From 98a4b8da7e64e1f7d6250994e1e9697e9a234477 Mon Sep 17 00:00:00 2001 From: rng Date: Wed, 8 Jan 2025 14:51:21 +1100 Subject: [PATCH 1/9] Refactor and version update --- Dockerfile | 3 +- README.md | 24 +- data_access_service/core/api.py | 4 +- data_access_service/core/restapi.py | 16 +- environment.yml | 2 +- poetry.lock | 3312 ++++++++++++++++----------- pyproject.toml | 7 +- 7 files changed, 2018 insertions(+), 1350 deletions(-) diff --git a/Dockerfile b/Dockerfile index 0db339f..8f0d023 100644 --- a/Dockerfile +++ b/Dockerfile @@ -3,7 +3,8 @@ FROM python:3.10-slim WORKDIR /app RUN useradd -l -m -s /bin/bash appuser -COPY pyproject.toml poetry.lock ./ +COPY pyproject.toml poetry.lock README.md ./ +COPY data_access_service ./data_access_service # For Docker build to understand the possible env RUN apt update && \ diff --git a/README.md b/README.md index 065949c..69a7c58 100644 --- a/README.md +++ b/README.md @@ -55,12 +55,34 @@ aodn_cloud_optimised = { git = "https://github.com/aodn/aodn_cloud_optimised.git ``` 2. **Install dependencies using Poetry:** - ```bash # after cloning the repo with git clone command $ cd data-access-service $ poetry install ``` + ```bash + # You should not need to install lib locally, if your python version is correct. + # https://arrow.apache.org/install/ + sudo apt update + sudo apt install -y -V ca-certificates lsb-release wget + wget https://apache.jfrog.io/artifactory/arrow/$(lsb_release --id --short | tr 'A-Z' 'a-z')/apache-arrow-apt-source-latest-$(lsb_release --codename --short).deb + sudo apt install -y -V ./apache-arrow-apt-source-latest-$(lsb_release --codename --short).deb + sudo apt update + sudo apt install -y -V libarrow-dev # For C++ + sudo apt install -y -V libarrow-glib-dev # For GLib (C) + sudo apt install -y -V libarrow-dataset-dev # For Apache Arrow Dataset C++ + sudo apt install -y -V libarrow-dataset-glib-dev # For Apache Arrow Dataset GLib (C) + sudo apt install -y -V libarrow-acero-dev # For Apache Arrow Acero + sudo apt install -y -V libarrow-flight-dev # For Apache Arrow Flight C++ + sudo apt install -y -V libarrow-flight-glib-dev # For Apache Arrow Flight GLib (C) + sudo apt install -y -V libarrow-flight-sql-dev # For Apache Arrow Flight SQL C++ + sudo apt install -y -V libarrow-flight-sql-glib-dev # For Apache Arrow Flight SQL GLib (C) + sudo apt install -y -V libgandiva-dev # For Gandiva C++ + sudo apt install -y -V libgandiva-glib-dev # For Gandiva GLib (C) + sudo apt install -y -V libparquet-dev # For Apache Parquet C++ + sudo apt install -y -V libparquet-glib-dev # For Apache Parquet GLib (C) + sudo apt install -y ninja-build + ``` 3. **Run the app:** diff --git a/data_access_service/core/api.py b/data_access_service/core/api.py index 5f59381..6ec2c71 100644 --- a/data_access_service/core/api.py +++ b/data_access_service/core/api.py @@ -5,7 +5,7 @@ from datetime import timedelta, datetime from io import BytesIO from typing import Optional -from aodn_cloud_optimised import ParquetDataQuery +from aodn_cloud_optimised import DataQuery from data_access_service.core.descriptor import Depth, Descriptor log = logging.getLogger(__name__) @@ -37,7 +37,7 @@ def __init__(self): # UUID to metadata mapper and init it, a scheduler need to # updated it as times go - self._instance = ParquetDataQuery.GetAodn() + self._instance = DataQuery.GetAodn() self._metadata = self._instance.get_metadata() self._create_uuid_dataset_map() diff --git a/data_access_service/core/restapi.py b/data_access_service/core/restapi.py index b9dc878..4bfaa33 100644 --- a/data_access_service/core/restapi.py +++ b/data_access_service/core/restapi.py @@ -130,7 +130,6 @@ def _verify_to_index_flag_param(flag: str) -> bool: else: return False - def _response_json(filtered: DataFrame, compress: bool): ddf: dask.dataframe.DataFrame = dd.from_pandas( filtered, npartitions=len(filtered.index) // RECORD_PER_PARTITION + 1 @@ -206,13 +205,13 @@ def get_raw_metadata(uuid): return app.api.get_raw_meta_data(uuid) -@restapi.route("data//has_data", methods=["GET"]) +@restapi.route("/data//has_data", methods=["GET"]) def data_check(uuid): start_date = _verify_datatime_param( - "start_date", request.args.get("start_date", default=None, type=str) + "start_date", request.args.get("start_date", default="1970-01-01") ) end_date = _verify_datatime_param( - "end_date", request.args.get("end_date", default=None, type=str) + "end_date", request.args.get("end_date", default=datetime.datetime.now().strftime("%Y-%m-%d")) ) has_data = str(app.api.has_data(uuid, start_date, end_date)).lower() return Response(has_data, mimetype="application/json") @@ -222,21 +221,20 @@ def data_check(uuid): def get_data(uuid): log.info("Request details: %s", json.dumps(request.args.to_dict(), indent=2)) start_date = _verify_datatime_param( - "start_date", request.args.get("start_date", default=None, type=str) + "start_date", request.args.get("start_date", default="1970-01-01") ) end_date = _verify_datatime_param( - "end_date", request.args.get("end_date", default=None, type=str) + "end_date", request.args.get("end_date", default=datetime.datetime.now().strftime("%Y-%m-%d")) ) - result: Optional[pd.DataFrame] = app.api.get_dataset_data( uuid=uuid, date_start=start_date, date_end=end_date ) start_depth = _verify_depth_param( - "start_depth", request.args.get("start_depth", default=None, type=numpy.double) + "start_depth", numpy.double(request.args.get("start_depth", default=0.0)) ) end_depth = _verify_depth_param( - "end_depth", request.args.get("end_depth", default=None, type=numpy.double) + "end_depth", numpy.double(request.args.get("end_depth", default=1.0)) ) is_to_index = _verify_to_index_flag_param( diff --git a/environment.yml b/environment.yml index fda4c14..00dfb12 100644 --- a/environment.yml +++ b/environment.yml @@ -3,7 +3,7 @@ channels: - conda-forge - defaults dependencies: - - python>=3.10.14 + - python=3.10.14 - pip<24.1 - pip: - poetry diff --git a/poetry.lock b/poetry.lock index 09a07b7..64f4f6b 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,145 +1,141 @@ -# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.0.0 and should not be changed by hand. 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[metadata] -lock-version = "2.0" +lock-version = "2.1" python-versions = "^3.10.14" -content-hash = "d8a1090ec33e8072262ccea5c9f2a2c013179339346e9513fbc21d663940ebd9" +content-hash = "13068b901c91f52cd56308171d5d4f9c39ba96ccc039ad83ba3b91b0a3ee6488" diff --git a/pyproject.toml b/pyproject.toml index d4ed5de..8f9509b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -15,11 +15,11 @@ gunicorn = "22.0.0" gevent = "24.2.1" h5py = "3.11.0" jsonify = "^0.5" -matplotlib = "3.9.1" +matplotlib = "3.10.0" pandas = "^2.2.3" pyarrow = "17.0.0" python = "^3.10.14" -python-levenshtein = "~0.25.1" +python-levenshtein = "^0.25.1" scipy = "1.14.0" logging = "^0.4.9.6" requests = "2.32.3" @@ -30,9 +30,10 @@ cryptography = "<43.0.0" cartopy = "^0.24.1" gsw = "^3.6.19" seaborn = "^0.13.2" +windrose = ">=1.9.2" # Dependency from a GitHub repository -aodn_cloud_optimised = { git = "https://github.com/aodn/aodn_cloud_optimised.git", tag = "v0.1.27" } +aodn_cloud_optimised = { git = "https://github.com/aodn/aodn_cloud_optimised.git", tag = "v0.1.32" } pytest = "^8.3.4" [build-system] From 851fe9bae87c3606526cf8b430e3e333b5f15aef Mon Sep 17 00:00:00 2001 From: rng Date: Wed, 8 Jan 2025 16:14:15 +1100 Subject: [PATCH 2/9] Improve speed of has_data --- data_access_service/core/api.py | 24 +++++++----------------- data_access_service/core/restapi.py | 23 +++++++++++++++-------- 2 files changed, 22 insertions(+), 25 deletions(-) diff --git a/data_access_service/core/api.py b/data_access_service/core/api.py index 6ec2c71..b6695ce 100644 --- a/data_access_service/core/api.py +++ b/data_access_service/core/api.py @@ -77,25 +77,15 @@ def get_raw_meta_data(self, uuid: str): return value else: return None - + """ + Given a time range, we find if this uuid temporal cover the whole range + """ def has_data(self, uuid: str, start_date: datetime, end_date: datetime): md: Descriptor = self._cached.get(uuid) if md is not None: - ds: ParquetDataQuery.Dataset = self._instance.get_dataset(md.dname) - while start_date <= end_date: - - # currently use 366 days as a period, to make sure 1 query can cover 1 year - period_end = start_date + timedelta(days=366) - log.info(f"Checking data for {start_date} to {period_end}") - if period_end > end_date: - period_end = end_date - - if not ds.get_data( - start_date, period_end, None, None, None, None, None - ).empty: - return True - else: - start_date = period_end + timedelta(days=1) + ds: DataQuery.Dataset = self._instance.get_dataset(md.dname) + te = ds.get_temporal_extent() + return start_date <= te[0] and te[1] <= end_date return False def get_dataset_data( @@ -112,7 +102,7 @@ def get_dataset_data( md: Descriptor = self._cached.get(uuid) if md is not None: - ds: ParquetDataQuery.Dataset = self._instance.get_dataset(md.dname) + ds: DataQuery.Dataset = self._instance.get_dataset(md.dname) # Default get 10 days of data if date_start is None: diff --git a/data_access_service/core/restapi.py b/data_access_service/core/restapi.py index 4bfaa33..4e1b477 100644 --- a/data_access_service/core/restapi.py +++ b/data_access_service/core/restapi.py @@ -26,7 +26,8 @@ log = logging.getLogger(__name__) RECORD_PER_PARTITION: Optional[int] = 1000 - +DATE_FORMAT = "%Y-%m-%d %H:%M:%S%z" +MIN_DATE = "1970-01-01T00:00:00Z" # Make all non-numeric and str field to str so that json do not throw serializable error def convert_non_numeric_to_str(df): @@ -206,25 +207,31 @@ def get_raw_metadata(uuid): @restapi.route("/data//has_data", methods=["GET"]) -def data_check(uuid): +def has_data(uuid): start_date = _verify_datatime_param( - "start_date", request.args.get("start_date", default="1970-01-01") + "start_date", request.args.get("start_date", default=MIN_DATE) ) end_date = _verify_datatime_param( - "end_date", request.args.get("end_date", default=datetime.datetime.now().strftime("%Y-%m-%d")) + "end_date", request.args.get( + "end_date", + default=datetime.datetime.now(datetime.timezone.utc).strftime(DATE_FORMAT) + ) ) - has_data = str(app.api.has_data(uuid, start_date, end_date)).lower() - return Response(has_data, mimetype="application/json") + result = str(app.api.has_data(uuid, start_date, end_date)).lower() + return Response(result, mimetype="application/json") @restapi.route("/data/", methods=["GET"]) def get_data(uuid): log.info("Request details: %s", json.dumps(request.args.to_dict(), indent=2)) start_date = _verify_datatime_param( - "start_date", request.args.get("start_date", default="1970-01-01") + "start_date", request.args.get("start_date", default=MIN_DATE) ) end_date = _verify_datatime_param( - "end_date", request.args.get("end_date", default=datetime.datetime.now().strftime("%Y-%m-%d")) + "end_date", request.args.get( + "end_date", + default=datetime.datetime.now(datetime.timezone.utc).strftime(DATE_FORMAT) + ) ) result: Optional[pd.DataFrame] = app.api.get_dataset_data( uuid=uuid, date_start=start_date, date_end=end_date From 99a62f1242fa3fa2e5ec48901437b0963232b229 Mon Sep 17 00:00:00 2001 From: rng Date: Wed, 8 Jan 2025 16:39:21 +1100 Subject: [PATCH 3/9] Fix issue with query --- data_access_service/core/api.py | 14 ++++++++++++-- data_access_service/core/restapi.py | 12 ++++++------ 2 files changed, 18 insertions(+), 8 deletions(-) diff --git a/data_access_service/core/api.py b/data_access_service/core/api.py index b6695ce..c4ca5fd 100644 --- a/data_access_service/core/api.py +++ b/data_access_service/core/api.py @@ -2,7 +2,7 @@ import pandas as pd import logging -from datetime import timedelta, datetime +from datetime import timedelta, datetime, timezone from io import BytesIO from typing import Optional from aodn_cloud_optimised import DataQuery @@ -106,7 +106,17 @@ def get_dataset_data( # Default get 10 days of data if date_start is None: - date_start = datetime.now() - timedelta(days=10) + date_start = datetime.now(timezone.utc) - timedelta(days=10) + + # The get_data call the pyarrow and compare only works with non timezone datetime + # now make sure the timezone is correctly convert to utc then remove it. + # As get_date datetime are all utc, but the pyarrow do not support compare of datetime vs + # datetime with timezone. + if date_start.tzinfo is not None: + date_start = date_start.astimezone(timezone.utc).replace(tzinfo=None) + + if date_end.tzinfo is not None: + date_end = date_end.astimezone(timezone.utc).replace(tzinfo=None) return ds.get_data( date_start, date_end, lat_min, lat_max, lon_min, lon_max, scalar_filter diff --git a/data_access_service/core/restapi.py b/data_access_service/core/restapi.py index 4e1b477..298b2f7 100644 --- a/data_access_service/core/restapi.py +++ b/data_access_service/core/restapi.py @@ -238,27 +238,27 @@ def get_data(uuid): ) start_depth = _verify_depth_param( - "start_depth", numpy.double(request.args.get("start_depth", default=0.0)) + "start_depth", numpy.double(request.args.get("start_depth", default=-1.0)) ) end_depth = _verify_depth_param( - "end_depth", numpy.double(request.args.get("end_depth", default=1.0)) + "end_depth", numpy.double(request.args.get("end_depth", default=-1.0)) ) is_to_index = _verify_to_index_flag_param( - request.args.get("is_to_index", default=None, type=str) + request.args.get("is_to_index", default=None) ) # The cloud optimized format is fast to lookup if there is an index, some field isn't part of the # index and therefore will not gain to filter by those field, indexed fields are site_code, timestamp, polygon # Depth is below sea level zero, so logic slightly diff - if start_depth is not None and end_depth is not None: + if start_depth > 0 and end_depth > 0: filtered = result[ (result["DEPTH"] <= start_depth) & (result["DEPTH"] >= end_depth) ] - elif start_depth is not None: + elif start_depth > 0: filtered = result[(result["DEPTH"] <= start_depth)] - elif end_depth is not None: + elif end_depth > 0: filtered = result[result["DEPTH"] >= end_depth] else: filtered = result From 1d49bb36276eedddd9f5f3b28754f51162ebed4f Mon Sep 17 00:00:00 2001 From: rng Date: Thu, 9 Jan 2025 10:20:40 +1100 Subject: [PATCH 4/9] Add temporal_extents call --- data_access_service/core/api.py | 8 ++++++++ data_access_service/core/restapi.py | 9 +++++++++ 2 files changed, 17 insertions(+) diff --git