Merge pull request #12 from mlibrary/DWI-32-cronjob

DWI-32 cronjob

.github/workflows/tests.yaml

@@ -3,7 +3,7 @@ name: Run Tests
 on: push
 
 jobs:
-  test:
+  test-python:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
@@ -26,4 +26,22 @@ jobs:
       - name: Run tests
         env:
           CI: "true"
-        run: poetry run pytest 
+        run: poetry run pytest 
+
+  test-bash:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup Bats and bats libs
+        id: setup-bats
+        uses: bats-core/[email protected]
+      - name: Setup Shell Mock
+        run: wget -P /opt/ https://github.com/boschresearch/shellmock/releases/download/0.9.1/shellmock.bash 
+      - run: ls /opt
+      - name: Run tests
+        shell: bash
+        env:
+         BATS_LIB_PATH: ${{ steps.setup-bats.outputs.lib-path }}
+         SHELLMOCK_PATH: /opt/shellmock.bash
+         TERM: xterm
+        run: bats ./bin/**/*_test.sh

.gitignore

@@ -14,4 +14,6 @@ htmlcov/
 .coverage
 .gnupg
 requirements.txt
-docs/_build
+
+docs/_build
+bin/digifeeds/*.config

Dockerfile

@@ -68,7 +68,18 @@ RUN poetry export --without dev -f requirements.txt --output requirements.txt
 # We want poetry on in development
 FROM poetry AS development
 RUN apt-get update -yqq && apt-get install -yqq --no-install-recommends \
-   git
+   git \
+   bats \
+   bats-assert \
+   bats-file\
+   wget\
+   zip\
+   unzip
+
+RUN wget -P /opt/ https://github.com/boschresearch/shellmock/releases/download/0.9.1/shellmock.bash && \
+  chown ${UID}:${GID} /opt/shellmock.bash
+
+ENV SHELLMOCK_PATH=/opt/shellmock.bash
 
 # Switch to the non-root user "user"
 USER app
@@ -84,4 +95,4 @@ COPY --chown=${UID}:${GID} --from=build "/app/requirements.txt" /app/requirement
 
 RUN pip install -r /app/requirements.txt
 
-USER app
+USER app

bin/digifeeds/upload_to_s3.config.example

@@ -0,0 +1,3 @@
+input_directory="some/path/to/input/directory"
+processed_directory="some/path/to/processed/directory"
+digifeeds_bucket="rclone_remote_to_s3_bucket"

