Merge pull request 'changes in copy script' (#438) from antonis.lempesis/dnet-hadoop:beta into beta

Reviewed-on: D-Net/dnet-hadoop#438

dhp-workflows/dhp-stats-hist-snaps/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-hist-snaps/oozie_app/copyDataToImpalaCluster.sh

@@ -8,6 +8,8 @@ fi
 
 export HADOOP_USER_NAME=$2
 
+SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR=0
+
 
 # Set the active HDFS node of OCEAN and IMPALA cluster.
 OCEAN_HDFS_NODE='hdfs://nameservice1'
@@ -30,7 +32,9 @@ while [ $COUNTER -lt 3 ]; do
 done
 if [ -z "$IMPALA_HDFS_NODE" ]; then
     echo -e "\n\nERROR: PROBLEM WHEN SETTING THE HDFS-NODE FOR IMPALA CLUSTER! | AFTER ${COUNTER} RETRIES.\n\n"
+    if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
       exit 1
+    fi
 fi
 echo -e "Active IMPALA HDFS Node: ${IMPALA_HDFS_NODE} , after ${COUNTER} retries.\n\n"
 
@@ -39,26 +43,25 @@ IMPALA_CONFIG_FILE='/etc/impala_cluster/hdfs-site.xml'
 
 IMPALA_HDFS_DB_BASE_PATH="${IMPALA_HDFS_NODE}/user/hive/warehouse"
 
-
 # Set sed arguments.
 LOCATION_HDFS_NODE_SED_ARG="s|${OCEAN_HDFS_NODE}|${IMPALA_HDFS_NODE}|g" # This requires to be used with "sed -e" in order to have the "|" delimiter (as the "/" conflicts with the URIs)
 
-# Set the SED command arguments for column-names with reserved words:
-DATE_SED_ARG_1='s/[[:space:]]\date[[:space:]]/\`date\`/g'
-DATE_SED_ARG_2='s/\.date,/\.\`date\`,/g'  # the "date" may be part of a larger field name like "datestamp" or "date_aggregated", so we need to be careful with what we are replacing.
-DATE_SED_ARG_3='s/\.date[[:space:]]/\.\`date\` /g'
 
-HASH_SED_ARG_1='s/[[:space:]]\hash[[:space:]]/\`hash\`/g'
+function print_elapsed_time()
-HASH_SED_ARG_2='s/\.hash,/\.\`hash\`,/g'
+{
-HASH_SED_ARG_3='s/\.hash[[:space:]]/\.\`hash\` /g'
+  start_time=$1
-
+  end_time=$(date +%s)
-LOCATION_SED_ARG_1='s/[[:space:]]\location[[:space:]]/\`location\`/g'
+  elapsed_time=$(($end_time-$start_time))
-LOCATION_SED_ARG_2='s/\.location,/\.\`location\`,/g'
+  hours=$((elapsed_time / 3600))
-LOCATION_SED_ARG_3='s/\.location[[:space:]]/\.\`location\` /g'
+  minutes=$(((elapsed_time % 3600) / 60))
+  seconds=$((elapsed_time % 60))
+  printf "\nElapsed time: %02d:%02d:%02d\n\n" $hours $minutes $seconds
+}
 
 
 function copydb() {
   db=$1
+  start_db_time=$(date +%s)
   echo -e "\nStart processing db: '${db}'..\n"
 
   # Delete the old DB from Impala cluster (if exists).
@@ -67,8 +70,10 @@ function copydb() {
   if [ -n "$log_errors" ]; then
     echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN DROPPING THE OLD DATABASE! EXITING...\n\n"
     rm -f error.log
+    if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
       exit 2
     fi
+  fi
 
   echo -e "\n\nCopying files of '${db}', from Ocean to Impala cluster..\n"
   # Using max-bandwidth of: 70 * 150 Mb/s = 10.5 Gb/s
@@ -91,8 +96,10 @@ function copydb() {
   else
     echo -e "\n\nERROR: FAILED TO TRANSFER THE FILES OF '${db}', WITH 'hadoop distcp'. GOT EXIT STATUS: $?\n\n"
     rm -f error.log
+    if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
       exit 3
     fi
+  fi
 
   # In case we ever use this script for a writable DB (using inserts/updates), we should perform the following costly operation as well..
   #hdfs dfs -conf ${IMPALA_CONFIG_FILE} -chmod -R 777 ${TEMP_SUBDIR_FULLPATH}/${db}.db
@@ -109,17 +116,13 @@ function copydb() {
   num_tables=0
 