a/data_access_service/core/api.py b/data_access_service/core/api.py index c4ca5fd..526b934 100644 --- a/data_access_service/core/api.py +++ b/data_access_service/core/api.py @@ -88,6 +88,14 @@ def has_data(self, uuid: str, start_date: datetime, end_date: datetime): return start_date <= te[0] and te[1] <= end_date return False + def get_temporal_extent(self, uuid: str) -> (datetime, datetime): + md: Descriptor = self._cached.get(uuid) + if md is not None: + ds: DataQuery.Dataset = self._instance.get_dataset(md.dname) + return ds.get_temporal_extent() + else: + return () + def get_dataset_data( self, uuid: str, diff --git a/data_access_service/core/restapi.py b/data_access_service/core/restapi.py index 298b2f7..f66555c 100644 --- a/data_access_service/core/restapi.py +++ b/data_access_service/core/restapi.py @@ -220,6 +220,15 @@ def has_data(uuid): result = str(app.api.has_data(uuid, start_date, end_date)).lower() return Response(result, mimetype="application/json") +@restapi.route("/data//temporal_extent", methods=["GET"]) +def get_temporal_extent(uuid): + temp: (datetime, datetime) = app.api.get_temporal_extent(uuid) + result = { + "start": temp[0].strftime(DATE_FORMAT), + "end": temp[1].strftime(DATE_FORMAT) + } + return Response(json.dumps(result), mimetype="application/json") + @restapi.route("/data/", methods=["GET"]) def get_data(uuid): From 0f8ff1df535bf6b3a87cc32d5ef63d7312df91de Mon Sep 17 00:00:00 2001 From: rng Date: Thu, 9 Jan 2025 10:33:26 +1100 Subject: [PATCH 5/9] Make return array as temporal can be disjoint --- data_access_service/core/restapi.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/data_access_service/core/restapi.py b/data_access_service/core/restapi.py index f66555c..716a71b 100644 --- a/data_access_service/core/restapi.py +++ b/data_access_service/core/restapi.py @@ -223,10 +223,10 @@ def has_data(uuid): @restapi.route("/data//temporal_extent", methods=["GET"]) def get_temporal_extent(uuid): temp: (datetime, datetime) = app.api.get_temporal_extent(uuid) - result = { + result = [{ "start": temp[0].strftime(DATE_FORMAT), "end": temp[1].strftime(DATE_FORMAT) - } + }] return Response(json.dumps(result), mimetype="application/json") From 255308c70f2cc7a8456471fcc640788ed50b9b41 Mon Sep 17 00:00:00 2001 From: rng Date: Thu, 9 Jan 2025 10:38:53 +1100 Subject: [PATCH 6/9] match convention --- data_access_service/core/restapi.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/data_access_service/core/restapi.py b/data_access_service/core/restapi.py index 716a71b..d77835b 100644 --- a/data_access_service/core/restapi.py +++ b/data_access_service/core/restapi.py @@ -224,8 +224,8 @@ def has_data(uuid): def get_temporal_extent(uuid): temp: (datetime, datetime) = app.api.get_temporal_extent(uuid) result = [{ - "start": temp[0].strftime(DATE_FORMAT), - "end": temp[1].strftime(DATE_FORMAT) + "start_date": temp[0].strftime(DATE_FORMAT), + "end_date": temp[1].strftime(DATE_FORMAT) }] return Response(json.dumps(result), mimetype="application/json") From 926a01874a87990697c93aba4be5cf9010d8f4d4 Mon Sep 17 00:00:00 2001 From: rng Date: Thu, 9 Jan 2025 12:11:10 +1100 Subject: [PATCH 7/9] Missing T in the date format --- data_access_service/core/restapi.