From 065916c95df908973ab8c8950332711cebf7d3f0 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 28 Aug 2023 12:52:53 +0000 Subject: [PATCH 01/14] Update pyarrow requirement from ~=12.0.0 to ~=13.0.0 Updates the requirements on [pyarrow](https://github.com/apache/arrow) to permit the latest version. - [Commits](https://github.com/apache/arrow/compare/go/v12.0.0...go/v13.0.0) --- updated-dependencies: - dependency-name: pyarrow dependency-type: direct:production ... Signed-off-by: dependabot[bot] --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 4975d6c3..1d797e93 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -40,7 +40,7 @@ dependencies = [ "pandas~=2.0", "pex~=2.1", "publicsuffixlist~=0.9.3", - "pyarrow~=12.0.0", + "pyarrow~=13.0.0", "pycld3~=0.22.0", "pylint~=2.16", "pyspark~=3.0", From 69c477b6b4a064bd0f82120e24a5bb2379c2c58f Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 28 Aug 2023 12:53:22 +0000 Subject: [PATCH 02/14] Update approvaltests requirement from ~=8.2 to ~=9.0 Updates the requirements on [approvaltests](https://github.com/approvals/ApprovalTests.Python) to permit the latest version. - [Release notes](https://github.com/approvals/ApprovalTests.Python/releases) - [Commits](https://github.com/approvals/ApprovalTests.Python/compare/v8.2.0...v9.0.0) --- updated-dependencies: - dependency-name: approvaltests dependency-type: direct:production ... Signed-off-by: dependabot[bot] --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 4975d6c3..12389b50 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -60,7 +60,7 @@ dynamic = ["version"] [project.optional-dependencies] tests = [ - "approvaltests~=8.2", + "approvaltests~=9.0", "flake8~=6.0", "pylint~=2.12", "pytest~=7.2", From 0011506ba5ee8a768ef9169fe22410a588d5388c Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 11 Sep 2023 12:28:30 +0000 Subject: [PATCH 03/14] Update dataclasses-json requirement from ~=0.5.7 to ~=0.6.0 Updates the requirements on [dataclasses-json](https://github.com/lidatong/dataclasses-json) to permit the latest version. - [Release notes](https://github.com/lidatong/dataclasses-json/releases) - [Commits](https://github.com/lidatong/dataclasses-json/compare/v0.5.7...v0.6.0) --- updated-dependencies: - dependency-name: dataclasses-json dependency-type: direct:production ... Signed-off-by: dependabot[bot] --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 1d797e93..0f4125e7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -27,7 +27,7 @@ dependencies = [ "beautifulsoup4~=4.11", "bleach~=6.0", "click~=8.1", - "dataclasses-json~=0.5.7", + "dataclasses-json~=0.6.0", "diskcache~=5.4", "fasttext-langdetect~=1.0", "fastwarc~=0.14.0", From c23913c4f852ad9c351f450b65cf64e5f234ce4b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Maik=20Fr=C3=B6be?= Date: Wed, 25 Oct 2023 08:55:21 +0000 Subject: [PATCH 04/14] Prepare embedding of queries --- notebooks/calculate-sbert-embeddings.ipynb | 442 +++++++++++++++++++++ 1 file changed, 442 insertions(+) create mode 100644 notebooks/calculate-sbert-embeddings.ipynb diff --git a/notebooks/calculate-sbert-embeddings.ipynb b/notebooks/calculate-sbert-embeddings.ipynb new file mode 100644 index 00000000..2f71cebb --- /dev/null +++ b/notebooks/calculate-sbert-embeddings.ipynb @@ -0,0 +1,442 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "id": "dbd905f6-46f6-48f8-874f-8f9d036b5e54", + "metadata": {}, + "outputs": [], + "source": [ + "# Calculate sBERT Embeddings" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "12037192-0b2a-4eea-aee7-4aca617914f5", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'3.8.13 | packaged by conda-forge | (default, Mar 25 2022, 06:04:10) \\n[GCC 10.3.0]'" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "import sys\n", + "\n", + "sys.version" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "89422d77-a927-46f1-85de-19bd9d548b03", + "metadata": {}, + "outputs": [], + "source": [ + "def transform_to_sbert_embeddings(input):\n", + " import os\n", + " import json\n", + " import sys\n", + " # I created the venv-environment below using \n", + " \n", + " #VENV_LIB_DIR = '/mnt/ceph/storage/data-in-progress/data-research/web-search/ECIR-22/ecir22-zero-shot/sbert-env/lib/python3.8/site-packages'\n", + " #VENV_LIB_DIR = '/mnt/ceph/storage/data-in-progress/data-research/web-search/ECIR-22/ecir22-zero-shot/sbert-env-python3.7/lib/python3.7/site-packages'\n", + " VENV_LIB_DIR = '/mnt/ceph/storage/data-in-progress/data-research/web-search/ECIR-22/ecir22-zero-shot/sbert-env-python3.8/lib/python3.8/site-packages'\n", + " if VENV_LIB_DIR not in sys.path:\n", + " sys.path = [VENV_LIB_DIR] + sys.path\n", + " os.environ['SENTENCE_TRANSFORMERS_HOME'] = '/mnt/ceph/storage/data-in-progress/data-research/web-search/ECIR-22/ecir22-zero-shot/sbert-env/sentence-transformer-home'\n", + " from sentence_transformers import SentenceTransformer\n", + " sbert_model = SentenceTransformer('paraphrase-MiniLM-L6-v2')\n", + " return json.dumps(sbert_model.encode(input).tolist())" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "id": "a231e76c-1e8f-416f-a338-097a6c7e2b37", + "metadata": {}, + "outputs": [ + { + "ename": "ImportError", + "evalue": "Failed to load PyTorch C extensions:\n It appears that PyTorch has loaded the `torch/_C` folder\n of the PyTorch repository rather than the C extensions which\n are expected in the `torch._C` namespace. This can occur when\n using the `install` workflow. e.g.\n $ python setup.py install && python -c \"import torch\"\n\n This error can generally be solved using the `develop` workflow\n $ python setup.py develop && python -c \"import torch\" # This should succeed\n or by running Python from a different directory.", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mImportError\u001b[0m Traceback (most recent call last)", + "Cell \u001b[0;32mIn [3], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[43mtransform_to_sbert_embeddings\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mhello world foo\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m)\u001b[49m\n", + "Cell \u001b[0;32mIn [2], line 12\u001b[0m, in \u001b[0;36mtransform_to_sbert_embeddings\u001b[0;34m(input)\u001b[0m\n\u001b[1;32m 10\u001b[0m sys\u001b[38;5;241m.\u001b[39mpath \u001b[38;5;241m=\u001b[39m [VENV_LIB_DIR] \u001b[38;5;241m+\u001b[39m sys\u001b[38;5;241m.\u001b[39mpath\n\u001b[1;32m 11\u001b[0m os\u001b[38;5;241m.