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Merge branch 'beta' into rest-collector-request-header-map

This commit is contained in:
Alessia Bardi 2024-05-29 15:46:23 +02:00
parent 1b165a14a0 e996787be2
commit c5f4da16a4
7 changed files with 110 additions and 45 deletions
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19
dhp-common/pom.xml
View File

@ -169,4 +169,23 @@
</dependency>
</dependencies>
<!-- dependencies required on JDK9+ because J2EE has been removed -->
<profiles>
<profile>
<id>spark-34</id>
<dependencies>
<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
<version>2.2.11</version>
</dependency>
<dependency>
<groupId>com.sun.xml.ws</groupId>
<artifactId>jaxws-ri</artifactId>
<version>2.3.3</version>
<type>pom</type>
</dependency>
</dependencies>
</profile>
</profiles>
</project>

6
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/crossref/irish_funder.json
View File

@ -625,12 +625,6 @@
"name": "Alimentary Health",
"synonym": []
},
{
"id": "501100011103",
"uri": "http://dx.doi.org/10.13039/501100011103",
"name": "Rann\u00eds",
"synonym": []
},
{
"id": "501100012354",
"uri": "http://dx.doi.org/10.13039/501100012354",

6
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/rest/OsfPreprintCollectorTest.java
View File

@ -39,8 +39,8 @@ public class OsfPreprintCollectorTest {
private final String resumptionType = "page";
private final String resumptionXpath = "/*/*[local-name()='links']/*[local-name()='next']";
private final String resultSizeParam = "";
private final String resultSizeValue = "";
private final String resultSizeParam = "page[size]";
private final String resultSizeValue = "100";
private final String resultFormatParam = "format";
private final String resultFormatValue = "json";
@ -74,7 +74,7 @@ public class OsfPreprintCollectorTest {
final AtomicInteger i = new AtomicInteger(0);
final Stream<String> stream = this.rcp.collect(this.api, new AggregatorReport());
stream.limit(200).forEach(s -> {
stream.limit(2000).forEach(s -> {
Assertions.assertTrue(s.length() > 0);
i.incrementAndGet();
log.info(s);

31
dhp-workflows/dhp-stats-hist-snaps/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-hist-snaps/oozie_app/copyDataToImpalaCluster.sh
View File

@ -72,6 +72,8 @@ function copydb() {
rm -f error.log
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 2
else
return 2
fi
fi
@ -90,19 +92,30 @@ function copydb() {
-pb \
${OCEAN_HDFS_NODE}/user/hive/warehouse/${db}.db ${IMPALA_HDFS_DB_BASE_PATH}
# Check the exit status of the "hadoop distcp" command.
if [ $? -eq 0 ]; then
echo -e "\nSuccessfully copied the files of '${db}'.\n"
if [ $? -eq 0 ]; then # Check the exit status of the "hadoop distcp" command.
echo -e "\nSuccessfully copied the files of '${db}' from Ocean to Impala cluster.\n"
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
else
return 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
# Give WRITE and EXECUTE permissions to the DBs' directory only, in order to be able to create more tables later, on top of that DB.
hdfs dfs -conf ${IMPALA_CONFIG_FILE} -chmod u+wx ${IMPALA_HDFS_DB_BASE_PATH}/${db}.db
# In case we ever use this script for a writable DB (using inserts/updates), we should perform the costly recursive operation as well, using the "-R" param.
if [ $? -ne 0 ]; then # Check the exit status..
echo -e "\n\nERROR: FAILED TO ASSIGN WRITE AND EXECUTE PERMISSIONS TO THE DIRECTORY OF DB: '${db}'. GOT EXIT STATUS: $?\n\n"
rm -f error.log
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 4
else
return 4
fi
fi
echo -e "\nCreating schema for db: '${db}'\n"
@ -131,7 +144,7 @@ function copydb() {
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"
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 4
exit 5
fi
else
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create table ${db}.${i} like parquet '${CURRENT_PRQ_FILE}' stored as parquet;" |& tee error.log
@ -139,7 +152,7 @@ function copydb() {
if [ -n "$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
exit 6
fi
fi
fi
@ -185,7 +198,7 @@ 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"
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 6
exit 7
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${all_create_view_statements[@]}\n"
@ -215,7 +228,7 @@ function copydb() {
echo -e "\n\nERROR: 1 OR MORE ENTITIES OF DB '${db}' FAILED TO BE COPIED TO IMPALA CLUSTER!\n\n"
rm -f error.log
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 7
exit 8
fi
fi

31
dhp-workflows/dhp-stats-monitor-irish/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor-irish/oozie_app/copyDataToImpalaCluster.sh
View File

@ -72,6 +72,8 @@ function copydb() {
rm -f error.log
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 2
else
return 2
fi
fi
@ -90,19 +92,30 @@ function copydb() {
-pb \
${OCEAN_HDFS_NODE}/user/hive/warehouse/${db}.db ${IMPALA_HDFS_DB_BASE_PATH}
# Check the exit status of the "hadoop distcp" command.
if [ $? -eq 0 ]; then
echo -e "\nSuccessfully copied the files of '${db}'.\n"
if [ $? -eq 0 ]; then # Check the exit status of the "hadoop distcp" command.
echo -e "\nSuccessfully copied the files of '${db}' from Ocean to Impala cluster.\n"
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
else
return 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
# Give WRITE and EXECUTE permissions to the DBs' directory only, in order to be able to create more tables later, on top of that DB.
hdfs dfs -conf ${IMPALA_CONFIG_FILE} -chmod u+wx ${IMPALA_HDFS_DB_BASE_PATH}/${db}.db
# In case we ever use this script for a writable DB (using inserts/updates), we should perform the costly recursive operation as well, using the "-R" param.
if [ $? -ne 0 ]; then # Check the exit status..
echo -e "\n\nERROR: FAILED TO ASSIGN WRITE AND EXECUTE PERMISSIONS TO THE DIRECTORY OF DB: '${db}'. GOT EXIT STATUS: $?\n\n"
rm -f error.log
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 4
else
return 4
fi
fi
echo -e "\nCreating schema for db: '${db}'\n"
@ -131,7 +144,7 @@ function copydb() {
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"
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 4
exit 5
fi
else
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create table ${db}.${i} like parquet '${CURRENT_PRQ_FILE}' stored as parquet;" |& tee error.log
@ -139,7 +152,7 @@ function copydb() {
if [ -n "$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
exit 6
fi
fi
fi
@ -185,7 +198,7 @@ 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"
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 6
exit 7
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${all_create_view_statements[@]}\n"
@ -215,7 +228,7 @@ function copydb() {
echo -e "\n\nERROR: 1 OR MORE ENTITIES OF DB '${db}' FAILED TO BE COPIED TO IMPALA CLUSTER!\n\n"
rm -f error.log
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 7
exit 8
fi
fi