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/data_access_service/core/restapi.py b/data_access_service/core/restapi.py index d77835b..7895548 100644 --- a/data_access_service/core/restapi.py +++ b/data_access_service/core/restapi.py @@ -26,7 +26,7 @@ log = logging.getLogger(__name__) RECORD_PER_PARTITION: Optional[int] = 1000 -DATE_FORMAT = "%Y-%m-%d %H:%M:%S%z" +DATE_FORMAT = "%Y-%m-%dT%H:%M:%S%z" MIN_DATE = "1970-01-01T00:00:00Z" # Make all non-numeric and str field to str so that json do not throw serializable error From 1aaab4d6999e3a781af46a51b2b5a8457c2b9a46 Mon Sep 17 00:00:00 2001 From: rng Date: Fri, 10 Jan 2025 17:29:37 +1100 Subject: [PATCH 8/9] incorrect option fix --- .github/workflows/test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 9991b13..60c4ab0 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -26,7 +26,7 @@ jobs: version: "latest" - name: Install dependencies run: | - poetry lock --no-update + poetry lock poetry install - name: Run pre-commit checks run: | From 8b5e82bf52ef39befcfb08e56a34327887f3e41e Mon Sep 17 00:00:00 2001 From: rng Date: Fri, 10 Jan 2025 17:35:35 +1100 Subject: [PATCH 9/9] pre-commit fix --- data_access_service/core/api.py | 2 ++ data_access_service/core/restapi.py | 27 +++++++++++++++++---------- 2 files changed, 19 insertions(+), 10 deletions(-) diff --git a/data_access_service/core/api.py b/data_access_service/core/api.py index 526b934..e2db7f8 100644 --- a/data_access_service/core/api.py +++ b/data_access_service/core/api.py @@ -77,9 +77,11 @@ def get_raw_meta_data(self, uuid: str): return value else: return None + """ Given a time range, we find if this uuid temporal cover the whole range """ + def has_data(self, uuid: str, start_date: datetime, end_date: datetime): md: Descriptor = self._cached.get(uuid) if md is not None: diff --git a/data_access_service/core/restapi.py b/data_access_service/core/restapi.py index 7895548..ccf1c16 100644 --- a/data_access_service/core/restapi.py +++ b/data_access_service/core/restapi.py @@ -29,6 +29,7 @@ DATE_FORMAT = "%Y-%m-%dT%H:%M:%S%z" MIN_DATE = "1970-01-01T00:00:00Z" + # Make all non-numeric and str field to str so that json do not throw serializable error def convert_non_numeric_to_str(df): def convert_value(value): @@ -131,6 +132,7 @@ def _verify_to_index_flag_param(flag: str) -> bool: else: return False + def _response_json(filtered: DataFrame, compress: bool): ddf: dask.dataframe.DataFrame = dd.from_pandas( filtered, npartitions=len(filtered.index) // RECORD_PER_PARTITION + 1 @@ -212,21 +214,25 @@ def has_data(uuid): "start_date", request.args.get("start_date", default=MIN_DATE) ) end_date = _verify_datatime_param( - "end_date", request.args.get( + "end_date", + request.args.get( "end_date", - default=datetime.datetime.now(datetime.timezone.utc).strftime(DATE_FORMAT) - ) + default=datetime.datetime.now(datetime.timezone.utc).strftime(DATE_FORMAT), + ), ) result = str(app.api.has_data(uuid, start_date, end_date)).lower() return Response(result, mimetype="application/json") + @restapi.route("/data//temporal_extent", methods=["GET"]) def get_temporal_extent(uuid): temp: (datetime, datetime) = app.api.get_temporal_extent(uuid) - result = [{ - "start_date": temp[0].strftime(DATE_FORMAT), - "end_date": temp[1].strftime(DATE_FORMAT) - }] + result = [ + { + "start_date": temp[0].strftime(DATE_FORMAT), + "end_date": temp[1].strftime(DATE_FORMAT), + } + ] return Response(json.dumps(result), mimetype="application/json") @@ -237,10 +243,11 @@ def get_data(uuid): "start_date", request.args.get("start_date", default=MIN_DATE) ) end_date = _verify_datatime_param( - "end_date", request.args.get( + "end_date", + request.args.get( "end_date", - default=datetime.datetime.now(datetime.timezone.utc).strftime(DATE_FORMAT) - ) + default=datetime.datetime.now(datetime.timezone.utc).strftime(DATE_FORMAT), + ), ) result: Optional[pd.DataFrame] = app.api.get_dataset_data( uuid=uuid, date_start=start_date, date_end=end_date