\u001b[39menviron[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mSENTENCE_TRANSFORMERS_HOME\u001b[39m\u001b[38;5;124m'\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124m/mnt/ceph/storage/data-in-progress/data-research/web-search/ECIR-22/ecir22-zero-shot/sbert-env/sentence-transformer-home\u001b[39m\u001b[38;5;124m'\u001b[39m\n\u001b[0;32m---> 12\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01msentence_transformers\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m SentenceTransformer\n\u001b[1;32m 13\u001b[0m sbert_model \u001b[38;5;241m=\u001b[39m SentenceTransformer(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mparaphrase-MiniLM-L6-v2\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m 14\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m json\u001b[38;5;241m.\u001b[39mdumps(sbert_model\u001b[38;5;241m.\u001b[39mencode(\u001b[38;5;28minput\u001b[39m)\u001b[38;5;241m.\u001b[39mtolist())\n", + "File \u001b[0;32m/mnt/ceph/storage/data-in-progress/data-research/web-search/ECIR-22/ecir22-zero-shot/sbert-env-python3.7/lib/python3.7/site-packages/sentence_transformers/__init__.py:3\u001b[0m\n\u001b[1;32m 1\u001b[0m __version__ \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m2.0.0\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 2\u001b[0m __MODEL_HUB_ORGANIZATION__ \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124msentence-transformers\u001b[39m\u001b[38;5;124m'\u001b[39m\n\u001b[0;32m----> 3\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mdatasets\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m SentencesDataset, ParallelSentencesDataset\n\u001b[1;32m 4\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mLoggingHandler\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m LoggingHandler\n\u001b[1;32m 5\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mSentenceTransformer\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m SentenceTransformer\n", + "File \u001b[0;32m/mnt/ceph/storage/data-in-progress/data-research/web-search/ECIR-22/ecir22-zero-shot/sbert-env-python3.7/lib/python3.7/site-packages/sentence_transformers/datasets/__init__.py:1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mDenoisingAutoEncoderDataset\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m DenoisingAutoEncoderDataset\n\u001b[1;32m 2\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mNoDuplicatesDataLoader\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m NoDuplicatesDataLoader\n\u001b[1;32m 3\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mParallelSentencesDataset\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m ParallelSentencesDataset\n", + "File \u001b[0;32m/mnt/ceph/storage/data-in-progress/data-research/web-search/ECIR-22/ecir22-zero-shot/sbert-env-python3.7/lib/python3.7/site-packages/sentence_transformers/datasets/DenoisingAutoEncoderDataset.py:1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mtorch\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mutils\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mdata\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m Dataset\n\u001b[1;32m 2\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mtyping\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m List\n\u001b[1;32m 3\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mreaders\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mInputExample\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m InputExample\n", + "File \u001b[0;32m/mnt/ceph/storage/data-in-progress/data-research/web-search/ECIR-22/ecir22-zero-shot/sbert-env-python3.7/lib/python3.7/site-packages/torch/__init__.py:214\u001b[0m\n\u001b[1;32m 212\u001b[0m \u001b[38;5;66;03m# The __file__ check only works for Python 3.7 and above.\u001b[39;00m\n\u001b[1;32m 213\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m sys\u001b[38;5;241m.\u001b[39mversion_info \u001b[38;5;241m>\u001b[39m\u001b[38;5;241m=\u001b[39m (\u001b[38;5;241m3\u001b[39m, \u001b[38;5;241m7\u001b[39m) \u001b[38;5;129;01mand\u001b[39;00m _C_for_compiled_check\u001b[38;5;241m.\u001b[39m\u001b[38;5;18m__file__\u001b[39m \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[0;32m--> 214\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mImportError\u001b[39;00m(textwrap\u001b[38;5;241m.\u001b[39mdedent(\u001b[38;5;124m'''\u001b[39m\n\u001b[1;32m 215\u001b[0m \u001b[38;5;124m Failed to load PyTorch C extensions:\u001b[39m\n\u001b[1;32m 216\u001b[0m \u001b[38;5;124m It appears that PyTorch has loaded the `torch/_C` folder\u001b[39m\n\u001b[1;32m 217\u001b[0m \u001b[38;5;124m of the PyTorch repository rather than the C extensions which\u001b[39m\n\u001b[1;32m 218\u001b[0m \u001b[38;5;124m are expected in the `torch._C` namespace. This can occur when\u001b[39m\n\u001b[1;32m 219\u001b[0m \u001b[38;5;124m using the `install` workflow. e.g.\u001b[39m\n\u001b[1;32m 220\u001b[0m \u001b[38;5;124m $ python setup.py install && python -c \u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mimport torch\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 221\u001b[0m \n\u001b[1;32m 222\u001b[0m \u001b[38;5;124m This error can generally be solved using the `develop` workflow\u001b[39m\n\u001b[1;32m 223\u001b[0m \u001b[38;5;124m $ python setup.py develop && python -c \u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mimport torch\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m # This should succeed\u001b[39m\n\u001b[1;32m 224\u001b[0m \u001b[38;5;124m or by running Python from a different directory.\u001b[39m\n\u001b[1;32m 225\u001b[0m \u001b[38;5;124m \u001b[39m\u001b[38;5;124m'''\u001b[39m)\u001b[38;5;241m.\u001b[39mstrip()) \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[1;32m 226\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;66;03m# If __file__ is not None the cause is unknown, so just re-raise.\u001b[39;00m\n\u001b[1;32m 229\u001b[0m __all__ \u001b[38;5;241m+\u001b[39m\u001b[38;5;241m=\u001b[39m [name \u001b[38;5;28;01mfor\u001b[39;00m name \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mdir\u001b[39m(_C)\n\u001b[1;32m 230\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m name[\u001b[38;5;241m0\u001b[39m] \u001b[38;5;241m!=\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124m_\u001b[39m\u001b[38;5;124m'\u001b[39m \u001b[38;5;129;01mand\u001b[39;00m\n\u001b[1;32m 231\u001b[0m \u001b[38;5;129;01mnot\u001b[39;00m name\u001b[38;5;241m.\u001b[39mendswith(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mBase\u001b[39m\u001b[38;5;124m'\u001b[39m)]\n", + "\u001b[0;31mImportError\u001b[0m: Failed to load PyTorch C extensions:\n It appears that PyTorch has loaded the `torch/_C` folder\n of the PyTorch repository rather than the C extensions which\n are expected in the `torch._C` namespace. This can occur when\n using the `install` workflow. e.g.\n $ python setup.py install && python -c \"import torch\"\n\n This error can generally be solved using the `develop` workflow\n $ python setup.py develop && python -c \"import torch\" # This should succeed\n or by running Python from a different directory." + ] + } + ], + "source": [ + "transform_to_sbert_embeddings('hello world foo')" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "id": "bb71c6e5-4c33-4e81-9334-5f0ee017b8d0", + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "22/02/08 14:21:56 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable\n", + "22/02/08 14:21:58 WARN Utils: spark.executor.instances less than spark.dynamicAllocation.minExecutors is invalid, ignoring its setting, please update your configs.\n", + "22/02/08 14:21:59 WARN Client: Neither spark.yarn.jars nor spark.yarn.archive is set, falling back to uploading libraries under SPARK_HOME.\n", + "22/02/08 14:22:14 WARN Utils: spark.executor.instances less than spark.dynamicAllocation.minExecutors is invalid, ignoring its setting, please update your configs.\n" + ] + }, + { + "data": { + "text/html": [ + "\n", + "
