{ "cells": [ { "cell_type": "code", "execution_count": 1, "id": "e71279e2", "metadata": { "execution": { "iopub.execute_input": "2026-01-03T05:06:29.218342Z", "iopub.status.busy": "2026-01-03T05:06:29.217998Z" }, "papermill": { "duration": null, "end_time": null, "exception": false, "start_time": "2026-01-03T05:06:29.213366", "status": "running" }, "tags": [] }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "-> Đã kết nối với Hugging Face Repo: enzosama154/BRCancer\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Đọc file Excel thành công.\n", "Tra cứu UUID cho 1095 IDs...\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "-> Đã tìm thấy 0 file đã xử lý trước đó (sẽ bỏ qua).\n", "Đang lấy danh sách file...\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "-> Tổng số file cần xử lý: 10000\n", "[1/10000] (0.00GB) Downloading: 277ef499-3b0f-429e-a5fd-b63b59ce731f.mirbase21.isoforms.quantification.txt (0.26 MB)... 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For such cases, it is recommended to upload in smaller batches or to use `HfApi().upload_large_folder(...)`/`hf upload-large-folder` instead. For more details, check out https://huggingface.co/docs/huggingface_hub/main/en/guides/upload#upload-a-large-folder.\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "1a6f72ebbb0c4a39aa3505b3348bb51b", "version_major": 2, "version_minor": 0 }, "text/plain": [ "Processing Files (0 / 0): | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "4674225379ae47518ef7c15ae448df40", "version_major": 2, "version_minor": 0 }, "text/plain": [ "New Data Upload: | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "-> Upload thành công!\n", "-> Đang xóa dữ liệu local để giải phóng bộ nhớ...\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "-> Đã làm trống thư mục. 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" ] }, { "name": "stderr", "output_type": "stream", "text": [ "It seems you are trying to upload a large folder at once. This might take some time and then fail if the folder is too large. For such cases, it is recommended to upload in smaller batches or to use `HfApi().upload_large_folder(...)`/`hf upload-large-folder` instead. 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" ] }, { "name": "stderr", "output_type": "stream", "text": [ "It seems you are trying to upload a large folder at once. This might take some time and then fail if the folder is too large. For such cases, it is recommended to upload in smaller batches or to use `HfApi().upload_large_folder(...)`/`hf upload-large-folder` instead. For more details, check out https://huggingface.co/docs/huggingface_hub/main/en/guides/upload#upload-a-large-folder.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "OK\n", "\n", "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", "CẢNH BÁO: Dung lượng đã đạt giới hạn (15.54 GB).\n", "Đang tiến hành upload lên Hugging Face và giải phóng bộ nhớ...\n", "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", "\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "17b67846f7ff4c33a2d3ea97e1e99ff5", "version_major": 2, "version_minor": 0 }, "text/plain": [ "Processing Files (0 / 0): | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "e521307f4227456dbaecf8cdb0c82c82", "version_major": 2, "version_minor": 0 }, "text/plain": [ "New Data Upload: | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "-> Upload thành công!\n", "-> Đang xóa dữ liệu local để giải phóng bộ nhớ...\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "-> Đã làm trống thư mục. 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For such cases, it is recommended to upload in smaller batches or to use `HfApi().upload_large_folder(...)`/`hf upload-large-folder` instead. For more details, check out https://huggingface.co/docs/huggingface_hub/main/en/guides/upload#upload-a-large-folder.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "OK\n", "\n", "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", "CẢNH BÁO: Dung lượng đã đạt giới hạn (15.99 GB).\n", "Đang tiến hành upload lên Hugging Face và giải phóng bộ nhớ...\n", "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", "\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "d8ee5d37dae44674ad2942c4943aa22f", "version_major": 2, "version_minor": 0 }, "text/plain": [ "Processing Files (0 / 0): | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "fbe467713b14422c9271674b23848b5d", "version_major": 2, "version_minor": 0 }, "text/plain": [ "New Data Upload: | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "Lỗi khi Upload: 503 Server Error: Service Unavailable for url: https://huggingface.co/api/datasets/enzosama154/BRCancer/commit/main\n", "[1371/10000] (15.99GB) Downloading: 3fa2c954-fdae-4808-8147-c45f3daa0f92_noid_Grn.idat (0.69 MB)... " ] }, { "name": "stderr", "output_type": "stream", "text": [ "It seems you are trying to upload a large folder at once. This might take some time and then fail if the folder is too large. For such cases, it is recommended to upload in smaller batches or to use `HfApi().upload_large_folder(...)`/`hf upload-large-folder` instead. For more details, check out https://huggingface.co/docs/huggingface_hub/main/en/guides/upload#upload-a-large-folder.