submission-prepare-files

#/bin/bash
# author Renzo Kottmann 2018-02-01

# This script creates symbolic links and md5 to the raw datafiles for
#  16S and 18 raw and workable datasets

# current dir (CWD) has to be sequence-data
#declare -r CWD=$(basename ${PWD})

#declare -r OSD_DIR='/bioinf/projects/osd/main/2015/06'

# from LGC
#declare -r LGC_RAW_18S_DATA_DIR=${OSD_DIR}'/pre-processing/18S/primer-clipping/lgc'
#declare -r LGC_WORKABLE_18S_DATA_DIR=${OSD_DIR}'/pre-processing/18S/quality-trimming/lgc'
#declare -r LGC_RAW_16S_DATA_DIR=${OSD_DIR}'/pre-processing/16S/primer-clipping/lgc'
#declare -r LGC_WORKABLE_16S_DATA_DIR=${OSD_DIR}'/pre-processing/16S/quality-trimming/lgc'

declare -r DEBUG='true'


function log::debug () {
  test -z "${DEBUG}" && { echo "ERROR: DEBUG variable not set"; exit 100; }
  test -n "${DEBUG}" && echo "DEBUG ${1}" 1>&2;
}


function log::error () {
   test -z "${DEBUG}" && { echo "ERROR: DEBUG variable not set"; exit 100; }
   test -n "${DEBUG}" && echo "ERROR ${1}" 1>&2;
}


function check_empty_var() {
    if [[ ! ${1} ]]; then
        log::error "Variable is empty";
        return 100
    fi
    return 0
}


function _check_required_programs() {

    # Required program(s)
    #req_progs=(readlink date md5)
    for p in ${@}; do
	hash "${p}" 2>&- || \
	    { echo >&2 " Required program \"${p}\" not installed or in search PATH.";
        exit 1;
      }
    done
}

function create_dir_structure {


  echo "Current base dirname=${CWD}"
  check_empty_var "${1}" || exit 999

  local -r SUBMISSION_DIR="${1}"

  mkdir -pv "${SUBMISSION_DIR}"

}


function blacklist() {

  #
  # delete blacklist: OSD_R[12]-_16S
  #
  echo "Deleting: ${BLACKLIST}"
  rm  ${BLACKLIST}
}

function calc_md5() {

  ## doing all md5 for 18S or 16S
  echo 'creating md5s'
  for i in *.fasta.gz ; do
    echo "md5 for ${i}"
    md5sum ${i} > ${i}.md5;
  done

  chmod 664 *.md5
}


function create_usage() {
    cat <<EOF

Usage: ${BASH_SOURCE} [Options] directory

Options:

  -n, --subsmission-name   Give of a submission to be done e.g. myosd or osd
  -s, --sequencing-center  Provide a sequencing center name e.g. LGC_GENOMICS

  -c, --campaign-name      Provide a campaign name e.g. OSD2014 or MYOSD2016

  -d, --data-set           Provide the data set name e.g. 18S, 16S or shotgun

  -p, --processing-status  Provide a th (pre-) processing status of sequences e.g. RAW or WORKABLE

  --primer                 Provide a primer pair name used for sequencing e.g. alma_alma or NONE in case of shotgun

EOF
}

function main() {

  local SUBMISSION_NAME='unknown'
  log::debug "Num options=$#"
  log::debug "first option=${1}="

declare -r RUN="${@}"

  check_empty_var "${1}" || { log::debug 'Provide options';  create_usage; }
  _check_required_programs md5sum readlink

  while [[ $# -gt 0 ]]; do

    case ${1} in

      -n|--submission-name)
        shift;
        check_empty_var "${1}" || {
          log::error "Provide a submission name";
          exit 66
        }

        local -r SUBMISSION_NAME="${1}"
        shift;
        ;;

        -s|--sequencing-center)
          shift;
          check_empty_var "${1}" || {
            log::error "Provide a sequencing center name e.g. LGC_GENOMICS";
            exit 66
          }

          local -r SEQUENCING_CENTER="${1,,}"
          shift;
          ;;

        -c|--campaign-name)
          shift;
          check_empty_var "${1}" || {
            log::error "Provide a campaign name e.g. OSD or MYOSD";
            exit 66
          }

          local -r CAMPAIGN_NAME="${1}"
          shift;
          ;;

        -d|--data-set)
          shift;
          check_empty_var "${1}" || {
            log::error "Provide the sequencing data category e.g. RRNA or shotgun";
            exit 66
          }

          local -r DATA_SET="${1,,}"
          shift;
          ;;

