text stringlengths 5 22M | id stringlengths 12 177 | metadata dict | __index_level_0__ int64 0 1.37k |
|---|---|---|---|
# flake8: noqa
from .binarizer import MagnitudeBinarizer, ThresholdBinarizer, TopKBinarizer
from .masked_nn import MaskedLinear
| AdaMix/examples/research_projects/movement-pruning/emmental/modules/__init__.py/0 | {
"file_path": "AdaMix/examples/research_projects/movement-pruning/emmental/modules/__init__.py",
"repo_id": "AdaMix",
"token_count": 43
} | 41 |
#!/usr/bin/env python
import argparse
import glob
import logging
import os
import sys
import time
from collections import defaultdict
from pathlib import Path
from typing import Dict, List, Tuple
import numpy as np
import pytorch_lightning as pl
import torch
from torch.utils.data import DataLoader
from callbacks imp... | AdaMix/examples/research_projects/seq2seq-distillation/finetune.py/0 | {
"file_path": "AdaMix/examples/research_projects/seq2seq-distillation/finetune.py",
"repo_id": "AdaMix",
"token_count": 8351
} | 42 |
#!/usr/bin/env bash
python run_asr.py \
--output_dir="./wav2vec2-base-100h" \
--num_train_epochs="30" \
--per_device_train_batch_size="32" \
--per_device_eval_batch_size="32" \
--evaluation_strategy="steps" \
--save_total_limit="3" \
--save_steps="500" \
--eval_steps="100" \
--logging_steps="50" \
--learning_rate="5e-4... | AdaMix/examples/research_projects/wav2vec2/finetune_base_100.sh/0 | {
"file_path": "AdaMix/examples/research_projects/wav2vec2/finetune_base_100.sh",
"repo_id": "AdaMix",
"token_count": 249
} | 43 |
# Copyright 2020 The HuggingFace Team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicabl... | AdaMix/examples/tests/deepspeed/test_deepspeed.py/0 | {
"file_path": "AdaMix/examples/tests/deepspeed/test_deepspeed.py",
"repo_id": "AdaMix",
"token_count": 4436
} | 44 |
<jupyter_start><jupyter_text>How to export 🤗 Transformers Models to ONNX ? [ONNX](http://onnx.ai/) is open format for machine learning models. It allows to save your neural network's computation graph in a framework agnostic way, which might be particulary helpful when deploying deep learning models.Indeed, businesses... | AdaMix/notebooks/04-onnx-export.ipynb/0 | {
"file_path": "AdaMix/notebooks/04-onnx-export.ipynb",
"repo_id": "AdaMix",
"token_count": 5758
} | 45 |
#!/usr/bin/env python
# Copyright 2020 The HuggingFace Team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless... | AdaMix/scripts/fsmt/gen-card-facebook-wmt19.py/0 | {
"file_path": "AdaMix/scripts/fsmt/gen-card-facebook-wmt19.py",
"repo_id": "AdaMix",
"token_count": 2079
} | 46 |
# coding=utf-8
# Copyright 2018 The HuggingFace Inc. team.
# Copyright (c) 2018, NVIDIA CORPORATION. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.a... | AdaMix/src/transformers/benchmark/benchmark_tf.py/0 | {
"file_path": "AdaMix/src/transformers/benchmark/benchmark_tf.py",
"repo_id": "AdaMix",
"token_count": 5791
} | 47 |
# coding=utf-8
# Copyright 2018 The HuggingFace Inc. team.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable... | AdaMix/src/transformers/convert_slow_tokenizer.py/0 | {
"file_path": "AdaMix/src/transformers/convert_slow_tokenizer.py",
"repo_id": "AdaMix",
"token_count": 12334
} | 48 |
import time
import warnings
from abc import ABC
from typing import Optional
import torch
from .file_utils import add_start_docstrings
LOGITS_PROCESSOR_INPUTS_DOCSTRING = r"""
Args:
input_ids (:obj:`torch.LongTensor` of shape :obj:`(batch_size, sequence_length)`):
Indices of input sequence to... | AdaMix/src/transformers/generation_stopping_criteria.py/0 | {
"file_path": "AdaMix/src/transformers/generation_stopping_criteria.py",
"repo_id": "AdaMix",
"token_count": 1476
} | 49 |
# coding=utf-8
# Copyright 2018 The Google AI Language Team Authors and The HuggingFace Inc. team.
# Copyright (c) 2018, NVIDIA CORPORATION. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a cop... | AdaMix/src/transformers/models/bert/configuration_bert.py/0 | {
"file_path": "AdaMix/src/transformers/models/bert/configuration_bert.py",
"repo_id": "AdaMix",
"token_count": 4458
} | 50 |
# coding=utf-8
# Copyright (c) 2020, NVIDIA CORPORATION. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless re... | AdaMix/src/transformers/models/bert_generation/tokenization_bert_generation.py/0 | {
"file_path": "AdaMix/src/transformers/models/bert_generation/tokenization_bert_generation.py",
"repo_id": "AdaMix",
"token_count": 2216
} | 51 |
# coding=utf-8
# Copyright 2020 The HuggingFace Inc. team.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable... | AdaMix/src/transformers/models/convbert/convert_convbert_original_tf1_checkpoint_to_pytorch_and_tf2.py/0 | {
"file_path": "AdaMix/src/transformers/models/convbert/convert_convbert_original_tf1_checkpoint_to_pytorch_and_tf2.py",
"repo_id": "AdaMix",
"token_count": 723
} | 52 |
# Copyright 2020 The HuggingFace Team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicabl... | AdaMix/src/transformers/models/dialogpt/convert_dialogpt_original_pytorch_checkpoint_to_pytorch.py/0 | {
"file_path": "AdaMix/src/transformers/models/dialogpt/convert_dialogpt_original_pytorch_checkpoint_to_pytorch.py",
"repo_id": "AdaMix",
"token_count": 562
} | 53 |
# coding=utf-8
# Copyright 2019 The Google AI Language Team Authors and The HuggingFace Inc. team.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICEN... | AdaMix/src/transformers/models/electra/modeling_electra.py/0 | {
"file_path": "AdaMix/src/transformers/models/electra/modeling_electra.py",
"repo_id": "AdaMix",
"token_count": 25721
} | 54 |
# coding=utf-8
# Copyright 2019-present CNRS, Facebook Inc. and the HuggingFace Inc. team.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#... | AdaMix/src/transformers/models/flaubert/configuration_flaubert.py/0 | {
"file_path": "AdaMix/src/transformers/models/flaubert/configuration_flaubert.py",
