diff --git a/pyproject.toml b/pyproject.toml index 17be78f..b3e3a5c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -3,80 +3,69 @@ requires = ["hatchling"] build-backend = "hatchling.build" [tool.hatch.build.targets.wheel] -packages = ["src/DD_tools"] +packages = ["src/TreeOfLife_toolbox"] [project] -name = "DD_tools" +name = "TreeOfLife_toolbox" dynamic = ["version"] authors = [ { name = "Andrey Kopanev", email = "kopanev.1@osu.edu" }, { name = "Elizabeth G. Campolongo", email = "e.campolongo479@gmail.com" }, { name = "Matthew J. Thompson", email = "thompson.m.j@outlook.com" }, ] -description = "A tool for downloading files from a list of URLs in parallel." +description = "A tool for processing datasets that was downloaded using the distributed-downloader package." readme = "README.md" -requires-python = ">=3.8" +requires-python = ">=3.10, <3.12" classifiers = [ + "Development Status :: 4 - Beta", "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", "License :: OSI Approved :: MIT License", "Operating System :: OS Independent", ] dependencies = [ "attrs", "brotli", - "certifi", - "charset-normalizer", "cramjam", "cython", - "exceptiongroup", "fsspec", - "hatchling", - "idna", "inflate64", - "iniconfig", - "mpi4py < 4", + "mpi4py", "multivolumefile", - "numpy", "opencv-python", - "packaging", "pandas", "pathspec", "pillow", - "pip", - "pluggy", "psutil", - "py4j", "pyarrow", "pybcj", "pycryptodomex", "pyppmd", "pyspark", - "pytest", - "python-dateutil", "python-dotenv", - "pytz", "pyyaml", "pyzstd", "requests", "setuptools", - "six", "texttable", - "tomli", "trove-classifiers", "typing-extensions", - "tzdata", - "urllib3", "wheel" ] [project.optional-dependencies] -dev = ["pytest"] +dev = [ + "pytest", + "ruff" +] keywords = [ "parallel", "distributed", - "download", "url", + "mpi-applications", + "dataset-generation", ] [project.urls] @@ -84,5 +73,8 @@ Homepage = "https://github.com/Imageomics/distributed-downloader" Repository = "https://github.com/Imageomics/distributed-downloader.git" "Bug Tracker" = "https://github.com/Imageomics/distributed-downloader/issues" +[project.scripts] +tree_of_life_toolbox = "TreeOfLife_toolbox.main.main:main" + [tool.hatch.version] -path = "src/DD_tools/main/__about__.py" +path = "src/TreeOfLife_toolbox/main/__about__.py" diff --git a/scripts/tools_filter.slurm b/scripts/tools_filter.slurm index 4642e34..6aee3f6 100644 --- a/scripts/tools_filter.slurm +++ b/scripts/tools_filter.slurm @@ -19,11 +19,10 @@ executor_memory="64G" module load spark/3.4.1 module load miniconda3/23.3.1-py310 source "${REPO_ROOT}/.venv/bin/activate" -export PYTHONPATH=${PYTHONPATH}:"${REPO_ROOT}/src":"${REPO_ROOT}/distributed-downloader" pbs-spark-submit \ --driver-memory $driver_memory \ --executor-memory $executor_memory \ - "${REPO_ROOT}/src/distributed_downloader/tools/filter.py" \ + "${TOOLBOX_PATH}/main/filter.py" \ "${tool_name}" \ > "${logs_dir}/tool_filter.log" diff --git a/scripts/tools_scheduler.slurm b/scripts/tools_scheduler.slurm index e4fb6a2..ea35a32 100644 --- a/scripts/tools_scheduler.slurm +++ b/scripts/tools_scheduler.slurm @@ -19,7 +19,6 @@ module load miniconda3/23.3.1-py310 source "${REPO_ROOT}/.venv/bin/activate" export PYARROW_IGNORE_TIMEZONE=1 export I_MPI_JOB_RESPECT_PROCESS_PLACEMENT=0 -export PYTHONPATH=${PYTHONPATH}:"${REPO_ROOT}/src":"${REPO_ROOT}/distributed-downloader" srun \ --mpi=pmi2 \ @@ -28,4 +27,4 @@ srun \ --cpus-per-task=1 \ --mem=0 \ --output="${logs_dir}/tool_scheduler.log" \ - python "${REPO_ROOT}/src/distributed_downloader/tools/scheduler.py" "${tool_name}" + python "${TOOLBOX_PATH}/main/scheduler.py" "${tool_name}" diff --git a/scripts/tools_verifier.slurm b/scripts/tools_verifier.slurm index 98ca024..6a3b75e 100644 --- a/scripts/tools_verifier.slurm +++ b/scripts/tools_verifier.slurm @@ -19,7 +19,6 @@ module load miniconda3/23.3.1-py310 source "${REPO_ROOT}/.venv/bin/activate" export PYARROW_IGNORE_TIMEZONE=1 export I_MPI_JOB_RESPECT_PROCESS_PLACEMENT=0 -export PYTHONPATH=${PYTHONPATH}:"${REPO_ROOT}/src":"${REPO_ROOT}/distributed-downloader" srun \ --mpi=pmi2 \ @@ -28,4 +27,4 @@ srun \ --cpus-per-task=1 \ --mem=0 \ --output="${logs_dir}/tool_verifier.log" \ - python "${REPO_ROOT}/src/distributed_downloader/tools/verification.py" "${tool_name}" + python "${TOOLBOX_PATH}/main/verification.py" "${tool_name}" diff --git a/scripts/tools_worker.slurm b/scripts/tools_worker.slurm index 2ee2662..4856e62 100644 --- a/scripts/tools_worker.slurm +++ b/scripts/tools_worker.slurm @@ -19,7 +19,6 @@ module load miniconda3/23.3.1-py310 source "${REPO_ROOT}/.venv/bin/activate" export PYARROW_IGNORE_TIMEZONE=1 export I_MPI_JOB_RESPECT_PROCESS_PLACEMENT=0 -export PYTHONPATH=${PYTHONPATH}:"${REPO_ROOT}/src":"${REPO_ROOT}/distributed-downloader" srun \ --mpi=pmi2 \ @@ -28,4 +27,4 @@ srun \ --cpus-per-task="$TOOLS_CPU_PER_WORKER" \ --mem=0 \ --output="${logs_dir}/tool_worker-%2t.log" \ - python "${REPO_ROOT}/src/distributed_downloader/tools/runner.py" "${tool_name}" + python "${TOOLBOX_PATH}/main/runner.py" "${tool_name}" diff --git a/src/DD_tools/__init__.py b/src/DD_tools/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/src/TreeOfLife_toolbox/__init__.py b/src/TreeOfLife_toolbox/__init__.py new file mode 100644 index 0000000..aac4b80 --- /dev/null +++ b/src/TreeOfLife_toolbox/__init__.py @@ -0,0 +1 @@ +from TreeOfLife_toolbox import data_merging diff --git a/src/TreeOfLife_toolbox/data_merging/README.md b/src/TreeOfLife_toolbox/data_merging/README.md new file mode 100644 index 0000000..5b812e6 --- /dev/null +++ b/src/TreeOfLife_toolbox/data_merging/README.md @@ -0,0 +1,81 @@ +# Data Merging Tool + +This tool identifies and filters out duplicate images between a target dataset and a newly downloaded source dataset +based on image hash values. It's designed to ensure data uniqueness when integrating new data into an existing +repository. + +## What it does + +The tool performs the following steps: + +1. Scans a target dataset (existing data collection) +2. Scans a source dataset (newly downloaded data) +3. Identifies duplicate images by comparing `hashsum_original` values +4. Creates a filter table of duplicates that can be used for further processing +5. Filters out duplicated entries from the source dataset + +## Required fields in config + +- `merge_target`: Path to the target dataset folder that will be checked against the new dataset + +## Initial assumptions/preconditions + +**Target dataset:** + +- It follows the following structure: + + ``` + / + ├── server= + │ ├── data_.parquet + │ ├── data_.parquet + │ └── ... + └── server= + └── ... + ``` + + - Entries in the target dataset are unique on `hashsum_original` column + - Each file follows the `successes` scheme from `distributed-downloader` + +**Source dataset:** + +- It follows the following structure: + + ``` + // + ├── server_name= + │ ├── partition_id= + │ │ ├── successes.parquet + │ │ ├── errors.parquet + │ │ └── completed + │ └── partition_id= + │ ├── ... + └── server_name= + └── ... + ``` + +- Each file follows the `successes` scheme from `distributed-downloader` +- Entries in the source are unique on `hashsum_original` column + +## Post conditions + +After successful execution, the tool guarantees: + +- A CSV filter table is created containing metadata about all duplicated entries, including their source and target + UUIDs +- The duplicated records are accessible via the tool's filter table, showing the relationship between source and target + entries +- The number of duplicated entries is logged for verification +- Processing is distributed across available nodes for efficient execution +- Original data files remain untouched - this is a non-destructive analysis + +## Implementation Details + +The tool consists of three main components: + +1. **DataMergedDupCheckFilter** - Identifies duplicate records by comparing hashsums +2. **DataMergedDupCheckScheduleCreation** - Handles task scheduling for distributed processing +3. **DataMergedDupCheckRunner** - Executes the actual filtering process + +The implementation relies on Apache Spark for efficient distributed data processing, making it suitable for large +datasets. \ No newline at end of file diff --git a/src/TreeOfLife_toolbox/data_merging/__init__.py b/src/TreeOfLife_toolbox/data_merging/__init__.py new file mode 100644 index 0000000..b5696f1 --- /dev/null +++ b/src/TreeOfLife_toolbox/data_merging/__init__.py @@ -0,0 +1,5 @@ +from .classes import ( + DataMergedDupCheckFilter, + DataMergedDupCheckScheduleCreation, + DataMergedDupCheckRunner, +) diff --git a/src/TreeOfLife_toolbox/data_merging/classes.py b/src/TreeOfLife_toolbox/data_merging/classes.py new file mode 100644 index 0000000..179ab12 --- /dev/null +++ b/src/TreeOfLife_toolbox/data_merging/classes.py @@ -0,0 +1,122 @@ +from TreeOfLife_toolbox.main.config import Config +from TreeOfLife_toolbox.main.filters import FilterRegister, SparkFilterToolBase +from TreeOfLife_toolbox.main.runners import RunnerRegister, FilterRunnerTool +from TreeOfLife_toolbox.main.schedulers import DefaultScheduler, SchedulerRegister + + +@FilterRegister("merged_duplicated_check") +class DataMergedDupCheckFilter(SparkFilterToolBase): + """ + Filter that identifies duplicate records between a target dataset and a source dataset. + + This filter compares records based on their 'hashsum_original' column to identify + entries that exist in both the target dataset (specified by 'merge_target' in config) + and the source dataset (downloaded images). + + Attributes: + filter_name (str): Name identifier for the filter, set to "merged_duplicated_check". + merge_target (str): Path to the target dataset for duplicate checking. + """ + + def __init__(self, cfg: Config): + """ + Initialize the duplicate check filter with configuration. + + Args: + cfg (Config): Configuration object containing filter settings + including the 'merge_target' path. + """ + super().__init__(cfg) + + self.filter_name: str = "merged_duplicated_check" + self.merge_target: str = str(self.config["merge_target"]) + + def run(self): + """ + Execute the duplicate check process. + + This method: + 1. Reads the target dataset from the specified merge_target path + 2. Reads the source dataset from the downloaded_images_path + 3. Joins the datasets on 'hashsum_original' to find duplicates + 4. Saves the duplicate records and logs the count + + Returns: + None + """ + from pyspark.sql import DataFrame + import pyspark.sql.functions as func + + target_df: DataFrame = ( + self.spark.read.option("basePath", self.merge_target) + .parquet(self.merge_target + "/source=*/server=*/data_*.parquet") + .select("uuid", "source_id", "hashsum_original") + .withColumnsRenamed({"uuid": "uuid_main", "source_id": "source_id_main"}) + ) + + target_df = target_df.withColumn("file_main", func.input_file_name()) + + object_df = ( + self.spark.read.schema(self.success_scheme) + .option("basePath", self.downloaded_images_path) + .parquet(self.downloaded_images_path + "/*/*/successes.parquet") + .select( + "uuid", "source_id", "server_name", "partition_id", "hashsum_original" + ) + ) + + duplicate_records = object_df.join( + target_df, on=["hashsum_original"], how="inner" + ) + + self.save_filter(duplicate_records) + + self.logger.info(f"duplicated number: {duplicate_records.count()}") + + +@SchedulerRegister("merged_duplicated_check") +class DataMergedDupCheckScheduleCreation(DefaultScheduler): + """ + Scheduler for the duplicate check process. + + Extends the DefaultScheduler to handle scheduling of the + duplicate checking tasks. This scheduler is registered with + the "merged_duplicated_check" name. + + Attributes: + filter_name (str): Name identifier for the filter, set to "merged_duplicated_check". + """ + def __init__(self, cfg: Config): + """ + Initialize the duplicate check scheduler with configuration. + + Args: + cfg (Config): Configuration object for scheduling parameters. + """ + super().__init__(cfg) + + self.filter_name: str = "merged_duplicated_check" + + +@RunnerRegister("merged_duplicated_check") +class DataMergedDupCheckRunner(FilterRunnerTool): + """ + Runner for executing the duplicate check filter. + + Handles the execution flow of the duplicate checking process, + extending the FilterRunnerTool to provide specific functionality + for the merged_duplicated_check filter. + + Attributes: + filter_name (str): Name identifier for the filter, set to "merged_duplicated_check". + """ + def __init__(self, cfg: Config): + """ + Initialize the duplicate check runner with configuration. + + Args: + cfg (Config): Configuration object containing runner settings. + """ + super().__init__(cfg) + + self.filter_name: str = "merged_duplicated_check" diff --git a/src/DD_tools/main/__about__.py b/src/TreeOfLife_toolbox/main/__about__.py similarity index 100% rename from src/DD_tools/main/__about__.py rename to src/TreeOfLife_toolbox/main/__about__.py diff --git a/src/DD_tools/main/checkpoint.py b/src/TreeOfLife_toolbox/main/checkpoint.py similarity index 100% rename from src/DD_tools/main/checkpoint.py rename to src/TreeOfLife_toolbox/main/checkpoint.py diff --git a/src/DD_tools/main/config.py b/src/TreeOfLife_toolbox/main/config.py similarity index 100% rename from src/DD_tools/main/config.py rename to src/TreeOfLife_toolbox/main/config.py diff --git a/src/DD_tools/main/config_templates/tools.yaml b/src/TreeOfLife_toolbox/main/config_templates/tools.yaml similarity index 100% rename from src/DD_tools/main/config_templates/tools.yaml rename to src/TreeOfLife_toolbox/main/config_templates/tools.yaml diff --git a/src/DD_tools/main/filter.py b/src/TreeOfLife_toolbox/main/filter.py similarity index 85% rename from src/DD_tools/main/filter.py rename to src/TreeOfLife_toolbox/main/filter.py index 080e1a2..ed526c5 100644 --- a/src/DD_tools/main/filter.py +++ b/src/TreeOfLife_toolbox/main/filter.py @@ -1,10 +1,10 @@ import argparse import os -from DD_tools.main.checkpoint import Checkpoint -from DD_tools.main.config import Config -from DD_tools.main.registry import ToolsRegistryBase -from DD_tools.main.utils import init_logger +from TreeOfLife_toolbox.main.checkpoint import Checkpoint +from