        -p|--processing-status)
          shift;
          check_empty_var "${1}" || {
            log::error "Provide a th (pre-) processing status of sequences e.g. RAW or WORKABLE";
            exit 66
          }

          local -r PROCESSING_STATUS="${1,,}"
          shift;
          ;;

        --primer)
          shift;
          check_empty_var "${1}" || {
            log::error "Provide a the primer pair used for sequencing e.g. alma_alma or NONE in case of shotgung";
            exit 66
          }

          local -r PRIMER_PAIR="${1,,}"
          shift;
          ;;
        -o|--output-dir)
          shift;
          check_empty_var "${1}" || {
            log::error "Provide a output directory where files get created in";
            exit 66
          }

          local -r OUTPUT_BASE_DIR='/OSD2015_*/fasta/*'
          shift;
          ;;
        --file-pattern)
          shift;
          check_empty_var "${1}" || {
            log::error "Provide a bash compatible pattern for files to be included in submission preparation. This should be relative to directory provided as last argument. Without leading slash";
            exit 66
          }

          local -r DIR_PATTERN=${1}
          shift;
          ;;

        -h|--help)
          create_usage ;
          exit 0
          ;;

        *)

          log::debug  "Rest is source directory"
          #create_usage ;

                # now checking last argument
          if [[ -d ${1} ]]; then
            echo "directory=${1} exists. Can proceed..."
            #TODO check more about source dir, like does it have readable files etc.
            # need absolute path to source dit
            local -r SOURCE_DIR=$(readlink -f "${1}")
            log::debug "Source dir=${SOURCE_DIR}"
          else
            log::error "directory=${1} does not exist"
            exit 1
          fi
          shift;
          ;;

    esac
  done



  check_empty_var "${SUBMISSION_NAME}" || {
    log::error "SEQUENCING_CENTER missing but required"
    exit 66
  }
  check_empty_var "${SEQUENCING_CENTER}" || {
    log::error "SEQUENCING_CENTER missing but required"
    exit 66
  }
  check_empty_var "${CAMPAIGN_NAME}" || {
    log::error "CAMPAIGN_NAME missing but required"
    exit 66
  }
  check_empty_var "${DATA_SET}" || {
    log::error "DATA SET name missing but required"
    exit 66
  }
  check_empty_var "${PROCESSING_STATUS}" || {
    log::error "PROCESSING_STATUS missing but required"
    exit 66
  }
  check_empty_var "${PRIMER_PAIR}" || {
    log::error "PRIMER_PAIR missing but required"
    exit 66
  }
  check_empty_var "${DIR_PATTERN}" || {
    log::error "FILE PATTERN is missing but required"
    exit 66
  }



  local -r FILE_TAG="${CAMPAIGN_NAME}-${DATA_SET}-${PRIMER_PAIR}-${PROCESSING_STATUS}"
  local -r DESTINATION_DIR="${FILE_TAG}-${SUBMISSION_NAME}"

  create_dir_structure "${DESTINATION_DIR}"

  #cd "${SUBMISSION_NAME}"/workable


  shopt -s nullglob
  # TODO also add 2016-01-26
  #local -r TEST_PATTERN='OSD2015_*/fasta/*'

  for FILE in "${SOURCE_DIR}/"${DIR_PATTERN} ; do
    if [ -e "${FILE}" ] ; then
      fname="${DESTINATION_DIR}/"$(basename ${FILE});
      log::debug "new link name=${fname} of ${FILE}"
      ln -sf "${FILE}" "${fname}" || exit 1000;
    else
      echo "${FILE} does not exist"
    fi
  done

  # becaause of md5sum writing filepath in report need to do it local to file
  $( cd "${DESTINATION_DIR}";
     for FILE in * ; do
       log::debug "file=${FILE}";
       md5sum "./${FILE}" > "${FILE}.md5" || {
         log::error "Can not create md5sum" && exit 1000;
      };
     done
  ) || exit 9999

local -r CUR_DATE=$(date)

# ADDING README
cat > "${DESTINATION_DIR}/README.md" <<EOF
# Submission Perparation

This directory contains files from the submission preparation run with

Script: ${BASH_SOURCE}
Script Parameters: ${RUN}
Called from direcotry: ${PWD}
User: ${USER}
Time: ${CUR_DATE}

EOF

  echo "Done :)"
}

log::debug 'Hi script'
main "$@"