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Code cleanup #10

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merged 7 commits into from
May 6, 2024
+77 −365
Merged

Code cleanup #10

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781f77a
Remove auth. Input data is now public.
deflaux May 1, 2024
62fe14b
Remove auth. Input data is now public.
deflaux May 2, 2024
b98f6ed
Add Dockstore config file.
deflaux May 2, 2024
4dfe670
Remove obsolete parameters and outputs.
deflaux May 2, 2024
a200b34
Move files for original Docker image to separate directory.
deflaux May 2, 2024
c2d4366
Add Dockerfile for the public Docker image.
deflaux May 2, 2024
e516479
Update default parameter value in both places.
deflaux May 2, 2024
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5 changes: 5 additions & 0 deletions .dockstore.yml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
version: 1.2
workflows:
- subclass: WDL
primaryDescriptorPath: embedding_creation_script.wdl
name: EmbeddingCreation
20 changes: 5 additions & 15 deletions Dockerfile
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Expand Up @@ -2,19 +2,9 @@
# Use of this source code is governed by a BSD-style license that can be found in the LICENSE file or at
# https://developers.google.com/open-source/licenses/bsd

# Install gcloud so that we can access AWS secrets from Secret Manager.
FROM gcr.io/google.com/cloudsdktool/google-cloud-cli:slim as gcloud
# Start from the actual Docker image used to compute the embeddings in 2022 and 2023.
FROM gcr.io/terra-solutions-jump-cp-dev/embedding_creation:20221027_090451

FROM tensorflow/tensorflow:latest-gpu

ENV TFHUB_CACHE_DIR=/opt/hub_models

ADD cache_model.py /opt

RUN pip3 install apache-beam[gcp,dataframe] google-cloud-secret-manager fsspec[gcs,s3] imagecodecs Pillow tensorflow-hub tifffile tqdm \
&& rm -rf ~/.cache/pip \
&& python3 /opt/cache_model.py

COPY --from=gcloud /usr/lib/google-cloud-sdk /usr/lib/google-cloud-sdk

RUN ln -s /usr/lib/google-cloud-sdk/bin/gcloud /usr/bin/gcloud
# Add the finalized scripts
ADD scatter_wells_s3.py /opt
ADD embedding_creation.py /opt
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