   entities_on_ocean=`hive -e "show tables in ${db};" | sed 's/WARN:.*//g'`  # Get the tables and views without any potential the "WARN" logs.
-  for i in ${entities_on_ocean[@]}; do # Use un-quoted values, as the elemetns are single-words.
+  for i in ${entities_on_ocean[@]}; do # Use un-quoted values, as the elements are single-words.
     # Check if this is a view by showing the create-statement where it should print "create view" for a view, not the "create table". Unfortunately, there is no "show views" command.
-    create_entity_statement=`hive -e "show create table ${db}.${i};"` # It needs to happen in two stages, otherwise the "grep" is not able to match multi-line statement.
+    create_entity_statement=`hive --database ${db} -e "show create table ${i};"`  # We need to use the "--database", instead of including it inside the query, in order to return the statements with the '`' chars being in the right place to be used by impala-shell. However, we need to add the db-name in the "CREATE VIEW view_name" statement.
-
+    create_view_statement_test=`echo -e "$create_entity_statement" | grep 'CREATE VIEW'`  # It needs to happen in two stages, otherwise the "grep" is not able to match multi-line statement.
-    create_view_statement_test=`echo -e "$create_entity_statement" | grep 'CREATE VIEW'`
     if [ -n "$create_view_statement_test" ]; then
       echo -e "\n'${i}' is a view, so we will save its 'create view' statement and execute it on Impala, after all tables have been created.\n"
-      create_view_statement=`echo -e "$create_entity_statement" | sed 's/WARN:.*//g' | sed 's/\`//g' \
+      create_view_statement=`echo -e "$create_entity_statement" | sed 's/WARN:.*//g' | sed 's/"$/;/' | sed 's/^"//' | sed 's/\\"\\"/\"/g' | sed -e "${LOCATION_HDFS_NODE_SED_ARG}" | sed "s/CREATE VIEW /CREATE VIEW ${db}./"`
-        | sed 's/"$/;/' | sed 's/^"//' | sed 's/\\"\\"/\"/g' | sed -e "${LOCATION_HDFS_NODE_SED_ARG}" | sed "${DATE_SED_ARG_1}" | sed "${HASH_SED_ARG_1}" | sed "${LOCATION_SED_ARG_1}" \
-        | sed "${DATE_SED_ARG_2}" | sed "${HASH_SED_ARG_2}" | sed "${LOCATION_SED_ARG_2}" \
-        | sed "${DATE_SED_ARG_3}" | sed "${HASH_SED_ARG_3}" | sed "${LOCATION_SED_ARG_3}"`
       all_create_view_statements+=("$create_view_statement")
     else
       echo -e "\n'${i}' is a table, so we will check for its parquet files and create the table on Impala cluster.\n"
@@ -127,12 +130,17 @@ function copydb() {
       CURRENT_PRQ_FILE=`hdfs dfs -conf ${IMPALA_CONFIG_FILE} -ls -C "${IMPALA_HDFS_DB_BASE_PATH}/${db}.db/${i}/" | grep -v 'Found' | grep -v '_impala_insert_staging' |  head -1`
       if [ -z "$CURRENT_PRQ_FILE" ]; then # If there is not parquet-file inside.
           echo -e "\nERROR: THE TABLE \"${i}\" HAD NO FILES TO GET THE SCHEMA FROM! IT'S EMPTY!\n\n"
-          exit 4 # Comment out when testing a DB which has such a table, just for performing this exact test-check.
+          if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
+            exit 4
+          fi
       else
         impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create table ${db}.${i} like parquet '${CURRENT_PRQ_FILE}' stored as parquet;" |& tee error.log
         log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
         if [ -n "$log_errors" ]; then
           echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN CREATING TABLE '${i}'!\n\n"
+          if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
+            exit 5
+          fi
         fi
       fi
     fi
@@ -176,7 +184,9 @@ function copydb() {
 
     if [[ $new_num_of_views_to_retry -eq $previous_num_of_views_to_retry ]]; then
       echo -e "\n\nERROR: THE NUMBER OF VIEWS TO RETRY HAS NOT BEEN REDUCED! THE SCRIPT IS LIKELY GOING TO AN INFINITE-LOOP! EXITING..\n\n"
-      exit 5
+      if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
+        exit 6
+      fi
     elif [[ $new_num_of_views_to_retry -gt 0 ]]; then
       echo -e "\nTo be retried \"create_view_statements\" (${new_num_of_views_to_retry}):\n\n${all_create_view_statements[@]}\n"
     else
@@ -204,11 +214,14 @@ function copydb() {
   else
     echo -e "\n\nERROR: 1 OR MORE ENTITIES OF DB '${db}' FAILED TO BE COPIED TO IMPALA CLUSTER!\n\n"
     rm -f error.log
-    exit 6
+    if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
+      exit 7
+    fi
   fi
 
   rm -f error.log
-  echo -e "\n\nFinished processing db: ${db}\n\n"
+  echo -e "\n\nFinished processing db: ${db}\n"
+  print_elapsed_time start_db_time
 }
 
 

dhp-workflows/dhp-stats-monitor-irish/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor-irish/oozie_app/copyDataToImpalaCluster.sh

