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Fix Google Bucket Job #2686

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Fix Google Bucket Job #2686

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eda1b7c
Fix Google Bucket Job
BinamB Dec 12, 2024
59b31d1
fix file paths
BinamB Dec 13, 2024
4b1829a
Merge branch 'master' into chore/fix-google-replication
BinamB Dec 18, 2024
e4f2a76
Update Dockerfile json args
MaribelleHGomez Dec 18, 2024
72e44a7
use "
MaribelleHGomez Dec 18, 2024
278f669
Merge branch 'master' into chore/fix-google-replication
MaribelleHGomez Jan 14, 2025
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78 changes: 1 addition & 77 deletions .secrets.baseline
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Original file line number Diff line number Diff line change
Expand Up @@ -1275,29 +1275,6 @@
"line_number": 33
}
],
"kube/services/jobs/aws-bucket-replicate-job.yaml": [
{
"type": "Secret Keyword",
"filename": "kube/services/jobs/aws-bucket-replicate-job.yaml",
"hashed_secret": "deb02468778f4041fb189654698ac948e436732d",
"is_verified": false,
"line_number": 33
},
{
"type": "Secret Keyword",
"filename": "kube/services/jobs/aws-bucket-replicate-job.yaml",
"hashed_secret": "abe72fcb190ed9c73eb20e198c73a97605b95063",
"is_verified": false,
"line_number": 36
},
{
"type": "Secret Keyword",
"filename": "kube/services/jobs/aws-bucket-replicate-job.yaml",
"hashed_secret": "ca3cdac59f2bfa45cb014190e4509bf6becf28fb",
"is_verified": false,
"line_number": 42
}
],
"kube/services/jobs/bucket-manifest-job.yaml": [
{
"type": "Secret Keyword",
Expand Down Expand Up @@ -1703,29 +1680,6 @@
"line_number": 31
}
],
"kube/services/jobs/google-bucket-replicate-job.yaml": [
{
"type": "Secret Keyword",
"filename": "kube/services/jobs/google-bucket-replicate-job.yaml",
"hashed_secret": "b6f0ec0b08da77656ced48427841e28d7a8a81d6",
"is_verified": false,
"line_number": 35
},
{
"type": "Secret Keyword",
"filename": "kube/services/jobs/google-bucket-replicate-job.yaml",
"hashed_secret": "abe72fcb190ed9c73eb20e198c73a97605b95063",
"is_verified": false,
"line_number": 38
},
{
"type": "Secret Keyword",
"filename": "kube/services/jobs/google-bucket-replicate-job.yaml",
"hashed_secret": "ca3cdac59f2bfa45cb014190e4509bf6becf28fb",
"is_verified": false,
"line_number": 41
}
],
"kube/services/jobs/google-create-bucket-job.yaml": [
{
"type": "Secret Keyword",
Expand Down Expand Up @@ -2373,36 +2327,6 @@
"line_number": 43
}
],
"kube/services/jobs/replicate-validation-job.yaml": [
{
"type": "Secret Keyword",
"filename": "kube/services/jobs/replicate-validation-job.yaml",
"hashed_secret": "deb02468778f4041fb189654698ac948e436732d",
"is_verified": false,
"line_number": 34
},
{
"type": "Secret Keyword",
"filename": "kube/services/jobs/replicate-validation-job.yaml",
"hashed_secret": "b6f0ec0b08da77656ced48427841e28d7a8a81d6",
"is_verified": false,
"line_number": 37
},
{
"type": "Secret Keyword",
"filename": "kube/services/jobs/replicate-validation-job.yaml",
"hashed_secret": "abe72fcb190ed9c73eb20e198c73a97605b95063",
"is_verified": false,
"line_number": 40
},
{
"type": "Secret Keyword",
