forked from D-Net/dnet-hadoop
Merge branch 'master' of code-repo.d4science.org:D-Net/dnet-hadoop
This commit is contained in:
commit
4752d60421
|
|
@ -1048,5 +1048,10 @@
|
|||
"openaire_id": "re3data_____::r3d100010399",
|
||||
"datacite_name": "ZEW Forschungsdatenzentrum",
|
||||
"official_name": "ZEW Forschungsdatenzentrum"
|
||||
},
|
||||
"HBP.NEUROINF": {
|
||||
"openaire_id": "fairsharing_::2975",
|
||||
"datacite_name": "EBRAINS",
|
||||
"official_name": "EBRAINS"
|
||||
}
|
||||
}
|
||||
|
|
@ -15,4 +15,12 @@
|
|||
<name>oozie.action.sharelib.for.spark</name>
|
||||
<value>spark2</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>hiveMetastoreUris</name>
|
||||
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>pivotHistoryDatabase</name>
|
||||
<value>​</value>
|
||||
</property>
|
||||
</configuration>
|
||||
|
|
@ -198,6 +198,8 @@
|
|||
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
|
||||
<arg>--actionSetId</arg><arg>${actionSetId}</arg>
|
||||
<arg>--cutConnectedComponent</arg><arg>${cutConnectedComponent}</arg>
|
||||
<arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
|
||||
<arg>--pivotHistoryDatabase</arg><arg>${pivotHistoryDatabase}</arg>
|
||||
</spark>
|
||||
<ok to="PrepareOrgRels"/>
|
||||
<error to="Kill"/>
|
||||
|
|
|
|||
|
|
@ -73,12 +73,6 @@
|
|||
"name": "Irish Nephrology Society",
|
||||
"synonym": []
|
||||
},
|
||||
{
|
||||
"id": "100011062",
|
||||
"uri": "http://dx.doi.org/10.13039/100011062",
|
||||
"name": "Asian Spinal Cord Network",
|
||||
"synonym": []
|
||||
},
|
||||
{
|
||||
"id": "100011096",
|
||||
"uri": "http://dx.doi.org/10.13039/100011096",
|
||||
|
|
@ -223,12 +217,6 @@
|
|||
"name": "Global Brain Health Institute",
|
||||
"synonym": []
|
||||
},
|
||||
{
|
||||
"id": "100015776",
|
||||
"uri": "http://dx.doi.org/10.13039/100015776",
|
||||
"name": "Health and Social Care Board",
|
||||
"synonym": []
|
||||
},
|
||||
{
|
||||
"id": "100015992",
|
||||
"uri": "http://dx.doi.org/10.13039/100015992",
|
||||
|
|
@ -403,18 +391,6 @@
|
|||
"name": "Irish Hospice Foundation",
|
||||
"synonym": []
|
||||
},
|
||||
{
|
||||
"id": "501100001596",
|
||||
"uri": "http://dx.doi.org/10.13039/501100001596",
|
||||
"name": "Irish Research Council for Science, Engineering and Technology",
|
||||
"synonym": []
|
||||
},
|
||||
{
|
||||
"id": "501100001597",
|
||||
"uri": "http://dx.doi.org/10.13039/501100001597",
|
||||
"name": "Irish Research Council for the Humanities and Social Sciences",
|
||||
"synonym": []
|
||||
},
|
||||
{
|
||||
"id": "501100001598",
|
||||
"uri": "http://dx.doi.org/10.13039/501100001598",
|
||||
|
|
@ -515,7 +491,7 @@
|
|||
"id": "501100002081",
|
||||
"uri": "http://dx.doi.org/10.13039/501100002081",
|
||||
"name": "Irish Research Council",
|
||||
"synonym": []
|
||||
"synonym": ["501100001596", "501100001597"]
|
||||
},
|
||||
{
|
||||
"id": "501100002736",
|
||||
|
|
|
|||
|
|
@ -587,7 +587,15 @@ case object Crossref2Oaf {
|
|||
"10.13039/501100000266" | "10.13039/501100006041" | "10.13039/501100000265" | "10.13039/501100000270" |
|
||||
"10.13039/501100013589" | "10.13039/501100000271" =>
|
||||
generateSimpleRelationFromAward(funder, "ukri________", a => a)
|
||||
|
||||
//HFRI
|
||||
case "10.13039/501100013209" =>
|
||||
generateSimpleRelationFromAward(funder, "hfri________", a => a)
|
||||
val targetId = getProjectId("hfri________", "1e5e62235d094afd01cd56e65112fc63")
|
||||
queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)
|
||||
queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES)
|
||||
//ERASMUS+
|
||||
case "10.13039/501100010790" =>
|
||||
generateSimpleRelationFromAward(funder, "erasmusplus_", a => a)
|
||||
case _ => logger.debug("no match for " + funder.DOI.get)
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -185,6 +185,7 @@
|
|||
--executor-cores=${sparkExecutorCoresForJoining}
|
||||
--executor-memory=${sparkExecutorMemoryForJoining}
|
||||
--driver-memory=${sparkDriverMemoryForJoining}
|
||||
--conf spark.executor.memoryOverhead=${sparkExecutorMemoryForJoining}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
|
|
@ -212,6 +213,7 @@
|
|||
--executor-cores=${sparkExecutorCoresForJoining}
|
||||
--executor-memory=${sparkExecutorMemoryForJoining}
|
||||
--driver-memory=${sparkDriverMemoryForJoining}
|
||||
--conf spark.executor.memoryOverhead=${sparkExecutorMemoryForJoining}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
|
|
@ -239,6 +241,7 @@
|
|||
--executor-cores=${sparkExecutorCoresForJoining}
|
||||
--executor-memory=${sparkExecutorMemoryForJoining}
|
||||
--driver-memory=${sparkDriverMemoryForJoining}
|
||||
--conf spark.executor.memoryOverhead=${sparkExecutorMemoryForJoining}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
|
|
@ -266,6 +269,7 @@
|
|||
--executor-cores=${sparkExecutorCoresForJoining}
|
||||
--executor-memory=${sparkExecutorMemoryForJoining}
|
||||
--driver-memory=${sparkDriverMemoryForJoining}
|
||||
--conf spark.executor.memoryOverhead=${sparkExecutorMemoryForJoining}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
|
|
@ -293,6 +297,7 @@
|
|||
--executor-cores=${sparkExecutorCoresForJoining}
|
||||
--executor-memory=${sparkExecutorMemoryForJoining}
|
||||
--driver-memory=${sparkDriverMemoryForJoining}
|
||||
--conf spark.executor.memoryOverhead=${sparkExecutorMemoryForJoining}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
|
|
@ -320,6 +325,7 @@
|
|||
--executor-cores=${sparkExecutorCoresForJoining}
|
||||
--executor-memory=${sparkExecutorMemoryForJoining}
|
||||
--driver-memory=${sparkDriverMemoryForJoining}
|
||||
--conf spark.executor.memoryOverhead=${sparkExecutorMemoryForJoining}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
|
|
@ -347,6 +353,7 @@
|
|||
--executor-cores=${sparkExecutorCoresForJoining}
|
||||
--executor-memory=${sparkExecutorMemoryForJoining}
|
||||
--driver-memory=${sparkDriverMemoryForJoining}
|
||||
--conf spark.executor.memoryOverhead=${sparkExecutorMemoryForJoining}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
|
|
@ -386,6 +393,7 @@
|
|||
--executor-cores=${sparkExecutorCoresForJoining}
|
||||
--executor-memory=${sparkExecutorMemoryForJoining}
|
||||
--driver-memory=${sparkDriverMemoryForJoining}
|
||||
--conf spark.executor.memoryOverhead=${sparkExecutorMemoryForJoining}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
|
|
@ -414,6 +422,7 @@
|
|||
--executor-cores=${sparkExecutorCoresForJoining}
|
||||
--executor-memory=${sparkExecutorMemoryForJoining}
|
||||
--driver-memory=${sparkDriverMemoryForJoining}
|
||||
--conf spark.executor.memoryOverhead=${sparkExecutorMemoryForJoining}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
|
|
@ -442,6 +451,7 @@
|
|||
--executor-cores=${sparkExecutorCoresForJoining}
|
||||
--executor-memory=${sparkExecutorMemoryForJoining}
|
||||
--driver-memory=${sparkDriverMemoryForJoining}
|
||||
--conf spark.executor.memoryOverhead=${sparkExecutorMemoryForJoining}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
|
|
@ -470,6 +480,7 @@
|
|||
--executor-cores=${sparkExecutorCoresForJoining}
|
||||
--executor-memory=${sparkExecutorMemoryForJoining}
|
||||
--driver-memory=${sparkDriverMemoryForJoining}
|
||||
--conf spark.executor.memoryOverhead=${sparkExecutorMemoryForJoining}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
|
|
@ -498,6 +509,7 @@
|
|||
--executor-cores=${sparkExecutorCoresForJoining}
|
||||
--executor-memory=${sparkExecutorMemoryForJoining}
|
||||
--driver-memory=${sparkDriverMemoryForJoining}
|
||||
--conf spark.executor.memoryOverhead=${sparkExecutorMemoryForJoining}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
|
|
@ -526,6 +538,7 @@
|
|||
--executor-cores=${sparkExecutorCoresForJoining}
|
||||
--executor-memory=${sparkExecutorMemoryForJoining}
|
||||
--driver-memory=${sparkDriverMemoryForJoining}
|
||||
--conf spark.executor.memoryOverhead=${sparkExecutorMemoryForJoining}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
|
|
@ -554,6 +567,7 @@
|
|||
--executor-cores=${sparkExecutorCoresForJoining}
|
||||
--executor-memory=${sparkExecutorMemoryForJoining}
|
||||
--driver-memory=${sparkDriverMemoryForJoining}
|
||||
--conf spark.executor.memoryOverhead=${sparkExecutorMemoryForJoining}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
|
|
|
|||
|
|
@ -0,0 +1,32 @@
|
|||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
|
||||
<parent>
|
||||
<artifactId>dhp-workflows</artifactId>
|
||||
<groupId>eu.dnetlib.dhp</groupId>
|
||||
<version>1.2.5-SNAPSHOT</version>
|
||||
</parent>
|
||||
<modelVersion>4.0.0</modelVersion>
|
||||
<artifactId>dhp-stats-hist-snaps</artifactId>
|
||||
<dependencies>
|
||||
<dependency>
|
||||
<groupId>org.apache.spark</groupId>
|
||||
<artifactId>spark-core_2.11</artifactId>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.apache.spark</groupId>
|
||||
<artifactId>spark-sql_2.11</artifactId>
|
||||
</dependency>
|
||||
</dependencies>
|
||||
<build>
|
||||
<plugins>
|
||||
<plugin>
|
||||
<groupId>pl.project13.maven</groupId>
|
||||
<artifactId>git-commit-id-plugin</artifactId>
|
||||
<version>2.1.11</version>
|
||||
<configuration>
|
||||
<failOnNoGitDirectory>false</failOnNoGitDirectory>
|
||||
</configuration>
|
||||
</plugin>
|
||||
</plugins>
|
||||
</build>
|
||||
</project>
|
||||
|
|
@ -0,0 +1,30 @@
|
|||
<configuration>
|
||||
<property>
|
||||
<name>jobTracker</name>
|
||||
<value>${jobTracker}</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>nameNode</name>
|
||||
<value>${nameNode}</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.use.system.libpath</name>
|
||||
<value>true</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.action.sharelib.for.spark</name>
|
||||
<value>spark2</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>hive_metastore_uris</name>
|
||||
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>hive_jdbc_url</name>
|
||||
<value>jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000/;UseNativeQuery=1;?spark.executor.memory=22166291558;spark.yarn.executor.memoryOverhead=3225;spark.driver.memory=15596411699;spark.yarn.driver.memoryOverhead=1228</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.wf.workflow.notification.url</name>
|
||||
<value>{serviceUrl}/v1/oozieNotification/jobUpdate?jobId=$jobId%26status=$status</value>
|
||||
</property>
|
||||
</configuration>
|
||||
|
|
@ -0,0 +1,223 @@
|
|||
export PYTHON_EGG_CACHE=/home/$(whoami)/.python-eggs
|
||||
export link_folder=/tmp/impala-shell-python-egg-cache-$(whoami)
|
||||
if ! [ -L $link_folder ]
|
||||
then
|
||||
rm -Rf "$link_folder"
|
||||
ln -sfn ${PYTHON_EGG_CACHE}${link_folder} ${link_folder}
|
||||
fi
|
||||
|
||||
export HADOOP_USER_NAME=$2
|
||||
|
||||
|
||||
# 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}"
|
||||
|
||||
IMPALA_HDFS_NODE=''
|
||||
COUNTER=0
|
||||
while [ $COUNTER -lt 3 ]; do
|
||||
if hdfs dfs -test -e hdfs://impala-cluster-mn1.openaire.eu/tmp >/dev/null 2>&1; then
|
||||
IMPALA_HDFS_NODE='hdfs://impala-cluster-mn1.openaire.eu:8020'
|
||||
break
|
||||
elif hdfs dfs -test -e hdfs://impala-cluster-mn2.openaire.eu/tmp >/dev/null 2>&1; then
|
||||
IMPALA_HDFS_NODE='hdfs://impala-cluster-mn2.openaire.eu:8020'
|
||||
break
|
||||
else
|
||||
IMPALA_HDFS_NODE=''
|
||||
sleep 1
|
||||
fi
|
||||
((COUNTER++))
|
||||
done
|
||||
if [ -z "$IMPALA_HDFS_NODE" ]; then
|
||||
echo -e "\n\nERROR: PROBLEM WHEN SETTING THE HDFS-NODE FOR IMPALA CLUSTER! | AFTER ${COUNTER} RETRIES.\n\n"
|
||||
exit 1
|
||||
fi
|
||||
echo -e "Active IMPALA HDFS Node: ${IMPALA_HDFS_NODE} , after ${COUNTER} retries.\n\n"
|
||||
|
||||
IMPALA_HOSTNAME='impala-cluster-dn1.openaire.eu'
|
||||
IMPALA_CONFIG_FILE='/etc/impala_cluster/hdfs-site.xml'
|
||||
|
||||
IMPALA_HDFS_DB_BASE_PATH="${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'
|
||||
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'
|
||||
|
||||
|
||||
function copydb() {
|
||||
db=$1
|
||||
echo -e "\nStart processing db: '${db}'..\n"
|
||||
|
||||
# Delete the old DB from Impala cluster (if exists).
|
||||
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "drop database if exists ${db} cascade" |& tee error.log # impala-shell prints all logs in stderr, so wee need to capture them and put them in a file, in order to perform "grep" on them later
|
||||
log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
|
||||
if [ -n "$log_errors" ]; then
|
||||
echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN DROPPING THE OLD DATABASE! EXITING...\n\n"
|
||||
rm -f error.log
|
||||
return 1
|
||||
fi
|
||||
|
||||
# Make Impala aware of the deletion of the old DB immediately.
|
||||
sleep 1
|
||||
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
|
||||
|
||||
echo -e "\n\nCopying files of '${db}', from Ocean to Impala cluster..\n"
|
||||
# Using max-bandwidth of: 50 * 100 Mb/s = 5 Gb/s
|
||||
# Using max memory of: 50 * 6144 = 300 Gb
|
||||
# Using 1MB as a buffer-size.
|
||||
# The " -Ddistcp.dynamic.recordsPerChunk=50" arg is not available in our version of hadoop
|
||||
# The "ug" args cannot be used as we get a "User does not belong to hive" error.
|
||||
# The "p" argument cannot be used, as it blocks the files from being used, giving a "sticky bit"-error, even after applying chmod and chown onm the files.