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\n", + " " + ], + "text/plain": [ + "" + ] + }, + "execution_count": 3, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "import pyspark\n", + "\n", + "sc = pyspark.SparkContext()\n", + "sc" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "id": "0516471d-d328-4807-8707-d994a37adde1", + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "367013it [00:05, 73188.42it/s]\n" + ] + } + ], + "source": [ + "def load_queries(file_name):\n", + " ret = []\n", + " import json\n", + " from tqdm import tqdm\n", + " with open(file_name, 'r') as f:\n", + " for l in tqdm(f):\n", + " ret += [json.loads(l)]\n", + " return ret\n", + " \n", + "queries = load_queries('/mnt/ceph/storage/data-in-progress/data-research/web-search/ECIR-22/ecir22-zero-shot/msmarco-document-train.jsonl')" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "id": "a879be84-261c-437c-a060-75b116ce4263", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[{'id': '1185869',\n", + " 'contents': ')what was the immediate impact of the success of the manhattan project?',\n", + " 'target_document': ['D59219']},\n", + " {'id': '1185868',\n", + " 'contents': '_________ justice is designed to repair the harm to victim, the community and the offender caused by the offender criminal act. question 19 options:',\n", + " 'target_document': ['D59235']},\n", + " {'id': '1183785',\n", + " 'contents': 'elegxo meaning',\n", + " 'target_document': ['D576811']}]" + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "queries[:3]" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "id": "07d86350-c46c-4070-98b4-a3c0f8ab3767", + "metadata": {}, + "outputs": [], + "source": [ + "def append_sbert_embedding(i):\n", + " import json\n", + " i['sbert-embedding'] = transform_to_sbert_embeddings(i['contents'])\n", + " return json.dumps(i)\n", + "\n", + "sc.parallelize(queries, 10000)\\\n", + " .map(append_sbert_embedding)\\\n", + " .saveAsTextFile('ecir22/embeddings-ms-marco-train.jsonl')" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "id": "cfb67337-1425-4625-a9ba-d960b69652c1", + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "250it [00:00, 38687.13it/s]\n" + ] + } + ], + "source": [ + "robust04_desc_queries = load_queries('/mnt/ceph/storage/data-in-progress/data-research/web-search/ECIR-22/ecir22-zero-shot/robust04-descriptions.jsonl')\n", + "\n", + "sc.parallelize(robust04_desc_queries, 100)\\\n", + " .map(append_sbert_embedding)\\\n", + " .saveAsTextFile('ecir22/embeddings-robust04-descriptions.jsonl')" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "id": "f31203bd-6631-45e3-81ba-18254d722d65", + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "3151it [00:00, 108014.74it/s]\n" + ] + } + ], + "source": [ + "robust04_formulation_queries = load_queries('/mnt/ceph/storage/data-in-progress/data-research/web-search/ECIR-22/ecir22-zero-shot/culpepper-robust04-query-formulations.jsonl')\n", + "\n", + "sc.parallelize(robust04_formulation_queries, 100)\\\n", + " .map(append_sbert_embedding)\\\n", + " .saveAsTextFile('ecir22/culpepper-robust04-query-formulations.jsonl')" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "id": "f92e5c00-8dc0-4a2f-93f7-9e05ae681e5e", + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "250it [00:00, 41929.62it/s]\n" + ] + } + ], + "source": [ + "robust04_queries = load_queries('/mnt/ceph/storage/data-in-progress/data-research/web-search/ECIR-22/ecir22-zero-shot/trec-robust04.jsonl')\n", + "\n", + "sc.parallelize(robust04_queries, 10)\\\n", + " .map(append_sbert_embedding)\\\n", + " .saveAsTextFile('ecir22/embeddings-trec-robust04.jsonl')" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "id": "99aafba2-b9fb-42fb-b96c-b6a3f2c7958f", + "metadata": {}, + "outputs": [], + "source": [ + "sc.textFile('file:///mnt/ceph/storage/data-in-progress/data-research/web-search/ECIR-22/ecir22-zero-shot/msmarco-document-orcas.jsonl')\\\n", + " .repartition(100)\\\n", + " .saveAsTextFile('ecir22/original-ms-marco-orcas.jsonl')" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "id": "312a8d54-0d0a-4e8b-bca5-5f35a907e2c8", + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "1505it [00:00, 71136.36it/s]\n", + " \r" + ] + } + ], + "source": [ + "trec18_reformulations = load_queries('/mnt/ceph/storage/data-in-progress/data-research/web-search/ECIR-22/ecir22-zero-shot/culpepper-trec18-query-formulations.jsonl')\n", + "\n", + "sc.parallelize(trec18_reformulations, 10)\\\n", + " .map(append_sbert_embedding)\\\n", + " .saveAsTextFile('ecir22/embeddings-trec18-reformulations.jsonl')" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "id": "95ba9d06-0cdf-4945-aa35-24e40bd95fae", + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "50it [00:00, 10988.48it/s]\n", + " \r" + ] + } + ], + "source": [ + "trec18_reformulations = load_queries('/mnt/ceph/storage/data-in-progress/data-research/web-search/ECIR-22/ecir22-zero-shot/wapo-core-2018-descriptions.jsonl')\n", + "\n", + "sc.parallelize(trec18_reformulations, 10)\\\n", + " .map(append_sbert_embedding)\\\n", + " .saveAsTextFile('ecir22/embeddings-trec18-descriptions.jsonl')" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "id": "230170c7-db65-443a-8019-a6523e8f5121", + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "50it [00:00, 12575.12it/s]\n", + " \r" + ] + } + ], + "source": [ + "trec18_reformulations = load_queries('/mnt/ceph/storage/data-in-progress/data-research/web-search/ECIR-22/ecir22-zero-shot/wapo-core-2018-titles.jsonl')\n", + "\n", + "sc.parallelize(trec18_reformulations, 10)\\\n", + " .map(append_sbert_embedding)\\\n", + " .saveAsTextFile('ecir22/embeddings-trec18-titles.jsonl')" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "6dd83a4a-fe0c-4f0f-aaaf-156419bdb305", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Process \"ecir22/original-ms-marco-orcas.jsonl/part-*0\" and write to \"ecir22/embeddings-ms-marco-orcas/part-0.jsonl\".