"filename": "kube/services/jobs/replicate-validation-job.yaml",
"hashed_secret": "ca3cdac59f2bfa45cb014190e4509bf6becf28fb",
"is_verified": false,
"line_number": 43
}
],
"kube/services/jobs/s3sync-cronjob.yaml": [
{
"type": "Secret Keyword",
Expand Down Expand Up @@ -3253,5 +3177,5 @@
}
]
},
"generated_at": "2024-11-25T11:39:59Z"
"generated_at": "2024-12-13T06:58:14Z"
}
2 changes: 1 addition & 1 deletion Docker/awshelper/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -126,4 +126,4 @@ RUN git config --global user.email gen3 \
RUN export GEN3_HOME="$HOME/cloud-automation" \
&& bash -c 'source "$GEN3_HOME/gen3/gen3setup.sh" && gen3 help'

CMD /bin/bash
CMD ["/bin/bash"]
4 changes: 2 additions & 2 deletions kube/services/jobs/aws-bucket-replicate-job.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -88,13 +88,13 @@ spec:
args:
- "-c"
- |
cat /secrets/dcf_dataservice_settings > ./scripts/settings.py
cat /secrets/dcf_dataservice_settings > ./dcfdataservice/settings.py
echo """
[default]
region: us-east-1
""" > ~/.aws/config
aws configure set default.s3.max_concurrent_requests 1000
aws configure set default.s3.max_queue_size 10000
python replicate.py aws_replicate --release $RELEASE --quick_test $QUICK_TEST --bucket $GDC_BUCKET_NAME --thread_num $THREAD_NUM --manifest_file $MANIFEST_S3 --global_config "{\"chunk_size\": $CHUNK_SIZE, \"log_bucket\": \"$LOG_BUCKET\"}"
# python scripts/replicate.py indexing --thread_num 20 --manifest_file $MANIFEST_S3 --global_config "{\"chunk_size\": 3, \"log_bucket\": \"$LOG_BUCKET\"}"
# python dcfdataservice/replicate.py indexing --thread_num 20 --manifest_file $MANIFEST_S3 --global_config "{\"chunk_size\": 3, \"log_bucket\": \"$LOG_BUCKET\"}"
restartPolicy: Never
10 changes: 8 additions & 2 deletions kube/services/jobs/google-bucket-replicate-job.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -39,6 +39,9 @@ spec:
- name: creds-json-volume
secret:
secretName: "dcf-dataservice-json-secret"
- name: project-map-volume
configMap:
name: project-map-manifest
containers:
- name: datareplicate
GEN3_DATAREPLICATE_IMAGE
Expand Down Expand Up @@ -78,11 +81,14 @@ spec:
- name: "creds-json-volume"
mountPath: "/secrets/dcf_dataservice_credentials.json"
subPath: "dcf_dataservice_credentials.json"
- name: "project-map-volume"
mountPath: "/dcf-dataservice/GDC_project_map.json"
subPath: "GDC_project_map.json"
command: ["/bin/bash" ]
args:
- "-c"
- |
cat /secrets/dcf_dataservice_settings > ./scripts/settings.py
cat /secrets/dcf_dataservice_settings > ./dcfdataservice/settings.py
gcloud auth activate-service-account --key-file=/secrets/google_service_account_creds
export GOOGLE_APPLICATION_CREDENTIALS=/secrets/google_service_account_creds
export http_proxy='http://cloud-proxy.internal.io:3128'
Expand All @@ -97,7 +103,7 @@ spec:
fi
if [[ "$type" == "active" || "$type" == "legacy" ]]; then
rand_str="$(cat /dev/urandom | tr -dc 'a-zA-Z0-9' | fold -w 5 | head -n 1)"