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "OK\n", "\n", "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", "CẢNH BÁO: Dung lượng đã đạt giới hạn (15.99 GB).\n", "Đang tiến hành upload lên Hugging Face và giải phóng bộ nhớ...\n", "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", "\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "d93ce1e092f34a0f92a740e3da528a7d", "version_major": 2, "version_minor": 0 }, "text/plain": [ "Processing Files (0 / 0): | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "d495ae0aa3b7467abad07d10d439c31c", "version_major": 2, "version_minor": 0 }, "text/plain": [ "New Data Upload: | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "Lỗi khi Upload: 503 Server Error: Service Unavailable for url: https://huggingface.co/api/datasets/enzosama154/BRCancer/commit/main\n", "[1372/10000] (15.99GB) Downloading: nationwidechildrens.org_clinical.TCGA-BH-A0B4.xml (0.07 MB)... " ] }, { "name": "stderr", "output_type": "stream", "text": [ "It seems you are trying to upload a large folder at once. This might take some time and then fail if the folder is too large. For such cases, it is recommended to upload in smaller batches or to use `HfApi().upload_large_folder(...)`/`hf upload-large-folder` instead. For more details, check out https://huggingface.co/docs/huggingface_hub/main/en/guides/upload#upload-a-large-folder.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "OK\n", "\n", "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", "CẢNH BÁO: Dung lượng đã đạt giới hạn (15.99 GB).\n", "Đang tiến hành upload lên Hugging Face và giải phóng bộ nhớ...\n", "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", "\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "62754a8f77f44a6a998e584e58ec5a50", "version_major": 2, "version_minor": 0 }, "text/plain": [ "Processing Files (0 / 0): | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "a85ef8725a2748d1a04fb188067b4e1d", "version_major": 2, "version_minor": 0 }, "text/plain": [ "New Data Upload: | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "-> Upload thành công!\n", "-> Đang xóa dữ liệu local để giải phóng bộ nhớ...\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "-> Đã làm trống thư mục. 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For such cases, it is recommended to upload in smaller batches or to use `HfApi().upload_large_folder(...)`/`hf upload-large-folder` instead. For more details, check out https://huggingface.co/docs/huggingface_hub/main/en/guides/upload#upload-a-large-folder.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "OK\n", "\n", "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", "CẢNH BÁO: Dung lượng đã đạt giới hạn (15.69 GB).\n", "Đang tiến hành upload lên Hugging Face và giải phóng bộ nhớ...\n", "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", "\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "e0e4e3c2e34b4acda14510b01de7568c", "version_major": 2, "version_minor": 0 }, "text/plain": [ "Processing Files (0 / 0): | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "4435f81646334289a3e0c12b31e46447", "version_major": 2, "version_minor": 0 }, "text/plain": [ "New Data Upload: | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "-> Upload thành công!\n", "-> Đang xóa dữ liệu local để giải phóng bộ nhớ...\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "-> Đã làm trống thư mục. 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" ] }, { "name": "stderr", "output_type": "stream", "text": [ "It seems you are trying to upload a large folder at once. This might take some time and then fail if the folder is too large. For such cases, it is recommended to upload in smaller batches or to use `HfApi().upload_large_folder(...)`/`hf upload-large-folder` instead. For more details, check out https://huggingface.co/docs/huggingface_hub/main/en/guides/upload#upload-a-large-folder.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "OK\n", "\n", "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", "CẢNH BÁO: Dung lượng đã đạt giới hạn (15.49 GB).\n", "Đang tiến hành upload lên Hugging Face và giải phóng bộ nhớ...\n", "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", "\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "9e765614aff3478b91da0a9e0a032c9f", "version_major": 2, "version_minor": 0 }, "text/plain": [ "Processing Files (0 / 0): | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "ddcc03256e854f8dadf45b02d0730c5f", "version_major": 2, "version_minor": 0 }, "text/plain": [ "New Data Upload: | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "-> Upload thành công!\n", "-> Đang xóa dữ liệu local để giải phóng bộ nhớ...\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "-> Đã làm trống thư mục. 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For more details, check out https://huggingface.co/docs/huggingface_hub/main/en/guides/upload#upload-a-large-folder.\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "ebf7152f02294b4ea332074a6a7217a8", "version_major": 2, "version_minor": 0 }, "text/plain": [ "Processing Files (0 / 0): | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "0fcf9286d6fe436587ff84d70428fef1", "version_major": 2, "version_minor": 0 }, "text/plain": [ "New Data Upload: | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "-> Upload thành công!