\n", + "Process \"ecir22/original-ms-marco-orcas.jsonl/part-*1\" and write to \"ecir22/embeddings-ms-marco-orcas/part-1.jsonl\".\n", + "Process \"ecir22/original-ms-marco-orcas.jsonl/part-*2\" and write to \"ecir22/embeddings-ms-marco-orcas/part-2.jsonl\".\n" + ] + } + ], + "source": [ + "import json\n", + "\n", + "for part in range(10):\n", + " input_file = 'ecir22/original-ms-marco-orcas.jsonl/part-*' + str(part)\n", + " output_file = 'ecir22/embeddings-ms-marco-orcas/part-' + str(part) + '.jsonl'\n", + " \n", + " print('Process \"' + input_file + '\" and write to \"' + output_file +'\".')\n", + " sc.textFile(input_file)\\\n", + " .repartition(10000) \\\n", + " .map(lambda i: append_sbert_embedding(json.loads(i)))\\\n", + " .saveAsTextFile(output_file)\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "d9ce53ec-3829-49f1-bb9a-3fb204fdaadc", + "metadata": {}, + "outputs": [], + "source": [ + "# Run ORCAS simply via writing to hdfs (with 100 parts) and combining all parts again" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "id": "bd987dbb-7dfe-4dd5-b436-c7aca21c4c13", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'[-0.08469943702220917, 0.4564870297908783, 0.10086822509765625, -0.11005697399377823, 0.04533920809626579, -0.3661494851112366, 0.3580332398414612, -0.07830145955085754, -0.24362005293369293, 0.2736354470252991, 0.10803011804819107, -0.7733525633811951, -0.13244451582431793, 0.19357416033744812, 0.20357149839401245, 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"transform_to_sbert_embeddings('Hello World')" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.8.13" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} From f00413055c490c851a43547d1a89123261e53133 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Maik=20Fr=C3=B6be?= Date: Wed, 25 Oct 2023 08:59:49 +0000 Subject: [PATCH 05/14] mf --- notebooks/calculate-sbert-embeddings.ipynb | 221 ++------------------- 1 file changed, 14 insertions(+), 207 deletions(-) diff --git a/notebooks/calculate-sbert-embeddings.ipynb b/notebooks/calculate-sbert-embeddings.ipynb index 2f71cebb..8fce4c0f 100644 --- a/notebooks/calculate-sbert-embeddings.ipynb +++ b/notebooks/calculate-sbert-embeddings.ipynb @@ -12,7 +12,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": 3, "id": "12037192-0b2a-4eea-aee7-4aca617914f5", "metadata": {}, "outputs": [ @@ -22,7 +22,7 @@ "'3.8.13 | packaged by conda-forge | (default, Mar 25 2022, 06:04:10) \\n[GCC 10.3.0]'" ] }, - "execution_count": 2, + "execution_count": 3, "metadata": {}, "output_type": "execute_result" } @@ -35,7 +35,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": 4, "id": "89422d77-a927-46f1-85de-19bd9d548b03", "metadata": {}, "outputs": [], @@ -59,25 +59,19 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 5, "id": "a231e76c-1e8f-416f-a338-097a6c7e2b37", "metadata": {}, "outputs": [ { - "ename": "ImportError", - "evalue": "Failed to load PyTorch C extensions:\n It appears that PyTorch has loaded the `torch/_C` folder\n of the PyTorch repository rather than the C extensions which\n are expected in the `torch._C` namespace. This can occur when\n using the `install` workflow. e.g.\n $ python setup.py install && python -c \"import torch\"\n\n This error can generally be solved using the `develop` workflow\n $ python setup.py develop && python -c \"import torch\" # This should succeed\n or by running Python from a different directory.", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mImportError\u001b[0m Traceback (most recent call last)", - "Cell \u001b[0;32mIn [3], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[43mtransform_to_sbert_embeddings\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mhello world foo\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m)\u001b[49m\n", - "Cell \u001b[0;32mIn [2], line 12\u001b[0m, in \u001b[0;36mtransform_to_sbert_embeddings\u001b[0;34m(input)\u001b[0m\n\u001b[1;32m 10\u001b[0m sys\u001b[38;5;241m.\u001b[39mpath \u001b[38;5;241m=\u001b[39m [VENV_LIB_DIR] \u001b[38;5;241m+\u001b[39m sys\u001b[38;5;241m.\u001b[39mpath\n\u001b[1;32m 11\u001b[0m os\u001b[38;5;241m.\u001b[39menviron[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mSENTENCE_TRANSFORMERS_HOME\u001b[39m\u001b[38;5;124m'\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124m/mnt/ceph/storage/data-in-progress/data-research/web-search/ECIR-22/ecir22-zero-shot/sbert-env/sentence-transformer-home\u001b[39m\u001b[38;5;124m'\u001b[39m\n\u001b[0;32m---> 12\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01msentence_transformers\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m SentenceTransformer\n\u001b[1;32m 13\u001b[0m sbert_model \u001b[38;5;241m=\u001b[39m SentenceTransformer(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mparaphrase-MiniLM-L6-v2\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m 14\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m json\u001b[38;5;241m.\u001b[39mdumps(sbert_model\u001b[38;5;241m.\u001b[39mencode(\u001b[38;5;28minput\u001b[39m)\u001b[38;5;241m.\u001b[39mtolist())\n", - "File \u001b[0;32m/mnt/ceph/storage/data-in-progress/data-research/web-search/ECIR-22/ecir22-zero-shot/sbert-env-python3.7/lib/python3.7/site-packages/sentence_transformers/__init__.py:3\u001b[0m\n\u001b[1;32m 1\u001b[0m __version__ \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m2.0.0\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 2\u001b[0m __MODEL_HUB_ORGANIZATION__ \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124msentence-transformers\u001b[39m\u001b[38;5;124m'\u001b[39m\n\u001b[0;32m----> 3\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mdatasets\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m SentencesDataset, ParallelSentencesDataset\n\u001b[1;32m 4\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mLoggingHandler\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m LoggingHandler\n\u001b[1;32m 5\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mSentenceTransformer\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m SentenceTransformer\n", - "File \u001b[0;32m/mnt/ceph/storage/data-in-progress/data-research/web-search/ECIR-22/ecir22-zero-shot/sbert-env-python3.7/lib/python3.7/site-packages/sentence_transformers/datasets/__init__.py:1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mDenoisingAutoEncoderDataset\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m DenoisingAutoEncoderDataset\n\u001b[1;32m 2\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mNoDuplicatesDataLoader\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m NoDuplicatesDataLoader\n\u001b[1;32m 