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Miscellaneous updates to the copying operation to Impala Cluster: 

- Fix not breaking out of the VIEWS-infinite-loop when the "SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR" is set to "false".
- Exit the script when no HDFS-active-node was found, independently of the "SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR".
- Fix view_name-recognition in a log-message, by using the more advanced "Perl-Compatible Regular Expressions" in "grep".
- Add error-handling for "compute stats" errors.
This commit is contained in:
Lampros Smyrnaios 2024-06-18 14:40:41 +03:00 committed by Claudio Atzori
parent c67ef157d3
commit 3c9b8de892
4 changed files with 64 additions and 32 deletions
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24
dhp-workflows/dhp-stats-hist-snaps/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-hist-snaps/oozie_app/copyDataToImpalaCluster.sh
View File

@ -32,9 +32,7 @@ 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
exit 1 # This is fatal and we have to exit independently of the "SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR" config, as none of the DBs will be able to get transferred.
fi
echo -e "Active IMPALA HDFS Node: ${IMPALA_HDFS_NODE} , after ${COUNTER} retries.\n\n"
@ -148,7 +146,7 @@ function copydb() {
echo -e "\nERROR: THE TABLE \"${i}\" HAD NO FILES TO GET THE SCHEMA FROM! IT'S EMPTY!\n\n"
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 5
fi
fi # This error is not FATAL, do we do not return from this function, in normal circumstances.
else
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create table ${db}.${i} like parquet '${CURRENT_PRQ_FILE}' stored as parquet;" |& tee error.log
log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
@ -188,7 +186,7 @@ function copydb() {
specific_errors=`cat error.log | grep -E "FAILED: ParseException line 1:13 missing TABLE at 'view'|ERROR: AnalysisException: Could not resolve table reference:"`
if [ -n "$specific_errors" ]; then
echo -e "\nspecific_errors: ${specific_errors}\n"
echo -e "\nView '$(cat error.log | grep -Eo "Query: CREATE VIEW ([^\s]+)" | sed 's/Query: CREATE VIEW //g')' failed to be created, possibly because it depends on another view.\n"
echo -e "\nView '$(cat error.log | grep -Po "Query: CREATE VIEW ([^\s]+)" | sed 's/Query: CREATE VIEW //g')' failed to be created, possibly because it depends on another view.\n"
((new_num_of_views_to_retry++)) # Increment it here, instead of acquiring the array's size in the end, as that doesn't work for some reason.
else
all_create_view_statements=("${all_create_view_statements[@]/$create_view_statement}") # Remove the current successful statement from the list.
@ -200,9 +198,11 @@ function copydb() {
# Although the above command reduces the "active" elements to just the few to-be-retried, it does not manage to make the array return the its true size through the "${#all_create_view_statements[@]}" statement. So we use counters.
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"
echo -e "\n\nERROR: THE NUMBER OF VIEWS TO RETRY HAS NOT BEEN REDUCED! THE SCRIPT IS LIKELY GOING TO AN INFINITE-LOOP! BREAKING-OUT..\n\n"
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 7
else
break # Break form the inf-loop of views and continue by computing stats for the tables.
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"
@ -224,7 +224,15 @@ function copydb() {
# Invalidate metadata of this DB's tables, in order for Impala to be aware of all parquet files put inside the tables' directories, previously, by "hadoop distcp".
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA ${db}.${i}"
sleep 1
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "compute stats ${db}.${i}";
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "compute stats ${db}.${i}" |& tee error.log
log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
if [ -n "$log_errors" ]; then
echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN COMPUTING STATS FOR TABLE '${i}'!\n\n"
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
rm -f error.log
exit 8
fi # This error is not FATAL, do we do not return from this function, in normal circumstances.
fi
fi
done
@ -237,7 +245,7 @@ function copydb() {
else
echo -e "\n\nERROR: $((${#entities_on_ocean[@]} - ${#entities_on_impala[@]})) ENTITIES OF DB '${db}' FAILED TO BE COPIED TO IMPALA CLUSTER!\n\n\nFinished processing db: '${db}', after: $(print_elapsed_time start_db_time)\n"
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 8
exit 9
fi
fi
}

24
dhp-workflows/dhp-stats-monitor-irish/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor-irish/oozie_app/copyDataToImpalaCluster.sh
View File