"repo_id": "AdaMix",
"token_count": 3218
} | 55 |
# coding=utf-8
# Copyright 2021 The I-BERT Authors (Sehoon Kim, Amir Gholami, Zhewei Yao,
# Michael Mahoney, Kurt Keutzer - UC Berkeley) and The HuggingFace Inc. team.
# Copyright (c) 20121, NVIDIA CORPORATION. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use t... | AdaMix/src/transformers/models/ibert/configuration_ibert.py/0 | {
"file_path": "AdaMix/src/transformers/models/ibert/configuration_ibert.py",
"repo_id": "AdaMix",
"token_count": 2727
} | 56 |
# coding=utf-8
# Copyright 2020 The Allen Institute for AI team and The HuggingFace Inc. team.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2... | AdaMix/src/transformers/models/longformer/modeling_longformer.py/0 | {
"file_path": "AdaMix/src/transformers/models/longformer/modeling_longformer.py",
"repo_id": "AdaMix",
"token_count": 45243
} | 57 |
# Copyright 2020 The HuggingFace Team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicabl... | AdaMix/src/transformers/models/marian/convert_marian_to_pytorch.py/0 | {
"file_path": "AdaMix/src/transformers/models/marian/convert_marian_to_pytorch.py",
"repo_id": "AdaMix",
"token_count": 10947
} | 58 |
# coding=utf-8
# Copyright 2020 The Facebook AI Research Team Authors and The HuggingFace Inc. team.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LIC... | AdaMix/src/transformers/models/mbart/tokenization_mbart.py/0 | {
"file_path": "AdaMix/src/transformers/models/mbart/tokenization_mbart.py",
"repo_id": "AdaMix",
"token_count": 3852
} | 59 |
# MIT License
#
# Copyright (c) 2020 The Google AI Language Team Authors, The HuggingFace Inc. team and github/lonePatient
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restricti... | AdaMix/src/transformers/models/mobilebert/modeling_mobilebert.py/0 | {
"file_path": "AdaMix/src/transformers/models/mobilebert/modeling_mobilebert.py",
"repo_id": "AdaMix",
"token_count": 27705
} | 60 |
# coding=utf-8
# Copyright 2018 The Open AI Team Authors and The HuggingFace Inc. team.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# ... | AdaMix/src/transformers/models/openai/tokenization_openai.py/0 | {
"file_path": "AdaMix/src/transformers/models/openai/tokenization_openai.py",
"repo_id": "AdaMix",
"token_count": 3902
} | 61 |
# coding=utf-8
# Copyright 2021 The Fairseq Authors and The HuggingFace Inc. team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/... | AdaMix/src/transformers/models/speech_to_text/modeling_speech_to_text.py/0 | {
"file_path": "AdaMix/src/transformers/models/speech_to_text/modeling_speech_to_text.py",
"repo_id": "AdaMix",
"token_count": 27410
} | 62 |
# coding=utf-8
# Copyright 2020 Google Research and The HuggingFace Inc. team.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless re... | AdaMix/src/transformers/models/tapas/modeling_tapas.py/0 | {
"file_path": "AdaMix/src/transformers/models/tapas/modeling_tapas.py",
"repo_id": "AdaMix",
"token_count": 44590
} | 63 |
# coding=utf-8
# Copyright 2018 The HuggingFace Inc. team.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable... | AdaMix/src/transformers/models/xlm/convert_xlm_original_pytorch_checkpoint_to_pytorch.py/0 | {
"file_path": "AdaMix/src/transformers/models/xlm/convert_xlm_original_pytorch_checkpoint_to_pytorch.py",
"repo_id": "AdaMix",
"token_count": 1116
} | 64 |
# coding=utf-8
# Copyright 2018 Google AI, Google Brain and Carnegie Mellon University Authors and the HuggingFace Inc. team.
# Copyright (c) 2018, NVIDIA CORPORATION. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the Lice... | AdaMix/src/transformers/models/xlnet/modeling_xlnet.py/0 | {
"file_path": "AdaMix/src/transformers/models/xlnet/modeling_xlnet.py",
"repo_id": "AdaMix",
"token_count": 41251
} | 65 |
from typing import List, Union
import numpy as np
from ..file_utils import add_end_docstrings
from ..tokenization_utils import TruncationStrategy
from ..utils import logging
from .base import PIPELINE_INIT_ARGS, ArgumentHandler, Pipeline
logger = logging.get_logger(__name__)
class ZeroShotClassificationArgumentHa... | AdaMix/src/transformers/pipelines/zero_shot_classification.py/0 | {
"file_path": "AdaMix/src/transformers/pipelines/zero_shot_classification.py",
"repo_id": "AdaMix",
"token_count": 3416
} | 66 |
# Copyright 2020 The HuggingFace Team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicabl... | AdaMix/src/transformers/training_args_tf.py/0 | {
"file_path": "AdaMix/src/transformers/training_args_tf.py",
"repo_id": "AdaMix",
"token_count": 5960
} | 67 |
# coding=utf-8
# Copyright 2020 The HuggingFace Team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requir... | AdaMix/src/transformers/utils/model_parallel_utils.py/0 | {
"file_path": "AdaMix/src/transformers/utils/model_parallel_utils.py",
"repo_id": "AdaMix",
"token_count": 715
} | 68 |
# coding=utf-8
# Copyright 2021 The HuggingFace Inc. team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless r... | AdaMix/templates/adding_a_new_model/cookiecutter-template-{{cookiecutter.modelname}}/test_modeling_{{cookiecutter.lowercase_modelname}}.py/0 | {
"file_path": "AdaMix/templates/adding_a_new_model/cookiecutter-template-{{cookiecutter.modelname}}/test_modeling_{{cookiecutter.lowercase_modelname}}.py",