TreeOfLife_toolbox.main.config import Config +from TreeOfLife_toolbox.main.registry import ToolsRegistryBase +from TreeOfLife_toolbox.main.utils import init_logger if __name__ == "__main__": config_path = os.environ.get("CONFIG_PATH") diff --git a/src/DD_tools/main/filters.py b/src/TreeOfLife_toolbox/main/filters.py similarity index 93% rename from src/DD_tools/main/filters.py rename to src/TreeOfLife_toolbox/main/filters.py index 11c9426..385f18e 100644 --- a/src/DD_tools/main/filters.py +++ b/src/TreeOfLife_toolbox/main/filters.py @@ -7,10 +7,10 @@ from pyspark.sql import SparkSession from pyspark.sql.types import StructType -from DD_tools.main.config import Config -from DD_tools.main.registry import ToolsBase -from DD_tools.main.registry import ToolsRegistryBase -from DD_tools.main.utils import SuccessEntry +from TreeOfLife_toolbox.main.config import Config +from TreeOfLife_toolbox.main.registry import ToolsBase +from TreeOfLife_toolbox.main.registry import ToolsRegistryBase +from TreeOfLife_toolbox.main.utils import SuccessEntry FilterRegister = partial(ToolsRegistryBase.register, "filter") diff --git a/src/DD_tools/main/main.py b/src/TreeOfLife_toolbox/main/main.py similarity index 96% rename from src/DD_tools/main/main.py rename to src/TreeOfLife_toolbox/main/main.py index b3d5732..5272354 100644 --- a/src/DD_tools/main/main.py +++ b/src/TreeOfLife_toolbox/main/main.py @@ -1,15 +1,16 @@ import argparse import os from logging import Logger +from pathlib import Path from typing import Dict, List, Optional, TextIO, Tuple import pandas as pd from attr import Factory, define, field -from DD_tools.main.checkpoint import Checkpoint -from DD_tools.main.config import Config -from DD_tools.main.registry import ToolsRegistryBase -from DD_tools.main.utils import ( +from TreeOfLife_toolbox.main.checkpoint import Checkpoint +from TreeOfLife_toolbox.main.config import Config +from TreeOfLife_toolbox.main.registry import ToolsRegistryBase +from TreeOfLife_toolbox.main.utils import ( init_logger, ensure_created, truncate_paths, @@ -78,6 +79,7 @@ def __attrs_post_init__(self): def __init_environment(self) -> None: os.environ["CONFIG_PATH"] = self.config.config_path + os.environ["TOOLBOX_PATH"] = str(Path(__file__).parent.parent.resolve()) os.environ["ACCOUNT"] = self.config["account"] os.environ["PATH_TO_INPUT"] = self.config["path_to_input"] diff --git a/src/DD_tools/main/registry.py b/src/TreeOfLife_toolbox/main/registry.py similarity index 94% rename from src/DD_tools/main/registry.py rename to src/TreeOfLife_toolbox/main/registry.py index 12774dd..03cf9d6 100644 --- a/src/DD_tools/main/registry.py +++ b/src/TreeOfLife_toolbox/main/registry.py @@ -1,7 +1,7 @@ from typing import Dict, Type, Optional -from DD_tools.main.config import Config -from DD_tools.main.utils import init_logger +from TreeOfLife_toolbox.main.config import Config +from TreeOfLife_toolbox.main.utils import init_logger class ToolsRegistryBase(type): diff --git a/src/DD_tools/main/runner.py b/src/TreeOfLife_toolbox/main/runner.py similarity index 84% rename from src/DD_tools/main/runner.py rename to src/TreeOfLife_toolbox/main/runner.py index 214237e..77dcefa 100644 --- a/src/DD_tools/main/runner.py +++ b/src/TreeOfLife_toolbox/main/runner.py @@ -1,10 +1,10 @@ import argparse import os -from DD_tools.main.checkpoint import Checkpoint -from DD_tools.main.config import Config -from DD_tools.main.registry import ToolsRegistryBase -from DD_tools.main.utils import init_logger +from TreeOfLife_toolbox.main.checkpoint import