python dataflow_pipeline.py --runner DataflowRunner --project $PROJECT --job_name dcf-dataservice --autoscaling_algorithm NONE --num_worker $MAX_WORKERS --maxNumWorkers $MAX_WORKERS --staging_location gs://$LOG_BUCKET/$RELEASE/staging --temp_location gs://$LOG_BUCKET/$RELEASE/temp --output gs://$LOG_BUCKET/$RELEASE/$type/output_$rand_str --setup_file ./setup.py --input $MANIFEST_FILE --global_config "{\"release\": \"$RELEASE/$type\", \"log_bucket\": \"$LOG_BUCKET\"}" --requirements_file requirements.txt --extra_package indexclient-1.6.0.zip --requirements_file scripts/requirements.txt
python dataflow_pipeline.py --runner DataflowRunner --project $PROJECT --job_name dcf-dataservice --autoscaling_algorithm NONE --num_worker $MAX_WORKERS --maxNumWorkers $MAX_WORKERS --staging_location gs://$LOG_BUCKET/$RELEASE/staging --temp_location gs://$LOG_BUCKET/$RELEASE/temp --output gs://$LOG_BUCKET/$RELEASE/$type/output_$rand_str --setup_file ./setup.py --input $MANIFEST_FILE --global_config "{\"release\": \"$RELEASE/$type\", \"log_bucket\": \"$LOG_BUCKET\"}" --requirements_file requirements.txt --extra_package indexclient-1.6.0.zip --requirements_file dcfdataservice/requirements.txt
else
echo "Neither active nor legacy manifest is provided. Please check the manifest name!!!"
fi
Expand Down
13 changes: 10 additions & 3 deletions kube/services/jobs/replicate-validation-job.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -41,6 +41,9 @@ spec:
- name: creds-json-volume
secret:
secretName: "dcf-dataservice-json-secret"
- name: project-map-volume
configMap:
name: project-map-manifest
containers:
- name: datareplicate
GEN3_DATAREPLICATE_IMAGE
Expand All @@ -64,6 +67,8 @@ spec:
GEN3_FORCE_CREATE_MANIFEST
- name: LOG_BUCKET
GEN3_LOG_BUCKET
- name: MAP_FILE
value: "" # Default to empty string if not provided
volumeMounts:
- name: aws-cred-volume
mountPath: "/root/.aws/credentials"
Expand All @@ -76,7 +81,9 @@ spec:
subPath: "dcf_dataservice_settings"
- name: "creds-json-volume"
mountPath: "/secrets/dcf_dataservice_credentials.json"
subPath: "dcf_dataservice_credentials.json"
- name: "project-map-volume"
mountPath: "/dcf-dataservice/GDC_project_map.json"
subPath: "GDC_project_map.json"
command: ["/bin/bash" ]
args:
- "-c"
Expand All @@ -85,9 +92,9 @@ spec:
[default]
region: us-east-1
""" > ~/.aws/config
cat /secrets/dcf_dataservice_settings > ./scripts/settings.py
cat /secrets/dcf_dataservice_settings > ./dcfdataservice/settings.py
gcloud auth activate-service-account --key-file=/secrets/google_service_account_creds
export GOOGLE_APPLICATION_CREDENTIALS=/secrets/google_service_account_creds
gsutil cp $IGNORED_FILE /dcf-dataservice/ignored_files_manifest.csv
python replicate.py validate --global_config "{\"release\": \"$RELEASE\", \"manifest_files\":\"$MANIFEST_FILES\", \"out_manifests\": \"$OUT_FILES\", \"FORCE_CREATE_MANIFEST\": \"$FORCE_CREATE_MANIFEST\", \"log_bucket\": \"$LOG_BUCKET\", \"save_copied_objects\": 1}"
python replicate.py validate --global_config "{\"release\": \"$RELEASE\", \"manifest_files\":\"$MANIFEST_FILES\", \"out_manifests\": \"$OUT_FILES\", \"FORCE_CREATE_MANIFEST\": \"$FORCE_CREATE_MANIFEST\", \"log_bucket\": \"$LOG_BUCKET\", \"map_file\": \"$MAP_FILE\", \"save_copied_objects\": 1}"
restartPolicy: Never
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