diff --git a/.flake8 b/.flake8 index 7b0c786..e416c1f 100644 --- a/.flake8 +++ b/.flake8 @@ -6,6 +6,7 @@ max-complexity = 10 docstring-convention = google per-file-ignores = tests/*:S101,S301,S403 + tests/unit_tests/test_parquet.py:B908,DAR101 noxfile.py:DAR101 spectrum_io/raw/thermo_raw.py:S603,S404 spectrum_io/raw/msraw.py:S405,S314 diff --git a/.github/workflows/build_package.yml b/.github/workflows/build_package.yml index 00e9570..13d080e 100644 --- a/.github/workflows/build_package.yml +++ b/.github/workflows/build_package.yml @@ -9,7 +9,7 @@ jobs: strategy: matrix: os: [macos-latest, ubuntu-latest, windows-latest] - python: [3.8, 3.9] + python: ["3.9", "3.10"] steps: - uses: actions/checkout@v4 diff --git a/.github/workflows/publish_docs.yml b/.github/workflows/publish_docs.yml index 11d3f2e..9e46e49 100644 --- a/.github/workflows/publish_docs.yml +++ b/.github/workflows/publish_docs.yml @@ -13,7 +13,7 @@ jobs: - name: Setup Python uses: actions/setup-python@v4 with: - python-version: 3.8 + python-version: 3.9 - name: Install pip run: | diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml index d91eb1f..498ce29 100644 --- a/.github/workflows/run_tests.yml +++ b/.github/workflows/run_tests.yml @@ -19,47 +19,47 @@ jobs: matrix: include: - { - python-version: 3.8, + python-version: 3.9, os: ubuntu-latest, session: "pre-commit", } - { - python-version: 3.8, + python-version: 3.9, os: ubuntu-latest, session: "safety", } - { - python-version: 3.8, + python-version: 3.9, os: ubuntu-latest, session: "mypy", } - { - python-version: 3.8, + python-version: 3.9, os: ubuntu-latest, session: "tests", } - { - python-version: 3.8, + python-version: 3.9, os: windows-latest, session: "tests", } - { - python-version: 3.8, + python-version: 3.9, os: macos-latest, session: "tests", } - { - python-version: 3.8, + python-version: 3.9, os: ubuntu-latest, session: "typeguard", } - { - python-version: 3.8, + python-version: 3.9, os: ubuntu-latest, session: "xdoctest", } - { - python-version: 3.8, + python-version: 3.9, os: ubuntu-latest, session: "docs-build", } @@ -136,10 +136,10 @@ jobs: - name: Check out the repository uses: actions/checkout@v4 - - name: Set up Python 3.8 + - name: Set up Python 3.9 uses: actions/setup-python@v4 with: - python-version: 3.8 + python-version: 3.9 - name: Install Poetry run: | diff --git a/docs/spectrum_io.file.rst b/docs/spectrum_io.file.rst index b038996..7f977e5 100644 --- a/docs/spectrum_io.file.rst +++ b/docs/spectrum_io.file.rst @@ -20,6 +20,14 @@ spectrum\_io.file.hdf5 module :undoc-members: :show-inheritance: +spectrum\_io.file.parquet module +----------------------------- + +.. automodule:: spectrum_io.file.parquet + :members: + :undoc-members: + :show-inheritance: + Module contents --------------- diff --git a/noxfile.py b/noxfile.py index eb9b0a3..a62a8fb 100644 --- a/noxfile.py +++ b/noxfile.py @@ -18,7 +18,7 @@ sys.exit(1) package = "spectrum_io" -python_versions = ["3.8", "3.9"] +python_versions = ["3.9", "3.10"] nox.options.sessions = ( "pre-commit", "safety", @@ -125,9 +125,10 @@ def precommit(session: Session) -> None: @session(python=python_versions) def safety(session: Session) -> None: """Scan dependencies for insecure packages.""" + to_ignore = "--ignore=70612" requirements = session.poetry.export_requirements() session.install("safety") - session.run("safety", "check", "--full-report", f"--file={requirements}") + session.run("safety", "check", "--full-report", f"--file={requirements}", to_ignore) @session(python=python_versions) diff --git a/poetry.lock b/poetry.lock index c5f6d63..8ef987e 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2,13 +2,13 @@ [[package]] name = "alabaster" -version = "0.7.13" -description = "A configurable sidebar-enabled Sphinx theme" +version = "0.7.16" +description = "A light, configurable Sphinx theme" optional = false -python-versions = ">=3.6" +python-versions = ">=3.9" files = [ - {file = "alabaster-0.7.13-py3-none-any.whl", hash = "sha256:1ee19aca801bbabb5ba3f5f258e4422dfa86f82f3e9cefb0859b283cdd7f62a3"}, - {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"}, + {file = "alabaster-0.7.16-py3-none-any.whl", hash = "sha256:b46733c07dce03ae4e150330b975c75737fa60f0a7c591b6c8bf4928a28e2c92"}, + {file = "alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65"}, ] [[package]] @@ -42,17 +42,36 @@ stable = ["click (==8.1.3)", "h5py (==3.8.0)", "numba (==0.56.4)", "pandas (==1. 