#!/usr/bin/env bash
    # basic template bash script to run submit the clearinghouse submissions. This ought to run in most linux and unix(inc. MacOS) environments.
    # This is just an example, you may well have better ways to do this. This template may help you implement your own in bash or indeed python, R or rust et cetera.
    # N.B. please always refer to the API documentation, as that will be the most up to date.
    # ENA, EMBL-EBI, January 2024
    #
    echo " template script to run submit the clearinghouse submissions"
    echo "  run: script_name.py dir_path_to_submission_jsons"
    # echo "  suggestion, before the run: script submission_typescript.log as this will record the output"
    # echo "  please check the output for an errors, e.g. JSON to fix or resubmit"
    echo ""

    ##################################################################################################
    ##### Configurable portion
    # This where one can set environmental variables and credentials up, that are used subsequently.

    # Taking the first argument to the script from the command line. It is the directory containing the JSON annotation files to be submitted.
    submission_dir=$1

    #need a plain file to write and read the bearer key from, see later in this script. It will be automatically created with the name below
    export bearer_file="bearer_file"

    # this is my local bash (chmod 007 ~/.my_secrets), please contact your IT admin to see whether this is permissible or if they have a better solution
    my_protected_secret_file="~/.my_secrets"
    if ! [ -f ${my_protected_secret_file} ] ; then
        echo "${my_protected_secret_file}<--does not exist, so exiting"
        exit
    fi

    source ${my_protected_secret_file}
    #these below are the relevant contents of the configuration file, please uncomment and add your credentials
    #export my_email_address='my_email_name@redbrick.ac.uk'
    #export aai_test_user='my_test_username'
    #export aai_test_pass='my_test_password'
    #export aai_test_creds="${aai_test_user}:${aai_test_pass}"
    #
    #export aai_prod_user='my_prod_username'
    #export aai_prod_pass='my_prod_password'
    #export aai_prod_creds="${aai_prod_user}:${aai_prod_pass}"

    # set up the applicable server URL for the the test or production environment.
    # it is by default set up to submit to the test=developmental server.
    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_test_creds
    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
    fi

    ################################################################
    # Declaring Functions, that are called later in this bash script

    function re_run_bearer_file () {
      auth_url=$1
      credentials=$2
      echo "curl $auth_url" -u "$credentials"
      echo $bearer_file
      curl "$auth_url" -u "$credentials" 1> $bearer_file 2>/dev/null
      bearerkey=`cat $bearer_file`
      len=${#bearerkey}
      if [ $len -lt 100 ]; then
        echo "Invalid bearer key, so exiting script, try later."
        exit
      fi
      }

    function submit_2_clearinghouse () {
      export curation_json_file=$1
      echo $curation_json_file
      export bearerkey=`cat $bearer_file`
      export bearer="Authorization: Bearer $bearerkey"
      #echo $bearer
      # -T is needed for big files -d @ is slightly faster and puts it into memory
      cmd=`curl -X POST \"${url}\" -H \"accept: */*\"  -H \"Content-Type: application/json\"   -H \"${bearer}\"  -d @${curation_json_file}`
      #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
      echo " "
    }

    #########################################################################
    # configuration continued, this using the configurations and a function from above to
    # 1) ensure that you have a submission directory
    # 2) use the user name, password and applicable URL to create the bearer key.
    #    the bearer key identifies you to the applicable ClearingHouse server, so that you can submit the annotations.

    if [ ! -d $submission_dir ]; then
        echo "${submission_dir}<--is not a valid directory, so exiting"
        exit
    fi
    echo "submission_dir: -->"${submission_dir}

    # echo $creds
    # if one needs, 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 bearer key frequently as it times out within an hour...

    re_run_bearer_file $auth_url $creds
    export bearerkey=`cat $bearer_file`
    export bearer="Authorization: Bearer $bearerkey"

    ##################################################################################################
    # now processing every json file in your submission directory
    for file in $submission_dir/*.json
    do
        echo $file
        echo $bearer
        submit_2_clearinghouse $file
        sleep 0.1 # wait 0.1 seconds
        re_run_bearer_file $auth_url $creds
    done
    message_contents="Attempted to process all files in ${submission_dir} . Please do check the logfiles for any errors."
    echo ${message_contents} | mail -s "ClearingHouse submission finished" ${my_email_address}
    echo "end of script: ${0}"
    ################################################################################################