|
||||
hadoop distcp -Dmapreduce.map.memory.mb=6144 -m 70 -bandwidth 150 \
|
||||
-numListstatusThreads 40 \
|
||||
-copybuffersize 1048576 \
|
||||
-strategy dynamic \
|
||||
-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"
|
||||
else
|
||||
echo -e "\n\nERROR: FAILED TO TRANSFER THE FILES OF '${db}', WITH 'hadoop distcp'. GOT WITH EXIT STATUS: $?\n\n"
|
||||
rm -f error.log
|
||||
return 2
|
||||
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
|
||||
|
||||
echo -e "\nCreating schema for db: '${db}'\n"
|
||||
|
||||
# create the new database (with the same name)
|
||||
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create database ${db}"
|
||||
|
||||
# Make Impala aware of the creation of the new DB immediately.
|
||||
sleep 1
|
||||
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
|
||||
sleep 1
|
||||
# Because "Hive" and "Impala" do not have compatible schemas, we cannot use the "show create table <name>" output from hive to create the exact same table in impala.
|
||||
# So, we have to find at least one parquet file (check if it's there) from the table in the ocean cluster for impala to use it to extract the table-schema itself from that file.
|
||||
|
||||
all_create_view_statements=()
|
||||
|
||||
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.
|
||||
# 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_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' \
|
||||
| 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"
|
||||
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"
|
||||
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 '${i}'!\n\n"
|
||||
fi
|
||||
fi
|
||||
fi
|
||||
done
|
||||
|
||||
echo -e "\nAll tables have been created, going to create the views..\n"
|
||||
|
||||
# Time to loop through the views and create them.
|
||||
# At this point all table-schemas should have been created.
|
||||
|
||||
previous_num_of_views_to_retry=${#all_create_view_statements}
|
||||
if [[ $previous_num_of_views_to_retry -gt 0 ]]; then
|
||||
echo -e "\nAll_create_view_statements:\n\n${all_create_view_statements[@]}\n" # DEBUG
|
||||
# Make Impala aware of the new tables, so it knows them when creating the views.
|
||||
sleep 1
|
||||
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
|
||||
sleep 1
|
||||
else
|
||||
echo -e "\nDB '${db}' does not contain any views.\n"
|
||||
fi
|
||||
|
||||
level_counter=0
|
||||
while [[ ${#all_create_view_statements[@]} -gt 0 ]]; do
|
||||
((level_counter++))
|
||||
# The only accepted reason for a view to not be created, is if it depends on another view, which has not been created yet.
|
||||
# In this case, we should retry creating this particular view again.
|
||||
should_retry_create_view_statements=()
|
||||
|
||||
for create_view_statement in "${all_create_view_statements[@]}"; do # Here we use double quotes, as the elements are phrases, instead of single-words.
|
||||
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "${create_view_statement}" |& tee error.log # impala-shell prints all logs in stderr, so wee need to capture them and put them in a file, in order to perform "grep" on them later
|
||||
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 "CREATE VIEW " | sed 's/CREATE VIEW //g' | sed 's/ as select .*//g')' failed to be created, possibly because it depends on another view.\n"
|
||||
should_retry_create_view_statements+=("$create_view_statement")
|
||||
else
|
||||
sleep 1 # Wait a bit for Impala to register that the view was created, before possibly referencing it by another view.
|
||||
fi
|
||||
done
|
||||
|
||||
new_num_of_views_to_retry=${#should_retry_create_view_statements}
|
||||
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"
|
||||
return 3
|
||||
elif [[ $new_num_of_views_to_retry -gt 0 ]]; then
|
||||
echo -e "\nTo be retried \"create_view_statements\":\n\n${should_retry_create_view_statements[@]}\n"
|
||||
previous_num_of_views_to_retry=$new_num_of_views_to_retry
|
||||
else
|
||||
echo -e "\nFinished creating views, for db: '${db}', in level-${level_counter}.\n"
|
||||
fi
|
||||
all_create_view_statements=("${should_retry_create_view_statement[@]}") # This is needed in any case to either move forward with the rest of the views or stop at 0 remaining views.
|
||||
done
|
||||
|
||||
sleep 1
|
||||
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
|
||||
sleep 1
|
||||
|
||||
echo -e "\nComputing stats for tables..\n"
|
||||
entities_on_impala=`impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} --delimited -q "show tables in ${db}"`
|
||||
for i in ${entities_on_impala[@]}; do # Use un-quoted values, as the elemetns are single-words.
|
||||
# Taking the create table statement from the Ocean cluster, just to check if its a view, as the output is easier than using impala-shell from Impala cluster.
|
||||
create_view_statement=`hive -e "show create table ${db}.${i};" | grep "CREATE VIEW"` # This grep works here, as we do not want to match multiple-lines.
|
||||
if [ -z "$create_view_statement" ]; then # If it's a table, then go load the data to it.
|
||||
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "compute stats ${db}.${i}";
|
||||
fi
|
||||
done
|
||||
|
||||
if [ "${entities_on_impala[@]}" == "${entities_on_ocean[@]}" ]; then
|
||||
echo -e "\nAll entities have been copied to Impala cluster.\n"
|
||||
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
|
||||
return 4
|
||||
fi
|
||||
|
||||
rm -f error.log
|
||||
echo -e "\n\nFinished processing db: ${db}\n\n"
|
||||
}
|
||||
|
||||
|
||||
MONITOR_DB=$1
|
||||
#HADOOP_USER_NAME=$2
|
||||
copydb $MONITOR_DB
|
||||
|
||||
|
|
@ -0,0 +1,41 @@
|
|||
export PYTHON_EGG_CACHE=/home/$(whoami)/.python-eggs
|
||||
export link_folder=/tmp/impala-shell-python-egg-cache-$(whoami)
|
||||
if ! [ -L $link_folder ]
|
||||
then
|
||||
rm -Rf "$link_folder"
|
||||
ln -sfn ${PYTHON_EGG_CACHE}${link_folder} ${link_folder}
|
||||
fi
|
||||
|
||||
SOURCE=$1
|
||||
PRODUCTION=$2
|
||||
SHADOW=$3
|
||||
MONITOR_PROD=$4
|
||||
MONITOR_IRISH_PROD=$5
|
||||
|
||||
|
||||
echo ${SOURCE}
|
||||
echo ${PRODUCTION}
|
||||
|
||||
#echo "Updating ${PRODUCTION} monitor database old cluster"
|
||||
#impala-shell -q "create database if not exists ${PRODUCTION}"
|
||||
#impala-shell -d ${PRODUCTION} -q "show tables" --delimited | sed "s/^/drop view if exists ${PRODUCTION}./" | sed "s/$/;/" | impala-shell -c -f -
|
||||
#impala-shell -d ${SOURCE} -q "show tables" --delimited | sed "s/\(.*\)/create view ${PRODUCTION}.\1 as select * from ${SOURCE}.\1;/" | impala-shell -c -f -
|
||||
|
||||
echo "Updating ${PRODUCTION} historical snapshots database"
|
||||
impala-shell -i impala-cluster-dn1.openaire.eu -q "create database if not exists ${PRODUCTION}"
|
||||
impala-shell -i impala-cluster-dn1.openaire.eu -d ${PRODUCTION} -q "show tables" --delimited | sed "s/^/drop view if exists ${PRODUCTION}./" | sed "s/$/;/" | impala-shell -i impala-cluster-dn1.openaire.eu -c -f -
|
||||
impala-shell -i impala-cluster-dn1.openaire.eu -d ${SOURCE} -q "show tables" --delimited | sed "s/\(.*\)/create view ${PRODUCTION}.\1 as select * from ${SOURCE}.\1;/" | impala-shell -i impala-cluster-dn1.openaire.eu -c -f -
|
||||
echo "Production monitor db ready!"
|
||||
|
||||
impala-shell -i impala-cluster-dn1.openaire.eu -q "drop view ${MONITOR_PROD}.historical_snapshots"
|
||||
impala-shell -i impala-cluster-dn1.openaire.eu -q "drop view ${MONITOR_PROD}.historical_snapshots_fos"
|
||||
|
||||
impala-shell -i impala-cluster-dn1.openaire.eu -q "create view ${MONITOR_PROD}.historical_snapshots as select * from ${SOURCE}.historical_snapshots"
|
||||
impala-shell -i impala-cluster-dn1.openaire.eu -q "create view ${MONITOR_PROD}.historical_snapshots_fos as select * from ${SOURCE}.historical_snapshots_fos"
|
||||
|
||||
impala-shell -i impala-cluster-dn1.openaire.eu -q "drop view ${MONITOR_IRISH_PROD}.historical_snapshots_irish"
|
||||
impala-shell -i impala-cluster-dn1.openaire.eu -q "drop view ${MONITOR_IRISH_PROD}.historical_snapshots_irish_fos"
|
||||
|
||||
|
||||
impala-shell -i impala-cluster-dn1.openaire.eu -q "create view ${MONITOR_IRISH_PROD}.historical_snapshots_irish as select * from ${SOURCE}.historical_snapshots_irish"
|
||||
impala-shell -i impala-cluster-dn1.openaire.eu -q "create view ${MONITOR_IRISH_PROD}.historical_snapshots_irish_fos as select * from ${SOURCE}.historical_snapshots_irish"
|
||||
|
|
@ -0,0 +1,27 @@
|
|||
export PYTHON_EGG_CACHE=/home/$(whoami)/.python-eggs
|
||||
export link_folder=/tmp/impala-shell-python-egg-cache-$(whoami)
|
||||
if ! [ -L $link_folder ]
|
||||
then
|
||||
rm -Rf "$link_folder"
|
||||
ln -sfn ${PYTHON_EGG_CACHE}${link_folder} ${link_folder}
|
||||
fi
|
||||
|
||||
export SOURCE=$1
|
||||
export TARGET=$2
|
||||
export SHADOW=$3
|
||||
export SCRIPT_PATH=$4
|
||||
|
||||
|
||||
export HIVE_OPTS="-hiveconf mapred.job.queue.name=analytics -hiveconf hive.spark.client.connect.timeout=120000ms -hiveconf hive.spark.client.server.connect.timeout=300000ms -hiveconf spark.executor.memory=19166291558 -hiveconf spark.yarn.executor.memoryOverhead=3225 -hiveconf spark.driver.memory=11596411699 -hiveconf spark.yarn.driver.memoryOverhead=1228"
|
||||
export HADOOP_USER_NAME="oozie"
|
||||
|
||||
echo "Getting file from " $4
|
||||
hdfs dfs -copyToLocal $4
|
||||
|
||||
#update Monitor DB IRISH
|
||||
#cat CreateDB.sql | sed "s/SOURCE/$1/g" | sed "s/TARGET/$2/g1" | sed "s/GRAPHDB/$3/g1" > foo
|
||||
cat buildIrishMonitorDB.sql | sed "s/SOURCE/$1/g" | sed "s/TARGET/$2/g1" > foo
|
||||
hive $HIVE_OPTS -f foo
|
||||
|
||||
echo "Hive shell finished"
|
||||
|
||||
|
|
@ -0,0 +1,82 @@
|
|||
INSERT INTO ${hist_db_name}.historical_snapshots_fos_tmp
|
||||
SELECT * FROM ${hist_db_name_prev}.historical_snapshots_fos;
|
||||
|
||||
INSERT INTO ${hist_db_name}.historical_snapshots_fos_tmp
|
||||
select
|
||||
cast(${hist_date} as STRING),
|
||||
count(distinct r.id),
|
||||
r.type,
|
||||
rf.lvl1,
|
||||
rf.lvl2,
|
||||
pf.publicly_funded,
|
||||
r.access_mode,
|
||||
r.gold,
|
||||
r.green,
|
||||
coalesce(gl.green_with_license,0),
|
||||
h.is_hybrid,
|
||||
b.is_bronze_oa,
|
||||
d.in_diamond_journal,
|
||||
t.is_transformative,
|
||||
pr.refereed
|
||||
from ${stats_db_name}.result r
|
||||
left outer join ${stats_db_name}.result_fos rf on rf.id=r.id
|
||||
left outer join ${stats_db_name}.indi_pub_publicly_funded pf on pf.id=r.id
|
||||
left outer join ${stats_db_name}.indi_pub_green_with_license gl on gl.id=r.id
|
||||
left outer join ${stats_db_name}.indi_pub_bronze_oa b on b.id=r.id
|
||||
left outer join ${stats_db_name}.indi_pub_diamond d on d.id=r.id
|
||||
left outer join ${stats_db_name}.indi_pub_in_transformative t on t.id=r.id
|
||||
left outer join ${stats_db_name}.indi_pub_hybrid h on h.id=r.id
|
||||
left outer join ${stats_db_name}.result_refereed pr on pr.id=r.id
|
||||
group by r.green, r.gold, r.access_mode, r.type, rf.lvl1,rf.lvl2, pf.publicly_funded,r.green, gl.green_with_license,b.is_bronze_oa,d.in_diamond_journal,t.is_transformative,h.is_hybrid,pr.refereed;
|
||||
|
||||
drop table if exists ${hist_db_name}.historical_snapshots_fos purge;
|
||||
|
||||
CREATE TABLE ${hist_db_name}.historical_snapshots_fos STORED AS PARQUET AS
|
||||
SELECT * FROM ${hist_db_name}.historical_snapshots_fos_tmp;
|
||||
|
||||
drop table if exists ${monitor_db_name}.historical_snapshots_fos purge;
|
||||
|
||||
create table ${monitor_db_name}.historical_snapshots_fos stored as parquet
|
||||
as select * from ${hist_db_name}.historical_snapshots_fos;
|
||||
|
||||
drop table ${hist_db_name}.historical_snapshots_fos_tmp purge;
|
||||
|
||||
INSERT INTO ${hist_db_name}.historical_snapshots_tmp as
|
||||
SELECT * FROM ${hist_db_name_prev}.historical_snapshots;
|
||||
|
||||
INSERT INTO ${hist_db_name}.historical_snapshots_tmp
|
||||
select
|
||||
cast(${hist_date} as STRING),
|
||||
count(distinct r.id),
|
||||
r.type,
|
||||
pf.publicly_funded,
|
||||
r.access_mode,
|
||||
r.gold,
|
||||
r.green,
|
||||
coalesce(gl.green_with_license,0),
|
||||
h.is_hybrid,
|
||||
b.is_bronze_oa,
|
||||
d.in_diamond_journal,