3\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mParallelSentencesDataset\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m ParallelSentencesDataset\n", - "File \u001b[0;32m/mnt/ceph/storage/data-in-progress/data-research/web-search/ECIR-22/ecir22-zero-shot/sbert-env-python3.7/lib/python3.7/site-packages/sentence_transformers/datasets/DenoisingAutoEncoderDataset.py:1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mtorch\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mutils\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mdata\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m Dataset\n\u001b[1;32m 2\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mtyping\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m List\n\u001b[1;32m 3\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mreaders\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mInputExample\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m InputExample\n", - "File \u001b[0;32m/mnt/ceph/storage/data-in-progress/data-research/web-search/ECIR-22/ecir22-zero-shot/sbert-env-python3.7/lib/python3.7/site-packages/torch/__init__.py:214\u001b[0m\n\u001b[1;32m 212\u001b[0m \u001b[38;5;66;03m# The __file__ check only works for Python 3.7 and above.\u001b[39;00m\n\u001b[1;32m 213\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m sys\u001b[38;5;241m.\u001b[39mversion_info \u001b[38;5;241m>\u001b[39m\u001b[38;5;241m=\u001b[39m (\u001b[38;5;241m3\u001b[39m, \u001b[38;5;241m7\u001b[39m) \u001b[38;5;129;01mand\u001b[39;00m _C_for_compiled_check\u001b[38;5;241m.\u001b[39m\u001b[38;5;18m__file__\u001b[39m \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[0;32m--> 214\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mImportError\u001b[39;00m(textwrap\u001b[38;5;241m.\u001b[39mdedent(\u001b[38;5;124m'''\u001b[39m\n\u001b[1;32m 215\u001b[0m \u001b[38;5;124m Failed to load PyTorch C extensions:\u001b[39m\n\u001b[1;32m 216\u001b[0m \u001b[38;5;124m It appears that PyTorch has loaded the `torch/_C` folder\u001b[39m\n\u001b[1;32m 217\u001b[0m \u001b[38;5;124m of the PyTorch repository rather than the C extensions which\u001b[39m\n\u001b[1;32m 218\u001b[0m \u001b[38;5;124m are expected in the `torch._C` namespace. This can occur when\u001b[39m\n\u001b[1;32m 219\u001b[0m \u001b[38;5;124m using the `install` workflow. e.g.\u001b[39m\n\u001b[1;32m 220\u001b[0m \u001b[38;5;124m $ python setup.py install && python -c \u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mimport torch\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 221\u001b[0m \n\u001b[1;32m 222\u001b[0m \u001b[38;5;124m This error can generally be solved using the `develop` workflow\u001b[39m\n\u001b[1;32m 223\u001b[0m \u001b[38;5;124m $ python setup.py develop && python -c \u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mimport torch\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m # This should succeed\u001b[39m\n\u001b[1;32m 224\u001b[0m \u001b[38;5;124m or by running Python from a different directory.\u001b[39m\n\u001b[1;32m 225\u001b[0m \u001b[38;5;124m \u001b[39m\u001b[38;5;124m'''\u001b[39m)\u001b[38;5;241m.\u001b[39mstrip()) \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[1;32m 226\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;66;03m# If __file__ is not None the cause is unknown, so just re-raise.\u001b[39;00m\n\u001b[1;32m 229\u001b[0m __all__ \u001b[38;5;241m+\u001b[39m\u001b[38;5;241m=\u001b[39m [name \u001b[38;5;28;01mfor\u001b[39;00m name \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mdir\u001b[39m(_C)\n\u001b[1;32m 230\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m name[\u001b[38;5;241m0\u001b[39m] \u001b[38;5;241m!=\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124m_\u001b[39m\u001b[38;5;124m'\u001b[39m \u001b[38;5;129;01mand\u001b[39;00m\n\u001b[1;32m 231\u001b[0m \u001b[38;5;129;01mnot\u001b[39;00m name\u001b[38;5;241m.\u001b[39mendswith(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mBase\u001b[39m\u001b[38;5;124m'\u001b[39m)]\n", - "\u001b[0;31mImportError\u001b[0m: Failed to load PyTorch C extensions:\n It appears that PyTorch has loaded the `torch/_C` folder\n of the PyTorch repository rather than the C extensions which\n are expected in the `torch._C` namespace. This can occur when\n using the `install` workflow. e.g.\n $ python setup.py install && python -c \"import torch\"\n\n This error can generally be solved using the `develop` workflow\n $ python setup.py develop && python -c \"import torch\" # This should succeed\n or by running Python from a different directory." - ] + "data": { + "text/plain": [ + "'[-0.2869361340999603, 0.21075160801410675, 0.17087240517139435, -0.21817827224731445, 0.30960220098495483, -0.4539799094200134, 0.6447420716285706, -0.42383041977882385, 0.057523518800735474, 0.29355257749557495, -0.056013356894254684, -0.9076987504959106, 0.13708749413490295, 0.14686094224452972, 0.666681706905365, -0.11197157204151154, 0.11379440128803253, -0.5456849336624146, -0.6463279724121094, -0.5853947401046753, -0.2384648621082306, 0.05953194573521614, 0.20145022869110107, 0.18753255903720856, 0.06930533051490784, 0.08370830863714218, -0.12975147366523743, 0.19339627027511597, 0.8819394111633301, 0.22021707892417908, 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"stream", - "text": [ - "250it [00:00, 38687.13it/s]\n" - ] - } - ], - "source": [ - "robust04_desc_queries = load_queries('/mnt/ceph/storage/data-in-progress/data-research/web-search/ECIR-22/ecir22-zero-shot/robust04-descriptions.jsonl')\n", - "\n", - "sc.parallelize(robust04_desc_queries, 100)\\\n", - " .map(append_sbert_embedding)\\\n", - " .saveAsTextFile('ecir22/embeddings-robust04-descriptions.jsonl')" - ] - }, - { - "cell_type": "code", - "execution_count": 8, - "id": "f31203bd-6631-45e3-81ba-18254d722d65", - "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "3151it [00:00, 108014.74it/s]\n" - ] - } - ], - "source": [ - "robust04_formulation_queries = load_queries('/mnt/ceph/storage/data-in-progress/data-research/web-search/ECIR-22/ecir22-zero-shot/culpepper-robust04-query-formulations.jsonl')\n", - "\n", - "sc.parallelize(robust04_formulation_queries, 100)\\\n", - " .map(append_sbert_embedding)\\\n", - " .saveAsTextFile('ecir22/culpepper-robust04-query-formulations.jsonl')" - ] - }, - { - "cell_type": "code", - "execution_count": 13, - "id": "f92e5c00-8dc0-4a2f-93f7-9e05ae681e5e", - "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "250it [00:00, 41929.62it/s]\n" - ] - } - ], - "source": [ - "robust04_queries = load_queries('/mnt/ceph/storage/data-in-progress/data-research/web-search/ECIR-22/ecir22-zero-shot/trec-robust04.jsonl')\n", - "\n", - "sc.parallelize(robust04_queries, 