From 6494cd712f0758d93068bcac67786fe0eb55e50d Mon Sep 17 00:00:00 2001 From: Amy Unruh Date: Tue, 28 Sep 2021 16:31:22 -0700 Subject: [PATCH 1/3] bump the docker image versions for the Terra notebooks --- notebooks/mnist_survival_analysis_demo.ipynb | 2 +- notebooks/terra_featured_workspace/image_annotations_demo.ipynb | 2 +- .../review_model_results_interactive.ipynb | 2 +- .../review_one_sample_interactive.ipynb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/notebooks/mnist_survival_analysis_demo.ipynb b/notebooks/mnist_survival_analysis_demo.ipynb index b823da30d..2c697dadb 100644 --- a/notebooks/mnist_survival_analysis_demo.ipynb +++ b/notebooks/mnist_survival_analysis_demo.ipynb @@ -23,7 +23,7 @@ "## Setup\n", "\n", "
\n", - " If you're running this notebook on Terra, use custom Docker image: ghcr.io/broadinstitute/ml4h/ml4h_terra:20210902_181409.
\n", + " If you're running this notebook on Terra, use custom Docker image: ghcr.io/broadinstitute/ml4h/ml4h_terra:20210928_221837.
\n", " This notebook will run fine on a CPU, but you can also run it on a GPU-enabled Cloud Environment if you like.\n", "
" ] diff --git a/notebooks/terra_featured_workspace/image_annotations_demo.ipynb b/notebooks/terra_featured_workspace/image_annotations_demo.ipynb index ffbb4b2d6..5b302f161 100644 --- a/notebooks/terra_featured_workspace/image_annotations_demo.ipynb +++ b/notebooks/terra_featured_workspace/image_annotations_demo.ipynb @@ -24,7 +24,7 @@ "# Setup\n", "\n", "
\n", - " This notebook assumes Terra is running custom Docker image ghcr.io/broadinstitute/ml4h/ml4h_terra:20210902_181409.\n", + " This notebook assumes Terra is running custom Docker image ghcr.io/broadinstitute/ml4h/ml4h_terra:20210928_221837.\n", "
" ] }, diff --git a/notebooks/terra_featured_workspace/review_model_results_interactive.ipynb b/notebooks/terra_featured_workspace/review_model_results_interactive.ipynb index 94cd35440..19363d123 100644 --- a/notebooks/terra_featured_workspace/review_model_results_interactive.ipynb +++ b/notebooks/terra_featured_workspace/review_model_results_interactive.ipynb @@ -22,7 +22,7 @@ "# Setup\n", "\n", "
\n", - " This notebook assumes Terra is running custom Docker image ghcr.io/broadinstitute/ml4h/ml4h_terra:20210902_181409.\n", + " This notebook assumes Terra is running custom Docker image ghcr.io/broadinstitute/ml4h/ml4h_terra:20210928_221837.\n", "
" ] }, diff --git a/notebooks/terra_featured_workspace/review_one_sample_interactive.ipynb b/notebooks/terra_featured_workspace/review_one_sample_interactive.ipynb index 7d9ebcebd..bd3626fae 100644 --- a/notebooks/terra_featured_workspace/review_one_sample_interactive.ipynb +++ b/notebooks/terra_featured_workspace/review_one_sample_interactive.ipynb @@ -22,7 +22,7 @@ "# Setup\n", "\n", "
\n", - " This notebook assumes Terra is running custom Docker image ghcr.io/broadinstitute/ml4h/ml4h_terra:20210902_181409.\n", + " This notebook assumes Terra is running custom Docker image ghcr.io/broadinstitute/ml4h/ml4h_terra:20210928_221837.\n", "
" ] }, From be0ec7281bdf1cd3b622791daa3176e409abfdaa Mon Sep 17 00:00:00 2001 From: Amy Unruh Date: Tue, 28 Sep 2021 16:57:27 -0700 Subject: [PATCH 2/3] typo fix --- .../review_one_sample_interactive.