|
||||
t.is_transformative,
|
||||
pr.refereed
|
||||
from ${stats_db_name}.result r
|
||||
left outer join ${stats_db_name}.indi_pub_publicly_funded pf on pf.id=r.id
|
||||
left outer join ${stats_db_name}.indi_pub_green_with_license gl on gl.id=r.id
|
||||
left outer join ${stats_db_name}.indi_pub_bronze_oa b on b.id=r.id
|
||||
left outer join ${stats_db_name}.indi_pub_diamond d on d.id=r.id
|
||||
left outer join ${stats_db_name}.indi_pub_in_transformative t on t.id=r.id
|
||||
left outer join ${stats_db_name}.indi_pub_hybrid h on h.id=r.id
|
||||
left outer join ${stats_db_name}.result_refereed pr on pr.id=r.id
|
||||
group by r.green, r.gold, r.access_mode, r.type, pf.publicly_funded,r.green, gl.green_with_license,b.is_bronze_oa,d.in_diamond_journal,t.is_transformative,h.is_hybrid,pr.refereed;
|
||||
|
||||
drop table if exists ${hist_db_name}.historical_snapshots purge;
|
||||
|
||||
CREATE TABLE ${hist_db_name}.historical_snapshots STORED AS PARQUET AS
|
||||
SELECT * FROM ${hist_db_name}.historical_snapshots_tmp;
|
||||
|
||||
drop table if exists ${monitor_db_name}.historical_snapshots purge;
|
||||
|
||||
create table ${monitor_db_name}.historical_snapshots stored as parquet
|
||||
as select * from ${hist_db_name}.historical_snapshots;
|
||||
|
||||
drop table ${hist_db_name}.historical_snapshots_tmp purge;
|
||||
|
|
@ -0,0 +1,91 @@
|
|||
INSERT INTO ${hist_db_name}.historical_snapshots_fos_irish_tmp
|
||||
SELECT * FROM ${hist_db_name_prev}.historical_snapshots_irish_fos;
|
||||
|
||||
INSERT INTO ${hist_db_name}.historical_snapshots_fos_irish_tmp
|
||||
select
|
||||
cast(${hist_date} as STRING),
|
||||
count(distinct r.id),
|
||||
r.type,
|
||||
rf.lvl1,
|
||||
rf.lvl2,
|
||||
pf.publicly_funded,
|
||||
r.access_mode,
|
||||
r.gold,
|
||||
r.green,
|
||||
coalesce(gl.green_with_license,0),
|
||||
h.is_hybrid,
|
||||
b.is_bronze_oa,
|
||||
d.in_diamond_journal,
|
||||
t.is_transformative,
|
||||
pr.refereed
|
||||
from ${stats_irish_db_name}.result r
|
||||
left outer join ${stats_irish_db_name}.result_fos rf on rf.id=r.id
|
||||
left outer join ${stats_irish_db_name}.indi_pub_publicly_funded pf on pf.id=r.id
|
||||
left outer join ${stats_irish_db_name}.indi_pub_green_with_license gl on gl.id=r.id
|
||||
left outer join ${stats_irish_db_name}.indi_pub_bronze_oa b on b.id=r.id
|
||||
left outer join ${stats_irish_db_name}.indi_pub_diamond d on d.id=r.id
|
||||
left outer join ${stats_irish_db_name}.indi_pub_in_transformative t on t.id=r.id
|
||||
left outer join ${stats_irish_db_name}.indi_pub_hybrid h on h.id=r.id
|
||||
left outer join ${stats_irish_db_name}.result_refereed pr on pr.id=r.id
|
||||
group by r.green, r.gold, r.access_mode, r.type, rf.lvl1,rf.lvl2, pf.publicly_funded,r.green, gl.green_with_license,b.is_bronze_oa,d.in_diamond_journal,t.is_transformative,h.is_hybrid,pr.refereed;
|
||||
|
||||
drop table if exists ${hist_db_name}.historical_snapshots_irish_fos purge;
|
||||
|
||||
CREATE TABLE ${hist_db_name}.historical_snapshots_irish_fos STORED AS PARQUET AS
|
||||
SELECT * FROM ${hist_db_name}.historical_snapshots_fos_irish_tmp;
|
||||
|
||||
drop table if exists ${monitor_irish_db_name}.historical_snapshots_irish_fos purge;
|
||||
|
||||
create table ${monitor_irish_db_name}.historical_snapshots_irish_fos stored as parquet
|
||||
as select * from ${hist_db_name}.historical_snapshots_irish_fos;
|
||||
|
||||
drop table ${hist_db_name}.historical_snapshots_fos_irish_tmp purge;
|
||||
|
||||
INSERT INTO ${hist_db_name}.historical_snapshots_irish_tmp
|
||||
SELECT * FROM ${hist_db_name_prev}.historical_snapshots_irish;
|
||||
|
||||
INSERT INTO ${hist_db_name}.historical_snapshots_irish_tmp
|
||||
select
|
||||
cast(${hist_date} as STRING),
|
||||
count(distinct r.id),
|
||||
r.type,
|
||||
pf.publicly_funded,
|
||||
r.access_mode,
|
||||
r.gold,
|
||||
r.green,
|
||||
coalesce(gl.green_with_license,0),
|
||||
h.is_hybrid,
|
||||
b.is_bronze_oa,
|
||||
d.in_diamond_journal,
|
||||
t.is_transformative,
|
||||
pr.refereed
|
||||
from ${stats_irish_db_name}.result r
|
||||
left outer join ${stats_irish_db_name}.indi_pub_publicly_funded pf on pf.id=r.id
|
||||
left outer join ${stats_irish_db_name}.indi_pub_green_with_license gl on gl.id=r.id
|
||||
left outer join ${stats_irish_db_name}.indi_pub_bronze_oa b on b.id=r.id
|
||||
left outer join ${stats_irish_db_name}.indi_pub_diamond d on d.id=r.id
|
||||
left outer join ${stats_irish_db_name}.indi_pub_in_transformative t on t.id=r.id
|
||||
left outer join ${stats_irish_db_name}.indi_pub_hybrid h on h.id=r.id
|
||||
left outer join ${stats_irish_db_name}.result_refereed pr on pr.id=r.id
|
||||
group by r.green, r.gold, r.access_mode, r.type, pf.publicly_funded,r.green, gl.green_with_license,b.is_bronze_oa,d.in_diamond_journal,t.is_transformative,h.is_hybrid,pr.refereed;
|
||||
|
||||
|
||||
drop table if exists ${hist_db_name}.historical_snapshots_irish purge;
|
||||
|
||||
CREATE TABLE ${hist_db_name}.historical_snapshots_irish STORED AS PARQUET AS
|
||||
SELECT * FROM ${hist_db_name}.historical_snapshots_irish_tmp;
|
||||
|
||||
drop table if exists ${monitor_irish_db_name}.historical_snapshots_irish purge;
|
||||
|
||||
create table ${monitor_irish_db_name}.historical_snapshots_irish stored as parquet
|
||||
as select * from ${hist_db_name}.historical_snapshots_irish;
|
||||
|
||||
drop table ${hist_db_name}.historical_snapshots_irish_tmp purge;
|
||||
|
||||
|
||||
drop table if exists ${monitor_irish_db_name}.historical_snapshots_irish_fos purge;
|
||||
|
||||
create table ${monitor_irish_db_name}.historical_snapshots_irish_fos stored as parquet
|
||||
as select * from ${hist_db_name}.historical_snapshots_irish_fos;
|
||||
|
||||
drop table ${hist_db_name}.historical_snapshots_fos_irish_tmp purge;
|
||||
|
|
@ -0,0 +1,92 @@
|
|||
--------------------------------------------------------------
|
||||
--------------------------------------------------------------
|
||||
-- Historical Snapshots database creation
|
||||
--------------------------------------------------------------
|
||||
--------------------------------------------------------------
|
||||
|
||||
DROP database IF EXISTS ${hist_db_name} CASCADE;
|
||||
CREATE database ${hist_db_name};
|
||||
|
||||
drop table if exists ${hist_db_name}.historical_snapshots_fos_tmp purge;
|
||||
|
||||
CREATE TABLE ${hist_db_name}.historical_snapshots_fos_tmp
|
||||
(
|
||||
hist_date STRING,
|
||||
total INT,
|
||||
type STRING,
|
||||
lvl1 STRING,
|
||||
lvl2 STRING,
|
||||
publicly_funded INT,
|
||||
accessrights STRING,
|
||||
gold INT,
|
||||
green INT,
|
||||
green_with_license INT,
|
||||
hybrid INT,
|
||||
bronze INT,
|
||||
diamond INT,
|
||||
transformative INT,
|
||||
peer_reviewed STRING
|
||||
)
|
||||
CLUSTERED BY (hist_date) INTO 100 buckets stored as orc tblproperties ('transactional' = 'true');
|
||||
|
||||
drop table if exists ${hist_db_name}.historical_snapshots_fos_irish_tmp purge;
|
||||
|
||||
CREATE TABLE ${hist_db_name}.historical_snapshots_fos_irish_tmp
|
||||
(
|
||||
hist_date STRING,
|
||||
total INT,
|
||||
type STRING,
|
||||
lvl1 STRING,
|
||||
lvl2 STRING,
|
||||
publicly_funded INT,
|
||||
accessrights STRING,
|
||||
gold INT,
|
||||
green INT,
|
||||
green_with_license INT,
|
||||
hybrid INT,
|
||||
bronze INT,
|
||||
diamond INT,
|
||||
transformative INT,
|
||||
peer_reviewed STRING
|
||||
)
|
||||
CLUSTERED BY (hist_date) INTO 100 buckets stored as orc tblproperties ('transactional' = 'true');
|
||||
|
||||
drop table if exists ${hist_db_name}.historical_snapshots_tmp purge;
|
||||
|
||||
CREATE TABLE ${hist_db_name}.historical_snapshots_tmp
|
||||
(
|
||||
hist_date STRING,
|
||||
total INT,
|
||||
type STRING,
|
||||
publicly_funded INT,
|
||||
accessrights STRING,
|
||||
gold INT,
|
||||
green INT,
|
||||
green_with_license INT,
|
||||
hybrid INT,
|
||||
bronze INT,
|
||||
diamond INT,
|
||||
transformative INT,
|
||||
peer_reviewed STRING
|
||||
)
|
||||
CLUSTERED BY (hist_date) INTO 100 buckets stored as orc tblproperties ('transactional' = 'true');
|
||||
|
||||
drop table if exists ${hist_db_name}.historical_snapshots_irish_tmp purge;
|
||||
|
||||
CREATE TABLE ${hist_db_name}.historical_snapshots_irish_tmp
|
||||
(
|
||||
hist_date STRING,
|
||||
total INT,
|
||||
type STRING,
|
||||
publicly_funded INT,
|
||||
accessrights STRING,
|
||||
gold INT,
|
||||
green INT,
|
||||
green_with_license INT,
|
||||
hybrid INT,
|
||||
bronze INT,
|
||||
diamond INT,
|
||||
transformative INT,
|
||||
peer_reviewed STRING
|
||||
)
|
||||
CLUSTERED BY (hist_date) INTO 100 buckets stored as orc tblproperties ('transactional' = 'true');
|
||||
|
|
@ -0,0 +1,159 @@
|
|||
<workflow-app name="Stats Hist Snapshots" xmlns="uri:oozie:workflow:0.5">
|
||||
<parameters>
|
||||
<property>
|
||||
<name>hist_db_name</name>
|
||||
<description>the target hist database name</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>hist_db_name_prev</name>
|
||||
<description>the hist database name of previous_month</description>
|
||||
</property>
|
||||
|
||||
<property>
|
||||
<name>stats_db_name</name>
|
||||
<description>the stats db name</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>stats_irish_db_name</name>
|
||||
<description>the stats irish db name</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>monitor_db_name</name>
|
||||
<description>the monitor db name</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>monitor_irish_db_name</name>
|
||||
<description>the irish monitor db name</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>hist_db_prod_name</name>
|
||||
<description>the production db</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>hist_db_shadow_name</name>
|
||||
<description>the production shadow db</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>hist_date</name>
|
||||
<description>the snaps date</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>hive_metastore_uris</name>
|
||||
<description>hive server metastore URIs</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>hive_jdbc_url</name>
|
||||
<description>hive server jdbc url</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>hive_timeout</name>
|
||||
<description>the time period, in seconds, after which Hive fails a transaction if a Hive client has not sent a hearbeat. The default value is 300 seconds.</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>hadoop_user_name</name>
|
||||
<description>user name of the wf owner</description>
|
||||
</property>
|
||||
</parameters>
|
||||
|
||||
<global>
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<configuration>
|
||||
<property>
|
||||
<name>hive.metastore.uris</name>
|
||||
<value>${hive_metastore_uris}</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>hive.txn.timeout</name>
|
||||
<value>${hive_timeout}</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>mapred.job.queue.name</name>
|
||||
<value>analytics</value>
|
||||
</property>
|
||||
</configuration>
|
||||
</global>
|
||||
|
||||
<start to="resume_from"/>
|
||||
<decision name="resume_from">
|
||||
<switch>
|
||||
<case to="CreateDB">${wf:conf('resumeFrom') eq 'CreateDB'}</case>
|
||||
<case to="BuildHistSnaps">${wf:conf('resumeFrom') eq 'BuildHistSnaps'}</case>
|
||||
<case to="BuildHistSnapsIrish">${wf:conf('resumeFrom') eq 'BuildHistSnapsIrish'}</case>
|
||||
<case to="Step2-copyDataToImpalaCluster">${wf:conf('resumeFrom') eq 'Step2-copyDataToImpalaCluster'}</case>
|
||||
<case to="Step3-finalizeImpalaCluster">${wf:conf('resumeFrom') eq 'Step3-finalizeImpalaCluster'}</case>
|
||||
<default to="BuildHistSnaps"/>
|
||||
</switch>
|
||||
</decision>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
<action name="CreateDB">
|
||||
<hive2 xmlns="uri:oozie:hive2-action:0.1">
|
||||
<jdbc-url>${hive_jdbc_url}</jdbc-url>
|
||||
<script>scripts/CreateDB.sql</script>
|
||||
<param>hist_db_name=${hist_db_name}</param>
|
||||
</hive2>
|
||||
<ok to="BuildHistSnaps"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="BuildHistSnaps">
|
||||
<hive2 xmlns="uri:oozie:hive2-action:0.1">
|
||||