Checkpoint +from TreeOfLife_toolbox.main.config import Config +from TreeOfLife_toolbox.main.registry import ToolsRegistryBase +from TreeOfLife_toolbox.main.utils import init_logger if __name__ == "__main__": config_path = os.environ.get("CONFIG_PATH") diff --git a/src/DD_tools/main/runners.py b/src/TreeOfLife_toolbox/main/runners.py similarity index 98% rename from src/DD_tools/main/runners.py rename to src/TreeOfLife_toolbox/main/runners.py index cd875d3..bfb5d5e 100644 --- a/src/DD_tools/main/runners.py +++ b/src/TreeOfLife_toolbox/main/runners.py @@ -6,8 +6,8 @@ import pandas as pd -from DD_tools.main.config import Config -from DD_tools.main.registry import ToolsBase, ToolsRegistryBase +from TreeOfLife_toolbox.main.config import Config +from TreeOfLife_toolbox.main.registry import ToolsBase, ToolsRegistryBase RunnerRegister = partial(ToolsRegistryBase.register, "runner") diff --git a/src/DD_tools/main/scheduler.py b/src/TreeOfLife_toolbox/main/scheduler.py similarity index 87% rename from src/DD_tools/main/scheduler.py rename to src/TreeOfLife_toolbox/main/scheduler.py index 707b656..d686ae6 100644 --- a/src/DD_tools/main/scheduler.py +++ b/src/TreeOfLife_toolbox/main/scheduler.py @@ -1,10 +1,10 @@ import argparse import os -from DD_tools.main.checkpoint import Checkpoint -from DD_tools.main.config import Config -from DD_tools.main.registry import ToolsRegistryBase -from DD_tools.main.utils import init_logger +from TreeOfLife_toolbox.main.checkpoint import Checkpoint +from TreeOfLife_toolbox.main.config import Config +from TreeOfLife_toolbox.main.registry import ToolsRegistryBase +from TreeOfLife_toolbox.main.utils import init_logger if __name__ == "__main__": config_path = os.environ.get("CONFIG_PATH") diff --git a/src/DD_tools/main/schedulers.py b/src/TreeOfLife_toolbox/main/schedulers.py similarity index 90% rename from src/DD_tools/main/schedulers.py rename to src/TreeOfLife_toolbox/main/schedulers.py index ed70a9c..6b2c6e2 100644 --- a/src/DD_tools/main/schedulers.py +++ b/src/TreeOfLife_toolbox/main/schedulers.py @@ -5,8 +5,8 @@ import pandas as pd -from DD_tools.main.config import Config -from DD_tools.main.registry import ToolsBase, ToolsRegistryBase +from TreeOfLife_toolbox.main.config import Config +from TreeOfLife_toolbox.main.registry import ToolsBase, ToolsRegistryBase SchedulerRegister = partial(ToolsRegistryBase.register, "scheduler") diff --git a/src/DD_tools/main/utils.py b/src/TreeOfLife_toolbox/main/utils.py similarity index 100% rename from src/DD_tools/main/utils.py rename to src/TreeOfLife_toolbox/main/utils.py diff --git a/src/DD_tools/main/verification.py b/src/TreeOfLife_toolbox/main/verification.py similarity index 85% rename from src/DD_tools/main/verification.py rename to src/TreeOfLife_toolbox/main/verification.py index 742bb86..31d2561 100644 --- a/src/DD_tools/main/verification.py +++ b/src/TreeOfLife_toolbox/main/verification.py @@ -3,11 +3,11 @@ import pandas as pd -from DD_tools.main.checkpoint import Checkpoint -from DD_tools.main.config import Config -from DD_tools.main.registry import ToolsRegistryBase -from DD_tools.main.runners import MPIRunnerTool -from DD_tools.main.utils import init_logger +from TreeOfLife_toolbox.main.checkpoint import Checkpoint +from TreeOfLife_toolbox.main.config import Config +from TreeOfLife_toolbox.main.registry import ToolsRegistryBase +from TreeOfLife_toolbox.main.runners import MPIRunnerTool +from TreeOfLife_toolbox.main.utils import init_logger if __name__ == "__main__": config_path = os.environ.get("CONFIG_PATH")