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python_version < "3.10" -joblib==1.4.0 ; python_version >= "3.8" and python_full_version < "3.11.0" -kiwisolver==1.4.5 ; python_version >= "3.8" and python_full_version < "3.11.0" -llvmlite==0.41.1 ; python_version >= "3.8" and python_full_version < "3.11.0" -lxml==4.9.4 ; python_full_version >= "3.8.0" and python_full_version < "3.11.0" -markdown-it-py==3.0.0 ; python_version >= "3.8" and python_full_version < "3.11.0" -matplotlib==3.7.5 ; python_version >= "3.8" and python_full_version < "3.11.0" -mdurl==0.1.2 ; python_version >= "3.8" and python_full_version < "3.11.0" -moepy==1.1.4 ; python_full_version >= "3.8.0" and python_full_version < "3.11.0" -numba==0.58.1 ; python_version >= "3.8" and python_full_version < "3.11.0" -numpy==1.24.4 ; python_version >= "3.8" and python_full_version < "3.11.0" -packaging==24.0 ; python_version >= "3.8" and python_full_version < "3.11.0" -pandas==1.5.3 ; python_version >= "3.8" and python_full_version < "3.11.0" -pillow==10.3.0 ; python_version >= "3.8" and python_full_version < "3.11.0" -psutil==5.9.8 ; python_version >= "3.8" and python_full_version < "3.11.0" -pygments==2.17.2 ; python_full_version >= "3.8.0" and python_full_version < "3.11.0" -pymzml==2.5.9 ; python_full_version >= "3.8.0" and python_full_version < "3.11.0" -pyparsing==3.1.2 ; python_version >= "3.8" and python_full_version < "3.11.0" -pyteomics==4.7.2 ; python_full_version >= "3.8.0" and python_full_version < "3.11.0" -python-dateutil==2.9.0.post0 ; python_version >= "3.8" and python_full_version < "3.11.0" -pytz==2024.1 ; python_version >= "3.8" and python_full_version < "3.11.0" -pyyaml==6.0.1 ; python_full_version >= "3.8.0" and python_full_version < "3.11.0" -pyzstd==0.15.10 ; python_version >= "3.8" and python_full_version < "3.11.0" -regex==2024.4.16 ; python_full_version >= "3.8.0" and python_full_version < "3.11.0" -rich==13.7.1 ; python_full_version >= "3.8.0" and python_full_version < "3.11.0" -scikit-learn==1.3.2 ; python_version >= "3.8" and python_full_version < "3.11.0" -scipy==1.10.1 ; python_version >= "3.8" and python_full_version < "3.11.0" -six==1.16.0 ; python_version >= "3.8" and python_full_version < "3.11.0" -sortedcontainers==2.4.0 ; python_full_version >= "3.8.0" and python_full_version < "3.11.0" -spectrum-fundamentals==0.5.2 ; python_full_version >= "3.8.0" and python_full_version < "3.11.0" -threadpoolctl==3.4.0 ; python_version >= "3.8" and python_full_version < "3.11.0" -tqdm==4.66.2 ; python_version >= "3.8" and python_full_version < "3.11.0" -typing-extensions==4.11.0 ; python_version >= "3.8" and python_version < "3.9" -zipp==3.18.1 ; python_version >= "3.8" and python_version < "3.10" +alphatims==1.0.8 ; python_version >= "3.9" and python_full_version < "3.11.0" +click==8.1.7 ; python_version >= "3.9" and python_full_version < "3.11.0" +colorama==0.4.6 ; python_version >= "3.9" and python_full_version < "3.11.0" and platform_system == "Windows" +contourpy==1.1.1 ; python_version >= "3.9" and python_full_version < "3.11.0" +cycler==0.12.1 ; python_version >= "3.9" and python_full_version < "3.11.0" +fonttools==4.51.0 ; python_version >= "3.9" and python_full_version < "3.11.0" +h5py==3.11.0 ; python_version >= "3.9" and python_full_version < "3.11.0" +importlib-metadata==7.1.0 ; python_version >= "3.9" and python_version < "3.9" +importlib-resources==6.4.0 ; python_version >= "3.9" and