\n", "-> Đang xóa dữ liệu local để giải phóng bộ nhớ...\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "-> Đã làm trống thư mục. 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" ] }, { "name": "stderr", "output_type": "stream", "text": [ "It seems you are trying to upload a large folder at once. This might take some time and then fail if the folder is too large. For such cases, it is recommended to upload in smaller batches or to use `HfApi().upload_large_folder(...)`/`hf upload-large-folder` instead. 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For more details, check out https://huggingface.co/docs/huggingface_hub/main/en/guides/upload#upload-a-large-folder.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "OK\n", "\n", "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", "CẢNH BÁO: Dung lượng đã đạt giới hạn (15.34 GB).\n", "Đang tiến hành upload lên Hugging Face và giải phóng bộ nhớ...\n", "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", "\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "65194c9c6d494f298aeaf2b81d7253c8", "version_major": 2, "version_minor": 0 }, "text/plain": [ "Processing Files (0 / 0): | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "9bb3388974b3404ab1d61c94eb7ed27c", "version_major": 2, "version_minor": 0 }, "text/plain": [ "New Data Upload: | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "-> Upload thành công!\n", "-> Đang xóa dữ liệu local để giải phóng bộ nhớ...\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "-> Đã làm trống thư mục. 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" ] }, { "name": "stderr", "output_type": "stream", "text": [ "It seems you are trying to upload a large folder at once. This might take some time and then fail if the folder is too large. For such cases, it is recommended to upload in smaller batches or to use `HfApi().upload_large_folder(...)`/`hf upload-large-folder` instead. 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" ] }, { "name": "stderr", "output_type": "stream", "text": [ "It seems you are trying to upload a large folder at once. This might take some time and then fail if the folder is too large. For such cases, it is recommended to upload in smaller batches or to use `HfApi().upload_large_folder(...)`/`hf upload-large-folder` instead. For more details, check out https://huggingface.co/docs/huggingface_hub/main/en/guides/upload#upload-a-large-folder.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "OK\n", "\n", "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", "CẢNH BÁO: Dung lượng đã đạt giới hạn (15.27 GB).\n", "Đang tiến hành upload lên Hugging Face và giải phóng bộ nhớ...\n", "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", "\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "579a873ee748408ab54e8a52b52393f3", "version_major": 2, "version_minor": 0 }, "text/plain": [ "Processing Files (0 / 0): | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "62d75efd54ac40ce87513b34ded1eda2", "version_major": 2, "version_minor": 0 }, "text/plain": [ "New Data Upload: | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "-> Upload thành công!\n", "-> Đang xóa dữ liệu local để giải phóng bộ nhớ...\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "-> Đã làm trống thư mục. 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" ] }, { "name": "stderr", "output_type": "stream", "text": [ "It seems you are trying to upload a large folder at once. This might take some time and then fail if the folder is too large. For such cases, it is recommended to upload in smaller batches or to use `HfApi().upload_large_folder(...)`/`hf upload-large-folder` instead. 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For such cases, it is recommended to upload in smaller batches or to use `HfApi().upload_large_folder(...)`/`hf upload-large-folder` instead. For more details, check out https://huggingface.co/docs/huggingface_hub/main/en/guides/upload#upload-a-large-folder.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "OK\n", "\n", "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", "CẢNH BÁO: Dung lượng đã đạt giới hạn (15.23 GB).\n", "Đang tiến hành upload lên Hugging Face và giải phóng bộ nhớ...\n", "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", "\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "39c0666ae7324339a5ba76193c031f31", "version_major": 2, "version_minor": 0 }, "text/plain": [ "Processing Files (0 / 0): | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "de9e0c7777a64ae785c72d77800c25fe", "version_major": 2, "version_minor": 0 }, "text/plain": [ "New Data Upload: | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "-> Upload thành công!\n", "-> Đang xóa dữ liệu local để giải phóng bộ nhớ...\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "-> Đã làm trống thư mục. 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For such cases, it is recommended to upload in smaller batches or to use `HfApi().upload_large_folder(...)`/`hf upload-large-folder` instead. For more details, check out https://huggingface.co/docs/huggingface_hub/main/en/guides/upload#upload-a-large-folder.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "OK\n", "\n", "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", "CẢNH BÁO: Dung lượng đã đạt giới hạn (15.01 GB).