"repo_id": "AdaMix",
"token_count": 19917
} | 69 |
{
"model_type": "roberta"
} | AdaMix/tests/fixtures/dummy-config.json/0 | {
"file_path": "AdaMix/tests/fixtures/dummy-config.json",
"repo_id": "AdaMix",
"token_count": 15
} | 70 |
# coding=utf-8
# Copyright 2021 HuggingFace Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or ag... | AdaMix/tests/test_feature_extraction_common.py/0 | {
"file_path": "AdaMix/tests/test_feature_extraction_common.py",
"repo_id": "AdaMix",
"token_count": 760
} | 71 |
# coding=utf-8
# Copyright 2020 The HuggingFace Team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requir... | AdaMix/tests/test_modeling_flaubert.py/0 | {
"file_path": "AdaMix/tests/test_modeling_flaubert.py",
"repo_id": "AdaMix",
"token_count": 6950
} | 72 |
# coding=utf-8
# Copyright 2020 The HuggingFace Inc. team, Microsoft Corporation.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless... | AdaMix/tests/test_modeling_mpnet.py/0 | {
"file_path": "AdaMix/tests/test_modeling_mpnet.py",
"repo_id": "AdaMix",
"token_count": 4330
} | 73 |
# coding=utf-8
# Copyright 2021 The HuggingFace Inc. team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless r... | AdaMix/tests/test_modeling_tf_blenderbot.py/0 | {
"file_path": "AdaMix/tests/test_modeling_tf_blenderbot.py",
"repo_id": "AdaMix",
"token_count": 6114
} | 74 |
# coding=utf-8
# Copyright 2021 The HuggingFace Inc. team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless r... | AdaMix/tests/test_modeling_tf_marian.py/0 | {
"file_path": "AdaMix/tests/test_modeling_tf_marian.py",
"repo_id": "AdaMix",
"token_count": 7767
} | 75 |
# coding=utf-8
# Copyright 2021 The HuggingFace Inc. team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless r... | AdaMix/tests/test_modeling_wav2vec2.py/0 | {
"file_path": "AdaMix/tests/test_modeling_wav2vec2.py",
"repo_id": "AdaMix",
"token_count": 10374
} | 76 |
# coding=utf-8
# Copyright 2020 The HuggingFace Team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requir... | AdaMix/tests/test_tokenization_bert_generation.py/0 | {
"file_path": "AdaMix/tests/test_tokenization_bert_generation.py",
"repo_id": "AdaMix",
"token_count": 3378
} | 77 |
# coding=utf-8
# Copyright 2018 Google T5 Authors and HuggingFace Inc. team.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requ... | AdaMix/tests/test_tokenization_t5.py/0 | {
"file_path": "AdaMix/tests/test_tokenization_t5.py",
"repo_id": "AdaMix",
"token_count": 4402
} | 78 |
# Copyright 2020 The HuggingFace Team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicabl... | AdaMix/tests/test_versions_utils.py/0 | {
"file_path": "AdaMix/tests/test_versions_utils.py",
"repo_id": "AdaMix",
"token_count": 1673
} | 79 |
---
- step:
name: Execute python examples/text-classification/run_glue.py
image: pytorch/pytorch:nightly-devel-cuda10.0-cudnn7
command:
- python /valohai/repository/utils/download_glue_data.py --data_dir=/glue_data
- pip install -e .
- pip install -r examples/requirements.txt
- pyth... | AdaMix/valohai.yaml/0 | {
"file_path": "AdaMix/valohai.yaml",
"repo_id": "AdaMix",
"token_count": 1425
} | 80 |
# AirSim Drone Racing Lab
<img src="https://github.com/madratman/airsim_neurips_gifs/blob/master/imgs/neurips_b99_3_drones.gif?raw=true" width="275"> <img src="https://github.com/madratman/airsim_neurips_gifs/blob/master/imgs/neurips_soccer_field_8_drones.gif?raw=true" width="275"> <img src="https://github.com/madrat... | AirSim-Drone-Racing-Lab/README.md/0 | {
"file_path": "AirSim-Drone-Racing-Lab/README.md",
"repo_id": "AirSim-Drone-Racing-Lab",
"token_count": 643
} | 81 |
# Learning Visuomotor Policies for Aerial Navigation Using Cross-Modal Representations
This repository provides a code base to evaluate and train models from the paper "*Learning Visuomotor Policies for Aerial Navigation Using Cross-Modal Representations*".
ArXiv pre-print: [https://arxiv... | AirSim-Drone-Racing-VAE-Imitation/README.md/0 | {
"file_path": "AirSim-Drone-Racing-VAE-Imitation/README.md",
"repo_id": "AirSim-Drone-Racing-VAE-Imitation",
"token_count": 2060
} | 82 |
import tensorflow as tf
import os
import sys
curr_dir = os.path.dirname(os.path.abspath(__file__))
# imports
import_path = os.path.join(curr_dir, '..')
sys.path.insert(0, import_path)
import racing_models
import racing_utils
###########################################
# DEFINE TRAINING META PARAMETERS
base_path = '/... | AirSim-Drone-Racing-VAE-Imitation/imitation_learning/train_bc.py/0 | {
"file_path": "AirSim-Drone-Racing-VAE-Imitation/imitation_learning/train_bc.py",
"repo_id": "AirSim-Drone-Racing-VAE-Imitation",
"token_count": 2264
} | 83 |
from utils import AirSimSettingsCreator
AirSimSettingsCreator().write_airsim_neurips_baseline_settings_file() | AirSim-NeurIPS2019-Drone-Racing/baselines/generate_settings_file.py/0 | {
"file_path": "AirSim-NeurIPS2019-Drone-Racing/baselines/generate_settings_file.py",
"repo_id": "AirSim-NeurIPS2019-Drone-Racing",
"token_count": 33
} | 84 |
# -------------------------------------------------------------------------
# Copyright (c) Microsoft Corporation. All rights reserved.
# Licensed under the MIT License. See License in the project root for
# license information.
# --------------------------------------------------------------------------
VERSION = "0.... | ApplicationInsights-Python/azure-monitor-events-extension/azure/monitor/events/extension/_version.py/0 | {
"file_path": "ApplicationInsights-Python/azure-monitor-events-extension/azure/monitor/events/extension/_version.py",
"repo_id": "ApplicationInsights-Python",
"token_count": 52
} | 85 |
#!/bin/bash
set -e
get_latest_release() {
curl --silent "https://api.github.com/repos/$1/releases/latest" |
grep '"tag_name":' | sed -E 's/.*"v([^"]+)".*/\1/'
}
VERSION=${1:-"$(get_latest_release cli/cli)"}
INSTALL_DIR=${2:-"$HOME/.local/bin"}
CMD=gh
NAME="GitHub CLI"
echo -e "\e[34m»»» 📦 \e[32mInstalling \e[33... | AzureTRE/.devcontainer/scripts/gh.sh/0 | {
"file_path": "AzureTRE/.devcontainer/scripts/gh.sh",
"repo_id": "AzureTRE",
"token_count": 384
} | 86 |
.PHONY: bootstrap-init mgmt-deploy mgmt-destroy build-api-image push-api-image deploy-tre destroy-tre letsencrypt
.DEFAULT_GOAL := help
SHELL:=/bin/bash
MAKEFILE_FULLPATH := $(abspath $(lastword $(MAKEFILE_LIST)))
MAKEFILE_DIR := $(dir $(MAKEFILE_FULLPATH))
IMAGE_NAME_PREFIX?="microsoft/azuretre"
ACR_DOMAIN_SUFFIX?=`a... | AzureTRE/Makefile/0 | {
"file_path": "AzureTRE/Makefile",
"repo_id": "AzureTRE",
"token_count": 7647
} | 87 |
__version__ = "0.7.1"
| AzureTRE/airlock_processor/_version.py/0 | {
"file_path": "AzureTRE/airlock_processor/_version.py",
"repo_id": "AzureTRE",
"token_count": 12
} | 88 |
__version__ = "0.18.6"
| AzureTRE/api_app/_version.py/0 | {
"file_path": "AzureTRE/api_app/_version.py",
"repo_id": "AzureTRE",
"token_count": 12
} | 89 |
from datetime import datetime
from dateutil.relativedelta import relativedelta
from fastapi import APIRouter, Depends, Query, HTTPException, status
from fastapi.responses import JSONResponse
from typing import Optional
from pydantic import UUID4
from models.schemas.costs import get_cost_report_responses, get_workspac... | AzureTRE/api_app/api/routes/costs.py/0 | {
"file_path": "AzureTRE/api_app/api/routes/costs.py",
"repo_id": "AzureTRE",
"token_count": 3055
} | 90 |
import uuid
from typing import List, Tuple
from pydantic import parse_obj_as
from db.repositories.resources_history import ResourceHistoryRepository
from models.domain.resource_template import ResourceTemplate
from models.domain.authentication import User
from db.repositories.resource_templates import ResourceTemplate... | AzureTRE/api_app/db/repositories/workspace_services.py/0 | {
"file_path": "AzureTRE/api_app/db/repositories/workspace_services.py",
"repo_id": "AzureTRE",
"token_count": 1530
} | 91 |
from enum import Enum
class RequestAction(str, Enum):
Install = "install"
UnInstall = "uninstall"
Upgrade = "upgrade"
| AzureTRE/api_app/models/domain/request_action.py/0 | {
"file_path": "AzureTRE/api_app/models/domain/request_action.py",
"repo_id": "AzureTRE",
"token_count": 47
} | 92 |
from typing import List
from pydantic import BaseModel, Field
from models.domain.operation import Operation
def get_sample_operation(operation_id: str) -> dict:
return {
"id": operation_id,
"resourceId": "933ad738-7265-4b5f-9eae-a1a62928772e",
"resourcePath": "/workspaces/933ad738-7265-4b5... | AzureTRE/api_app/models/schemas/operation.py/0 | {
"file_path": "AzureTRE/api_app/models/schemas/operation.py",
"repo_id": "AzureTRE",
"token_count": 882
} | 93 |
# RG
CORE_RESOURCE_GROUP_NAME = "rg-{}"
WORKSPACE_RESOURCE_GROUP_NAME = "rg-{}-ws-{}"
IMPORT_TYPE = "import"
EXPORT_TYPE = "export"
# Import
STORAGE_ACCOUNT_NAME_IMPORT_EXTERNAL = "stalimex{}"
STORAGE_ACCOUNT_NAME_IMPORT_INPROGRESS = "stalimip{}"
STORAGE_ACCOUNT_NAME_IMPORT_APPROVED = "stalimappws{}"
STORAGE_ACCOUNT_N... | AzureTRE/api_app/resources/constants.py/0 | {
"file_path": "AzureTRE/api_app/resources/constants.py",
"repo_id": "AzureTRE",
"token_count": 313
} | 94 |
from abc import abstractmethod
from typing import List
from fastapi.security import OAuth2AuthorizationCodeBearer
from models.domain.workspace import Workspace, WorkspaceRole
from models.domain.authentication import User, RoleAssignment
class AuthConfigValidationError(Exception):
"""Raised when the input auth in... | AzureTRE/api_app/services/access_service.py/0 | {
"file_path": "AzureTRE/api_app/services/access_service.py",
"repo_id": "AzureTRE",
"token_count": 290
} | 95 |
import pytest
from httpx import AsyncClient
from starlette.status import HTTP_422_UNPROCESSABLE_ENTITY
pytestmark = pytest.mark.asyncio
async def test_frw_validation_error_format(app):
@app.get("/wrong_path/{param}")
def route_for_test(param: int) -> None: # pragma: no cover
pass
async with A... | AzureTRE/api_app/tests_ma/test_api/test_errors/test_422_error.py/0 | {
"file_path": "AzureTRE/api_app/tests_ma/test_api/test_errors/test_422_error.py",
"repo_id": "AzureTRE",
"token_count": 203
} | 96 |
from mock import patch