python_version < "3.10" +joblib==1.4.0 ; python_version >= "3.9" and python_full_version < "3.11.0" +kiwisolver==1.4.5 ; python_version >= "3.9" and python_full_version < "3.11.0" +llvmlite==0.41.1 ; python_version >= "3.9" and python_full_version < "3.11.0" +lxml==4.9.4 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" +markdown-it-py==3.0.0 ; python_version >= "3.9" and python_full_version < "3.11.0" +matplotlib==3.7.5 ; python_version >= "3.9" and python_full_version < "3.11.0" +mdurl==0.1.2 ; python_version >= "3.9" and python_full_version < "3.11.0" +moepy==1.1.4 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" +numba==0.58.1 ; python_version >= "3.9" and python_full_version < "3.11.0" +numpy==1.24.4 ; python_version >= "3.9" and python_full_version < "3.11.0" +packaging==24.0 ; python_version >= "3.9" and python_full_version < "3.11.0" +pandas==1.5.3 ; python_version >= "3.9" and python_full_version < "3.11.0" +pillow==10.3.0 ; python_version >= "3.9" and python_full_version < "3.11.0" +psutil==5.9.8 ; python_version >= "3.9" and python_full_version < "3.11.0" +pyarrow==16.1.0 ; python_full_version >= "3.9" and python_full_version < "3.11.0" +pygments==2.17.2 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" +pymzml==2.5.9 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" +pyparsing==3.1.2 ; python_version >= "3.9" and python_full_version < "3.11.0" +pyteomics==4.7.2 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" +python-dateutil==2.9.0.post0 ; python_version >= "3.9" and python_full_version < "3.11.0" +pytz==2024.1 ; python_version >= "3.9" and python_full_version < "3.11.0" +pyyaml==6.0.1 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" +pyzstd==0.15.10 ; python_version >= "3.9" and python_full_version < "3.11.0" +regex==2024.4.16 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" +rich==13.7.1 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" +scikit-learn==1.3.2 ; python_version >= "3.9" and python_full_version < "3.11.0" +scipy==1.10.1 ; python_version >= "3.9" and python_full_version < "3.11.0" +six==1.16.0 ; python_version >= "3.9" and python_full_version < "3.11.0" +sortedcontainers==2.4.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" +spectrum-fundamentals==0.5.2 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" +threadpoolctl==3.4.0 ; python_version >= "3.9" and python_full_version < "3.11.0" +tqdm==4.66.2 ; python_version >= "3.9" and python_full_version < "3.11.0" +typing-extensions==4.11.0 ; python_version >= "3.9" and python_version < "3.9" +zipp==3.18.1 ; python_version >= "3.9" and python_version < "3.10" diff --git a/spectrum_io/file/__init__.py b/spectrum_io/file/__init__.py index 35dc193..9aa3dba 100644 --- a/spectrum_io/file/__init__.py +++ b/spectrum_io/file/__init__.py @@ -2,6 +2,6 @@ import logging -from . import csv, hdf5 +from . import csv, hdf5, parquet logger = logging.getLogger(__name__) diff --git a/spectrum_io/file/parquet.ipynb b/spectrum_io/file/parquet.ipynb new file mode 100644 index 0000000..5d63ee5 --- /dev/null +++ b/spectrum_io/file/parquet.ipynb @@ -0,0 +1,902 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "from pathlib import Path\n", + "from typing import Union\n", + "\n", + "import datasets\n", + "import pandas as pd\n", + "import pyarrow as pa\n", + "import pyarrow.feather as feather\n", + "import pyarrow.parquet as pq\n", + "import scipy\n", + "\n", + "from parquet import *" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "root_path = Path(\"/cmnfs/proj/prosit_astral/datasets/parquet\")\n", + "train_path = root_path / \"train\"" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "385ec5beebab46e6933deda6d071ca39", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [ + "Resolving data files: 0%| | 0/78 [00:00\u001b[39m max_shard_size:\n\u001b[0;32m-> 1997\u001b[0m num_examples, num_bytes \u001b[39m=\u001b[39m writer\u001b[39m.