@@ -8,6 +8,9 @@ fi
 
 export HADOOP_USER_NAME=$2
 
+SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR=0
+
+
 # Set the active HDFS node of OCEAN and IMPALA cluster.
 OCEAN_HDFS_NODE='hdfs://nameservice1'
 echo -e "\nOCEAN HDFS virtual-name which resolves automatically to the active-node: ${OCEAN_HDFS_NODE}"
@@ -29,7 +32,9 @@ while [ $COUNTER -lt 3 ]; do
 done
 if [ -z "$IMPALA_HDFS_NODE" ]; then
     echo -e "\n\nERROR: PROBLEM WHEN SETTING THE HDFS-NODE FOR IMPALA CLUSTER! | AFTER ${COUNTER} RETRIES.\n\n"
+    if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
       exit 1
+    fi
 fi
 echo -e "Active IMPALA HDFS Node: ${IMPALA_HDFS_NODE} , after ${COUNTER} retries.\n\n"
 
@@ -38,26 +43,25 @@ IMPALA_CONFIG_FILE='/etc/impala_cluster/hdfs-site.xml'
 
 IMPALA_HDFS_DB_BASE_PATH="${IMPALA_HDFS_NODE}/user/hive/warehouse"
 
-
 # Set sed arguments.
 LOCATION_HDFS_NODE_SED_ARG="s|${OCEAN_HDFS_NODE}|${IMPALA_HDFS_NODE}|g" # This requires to be used with "sed -e" in order to have the "|" delimiter (as the "/" conflicts with the URIs)
 
-# Set the SED command arguments for column-names with reserved words:
-DATE_SED_ARG_1='s/[[:space:]]\date[[:space:]]/\`date\`/g'
-DATE_SED_ARG_2='s/\.date,/\.\`date\`,/g'  # the "date" may be part of a larger field name like "datestamp" or "date_aggregated", so we need to be careful with what we are replacing.
-DATE_SED_ARG_3='s/\.date[[:space:]]/\.\`date\` /g'
 
-HASH_SED_ARG_1='s/[[:space:]]\hash[[:space:]]/\`hash\`/g'
+function print_elapsed_time()
-HASH_SED_ARG_2='s/\.hash,/\.\`hash\`,/g'
+{
-HASH_SED_ARG_3='s/\.hash[[:space:]]/\.\`hash\` /g'
+  start_time=$1
-
+  end_time=$(date +%s)
-LOCATION_SED_ARG_1='s/[[:space:]]\location[[:space:]]/\`location\`/g'
+  elapsed_time=$(($end_time-$start_time))
-LOCATION_SED_ARG_2='s/\.location,/\.\`location\`,/g'
+  hours=$((elapsed_time / 3600))
-LOCATION_SED_ARG_3='s/\.location[[:space:]]/\.\`location\` /g'
+  minutes=$(((elapsed_time % 3600) / 60))
+  seconds=$((elapsed_time % 60))
+  printf "\nElapsed time: %02d:%02d:%02d\n\n" $hours $minutes $seconds
+}
 
 
 function copydb() {
   db=$1
+  start_db_time=$(date +%s)
   echo -e "\nStart processing db: '${db}'..\n"
 
   # Delete the old DB from Impala cluster (if exists).
@@ -66,8 +70,10 @@ function copydb() {
   if [ -n "$log_errors" ]; then
     echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN DROPPING THE OLD DATABASE! EXITING...\n\n"
     rm -f error.log
+    if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
       exit 2
     fi
+  fi
 
   echo -e "\n\nCopying files of '${db}', from Ocean to Impala cluster..\n"
   # Using max-bandwidth of: 70 * 150 Mb/s = 10.5 Gb/s
@@ -90,8 +96,10 @@ function copydb() {
   else
     echo -e "\n\nERROR: FAILED TO TRANSFER THE FILES OF '${db}', WITH 'hadoop distcp'. GOT EXIT STATUS: $?\n\n"
     rm -f error.log
+    if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
       exit 3
     fi
+  fi
 
   # In case we ever use this script for a writable DB (using inserts/updates), we should perform the following costly operation as well..
   #hdfs dfs -conf ${IMPALA_CONFIG_FILE} -chmod -R 777 ${TEMP_SUBDIR_FULLPATH}/${db}.db
@@ -108,17 +116,13 @@ function copydb() {
   num_tables=0
 