\n", "Đang tiến hành upload lên Hugging Face và giải phóng bộ nhớ...\n", "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", "\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "616cef647a734d18a1c5a18b5c9d1b9a", "version_major": 2, "version_minor": 0 }, "text/plain": [ "Processing Files (0 / 0): | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "66506de08c9d4326a318f44c661b7b41", "version_major": 2, "version_minor": 0 }, "text/plain": [ "New Data Upload: | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "-> Upload thành công!\n", "-> Đang xóa dữ liệu local để giải phóng bộ nhớ...\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "-> Đã làm trống thư mục. 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" ] }, { "name": "stderr", "output_type": "stream", "text": [ "It seems you are trying to upload a large folder at once. This might take some time and then fail if the folder is too large. For such cases, it is recommended to upload in smaller batches or to use `HfApi().upload_large_folder(...)`/`hf upload-large-folder` instead. 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" ] }, { "name": "stderr", "output_type": "stream", "text": [ "It seems you are trying to upload a large folder at once. This might take some time and then fail if the folder is too large. For such cases, it is recommended to upload in smaller batches or to use `HfApi().upload_large_folder(...)`/`hf upload-large-folder` instead. For more details, check out https://huggingface.co/docs/huggingface_hub/main/en/guides/upload#upload-a-large-folder.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "OK\n", "\n", "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", "CẢNH BÁO: Dung lượng đã đạt giới hạn (15.49 GB).\n", "Đang tiến hành upload lên Hugging Face và giải phóng bộ nhớ...\n", "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", "\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "d2c7c3237f2940bf8d3d504029836200", "version_major": 2, "version_minor": 0 }, "text/plain": [ "Processing Files (0 / 0): | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "753f25ce756b47239bf1510c50576596", "version_major": 2, "version_minor": 0 }, "text/plain": [ "New Data Upload: | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "-> Upload thành công!\n", "-> Đang xóa dữ liệu local để giải phóng bộ nhớ...\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "-> Đã làm trống thư mục. 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" ] }, { "name": "stdout", "output_type": "stream", "text": [ "OK\n", "[8075/10000] (14.76GB) Downloading: SHUCK_p_TCGAb74and75_SNP_N_GenomeWideSNP_6_B04_731082.nocnv_grch38.seg.v2.txt (0.00 MB)... " ] }, { "name": "stdout", "output_type": "stream", "text": [ "OK\n", "[8076/10000] (14.76GB) Downloading: 54aca121-5b70-4833-84ac-c7506a57bd02.rna_seq.augmented_star_gene_counts.tsv (4.03 MB)... " ] }, { "name": "stdout", "output_type": "stream", "text": [ "OK\n", "[8077/10000] (14.76GB) Downloading: TCGA-A2-A0EM-01Z-00-DX1.305CF011-7451-4880-9A5D-AB4432CF53A5.svs (751.14 MB)... " ] }, { "name": "stderr", "output_type": "stream", "text": [ "It seems you are trying to upload a large folder at once. This might take some time and then fail if the folder is too large. For such cases, it is recommended to upload in smaller batches or to use `HfApi().upload_large_folder(...)`/`hf upload-large-folder` instead. For more details, check out https://huggingface.co/docs/huggingface_hub/main/en/guides/upload#upload-a-large-folder.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "OK\n", "\n", "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", "CẢNH BÁO: Dung lượng đã đạt giới hạn (15.49 GB).\n", "Đang tiến hành upload lên Hugging Face và giải phóng bộ nhớ...\n", "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", "\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "44a55040b4d740069220e55ff253065b", "version_major": 2, "version_minor": 0 }, "text/plain": [ "Processing Files (0 / 0): | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "8f3b2d7eaef04feaace5d00f340d0084", "version_major": 2, "version_minor": 0 }, "text/plain": [ "New Data Upload: | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "Lỗi khi Upload: 503 Server Error: Service Unavailable for url: https://huggingface.co/api/datasets/enzosama154/BRCancer/commit/main\n", "[8078/10000] (15.49GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-AC-A3W6.xml (0.05 MB)... " ] }, { "name": "stderr", "output_type": "stream", "text": [ "It seems you are trying to upload a large folder at once. This might take some time and then fail if the folder is too large. For such cases, it is recommended to upload in smaller batches or to use `HfApi().upload_large_folder(...)`/`hf upload-large-folder` instead. For more details, check out https://huggingface.co/docs/huggingface_hub/main/en/guides/upload#upload-a-large-folder.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "OK\n", "\n", "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", "CẢNH BÁO: Dung lượng đã đạt giới hạn (15.49 GB).\n", "Đang tiến hành upload lên Hugging Face và giải phóng bộ nhớ...