import pytest
from azure.identity.aio import (
DefaultAzureCredential as DefaultAzureCredentialASync,
ManagedIdentityCredential as ManagedIdentityCredentialASync
)
from core.credentials import get_credential_async
pytestmark = pytest.mark.asyncio
@patch("core.credentials.MANAGED_IDEN... | AzureTRE/api_app/tests_ma/test_core/test_credentials.py/0 | {
"file_path": "AzureTRE/api_app/tests_ma/test_core/test_credentials.py",
"repo_id": "AzureTRE",
"token_count": 261
} | 97 |
from unittest.mock import AsyncMock
from mock import patch, MagicMock
import pytest
import pytest_asyncio
from db.errors import EntityDoesNotExist, ResourceIsNotDeployed
from db.repositories.workspace_services import WorkspaceServiceRepository
from db.repositories.operations import OperationRepository
from models.doma... | AzureTRE/api_app/tests_ma/test_db/test_repositories/test_workpaces_service_repository.py/0 | {
"file_path": "AzureTRE/api_app/tests_ma/test_db/test_repositories/test_workpaces_service_repository.py",
"repo_id": "AzureTRE",
"token_count": 1880
} | 98 |
### Get health status (no auth)
GET {{baseUrl}}/health
Accept: application/json
| AzureTRE/api_http_requests/API Other Endpoints.http/0 | {
"file_path": "AzureTRE/api_http_requests/API Other Endpoints.http",
"repo_id": "AzureTRE",
"token_count": 24
} | 99 |
import sys
from typing import Union
import click
import json
import msal
import os
from httpx import Client, Response
from logging import Logger
from pathlib import Path
from tre.authentication import get_auth_token_client_credentials, get_public_client_application
class ApiException(click.ClickException):
"""A... | AzureTRE/cli/tre/api_client.py/0 | {
"file_path": "AzureTRE/cli/tre/api_client.py",
"repo_id": "AzureTRE",
"token_count": 3736
} | 100 |
import logging
import click
from tre.commands.operation import get_operation_id_completion, operation_show
from tre.output import output_option, query_option
from .contexts import pass_shared_service_operation_context, SharedServiceOperationContext
def operation_id_completion(ctx: click.Context, param: click.Parame... | AzureTRE/cli/tre/commands/shared_services/operation.py/0 | {
"file_path": "AzureTRE/cli/tre/commands/shared_services/operation.py",
"repo_id": "AzureTRE",
"token_count": 675
} | 101 |
import logging
import click
from tre.api_client import ApiClient
from tre.commands.operation import operations_list
from tre.output import output_option, query_option
from .contexts import UserResourceContext, pass_user_resource_context
@click.group(name="operations", help="List operations ")
def user_resource_opera... | AzureTRE/cli/tre/commands/workspaces/workspace_services/user_resources/operations.py/0 | {
"file_path": "AzureTRE/cli/tre/commands/workspaces/workspace_services/user_resources/operations.py",
"repo_id": "AzureTRE",
"token_count": 483
} | 102 |
output "event_grid_status_changed_topic_endpoint" {
value = azurerm_eventgrid_topic.status_changed.endpoint
}
output "event_grid_airlock_notification_topic_endpoint" {
value = azurerm_eventgrid_topic.airlock_notification.endpoint
}
output "service_bus_step_result_queue" {
value = azurerm_servicebus_queue.step_r... | AzureTRE/core/terraform/airlock/outputs.tf/0 | {
"file_path": "AzureTRE/core/terraform/airlock/outputs.tf",
"repo_id": "AzureTRE",
"token_count": 198
} | 103 |
#!/bin/bash
set -o errexit
set -o pipefail
set -o nounset
# set -o xtrace
terraform_wrapper_path="../../devops/scripts/terraform_wrapper.sh"
# This variables are loaded in for us
# shellcheck disable=SC2154
terraform init -input=false -backend=true -reconfigure \
-backend-config="resource_group_name=${TF_VAR_mgm... | AzureTRE/core/terraform/migrate.sh/0 | {
"file_path": "AzureTRE/core/terraform/migrate.sh",
"repo_id": "AzureTRE",
"token_count": 4282
} | 104 |
#!/bin/bash
cat << EOF > 'validation.txt'
${CERTBOT_VALIDATION}
EOF
# shellcheck disable=SC2016
az storage blob upload \
--account-name "${STORAGE_ACCOUNT}" \
--auth-mode login \
--container-name '$web' \
--file 'validation.txt' \
--name ".well-known/acme-challenge/${CERTBOT_TOKEN}" \
--no-pro... | AzureTRE/core/terraform/scripts/auth-hook.sh/0 | {
"file_path": "AzureTRE/core/terraform/scripts/auth-hook.sh",
"repo_id": "AzureTRE",
"token_count": 153
} | 105 |
#!/bin/bash
# This script is designed to be `source`d to create reusable helper functions
# Grants admin consent for the given app permission.
#
# Parameters:
# 1. principalId is the object ID of the service principal/managed application
# 2. resourceId is the object ID of the resource service principal (can in s... | AzureTRE/devops/scripts/aad/grant_admin_consent.sh/0 | {
"file_path": "AzureTRE/devops/scripts/aad/grant_admin_consent.sh",
"repo_id": "AzureTRE",
"token_count": 479
} | 106 |
#!/bin/bash
set -o errexit
set -o pipefail
set -o nounset
# Uncomment this line to see each command for debugging (careful: this will show secrets!)
# set -o xtrace
base_url="${TRE_URL}"
cli_env_file="${HOME}/.config/tre/environment.json"
# Are we already signed in?
already_signed_in=0
got_token_from_cli=$(tre get-to... | AzureTRE/devops/scripts/ensure_cli_signed_in.sh/0 | {