\u001b[39;49mfinalize()\n\u001b[1;32m 1998\u001b[0m writer\u001b[39m.\u001b[39mclose()\n", + "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/datasets/arrow_writer.py:607\u001b[0m, in \u001b[0;36mArrowWriter.finalize\u001b[0;34m(self, close_stream)\u001b[0m\n\u001b[1;32m 606\u001b[0m \u001b[39mif\u001b[39;00m close_stream:\n\u001b[0;32m--> 607\u001b[0m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49mstream\u001b[39m.\u001b[39;49mclose()\n\u001b[1;32m 608\u001b[0m \u001b[39melse\u001b[39;00m:\n", + "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/fsspec/implementations/local.py:407\u001b[0m, in \u001b[0;36mLocalFileOpener.close\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 406\u001b[0m \u001b[39mdef\u001b[39;00m \u001b[39mclose\u001b[39m(\u001b[39mself\u001b[39m):\n\u001b[0;32m--> 407\u001b[0m \u001b[39mreturn\u001b[39;00m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49mf\u001b[39m.\u001b[39;49mclose()\n", + "\u001b[0;31mKeyboardInterrupt\u001b[0m: ", + "\nDuring handling of the above exception, another exception occurred:\n", + "\u001b[0;31mValueError\u001b[0m Traceback (most recent call last)", + "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/datasets/builder.py:2027\u001b[0m, in \u001b[0;36mArrowBasedBuilder._prepare_split_single\u001b[0;34m(self, gen_kwargs, fpath, file_format, max_shard_size, job_id)\u001b[0m\n\u001b[1;32m 2026\u001b[0m num_shards \u001b[39m=\u001b[39m shard_id \u001b[39m+\u001b[39m \u001b[39m1\u001b[39m\n\u001b[0;32m-> 2027\u001b[0m num_examples, num_bytes \u001b[39m=\u001b[39m writer\u001b[39m.\u001b[39;49mfinalize()\n\u001b[1;32m 2028\u001b[0m writer\u001b[39m.\u001b[39mclose()\n", + "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/datasets/arrow_writer.py:602\u001b[0m, in \u001b[0;36mArrowWriter.finalize\u001b[0;34m(self, close_stream)\u001b[0m\n\u001b[1;32m 601\u001b[0m \u001b[39mif\u001b[39;00m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mpa_writer \u001b[39mis\u001b[39;00m \u001b[39mNone\u001b[39;00m \u001b[39mand\u001b[39;00m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mschema:\n\u001b[0;32m--> 602\u001b[0m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49m_build_writer(\u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49mschema)\n\u001b[1;32m 603\u001b[0m \u001b[39mif\u001b[39;00m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mpa_writer \u001b[39mis\u001b[39;00m \u001b[39mnot\u001b[39;00m \u001b[39mNone\u001b[39;00m:\n", + "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/datasets/arrow_writer.py:404\u001b[0m, in \u001b[0;36mArrowWriter._build_writer\u001b[0;34m(self, inferred_schema)\u001b[0m\n\u001b[1;32m 403\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39m_schema \u001b[39m=\u001b[39m schema\n\u001b[0;32m--> 404\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mpa_writer \u001b[39m=\u001b[39m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49m_WRITER_CLASS(\u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49mstream, schema)\n", + "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/pyarrow/ipc.py:85\u001b[0m, in \u001b[0;36mRecordBatchStreamWriter.__init__\u001b[0;34m(self, sink, schema, use_legacy_format, options)\u001b[0m\n\u001b[1;32m 84\u001b[0m options \u001b[39m=\u001b[39m _get_legacy_format_default(use_legacy_format, options)\n\u001b[0;32m---> 85\u001b[0m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49m_open(sink, schema, options\u001b[39m=\u001b[39;49moptions)\n", + "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/pyarrow/ipc.pxi:582\u001b[0m, in \u001b[0;36mpyarrow.lib._RecordBatchStreamWriter._open\u001b[0;34m()\u001b[0m\n", + "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/pyarrow/io.pxi:2097\u001b[0m, in \u001b[0;36mpyarrow.lib.get_writer\u001b[0;34m()\u001b[0m\n", + "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/pyarrow/io.pxi:232\u001b[0m, in \u001b[0;36mpyarrow.lib.NativeFile.get_output_stream\u001b[0;34m()\u001b[0m\n", + "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/pyarrow/io.pxi:246\u001b[0m, in \u001b[0;36mpyarrow.lib.NativeFile._assert_writable\u001b[0;34m()\u001b[0m\n", + "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/pyarrow/io.pxi:237\u001b[0m, in \u001b[0;36mpyarrow.lib.NativeFile._assert_open\u001b[0;34m()\u001b[0m\n", + "\u001b[0;31mValueError\u001b[0m: I/O operation on closed file", + "\nThe above exception was the direct cause of the following exception:\n", + "\u001b[0;31mDatasetGenerationError\u001b[0m Traceback (most recent call last)", + "\u001b[1;32m/cmnfs/home/students/j.schlensok/spectrum_io/spectrum_io/file/parquet.ipynb Cell 3\u001b[0m line \u001b[0;36m1\n\u001b[0;32m----> 1\u001b[0m ds \u001b[39m=\u001b[39m datasets\u001b[39m.\u001b[39;49mload_dataset(\u001b[39mstr\u001b[39;49m(root_path))\n", + "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/datasets/load.py:2609\u001b[0m, in \u001b[0;36mload_dataset\u001b[0;34m(path, name, data_dir, data_files, split, cache_dir, features, download_config, download_mode, verification_mode, ignore_verifications, keep_in_memory, save_infos, revision, token, use_auth_token, task, streaming, num_proc, storage_options, trust_remote_code, **config_kwargs)\u001b[0m\n\u001b[1;32m 2606\u001b[0m \u001b[39mreturn\u001b[39;00m builder_instance\u001b[39m.\u001b[39mas_streaming_dataset(split\u001b[39m=\u001b[39msplit)\n\u001b[1;32m 2608\u001b[0m \u001b[39m# Download and prepare data\u001b[39;00m\n\u001b[0;32m-> 2609\u001b[0m builder_instance\u001b[39m.\u001b[39;49mdownload_and_prepare(\n\u001b[1;32m 2610\u001b[0m download_config\u001b[39m=\u001b[39;49mdownload_config,\n\u001b[1;32m 2611\u001b[0m download_mode\u001b[39m=\u001b[39;49mdownload_mode,\n\u001b[1;32m 2612\u001b[0m verification_mode\u001b[39m=\u001b[39;49mverification_mode,\n\u001b[1;32m 2613\u001b[0m num_proc\u001b[39m=\u001b[39;49mnum_proc,\n\u001b[1;32m 2614\u001b[0m storage_options\u001b[39m=\u001b[39;49mstorage_options,\n\u001b[1;32m 2615\u001b[0m )\n\u001b[1;32m 2617\u001b[0m \u001b[39m# Build dataset for splits\u001b[39;00m\n\u001b[1;32m 2618\u001b[0m keep_in_memory \u001b[39m=\u001b[39m (\n\u001b[1;32m 2619\u001b[0m keep_in_memory \u001b[39mif\u001b[39;00m keep_in_memory \u001b[39mis\u001b[39;00m \u001b[39mnot\u001b[39;00m \u001b[39mNone\u001b[39;00m \u001b[39melse\u001b[39;00m is_small_dataset(builder_instance\u001b[39m.\u001b[39minfo\u001b[39m.\u001b[39mdataset_size)\n\u001b[1;32m 2620\u001b[0m )\n", + "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/datasets/builder.py:1027\u001b[0m, in \u001b[0;36mDatasetBuilder.download_and_prepare\u001b[0;34m(self, output_dir, download_config, download_mode, verification_mode, ignore_verifications, try_from_hf_gcs, dl_manager, base_path, use_auth_token, file_format, max_shard_size, num_proc, storage_options, **download_and_prepare_kwargs)\u001b[0m\n\u001b[1;32m 1025\u001b[0m \u001b[39mif\u001b[39;00m num_proc \u001b[39mis\u001b[39;00m \u001b[39mnot\u001b[39;00m \u001b[39mNone\u001b[39;00m:\n\u001b[1;32m 1026\u001b[0m prepare_split_kwargs[\u001b[39m\"\u001b[39m\u001b[39mnum_proc\u001b[39m\u001b[39m\"\u001b[39m] \u001b[39m=\u001b[39m num_proc\n\u001b[0;32m-> 1027\u001b[0m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49m_download_and_prepare(\n\u001b[1;32m 1028\u001b[0m dl_manager\u001b[39m=\u001b[39;49mdl_manager,\n\u001b[1;32m 1029\u001b[0m verification_mode\u001b[39m=\u001b[39;49mverification_mode,\n\u001b[1;32m 1030\u001b[0m \u001b[39m*\u001b[39;49m\u001b[39m*\u001b[39;49mprepare_split_kwargs,\n\u001b[1;32m 1031\u001b[0m \u001b[39m*\u001b[39;49m\u001b[39m*\u001b[39;49mdownload_and_prepare_kwargs,\n\u001b[1;32m 1032\u001b[0m )\n\u001b[1;32m 1033\u001b[0m \u001b[39m# Sync info\u001b[39;00m\n\u001b[1;32m 1034\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39minfo\u001b[39m.\u001b[39mdataset_size \u001b[39m=\u001b[39m \u001b[39msum\u001b[39m(split\u001b[39m.