cleaned up, making it easy to switch between test and prod

Author: Woolly-at-EBI

src/run_submit_clearhouse.sh

@@ -1,20 +1,38 @@
 # script to run submit the clearinghouse submissions
+#
+# Peter Woollard, ENA, EMBL-EBI, March 2023
 echo "script to run submit the clearinghouse submissions"
-# set environment variables and credentials up
+
+##################################################################################################
+##### Configurable portion
+# set environment variables and credentials up - this is my local bash (only readable by me), suggest you doing something similar
 source ~/.ayup
-url="https://www.ebi.ac.uk/ena/clearinghouse/api/curations"
-url="https://wwwdev.ebi.ac.uk/ena/clearinghouse/api/curations"
-auth_url='https://explore.api.aai.ebi.ac.uk/auth'
-creds=$aai_test2_creds
-echo $creds
+
+TEST=1
+if [ $TEST -eq 1 ]; then
+  echo "using test credentials and setup"
+  url="https://wwwdev.ebi.ac.uk/ena/clearinghouse/api/curations"
+  auth_url='https://explore.api.aai.ebi.ac.uk/auth'
+  creds=$aai_test2_creds
+  submission_dir="/Users/woollard/projects/bluecloud/clearinghouse/submission_data/test/splits/"
+  submission_dir="/Users/woollard/projects/bluecloud/clearinghouse/submission_data/full/splits/"
+else
+  #PROD
+  echo "using production credentials and setup"
+  url="https://www.ebi.ac.uk/ena/clearinghouse/api/curations"
+  auth_url='https://api.aai.ebi.ac.uk/auth'
+  creds=$aai_prod_creds
+  submission_dir="/Users/woollard/projects/bluecloud/clearinghouse/submission_data/full/splits/"
+fi
+
+# echo $creds
 # if meed to renew the bearer ( the below is for the test):
 #curl 'https://explore.api.aai.ebi.ac.uk/auth'  -u $aai_test2_creds 1> bearer_file 2>/dev/null
 #re-running the bearerkey frequently as it times out within an hour
 
-submission_dir="/Users/woollard/projects/bluecloud/clearinghouse/submission_data/full/splits/"
-# submission_dir="/Users/woollard/projects/bluecloud/clearinghouse/submission_data/test/splits/"
 
-bearer_file="bearer_file"
+##################################################################################################
+echo "submission_dir: "$submission_dir
 
 function re_run_bearer_file () {
   auth_url=$1
@@ -30,23 +48,19 @@ function re_run_bearer_file () {
   }
 
 re_run_bearer_file $auth_url $creds
-echo $bearerkey "<<<<<<<<<<<<<<<<<<"
-
 export bearerkey=`cat $bearer_file`
 export bearer="Authorization: Bearer $bearerkey"
 
 function submit_2_clearinghouse () {
-
   export curation_json_file=$1
   echo $curation_json_file
   export bearerkey=`cat $bearer_file`
   export bearer="Authorization: Bearer $bearerkey"
   #echo $bearer
-
-  # would not run bre
+  # -T is needed for big files -d @ is slightly faster and puts it into memoru
   cmd=`echo curl -X POST \"${url}\" -H \"accept: */*\"  -H \"Content-Type: application/json\"   -H \"${bearer}\"  -T ${curation_json_file}`
   cmd=`echo curl -X POST \"${url}\" -H \"accept: */*\"  -H \"Content-Type: application/json\"   -H \"${bearer}\"  -d @${curation_json_file}`
-  # cmd=`echo echo "ayup"`
+  #could not get to both see the command and execute it, so doing the dirty way via a new file
   echo $cmd
   echo $cmd > run_me.sh
   time sh ./run_me.sh
@@ -55,15 +69,14 @@ function submit_2_clearinghouse () {
 }
 
 for file in $submission_dir/*.json
-  do
+do
     echo $file
     echo $bearer
     submit_2_clearinghouse $file
     sleep 0.1 # wait 0.1 seconds
     re_run_bearer_file $auth_url $creds
-  done
-
+done
 
-curation_json_file="/Users/woollard/projects/bluecloud/clearinghouse/submission_data/IHO-EEZ:intersect_MARREGION.json"
+#end of script