"file_path": "AzureTRE/devops/scripts/ensure_cli_signed_in.sh",
"repo_id": "AzureTRE",
"token_count": 590
} | 107 |
#!/bin/bash
set -o errexit
set -o pipefail
set -o nounset
# Uncomment this line to see each command for debugging (careful: this will show secrets!)
# set -o xtrace
# Find all terraform folders and create/upgrade lock files.
# Run from root folder
find . -type d -name terraform -not -path "*/.cnab/*" -exec echo In Di... | AzureTRE/devops/scripts/upgrade_lock_files.sh/0 | {
"file_path": "AzureTRE/devops/scripts/upgrade_lock_files.sh",
"repo_id": "AzureTRE",
"token_count": 132
} | 108 |
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<svg
viewBox="0 0 34 34"
class=""
role="presentation"
focusable="false"
id="FxSymbol0-03d"
data-type="1"
version="1.1"
sodipodi:docname="azure-tre-logo.svg"
inkscape:version="1.1.2 (b8e25be833, 2022-02-05)"
xmlns:inkscape="http://www.i... | AzureTRE/docs/assets/azure-tre-logo.svg/0 | {
"file_path": "AzureTRE/docs/assets/azure-tre-logo.svg",
"repo_id": "AzureTRE",
"token_count": 3310
} | 109 |
# Network Architecture
The Trusted Research Environment (TRE) network topology is based on [hub-spoke](https://docs.microsoft.com/en-us/azure/architecture/reference-architectures/hybrid-networking/hub-spoke). The TRE Core VNET ([Azure Virtual Network](https://docs.microsoft.com/en-us/azure/virtual-network/virtual-netw... | AzureTRE/docs/azure-tre-overview/networking.md/0 | {
"file_path": "AzureTRE/docs/azure-tre-overview/networking.md",
"repo_id": "AzureTRE",
"token_count": 1211
} | 110 |
# TRE Client UX
## Name
The Client Identity is typically called `<TRE_ID> UX` within the Microsoft Entra ID Portal.
## Purpose
This identity is used by any public facing client application so that user impersonation can occur to the Core API and any Workspace Applications.
## Application Roles
This application does ... | AzureTRE/docs/tre-admins/identities/client.md/0 | {
"file_path": "AzureTRE/docs/tre-admins/identities/client.md",
"repo_id": "AzureTRE",
"token_count": 850
} | 111 |
# Installing base workspace
## Publishing and registering the base workspace bundle
Run the following in a terminal to build, publish and register the base workpace bundle:
```cmd
make workspace_bundle BUNDLE=base
```
This will prepare the template for use with your TRE.
## Create Base Workspace
Workspace can be ... | AzureTRE/docs/tre-admins/setup-instructions/ui-install-base-workspace.md/0 | {
"file_path": "AzureTRE/docs/tre-admins/setup-instructions/ui-install-base-workspace.md",
"repo_id": "AzureTRE",
"token_count": 886
} | 112 |
# TRE Web User Interface
This project contains a React-based web UI which covers the core aspects of a TRE, for researchers and workspace owners.
## Chosen UI Stack + Components
The UI is built upon several popular web frameworks:
- React v18 (created via create-react-app, with all build configurations left as defaul... | AzureTRE/docs/tre-developers/ui.md/0 | {
"file_path": "AzureTRE/docs/tre-developers/ui.md",
"repo_id": "AzureTRE",
"token_count": 1179
} | 113 |
# Azure Health Data Services Workspace Service
See [Azure Health Data Services Documentation](https://learn.microsoft.com/en-us/azure/healthcare-apis/healthcare-apis-overview).
## Prerequisites
- [A base workspace deployed](https://microsoft.github.io/AzureTRE/tre-templates/workspaces/base/)
## Azure Healthcare Wor... | AzureTRE/docs/tre-templates/workspace-services/health_services.md/0 | {
"file_path": "AzureTRE/docs/tre-templates/workspace-services/health_services.md",
"repo_id": "AzureTRE",
"token_count": 372
} | 114 |
import os
import pytest
import asyncio
import logging
from azure.core.exceptions import ResourceNotFoundError
from azure.storage.blob import ContainerClient
from airlock.request import post_request, get_request, upload_blob_using_sas, wait_for_status
from resources.resource import get_resource, post_resource
from res... | AzureTRE/e2e_tests/test_airlock.py/0 | {
"file_path": "AzureTRE/e2e_tests/test_airlock.py",
"repo_id": "AzureTRE",
"token_count": 3682
} | 115 |
import os
import uuid
from azure.servicebus import ServiceBusClient, ServiceBusMessage
CREATE_WORKSPACE_REQUEST_DATA_FILE = "createWorkspaceRequestData.json"
def send_service_bus_message(service_bus_connection_string, service_bus_queue_name, correlation_id):
with open(CREATE_WORKSPACE_REQUEST_DATA_FILE, "r") a... | AzureTRE/resource_processor/test_tools/service_bus_message_sender/send_message_to_servicebus.py/0 | {
"file_path": "AzureTRE/resource_processor/test_tools/service_bus_message_sender/send_message_to_servicebus.py",
"repo_id": "AzureTRE",
"token_count": 556
} | 116 |
resource "azurerm_network_interface" "jumpbox_nic" {
name = "nic-vm-${var.tre_id}"
resource_group_name = data.azurerm_resource_group.rg.name
location = data.azurerm_resource_group.rg.location
tags = local.tre_shared_service_tags
ip_configuration {
name ... | AzureTRE/templates/shared_services/admin-vm/terraform/admin-jumpbox.tf/0 | {
"file_path": "AzureTRE/templates/shared_services/admin-vm/terraform/admin-jumpbox.tf",
"repo_id": "AzureTRE",
"token_count": 1252
} | 117 |
{
"$schema": "http://json-schema.org/draft-07/schema",
"$id": "https://github.com/microsoft/AzureTRE/templates/shared_services/airlock_notifier/template_schema.json",
"type": "object",
"title": "Airlock Notifier Shared Service",
"description": "A shared service notifying on Airlock operations",
"required":... | AzureTRE/templates/shared_services/airlock_notifier/template_schema.json/0 | {
"file_path": "AzureTRE/templates/shared_services/airlock_notifier/template_schema.json",
"repo_id": "AzureTRE",
"token_count": 1008
} | 118 |
---
schemaVersion: 1.0.0
name: tre-shared-service-cyclecloud
version: 0.5.5
description: "An Azure TRE Shared Service Template for Azure Cyclecloud"
registry: azuretre
dockerfile: Dockerfile.tmpl
credentials:
- name: azure_tenant_id
env: ARM_TENANT_ID
- name: azure_subscription_id
env: ARM_SUBSCRIPTION_ID
... | AzureTRE/templates/shared_services/cyclecloud/porter.yaml/0 | {
"file_path": "AzureTRE/templates/shared_services/cyclecloud/porter.yaml",
"repo_id": "AzureTRE",
"token_count": 2416
} | 119 |
# This file is maintained automatically by "terraform init".
# Manual edits may be lost in future updates.
provider "registry.terraform.io/databricks/databricks" {
version = "1.5.0"
constraints = "1.5.0"
hashes = [
"h1:UJe5L/BteOU7M5ewRLzuUjiewYFLF695eLp3hMKVR6M=",
"zh:0fa9ca13d977a8dcb46254f07c9be73... | AzureTRE/templates/shared_services/databricks-auth/terraform/.terraform.lock.hcl/0 | {
"file_path": "AzureTRE/templates/shared_services/databricks-auth/terraform/.terraform.lock.hcl",
"repo_id": "AzureTRE",
"token_count": 1286
} | 120 |
data "azurerm_subnet" "firewall" {
name = "AzureFirewallSubnet"
virtual_network_name = "vnet-${var.tre_id}"
resource_group_name = local.core_resource_group_name
}
data "azurerm_subnet" "firewall_management" {
name = "AzureFirewallManagementSubnet"
virtual_network_name = "vnet... | AzureTRE/templates/shared_services/firewall/terraform/data.tf/0 | {
"file_path": "AzureTRE/templates/shared_services/firewall/terraform/data.tf",
"repo_id": "AzureTRE",
"token_count": 1169
} | 121 |
{
"$schema": "http://json-schema.org/draft-07/schema",
"$id": "https://github.com/microsoft/AzureTRE/templates/shared_services/gitea/template_schema.json",
"type": "object",
"title": "Gitea - Git Mirror",
"description": "The Gitea shared service is typically used for mirroring external Git repositories.",
"... | AzureTRE/templates/shared_services/gitea/template_schema.json/0 | {
"file_path": "AzureTRE/templates/shared_services/gitea/template_schema.json",
"repo_id": "AzureTRE",
"token_count": 2787
} | 122 |
#!/bin/bash
set -o pipefail
set -o nounset
# set -o xtrace
if [ -z "$1" ]
then
echo 'Nexus password needs to be passed as argument'
fi
timeout=300
echo 'Checking for ./nexus_repos_config directory...'
while [ ! -d "$(dirname "${BASH_SOURCE[0]}")"/nexus_repos_config ]; do
# Wait for ./nexus_repos_config with j... | AzureTRE/templates/shared_services/sonatype-nexus-vm/scripts/configure_nexus_repos.sh/0 | {
"file_path": "AzureTRE/templates/shared_services/sonatype-nexus-vm/scripts/configure_nexus_repos.sh",
"repo_id": "AzureTRE",
"token_count": 782
} | 123 |
resource "azurerm_storage_account" "aml" {
name = local.storage_name
location = data.azurerm_resource_group.ws.location
resource_group_name = data.azurerm_resource_group.ws.name
account_tier = "Standard"
account_replication_type = "GRS"
tags ... | AzureTRE/templates/workspace_services/azureml/terraform/storage.tf/0 | {
"file_path": "AzureTRE/templates/workspace_services/azureml/terraform/storage.tf",
"repo_id": "AzureTRE",
"token_count": 1166
} | 124 |
ID=__CHANGE_ME__
WORKSPACE_ID=__CHANGE_ME__
AZURE_LOCATION=__CHANGE_ME__
HOST_SUBNET_ADDRESS_PREFIX=__CHANGE_ME__
CONTAINER_SUBNET_ADDRESS_PREFIX=__CHANGE_ME__
| AzureTRE/templates/workspace_services/databricks/.env.sample/0 | {
"file_path": "AzureTRE/templates/workspace_services/databricks/.env.sample",
"repo_id": "AzureTRE",
"token_count": 80
} | 125 |
#!/usr/bin/env sh
echo >&2 "oauth exited. code=${1}"
# terminate other services to exit from the container
exec s6-svscanctl -t /var/run/s6/services
| AzureTRE/templates/workspace_services/guacamole/guacamole-server/docker/services/oauth/finish/0 | {
"file_path": "AzureTRE/templates/workspace_services/guacamole/guacamole-server/docker/services/oauth/finish",
"repo_id": "AzureTRE",
"token_count": 54
} | 126 |
/**
*
*/
package org.apache.guacamole.auth.azuretre;
| AzureTRE/templates/workspace_services/guacamole/guacamole-server/guacamole-auth-azure/src/main/java/org/apache/guacamole/auth/azuretre/package-info.java/0 | {
"file_path": "AzureTRE/templates/workspace_services/guacamole/guacamole-server/guacamole-auth-azure/src/main/java/org/apache/guacamole/auth/azuretre/package-info.java",
"repo_id": "AzureTRE",
"token_count": 23
} | 127 |
{
"$schema": "http://json-schema.org/draft-07/schema",
"$id": "https://github.com/microsoft/AzureTRE/templates/workspace_services/guacamole/template_schema.json",
"type": "object",
"title": "Apache Guacamole - Virtual Desktop Service",
"description": "Enables Windows and Linux virtual machines to be accessed ... | AzureTRE/templates/workspace_services/guacamole/template_schema.json/0 | {
"file_path": "AzureTRE/templates/workspace_services/guacamole/template_schema.json",
"repo_id": "AzureTRE",
"token_count": 3143
} | 128 |
variable "workspace_id" {
type = string
}
variable "tre_id" {
type = string
}
variable "parent_service_id" {
type = string
}
variable "tre_resource_id" {
type = string
}
variable "image" {
type = string
}
variable "vm_size" {
type = string
}
variable "shared_storage_access" {
type = bool
}
variable "share... | AzureTRE/templates/workspace_services/guacamole/user_resources/guacamole-azure-linuxvm/terraform/variables.tf/0 | {
"file_path": "AzureTRE/templates/workspace_services/guacamole/user_resources/guacamole-azure-linuxvm/terraform/variables.tf",
"repo_id": "AzureTRE",
"token_count": 152
} | 129 |
variable "workspace_id" {
type = string