10)\\\n", - " .map(append_sbert_embedding)\\\n", - " .saveAsTextFile('ecir22/embeddings-trec-robust04.jsonl')" - ] - }, - { - "cell_type": "code", - "execution_count": 15, - "id": "99aafba2-b9fb-42fb-b96c-b6a3f2c7958f", - "metadata": {}, - "outputs": [], - "source": [ - "sc.textFile('file:///mnt/ceph/storage/data-in-progress/data-research/web-search/ECIR-22/ecir22-zero-shot/msmarco-document-orcas.jsonl')\\\n", - " .repartition(100)\\\n", - " .saveAsTextFile('ecir22/original-ms-marco-orcas.jsonl')" - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "id": "312a8d54-0d0a-4e8b-bca5-5f35a907e2c8", - "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "1505it [00:00, 71136.36it/s]\n", - " \r" - ] - } - ], - "source": [ - "trec18_reformulations = load_queries('/mnt/ceph/storage/data-in-progress/data-research/web-search/ECIR-22/ecir22-zero-shot/culpepper-trec18-query-formulations.jsonl')\n", - "\n", - "sc.parallelize(trec18_reformulations, 10)\\\n", - " .map(append_sbert_embedding)\\\n", - " .saveAsTextFile('ecir22/embeddings-trec18-reformulations.jsonl')" - ] - }, - { - "cell_type": "code", - "execution_count": 9, - "id": "95ba9d06-0cdf-4945-aa35-24e40bd95fae", - "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "50it [00:00, 10988.48it/s]\n", - " \r" - ] - } - ], - "source": [ - "trec18_reformulations = load_queries('/mnt/ceph/storage/data-in-progress/data-research/web-search/ECIR-22/ecir22-zero-shot/wapo-core-2018-descriptions.jsonl')\n", - "\n", - "sc.parallelize(trec18_reformulations, 10)\\\n", - " .map(append_sbert_embedding)\\\n", - " .saveAsTextFile('ecir22/embeddings-trec18-descriptions.jsonl')" - ] - }, - { - "cell_type": "code", - "execution_count": 10, - "id": "230170c7-db65-443a-8019-a6523e8f5121", - "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "50it [00:00, 12575.12it/s]\n", - " \r" - ] - } - ], - "source": [ - "trec18_reformulations = load_queries('/mnt/ceph/storage/data-in-progress/data-research/web-search/ECIR-22/ecir22-zero-shot/wapo-core-2018-titles.jsonl')\n", - "\n", - "sc.parallelize(trec18_reformulations, 10)\\\n", - " .map(append_sbert_embedding)\\\n", - " .saveAsTextFile('ecir22/embeddings-trec18-titles.jsonl')" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "6dd83a4a-fe0c-4f0f-aaaf-156419bdb305", - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Process \"ecir22/original-ms-marco-orcas.jsonl/part-*0\" and write to \"ecir22/embeddings-ms-marco-orcas/part-0.jsonl\".\n", - "Process \"ecir22/original-ms-marco-orcas.jsonl/part-*1\" and write to \"ecir22/embeddings-ms-marco-orcas/part-1.jsonl\".\n", - "Process \"ecir22/original-ms-marco-orcas.jsonl/part-*2\" and write to \"ecir22/embeddings-ms-marco-orcas/part-2.jsonl\".\n" - ] - } - ], - "source": [ - "import json\n", - "\n", - "for part in range(10):\n", - " input_file = 'ecir22/original-ms-marco-orcas.jsonl/part-*' + str(part)\n", - " output_file = 'ecir22/embeddings-ms-marco-orcas/part-' + str(part) + '.jsonl'\n", - " \n", - " print('Process \"' + input_file + '\" and write to \"' + output_file +'\".')\n", - " sc.textFile(input_file)\\\n", - " .repartition(10000) \\\n", - " .map(lambda i: append_sbert_embedding(json.loads(i)))\\\n", - " .saveAsTextFile(output_file)\n" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "d9ce53ec-3829-49f1-bb9a-3fb204fdaadc", - "metadata": {}, - "outputs": [], - "source": [ - "# Run ORCAS simply via writing to hdfs (with 100 parts) and combining all parts again" + " .saveAsTextFile(todo-find-directory-in-aql)" ] }, { @@ -405,7 +212,7 @@ { "data": { "text/plain": [ - "'[-0.08469943702220917, 0.4564870297908783, 0.10086822509765625, -0.11005697399377823, 0.04533920809626579, -0.3661494851112366, 0.3580332398414612, -0.07830145955085754, -0.24362005293369293, 0.2736354470252991, 0.10803011804819107, -0.7733525633811951, -0.13244451582431793, 0.19357416033744812, 0.20357149839401245, -0.36997082829475403, 0.3396165668964386, -0.6763170957565308, -0.849643886089325, -0.19371700286865234, -0.230658158659935, -0.02822048030793667, 0.34298205375671387, 0.20185132324695587, 0.24069765210151672, -0.27264273166656494, 0.07051801681518555, 0.28514087200164795, 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-0.14925692975521088, 0.17321136593818665, -0.2907690107822418, 0.23555323481559753, 0.7190688252449036, -0.5451159477233887, -0.2757304906845093, 0.13347133994102478, -0.20016296207904816, -0.16077686846256256, -0.06611384451389313, -0.18512988090515137, -0.5091965794563293, 0.09560314565896988, 0.21853826940059662, 0.2611772119998932, -0.00016783177852630615, 0.011892130598425865, 0.5450518131256104, 0.46314629912376404, -0.3741258680820465, -0.35845592617988586, -0.0242062509059906, -0.3381757140159607, -0.31798040866851807, 0.3382136821746826, -0.3494700491428375, -0.18475615978240967, -0.010816290974617004, -0.11279979348182678, 0.16977845132350922, -0.01769975572824478, 0.5151262283325195, 0.3195383846759796, -0.6560266017913818, -0.3686582148075104, 0.14153507351875305]'" ] }, "execution_count": 6, From f69c11f94c93a893ff7b99a518a51aa1334a61b1 Mon Sep 17 00:00:00 2001 From: Jan Heinrich Reimer Date: Wed, 1 Nov 2023 12:34:21 +0100 Subject: [PATCH 06/14] Remove IDE config from Git --- .gitignore | 109 +------------------ .idea/.gitignore | 11 -- .idea/.name | 1 - .idea/codeStyles/codeStyleConfig.xml | 5 - .idea/inspectionProfiles/Project_Default.xml | 16 --- .idea/misc.xml | 6 - .idea/modules.xml | 8 -- .idea/php.xml | 12 -- .idea/vcs.xml | 6 - 9 files changed, 2 insertions(+), 172 deletions(-) delete mode 100644 .idea/.gitignore delete mode 100644 .idea/.name delete mode 100644 .idea/codeStyles/codeStyleConfig.xml delete mode 100644 .idea/inspectionProfiles/Project_Default.xml delete mode 100644 .idea/misc.xml delete mode 100644 .idea/modules.xml delete mode 100644 .idea/php.xml delete mode 100644 .idea/vcs.xml diff --git a/.gitignore b/.gitignore index 25d52720..8bd84a93 100644 --- a/.gitignore +++ b/.gitignore @@ -1,112 +1,7 @@ ### JetBrains ### -# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio, WebStorm and Rider -# Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839 - -# User-specific stuff -.idea/**/workspace.xml -.idea/**/tasks.xml -.idea/**/usage.statistics.xml -.idea/**/dictionaries -.idea/**/shelf - -# AWS User-specific -.idea/**/aws.xml - -# Generated files -.idea/**/contentModel.xml -*.iml - -# Sensitive or high-churn files -.idea/**/dataSources/ -.idea/**/dataSources.ids -.idea/**/dataSources.local.xml -.idea/**/sqlDataSources.xml -.idea/**/dynamic.xml -.idea/**/uiDesigner.xml -.idea/**/dbnavigator.xml - -# Gradle -.idea/**/gradle.xml -.idea/**/libraries - -# Gradle and Maven with auto-import -# When using Gradle or Maven with auto-import, you should exclude module files, -# since they will