@ -32,9 +32,7 @@ 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
exit 1 # This is fatal and we have to exit independently of the "SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR" config, as none of the DBs will be able to get transferred.
fi
echo -e "Active IMPALA HDFS Node: ${IMPALA_HDFS_NODE} , after ${COUNTER} retries.\n\n"
@ -148,7 +146,7 @@ function copydb() {
echo -e "\nERROR: THE TABLE \"${i}\" HAD NO FILES TO GET THE SCHEMA FROM! IT'S EMPTY!\n\n"
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 5
fi
fi # This error is not FATAL, do we do not return from this function, in normal circumstances.
else
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create table ${db}.${i} like parquet '${CURRENT_PRQ_FILE}' stored as parquet;" |& tee error.log
log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
@ -188,7 +186,7 @@ function copydb() {
specific_errors=`cat error.log | grep -E "FAILED: ParseException line 1:13 missing TABLE at 'view'|ERROR: AnalysisException: Could not resolve table reference:"`
if [ -n "$specific_errors" ]; then
echo -e "\nspecific_errors: ${specific_errors}\n"
echo -e "\nView '$(cat error.log | grep -Eo "Query: CREATE VIEW ([^\s]+)" | sed 's/Query: CREATE VIEW //g')' failed to be created, possibly because it depends on another view.\n"
echo -e "\nView '$(cat error.log | grep -Po "Query: CREATE VIEW ([^\s]+)" | sed 's/Query: CREATE VIEW //g')' failed to be created, possibly because it depends on another view.\n"
((new_num_of_views_to_retry++)) # Increment it here, instead of acquiring the array's size in the end, as that doesn't work for some reason.
else
all_create_view_statements=("${all_create_view_statements[@]/$create_view_statement}") # Remove the current successful statement from the list.
@ -200,9 +198,11 @@ function copydb() {
# Although the above command reduces the "active" elements to just the few to-be-retried, it does not manage to make the array return the its true size through the "${#all_create_view_statements[@]}" statement. So we use counters.
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"
echo -e "\n\nERROR: THE NUMBER OF VIEWS TO RETRY HAS NOT BEEN REDUCED! THE SCRIPT IS LIKELY GOING TO AN INFINITE-LOOP! BREAKING-OUT..\n\n"
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 7
else
break # Break form the inf-loop of views and continue by computing stats for the tables.
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"
@ -224,7 +224,15 @@ function copydb() {
# Invalidate metadata of this DB's tables, in order for Impala to be aware of all parquet files put inside the tables' directories, previously, by "hadoop distcp".
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA ${db}.${i}"
sleep 1
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "compute stats ${db}.${i}";
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "compute stats ${db}.${i}" |& tee error.log
log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
if [ -n "$log_errors" ]; then
echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN COMPUTING STATS FOR TABLE '${i}'!\n\n"
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
rm -f error.log
exit 8
fi # This error is not FATAL, do we do not return from this function, in normal circumstances.
fi
fi
done
@ -237,7 +245,7 @@ function copydb() {
else
echo -e "\n\nERROR: $((${#entities_on_ocean[@]} - ${#entities_on_impala[@]})) ENTITIES OF DB '${db}' FAILED TO BE COPIED TO IMPALA CLUSTER!\n\n\nFinished processing db: '${db}', after: $(print_elapsed_time start_db_time)\n"
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 8
exit 9
fi
fi
}

24
dhp-workflows/dhp-stats-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor/oozie_app/copyDataToImpalaCluster.sh
View File

@ -32,9 +32,7 @@ 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
exit 1 # This is fatal and we have to exit independently of the "SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR" config, as none of the DBs will be able to get transferred.
fi
echo -e "Active IMPALA HDFS Node: ${IMPALA_HDFS_NODE} , after ${COUNTER} retries.\n\n"
@ -148,7 +146,7 @@ function copydb() {
echo -e "\nERROR: THE TABLE \"${i}\" HAD NO FILES TO GET THE SCHEMA FROM! IT'S EMPTY!\n\n"
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 5
fi
fi # This error is not FATAL, do we do not return from this function, in normal circumstances.
else
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create table ${db}.${i} like parquet '${CURRENT_PRQ_FILE}' stored as parquet;" |& tee error.log
log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
@ -188,7 +186,7 @@ function copydb() {
specific_errors=`cat error.log | grep -E "FAILED: ParseException line 1:13 missing TABLE at 'view'|ERROR: AnalysisException: Could not resolve table reference:"`
if [ -n "$specific_errors" ]; then
echo -e "\nspecific_errors: ${specific_errors}\n"
echo -e "\nView '$(cat error.log | grep -Eo "Query: CREATE VIEW ([^\s]+)" | sed 's/Query: CREATE VIEW //g')' failed to be created, possibly because it depends on another view.\n"
echo -e "\nView '$(cat error.log | grep -Po "Query: CREATE VIEW ([^\s]+)" | sed 's/Query: CREATE VIEW //g')' failed to be created, possibly because it depends on another view.\n"
((new_num_of_views_to_retry++)) # Increment it here, instead of acquiring the array's size in the end, as that doesn't work for some reason.
else
all_create_view_statements=("${all_create_view_statements[@]/$create_view_statement}") # Remove the current successful statement from the list.
@ -200,9 +198,11 @@ function copydb() {
# Although the above command reduces the "active" elements to just the few to-be-retried, it does not manage to make the array return the its true size through the "${#all_create_view_statements[@]}" statement. So we use counters.
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"
echo -e "\n\nERROR: THE NUMBER OF VIEWS TO RETRY HAS NOT BEEN REDUCED! THE SCRIPT IS LIKELY GOING TO AN INFINITE-LOOP! BREAKING-OUT..\n\n"
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 7
else
break # Break form the inf-loop of views and continue by computing stats for the tables.
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"
@ -224,7 +224,15 @@ function copydb() {
# Invalidate metadata of this DB's tables, in order for Impala to be aware of all parquet files put inside the tables' directories, previously, by "hadoop distcp".
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA ${db}.${i}"
sleep 1
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "compute stats ${db}.${i}";
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "compute stats ${db}.${i}" |& tee error.log
log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
if [ -n "$log_errors" ]; then
echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN COMPUTING STATS FOR TABLE '${i}'!\n\n"
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
rm -f error.log
exit 8
fi # This error is not FATAL, do we do not return from this function, in normal circumstances.
fi
fi
done
@ -237,7 +245,7 @@ function copydb() {
else
echo -e "\n\nERROR: $((${#entities_on_ocean[@]} - ${#entities_on_impala[@]})) ENTITIES OF DB '${db}' FAILED TO BE COPIED TO IMPALA CLUSTER!\n\n\nFinished processing db: '${db}', after: $(print_elapsed_time start_db_time)\n"
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 8
exit 9
fi
fi
}