bin/digifeeds/upload_to_s3.sh

@@ -0,0 +1,242 @@
+#! /bin/bash
+
+###########
+# CONSTANTS
+###########
+
+# For push gateway
+START_TIME=$(date '+%s')
+
+# Directory this script lives in
+SCRIPT_DIR=$(cd -- "$(dirname -- "${BASH_SOURCE[0]}")" &>/dev/null && pwd)
+
+APP_ENV=${APP_ENV:-"production"}
+
+if [[ $APP_ENV != "test" ]]; then
+  # CONFIG
+  # Variables contained in the config file:
+  #
+  # input_directory: path to the input directory
+  # processed_directory: path to the directory  of processed files+%
+  # digifeeds_bucket: rclone remote for the digifeeds bucket
+  #
+  # timestamp: used for testing timestamps; should be ommited in production
+  # send_metrics: when "false" metrics don't get sent;
+  # APP_ENV: when "test" the main script is not executed
+  CONFIG_FILE=${1:-$SCRIPT_DIR/upload_to_s3.config}
+  # shellcheck source=/dev/null
+  source "$CONFIG_FILE"
+fi
+if ! input_directory=${input_directory:?}; then exit 1; fi
+if ! processed_directory=${processed_directory:?}; then exit 1; fi
+if ! digifeeds_bucket=${digifeeds_bucket:?}; then exit 1; fi
+send_metrics=${send_metrics:-"true"}
+
+# matches .tif and .jp2 files with 8 digit file names that start with 0 OR
+# checksum.md5 files
+# examples that match:
+#   01234567.tif
+#   01234567.jp2
+#   checksum.md5
+IMGAWK='/^(0[0-9][0-9][0-9][0-9][0-9][0-9][0-9]\.(tif|jp2)|checksum\.md5)$/'
+
+# For push gateway
+JOB_NAME="aim_digifeeds_upload_to_aws"
+
+###########
+# COUNTERS
+###########
+files_processed_total=0
+image_order_errors_total=0
+upload_errors_total=0
+errors_total=0
+
+###########
+# FUNCTIONS
+###########
+
+log_info() {
+  echo "$(date --rfc-3339=seconds) - INFO: $*"
+}
+
+log_error() {
+  echo "$(date --rfc-3339=seconds) - ERROR: $*"
+}
+log_debug() {
+  [[ ${DEBUG:-false} == "true" ]] && echo "$(date --rfc-3339=seconds) - DEBUG: $*"
+}
+
+#equivalent to ls
+list_files() {
+  local path=$1
+  find "$path" -maxdepth 1 ! -printf '%P\n'
+}
+
+# Gets the last count from a job in the push gateway push gateway
+last_count() {
+  local metric=$1
+  pushgateway_advanced -j $JOB_NAME -q "${metric}"
+}
+
+verify_image_order() {
+  #Sort the array
+  mapfile -t sorted < <(printf '%s\n' "$@" | sort)
+
+  local cnt=0
+  for arg in "${sorted[@]}"; do
+    cnt=$((cnt + 1))
+    int=${arg:0:8}
+    [ $((10#$int)) != $cnt ] && return 1
+  done
+  return 0
+}
+
+zip_it() {
+  local barcode_path=$1
+  cd "$barcode_path" || return 1
+  list_files . | awk "$IMGAWK" | xargs zip -rq "$barcode_path".zip
+  local zip_return=$?
+  #Go back to  previous directory; Don't print the output.
+  cd - >/dev/null || return 1
+  return $zip_return
+}
+
+verify_zip() {
+  local barcode_path=$1
+
+  local files_in_dir
+  if ! files_in_dir=$(list_files "$barcode_path" | awk "$IMGAWK" | sort); then
+    return 1
+  fi
+  local files_in_zip
+  if ! files_in_zip=$(zipinfo -1 "$barcode_path".zip | sort); then
+    return 1
+  fi
+
+  if [ "$files_in_dir" == "$files_in_zip" ]; then
+    return 0
+  else
+    return 1
+  fi
+}
+
+print_metrics() {
+  local fp_current_total=$1
+  local image_order_errors_current_total=$2
+  local upload_errors_current_total=$3
+  local errors_current_total=$4
+
+  local fp_metric="${JOB_NAME}_files_processed_total"
+  local fp_last
+  fp_last=$(last_count $fp_metric)
+  local fp_total=$((fp_last + fp_current_total))
+
+  local image_order_errors_metric="${JOB_NAME}_image_order_errors_total"
+  local image_order_errors_last
+  image_order_errors_last=$(last_count $image_order_errors_metric)
+  local image_order_errors_total=$((image_order_errors_last + image_order_errors_current_total))
+
+  local upload_errors_metric="${JOB_NAME}_upload_errors_total"
+  local upload_errors_last
+  upload_errors_last=$(last_count $upload_errors_metric)
+  local upload_errors_total=$((upload_errors_last + upload_errors_current_total))
+
+  local errors_metric="${JOB_NAME}_errors_total"
+  local errors_last
+  errors_last=$(last_count $errors_metric)
+  local errors_total=$((errors_last + errors_current_total))
+
+  cat <<EOMETRICS
+# HELP ${fp_metric} Count of digifeeds zip files sent to S3
+# TYPE ${fp_metric} counter
+$fp_metric $fp_total
+# HELP ${image_order_errors_metric} Count of folders where there are missing pages of images 
+# TYPE ${image_order_errors_metric} counter
+${image_order_errors_metric} $image_order_errors_total
+# HELP ${upload_errors_metric} Count of errors when uploading digifeeds zip files to S3
+# TYPE ${upload_errors_metric} counter
+${upload_errors_metric} $upload_errors_total
+# HELP ${errors_metric} Count of all errors relating ot uploading digifeeds files sent to S3
+# TYPE ${errors_metric} counter
+${errors_metric} $errors_total
+EOMETRICS
+}
+
+main() {
+  TIMESTAMP=${timestamp:-$(date +%F_%H-%M-%S)} #YYY-MM-DD_hh-mm-ss
+
+  #This is so that the script works on empty directories.
+  shopt -s nullglob
+
+  for barcode_path in "${input_directory}"/*/; do
+    local barcode
+    barcode=$(basename "${barcode_path%%/}")
+
+    log_info "Copying $barcode"
+
+    log_debug "Verifying image order $barcode"
+    #8 digits, ends in .tif or .jp2
+    filter_regex='[[:digit:]]{8}\.tif$|[[:digit:]]{8}\.jp2$'
+    local image_list
+    image_list=$(list_files "$barcode_path" | grep -E "$filter_regex")
+    if ! verify_image_order "$image_list"; then
+      log_error "Image order incorrect for $barcode"
+      image_order_errors_total=$((image_order_errors_total + 1))
+      errors_total=$((errors_total + 1))
+      continue
+    fi
+
+    log_debug "Zipping $barcode"
+    if ! zip_it "$input_directory"/"$barcode"; then
+      log_error "Failed to zip $barcode"
+      errors_total=$((errors_total + 1))
+      continue
+    fi
+
+    log_debug "Verifying zip of $barcode"
+    if ! verify_zip "$input_directory"/"$barcode"; then
+      log_error "$barcode.zip does not contain the correct files"
+      errors_total=$((errors_total + 1))
+      continue
+    fi
+
+    log_debug "Sending $barcode to S3"
+    if ! rclone copy "$input_directory"/"$barcode".zip "$digifeeds_bucket":; then
+      log_error "Failed to copy $barcode"
+      upload_errors_total=$((upload_errors_total + 1))
+      errors_total=$((errors_total + 1))
+      continue
+    fi
+
+    log_debug "Verifying barcode in S3"
+    if ! rclone check "$input_directory"/"$barcode".zip "$digifeeds_bucket":; then
+      log_error "$barcode not found in S3"
+      upload_errors_total=$((upload_errors_total + 1))
+      errors_total=$((errors_total + 1))
+      continue
+    fi
+
+    log_info "Moving $barcode to processed"
+    mv "$input_directory"/"$barcode".zip "$processed_directory"/"${TIMESTAMP}"_"${barcode}".zip
+    mv "$input_directory"/"$barcode" "$processed_directory"/"${TIMESTAMP}"_"${barcode}"
+    files_processed_total=$((files_processed_total + 1))
+  done
+
+  log_info "Total files processed: $files_processed_total"
+  log_info "Total errors image order: $image_order_errors_total "
+  log_info "Total errors uploading to S3: $upload_errors_total"
+  log_info "Total errors: $errors_total"
+}
+
+if [[ $APP_ENV != "test" ]]; then
+
+  log_info "=====Start $(date)====="
+
+  main
+
+  if [ "$send_metrics" != "false" ]; then
+    print_metrics $files_processed_total $image_order_errors_total $upload_errors_total $errors_total | /usr/local/bin/pushgateway_advanced -j $JOB_NAME
+    /usr/local/bin/pushgateway -j $JOB_NAME -b "$START_TIME"
+  fi
+  log_info "=====End $(date)====="
+fi