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* first try!!!! * prep helix for launch * add helix name fix * udpate version
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,73 @@ | ||
| main: | ||
| params: [args] | ||
| steps: | ||
| - init: | ||
| assign: | ||
| - projectId: ${sys.get_env("GOOGLE_CLOUD_PROJECT_ID")} | ||
| - region: "us-central1" | ||
| - batchApi: "batch.googleapis.com/v1" | ||
| - batchApiUrl: ${ "https://" + batchApi + "/projects/" + projectId + "/locations/" + region + "/jobs"} | ||
| - jobId: ${ "helix-gisaid-" + string(int(sys.now()))} | ||
| - newFile: ${args.data.name} | ||
| - logCreateBatchJob: | ||
| call: sys.log | ||
| args: | ||
| data: ${ "Creating and running the batch job " + jobId} | ||
| - createAndRunBatchJob: | ||
| call: http.post | ||
| args: | ||
| url: ${batchApiUrl} | ||
| query: | ||
| job_id: ${jobId} | ||
| headers: | ||
| Content-Type: application/json | ||
| auth: | ||
| type: OAuth2 | ||
| body: | ||
| taskGroups: | ||
| - taskSpec: | ||
| runnables: | ||
| - container: | ||
| imageUri: "us-docker.pkg.dev/general-theiagen/theiagen/terra-tools:2023-08-08-2" | ||
| entrypoint: "/bin/bash" | ||
| volumes: | ||
| - "/mnt/disks/cdph_helix_gisaid_staging:/data" | ||
| - "/mnt/disks/cdph_helix_gisaid_staging/.config:/.config" | ||
| commands: | ||
| - "-c" | ||
| - ${ "bash /data/standard-dashboard.sh -d gs://cdph_helix_gisaid_staging -s no -b /data/input_gisaid -o /data -t gs://cdph_helix_gisaid -g gs://fc-6f47810a-0cc3-4e68-b8f0-12cde24d5893 -r helix_gisaid -p cdc-terrabio-taborda-manual -w dataAnalysis_SARS-CoV-2_Helix -q no -m false -i " + newFile + " -k true -x true"} | ||
| volumes: | ||
| - gcs: | ||
| remotePath: "cdph_helix_gisaid_staging" | ||
| mountPath: "/mnt/disks/cdph_helix_gisaid_staging" | ||
| taskCount: 1 | ||
| logsPolicy: | ||
| destination: CLOUD_LOGGING | ||
| result: createAndRunBatchJobResponse | ||
| - getJob: | ||
| call: http.get | ||
| args: | ||
| url: ${batchApiUrl + "/" + jobId} | ||
| auth: | ||
| type: OAuth2 | ||
| result: getJobResult | ||
| - logState: | ||
| call: sys.log | ||
| args: | ||
| data: ${ "Current job state " + getJobResult.body.status.state} | ||
| - checkState: | ||
| switch: | ||
| - condition: ${getJobResult.body.status.state == "SUCCEEDED"} | ||
| next: returnResult | ||
| - condition: ${getJobResult.body.status.state == "FAILED"} | ||
| next: returnResult | ||
| next: sleep | ||
| - sleep: | ||
| call: sys.sleep | ||
| args: | ||
| seconds: 10 | ||
| next: getJob | ||
| - returnResult: | ||
| return: | ||
| jobId: ${jobId} | ||
| status: "OK" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| gcloud eventarc triggers create helix-gisaid-trigger \ | ||
| --destination-workflow=helix-gisaid \ | ||
| --destination-workflow-location=us-central1 \ | ||
| --event-filters="type=google.cloud.storage.object.v1.finalized" \ | ||
| --event-filters="bucket=cdph_helix_gisaid" \ | ||
| --location=us \ | ||
| --service-account="[email protected]" |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,2 @@ | ||
| gcloud workflows deploy helix-gisaid \ | ||
| --source=helix-gisaid-data-workflow.yaml |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,34 @@ | ||
| #!/bin/bash | ||
|
|
||
| gcp_uri=$1 | ||
| terra_project=$2 | ||
| terra_workspace=$3 | ||
| root_entity=$4 | ||
| output_dir=$5 | ||
| alt_delimiter=$6 | ||
|
|
||
| date_tag=$7 | ||
| set_name=${date_tag}-set | ||
|
|
||
| # set default for $alt_delimiter in case user does not specify one | ||
| if [ -z $alt_delimiter ]; then | ||
| alt_delimiter="_" | ||
| fi | ||
|
|
||
| assembly_files=$(gsutil ls ${gcp_uri}/*.fasta | awk -F'/' '{ print $NF }') | ||
|
|
||
| # make set table header | ||
| echo -e "membership:${root_entity}_set_id\t${root_entity}" > ${output_dir}/${set_name}.tsv | ||
|
|
||
| for assembly in $assembly_files; do | ||
| # capture samplename from assembly filename | ||
| samplename=$(echo ${assembly} | awk -F "${alt_delimiter}|.fasta" '{ print $1 }') | ||
| # write samplename to the set | ||
| echo -e "${set_name}\t${samplename}" >> ${output_dir}/${set_name}.tsv | ||
| done | ||
|
|
||
| # remove duplicates from tsv if samplename not unique | ||
| awk '!a[$1]++' ${output_dir}/${set_name}.tsv > temp.tsv && mv temp.tsv ${output_dir}/${set_name}.tsv | ||
|
|
||
| # Import Terra table to sepcified terra_workspace | ||
| python3 /scripts/import_large_tsv/import_large_tsv.py --project ${terra_project} --workspace ${terra_workspace} --tsv ${output_dir}/${set_name}.tsv |