\u001b[39mnum_bytes \u001b[39mfor\u001b[39;00m split \u001b[39min\u001b[39;00m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39minfo\u001b[39m.\u001b[39msplits\u001b[39m.\u001b[39mvalues())\n", + "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/datasets/builder.py:1122\u001b[0m, in \u001b[0;36mDatasetBuilder._download_and_prepare\u001b[0;34m(self, dl_manager, verification_mode, **prepare_split_kwargs)\u001b[0m\n\u001b[1;32m 1118\u001b[0m split_dict\u001b[39m.\u001b[39madd(split_generator\u001b[39m.\u001b[39msplit_info)\n\u001b[1;32m 1120\u001b[0m \u001b[39mtry\u001b[39;00m:\n\u001b[1;32m 1121\u001b[0m \u001b[39m# Prepare split will record examples associated to the split\u001b[39;00m\n\u001b[0;32m-> 1122\u001b[0m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49m_prepare_split(split_generator, \u001b[39m*\u001b[39;49m\u001b[39m*\u001b[39;49mprepare_split_kwargs)\n\u001b[1;32m 1123\u001b[0m \u001b[39mexcept\u001b[39;00m \u001b[39mOSError\u001b[39;00m \u001b[39mas\u001b[39;00m e:\n\u001b[1;32m 1124\u001b[0m \u001b[39mraise\u001b[39;00m \u001b[39mOSError\u001b[39;00m(\n\u001b[1;32m 1125\u001b[0m \u001b[39m\"\u001b[39m\u001b[39mCannot find data file. \u001b[39m\u001b[39m\"\u001b[39m\n\u001b[1;32m 1126\u001b[0m \u001b[39m+\u001b[39m (\u001b[39mself\u001b[39m\u001b[39m.\u001b[39mmanual_download_instructions \u001b[39mor\u001b[39;00m \u001b[39m\"\u001b[39m\u001b[39m\"\u001b[39m)\n\u001b[1;32m 1127\u001b[0m \u001b[39m+\u001b[39m \u001b[39m\"\u001b[39m\u001b[39m\\n\u001b[39;00m\u001b[39mOriginal error:\u001b[39m\u001b[39m\\n\u001b[39;00m\u001b[39m\"\u001b[39m\n\u001b[1;32m 1128\u001b[0m \u001b[39m+\u001b[39m \u001b[39mstr\u001b[39m(e)\n\u001b[1;32m 1129\u001b[0m ) \u001b[39mfrom\u001b[39;00m \u001b[39mNone\u001b[39;00m\n", + "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/datasets/builder.py:1882\u001b[0m, in \u001b[0;36mArrowBasedBuilder._prepare_split\u001b[0;34m(self, split_generator, file_format, num_proc, max_shard_size)\u001b[0m\n\u001b[1;32m 1880\u001b[0m job_id \u001b[39m=\u001b[39m \u001b[39m0\u001b[39m\n\u001b[1;32m 1881\u001b[0m \u001b[39mwith\u001b[39;00m pbar:\n\u001b[0;32m-> 1882\u001b[0m \u001b[39mfor\u001b[39;00m job_id, done, content \u001b[39min\u001b[39;00m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39m_prepare_split_single(\n\u001b[1;32m 1883\u001b[0m gen_kwargs\u001b[39m=\u001b[39mgen_kwargs, job_id\u001b[39m=\u001b[39mjob_id, \u001b[39m*\u001b[39m\u001b[39m*\u001b[39m_prepare_split_args\n\u001b[1;32m 1884\u001b[0m ):\n\u001b[1;32m 1885\u001b[0m \u001b[39mif\u001b[39;00m done:\n\u001b[1;32m 1886\u001b[0m result \u001b[39m=\u001b[39m content\n", + "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/datasets/builder.py:2038\u001b[0m, in \u001b[0;36mArrowBasedBuilder._prepare_split_single\u001b[0;34m(self, gen_kwargs, fpath, file_format, max_shard_size, job_id)\u001b[0m\n\u001b[1;32m 2036\u001b[0m \u001b[39mif\u001b[39;00m \u001b[39misinstance\u001b[39m(e, DatasetGenerationError):\n\u001b[1;32m 2037\u001b[0m \u001b[39mraise\u001b[39;00m\n\u001b[0;32m-> 2038\u001b[0m \u001b[39mraise\u001b[39;00m DatasetGenerationError(\u001b[39m\"\u001b[39m\u001b[39mAn error occurred while generating the dataset\u001b[39m\u001b[39m\"\u001b[39m) \u001b[39mfrom\u001b[39;00m \u001b[39me\u001b[39;00m\n\u001b[1;32m 2040\u001b[0m \u001b[39myield\u001b[39;00m job_id, \u001b[39mTrue\u001b[39;00m, (total_num_examples, total_num_bytes, writer\u001b[39m.