description = "TRE workspace ID"
}
variable "aad_authority_url" {
type = string
description = "Active directory"
}
variable "tre_id" {
type = string
description = "TRE ID"
}
variable "tre_resource_id" {
type = string
description = "R... | AzureTRE/templates/workspace_services/health-services/terraform/variables.tf/0 | {
"file_path": "AzureTRE/templates/workspace_services/health-services/terraform/variables.tf",
"repo_id": "AzureTRE",
"token_count": 423
} | 130 |
# Azure Provider source and version being used
terraform {
required_providers {
azurerm = {
source = "hashicorp/azurerm"
version = "=2.97.0"
}
random = {
source = "hashicorp/random"
version = "=3.4.2"
}
local = {
source = "hashicorp/local"
version = "=2.4.0"
... | AzureTRE/templates/workspace_services/innereye/terraform/main.tf/0 | {
"file_path": "AzureTRE/templates/workspace_services/innereye/terraform/main.tf",
"repo_id": "AzureTRE",
"token_count": 562
} | 131 |
---
schemaVersion: 1.0.0
name: tre-service-mlflow
version: 0.7.7
description: "An Azure TRE service for MLflow machine learning lifecycle"
dockerfile: Dockerfile.tmpl
registry: azuretre
custom:
runtime_image:
name: mlflow-server
build:
version_file: mlflow-server/version.txt
docker_file: mlflow-s... | AzureTRE/templates/workspace_services/mlflow/porter.yaml/0 | {
"file_path": "AzureTRE/templates/workspace_services/mlflow/porter.yaml",
"repo_id": "AzureTRE",
"token_count": 1715
} | 132 |
---
schemaVersion: 1.0.0
name: tre-workspace-service-mysql
version: 1.0.1
description: "A MySQL workspace service"
registry: azuretre
dockerfile: Dockerfile.tmpl
credentials:
- name: azure_tenant_id
env: ARM_TENANT_ID
- name: azure_subscription_id
env: ARM_SUBSCRIPTION_ID
- name: azure_client_id
env:... | AzureTRE/templates/workspace_services/mysql/porter.yaml/0 | {
"file_path": "AzureTRE/templates/workspace_services/mysql/porter.yaml",
"repo_id": "AzureTRE",
"token_count": 1578
} | 133 |
#!/bin/bash
set -o errexit
set -o pipefail
set -o nounset
psql -v ON_ERROR_STOP=1 -e "$OHDSI_ADMIN_CONNECTION_STRING" -f "../sql/atlas_create_security.sql"
psql -v ON_ERROR_STOP=1 -e "$OHDSI_ADMIN_CONNECTION_STRING" -f "../sql/atlas_default_roles.sql"
count=1
for i in ${ATLAS_USERS//,/ }
do
if [ "$(("$count" % 2... | AzureTRE/templates/workspace_services/ohdsi/scripts/atlas_security.sh/0 | {
"file_path": "AzureTRE/templates/workspace_services/ohdsi/scripts/atlas_security.sh",
"repo_id": "AzureTRE",
"token_count": 598
} | 134 |
resource "terraform_data" "add_data_source" {
count = var.configure_data_source ? 1 : 0
triggers_replace = {
postgres_database_id = azurerm_postgresql_flexible_server_database.db.id
}
provisioner "local-exec" {
environment = {
OHDSI_WEB_API_URL = local.ohdsi_webapi_fqdn
OHDSI_WEB_AP... | AzureTRE/templates/workspace_services/ohdsi/terraform/data_source.tf/0 | {
"file_path": "AzureTRE/templates/workspace_services/ohdsi/terraform/data_source.tf",
"repo_id": "AzureTRE",
"token_count": 673
} | 135 |
# HACK: PR #3769: Remove file when base workspace release updated
output "vnet_id" {
value = azurerm_virtual_network.ws.id
}
| AzureTRE/templates/workspaces/airlock-import-review/terraform/network_output.terraform/0 | {
"file_path": "AzureTRE/templates/workspaces/airlock-import-review/terraform/network_output.terraform",
"repo_id": "AzureTRE",
"token_count": 43
} | 136 |
# 'Approved' storage account
resource "azurerm_storage_account" "sa_import_approved" {
name = local.import_approved_storage_name
location = var.location
resource_group_name = var.ws_resource_group_name
account_tier = "Standard"
a... | AzureTRE/templates/workspaces/base/terraform/airlock/storage_accounts.tf/0 | {
"file_path": "AzureTRE/templates/workspaces/base/terraform/airlock/storage_accounts.tf",
"repo_id": "AzureTRE",
"token_count": 4266
} | 137 |
resource "azurerm_virtual_network" "ws" {
name = "vnet-${local.workspace_resource_name_suffix}"
location = var.location
resource_group_name = var.ws_resource_group_name
address_space = local.address_spaces
tags = var.tre_workspace_tags
lifecycle { ignore_chang... | AzureTRE/templates/workspaces/base/terraform/network/network.tf/0 | {
"file_path": "AzureTRE/templates/workspaces/base/terraform/network/network.tf",
"repo_id": "AzureTRE",
"token_count": 1451
} | 138 |
import { Configuration, PublicClientApplication } from "@azure/msal-browser";
import config from "./config.json"
// MSAL configuration
const configuration: Configuration = {
auth: {
clientId: config.rootClientId,
authority: `${config.activeDirectoryUri}/${config.rootTenantId}`,
redirectUri... | AzureTRE/ui/app/src/authConfig.ts/0 | {
"file_path": "AzureTRE/ui/app/src/authConfig.ts",
"repo_id": "AzureTRE",
"token_count": 201
} | 139 |
import React, { useCallback, useContext, useState } from 'react';
import { ComponentAction, VMPowerStates, Resource } from '../../models/resource';
import { Callout, DefaultPalette, FontWeights, IconButton, IStackStyles, IStyle, mergeStyleSets, PrimaryButton, Shimmer, Stack, Text, TooltipHost } from '@fluentui/react';
... | AzureTRE/ui/app/src/components/shared/ResourceCard.tsx/0 | {
"file_path": "AzureTRE/ui/app/src/components/shared/ResourceCard.tsx",
"repo_id": "AzureTRE",
"token_count": 4374
} | 140 |
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