\n", "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", "\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "c9e976f1f9ed4e08b6f5a7b8cf40ad88", "version_major": 2, "version_minor": 0 }, "text/plain": [ "Processing Files (0 / 0): | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "e19e536cfdf34829964bf6663a2337d5", "version_major": 2, "version_minor": 0 }, "text/plain": [ "New Data Upload: | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "-> Upload thành công!\n", "-> Đang xóa dữ liệu local để giải phóng bộ nhớ...\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "-> Đã làm trống thư mục. 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For such cases, it is recommended to upload in smaller batches or to use `HfApi().upload_large_folder(...)`/`hf upload-large-folder` instead. For more details, check out https://huggingface.co/docs/huggingface_hub/main/en/guides/upload#upload-a-large-folder.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "OK\n", "\n", "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", "CẢNH BÁO: Dung lượng đã đạt giới hạn (15.70 GB).\n", "Đang tiến hành upload lên Hugging Face và giải phóng bộ nhớ...\n", "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", "\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "a029e906ea6a4e6d95d2fc2b1bf6cb77", "version_major": 2, "version_minor": 0 }, "text/plain": [ "Processing Files (0 / 0): | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "67958872251b49bfb4c371f81c701db0", "version_major": 2, "version_minor": 0 }, "text/plain": [ "New Data Upload: | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "Lỗi khi Upload: 503 Server Error: Service Unavailable for url: https://huggingface.co/api/datasets/enzosama154/BRCancer/commit/main\n", "[8623/10000] (15.70GB) Downloading: TCGA-BRCA.84e50324-d98b-4fa7-b6df-27714ed34a48.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... " ] }, { "name": "stderr", "output_type": "stream", "text": [ "It seems you are trying to upload a large folder at once. This might take some time and then fail if the folder is too large. For such cases, it is recommended to upload in smaller batches or to use `HfApi().upload_large_folder(...)`/`hf upload-large-folder` instead. For more details, check out https://huggingface.co/docs/huggingface_hub/main/en/guides/upload#upload-a-large-folder.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "OK\n", "\n", "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", "CẢNH BÁO: Dung lượng đã đạt giới hạn (15.70 GB).\n", "Đang tiến hành upload lên Hugging Face và giải phóng bộ nhớ...\n", "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", "\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "6af257bced784802ba7b1262e2592d19", "version_major": 2, "version_minor": 0 }, "text/plain": [ "Processing Files (0 / 0): | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "720072c2231f43fbab941f8d171920ce", "version_major": 2, "version_minor": 0 }, "text/plain": [ "New Data Upload: | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "Lỗi khi Upload: 503 Server Error: Service Unavailable for url: https://huggingface.co/api/datasets/enzosama154/BRCancer/commit/main\n", "[8624/10000] (15.70GB) Downloading: TCGA-E9-A1RC-01A-11D-A898-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.16 MB)... " ] }, { "name": "stderr", "output_type": "stream", "text": [ "It seems you are trying to upload a large folder at once. This might take some time and then fail if the folder is too large. For such cases, it is recommended to upload in smaller batches or to use `HfApi().upload_large_folder(...)`/`hf upload-large-folder` instead. For more details, check out https://huggingface.co/docs/huggingface_hub/main/en/guides/upload#upload-a-large-folder.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "OK\n", "\n", "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", "CẢNH BÁO: Dung lượng đã đạt giới hạn (15.70 GB).\n", "Đang tiến hành upload lên Hugging Face và giải phóng bộ nhớ...\n", "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", "\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "fbc74654167e44a99feb26c1f99a59a9", "version_major": 2, "version_minor": 0 }, "text/plain": [ "Processing Files (0 / 0): | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "53d36bd1e94d46ff8ef5dd2d0aa30f65", "version_major": 2, "version_minor": 0 }, "text/plain": [ "New Data Upload: | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "Lỗi khi Upload: 503 Server Error: Service Unavailable for url: https://huggingface.co/api/datasets/enzosama154/BRCancer/commit/main\n", "[8625/10000] (15.70GB) Downloading: TCGA-E9-A1RC-11A-01-TSA.eb86cac2-b5e3-479b-aecf-e5ee73bc5d77.svs (40.56 MB)... " ] }, { "name": "stderr", "output_type": "stream", "text": [ "It seems you are trying to upload a large folder at once. This might take some time and then fail if the folder is too large. For such cases, it is recommended to upload in smaller batches or to use `HfApi().upload_large_folder(...)`/`hf upload-large-folder` instead. For more details, check out https://huggingface.co/docs/huggingface_hub/main/en/guides/upload#upload-a-large-folder.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "OK\n", "\n", "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", "CẢNH BÁO: Dung lượng đã đạt giới hạn (15.74 GB).