<jdbc-url>${hive_jdbc_url}</jdbc-url>
|
||||
<script>scripts/BuildHistSnapsAll.sql</script>
|
||||
<param>hist_db_name=${hist_db_name}</param>
|
||||
<param>hist_db_name_prev=${hist_db_name_prev}</param>
|
||||
<param>stats_db_name=${stats_db_name}</param>
|
||||
<param>monitor_db_name=${monitor_db_name}</param>
|
||||
<param>hist_date=${hist_date}</param>
|
||||
</hive2>
|
||||
<ok to="BuildHistSnapsIrish"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="BuildHistSnapsIrish">
|
||||
<hive2 xmlns="uri:oozie:hive2-action:0.1">
|
||||
<jdbc-url>${hive_jdbc_url}</jdbc-url>
|
||||
<script>scripts/BuildHistSnapsIrish.sql</script>
|
||||
<param>hist_db_name=${hist_db_name}</param>
|
||||
<param>hist_db_name_prev=${hist_db_name_prev}</param>
|
||||
<param>stats_irish_db_name=${stats_irish_db_name}</param>
|
||||
<param>monitor_irish_db_name=${monitor_irish_db_name}</param>
|
||||
<param>hist_date=${hist_date}</param>
|
||||
</hive2>
|
||||
<ok to="Step2-copyDataToImpalaCluster"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
<action name="Step2-copyDataToImpalaCluster">
|
||||
<shell xmlns="uri:oozie:shell-action:0.1">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<exec>copyDataToImpalaCluster.sh</exec>
|
||||
<argument>${hist_db_name}</argument>
|
||||
<argument>${hadoop_user_name}</argument>
|
||||
<file>copyDataToImpalaCluster.sh</file>
|
||||
</shell>
|
||||
<ok to="Step3-finalizeImpalaCluster"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
<action name="Step3-finalizeImpalaCluster">
|
||||
<shell xmlns="uri:oozie:shell-action:0.1">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<exec>finalizeImpalaCluster.sh</exec>
|
||||
<argument>${hist_db_name}</argument>
|
||||
<argument>${hist_db_prod_name}</argument>
|
||||
<argument>${hist_db_shadow_name}</argument>
|
||||
<argument>${monitor_db_prod_name}</argument>
|
||||
<argument>${monitor_irish_db_prod_name}</argument>
|
||||
<file>finalizeImpalaCluster.sh</file>
|
||||
</shell>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
||||
|
|
@ -0,0 +1,32 @@
|
|||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
|
||||
<parent>
|
||||
<artifactId>dhp-workflows</artifactId>
|
||||
<groupId>eu.dnetlib.dhp</groupId>
|
||||
<version>1.2.5-SNAPSHOT</version>
|
||||
</parent>
|
||||
<modelVersion>4.0.0</modelVersion>
|
||||
<artifactId>dhp-stats-monitor-irish</artifactId>
|
||||
<dependencies>
|
||||
<dependency>
|
||||
<groupId>org.apache.spark</groupId>
|
||||
<artifactId>spark-core_2.11</artifactId>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.apache.spark</groupId>
|
||||
<artifactId>spark-sql_2.11</artifactId>
|
||||
</dependency>
|
||||
</dependencies>
|
||||
<build>
|
||||
<plugins>
|
||||
<plugin>
|
||||
<groupId>pl.project13.maven</groupId>
|
||||
<artifactId>git-commit-id-plugin</artifactId>
|
||||
<version>2.1.11</version>
|
||||
<configuration>
|
||||
<failOnNoGitDirectory>false</failOnNoGitDirectory>
|
||||
</configuration>
|
||||
</plugin>
|
||||
</plugins>
|
||||
</build>
|
||||
</project>
|
||||
|
|
@ -0,0 +1,30 @@
|
|||
<configuration>
|
||||
<property>
|
||||
<name>jobTracker</name>
|
||||
<value>${jobTracker}</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>nameNode</name>
|
||||
<value>${nameNode}</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.use.system.libpath</name>
|
||||
<value>true</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.action.sharelib.for.spark</name>
|
||||
<value>spark2</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>hive_metastore_uris</name>
|
||||
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>hive_jdbc_url</name>
|
||||
<value>jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000/;UseNativeQuery=1;?spark.executor.memory=22166291558;spark.yarn.executor.memoryOverhead=3225;spark.driver.memory=15596411699;spark.yarn.driver.memoryOverhead=1228</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.wf.workflow.notification.url</name>
|
||||
<value>{serviceUrl}/v1/oozieNotification/jobUpdate?jobId=$jobId%26status=$status</value>
|
||||
</property>
|
||||
</configuration>
|
||||
|
|
@ -0,0 +1,222 @@
|
|||
export PYTHON_EGG_CACHE=/home/$(whoami)/.python-eggs
|
||||
export link_folder=/tmp/impala-shell-python-egg-cache-$(whoami)
|
||||
if ! [ -L $link_folder ]
|
||||
then
|
||||
rm -Rf "$link_folder"
|
||||
ln -sfn ${PYTHON_EGG_CACHE}${link_folder} ${link_folder}
|
||||
fi
|
||||
|
||||
export HADOOP_USER_NAME=$2
|
||||
|
||||
# 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}"
|
||||
|
||||
IMPALA_HDFS_NODE=''
|
||||
COUNTER=0
|
||||
while [ $COUNTER -lt 3 ]; do
|
||||
if hdfs dfs -test -e hdfs://impala-cluster-mn1.openaire.eu/tmp >/dev/null 2>&1; then
|
||||
IMPALA_HDFS_NODE='hdfs://impala-cluster-mn1.openaire.eu:8020'
|
||||
break
|
||||
elif hdfs dfs -test -e hdfs://impala-cluster-mn2.openaire.eu/tmp >/dev/null 2>&1; then
|
||||
IMPALA_HDFS_NODE='hdfs://impala-cluster-mn2.openaire.eu:8020'
|
||||
break
|
||||
else
|
||||
IMPALA_HDFS_NODE=''
|
||||
sleep 1
|
||||
fi
|
||||
((COUNTER++))
|
||||
done
|
||||
if [ -z "$IMPALA_HDFS_NODE" ]; then
|
||||
echo -e "\n\nERROR: PROBLEM WHEN SETTING THE HDFS-NODE FOR IMPALA CLUSTER! | AFTER ${COUNTER} RETRIES.\n\n"
|
||||
exit 1
|
||||
fi
|
||||
echo -e "Active IMPALA HDFS Node: ${IMPALA_HDFS_NODE} , after ${COUNTER} retries.\n\n"
|
||||
|
||||
IMPALA_HOSTNAME='impala-cluster-dn1.openaire.eu'
|
||||
IMPALA_CONFIG_FILE='/etc/impala_cluster/hdfs-site.xml'
|
||||
|
||||
IMPALA_HDFS_DB_BASE_PATH="${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'
|
||||
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'
|
||||
|
||||
|
||||
function copydb() {
|
||||
db=$1
|
||||
echo -e "\nStart processing db: '${db}'..\n"
|
||||
|
||||
# Delete the old DB from Impala cluster (if exists).
|
||||
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "drop database if exists ${db} cascade" |& tee error.log # impala-shell prints all logs in stderr, so wee need to capture them and put them in a file, in order to perform "grep" on them later
|
||||
log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
|
||||
if [ -n "$log_errors" ]; then
|
||||
echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN DROPPING THE OLD DATABASE! EXITING...\n\n"
|
||||
rm -f error.log
|
||||
return 1
|
||||
fi
|
||||
|
||||
# Make Impala aware of the deletion of the old DB immediately.
|
||||
sleep 1
|
||||
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
|
||||
|
||||
echo -e "\n\nCopying files of '${db}', from Ocean to Impala cluster..\n"
|
||||
# Using max-bandwidth of: 50 * 100 Mb/s = 5 Gb/s
|
||||
# Using max memory of: 50 * 6144 = 300 Gb
|
||||
# Using 1MB as a buffer-size.
|
||||
# The " -Ddistcp.dynamic.recordsPerChunk=50" arg is not available in our version of hadoop
|
||||
# The "ug" args cannot be used as we get a "User does not belong to hive" error.
|
||||
# The "p" argument cannot be used, as it blocks the files from being used, giving a "sticky bit"-error, even after applying chmod and chown onm the files.
|
||||
hadoop distcp -Dmapreduce.map.memory.mb=6144 -m 70 -bandwidth 150 \
|
||||
-numListstatusThreads 40 \
|
||||
-copybuffersize 1048576 \
|
||||
-strategy dynamic \
|
||||
-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"
|
||||
else
|
||||
echo -e "\n\nERROR: FAILED TO TRANSFER THE FILES OF '${db}', WITH 'hadoop distcp'. GOT WITH EXIT STATUS: $?\n\n"
|
||||
rm -f error.log
|
||||
return 2
|
||||
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
|
||||
|
||||
echo -e "\nCreating schema for db: '${db}'\n"
|
||||
|
||||
# create the new database (with the same name)
|
||||
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create database ${db}"
|
||||
|
||||
# Make Impala aware of the creation of the new DB immediately.
|
||||
sleep 1
|
||||
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
|
||||
sleep 1
|
||||
# Because "Hive" and "Impala" do not have compatible schemas, we cannot use the "show create table <name>" output from hive to create the exact same table in impala.
|
||||
# So, we have to find at least one parquet file (check if it's there) from the table in the ocean cluster for impala to use it to extract the table-schema itself from that file.
|
||||
|
||||
all_create_view_statements=()
|
||||
|
||||
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.
|
||||
# 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_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' \
|
||||
| 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"
|
||||
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"
|
||||
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 '${i}'!\n\n"
|
||||
fi
|
||||
fi
|
||||
fi
|
||||
done
|
||||
|
||||
echo -e "\nAll tables have been created, going to create the views..\n"
|
||||
|
||||
# Time to loop through the views and create them.
|
||||
# At this point all table-schemas should have been created.
|
||||
|
||||
previous_num_of_views_to_retry=${#all_create_view_statements}
|
||||
if [[ $previous_num_of_views_to_retry -gt 0 ]]; then
|
||||
echo -e "\nAll_create_view_statements:\n\n${all_create_view_statements[@]}\n" # DEBUG
|
||||
# Make Impala aware of the new tables, so it knows them when creating the views.
|
||||
sleep 1
|
||||
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
|
||||
sleep 1
|
||||
else
|
||||
echo -e "\nDB '${db}' does not contain any views.\n"
|
||||
fi
|
||||
|
||||
level_counter=0
|
||||
while [[ ${#all_create_view_statements[@]} -gt 0 ]]; do
|
||||
((level_counter++))
|
||||
# The only accepted reason for a view to not be created, is if it depends on another view, which has not been created yet.
|
||||
# In this case, we should retry creating this particular view again.
|
||||
should_retry_create_view_statements=()
|
||||
|
||||
for create_view_statement in "${all_create_view_statements[@]}"; do # Here we use double quotes, as the elements are phrases, instead of single-words.
|
||||
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "${create_view_statement}" |& tee error.log # impala-shell prints all logs in stderr, so wee need to capture them and put them in a file, in order to perform "grep" on them later
|
||||
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 "CREATE VIEW " | sed 's/CREATE VIEW //g' | sed 's/ as select .*//g')' failed to be created, possibly because it depends on another view.\n"
|
||||
should_retry_create_view_statements+=("$create_view_statement")
|
||||
else
|
||||
sleep 1 # Wait a bit for Impala to register that the view was created, before possibly referencing it by another view.
|
||||
fi
|
||||
done
|
||||
|
||||
new_num_of_views_to_retry=${#should_retry_create_view_statements}
|
||||
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"
|
||||
return 3
|
||||
elif [[ $new_num_of_views_to_retry -gt 0 ]]; then
|
||||
echo -e "\nTo be retried \"create_view_statements\":\n\n${should_retry_create_view_statements[@]}\n"
|
||||
previous_num_of_views_to_retry=$new_num_of_views_to_retry
|
||||
else
|
||||
echo -e "\nFinished creating views, for db: '${db}', in level-${level_counter}.\n"
|
||||
fi
|
||||
all_create_view_statements=("${should_retry_create_view_statement[@]}") # This is needed in any case to either move forward with the rest of the views or stop at 0 remaining views.
|
||||
done
|
||||
|
||||
sleep 1
|
||||
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
|
||||
sleep 1
|
||||
|
||||
echo -e "\nComputing stats for tables..\n"
|
||||
entities_on_impala=`impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} --delimited -q "show tables in ${db}"`
|
||||
for i in ${entities_on_impala[@]}; do # Use un-quoted values, as the elemetns are single-words.
|
||||
# Taking the create table statement from the Ocean cluster, just to check if its a view, as the output is easier than using impala-shell from Impala cluster.
|
||||
create_view_statement=`hive -e "show create table ${db}.${i};" | grep "CREATE VIEW"` # This grep works here, as we do not want to match multiple-lines.
|
||||
if [ -z "$create_view_statement" ]; then # If it's a table, then go load the data to it.