be recreated, and may cause churn. Uncomment if using -# auto-import. -# .idea/artifacts -# .idea/compiler.xml -# .idea/jarRepositories.xml -# .idea/modules.xml -# .idea/*.iml -# .idea/modules -# *.iml -# *.ipr - -# CMake -cmake-build-*/ - -# Mongo Explorer plugin -.idea/**/mongoSettings.xml - -# File-based project format -*.iws - -# IntelliJ +.idea out/ - -# mpeltonen/sbt-idea plugin -.idea_modules/ - -# JIRA plugin -atlassian-ide-plugin.xml - -# Cursive Clojure plugin -.idea/replstate.xml - -# SonarLint plugin -.idea/sonarlint/ - -# Crashlytics plugin (for Android Studio and IntelliJ) -com_crashlytics_export_strings.xml -crashlytics.properties -crashlytics-build.properties -fabric.properties - -# Editor-based Rest Client -.idea/httpRequests - -# Android studio 3.1+ serialized cache file -.idea/caches/build_file_checksums.ser - -### JetBrains Patch ### -# Comment Reason: https://github.com/joeblau/gitignore.io/issues/186#issuecomment-215987721 - -# *.iml -# modules.xml -# .idea/misc.xml -# *.ipr - -# Sonarlint plugin -# https://plugins.jetbrains.com/plugin/7973-sonarlint -.idea/**/sonarlint/ - -# SonarQube Plugin -# https://plugins.jetbrains.com/plugin/7238-sonarqube-community-plugin -.idea/**/sonarIssues.xml - -# Markdown Navigator plugin -# https://plugins.jetbrains.com/plugin/7896-markdown-navigator-enhanced -.idea/**/markdown-navigator.xml -.idea/**/markdown-navigator-enh.xml -.idea/**/markdown-navigator/ - -# Cache file creation bug -# See https://youtrack.jetbrains.com/issue/JBR-2257 -.idea/$CACHE_FILE$ - -# CodeStream plugin -# https://plugins.jetbrains.com/plugin/12206-codestream -.idea/codestream.xml +*.iml ### LaTeX ### ## Core latex/pdflatex auxiliary files: diff --git a/.idea/.gitignore b/.idea/.gitignore deleted file mode 100644 index f55d62cf..00000000 --- a/.idea/.gitignore +++ /dev/null @@ -1,11 +0,0 @@ -# Default ignored files -/shelf/ -/workspace.xml -# Editor-based HTTP Client requests -/httpRequests/ -# Datasource local storage ignored files -/dataSources/ -/dataSources.local.xml -# Zeppelin ignored files -/ZeppelinRemoteNotebooks/ -discord.xml diff --git a/.idea/.name b/.idea/.name deleted file mode 100644 index 05a982c1..00000000 --- a/.idea/.name +++ /dev/null @@ -1 +0,0 @@ -archive-query-log \ No newline at end of file diff --git a/.idea/codeStyles/codeStyleConfig.xml b/.idea/codeStyles/codeStyleConfig.xml deleted file mode 100644 index a55e7a17..00000000 --- a/.idea/codeStyles/codeStyleConfig.xml +++ /dev/null @@ -1,5 +0,0 @@ - - - - \ No newline at end of file diff --git a/.idea/inspectionProfiles/Project_Default.xml b/.idea/inspectionProfiles/Project_Default.xml deleted file mode 100644 index 64fbba6f..00000000 --- a/.idea/inspectionProfiles/Project_Default.xml +++ /dev/null @@ -1,16 +0,0 @@ - - - - \ No newline at end of file diff --git a/.idea/misc.xml b/.idea/misc.xml deleted file mode 100644 index cb0abd88..00000000 --- a/.idea/misc.xml +++ /dev/null @@ -1,6 +0,0 @@ - - - - - - \ No newline at end of file diff --git a/.idea/modules.xml b/.idea/modules.xml deleted file mode 100644 index c2d87291..00000000 --- a/.idea/modules.xml +++ /dev/null @@ -1,8 +0,0 @@ - - - - - - - - \ No newline at end of file diff --git a/.idea/php.xml b/.idea/php.xml deleted file mode 100644 index f5f27444..00000000 --- a/.idea/php.xml +++ /dev/null @@ -1,12 +0,0 @@ - - - - - - - - - \ No newline at end of file diff --git a/.idea/vcs.xml b/.idea/vcs.xml deleted file mode 100644 index 35eb1ddf..00000000 --- a/.idea/vcs.xml +++ /dev/null @@ -1,6 +0,0 @@ - - - - - - \ No newline at end of file From 81ab4b39b8e0371c9255ce76660c04ff24322fb3 Mon Sep 17 00:00:00 2001 From: Jan Heinrich Reimer Date: Wed, 1 Nov 2023 12:35:01 +0100 Subject: [PATCH 07/14] Fix Pyspark dependency --- pyproject.toml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index dc30e63e..5e069151 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -43,8 +43,7 @@ dependencies = [ "pyarrow~=13.0.0", 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\u041f\u0440\u043e\u0434\u043e\u043b\u0436\u0438\u0442\u0435\u043b\u044c\u043d\u043e\u0441\u0442\u044c: 5:44", + "url": "https://www.youtube.com/watch?v=ds9_dy0zD_8" + } + ], + "timestamp": 1582390054, + "url": "https://www.youtube.com/results?search_query=%E4%B8%8A%E8%B6%8A%E7%B7%9A+%E3%83%AB%E3%83%BC%E3%83%97" +} From a99885f974790b8a7f856c1e5e2179db37f1f5c2 Mon Sep 17 00:00:00 2001 From: Jan Heinrich Reimer Date: Wed, 1 Nov 2023 13:46:12 +0100 Subject: [PATCH 09/14] Fix CI --- .github/workflows/ci.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index c4ab45a5..f293a84f 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -70,7 +70,6 @@ jobs: - name: "📤 Upload coverage to Codecov" uses: codecov/codecov-action@v2 with: - fail_ci_if_error: true token: ${{ secrets.CODECOV_TOKEN }} release: name: "🚀 Create GitHub release" From 0d1cb0a349c91f5c1728e2185a96bd01ba5322bc Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 1 Nov 2023 12:47:34 +0000 Subject: [PATCH 10/14] Update seaborn requirement from ~=0.12.2 to ~=0.13.0 Updates the requirements on [seaborn](https://github.com/mwaskom/seaborn) to permit the latest version. - [Release notes](https://github.com/mwaskom/seaborn/releases) - [Commits](https://github.com/mwaskom/seaborn/compare/v0.12.2...v0.13.0) --- updated-dependencies: - dependency-name: seaborn dependency-type: direct:production ... Signed-off-by: dependabot[bot] --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 5e069151..62b1c058 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -49,7 +49,7 @@ dependencies = [ "ranx~=0.3.6", "requests~=2.28", "requests-html~=0.10.0", - "seaborn~=0.12.2", + "seaborn~=0.13.0", "tqdm~=4.64", "unidecode~=1.3", "urllib3~=1.26", From 0e2063c6f65eb5092a60f60eba44a0b7d36e225a Mon Sep 17 00:00:00 2001 From: Jan Heinrich Reimer Date: Wed, 1 Nov 2023 13:56:02 +0100 Subject: [PATCH 11/14] Fix names --- README.md | 16 ++++++++-------- cli | 2 +- slurm-cli | 2 +- 3 files changed, 10 insertions(+), 10 deletions(-) diff --git a/README.md b/README.md index 139da807..8aabfeb4 100644 --- a/README.md +++ b/README.md @@ -59,10 +59,10 @@ If you want to learn more about each step here are some more detailed guides: Let's start with a small example and construct a query log for the [ChatNoir](https://chatnoir.eu) search engine: -1. `python -m web_archive_query_log make archived-urls chatnoir` -2. `python -m web_archive_query_log make archived-query-urls chatnoir` -3. `python -m web_archive_query_log make archived-raw-serps chatnoir` -4. `python -m web_archive_query_log make archived-parsed-serps chatnoir` +1. `python -m archive_query_log make archived-urls chatnoir` +2. `python -m archive_query_log make archived-query-urls chatnoir` +3. `python -m archive_query_log