From 6e61ebeda3d99dbff187176d04a2c0495140b33c Mon Sep 17 00:00:00 2001
From: Don Freed <donfreed12@gmail.com>
Date: Mon, 10 Jul 2023 20:10:33 -0700
Subject: [PATCH] Use the requester project for file upload

- Update the container base image
- Update the default container image
- Respect the requester project for log upload
---
 pipeline_scripts/Dockerfile      |  6 +++---
 pipeline_scripts/gc_functions.sh |  6 +++---
 pipeline_scripts/gc_germline.sh  | 12 ++++++------
 pipeline_scripts/gc_somatic.sh   | 14 +++++++-------
 runner/runner_default.json       |  2 +-
 runner/sentieon_runner.py        | 11 ++++++++---
 6 files changed, 28 insertions(+), 23 deletions(-)

diff --git a/pipeline_scripts/Dockerfile b/pipeline_scripts/Dockerfile
index 20385b1..b3a85ec 100644
--- a/pipeline_scripts/Dockerfile
+++ b/pipeline_scripts/Dockerfile
@@ -1,4 +1,4 @@
-FROM google/cloud-sdk:367.0.0-slim as downloader
+FROM google/cloud-sdk:437.0.1-slim as downloader
 
 # Install samtools
 RUN apt-get update && \
@@ -22,9 +22,9 @@ RUN curl -Lo samblaster-v.0.1.24.tar.gz https://github.com/GregoryFaust/samblast
   make && \
   cp samblaster /usr/local/bin/
 
-FROM google/cloud-sdk:367.0.0-slim
+FROM google/cloud-sdk:437.0.1-slim
 
-LABEL container.base.image="google/cloud-sdk:367.0.0-slim"
+LABEL container.base.image="google/cloud-sdk:437.0.1-slim"
 
 COPY --from=downloader /usr/local/bin/samtools /usr/local/bin
 COPY --from=downloader /usr/local/bin/samblaster /usr/local/bin
diff --git a/pipeline_scripts/gc_functions.sh b/pipeline_scripts/gc_functions.sh
index 91e8604..a1a5c7b 100644
--- a/pipeline_scripts/gc_functions.sh
+++ b/pipeline_scripts/gc_functions.sh
@@ -88,7 +88,7 @@ upload_metrics()
     eval "fun_metrics_cmd2=\$$fun_var_cmd2"
     if [[ -n "$fun_metrics_cmd2" && -z "$fun_metrics_cmd1" && -f "${fun_metrics_files[0]}" ]]; then
         (run "$fun_metrics_cmd2" "Plotting metrics results." &&
-            gsutil cp ${fun_metrics_files[@]} "$out_metrics" &&
+            gsutil ${REQUESTER_PROJECT:+-u $REQUESTER_PROJECT} cp ${fun_metrics_files[@]} "$out_metrics" &&
             rm ${fun_metrics_files[@]}) &
         eval "$fun_pid=$! "
         eval "$fun_var_cmd2=''"
@@ -297,7 +297,7 @@ bwa_mem_align()
         fi
         bwa_cmd="$bwa_cmd | $release_dir/bin/sentieon util sort ${fun_util_sort_xargs} --block_size 512M -o $local_bam -t $nt --sam2bam -i -"
         run "$bwa_cmd" "BWA-mem and sorting"
-        gsutil cp $bwa_log "$out_bam"
+        gsutil ${REQUESTER_PROJECT:+-u $REQUESTER_PROJECT} cp $bwa_log "$out_bam"
         fun_bam_dest+=($local_bam)
     done
     echo "BWA ended"
@@ -444,7 +444,7 @@ run_bqsr_post()
         run "$cmd" "BQSR post"
         run "$fun_bqsr_cmd3" "BQSR CSV"
         run "$fun_bqsr_cmd4" "BQSR plot"
-        gsutil cp $fun_plot "$out_metrics" &
+        gsutil ${REQUESTER_PROJECT:+-u $REQUESTER_PROJECT} cp $fun_plot "$out_metrics" &
         eval "$fun_upload_pid=$1 "
     fi
 