|
||||
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "compute stats ${db}.${i}";
|
||||
fi
|
||||
done
|
||||
|
||||
if [ "${entities_on_impala[@]}" == "${entities_on_ocean[@]}" ]; then
|
||||
echo -e "\nAll entities have been copied to Impala cluster.\n"
|
||||
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
|
||||
return 4
|
||||
fi
|
||||
|
||||
rm -f error.log
|
||||
echo -e "\n\nFinished processing db: ${db}\n\n"
|
||||
}
|
||||
|
||||
|
||||
MONITOR_DB=$1
|
||||
#HADOOP_USER_NAME=$2
|
||||
copydb $MONITOR_DB
|
||||
|
||||
|
|
@ -0,0 +1,23 @@
|
|||
export PYTHON_EGG_CACHE=/home/$(whoami)/.python-eggs
|
||||
export link_folder=/tmp/impala-shell-python-egg-cache-$(whoami)
|
||||
if ! [ -L $link_folder ]
|
||||
then
|
||||
rm -Rf "$link_folder"
|
||||
ln -sfn ${PYTHON_EGG_CACHE}${link_folder} ${link_folder}
|
||||
fi
|
||||
|
||||
SOURCE=$1
|
||||
PRODUCTION=$2
|
||||
echo ${SOURCE}
|
||||
echo ${PRODUCTION}
|
||||
|
||||
#echo "Updating ${PRODUCTION} monitor database old cluster"
|
||||
#impala-shell -q "create database if not exists ${PRODUCTION}"
|
||||
#impala-shell -d ${PRODUCTION} -q "show tables" --delimited | sed "s/^/drop view if exists ${PRODUCTION}./" | sed "s/$/;/" | impala-shell -c -f -
|
||||
#impala-shell -d ${SOURCE} -q "show tables" --delimited | sed "s/\(.*\)/create view ${PRODUCTION}.\1 as select * from ${SOURCE}.\1;/" | impala-shell -c -f -
|
||||
|
||||
echo "Updating ${PRODUCTION} monitor database"
|
||||
impala-shell -i impala-cluster-dn1.openaire.eu -q "create database if not exists ${PRODUCTION}"
|
||||
impala-shell -i impala-cluster-dn1.openaire.eu -d ${PRODUCTION} -q "show tables" --delimited | sed "s/^/drop view if exists ${PRODUCTION}./" | sed "s/$/;/" | impala-shell -i impala-cluster-dn1.openaire.eu -c -f -
|
||||
impala-shell -i impala-cluster-dn1.openaire.eu -d ${SOURCE} -q "show tables" --delimited | sed "s/\(.*\)/create view ${PRODUCTION}.\1 as select * from ${SOURCE}.\1;/" | impala-shell -i impala-cluster-dn1.openaire.eu -c -f -
|
||||
echo "Production monitor db ready!"
|
||||
|
|
@ -0,0 +1,28 @@
|
|||
export PYTHON_EGG_CACHE=/home/$(whoami)/.python-eggs
|
||||
export link_folder=/tmp/impala-shell-python-egg-cache-$(whoami)
|
||||
if ! [ -L $link_folder ]
|
||||
then
|
||||
rm -Rf "$link_folder"
|
||||
ln -sfn ${PYTHON_EGG_CACHE}${link_folder} ${link_folder}
|
||||
fi
|
||||
|
||||
export SOURCE=$1
|
||||
export TARGET=$2
|
||||
export SHADOW=$3
|
||||
export SCRIPT_PATH=$4
|
||||
export GRAPHDB=$5
|
||||
|
||||
|
||||
export HIVE_OPTS="-hiveconf mapred.job.queue.name=analytics -hiveconf hive.spark.client.connect.timeout=120000ms -hiveconf hive.spark.client.server.connect.timeout=300000ms -hiveconf spark.executor.memory=19166291558 -hiveconf spark.yarn.executor.memoryOverhead=3225 -hiveconf spark.driver.memory=11596411699 -hiveconf spark.yarn.driver.memoryOverhead=1228"
|
||||
export HADOOP_USER_NAME="oozie"
|
||||
|
||||
echo "Getting file from " $4
|
||||
hdfs dfs -copyToLocal $4
|
||||
|
||||
#update Monitor DB IRISH
|
||||
#cat CreateDB.sql | sed "s/SOURCE/$1/g" | sed "s/TARGET/$2/g1" | sed "s/GRAPHDB/$3/g1" > foo
|
||||
cat buildIrishMonitorDB.sql | sed "s/SOURCE/$1/g" | sed "s/TARGET/$2/g1" | sed "s/GRAPHDB/$5/g1" > foo
|
||||
hive $HIVE_OPTS -f foo
|
||||
|
||||
echo "Hive shell finished"
|
||||
|
||||
|
|
@ -0,0 +1,241 @@
|
|||
drop database if exists TARGET cascade;
|
||||
create database if not exists TARGET;
|
||||
|
||||
create view if not exists TARGET.category as select * from SOURCE.category;
|
||||
create view if not exists TARGET.concept as select * from SOURCE.concept;
|
||||
create view if not exists TARGET.context as select * from SOURCE.context;
|
||||
create view if not exists TARGET.country as select * from SOURCE.country;
|
||||
create view if not exists TARGET.countrygdp as select * from SOURCE.countrygdp;
|
||||
create view if not exists TARGET.creation_date as select * from SOURCE.creation_date;
|
||||
--create view if not exists TARGET.funder as select * from SOURCE.funder;
|
||||
create view if not exists TARGET.fundref as select * from SOURCE.fundref;
|
||||
create view if not exists TARGET.rndexpenditure as select * from SOURCE.rndexpediture;
|
||||
create view if not exists TARGET.rndgdpexpenditure as select * from SOURCE.rndgdpexpenditure;
|
||||
create view if not exists TARGET.doctoratestudents as select * from SOURCE.doctoratestudents;
|
||||
create view if not exists TARGET.totalresearchers as select * from SOURCE.totalresearchers;
|
||||
create view if not exists TARGET.totalresearchersft as select * from SOURCE.totalresearchersft;
|
||||
create view if not exists TARGET.hrrst as select * from SOURCE.hrrst;
|
||||
|
||||
drop table if exists TARGET.irish_funders;
|
||||
|
||||
create TEMPORARY table TARGET.irish_funders as
|
||||
select distinct xpath_string(fundingtree[0].value, '//funder/name') as funder from GRAPHDB.project
|
||||
where xpath_string(fundingtree[0].value, '//funder/jurisdiction')='IE';
|
||||
--create TEMPORARY table TARGET.irish_funders as
|
||||
--select distinct name as funder from SOURCE.fundref where country='IE';
|
||||
|
||||
drop table if exists TARGET.result;
|
||||
|
||||
create table TARGET.result stored as parquet as
|
||||
select distinct * from (
|
||||
select r.*
|
||||
from SOURCE.result r
|
||||
join SOURCE.result_projects rp on rp.id=r.id
|
||||
join SOURCE.project p on p.id=rp.project
|
||||
join openaire_prod_stats_monitor_ie_20231226b.irish_funders irf on irf.funder=p.funder
|
||||
union all
|
||||
select r.*
|
||||
from SOURCE.result r
|
||||
join SOURCE.result_organization ro on ro.id=r.id
|
||||
join SOURCE.organization o on o.id=ro.organization and o.country='IE'
|
||||
union all
|
||||
select r.*
|
||||
from SOURCE.result r
|
||||
join SOURCE.result_pids pid on pid.id=r.id
|
||||
join stats_ext.transformative_facts tf on tf.doi=pid.pid
|
||||
) foo;
|
||||
|
||||
create view if not exists TARGET.category as select * from SOURCE.category;
|
||||
create view if not exists TARGET.concept as select * from SOURCE.concept;
|
||||
create view if not exists TARGET.context as select * from SOURCE.context;
|
||||
create view if not exists TARGET.country as select * from SOURCE.country;
|
||||
create view if not exists TARGET.countrygdp as select * from SOURCE.countrygdp;
|
||||
create view if not exists TARGET.creation_date as select * from SOURCE.creation_date;
|
||||
|
||||
create table TARGET.funder stored as parquet as select * from SOURCE.funder where country='IE';
|
||||
|
||||
create view if not exists TARGET.fundref as select * from SOURCE.fundref;
|
||||
create view if not exists TARGET.rndexpenditure as select * from SOURCE.rndexpediture;
|
||||
create view if not exists TARGET.rndgdpexpenditure as select * from SOURCE.rndgdpexpenditure;
|
||||
create view if not exists TARGET.doctoratestudents as select * from SOURCE.doctoratestudents;
|
||||
create view if not exists TARGET.totalresearchers as select * from SOURCE.totalresearchers;
|
||||
create view if not exists TARGET.totalresearchersft as select * from SOURCE.totalresearchersft;
|
||||
create view if not exists TARGET.hrrst as select * from SOURCE.hrrst;
|
||||
--create view if not exists TARGET.graduatedoctorates as select * from SOURCE.graduatedoctorates;
|
||||
|
||||
create table TARGET.result_citations stored as parquet as select * from SOURCE.result_citations orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.result_references_oc stored as parquet as select * from SOURCE.result_references_oc orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.result_citations_oc stored as parquet as select * from SOURCE.result_citations_oc orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.result_classifications stored as parquet as select * from SOURCE.result_classifications orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.result_apc stored as parquet as select * from SOURCE.result_apc orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.result_concepts stored as parquet as select * from SOURCE.result_concepts orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.result_datasources stored as parquet as select * from SOURCE.result_datasources orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.result_fundercount stored as parquet as select * from SOURCE.result_fundercount orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.result_gold stored as parquet as select * from SOURCE.result_gold orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.result_greenoa stored as parquet as select * from SOURCE.result_greenoa orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.result_languages stored as parquet as select * from SOURCE.result_languages orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.result_licenses stored as parquet as select * from SOURCE.result_licenses orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.licenses_normalized STORED AS PARQUET as select * from SOURCE.licenses_normalized;
|
||||
|
||||
create table TARGET.result_oids stored as parquet as select * from SOURCE.result_oids orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.result_organization stored as parquet as select * from SOURCE.result_organization orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.result_peerreviewed stored as parquet as select * from SOURCE.result_peerreviewed orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.result_pids stored as parquet as select * from SOURCE.result_pids orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.result_projectcount stored as parquet as select * from SOURCE.result_projectcount orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.result_projects stored as parquet as select * from SOURCE.result_projects orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.result_refereed stored as parquet as select * from SOURCE.result_refereed orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.result_sources stored as parquet as select * from SOURCE.result_sources orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.result_topics stored as parquet as select * from SOURCE.result_topics orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.result_fos stored as parquet as select * from SOURCE.result_fos orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.result_accessroute stored as parquet as select * from SOURCE.result_accessroute orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.result_instance stored as parquet as select * from SOURCE.result_instance orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.result_orcid stored as parquet as select * from SOURCE.result_orcid orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create view TARGET.foo1 as select * from SOURCE.result_result rr where rr.source in (select id from TARGET.result);
|
||||
create view TARGET.foo2 as select * from SOURCE.result_result rr where rr.target in (select id from TARGET.result);
|
||||
create table TARGET.result_result STORED AS PARQUET as select distinct * from (select * from TARGET.foo1 union all select * from TARGET.foo2) foufou;
|
||||
drop view TARGET.foo1;
|
||||
drop view TARGET.foo2;
|
||||
|
||||
-- datasources
|
||||
create view if not exists TARGET.datasource as select * from SOURCE.datasource;
|
||||
create view if not exists TARGET.datasource_oids as select * from SOURCE.datasource_oids;
|
||||
create view if not exists TARGET.datasource_organizations as select * from SOURCE.datasource_organizations;
|
||||
create view if not exists TARGET.datasource_sources as select * from SOURCE.datasource_sources;
|
||||
|
||||
create table TARGET.datasource_results stored as parquet as select id as result, datasource as id from TARGET.result_datasources;
|
||||
|
||||
-- organizations
|
||||
create view if not exists TARGET.organization as select * from SOURCE.organization;
|
||||
create view if not exists TARGET.organization_datasources as select * from SOURCE.organization_datasources;
|
||||
create view if not exists TARGET.organization_pids as select * from SOURCE.organization_pids;
|
||||
create view if not exists TARGET.organization_projects as select * from SOURCE.organization_projects;
|
||||
create view if not exists TARGET.organization_sources as select * from SOURCE.organization_sources;
|
||||
|
||||
-- projects
|
||||
create view if not exists TARGET.project as select * from SOURCE.project;
|
||||
create view if not exists TARGET.project_oids as select * from SOURCE.project_oids;
|
||||
create view if not exists TARGET.project_organizations as select * from SOURCE.project_organizations;
|
||||
create view if not exists TARGET.project_resultcount as select * from SOURCE.project_resultcount;
|
||||
create view if not exists TARGET.project_classification as select * from SOURCE.project_classification;
|
||||
create view if not exists TARGET.project_organization_contribution as select * from SOURCE.project_organization_contribution;
|
||||
|
||||
create table TARGET.project_results stored as parquet as select id as result, project as id from TARGET.result_projects;
|
||||
|
||||
|
||||
-- indicators
|
||||
-- Sprint 1 ----
|
||||
create table TARGET.indi_pub_green_oa stored as parquet as select * from SOURCE.indi_pub_green_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.indi_pub_grey_lit stored as parquet as select * from SOURCE.indi_pub_grey_lit orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.indi_pub_doi_from_crossref stored as parquet as select * from SOURCE.indi_pub_doi_from_crossref orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
-- Sprint 2 ----
|
||||
create table TARGET.indi_result_has_cc_licence stored as parquet as select * from SOURCE.indi_result_has_cc_licence orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.indi_result_has_cc_licence_url stored as parquet as select * from SOURCE.indi_result_has_cc_licence_url orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.indi_pub_has_abstract stored as parquet as select * from SOURCE.indi_pub_has_abstract orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.indi_result_with_orcid stored as parquet as select * from SOURCE.indi_result_with_orcid orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
---- Sprint 3 ----
|
||||
create table TARGET.indi_funded_result_with_fundref stored as parquet as select * from SOURCE.indi_funded_result_with_fundref orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create view TARGET.indi_result_org_collab as select * from SOURCE.indi_result_org_collab;
|
||||
create view TARGET.indi_result_org_country_collab as select * from SOURCE.indi_result_org_country_collab;
|
||||
create view TARGET.indi_project_collab_org as select * from SOURCE.indi_project_collab_org;
|
||||
create view TARGET.indi_project_collab_org_country as select * from SOURCE.indi_project_collab_org_country;
|
||||
create view TARGET.indi_funder_country_collab as select * from SOURCE.indi_funder_country_collab;
|
||||
create view TARGET.indi_result_country_collab as select * from SOURCE.indi_result_country_collab;
|
||||
---- Sprint 4 ----
|
||||
create table TARGET.indi_pub_diamond stored as parquet as select * from SOURCE.indi_pub_diamond orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.indi_pub_in_transformative stored as parquet as select * from SOURCE.indi_pub_in_transformative orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.indi_pub_closed_other_open stored as parquet as select * from SOURCE.indi_pub_closed_other_open orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