   entities_on_ocean=`hive -e "show tables in ${db};" | sed 's/WARN:.*//g'`  # Get the tables and views without any potential the "WARN" logs.
-  for i in ${entities_on_ocean[@]}; do # Use un-quoted values, as the elemetns are single-words.
+  for i in ${entities_on_ocean[@]}; do # Use un-quoted values, as the elements are single-words.
     # Check if this is a view by showing the create-statement where it should print "create view" for a view, not the "create table". Unfortunately, there is no "show views" command.
-    create_entity_statement=`hive -e "show create table ${db}.${i};"` # It needs to happen in two stages, otherwise the "grep" is not able to match multi-line statement.
+    create_entity_statement=`hive --database ${db} -e "show create table ${i};"`  # We need to use the "--database", instead of including it inside the query, in order to return the statements with the '`' chars being in the right place to be used by impala-shell. However, we need to add the db-name in the "CREATE VIEW view_name" statement.
-
+    create_view_statement_test=`echo -e "$create_entity_statement" | grep 'CREATE VIEW'`  # It needs to happen in two stages, otherwise the "grep" is not able to match multi-line statement.
-    create_view_statement_test=`echo -e "$create_entity_statement" | grep 'CREATE VIEW'`
     if [ -n "$create_view_statement_test" ]; then
       echo -e "\n'${i}' is a view, so we will save its 'create view' statement and execute it on Impala, after all tables have been created.\n"
-      create_view_statement=`echo -e "$create_entity_statement" | sed 's/WARN:.*//g' | sed 's/\`//g' \
+      create_view_statement=`echo -e "$create_entity_statement" | sed 's/WARN:.*//g' | sed 's/"$/;/' | sed 's/^"//' | sed 's/\\"\\"/\"/g' | sed -e "${LOCATION_HDFS_NODE_SED_ARG}" | sed "s/CREATE VIEW /CREATE VIEW ${db}./"`
-        | sed 's/"$/;/' | sed 's/^"//' | sed 's/\\"\\"/\"/g' | sed -e "${LOCATION_HDFS_NODE_SED_ARG}" | sed "${DATE_SED_ARG_1}" | sed "${HASH_SED_ARG_1}" | sed "${LOCATION_SED_ARG_1}" \
-        | sed "${DATE_SED_ARG_2}" | sed "${HASH_SED_ARG_2}" | sed "${LOCATION_SED_ARG_2}" \
-        | sed "${DATE_SED_ARG_3}" | sed "${HASH_SED_ARG_3}" | sed "${LOCATION_SED_ARG_3}"`
       all_create_view_statements+=("$create_view_statement")
     else
       echo -e "\n'${i}' is a table, so we will check for its parquet files and create the table on Impala cluster.\n"
@@ -126,12 +130,17 @@ function copydb() {
       CURRENT_PRQ_FILE=`hdfs dfs -conf ${IMPALA_CONFIG_FILE} -ls -C "${IMPALA_HDFS_DB_BASE_PATH}/${db}.db/${i}/" | grep -v 'Found' | grep -v '_impala_insert_staging' |  head -1`
       if [ -z "$CURRENT_PRQ_FILE" ]; then # If there is not parquet-file inside.
           echo -e "\nERROR: THE TABLE \"${i}\" HAD NO FILES TO GET THE SCHEMA FROM! IT'S EMPTY!\n\n"
-          exit 4 # Comment out when testing a DB which has such a table, just for performing this exact test-check.
+          if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
+            exit 4
+          fi
       else
         impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create table ${db}.${i} like parquet '${CURRENT_PRQ_FILE}' stored as parquet;" |& tee error.log
         log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
         if [ -n "$log_errors" ]; then
           echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN CREATING TABLE '${i}'!\n\n"
+          if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
+            exit 5
+          fi
         fi
       fi
     fi
@@ -175,7 +184,9 @@ function copydb() {
 
     if [[ $new_num_of_views_to_retry -eq $previous_num_of_views_to_retry ]]; then
       echo -e "\n\nERROR: THE NUMBER OF VIEWS TO RETRY HAS NOT BEEN REDUCED! THE SCRIPT IS LIKELY GOING TO AN INFINITE-LOOP! EXITING..\n\n"
-      exit 5
+      if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
+        exit 6
+      fi
     elif [[ $new_num_of_views_to_retry -gt 0 ]]; then
       echo -e "\nTo be retried \"create_view_statements\" (${new_num_of_views_to_retry}):\n\n${all_create_view_statements[@]}\n"
     else
@@ -203,11 +214,14 @@ function copydb() {
   else
     echo -e "\n\nERROR: 1 OR MORE ENTITIES OF DB '${db}' FAILED TO BE COPIED TO IMPALA CLUSTER!\n\n"
     rm -f error.log
-    exit 6
+    if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
+      exit 7
+    fi
   fi
 
   rm -f error.log
-  echo -e "\n\nFinished processing db: ${db}\n\n"
+  echo -e "\n\nFinished processing db: ${db}\n"
+  print_elapsed_time start_db_time
 }
 
 

dhp-workflows/dhp-stats-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor/oozie_app/copyDataToImpalaCluster.sh

@@ -8,6 +8,9 @@ fi
 
 export HADOOP_USER_NAME=$2
 
+SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR=0
+
+
 # Set the active HDFS node of OCEAN and IMPALA cluster.
 OCEAN_HDFS_NODE='hdfs://nameservice1'
 echo -e "\nOCEAN HDFS virtual-name which resolves automatically to the active-node: ${OCEAN_HDFS_NODE}"
@@ -29,7 +32,9 @@ while [ $COUNTER -lt 3 ]; do
 done
 if [ -z "$IMPALA_HDFS_NODE" ]; then
     echo -e "\n\nERROR: PROBLEM WHEN SETTING THE HDFS-NODE FOR IMPALA CLUSTER! | AFTER ${COUNTER} RETRIES.\n\n"
+    if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
       exit 1
+    fi
 fi
 echo -e "Active IMPALA HDFS Node: ${IMPALA_HDFS_NODE} , after ${COUNTER} retries.\n\n"
 