\n", "Đang tiến hành upload lên Hugging Face và giải phóng bộ nhớ...\n", "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", "\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "02bb23eb6ce048b79c8efdd09f1cdb3a", "version_major": 2, "version_minor": 0 }, "text/plain": [ "Processing Files (0 / 0): | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "86d2fb926e294389a66d41c2cb3277c6", "version_major": 2, "version_minor": 0 }, "text/plain": [ "New Data Upload: | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "Lỗi khi Upload: 503 Server Error: Service Unavailable for url: https://huggingface.co/api/datasets/enzosama154/BRCancer/commit/main\n", "[8626/10000] (15.74GB) Downloading: MOHEL_p_TCGA_271_274_275_N_GenomeWideSNP_6_A02_1320380.grch38.seg.v2.txt (0.02 MB)... " ] }, { "name": "stderr", "output_type": "stream", "text": [ "It seems you are trying to upload a large folder at once. This might take some time and then fail if the folder is too large. For such cases, it is recommended to upload in smaller batches or to use `HfApi().upload_large_folder(...)`/`hf upload-large-folder` instead. For more details, check out https://huggingface.co/docs/huggingface_hub/main/en/guides/upload#upload-a-large-folder.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "OK\n", "\n", "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", "CẢNH BÁO: Dung lượng đã đạt giới hạn (15.74 GB).\n", "Đang tiến hành upload lên Hugging Face và giải phóng bộ nhớ...\n", "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", "\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "82c2c6d951cc4ee98d4d7d758f973f11", "version_major": 2, "version_minor": 0 }, "text/plain": [ "Processing Files (0 / 0): | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "4cf39eda3c9d4957bcf0ed7d62c84dfb", "version_major": 2, "version_minor": 0 }, "text/plain": [ "New Data Upload: | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "Lỗi khi Upload: 503 Server Error: Service Unavailable for url: https://huggingface.co/api/datasets/enzosama154/BRCancer/commit/main\n", "[8627/10000] (15.74GB) Downloading: MOHEL_p_TCGA_271_274_275_N_GenomeWideSNP_6_B03_1320358.grch38.seg.v2.txt (0.02 MB)... " ] }, { "name": "stderr", "output_type": "stream", "text": [ "It seems you are trying to upload a large folder at once. This might take some time and then fail if the folder is too large. For such cases, it is recommended to upload in smaller batches or to use `HfApi().upload_large_folder(...)`/`hf upload-large-folder` instead. For more details, check out https://huggingface.co/docs/huggingface_hub/main/en/guides/upload#upload-a-large-folder.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "OK\n", "\n", "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", "CẢNH BÁO: Dung lượng đã đạt giới hạn (15.74 GB).\n", "Đang tiến hành upload lên Hugging Face và giải phóng bộ nhớ...\n", "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", "\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "1ba9ebca2efd4a709aff90ed0b5d69f3", "version_major": 2, "version_minor": 0 }, "text/plain": [ "Processing Files (0 / 0): | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "2588a22c9d104621a3945efa67e73ece", "version_major": 2, "version_minor": 0 }, "text/plain": [ "New Data Upload: | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "-> Upload thành công!\n", "-> Đang xóa dữ liệu local để giải phóng bộ nhớ...\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "-> Đã làm trống thư mục. 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" ] }, { "name": "stderr", "output_type": "stream", "text": [ "It seems you are trying to upload a large folder at once. This might take some time and then fail if the folder is too large. For such cases, it is recommended to upload in smaller batches or to use `HfApi().upload_large_folder(...)`/`hf upload-large-folder` instead. 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" ] }, { "name": "stdout", "output_type": "stream", "text": [ "OK\n", "[9772/10000] (14.19GB) Downloading: TCGA-BRCA.31fad9a6-80ba-4ed8-862a-d8e17816c645.gene_level_copy_number.v36.tsv (3.29 MB)... " ] }, { "name": "stdout", "output_type": "stream", "text": [ "OK\n", "[9773/10000] (14.19GB) Downloading: TCGA-E9-A249-01Z-00-DX1.CA244384-FD89-44F6-8F94-A060A4C241CA.svs (1164.34 MB)... " ] }, { "name": "stderr", "output_type": "stream", "text": [ "It seems you are trying to upload a large folder at once. This might take some time and then fail if the folder is too large. For such cases, it is recommended to upload in smaller batches or to use `HfApi().upload_large_folder(...)`/`hf upload-large-folder` instead. For more details, check out https://huggingface.co/docs/huggingface_hub/main/en/guides/upload#upload-a-large-folder.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "OK\n", "\n", "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", "CẢNH BÁO: Dung lượng đã đạt giới hạn (15.33 GB).\n", "Đang tiến hành upload lên Hugging Face và giải phóng bộ nhớ...