\u001b[39m_features, num_shards, shard_lengths)\n", + "\u001b[0;31mDatasetGenerationError\u001b[0m: An error occurred while generating the dataset" + ] + } + ], + "source": [ + "ds = datasets.load_dataset(str(root_path))" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [], + "source": [ + "input_test_file = Path.cwd().parent.parent.parent / \"oktoberfest/data/intensity_data.parquet\"\n", + "raw_data = {\n", + " \"intensities\": [\n", + " [4e-5, 0., -1., 0., 0., -1., 0.03, 0., -1., 0.4],\n", + " [.3, 0., -1., 1., 0., -1., 0.4, 0., -1., 0.05],\n", + " [.04, 0., 0., 0., 0., 0., 2e-3, 0., 0., .13]\n", + " ],\n", + " \"sequence\": [\"SVFLTFLR\", \"KTSQIFLAK\", \"SPVGRVTPKEWR\"],\n", + " \"precursor_charge_onehot\": [\n", + " [0, 1, 0, 0, 0, 0],\n", + " [0, 1, 0, 0, 0, 0],\n", + " [0, 0, 1, 0, 0, 0],\n", + " ],\n", + " \"collision_energy_normed\": [.25, .28, .28]\n", + "}" + ] + }, + { + "cell_type": "code", + "execution_count": 42, + "metadata": {}, + "outputs": [], + "source": [ + "output_path = Path.cwd() / \"temp\"\n", + "output_path.mkdir(exist_ok=True)\n", + "\n", + "df = pd.DataFrame(raw_data)\n", + "\n", + "#df2 = pd.concat([df, df], keys=['1', '2'], names=[\"dataset\", \"index\"])\n", + "df2 = pd.concat([df.assign(dataset='1'), df.assign(dataset='2')])\n", + "table = pa.Table.from_pandas(df2)\n", + "\n", + "pq.write_to_dataset(\n", + " table,\n", + " root_path=output_path,\n", + " partition_cols=[\"dataset\"],\n", + " existing_data_behavior=\"delete_matching\",\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": 43, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "pyarrow.Table\n", + "intensities: list\n", + " child 0, item: double\n", + "sequence: string\n", + "precursor_charge_onehot: list\n", + " child 0, item: int64\n", + "collision_energy_normed: double\n", + "dataset: string\n", + "__index_level_0__: int64\n", + "----\n", + "intensities: [[[0.00004,0,-1,0,0,-1,0.03,0,-1,0.4],[0.3,0,-1,1,0,-1,0.4,0,-1,0.05],...,[0.3,0,-1,1,0,-1,0.4,0,-1,0.05],[0.04,0,0,0,0,0,0.002,0,0,0.13]]]\n", + "sequence: [[\"SVFLTFLR\",\"KTSQIFLAK\",\"SPVGRVTPKEWR\",\"SVFLTFLR\",\"KTSQIFLAK\",\"SPVGRVTPKEWR\"]]\n", + "precursor_charge_onehot: [[[0,1,0,0,0,0],[0,1,0,0,0,0],...,[0,1,0,0,0,0],[0,0,1,0,0,0]]]\n", + "collision_energy_normed: [[0.25,0.28,0.28,0.25,0.28,0.28]]\n", + "dataset: [[\"1\",\"1\",\"1\",\"2\",\"2\",\"2\"]]\n", + "__index_level_0__: [[0,1,2,0,1,2]]" + ] + }, + "execution_count": 43, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "table" + ] + }, + { + "cell_type": "code", + "execution_count": 44, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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intensitiessequenceprecursor_charge_onehotcollision_energy_normed
0[4e-05, 0.0, -1.0, 0.0, 0.0, -1.0, 0.03, 0.0, ...SVFLTFLR[0, 1, 0, 0, 0, 0]0.25
1[0.3, 0.0, -1.0, 1.0, 0.0, -1.0, 0.4, 0.0, -1....KTSQIFLAK[0, 1, 0, 0, 0, 0]0.28
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intensitiessequenceprecursor_charge_onehotcollision_energy_aligned_normed
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Careful: If all of these are strings of ints, + Parquet will convert them to raw integers! + + :raises NotImplementedError: if anything else but a Pandas DataFrame is used as the dataset + """ + if all(isinstance(x, pd.DataFrame) for x in datasets): + df = pd.concat([dataset.assign(dataset=name) for dataset, name in zip(datasets, dataset_names)]) + table = pa.Table.from_pandas(df) + else: + raise NotImplementedError + + if isinstance(path, str): + path = Path(path) + path.mkdir(exist_ok=True) + + pq.write_to_dataset( + table, + root_path=path, + partition_cols=["dataset"], + existing_data_behavior="delete_matching", + ) diff --git a/spectrum_io/raw/msraw.py b/spectrum_io/raw/msraw.py index f85708e..9157716 100644 --- a/spectrum_io/raw/msraw.py +++ b/spectrum_io/raw/msraw.py @@ -217,7 +217,7 @@ def _read_mzml_pyteomics(file_list: List[Path], *args, **kwargs) -> pd.DataFrame for file_path in file_list: mass_analyzer = get_mass_analyzer(file_path) logger.info(f"Reading mzML file: {file_path}") - data_iter = mzml.read(source=str(file_path), *args, **kwargs) + data_iter = mzml.read(str(file_path), *args, **kwargs) file_name = file_path.stem try: instrument_params = data_iter.get_by_id("commonInstrumentParams") diff --git a/tests/unit_tests/test_parquet.py b/tests/unit_tests/test_parquet.py new file mode 100644 index 0000000..61e9cf9 --- /dev/null +++ b/tests/unit_tests/test_parquet.py @@ -0,0 +1,101 @@ +import shutil +import sys +from contextlib import nullcontext +from pathlib import Path + +import pandas as pd +import pyarrow as pa +import pyarrow.parquet as pq +import pytest +import scipy + +if "typeguard" in sys.modules: + from typeguard import suppress_type_checks + +from spectrum_io.file import parquet + + +class TestParquet: + """Test class to check Parquet file I/O.""" + + def test_read_file(self, raw_data, tmpdir): + """Test read operation for a single dataset.""" + output_path = Path(tmpdir / "table.parquet") + pq.write_table(pa.Table.from_pydict(raw_data), output_path) + df = parquet.read_file(output_path) + output_path.unlink() + pd.testing.assert_frame_equal(df, pd.DataFrame(raw_data)) + + def test_write_file(self, raw_data, tmpdir): + """Check write operation for a single dataset.""" + output_path = Path(tmpdir / "table.parquet") + df = pd.DataFrame(raw_data) + parquet.write_file(df, output_path) + pd.testing.assert_frame_equal(df, pd.read_parquet(output_path)) + output_path.unlink() + + def test_read_write_partition(self, raw_data, tmpdir): + """Check whether data is unmodified after being written to and then read from a partitioned dataset.""" + output_path = Path(tmpdir / "partition") + df = pd.DataFrame(raw_data) + parquet.write_partition([df, df], output_path, ["dataset_1", "dataset_2"]) + read_df = parquet.read_partition(output_path, "dataset_1") + shutil.rmtree(output_path) + pd.testing.assert_frame_equal(read_df, df) + + def test_read_write_partition_integer_key(self, raw_data, tmpdir): + """Check whether Parquet's under-the-hood conversion of string to integer keys is handled seamlessly.""" + output_path = Path(tmpdir / "partition") + df = pd.DataFrame(raw_data) + parquet.write_partition([df, df], output_path, ["1", "2"]) + read_df = parquet.read_partition(output_path, "1") + shutil.rmtree(output_path) + pd.testing.assert_frame_equal(read_df, df) + + def test_modify_partition(self, raw_data, tmpdir): + """Check whether file content stays the same when writing new data to the same partitioned directory.""" + output_path = Path(tmpdir / "partition") + df = pd.DataFrame(raw_data) + parquet.write_partition([df, df], output_path, ["1", "2"]) + parquet.write_partition([df, df, df], output_path, ["1", "2", "3"]) + read_df = parquet.read_partition(output_path, "2") + shutil.rmtree(output_path) + pd.testing.assert_frame_equal(read_df, df) + + def test_write_not_implemented(self, raw_data, tmpdir): + """Check whether write_file() raises a NotImplementedError if provided with an unsupported object.""" + with pytest.raises(NotImplementedError): + with suppress_type_checks() if "typeguard" in sys.modules else nullcontext(): + output_path = Path(tmpdir / "table.parquet") + df = pd.DataFrame(raw_data).to_numpy() + parquet.write_file(df, output_path) + output_path.unlink() + + def test_read_write_partition_not_implemented(self, raw_data, tmpdir): + """Check whether write_partition() raises a NotImplementedError if provided with an unsupported object.""" + with pytest.raises(NotImplementedError): + with suppress_type_checks() if "typeguard" in sys.modules else nullcontext(): + output_path = Path(tmpdir / "partition") + df = pd.DataFrame(raw_data).to_numpy() + parquet.write_partition([df, df], output_path, ["dataset_1", "dataset_2"]) + output_path.unlink() + + +@pytest.fixture +def raw_data(): + """Simple toy MS data containing float, list[float], str, int, and list[int].""" + return { + "scan_number": [1, 234, 5678], + "intensities": [ + [4e-5, 0.0, -1.0, 0.0, 0.0, -1.0, 0.03, 0.0, -1.0, 0.4], + [0.3, 0.0, -1.0, 1.0, 0.0, -1.0, 0.4, 0.0, -1.0, 0.05], + [0.04, 0.0, 0.0, 0.0, 0.0, 0.0, 2e-3, 0.0, 0.0, 0.13], + ], + "sequence": ["SVFLTFLR", "KTSQIFLAK", "SPVGRVTPKEWR"], + "precursor_charge_onehot": [ + [0, 1, 0, 0, 0, 0], + [0, 1, 0, 0, 0, 0], + [0, 0, 1, 0, 0, 0], + ], + "collision_energy_normed": [0.250827308624, 0.288798207462, 0.2887064038764], + }