@@ -38,26 +43,25 @@ IMPALA_CONFIG_FILE='/etc/impala_cluster/hdfs-site.xml'
 
 IMPALA_HDFS_DB_BASE_PATH="${IMPALA_HDFS_NODE}/user/hive/warehouse"
 
-
 # Set sed arguments.
 LOCATION_HDFS_NODE_SED_ARG="s|${OCEAN_HDFS_NODE}|${IMPALA_HDFS_NODE}|g" # This requires to be used with "sed -e" in order to have the "|" delimiter (as the "/" conflicts with the URIs)
 
-# Set the SED command arguments for column-names with reserved words:
-DATE_SED_ARG_1='s/[[:space:]]\date[[:space:]]/\`date\`/g'
-DATE_SED_ARG_2='s/\.date,/\.\`date\`,/g'  # the "date" may be part of a larger field name like "datestamp" or "date_aggregated", so we need to be careful with what we are replacing.
-DATE_SED_ARG_3='s/\.date[[:space:]]/\.\`date\` /g'
 
-HASH_SED_ARG_1='s/[[:space:]]\hash[[:space:]]/\`hash\`/g'
+function print_elapsed_time()
-HASH_SED_ARG_2='s/\.hash,/\.\`hash\`,/g'
+{
-HASH_SED_ARG_3='s/\.hash[[:space:]]/\.\`hash\` /g'
+  start_time=$1
-
+  end_time=$(date +%s)
-LOCATION_SED_ARG_1='s/[[:space:]]\location[[:space:]]/\`location\`/g'
+  elapsed_time=$(($end_time-$start_time))
-LOCATION_SED_ARG_2='s/\.location,/\.\`location\`,/g'
+  hours=$((elapsed_time / 3600))
-LOCATION_SED_ARG_3='s/\.location[[:space:]]/\.\`location\` /g'
+  minutes=$(((elapsed_time % 3600) / 60))
+  seconds=$((elapsed_time % 60))
+  printf "\nElapsed time: %02d:%02d:%02d\n\n" $hours $minutes $seconds
+}
 
 
 function copydb() {
   db=$1
+  start_db_time=$(date +%s)
   echo -e "\nStart processing db: '${db}'..\n"
 
   # Delete the old DB from Impala cluster (if exists).
@@ -66,8 +70,10 @@ function copydb() {
   if [ -n "$log_errors" ]; then
     echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN DROPPING THE OLD DATABASE! EXITING...\n\n"
     rm -f error.log
+    if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
       exit 2
     fi
+  fi
 
   echo -e "\n\nCopying files of '${db}', from Ocean to Impala cluster..\n"
   # Using max-bandwidth of: 70 * 150 Mb/s = 10.5 Gb/s
@@ -90,8 +96,10 @@ function copydb() {
   else
     echo -e "\n\nERROR: FAILED TO TRANSFER THE FILES OF '${db}', WITH 'hadoop distcp'. GOT EXIT STATUS: $?\n\n"
     rm -f error.log
+    if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
       exit 3
     fi
+  fi
 
   # In case we ever use this script for a writable DB (using inserts/updates), we should perform the following costly operation as well..
   #hdfs dfs -conf ${IMPALA_CONFIG_FILE} -chmod -R 777 ${TEMP_SUBDIR_FULLPATH}/${db}.db
@@ -108,17 +116,13 @@ function copydb() {
   num_tables=0
 