24
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/copyDataToImpalaCluster.sh
View File

@ -30,9 +30,7 @@ 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
exit 1 # This is fatal and we have to exit independently of the "SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR" config, as none of the DBs will be able to get transferred.
fi
echo -e "Active IMPALA HDFS Node: ${IMPALA_HDFS_NODE} , after ${COUNTER} retries.\n\n"
@ -150,7 +148,7 @@ function copydb() {
echo -e "\nERROR: THE TABLE \"${i}\" HAD NO FILES TO GET THE SCHEMA FROM! IT'S EMPTY!\n\n"
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 5
fi
fi # This error is not FATAL, do we do not return from this function, in normal circumstances.
else
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create table ${db}.${i} like parquet '${CURRENT_PRQ_FILE}' stored as parquet;" |& tee error.log
log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
@ -190,7 +188,7 @@ function copydb() {
specific_errors=`cat error.log | grep -E "FAILED: ParseException line 1:13 missing TABLE at 'view'|ERROR: AnalysisException: Could not resolve table reference:"`
if [ -n "$specific_errors" ]; then
echo -e "\nspecific_errors: ${specific_errors}\n"
echo -e "\nView '$(cat error.log | grep -Eo "Query: CREATE VIEW ([^\s]+)" | sed 's/Query: CREATE VIEW //g')' failed to be created, possibly because it depends on another view.\n"
echo -e "\nView '$(cat error.log | grep -Po "Query: CREATE VIEW ([^\s]+)" | sed 's/Query: CREATE VIEW //g')' failed to be created, possibly because it depends on another view.\n"
((new_num_of_views_to_retry++)) # Increment it here, instead of acquiring the array's size in the end, as that doesn't work for some reason.
else
all_create_view_statements=("${all_create_view_statements[@]/$create_view_statement}") # Remove the current successful statement from the list.
@ -202,9 +200,11 @@ function copydb() {
# Although the above command reduces the "active" elements to just the few to-be-retried, it does not manage to make the array return the its true size through the "${#all_create_view_statements[@]}" statement. So we use counters.
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"
echo -e "\n\nERROR: THE NUMBER OF VIEWS TO RETRY HAS NOT BEEN REDUCED! THE SCRIPT IS LIKELY GOING TO AN INFINITE-LOOP! BREAKING-OUT..\n\n"
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 7
else
break # Break form the inf-loop of views and continue by computing stats for the tables.
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"
@ -226,7 +226,15 @@ function copydb() {
# Invalidate metadata of this DB's tables, in order for Impala to be aware of all parquet files put inside the tables' directories, previously, by "hadoop distcp".
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA ${db}.${i}"
sleep 1
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "compute stats ${db}.${i}";
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "compute stats ${db}.${i}" |& tee error.log
log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
if [ -n "$log_errors" ]; then
echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN COMPUTING STATS FOR TABLE '${i}'!\n\n"
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
rm -f error.log
exit 8
fi # This error is not FATAL, do we do not return from this function, in normal circumstances.
fi
fi
done
@ -239,7 +247,7 @@ function copydb() {
else
echo -e "\n\nERROR: $((${#entities_on_ocean[@]} - ${#entities_on_impala[@]})) ENTITIES OF DB '${db}' FAILED TO BE COPIED TO IMPALA CLUSTER!\n\n\nFinished processing db: '${db}', after: $(print_elapsed_time start_db_time)\n"
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 8
exit 9
fi
fi
}