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/notebooks/terra_featured_workspace/review_one_sample_interactive.ipynb b/notebooks/terra_featured_workspace/review_one_sample_interactive.ipynb index bd3626fae..e09050cfd 100644 --- a/notebooks/terra_featured_workspace/review_one_sample_interactive.ipynb +++ b/notebooks/terra_featured_workspace/review_one_sample_interactive.ipynb @@ -304,7 +304,7 @@ "source": [ "## View recent annotations\n", "\n", - "For the purposes of this demo we are storing and displaying only those annotations created within this session. The ml4h toolkit includes functionaltiy to also persist these annotations to durable storage." + "For the purposes of this demo we are storing and displaying only those annotations created within this session. The ml4h toolkit includes functionality to also persist these annotations to durable storage." ] }, { From 86cad7d763567c34d0fc65387da5d057a2153b64 Mon Sep 17 00:00:00 2001 From: Amy Unruh Date: Wed, 29 Sep 2021 11:16:52 -0700 Subject: [PATCH 3/3] update the terra docker image version in the 'review_results' notebooks --- notebooks/review_results/identify_a_sample_to_review.ipynb | 2 +- notebooks/review_results/image_annotations.ipynb | 2 +- notebooks/review_results/review_one_sample.ipynb | 2 +- .../test_error_handling_for_notebook_visualizations.ipynb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/notebooks/review_results/identify_a_sample_to_review.ipynb b/notebooks/review_results/identify_a_sample_to_review.ipynb index 528d06715..7b087a8f7 100644 --- a/notebooks/review_results/identify_a_sample_to_review.ipynb +++ b/notebooks/review_results/identify_a_sample_to_review.ipynb @@ -16,7 +16,7 @@ "
\n", " This notebook assumes:\n", "
    \n", - "
  • Terra is running custom Docker image ghcr.io/broadinstitute/ml4h/ml4h_terra:20210902_181409.
    • \n", + "
  • Terra is running custom Docker image ghcr.io/broadinstitute/ml4h/ml4h_terra:20210928_221837.
    • \n", "
  • ml4h is running custom Docker image gcr.io/broad-ml4cvd/deeplearning:tf2-latest-gpu.
    • \n", "
\n", "
" diff --git a/notebooks/review_results/image_annotations.ipynb b/notebooks/review_results/image_annotations.ipynb index 984dd0e33..f9a038c04 100644 --- a/notebooks/review_results/image_annotations.ipynb +++ b/notebooks/review_results/image_annotations.ipynb @@ -18,7 +18,7 @@ "
\n", " This notebook assumes\n", "
    \n", - "
  • Terra is running custom Docker image ghcr.io/broadinstitute/ml4h/ml4h_terra:20210902_181409.
    • \n", + "
  • Terra is running custom Docker image ghcr.io/broadinstitute/ml4h/ml4h_terra:20210928_221837.
    • \n", "
  • ml4h is running custom Docker image gcr.io/broad-ml4cvd/deeplearning:tf2-latest-gpu.
    • \n", "
\n", "
" diff --git a/notebooks/review_results/review_one_sample.ipynb b/notebooks/review_results/review_one_sample.ipynb index 3d025bb22..bb86858f0 100644 --- a/notebooks/review_results/review_one_sample.ipynb +++ b/notebooks/review_results/review_one_sample.ipynb @@ -16,7 +16,7 @@ "
\n", " This notebook assumes\n", "
    \n", - "
  • Terra is running custom Docker image ghcr.io/broadinstitute/ml4h/ml4h_terra:20210902_181409.
    • \n", + "
  • Terra is running custom Docker image ghcr.io/broadinstitute/ml4h/ml4h_terra:20210928_221837.
    • \n", "
  • ml4h is running custom Docker image gcr.io/broad-ml4cvd/deeplearning:tf2-latest-gpu.
    • \n", "
\n", "
" diff --git a/notebooks/review_results/test_error_handling_for_notebook_visualizations.ipynb b/notebooks/review_results/test_error_handling_for_notebook_visualizations.ipynb index fbe924d24..f9f417f71 100644 --- a/notebooks/review_results/test_error_handling_for_notebook_visualizations.ipynb +++ b/notebooks/review_results/test_error_handling_for_notebook_visualizations.ipynb @@ -21,7 +21,7 @@ "metadata": {}, "source": [ "
\n", - " Terra Users test with the most recent custom Docker image which has all the software dependencies preinstalled. (Currently: ghcr.io/broadinstitute/ml4h/ml4h_terra:20210902_181409)\n", + " Terra Users test with the most recent custom Docker image which has all the software dependencies preinstalled. (Currently: ghcr.io/broadinstitute/ml4h/ml4h_terra:20210928_221837)\n", "
" ] },