   entities_on_ocean=`hive -e "show tables in ${db};" | sed 's/WARN:.*//g'`  # Get the tables and views without any potential the "WARN" logs.
-  for i in ${entities_on_ocean[@]}; do # Use un-quoted values, as the elemetns are single-words.
+  for i in ${entities_on_ocean[@]}; do # Use un-quoted values, as the elements are single-words.
     # Check if this is a view by showing the create-statement where it should print "create view" for a view, not the "create table". Unfortunately, there is no "show views" command.
-    create_entity_statement=`hive -e "show create table ${db}.${i};"` # It needs to happen in two stages, otherwise the "grep" is not able to match multi-line statement.
+    create_entity_statement=`hive --database ${db} -e "show create table ${i};"`  # We need to use the "--database", instead of including it inside the query, in order to return the statements with the '`' chars being in the right place to be used by impala-shell. However, we need to add the db-name in the "CREATE VIEW view_name" statement.
-
+    create_view_statement_test=`echo -e "$create_entity_statement" | grep 'CREATE VIEW'`  # It needs to happen in two stages, otherwise the "grep" is not able to match multi-line statement.
-    create_view_statement_test=`echo -e "$create_entity_statement" | grep 'CREATE VIEW'`
     if [ -n "$create_view_statement_test" ]; then
       echo -e "\n'${i}' is a view, so we will save its 'create view' statement and execute it on Impala, after all tables have been created.\n"
-      create_view_statement=`echo -e "$create_entity_statement" | sed 's/WARN:.*//g' | sed 's/\`//g' \
+      create_view_statement=`echo -e "$create_entity_statement" | sed 's/WARN:.*//g' | sed 's/"$/;/' | sed 's/^"//' | sed 's/\\"\\"/\"/g' | sed -e "${LOCATION_HDFS_NODE_SED_ARG}" | sed "s/CREATE VIEW /CREATE VIEW ${db}./"`
-        | sed 's/"$/;/' | sed 's/^"//' | sed 's/\\"\\"/\"/g' | sed -e "${LOCATION_HDFS_NODE_SED_ARG}" | sed "${DATE_SED_ARG_1}" | sed "${HASH_SED_ARG_1}" | sed "${LOCATION_SED_ARG_1}" \
-        | sed "${DATE_SED_ARG_2}" | sed "${HASH_SED_ARG_2}" | sed "${LOCATION_SED_ARG_2}" \
-        | sed "${DATE_SED_ARG_3}" | sed "${HASH_SED_ARG_3}" | sed "${LOCATION_SED_ARG_3}"`
       all_create_view_statements+=("$create_view_statement")
     else
       echo -e "\n'${i}' is a table, so we will check for its parquet files and create the table on Impala cluster.\n"
@@ -126,12 +130,17 @@ function copydb() {
       CURRENT_PRQ_FILE=`hdfs dfs -conf ${IMPALA_CONFIG_FILE} -ls -C "${IMPALA_HDFS_DB_BASE_PATH}/${db}.db/${i}/" | grep -v 'Found' | grep -v '_impala_insert_staging' |  head -1`
       if [ -z "$CURRENT_PRQ_FILE" ]; then # If there is not parquet-file inside.
           echo -e "\nERROR: THE TABLE \"${i}\" HAD NO FILES TO GET THE SCHEMA FROM! IT'S EMPTY!\n\n"
-          exit 4 # Comment out when testing a DB which has such a table, just for performing this exact test-check.
+          if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
+            exit 4
+          fi
       else
         impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create table ${db}.${i} like parquet '${CURRENT_PRQ_FILE}' stored as parquet;" |& tee error.log
         log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
         if [ -n "$log_errors" ]; then
           echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN CREATING TABLE '${i}'!\n\n"
+          if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
+            exit 5
+          fi
         fi
       fi
     fi
@@ -175,7 +184,9 @@ function copydb() {
 
     if [[ $new_num_of_views_to_retry -eq $previous_num_of_views_to_retry ]]; then
       echo -e "\n\nERROR: THE NUMBER OF VIEWS TO RETRY HAS NOT BEEN REDUCED! THE SCRIPT IS LIKELY GOING TO AN INFINITE-LOOP! EXITING..\n\n"
-      exit 5
+      if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
+        exit 6
+      fi
     elif [[ $new_num_of_views_to_retry -gt 0 ]]; then
       echo -e "\nTo be retried \"create_view_statements\" (${new_num_of_views_to_retry}):\n\n${all_create_view_statements[@]}\n"
     else
@@ -203,11 +214,14 @@ function copydb() {
   else
     echo -e "\n\nERROR: 1 OR MORE ENTITIES OF DB '${db}' FAILED TO BE COPIED TO IMPALA CLUSTER!\n\n"
     rm -f error.log
-    exit 6
+    if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
+      exit 7
+    fi
   fi
 
   rm -f error.log
-  echo -e "\n\nFinished processing db: ${db}\n\n"
+  echo -e "\n\nFinished processing db: ${db}\n"
+  print_elapsed_time start_db_time
 }
 
 

dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/copyDataToImpalaCluster.sh

@@ -6,6 +6,8 @@ then
     ln -sfn ${PYTHON_EGG_CACHE}${link_folder} ${link_folder}
 fi
 
+SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR=0
+
 
 # Set the active HDFS node of OCEAN and IMPALA cluster.
 OCEAN_HDFS_NODE='hdfs://nameservice1'
@@ -28,7 +30,9 @@ while [ $COUNTER -lt 3 ]; do
 done
 if [ -z "$IMPALA_HDFS_NODE" ]; then
     echo -e "\n\nERROR: PROBLEM WHEN SETTING THE HDFS-NODE FOR IMPALA CLUSTER! | AFTER ${COUNTER} RETRIES.\n\n"
+    if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
       exit 1
+    fi
 fi
 echo -e "Active IMPALA HDFS Node: ${IMPALA_HDFS_NODE} , after ${COUNTER} retries.\n\n"
 
@@ -40,26 +44,26 @@ IMPALA_HDFS_DB_BASE_PATH="${IMPALA_HDFS_NODE}/user/hive/warehouse"
 # Set sed arguments.
 LOCATION_HDFS_NODE_SED_ARG="s|${OCEAN_HDFS_NODE}|${IMPALA_HDFS_NODE}|g" # This requires to be used with "sed -e" in order to have the "|" delimiter (as the "/" conflicts with the URIs)
 