---- Sprint 5 ----
|
||||
create table TARGET.indi_result_no_of_copies stored as parquet as select * from SOURCE.indi_result_no_of_copies orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
---- Sprint 6 ----
|
||||
create table TARGET.indi_pub_hybrid_oa_with_cc stored as parquet as select * from SOURCE.indi_pub_hybrid_oa_with_cc orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.indi_pub_bronze_oa stored as parquet as select * from SOURCE.indi_pub_bronze_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.indi_pub_downloads stored as parquet as select * from SOURCE.indi_pub_downloads orig where exists (select 1 from TARGET.result r where r.id=orig.result_id);
|
||||
|
||||
create table TARGET.indi_pub_downloads_datasource stored as parquet as select * from SOURCE.indi_pub_downloads_datasource orig where exists (select 1 from TARGET.result r where r.id=orig.result_id);
|
||||
|
||||
create table TARGET.indi_pub_downloads_year stored as parquet as select * from SOURCE.indi_pub_downloads_year orig where exists (select 1 from TARGET.result r where r.id=orig.result_id);
|
||||
|
||||
create table TARGET.indi_pub_downloads_datasource_year stored as parquet as select * from SOURCE.indi_pub_downloads_datasource_year orig where exists (select 1 from TARGET.result r where r.id=orig.result_id);
|
||||
|
||||
---- Sprint 7 ----
|
||||
create table TARGET.indi_pub_gold_oa stored as parquet as select * from SOURCE.indi_pub_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.indi_pub_hybrid stored as parquet as select * from SOURCE.indi_pub_hybrid orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create view TARGET.indi_org_fairness as select * from SOURCE.indi_org_fairness;
|
||||
create view TARGET.indi_org_fairness_pub_pr as select * from SOURCE.indi_org_fairness_pub_pr;
|
||||
create view TARGET.indi_org_fairness_pub_year as select * from SOURCE.indi_org_fairness_pub_year;
|
||||
create view TARGET.indi_org_fairness_pub as select * from SOURCE.indi_org_fairness_pub;
|
||||
create view TARGET.indi_org_fairness_year as select * from SOURCE.indi_org_fairness_year;
|
||||
create view TARGET.indi_org_findable_year as select * from SOURCE.indi_org_findable_year;
|
||||
create view TARGET.indi_org_findable as select * from SOURCE.indi_org_findable;
|
||||
create view TARGET.indi_org_openess as select * from SOURCE.indi_org_openess;
|
||||
create view TARGET.indi_org_openess_year as select * from SOURCE.indi_org_openess_year;
|
||||
create table TARGET.indi_pub_has_preprint stored as parquet as select * from SOURCE.indi_pub_has_preprint orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.indi_pub_in_subscribed stored as parquet as select * from SOURCE.indi_pub_in_subscribed orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.indi_result_with_pid stored as parquet as select * from SOURCE.indi_result_with_pid orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.indi_impact_measures stored as parquet as select * from SOURCE.indi_impact_measures orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.indi_pub_interdisciplinarity stored as parquet as select * from SOURCE.indi_pub_interdisciplinarity orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.result_apc_affiliations stored as parquet as select * from SOURCE.result_apc_affiliations orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.indi_is_project_result_after stored as parquet as select * from SOURCE.indi_is_project_result_after orig where exists (select 1 from TARGET.result r where r.id=orig.result_id);
|
||||
create view TARGET.indi_is_funder_plan_s as select * from SOURCE.indi_is_funder_plan_s;
|
||||
create view TARGET.indi_funder_fairness as select * from SOURCE.indi_funder_fairness;
|
||||
create view TARGET.indi_funder_openess as select * from SOURCE.indi_funder_openess;
|
||||
create view TARGET.indi_funder_findable as select * from SOURCE.indi_funder_findable;
|
||||
create view TARGET.indi_ris_fairness as select * from SOURCE.indi_ris_fairness;
|
||||
create view TARGET.indi_ris_openess as select * from SOURCE.indi_ris_openess;
|
||||
create view TARGET.indi_ris_findable as select * from SOURCE.indi_ris_findable;
|
||||
|
||||
create table TARGET.indi_pub_green_with_license stored as parquet as select * from SOURCE.indi_pub_green_with_license orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
create table TARGET.result_country stored as parquet as select * from SOURCE.result_country orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
create table TARGET.indi_pub_publicly_funded stored as parquet as select * from SOURCE.indi_pub_publicly_funded orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.indi_result_oa_with_license stored as parquet as select * from SOURCE.indi_result_oa_with_license orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
create table TARGET.indi_result_oa_without_license stored as parquet as select * from SOURCE.indi_result_oa_without_license orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.indi_result_under_transformative stored as parquet as select * from SOURCE.indi_result_under_transformative orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
|
@ -0,0 +1,118 @@
|
|||
<workflow-app name="Irish Monitor Update" xmlns="uri:oozie:workflow:0.5">
|
||||
<parameters>
|
||||
<property>
|
||||
<name>stats_db_name</name>
|
||||
<description>the target stats database name</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>graph_db_name</name>
|
||||
<description>the graph database name</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>monitor_irish_db_name</name>
|
||||
<description>the target monitor db name</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>monitor_irish_db_prod_name</name>
|
||||
<description>the name of the production monitor db</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>monitor_irish_db_shadow_name</name>
|
||||
<description>the name of the shadow monitor db</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>hive_metastore_uris</name>
|
||||
<description>hive server metastore URIs</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>hive_jdbc_url</name>
|
||||
<description>hive server jdbc url</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>hive_timeout</name>
|
||||
<description>the time period, in seconds, after which Hive fails a transaction if a Hive client has not sent a hearbeat. The default value is 300 seconds.</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>hadoop_user_name</name>
|
||||
<description>user name of the wf owner</description>
|
||||
</property>
|
||||
</parameters>
|
||||
|
||||
<global>
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<configuration>
|
||||
<property>
|
||||
<name>hive.metastore.uris</name>
|
||||
<value>${hive_metastore_uris}</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>hive.txn.timeout</name>
|
||||
<value>${hive_timeout}</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>mapred.job.queue.name</name>
|
||||
<value>analytics</value>
|
||||
</property>
|
||||
</configuration>
|
||||
</global>
|
||||
|
||||
<start to="resume_from"/>
|
||||
<decision name="resume_from">
|
||||
<switch>
|
||||
<case to="Step1-buildIrishMonitorDB">${wf:conf('resumeFrom') eq 'Step1-buildIrishMonitorDB'}</case>
|
||||
<case to="Step2-copyDataToImpalaCluster">${wf:conf('resumeFrom') eq 'Step2-copyDataToImpalaCluster'}</case>
|
||||
<case to="Step3-finalizeImpalaCluster">${wf:conf('resumeFrom') eq 'Step3-finalizeImpalaCluster'}</case>
|
||||
<default to="Step1-buildIrishMonitorDB"/>
|
||||
</switch>
|
||||
</decision>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
<action name="Step1-buildIrishMonitorDB">
|
||||
<shell xmlns="uri:oozie:shell-action:0.1">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<exec>monitor_irish.sh</exec>
|
||||
<argument>${stats_db_name}</argument>
|
||||
<argument>${monitor_irish_db_name}</argument>
|
||||
<argument>${monitor_irish_db_shadow_name}</argument>
|
||||
<argument>${wf:appPath()}/scripts/buildIrishMonitorDB.sql</argument>
|
||||
<argument>${graph_db_name}</argument>
|
||||
<file>monitor_irish.sh</file>
|
||||
</shell>
|
||||
<ok to="Step2-copyDataToImpalaCluster"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="Step2-copyDataToImpalaCluster">
|
||||
<shell xmlns="uri:oozie:shell-action:0.1">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<exec>copyDataToImpalaCluster.sh</exec>
|
||||
<argument>${monitor_irish_db_name}</argument>
|
||||
<argument>${hadoop_user_name}</argument>
|
||||
<file>copyDataToImpalaCluster.sh</file>
|
||||
</shell>
|
||||
<ok to="Step3-finalizeImpalaCluster"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="Step3-finalizeImpalaCluster">
|
||||
<shell xmlns="uri:oozie:shell-action:0.1">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<exec>finalizeImpalaCluster.sh</exec>
|
||||
<argument>${monitor_irish_db_name}</argument>
|
||||
<argument>${monitor_irish_db_prod_name}</argument>
|
||||
<argument>${monitor_irish_db_shadow_name}</argument>
|
||||
<file>finalizeImpalaCluster.sh</file>
|
||||
</shell>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
||||
|
|
@ -0,0 +1,32 @@
|
|||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
|
||||
<parent>
|
||||
<artifactId>dhp-workflows</artifactId>
|
||||
<groupId>eu.dnetlib.dhp</groupId>
|
||||
<version>1.2.5-SNAPSHOT</version>
|
||||
</parent>
|
||||
<modelVersion>4.0.0</modelVersion>
|
||||
<artifactId>dhp-stats-monitor-update</artifactId>
|
||||
<dependencies>
|
||||
<dependency>
|
||||
<groupId>org.apache.spark</groupId>
|
||||
<artifactId>spark-core_2.11</artifactId>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.apache.spark</groupId>
|
||||
<artifactId>spark-sql_2.11</artifactId>
|
||||
</dependency>
|
||||
</dependencies>
|
||||
<build>
|
||||
<plugins>
|
||||
<plugin>
|
||||
<groupId>pl.project13.maven</groupId>
|
||||
<artifactId>git-commit-id-plugin</artifactId>
|
||||
<version>2.1.11</version>
|
||||
<configuration>
|
||||
<failOnNoGitDirectory>false</failOnNoGitDirectory>
|
||||
</configuration>
|
||||
</plugin>
|
||||
</plugins>
|
||||
</build>
|
||||
</project>
|
||||
|
|
@ -0,0 +1,30 @@
|
|||
<configuration>
|
||||
<property>
|
||||
<name>jobTracker</name>
|
||||
<value>${jobTracker}</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>nameNode</name>
|
||||
<value>${nameNode}</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.use.system.libpath</name>
|
||||
<value>true</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.action.sharelib.for.spark</name>
|
||||
<value>spark2</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>hive_metastore_uris</name>
|
||||
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>hive_jdbc_url</name>
|
||||
<value>jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000/;UseNativeQuery=1;?spark.executor.memory=22166291558;spark.yarn.executor.memoryOverhead=3225;spark.driver.memory=15596411699;spark.yarn.driver.memoryOverhead=1228</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.wf.workflow.notification.url</name>
|
||||
<value>{serviceUrl}/v1/oozieNotification/jobUpdate?jobId=$jobId%26status=$status</value>
|
||||
</property>
|
||||
</configuration>
|
||||
|
|
@ -0,0 +1,223 @@
|
|||
export PYTHON_EGG_CACHE=/home/$(whoami)/.python-eggs
|
||||
export link_folder=/tmp/impala-shell-python-egg-cache-$(whoami)
|
||||
if ! [ -L $link_folder ]
|
||||
then
|
||||
rm -Rf "$link_folder"
|
||||
ln -sfn ${PYTHON_EGG_CACHE}${link_folder} ${link_folder}
|
||||
fi
|
||||
|
||||
export HADOOP_USER_NAME=$2
|
||||
|
||||
# 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}"
|
||||
|
||||
IMPALA_HDFS_NODE=''
|
||||
COUNTER=0
|
||||
while [ $COUNTER -lt 3 ]; do
|
||||
if hdfs dfs -test -e hdfs://impala-cluster-mn1.openaire.eu/tmp >/dev/null 2>&1; then
|
||||
IMPALA_HDFS_NODE='hdfs://impala-cluster-mn1.openaire.eu:8020'
|
||||
break
|
||||
elif hdfs dfs -test -e hdfs://impala-cluster-mn2.openaire.eu/tmp >/dev/null 2>&1; then
|
||||
IMPALA_HDFS_NODE='hdfs://impala-cluster-mn2.openaire.eu:8020'
|
||||
break
|
||||
else
|
||||
IMPALA_HDFS_NODE=''
|
||||
sleep 1
|
||||
fi
|
||||
((COUNTER++))
|
||||
done
|
||||
if [ -z "$IMPALA_HDFS_NODE" ]; then
|
||||
echo -e "\n\nERROR: PROBLEM WHEN SETTING THE HDFS-NODE FOR IMPALA CLUSTER! | AFTER ${COUNTER} RETRIES.\n\n"
|
||||
exit 1
|
||||
fi
|
||||
echo -e "Active IMPALA HDFS Node: ${IMPALA_HDFS_NODE} , after ${COUNTER} retries.\n\n"
|
||||
|
||||
IMPALA_HOSTNAME='impala-cluster-dn1.openaire.eu'
|
||||
IMPALA_CONFIG_FILE='/etc/impala_cluster/hdfs-site.xml'
|
||||
|
||||
IMPALA_HDFS_DB_BASE_PATH="${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'
|
||||
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'
|
||||
|
||||
|
||||
function copydb() {
|
||||
db=$1
|
||||
echo -e "\nStart processing db: '${db}'..\n"
|
||||
|
||||
# Delete the old DB from Impala cluster (if exists).
|
||||
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "drop database if exists ${db} cascade" |& tee error.log # impala-shell prints all logs in stderr, so wee need to capture them and put them in a file, in order to perform "grep" on them later
|
||||
log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
|
||||
if [ -n "$log_errors" ]; then
|
||||
echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN DROPPING THE OLD DATABASE! EXITING...\n\n"
|
||||
rm -f error.log
|
||||
return 1
|
||||
fi
|
||||
|
||||
# Make Impala aware of the deletion of the old DB immediately.
|
||||
sleep 1
|
||||
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
|
||||
|
||||
echo -e "\n\nCopying files of '${db}', from Ocean to Impala cluster..\n"
|
||||
# Using max-bandwidth of: 50 * 100 Mb/s = 5 Gb/s
|
||||
# Using max memory of: 50 * 6144 = 300 Gb
|
||||
# Using 1MB as a buffer-size.
|
||||
# The " -Ddistcp.dynamic.recordsPerChunk=50" arg is not available in our version of hadoop
|
||||
# The "ug" args cannot be used as we get a "User does not belong to hive" error.
|
||||
# The "p" argument cannot be used, as it blocks the files from being used, giving a "sticky bit"-error, even after applying chmod and chown onm the files.
|
||||
hadoop distcp -Dmapreduce.map.memory.mb=6144 -m 70 -bandwidth 150 \
|
||||
-numListstatusThreads 40 \
|
||||
-copybuffersize 1048576 \
|
||||
-strategy dynamic \
|
||||
-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"
|
||||
else
|
||||
echo -e "\n\nERROR: FAILED TO TRANSFER THE FILES OF '${db}', WITH 'hadoop distcp'. GOT WITH EXIT STATUS: $?\n\n"
|
||||
rm -f error.log
|
||||
return 2
|
||||
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
|
||||
|
||||
echo -e "\nCreating schema for db: '${db}'\n"
|
||||
|
||||
# create the new database (with the same name)
|
||||
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create database ${db}"
|
||||
|
||||
# Make Impala aware of the creation of the new DB immediately.
|
||||
sleep 1
|
||||
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
|
||||
sleep 1
|
||||
# Because "Hive" and "Impala" do not have compatible schemas, we cannot use the "show create table <name>" output from hive to create the exact same table in impala.