diff --git a/pipeline_scripts/gc_germline.sh b/pipeline_scripts/gc_germline.sh
index 4a10872..551a24c 100644
--- a/pipeline_scripts/gc_germline.sh
+++ b/pipeline_scripts/gc_germline.sh
@@ -102,7 +102,7 @@ output_ext="bam"
 run_mark_duplicates "" "$DEDUP" metrics_cmd1 "$local_bams_str" dedup_bam_str dedup_bams "$dedup_xargs" $output_ext "false" "${local_bams[@]}"
 if [[ "$DEDUP" != "nodup" ]]; then
     if [[ -z "$NO_METRICS" ]]; then
-        (gsutil cp $metrics_dir/dedup_metrics.txt "$out_metrics" &&
+        (gsutil ${REQUESTER_PROJECT:+-u $REQUESTER_PROJECT} cp $metrics_dir/dedup_metrics.txt "$out_metrics" &&
             rm $metrics_dir/dedup_metrics.txt) &
         upload_dedup_pid=$!
     else
@@ -131,7 +131,7 @@ if [[ -z "$NO_BAM_OUTPUT" && (-z "$bqsr_sites" || -z "$RECALIBRATED_OUTPUT" ) ]]
             upload_list+=" \"${bam}.crai\" "
         fi
     done
-    eval gsutil cp $upload_list "$out_bam" &
+    eval gsutil ${REQUESTER_PROJECT:+-u $REQUESTER_PROJECT} cp $upload_list "$out_bam" &
     upload_deduped_pid=$!
 fi
 
@@ -146,12 +146,12 @@ if [[ -n "$bqsr_sites" && -z "$NO_BAM_OUTPUT" && -n "$RECALIBRATED_OUTPUT" ]]; t
     outrecal=$work/recalibrated.bam
     cmd="$release_dir/bin/sentieon driver $dedup_bam_str -q $bqsr_table --algo ReadWriter $outrecal"
     (run "$cmd" "ReadWriter";
-        gsutil cp $outrecal ${outrecal}.bai "$out_bam") &
+        gsutil ${REQUESTER_PROJECT:+-u $REQUESTER_PROJECT} cp $outrecal ${outrecal}.bai "$out_bam") &
     upload_recal_pid=$!
 fi
 
 if [[ -n "$bqsr_sites" && -z "$NO_BAM_OUTPUT" && -z "$RECALIBRATED_OUTPUT" ]]; then
-    gsutil cp $bqsr_table "$out_bam" &
+    gsutil ${REQUESTER_PROJECT:+-u $REQUESTER_PROJECT} cp $bqsr_table "$out_bam" &
     upload_bqsr_pid=$!
 fi
 
@@ -218,7 +218,7 @@ if [[ -z $NO_HAPLOTYPER ]]; then
         run "$cmd" "DNAscope model apply"
     fi
 
-    gsutil cp $outfile ${outfile}.tbi "$out_variants" &
+    gsutil ${REQUESTER_PROJECT:+-u $REQUESTER_PROJECT} cp $outfile ${outfile}.tbi "$out_variants" &
     upload_vcf_pid=$!
 fi
 
@@ -240,7 +240,7 @@ fi
 if [[ -n $bqsr_cmd3 ]]; then
     run "$bqsr_cmd3" "BQSR CSV"
     run "$bqsr_cmd4" "BQSR plot"
-    gsutil cp $plot "$out_metrics" &
+    gsutil ${REQUESTER_PROJECT:+-u $REQUESTER_PROJECT} cp $plot "$out_metrics" &
     upload_bqsr_metrics_pid=$!
 fi
 
diff --git a/pipeline_scripts/gc_somatic.sh b/pipeline_scripts/gc_somatic.sh
index 9874538..f1baa8f 100644
--- a/pipeline_scripts/gc_somatic.sh
+++ b/pipeline_scripts/gc_somatic.sh
@@ -159,7 +159,7 @@ if [[ "$DEDUP" != "nodup" ]]; then
         if [[ -n "$dedup_bam_str" ]]; then
             to_upload+=" $metrics_dir/normal_dedup_metrics.txt"
         fi
-        (gsutil cp $to_upload "$out_metrics" &&
+        (gsutil ${REQUESTER_PROJECT:+-u $REQUESTER_PROJECT} cp $to_upload "$out_metrics" &&
             rm $metrics_dir/*_dedup_metrics.txt) &
         upload_dedup_pid=$!
     else
@@ -188,7 +188,7 @@ if [[ -z "$NO_BAM_OUTPUT" && -z "$REALIGN_SITES" ]]; then
             upload_list+=" \"${bam}.crai\" "
         fi
     done
-    eval gsutil cp $upload_list "$out_bam" &
+    eval gsutil ${REQUESTER_PROJECT:+-u $REQUESTER_PROJECT} cp $upload_list "$out_bam" &
     upload_deduped_pid=$!
 fi
 
