using sshpass to upload because curl no longer working for some reason

MRCIEU · Jan 16, 2025 · f172a2e · f172a2e
1 parent 349dda6
commit f172a2e
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Showing 3 changed files with 12 additions and 4 deletions.
diff --git a/bin/sshpass b/bin/sshpass
diff --git a/utils/archive.sh b/utils/archive.sh
@@ -62,7 +62,7 @@ if [[ $step = "00" ]];
 then
     cp config.env ${results_dir}/00
     cp ${genotype_input_list} ${results_dir}/00
-    cp ${genptype_processed_dir}/scratch/indep.bim ${results_dir}/00
+    cp ${genotype_processed_dir}/scratch/indep.bim ${results_dir}/00
 fi
 
 tar -czvf ${results_dir}/${cohort_name}_$step.tar.gz -C ${results_dir} $step

diff --git a/utils/upload.sh b/utils/upload.sh
@@ -33,13 +33,21 @@ cd ${results_dir}
 md5sum -c ${cohort_name}_${step}.tar.gz.md5
 
 sftp_address="lcgwassftp.blob.core.windows.net"
-sftp_username_full="lcgwassftp.analysts.${sftp_username}"
+sftp_username_full="lcgwassftp.testcontainer.${sftp_username}"
 
 read -s -p "Ready to upload? Press enter to continue: " anykey
 echo ""
 read -s -p "Enter SFTP password: " mypassword
 
-curl -1 -v -k "sftp://${sftp_address}/${sftp_username}/${cohort_name}_${step}.tar.gz" --user "${sftp_username_full}:${mypassword}" -T "${results_dir}/${cohort_name}_${step}.tar.gz"
-curl -1 -v -k "sftp://${sftp_address}/${sftp_username}/${cohort_name}_${step}.tar.gz.md5" --user "${sftp_username_full}:${mypassword}" -T "${results_dir}/${cohort_name}_${step}.tar.gz.md5"
+export SSHPASS=$mypassword
+${d}/bin/sshpass -e sftp -oBatchMode=no -b - ${sftp_username_full}@${sftp_address} << !
+   put ${results_dir}/${cohort_name}_${step}.tar.gz
+   put ${results_dir}/${cohort_name}_${step}.tar.gz.md5
+   bye
+!
+
+# This used to work and now doesn't - need to figure it out
+# curl -1 -v -k "sftp://${sftp_address}:22/${sftp_username}/${cohort_name}_${step}.tar.gz" --user "${sftp_username_full}:${mypassword}" -T "${results_dir}/${cohort_name}_${step}.tar.gz"
+# curl -1 -v -k "sftp://${sftp_address}:22/${sftp_username}/${cohort_name}_${step}.tar.gz.md5" --user "${sftp_username_full}:${mypassword}" -T "${results_dir}/${cohort_name}_${step}.tar.gz.md5"
 
 echo "Successfully uploaded ${cohort_name}_${step}.tar.gz and ${cohort_name}_${step}.tar.gz.md5. Many thanks indeed!"