.py +++ b/lib/catalog/owid/catalog/meta.py @@ -149,12 +149,8 @@ def __post_init__(self): if isinstance(self.date_published, (dt.date, int)): self.date_published = YearDateLatest(str(self.date_published)) - if self.date_published != "latest" and not is_year_or_date( - self.date_published - ): - raise ValueError( - "date_published should be either a year or a date or latest" - ) + if self.date_published != "latest" and not is_year_or_date(self.date_published): + raise ValueError("date_published should be either a year or a date or latest") # Minor is for cases where we only harmonized the countries or similar @@ -227,18 +223,14 @@ class VariableMeta(MetaBase): description_from_producer: Optional[str] = None # List of bullet points for the description key (can use markdown formatting) description_key: List[str] = field(default_factory=list) - origins: List[Origin] = field( - default_factory=list - ) # Origins is the new replacement for sources + origins: List[Origin] = field(default_factory=list) # Origins is the new replacement for sources # Use of `licenses` is discouraged, they should be captured in origins. licenses: List[License] = field(default_factory=list) unit: Optional[str] = None short_unit: Optional[str] = None # We keep display for the time being as the "less powerful sibling" of grapherConfig below display: Optional[Dict[str, Any]] = None - additional_info: Optional[Dict[str, Any]] = ( - None # Only used for internal bookkeeping - ) + additional_info: Optional[Dict[str, Any]] = None # Only used for internal bookkeeping # How much processing did we do to this data? processing_level: Optional[PROCESSING_LEVELS] = None @@ -428,9 +420,7 @@ def to_html(record: Any) -> Optional[str]: k, v_str ) ) - return '{}
    '.format( - "".join(rows) - ) + return '{}
    '.format("".join(rows)) elif isinstance(record, list): record = list(filter(None, record)) @@ -440,9 +430,7 @@ def to_html(record: Any) -> Optional[str]: rows = [] for item in record: rows.append("
  • {}
    • ".format(to_html(item))) - return '
      {}
    '.format( - "".join(rows) - ) + return '
      {}
    '.format("".join(rows)) else: return mistune.html(str(record)) # type: ignore @@ -472,14 +460,7 @@ def _deepcopy_dataclass(dc) -> Any: lis = type(v)(lis) setattr(dc, k, lis) elif isinstance(v, dict): - setattr( - dc, - k, - { - x: _deepcopy_dataclass(y) if is_dataclass(y) else y - for x, y in v.items() - }, - ) + setattr(dc, k, {x: _deepcopy_dataclass(y) if is_dataclass(y) else y for x, y in v.items()}) else: pass return dc diff --git a/tests/test_grapher_helpers.py b/tests/test_grapher_helpers.py index 7fa69703d02..84dd1bfbada 100644 --- a/tests/test_grapher_helpers.py +++ b/tests/test_grapher_helpers.py @@ -120,8 +120,7 @@ def test_ensure_source_per_variable_multiple_sources(): ) ) table.metadata.dataset = DatasetMeta( - description="Dataset description", - sources=[Source(name="s3", description="s3 description")], + description="Dataset description", sources=[Source(name="s3", description="s3 description")] ) table.metadata.description = "Table description" @@ -178,8 +177,7 @@ def _sample_table() -> Table: ) ) table.metadata.dataset = DatasetMeta( - description="Dataset description", - sources=[Source(name="s3", description="s3 description")], + description="Dataset description", sources=[Source(name="s3", description="s3 description")] ) table.metadata.description = "Table description" return table @@ -202,34 +200,17 @@ def test_adapt_table_for_grapher_multiindex(): table = _sample_table() out_table = gh._adapt_table_for_grapher(table, engine) - assert out_table.index.names == [ - "entityId", - "entityCode", - "entityName", - "year", - ] + assert out_table.index.names == ["entityId", "entityCode", "entityName", "year"] assert out_table.columns.tolist() == ["deaths", "sex"] table = _sample_table().set_index(["country", "year", "sex"]) out_table = gh._adapt_table_for_grapher(table, engine) - assert out_table.index.names == [ - "entityId", - "entityCode", - "entityName", - "year", - "sex", - ] + assert out_table.index.names == ["entityId", "entityCode", "entityName", "year", "sex"] assert out_table.columns.tolist() == ["deaths"] table = _sample_table().set_index(["sex"]) out_table = gh._adapt_table_for_grapher(table, engine) - assert out_table.index.names == [ - "entityId", - "entityCode", - "entityName", - "year", - "sex", - ] + assert out_table.index.names == ["entityId", "entityCode", "entityName", "year", "sex"] assert out_table.columns.tolist() == ["deaths"] @@ -282,12 +263,7 @@ def test_long_to_wide(): wide = gh.long_to_wide(table) - assert list(wide.columns) == [ - "deaths", - "deaths__age_10_18", - "deaths__age_19_25", - "deaths__age_26_30", - ] + assert list(wide.columns) == ["deaths", "deaths__age_10_18", "deaths__age_19_25", "deaths__age_26_30"] assert wide["deaths"].m.title == "Deaths" assert wide["deaths__age_10_18"].m.title == "Deaths - Age: 10-18" From 90d3ffb2844c4cef195e70bed48d52765b4faf3d Mon Sep 17 00:00:00 2001 From: Marigold Date: Thu, 19 Dec 2024 12:00:57 +0100 Subject: [PATCH 6/6] wip --- etl/grapher_import.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/etl/grapher_import.py b/etl/grapher_import.py index 51d41f757ad..f28dc834193 100644 --- a/etl/grapher_import.py +++ b/etl/grapher_import.py @@ -27,7 +27,7 @@ from sqlalchemy import select, text, update from sqlalchemy.engine.base import Engine from sqlalchemy.exc import NoResultFound -from sqlalchemy.ext.asyncio import AsyncEngine, AsyncSession +from sqlalchemy.ext.asyncio import AsyncEngine, AsyncSession, async_sessionmaker from sqlalchemy.orm import Session from apps.backport.datasync import data_metadata as dm @@ -117,7 +117,7 @@ def upsert_dataset( assert source.name source_ids[hash(source)] = _upsert_source_to_db(session, source, ds.id) - await session.commit() + session.commit() return DatasetUpsertResult(ds.id, source_ids)