|
||||
# So, we have to find at least one parquet file (check if it's there) from the table in the ocean cluster for impala to use it to extract the table-schema itself from that file.
|
||||
|
||||
all_create_view_statements=()
|
||||
|
||||
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.
|
||||
# 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_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' \
|
||||
| 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"
|
||||
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"
|
||||
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 '${i}'!\n\n"
|
||||
fi
|
||||
fi
|
||||
fi
|
||||
done
|
||||
|
||||
echo -e "\nAll tables have been created, going to create the views..\n"
|
||||
|
||||
# Time to loop through the views and create them.
|
||||
# At this point all table-schemas should have been created.
|
||||
|
||||
previous_num_of_views_to_retry=${#all_create_view_statements}
|
||||
if [[ $previous_num_of_views_to_retry -gt 0 ]]; then
|
||||
echo -e "\nAll_create_view_statements:\n\n${all_create_view_statements[@]}\n" # DEBUG
|
||||
# Make Impala aware of the new tables, so it knows them when creating the views.
|
||||
sleep 1
|
||||
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
|
||||
sleep 1
|
||||
else
|
||||
echo -e "\nDB '${db}' does not contain any views.\n"
|
||||
fi
|
||||
|
||||
level_counter=0
|
||||
while [[ ${#all_create_view_statements[@]} -gt 0 ]]; do
|
||||
((level_counter++))
|
||||
# The only accepted reason for a view to not be created, is if it depends on another view, which has not been created yet.
|
||||
# In this case, we should retry creating this particular view again.
|
||||
should_retry_create_view_statements=()
|
||||
|
||||
for create_view_statement in "${all_create_view_statements[@]}"; do # Here we use double quotes, as the elements are phrases, instead of single-words.
|
||||
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "${create_view_statement}" |& tee error.log # impala-shell prints all logs in stderr, so wee need to capture them and put them in a file, in order to perform "grep" on them later
|
||||
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 "CREATE VIEW " | sed 's/CREATE VIEW //g' | sed 's/ as select .*//g')' failed to be created, possibly because it depends on another view.\n"
|
||||
should_retry_create_view_statements+=("$create_view_statement")
|
||||
else
|
||||
sleep 1 # Wait a bit for Impala to register that the view was created, before possibly referencing it by another view.
|
||||
fi
|
||||
done
|
||||
|
||||
new_num_of_views_to_retry=${#should_retry_create_view_statements}
|
||||
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"
|
||||
return 3
|
||||
elif [[ $new_num_of_views_to_retry -gt 0 ]]; then
|
||||
echo -e "\nTo be retried \"create_view_statements\":\n\n${should_retry_create_view_statements[@]}\n"
|
||||
previous_num_of_views_to_retry=$new_num_of_views_to_retry
|
||||
else
|
||||
echo -e "\nFinished creating views, for db: '${db}', in level-${level_counter}.\n"
|
||||
fi
|
||||
all_create_view_statements=("${should_retry_create_view_statement[@]}") # This is needed in any case to either move forward with the rest of the views or stop at 0 remaining views.
|
||||
done
|
||||
|
||||
sleep 1
|
||||
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
|
||||
sleep 1
|
||||
|
||||
echo -e "\nComputing stats for tables..\n"
|
||||
entities_on_impala=`impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} --delimited -q "show tables in ${db}"`
|
||||
for i in ${entities_on_impala[@]}; do # Use un-quoted values, as the elemetns are single-words.
|
||||
# Taking the create table statement from the Ocean cluster, just to check if its a view, as the output is easier than using impala-shell from Impala cluster.
|
||||
create_view_statement=`hive -e "show create table ${db}.${i};" | grep "CREATE VIEW"` # This grep works here, as we do not want to match multiple-lines.
|
||||
if [ -z "$create_view_statement" ]; then # If it's a table, then go load the data to it.
|
||||
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "compute stats ${db}.${i}";
|
||||
fi
|
||||
done
|
||||
|
||||
if [ "${entities_on_impala[@]}" == "${entities_on_ocean[@]}" ]; then
|
||||
echo -e "\nAll entities have been copied to Impala cluster.\n"
|
||||
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
|
||||
return 4
|
||||
fi
|
||||
|
||||
rm -f error.log
|
||||
echo -e "\n\nFinished processing db: ${db}\n\n"
|
||||
}
|
||||
|
||||
|
||||
MONITOR_DB=$1
|
||||
|
||||
copydb $MONITOR_DB'_institutions'
|
||||
copydb $MONITOR_DB
|
||||
|
||||
|
|
@ -0,0 +1,57 @@
|
|||
export PYTHON_EGG_CACHE=/home/$(whoami)/.python-eggs
|
||||
export link_folder=/tmp/impala-shell-python-egg-cache-$(whoami)
|
||||
if ! [ -L $link_folder ]
|
||||
then
|
||||
rm -Rf "$link_folder"
|
||||
ln -sfn ${PYTHON_EGG_CACHE}${link_folder} ${link_folder}
|
||||
fi
|
||||
#
|
||||
#function createShadowDB() {
|
||||
# SOURCE=$1
|
||||
# SHADOW=$2
|
||||
#
|
||||
# # drop views from db
|
||||
# for i in `impala-shell -i impala-cluster-dn1.openaire.eu -d ${SHADOW} --delimited -q "show tables"`;
|
||||
# do
|
||||
# `impala-shell -i impala-cluster-dn1.openaire.eu -d ${SHADOW} -q "drop view $i;"`;
|
||||
# done
|
||||
#
|
||||
# impala-shell -i impala-cluster-dn1.openaire.eu -q "drop database ${SHADOW} CASCADE";
|
||||
# impala-shell -i impala-cluster-dn1.openaire.eu -q "create database if not exists ${SHADOW}";
|
||||
## impala-shell -i impala-cluster-dn1.openaire.eu -d ${SHADOW} -q "show tables" | sed "s/^/drop view if exists ${SHADOW}./" | sed "s/$/;/" | impala-shell -i impala-cluster-dn1.openaire.eu -f -
|
||||
# impala-shell -i impala-cluster-dn1.openaire.eu -d ${SOURCE} -q "show tables" --delimited | sed "s/\(.*\)/create view ${SHADOW}.\1 as select * from ${SOURCE}.\1;/" | impala-shell -i impala-cluster-dn1.openaire.eu -f -
|
||||
#}
|
||||
#
|
||||
#MONITOR_DB=$1
|
||||
#MONITOR_DB_SHADOW=$2
|
||||
#
|
||||
#createShadowDB $MONITOR_DB'_institutions' $MONITOR_DB'_institutions_shadow'
|
||||
#createShadowDB $MONITOR_DB $MONITOR_DB'_shadow'
|
||||
|
||||
SOURCE=$1
|
||||
PRODUCTION=$2
|
||||
echo ${SOURCE}
|
||||
echo ${PRODUCTION}
|
||||
|
||||
#echo "Updating ${PRODUCTION} monitor database old cluster"
|
||||
#impala-shell -q "create database if not exists ${PRODUCTION}"
|
||||
#impala-shell -d ${PRODUCTION} -q "show tables" --delimited | sed "s/^/drop view if exists ${PRODUCTION}./" | sed "s/$/;/" | impala-shell -c -f -
|
||||
#impala-shell -d ${SOURCE} -q "show tables" --delimited | sed "s/\(.*\)/create view ${PRODUCTION}.\1 as select * from ${SOURCE}.\1;/" | impala-shell -c -f -
|
||||
#
|
||||
#echo "Updating ${PRODUCTION}_institutions database old cluster"
|
||||
#impala-shell -q "create database if not exists ${PRODUCTION}_institutions"
|
||||
#impala-shell -d ${PRODUCTION}_institutions -q "show tables" --delimited | sed "s/^/drop view if exists ${PRODUCTION}_institutions./" | sed "s/$/;/" | impala-shell -c -f -
|
||||
#impala-shell -d ${SOURCE}_institutions -q "show tables" --delimited | sed "s/\(.*\)/create view ${PRODUCTION}_institutions.\1 as select * from ${SOURCE}_institutions.\1;/" | impala-shell -c -f -
|
||||
#echo "Production insitutions db ready!"
|
||||
|
||||
echo "Updating ${PRODUCTION} monitor database"
|
||||
impala-shell -i impala-cluster-dn1.openaire.eu -q "create database if not exists ${PRODUCTION}"
|
||||
impala-shell -i impala-cluster-dn1.openaire.eu -d ${PRODUCTION} -q "show tables" --delimited | sed "s/^/drop view if exists ${PRODUCTION}./" | sed "s/$/;/" | impala-shell -i impala-cluster-dn1.openaire.eu -c -f -
|
||||
impala-shell -i impala-cluster-dn1.openaire.eu -d ${SOURCE} -q "show tables" --delimited | sed "s/\(.*\)/create view ${PRODUCTION}.\1 as select * from ${SOURCE}.\1;/" | impala-shell -i impala-cluster-dn1.openaire.eu -c -f -
|
||||
echo "Production monitor db ready!"
|
||||
|
||||
echo "Updating ${PRODUCTION}_institutions database"
|
||||
impala-shell -i impala-cluster-dn1.openaire.eu -q "create database if not exists ${PRODUCTION}_institutions"
|
||||
impala-shell -i impala-cluster-dn1.openaire.eu -d ${PRODUCTION}_institutions -q "show tables" --delimited | sed "s/^/drop view if exists ${PRODUCTION}_institutions./" | sed "s/$/;/" | impala-shell -i impala-cluster-dn1.openaire.eu -c -f -
|
||||
impala-shell -i impala-cluster-dn1.openaire.eu -d ${SOURCE}_institutions -q "show tables" --delimited | sed "s/\(.*\)/create view ${PRODUCTION}_institutions.\1 as select * from ${SOURCE}_institutions.\1;/" | impala-shell -i impala-cluster-dn1.openaire.eu -c -f -
|
||||
echo "Production insitutions db ready!"
|
||||
|
|
@ -0,0 +1,60 @@
|
|||
export PYTHON_EGG_CACHE=/home/$(whoami)/.python-eggs
|
||||
export link_folder=/tmp/impala-shell-python-egg-cache-$(whoami)
|
||||
if ! [ -L $link_folder ]
|
||||
then
|
||||
rm -Rf "$link_folder"
|
||||
ln -sfn ${PYTHON_EGG_CACHE}${link_folder} ${link_folder}
|
||||
fi
|
||||
|
||||
export SOURCE=$1
|
||||
export TARGET=$2
|
||||
export SHADOW=$3
|
||||
export SCRIPT_PATH=$4
|
||||
export SCRIPT_PATH2=$5
|
||||
export SCRIPT_PATH2=$6
|
||||
|
||||
export HIVE_OPTS="-hiveconf mapred.job.queue.name=analytics -hiveconf hive.spark.client.connect.timeout=120000ms -hiveconf hive.spark.client.server.connect.timeout=300000ms -hiveconf spark.executor.memory=19166291558 -hiveconf spark.yarn.executor.memoryOverhead=3225 -hiveconf spark.driver.memory=11596411699 -hiveconf spark.yarn.driver.memoryOverhead=1228"
|
||||
export HADOOP_USER_NAME="oozie"
|
||||
|
||||
echo "Getting file from " $4
|
||||
hdfs dfs -copyToLocal $4
|
||||
|
||||
echo "Getting file from " $5
|
||||
hdfs dfs -copyToLocal $5
|
||||
|
||||
echo "Getting file from " $6
|
||||
hdfs dfs -copyToLocal $6
|
||||
|
||||
#update Monitor DB
|
||||
cat updateMonitorDBAll.sql | sed "s/SOURCE/$1/g" | sed "s/TARGET/$2/g1" > foo
|
||||
hive $HIVE_OPTS -f foo
|
||||
|
||||
#update Institutions DB
|
||||
cat updateMonitorDB_institutions.sql | sed "s/SOURCE/$1/g" | sed "s/TARGET/$2_institutions/g1" > foo
|
||||
hive $HIVE_OPTS -f foo
|
||||
cat updateMonitorDB.sql | sed "s/SOURCE/$1/g" | sed "s/TARGET/$2_institutions/g1" > foo
|
||||
hive $HIVE_OPTS -f foo
|
||||
|
||||
|
||||
|
||||
echo "Hive shell finished"
|
||||
|
||||
#echo "Updating shadow monitor insitutions database"
|
||||
#hive -e "drop database if exists ${SHADOW}_institutions cascade"
|
||||
#hive -e "create database if not exists ${SHADOW}_institutions"
|
||||
#hive $HIVE_OPTS --database ${2}_institutions -e "show tables" | grep -v WARN | sed "s/\(.*\)/create view ${SHADOW}_institutions.\1 as select * from ${2}_institutions.\1;/" > foo
|
||||
#hive -f foo
|
||||
#echo "Shadow db monitor insitutions ready!"
|
||||
#
|
||||
##update Monitor DB
|
||||
#cat updateMonitorDBAll.sql | sed "s/SOURCE/$1/g" | sed "s/TARGET/$2/g1" > foo
|
||||
#hive $HIVE_OPTS -f foo
|
||||
#
|
||||
#echo "Hive shell finished"
|
||||
#
|
||||
#echo "Updating shadow monitor database"
|
||||
#hive -e "drop database if exists ${SHADOW} cascade"
|
||||
#hive -e "create database if not exists ${SHADOW}"
|
||||
#hive $HIVE_OPTS --database ${2} -e "show tables" | grep -v WARN | sed "s/\(.*\)/create view ${SHADOW}.\1 as select * from ${2}.\1;/" > foo
|
||||
#hive -f foo
|
||||
#echo "Shadow db monitor insitutions ready!"