31
dhp-workflows/dhp-stats-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor/oozie_app/copyDataToImpalaCluster.sh
View File

@ -72,6 +72,8 @@ function copydb() {
rm -f error.log
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 2
else
return 2
fi
fi
@ -90,19 +92,30 @@ function copydb() {
-pb \
${OCEAN_HDFS_NODE}/user/hive/warehouse/${db}.db ${IMPALA_HDFS_DB_BASE_PATH}
# Check the exit status of the "hadoop distcp" command.
if [ $? -eq 0 ]; then
echo -e "\nSuccessfully copied the files of '${db}'.\n"
if [ $? -eq 0 ]; then # Check the exit status of the "hadoop distcp" command.
echo -e "\nSuccessfully copied the files of '${db}' from Ocean to Impala cluster.\n"
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
else
return 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
# Give WRITE and EXECUTE permissions to the DBs' directory only, in order to be able to create more tables later, on top of that DB.
hdfs dfs -conf ${IMPALA_CONFIG_FILE} -chmod u+wx ${IMPALA_HDFS_DB_BASE_PATH}/${db}.db
# In case we ever use this script for a writable DB (using inserts/updates), we should perform the costly recursive operation as well, using the "-R" param.
if [ $? -ne 0 ]; then # Check the exit status..
echo -e "\n\nERROR: FAILED TO ASSIGN WRITE AND EXECUTE PERMISSIONS TO THE DIRECTORY OF DB: '${db}'. GOT EXIT STATUS: $?\n\n"
rm -f error.log
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 4
else
return 4
fi
fi
echo -e "\nCreating schema for db: '${db}'\n"
@ -131,7 +144,7 @@ function copydb() {
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"
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 4
exit 5
fi
else
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create table ${db}.${i} like parquet '${CURRENT_PRQ_FILE}' stored as parquet;" |& tee error.log
@ -139,7 +152,7 @@ function copydb() {
if [ -n "$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
exit 6
fi
fi
fi
@ -185,7 +198,7 @@ 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"
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 6
exit 7
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${all_create_view_statements[@]}\n"
@ -215,7 +228,7 @@ function copydb() {
echo -e "\n\nERROR: 1 OR MORE ENTITIES OF DB '${db}' FAILED TO BE COPIED TO IMPALA CLUSTER!\n\n"
rm -f error.log
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 7
exit 8
fi
fi

31
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/copyDataToImpalaCluster.sh
View File

@ -74,6 +74,8 @@ function copydb() {
rm -f error.log
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 2
else
return 2
fi
fi
@ -92,19 +94,30 @@ function copydb() {
-pb \
${OCEAN_HDFS_NODE}/user/hive/warehouse/${db}.db ${IMPALA_HDFS_DB_BASE_PATH}
# Check the exit status of the "hadoop distcp" command.
if [ $? -eq 0 ]; then
echo -e "\nSuccessfully copied the files of '${db}'.\n"
if [ $? -eq 0 ]; then # Check the exit status of the "hadoop distcp" command.
echo -e "\nSuccessfully copied the files of '${db}' from Ocean to Impala cluster.\n"
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
else
return 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
# Give WRITE and EXECUTE permissions to the DBs' directory only, in order to be able to create more tables later, on top of that DB.
hdfs dfs -conf ${IMPALA_CONFIG_FILE} -chmod u+wx ${IMPALA_HDFS_DB_BASE_PATH}/${db}.db
# In case we ever use this script for a writable DB (using inserts/updates), we should perform the costly recursive operation as well, using the "-R" param.
if [ $? -ne 0 ]; then # Check the exit status..
echo -e "\n\nERROR: FAILED TO ASSIGN WRITE AND EXECUTE PERMISSIONS TO THE DIRECTORY OF DB: '${db}'. GOT EXIT STATUS: $?\n\n"
rm -f error.log
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 4
else
return 4
fi
fi
echo -e "\nCreating schema for db: '${db}'\n"
@ -133,7 +146,7 @@ function copydb() {
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"
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 4
exit 5
fi
else
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create table ${db}.${i} like parquet '${CURRENT_PRQ_FILE}' stored as parquet;" |& tee error.log
@ -141,7 +154,7 @@ function copydb() {
if [ -n "$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
exit 6
fi
fi
fi
@ -187,7 +200,7 @@ 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"
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 6
exit 7
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${all_create_view_statements[@]}\n"
@ -217,7 +230,7 @@ function copydb() {
echo -e "\n\nERROR: 1 OR MORE ENTITIES OF DB '${db}' FAILED TO BE COPIED TO IMPALA CLUSTER!\n\n"
rm -f error.log
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 7
exit 8
fi
fi