-# Set the SED command arguments for column-names with reserved words:
-DATE_SED_ARG_1='s/[[:space:]]\date[[:space:]]/\`date\`/g'
-DATE_SED_ARG_2='s/\.date,/\.\`date\`,/g'  # the "date" may be part of a larger field name like "datestamp" or "date_aggregated", so we need to be careful with what we are replacing.
-DATE_SED_ARG_3='s/\.date[[:space:]]/\.\`date\` /g'
-
-HASH_SED_ARG_1='s/[[:space:]]\hash[[:space:]]/\`hash\`/g'
-HASH_SED_ARG_2='s/\.hash,/\.\`hash\`,/g'
-HASH_SED_ARG_3='s/\.hash[[:space:]]/\.\`hash\` /g'
-
-LOCATION_SED_ARG_1='s/[[:space:]]\location[[:space:]]/\`location\`/g'
-LOCATION_SED_ARG_2='s/\.location,/\.\`location\`,/g'
-LOCATION_SED_ARG_3='s/\.location[[:space:]]/\.\`location\` /g'
-
 
 export HADOOP_USER_NAME=$6
 export PROD_USAGE_STATS_DB="openaire_prod_usage_stats"
 
 
+function print_elapsed_time()
+{
+  start_time=$1
+  end_time=$(date +%s)
+  elapsed_time=$(($end_time-$start_time))
+  hours=$((elapsed_time / 3600))
+  minutes=$(((elapsed_time % 3600) / 60))
+  seconds=$((elapsed_time % 60))
+  printf "\nElapsed time: %02d:%02d:%02d\n\n" $hours $minutes $seconds
+}
+
+
 function copydb() {
   db=$1
+  start_db_time=$(date +%s)
   echo -e "\nStart processing db: '${db}'..\n"
 
   # Delete the old DB from Impala cluster (if exists).
@@ -68,8 +72,10 @@ function copydb() {
   if [ -n "$log_errors" ]; then
     echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN DROPPING THE OLD DATABASE! EXITING...\n\n"
     rm -f error.log
+    if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
       exit 2
     fi
+  fi
 
   echo -e "\n\nCopying files of '${db}', from Ocean to Impala cluster..\n"
   # Using max-bandwidth of: 70 * 150 Mb/s = 10.5 Gb/s
@@ -92,8 +98,10 @@ function copydb() {
   else
     echo -e "\n\nERROR: FAILED TO TRANSFER THE FILES OF '${db}', WITH 'hadoop distcp'. GOT EXIT STATUS: $?\n\n"
     rm -f error.log
+    if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
       exit 3
     fi
+  fi
 
   # In case we ever use this script for a writable DB (using inserts/updates), we should perform the following costly operation as well..
   #hdfs dfs -conf ${IMPALA_CONFIG_FILE} -chmod -R 777 ${TEMP_SUBDIR_FULLPATH}/${db}.db
@@ -110,17 +118,13 @@ function copydb() {
   num_tables=0
 