make archived-raw-serps chatnoir` +4. `python -m archive_query_log make archived-parsed-serps chatnoir` Got the idea? Now you're ready to scrape your own query logs! To scale things up and understand the data, just keep on reading. For more details on how to add more search providers, see [below](#contribute). @@ -123,7 +123,7 @@ Fetch all archived URLs for a search provider from the Internet Archive's Waybac You can run this step with the following command line, where `` is the name of the search provider you want to fetch archived URLs from: ```shell: -python -m web_archive_query_log make archived-urls +python -m archive_query_log make archived-urls ``` This will create multiple files in the `archived-urls` subdirectory under the [data directory](#pro-tip--specify-a-custom-data-directory), based on the search provider's name (``), domain (``), and the Wayback Machine's CDX [page number][cdx-pagination] (``) from which the URLs were originally fetched: @@ -154,7 +154,7 @@ Parse and filter archived URLs that contain a query and may point to a search en You can run this step with the following command line, where `` is the name of the search provider you want to parse query URLs from: ```shell: -python -m web_archive_query_log make archived-query-urls +python -m archive_query_log make archived-query-urls ``` This will create multiple files in the `archived-query-urls` subdirectory under the [data directory](#pro-tip--specify-a-custom-data-directory), based on the search provider's name (``), domain (``), and the Wayback Machine's CDX [page number][cdx-pagination] (``) from which the URLs were originally fetched: @@ -191,7 +191,7 @@ Download the raw HTML content of archived search engine result pages (SERPs). You can run this step with the following command line, where `` is the name of the search provider you want to download raw SERP HTML contents from: ```shell: -python -m web_archive_query_log make archived-raw-serps +python -m archive_query_log make archived-raw-serps ``` This will create multiple files in the `archived-urls` subdirectory under the [data directory](#pro-tip--specify-a-custom-data-directory), based on the search provider's name (``), domain (``), and the Wayback Machine's CDX [page number][cdx-pagination] (``) from which the URLs were originally fetched. Archived raw SERPs are stored as 1GB-sized WARC chunk files, that is, WARC chunks are "filled" sequentially up to a size of 1GB each. If a chunk is full, a new chunk is created. @@ -228,7 +228,7 @@ Parse and filter archived SERPs from raw contents. You can run this step with the following command line, where `` is the name of the search provider you want to parse SERPs from: ```shell: -python -m web_archive_query_log make archived-parsed-serps +python -m archive_query_log make archived-parsed-serps ``` This will create multiple files in the `archived-serps` subdirectory under the [data directory](#pro-tip--specify-a-custom-data-directory), based on the search provider's name (``), domain (``), and the Wayback Machine's CDX [page number][cdx-pagination] (``) from which the URLs were originally fetched: diff --git a/cli b/cli index 388c4e24..5891ddd5 100755 --- a/cli +++ b/cli @@ -1,3 +1,3 @@ #!/bin/bash -e -pipenv run python -m web_archive_query_log "$@" +pipenv run python -m archive_query_log "$@" diff --git a/slurm-cli b/slurm-cli index bc4b09ce..417e1c38 100755 --- a/slurm-cli +++ b/slurm-cli @@ -12,5 +12,5 @@ srun \ --pty \ sh -c " cd /workspace - python -m pipenv run python -m web_archive_query_log $* + python -m pipenv run python -m archive_query_log $* " From 7976a2aa28ceda51ecbadebf4bcb7f6f26c599c5 Mon Sep 17 00:00:00 2001 From: Jan Heinrich Reimer Date: Wed, 1 Nov 2023 14:11:30 +0100 Subject: [PATCH 12/14] Remove duplicate test --- archive_query_log/results/test/test_qq_serp_parsing.py | 7 ------- 1 file changed, 7 deletions(-) diff --git a/archive_query_log/results/test/test_qq_serp_parsing.py b/archive_query_log/results/test/test_qq_serp_parsing.py index a5fa1833..389a98ec 100644 --- a/archive_query_log/results/test/test_qq_serp_parsing.py +++ b/archive_query_log/results/test/test_qq_serp_parsing.py @@ -94,13 +94,6 @@ def test_parse_query_qq_xing_xing_di_qiu_2_1582812539(): ) -def test_parse_query_qq_jin_cheng_wu_1319745059(): - verify_serp_parsing( - "https://web.archive.org/web/20111027195059id_/http://v.qq.com/search.html?pagetype=3&ms_key=%E9%87%91%E5%9F%8E%E6%AD%A6", - "qq", - ) - - def test_parse_query_qq_turn_that_finger_around_1324266860(): verify_serp_parsing( "https://web.archive.org/web/20111219035420id_/http://v.qq.com:80/search.html?pagetype=3&ms_key=Turn+That+Finger+Around", From 3cf086a8b0fbc381ac9c45dd796ed92b1ac8eb6b Mon Sep 17 00:00:00 2001 From: Jan Heinrich Reimer Date: Wed, 1 Nov 2023 15:44:20 +0100 Subject: [PATCH 13/14] Add TripAdvisor --- data/selected-services.yaml | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/data/selected-services.yaml b/data/selected-services.yaml index 8ccfceca..a976cb5b 100644 --- a/data/selected-services.yaml +++ b/data/selected-services.yaml @@ -26588,3 +26588,28 @@ interpreted_query_parsers: [] results_parsers: [] focused_url_prefixes: [] +- name: tripadvisor + public_suffix: net + alexa_domain: tripadvisor.com + alexa_rank: null + category: search-engine + notes: null + input_field: null + search_form: null + search_div: null + domains: + - tripadvisor.com + query_parsers: + - url_pattern: ^https?://[^/]+/Search\? + type: query_parameter + parameter: q + - url_pattern: ^https?://[^/]+/SearchForums\? + type: query_parameter + parameter: q + page_parsers: [] + offset_parsers: [] + interpreted_query_parsers: [] + results_parsers: [] + focused_url_prefixes: + - /Search? + - /SearchForums? From 3367559eac54f830995b788860afa1b424cd56f6 Mon Sep 17 00:00:00 2001 From: Jan Heinrich Reimer Date: Wed, 1 Nov 2023 15:57:59 +0100 Subject: [PATCH 14/14] Add TripAdvisor snippet parser --- data/selected-services.yaml | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/data/selected-services.yaml b/data/selected-services.yaml index a976cb5b..217b6c38 100644 --- a/data/selected-services.yaml +++ b/data/selected-services.yaml @@ -26608,8 +26608,17 @@ parameter: q page_parsers: [] offset_parsers: [] - interpreted_query_parsers: [] - results_parsers: [] + interpreted_query_parsers: + - url_pattern: ^https?://[^/]+/Search\? + type: html_selector + query_selector: div.SEARCH_LHN form#SEARCH_LHN_form input#mainSearch + results_parsers: + - url_pattern: ^https?://[^/]+/Search\? + type: html_selector + results_selector: div#SEARCH_RESULTS div.searchResult + url_selector: div.srHead a + title_selector: div.srHead + snippet_selector: div.srSnippet focused_url_prefixes: - /Search? - /SearchForums?