@@ -254,7 +254,7 @@ if [[ -n "$realigned_bam_str" ]]; then
 fi
 
 if [[ -n "$bqsr_sites" && -z "$NO_BAM_OUTPUT" ]]; then
-    gsutil cp $bqsr_table $tumor_bqsr_table "$out_bam" &
+    gsutil ${REQUESTER_PROJECT:+-u $REQUESTER_PROJECT} cp $bqsr_table $tumor_bqsr_table "$out_bam" &
     upload_bqsr_pid=$!
 fi
 
@@ -296,7 +296,7 @@ if [[ -n "$REALIGN_SITES" && -n "$RUN_TNSNV" && -n "$realigned_bam_str" ]]; then
     elif [[ -f "${corealigned_bam}.crai" ]]; then
         upload_list+=" ${corealigned_bam}.crai "
     fi
-    gsutil cp $upload_list "$out_bam" &
+    gsutil ${REQUESTER_PROJECT:+-u $REQUESTER_PROJECT} cp $upload_list "$out_bam" &
     upload_corealigned_pid=$!
 
     corealigned_bam_str=" -i $corealigned_bam "
@@ -310,7 +310,7 @@ elif [[ -n "$REALIGN_SITES" && -n "$RUN_TNSNV" ]]; then
             upload_list+=" \"${bam}.crai\" "
         fi
     done
-    eval gsutil cp $upload_list "$out_bam" &
+    eval gsutil ${REQUESTER_PROJECT:+-u $REQUESTER_PROJECT} cp $upload_list "$out_bam" &
     upload_corealigned_pid=$!
 
     corealigned_bam_str=" $tumor_realigned_bam_str "
@@ -350,7 +350,7 @@ if [[ -z "$NO_VCF" ]]; then
     fi
 
     run "$cmd" "Variant calling"
-    gsutil cp $vcf ${vcf}.tbi "$out_variants" &
+    gsutil ${REQUESTER_PROJECT:+-u $REQUESTER_PROJECT} cp $vcf ${vcf}.tbi "$out_variants" &
     upload_vcf_pid=$!
 fi
 
@@ -382,7 +382,7 @@ if [[ -n $tumor_bqsr_cmd3 ]]; then
     fi
     run "$tumor_bqsr_cmd3" "Tumor BQSR CSV"
     run "$tumor_bqsr_cmd4" "Tumor BQSR plot"
-    gsutil cp $upload_list $tumor_bqsr_plot "$out_metrics" &
+    gsutil ${REQUESTER_PROJECT:+-u $REQUESTER_PROJECT} cp $upload_list $tumor_bqsr_plot "$out_metrics" &
     upload_bqsr_metrics_pid=$!
 fi
 
diff --git a/runner/runner_default.json b/runner/runner_default.json
index de4940d..59cbd6c 100644
--- a/runner/runner_default.json
+++ b/runner/runner_default.json
@@ -34,7 +34,7 @@
   "CPU_PLATFORM": "Intel Broadwell",
   "PROJECT_ID": null,
   "REQUESTER_PROJECT": null,
-  "DOCKER_IMAGE": "sentieon/sentieon-google-cloud:0.2.4",
+  "DOCKER_IMAGE": "sentieon/sentieon-google-cloud:0.2.6",
   "CALLING_ARGS": null,
   "CALLING_ALGO": "Haplotyper",
   "DNASCOPE_MODEL": "https://s3.amazonaws.com/sentieon-release/other/SentieonDNAscopeModel1.0.model",
diff --git a/runner/sentieon_runner.py b/runner/sentieon_runner.py
index 674c229..3640e60 100644
--- a/runner/sentieon_runner.py
+++ b/runner/sentieon_runner.py
@@ -435,11 +435,16 @@ def main(
             "/bin/bash",
             "-c",
             (
-                "gsutil cp /google/logs/action/1/stderr "
+                "gsutil -u {} cp /google/logs/action/1/stderr "
                 '"{}/worker_logs/stderr.txt" && '
-                "gsutil cp /google/logs/action/1/stdout "
+                "gsutil -u {} cp /google/logs/action/1/stdout "
                 '"{}/worker_logs/stdout.txt"'
-            ).format(job_vars["OUTPUT_BUCKET"], job_vars["OUTPUT_BUCKET"]),
+            ).format(
+                job_vars["REQUESTER_PROJECT"],
+                job_vars["OUTPUT_BUCKET"],
+                job_vars["REQUESTER_PROJECT"],
+                job_vars["OUTPUT_BUCKET"]
+            ),
         ],
         "alwaysRun": True,
     }