\n", "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", "\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "708d69c81ae1443d8ff793f113b1a99d", "version_major": 2, "version_minor": 0 }, "text/plain": [ "Processing Files (0 / 0): | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "0a86482f8c2b4e83a0957ada3e32b15f", "version_major": 2, "version_minor": 0 }, "text/plain": [ "New Data Upload: | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "Lỗi khi Upload: 503 Server Error: Service Unavailable for url: https://huggingface.co/api/datasets/enzosama154/BRCancer/commit/main\n", "[9774/10000] (15.33GB) Downloading: HEIGH_p_TCGAb418_19_21_BCR_NSP_GenomeWideSNP_6_G04_1485732.nocnv_grch38.seg.v2.txt (0.00 MB)... " ] }, { "name": "stderr", "output_type": "stream", "text": [ "It seems you are trying to upload a large folder at once. This might take some time and then fail if the folder is too large. For such cases, it is recommended to upload in smaller batches or to use `HfApi().upload_large_folder(...)`/`hf upload-large-folder` instead. For more details, check out https://huggingface.co/docs/huggingface_hub/main/en/guides/upload#upload-a-large-folder.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "OK\n", "\n", "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", "CẢNH BÁO: Dung lượng đã đạt giới hạn (15.33 GB).\n", "Đang tiến hành upload lên Hugging Face và giải phóng bộ nhớ...\n", "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", "\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "731c71362e394e5b91347ce8b331cff5", "version_major": 2, "version_minor": 0 }, "text/plain": [ "Processing Files (0 / 0): | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "4588d4b2238d4845be32f56d595a830c", "version_major": 2, "version_minor": 0 }, "text/plain": [ "New Data Upload: | | 0.00B / 0.00B " ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "import pandas as pd\n", "import requests\n", "import os\n", "import shutil\n", "from kaggle_secrets import UserSecretsClient\n", "from huggingface_hub import HfApi, create_repo\n", "\n", "# 1. Lấy Token từ Secrets\n", "user_secrets = UserSecretsClient()\n", "hf_token = user_secrets.get_secret(\"HF_API_PAPER\")\n", "\n", "HF_REPO_ID = \"enzosama154/BRCancer\"\n", "REPO_TYPE = \"dataset\"\n", "\n", "# 3. Khởi tạo API\n", "api = HfApi(token=hf_token)\n", "\n", "# Tạo repo nếu chưa có (private để bảo mật dữ liệu y tế)\n", "try:\n", " create_repo(repo_id=HF_REPO_ID, repo_type=REPO_TYPE, private=True, exist_ok=True, token=hf_token)\n", " print(f\"-> Đã kết nối với Hugging Face Repo: {HF_REPO_ID}\")\n", "except Exception as e:\n", " print(f\"Lỗi kết nối HF: {e}\")\n", "\n", "INPUT_FILE_PATH = '/kaggle/input/databc/brca_clinical_withPAM50.xlsx'\n", "OUTPUT_ROOT_DIR = '/kaggle/working/gdc_data_organized'\n", "TRACKING_FILE = '/kaggle/working/tracking_downloaded.txt' # File lưu lịch sử tránh trùng\n", "LIMIT_SIZE_GB = 15.0 \n", "\n", "def get_folder_size_gb(folder_path):\n", " \"\"\"Tính tổng dung lượng thư mục (GB).\"\"\"\n", " total_size = 0\n", " for dirpath, dirnames, filenames in os.walk(folder_path):\n", " for f in filenames:\n", " fp = os.path.join(dirpath, f)\n", " if not os.path.islink(fp):\n", " total_size += os.path.getsize(fp)\n", " return total_size / (1024**3)\n", "\n", "def load_processed_files():\n", " \"\"\"Đọc danh sách các file ID đã tải xong từ file text.\"\"\"\n", " if os.path.exists(TRACKING_FILE):\n", " with open(TRACKING_FILE, 'r') as f:\n", " return set(line.strip() for line in f)\n", " return set()\n", "\n", "def save_processed_file(file_id):\n", " \"\"\"Lưu file ID vào danh sách đã hoàn thành.\"\"\"\n", " with open(TRACKING_FILE, 'a') as f:\n", " f.write(f\"{file_id}\\n\")\n", "\n", "def upload_and_clean(current_dir):\n", " \"\"\"\n", " Thực hiện đẩy dữ liệu lên HF và xóa dữ liệu local.\n", " \"\"\"\n", " print(\"\\n\" + \"!\"*50)\n", " print(f\"CẢNH BÁO: Dung lượng đã đạt giới hạn ({get_folder_size_gb(current_dir):.2f} GB).\")\n", " print(\"Đang tiến hành upload lên Hugging Face và giải phóng bộ nhớ...\")\n", " print(\"!\"*50 + \"\\n\")\n", " \n", " # 1. Upload lên Hugging Face\n", " try:\n", " api.upload_folder(\n", " folder_path=current_dir,\n", " repo_id=HF_REPO_ID,\n", " repo_type=REPO_TYPE,\n", " path_in_repo=\"data\", # Lưu vào thư mục 'data' trên HF\n", " ignore_patterns=[\"tracking_downloaded.txt\"], # Không upload file tracking\n", " commit_message=f\"Auto-upload batch data to clear storage\"\n", " )\n", " print(\"-> Upload thành công!\")\n", " except Exception as e:\n", " print(f\"Lỗi khi Upload: {e}\")\n", " return # Nếu lỗi thì không xóa để tránh mất dữ liệu\n", "\n", " # 2. Xóa dữ liệu local (giữ lại file tracking)\n", " print(\"-> Đang xóa dữ liệu local để giải phóng bộ nhớ...\")\n", " for item in os.listdir(current_dir):\n", " item_path = os.path.join(current_dir, item)\n", " # Không xóa file tracking và file CSV kết quả UUID\n", " if item in [\"tracking_downloaded.txt\", \"brca_clinical_with_uuid.csv\"]:\n", " continue\n", " \n", " try:\n", " if os.path.isfile(item_path) or os.path.islink(item_path):\n", " os.unlink(item_path)\n", " elif os.path.isdir(item_path):\n", " shutil.rmtree(item_path)\n", " except Exception as e:\n", " print(f\"Không thể xóa {item_path}: {e}\")\n", " \n", " print(f\"-> Đã làm trống thư mục. Dung lượng hiện tại: {get_folder_size_gb(current_dir):.2f} GB\")\n", " print(\"-\" * 50)\n", "\n", "# ==============================================================================\n", "# LOGIC CHÍNH: LẤY UUID VÀ DOWNLOAD\n", "# ==============================================================================\n", "\n", "def get_gdc_uuids_from_submitter_ids(submitter_ids):\n", " url = \"https://api.gdc.cancer.gov/cases\"\n", " params = {\n", " \"filters\": {\"op\": \"in\", \"content\": {\"field\": \"submitter_id\", \"value\": submitter_ids}},\n", " \"fields\": \"submitter_id,case_id\", \"format\": \"json\", \"size\": len(submitter_ids) + 1000\n", " }\n", " try:\n", " response = requests.post(url, json=params)\n", " response.raise_for_status()\n", " hits = response.json().get('data', {}).get('hits', [])\n", " return {item['submitter_id']: item['case_id'] for item in hits}\n", " except Exception as e:\n", " print(f\"Lỗi API: {e}\")\n", " return {}\n", "\n", "def download_smart_loop(case_uuids, root_dir):\n", " if not os.path.exists(root_dir):\n", " os.makedirs(root_dir)\n", "\n", " # Load danh sách các file đã tải trước đó (nếu chạy lại hoặc loop tiếp)\n", " processed_files = load_processed_files()\n", " print(f\"-> Đã tìm thấy {len(processed_files)} file đã xử lý trước đó (sẽ bỏ qua).\")\n", "\n", " # API endpoints\n", " files_endpt = \"https://api.gdc.cancer.gov/files\"\n", " data_endpt = \"https://api.gdc.cancer.gov/data\"\n", "\n", " # Filter lấy tất cả file Open\n", " filters = {\n", " \"op\": \"and\",\n", " \"content\": [\n", " {\"op\": \"in\", \"content\": {\"field\": \"cases.case_id\", \"value\": case_uuids}},\n", " {\"op\": \"in\", \"content\": {\"field\": \"access\", \"value\": [\"open\"]}}\n", " ]\n", " }\n", " \n", " params = {\n", " \"filters\": filters,\n", " \"fields\": \"file_id,file_name,file_size,data_format,cases.case_id\",\n", " \"format\": \"json\",\n", " \"size\": 10000 \n", " }\n", "\n", " print(\"Đang lấy danh sách file...\")\n", " response = requests.post(files_endpt, json=params)\n", " files_data = response.json().get('data', {}).get('hits', [])\n", " print(f\"-> Tổng số file cần xử lý: {len(files_data)}\")\n", "\n", " for idx, file_info in enumerate(files_data):\n", " file_id = file_info['file_id']\n", " file_name = file_info['file_name']\n", " file_size_mb = file_info['file_size'] / (1024 * 1024)\n", " \n", " # 1. KIỂM TRA TRÙNG LẶP\n", " if file_id in processed_files:\n", " continue # Bỏ qua nếu đã tải và upload rồi\n", "\n", " # 2. KIỂM TRA DUNG LƯỢNG TRƯỚC KHI TẢI TIẾP\n", " current_usage = get_folder_size_gb('/kaggle/working')\n", " if current_usage >= LIMIT_SIZE_GB:\n", " upload_and_clean('/kaggle/working')\n", " \n", " # 3. TẠO FOLDER VÀ TẢI\n", " case_id = file_info['cases'][0]['case_id'] if 'cases' in file_info else \"Unknown\"\n", " case_dir = os.path.join(root_dir, case_id)\n", " if not os.path.exists(case_dir):\n", " os.makedirs(case_dir)\n", " \n", " save_path = os.path.join(case_dir, file_name)\n", " \n", " print(f\"[{idx+1}/{len(files_data)}] ({current_usage:.2f}GB) Downloading: {file_name} ({file_size_mb:.2f} MB)...\", end=\" \")\n", " \n", " try:\n", " with requests.get(f\"{data_endpt}/{file_id}\", stream=True) as r:\n", " r.raise_for_status()\n", " with open(save_path, 'wb') as f:\n", " for chunk in r.iter_content(chunk_size=1024*1024):\n", " if chunk: f.write(chunk)\n", " print(\"OK\")\n", " \n", " # Ghi nhận đã tải xong\n", " save_processed_file(file_id)\n", " processed_files.add(file_id)\n", " \n", " except Exception as e:\n", " print(f\"LỖI: {e}\")\n", "\n", " # Upload lần cuối cùng sau khi chạy hết vòng lặp\n", " print(\"\\n-> Đã hoàn tất danh sách. Upload phần dữ liệu còn lại...\")\n", " upload_and_clean('/kaggle/working')\n", "\n", "# ==============================================================================\n", "# MAIN\n", "# ==============================================================================\n", "def main():\n", " try:\n", " df = pd.read_excel(INPUT_FILE_PATH)\n", " print(\"Đọc file Excel thành công.\")\n", " except Exception as e:\n", " print(f\"Lỗi đọc file: {e}\")\n", " return\n", "\n", " id_col = 'patient_id' if 'patient_id' in df.columns else 'sample_id'\n", " unique_ids = df[id_col].dropna().unique().tolist()\n", " \n", " if unique_ids:\n", " print(f\"Tra cứu UUID cho {len(unique_ids)} IDs...\")\n", " uuid_map = get_gdc_uuids_from_submitter_ids(unique_ids)\n", " valid_uuids = list(set(uuid_map.values()))\n", " \n", " # Map và lưu CSV\n", " df['case_uuid'] = df[id_col].map(uuid_map)\n", " df.to_csv('/kaggle/working/brca_clinical_with_uuid.csv', index=False)\n", " \n", " if valid_uuids:\n", " download_smart_loop(valid_uuids, OUTPUT_ROOT_DIR)\n", " else:\n", " print(\"Không có UUID hợp lệ.\")\n", " else:\n", " print(\"File input rỗng.\")\n", "\n", "if __name__ == \"__main__\":\n", " main()" ] } ], "metadata": { "kaggle": { "accelerator": "none", "dataSources": [ { "datasetId": 9181321, "sourceId": 14376718, "sourceType": "datasetVersion" } ], "dockerImageVersionId": 31234, "isGpuEnabled": false, "isInternetEnabled": true, "language": "python", "sourceType": "notebook" }, "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": "3.12.12" }, "papermill": { "default_parameters": {}, "duration": null, "end_time": null, "environment_variables": {}, "exception": null, "input_path": "__notebook__.ipynb", "output_path": "__notebook__.ipynb", "parameters": {}, "start_time": "2026-01-03T05:06:25.522693", "version": "2.6.0" } }, "nbformat": 4, "nbformat_minor": 5 }