   entities_on_ocean=`hive -e "show tables in ${db};" | sed 's/WARN:.*//g'`  # Get the tables and views without any potential the "WARN" logs.
-  for i in ${entities_on_ocean[@]}; do # Use un-quoted values, as the elemetns are single-words.
+  for i in ${entities_on_ocean[@]}; do # Use un-quoted values, as the elements are single-words.
     # Check if this is a view by showing the create-statement where it should print "create view" for a view, not the "create table". Unfortunately, there is no "show views" command.
-    create_entity_statement=`hive -e "show create table ${db}.${i};"` # It needs to happen in two stages, otherwise the "grep" is not able to match multi-line statement.
+    create_entity_statement=`hive --database ${db} -e "show create table ${i};"`  # We need to use the "--database", instead of including it inside the query, in order to return the statements with the '`' chars being in the right place to be used by impala-shell. However, we need to add the db-name in the "CREATE VIEW view_name" statement.
-
+    create_view_statement_test=`echo -e "$create_entity_statement" | grep 'CREATE VIEW'`  # It needs to happen in two stages, otherwise the "grep" is not able to match multi-line statement.
-    create_view_statement_test=`echo -e "$create_entity_statement" | grep 'CREATE VIEW'`
     if [ -n "$create_view_statement_test" ]; then
       echo -e "\n'${i}' is a view, so we will save its 'create view' statement and execute it on Impala, after all tables have been created.\n"
-      create_view_statement=`echo -e "$create_entity_statement" | sed 's/WARN:.*//g' | sed 's/\`//g' \
+      create_view_statement=`echo -e "$create_entity_statement" | sed 's/WARN:.*//g' | sed 's/"$/;/' | sed 's/^"//' | sed 's/\\"\\"/\"/g' | sed -e "${LOCATION_HDFS_NODE_SED_ARG}" | sed "s/CREATE VIEW /CREATE VIEW ${db}./"`
-        | sed 's/"$/;/' | sed 's/^"//' | sed 's/\\"\\"/\"/g' | sed -e "${LOCATION_HDFS_NODE_SED_ARG}" | sed "${DATE_SED_ARG_1}" | sed "${HASH_SED_ARG_1}" | sed "${LOCATION_SED_ARG_1}" \
-        | sed "${DATE_SED_ARG_2}" | sed "${HASH_SED_ARG_2}" | sed "${LOCATION_SED_ARG_2}" \
-        | sed "${DATE_SED_ARG_3}" | sed "${HASH_SED_ARG_3}" | sed "${LOCATION_SED_ARG_3}"`
       all_create_view_statements+=("$create_view_statement")
     else
       echo -e "\n'${i}' is a table, so we will check for its parquet files and create the table on Impala cluster.\n"
@@ -128,12 +132,17 @@ function copydb() {
       CURRENT_PRQ_FILE=`hdfs dfs -conf ${IMPALA_CONFIG_FILE} -ls -C "${IMPALA_HDFS_DB_BASE_PATH}/${db}.db/${i}/" | grep -v 'Found' | grep -v '_impala_insert_staging' |  head -1`
       if [ -z "$CURRENT_PRQ_FILE" ]; then # If there is not parquet-file inside.
           echo -e "\nERROR: THE TABLE \"${i}\" HAD NO FILES TO GET THE SCHEMA FROM! IT'S EMPTY!\n\n"
-          exit 4 # Comment out when testing a DB which has such a table, just for performing this exact test-check.
+          if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
+            exit 4
+          fi
       else
         impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create table ${db}.${i} like parquet '${CURRENT_PRQ_FILE}' stored as parquet;" |& tee error.log
         log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
         if [ -n "$log_errors" ]; then
           echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN CREATING TABLE '${i}'!\n\n"
+          if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
+            exit 5
+          fi
         fi
       fi
     fi
@@ -177,7 +186,9 @@ function copydb() {
 
     if [[ $new_num_of_views_to_retry -eq $previous_num_of_views_to_retry ]]; then
       echo -e "\n\nERROR: THE NUMBER OF VIEWS TO RETRY HAS NOT BEEN REDUCED! THE SCRIPT IS LIKELY GOING TO AN INFINITE-LOOP! EXITING..\n\n"
-      exit 5
+      if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
+        exit 6
+      fi
     elif [[ $new_num_of_views_to_retry -gt 0 ]]; then
       echo -e "\nTo be retried \"create_view_statements\" (${new_num_of_views_to_retry}):\n\n${all_create_view_statements[@]}\n"
     else
@@ -205,11 +216,14 @@ function copydb() {
   else
     echo -e "\n\nERROR: 1 OR MORE ENTITIES OF DB '${db}' FAILED TO BE COPIED TO IMPALA CLUSTER!\n\n"
     rm -f error.log
-    exit 6
+    if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
+      exit 7
+    fi
   fi
 
   rm -f error.log
-  echo -e "\n\nFinished processing db: ${db}\n\n"
+  echo -e "\n\nFinished processing db: ${db}\n"
+  print_elapsed_time start_db_time
 }
 
 STATS_DB=$1

dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql

@@ -129,11 +129,14 @@ create table ${stats_db_name}.result_fos stored as parquet as
 with
     lvl1 as (select id, topic from ${stats_db_name}.result_topics where topic like '__ %' and type='Fields of Science and Technology classification'),
     lvl2 as (select id, topic from ${stats_db_name}.result_topics where topic like '____ %' and type='Fields of Science and Technology classification'),
-    lvl3 as (select id, topic from ${stats_db_name}.result_topics where topic like '______ %' and type='Fields of Science and Technology classification')
+    lvl3 as (select id, topic from ${stats_db_name}.result_topics where topic like '______ %' and type='Fields of Science and Technology classification'),
-select lvl1.id, lvl1.topic as lvl1, lvl2.topic as lvl2, lvl3.topic as lvl3
+    lvl4 as (select id, topic from ${stats_db_name}.result_topics where topic like '________ %' and type='Fields of Science and Technology classification')
+select lvl1.id, lvl1.topic as lvl1, lvl2.topic as lvl2, lvl3.topic as lvl3, lvl4.topic as lvl4
 from lvl1
  join lvl2 on lvl1.id=lvl2.id and substr(lvl2.topic, 1, 2)=substr(lvl1.topic, 1, 2)
- join lvl3 on lvl3.id=lvl1.id and substr(lvl3.topic, 1, 4)=substr(lvl2.topic, 1, 4);
+ join lvl3 on lvl3.id=lvl1.id and substr(lvl3.topic, 1, 4)=substr(lvl2.topic, 1, 4)
+ join lvl4 on lvl4.id=lvl1.id and substr(lvl4.topic, 1, 6)=substr(lvl3.topic, 1, 6);
+
 
 DROP TABLE IF EXISTS ${stats_db_name}.result_organization purge;