|
||||
|
|
@ -0,0 +1,278 @@
|
|||
--drop database if exists TARGET cascade;
|
||||
--create database if not exists TARGET;
|
||||
--
|
||||
--create view if not exists TARGET.category as select * from SOURCE.category;
|
||||
--create view if not exists TARGET.concept as select * from SOURCE.concept;
|
||||
--create view if not exists TARGET.context as select * from SOURCE.context;
|
||||
--create view if not exists TARGET.country as select * from SOURCE.country;
|
||||
--create view if not exists TARGET.countrygdp as select * from SOURCE.countrygdp;
|
||||
--create view if not exists TARGET.creation_date as select * from SOURCE.creation_date;
|
||||
--create view if not exists TARGET.funder as select * from SOURCE.funder;
|
||||
--create view if not exists TARGET.fundref as select * from SOURCE.fundref;
|
||||
--create view if not exists TARGET.rndexpenditure as select * from SOURCE.rndexpediture;
|
||||
--create view if not exists TARGET.rndgdpexpenditure as select * from SOURCE.rndgdpexpenditure;
|
||||
--create view if not exists TARGET.doctoratestudents as select * from SOURCE.doctoratestudents;
|
||||
--create view if not exists TARGET.totalresearchers as select * from SOURCE.totalresearchers;
|
||||
--create view if not exists TARGET.totalresearchersft as select * from SOURCE.totalresearchersft;
|
||||
--create view if not exists TARGET.hrrst as select * from SOURCE.hrrst;
|
||||
--
|
||||
--create table TARGET.result stored as parquet as
|
||||
-- select distinct * from (
|
||||
-- select * from SOURCE.result r where exists (select 1 from SOURCE.result_projects rp join SOURCE.project p on rp.project=p.id where rp.id=r.id)
|
||||
-- union all
|
||||
-- select * from SOURCE.result r where exists (select 1 from SOURCE.result_concepts rc where rc.id=r.id)
|
||||
-- union all
|
||||
-- select * from SOURCE.result r where exists (select 1 from SOURCE.result_organization ro where ro.id=r.id and ro.organization in (
|
||||
-- 'openorgs____::b84450f9864182c67b8611b5593f4250', --"Athena Research and Innovation Center In Information Communication & Knowledge Technologies', --ARC"
|
||||
-- 'openorgs____::d41cf6bd4ab1b1362a44397e0b95c975', --National Research Council
|
||||
-- 'openorgs____::d2a09b9d5eabb10c95f9470e172d05d2', --??? Not exists ??
|
||||
-- 'openorgs____::d169c7407dd417152596908d48c11460', --Masaryk University
|
||||
-- 'openorgs____::1ec924b1759bb16d0a02f2dad8689b21', --University of Belgrade
|
||||
-- 'openorgs____::0ae431b820e4c33db8967fbb2b919150', --University of Helsinki
|
||||
-- 'openorgs____::759d59f05d77188faee99b7493b46805', --University of Minho
|
||||
-- 'openorgs____::cad284878801b9465fa51a95b1d779db', --Universidad Politécnica de Madrid
|
||||
-- 'openorgs____::eadc8da90a546e98c03f896661a2e4d4', --University of Göttingen
|
||||
-- 'openorgs____::c0286313e36479eff8676dba9b724b40', --National and Kapodistrian University of Athens
|
||||
-- -- 'openorgs____::c80a8243a5e5c620d7931c88d93bf17a', --Université Paris Diderot
|
||||
-- 'openorgs____::c08634f0a6b0081c3dc6e6c93a4314f3', --Bielefeld University
|
||||
-- 'openorgs____::6fc85e4a8f7ecaf4b0c738d010e967ea', --University of Southern Denmark
|
||||
-- 'openorgs____::3d6122f87f9a97a99d8f6e3d73313720', --Humboldt-Universität zu Berlin
|
||||
-- 'openorgs____::16720ada63d0fa8ca41601feae7d1aa5', --TU Darmstadt
|
||||
-- 'openorgs____::ccc0a066b56d2cfaf90c2ae369df16f5', --KU Leuven
|
||||
-- 'openorgs____::4c6f119632adf789746f0a057ed73e90', --University of the Western Cape
|
||||
-- 'openorgs____::ec3665affa01aeafa28b7852c4176dbd', --Rudjer Boskovic Institute
|
||||
-- 'openorgs____::5f31346d444a7f06a28c880fb170b0f6', --Ghent University
|
||||
-- 'openorgs____::2dbe47117fd5409f9c61620813456632', --University of Luxembourg
|
||||
-- 'openorgs____::6445d7758d3a40c4d997953b6632a368', --National Institute of Informatics (NII)
|
||||
-- 'openorgs____::b77c01aa15de3675da34277d48de2ec1', -- Valencia Catholic University Saint Vincent Martyr
|
||||
-- 'openorgs____::7fe2f66cdc43983c6b24816bfe9cf6a0', -- Unviersity of Warsaw
|
||||
-- 'openorgs____::15e7921fc50d9aa1229a82a84429419e', -- University Of Thessaly
|
||||
-- 'openorgs____::11f7919dadc8f8a7251af54bba60c956', -- Technical University of Crete
|
||||
-- 'openorgs____::84f0c5f5dbb6daf42748485924efde4b', -- University of Piraeus
|
||||
-- 'openorgs____::4ac562f0376fce3539504567649cb373', -- University of Patras
|
||||
-- 'openorgs____::3e8d1f8c3f6cd7f418b09f1f58b4873b', -- Aristotle University of Thessaloniki
|
||||
-- 'openorgs____::3fcef6e1c469c10f2a84b281372c9814', -- World Bank
|
||||
-- 'openorgs____::1698a2eb1885ef8adb5a4a969e745ad3', -- École des Ponts ParisTech
|
||||
-- 'openorgs____::e15adb13c4dadd49de4d35c39b5da93a', -- Nanyang Technological University
|
||||
-- 'openorgs____::4b34103bde246228fcd837f5f1bf4212', -- Autonomous University of Barcelona
|
||||
-- 'openorgs____::72ec75fcfc4e0df1a76dc4c49007fceb', -- McMaster University
|
||||
-- 'openorgs____::51c7fc556e46381734a25a6fbc3fd398', -- University of Modena and Reggio Emilia
|
||||
-- 'openorgs____::235d7f9ad18ecd7e6dc62ea4990cb9db', -- Bilkent University
|
||||
-- 'openorgs____::31f2fa9e05b49d4cf40a19c3fed8eb06', -- Saints Cyril and Methodius University of Skopje
|
||||
-- 'openorgs____::db7686f30f22cbe73a4fde872ce812a6', -- University of Milan
|
||||
-- 'openorgs____::b8b8ca674452579f3f593d9f5e557483', -- University College Cork
|
||||
-- 'openorgs____::38d7097854736583dde879d12dacafca' -- Brown University
|
||||
-- 'openorgs____::57784c9e047e826fefdb1ef816120d92', --Arts et Métiers ParisTech
|
||||
-- 'openorgs____::2530baca8a15936ba2e3297f2bce2e7e', -- University of Cape Town
|
||||
-- 'openorgs____::d11f981828c485cd23d93f7f24f24db1', -- Technological University Dublin
|
||||
-- 'openorgs____::5e6bf8962665cdd040341171e5c631d8', -- Delft University of Technology
|
||||
-- 'openorgs____::846cb428d3f52a445f7275561a7beb5d', -- University of Manitoba
|
||||
-- 'openorgs____::eb391317ed0dc684aa81ac16265de041', -- Universitat Rovira i Virgili
|
||||
-- 'openorgs____::66aa9fc2fceb271423dfabcc38752dc0', -- Lund University
|
||||
-- 'openorgs____::3cff625a4370d51e08624cc586138b2f' -- IMT Atlantique
|
||||
-- ) )) foo;
|
||||
--
|
||||
--ANALYZE TABLE TARGET.result COMPUTE STATISTICS;
|
||||
|
||||
create view if not exists TARGET.category as select * from SOURCE.category;
|
||||
create view if not exists TARGET.concept as select * from SOURCE.concept;
|
||||
create view if not exists TARGET.context as select * from SOURCE.context;
|
||||
create view if not exists TARGET.country as select * from SOURCE.country;
|
||||
create view if not exists TARGET.countrygdp as select * from SOURCE.countrygdp;
|
||||
create view if not exists TARGET.creation_date as select * from SOURCE.creation_date;
|
||||
create view if not exists TARGET.funder as select * from SOURCE.funder;
|
||||
create view if not exists TARGET.fundref as select * from SOURCE.fundref;
|
||||
create view if not exists TARGET.rndexpenditure as select * from SOURCE.rndexpediture;
|
||||
create view if not exists TARGET.rndgdpexpenditure as select * from SOURCE.rndgdpexpenditure;
|
||||
create view if not exists TARGET.doctoratestudents as select * from SOURCE.doctoratestudents;
|
||||
create view if not exists TARGET.totalresearchers as select * from SOURCE.totalresearchers;
|
||||
create view if not exists TARGET.totalresearchersft as select * from SOURCE.totalresearchersft;
|
||||
create view if not exists TARGET.hrrst as select * from SOURCE.hrrst;
|
||||
--create view if not exists TARGET.graduatedoctorates as select * from SOURCE.graduatedoctorates;
|
||||
|
||||
create table TARGET.result_citations stored as parquet as select * from SOURCE.result_citations orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_citations COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_references_oc stored as parquet as select * from SOURCE.result_references_oc orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_references_oc COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_citations_oc stored as parquet as select * from SOURCE.result_citations_oc orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_citations_oc COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_classifications stored as parquet as select * from SOURCE.result_classifications orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_classifications COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_apc stored as parquet as select * from SOURCE.result_apc orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_apc COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_concepts stored as parquet as select * from SOURCE.result_concepts orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_concepts COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_datasources stored as parquet as select * from SOURCE.result_datasources orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_datasources COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_fundercount stored as parquet as select * from SOURCE.result_fundercount orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_fundercount COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_gold stored as parquet as select * from SOURCE.result_gold orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_gold COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_greenoa stored as parquet as select * from SOURCE.result_greenoa orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_greenoa COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_languages stored as parquet as select * from SOURCE.result_languages orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_languages COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_licenses stored as parquet as select * from SOURCE.result_licenses orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_licenses COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.licenses_normalized STORED AS PARQUET as select * from SOURCE.licenses_normalized;
|
||||
--ANALYZE TABLE TARGET.licenses_normalized COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_oids stored as parquet as select * from SOURCE.result_oids orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_oids COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_organization stored as parquet as select * from SOURCE.result_organization orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_organization COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_peerreviewed stored as parquet as select * from SOURCE.result_peerreviewed orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_peerreviewed COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_pids stored as parquet as select * from SOURCE.result_pids orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_pids COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_projectcount stored as parquet as select * from SOURCE.result_projectcount orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_projectcount COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_projects stored as parquet as select * from SOURCE.result_projects orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_projects COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_refereed stored as parquet as select * from SOURCE.result_refereed orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_refereed COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_sources stored as parquet as select * from SOURCE.result_sources orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_sources COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_topics stored as parquet as select * from SOURCE.result_topics orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_topics COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_fos stored as parquet as select * from SOURCE.result_fos orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_fos COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_accessroute stored as parquet as select * from SOURCE.result_accessroute orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_accessroute COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_instance stored as parquet as select * from SOURCE.result_instance orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
create table TARGET.result_orcid stored as parquet as select * from SOURCE.result_orcid orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create view TARGET.foo1 as select * from SOURCE.result_result rr where rr.source in (select id from TARGET.result);
|
||||
create view TARGET.foo2 as select * from SOURCE.result_result rr where rr.target in (select id from TARGET.result);
|
||||
create table TARGET.result_result STORED AS PARQUET as select distinct * from (select * from TARGET.foo1 union all select * from TARGET.foo2) foufou;
|
||||
drop view TARGET.foo1;
|
||||
drop view TARGET.foo2;
|
||||
--ANALYZE TABLE TARGET.result_result COMPUTE STATISTICS;
|
||||
|
||||
-- datasources
|
||||
create view if not exists TARGET.datasource as select * from SOURCE.datasource;
|
||||
create view if not exists TARGET.datasource_oids as select * from SOURCE.datasource_oids;
|
||||
create view if not exists TARGET.datasource_organizations as select * from SOURCE.datasource_organizations;
|
||||
create view if not exists TARGET.datasource_sources as select * from SOURCE.datasource_sources;
|
||||
|
||||
create table TARGET.datasource_results stored as parquet as select id as result, datasource as id from TARGET.result_datasources;
|
||||
--ANALYZE TABLE TARGET.datasource_results COMPUTE STATISTICS;
|
||||
|
||||
-- organizations
|
||||
create view if not exists TARGET.organization as select * from SOURCE.organization;
|
||||
create view if not exists TARGET.organization_datasources as select * from SOURCE.organization_datasources;
|
||||
create view if not exists TARGET.organization_pids as select * from SOURCE.organization_pids;
|
||||
create view if not exists TARGET.organization_projects as select * from SOURCE.organization_projects;
|
||||
create view if not exists TARGET.organization_sources as select * from SOURCE.organization_sources;
|
||||
|
||||
-- projects
|
||||
create view if not exists TARGET.project as select * from SOURCE.project;
|
||||
create view if not exists TARGET.project_oids as select * from SOURCE.project_oids;
|
||||
create view if not exists TARGET.project_organizations as select * from SOURCE.project_organizations;
|
||||
create view if not exists TARGET.project_resultcount as select * from SOURCE.project_resultcount;
|
||||
create view if not exists TARGET.project_classification as select * from SOURCE.project_classification;
|
||||
create view if not exists TARGET.project_organization_contribution as select * from SOURCE.project_organization_contribution;
|
||||
|
||||
create table TARGET.project_results stored as parquet as select id as result, project as id from TARGET.result_projects;
|
||||
--ANALYZE TABLE TARGET.project_results COMPUTE STATISTICS;
|
||||
|
||||
-- indicators
|
||||
-- Sprint 1 ----
|
||||
create table TARGET.indi_pub_green_oa stored as parquet as select * from SOURCE.indi_pub_green_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.indi_pub_green_oa COMPUTE STATISTICS;
|
||||
create table TARGET.indi_pub_grey_lit stored as parquet as select * from SOURCE.indi_pub_grey_lit orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.indi_pub_grey_lit COMPUTE STATISTICS;
|
||||
create table TARGET.indi_pub_doi_from_crossref stored as parquet as select * from SOURCE.indi_pub_doi_from_crossref orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.indi_pub_doi_from_crossref COMPUTE STATISTICS;
|
||||
-- Sprint 2 ----
|
||||
create table TARGET.indi_result_has_cc_licence stored as parquet as select * from SOURCE.indi_result_has_cc_licence orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.indi_result_has_cc_licence COMPUTE STATISTICS;
|
||||
create table TARGET.indi_result_has_cc_licence_url stored as parquet as select * from SOURCE.indi_result_has_cc_licence_url orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.indi_result_has_cc_licence_url COMPUTE STATISTICS;
|
||||
create table TARGET.indi_pub_has_abstract stored as parquet as select * from SOURCE.indi_pub_has_abstract orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.indi_pub_has_abstract COMPUTE STATISTICS;
|
||||
create table TARGET.indi_result_with_orcid stored as parquet as select * from SOURCE.indi_result_with_orcid orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.indi_result_with_orcid COMPUTE STATISTICS;
|
||||
---- Sprint 3 ----
|
||||
create table TARGET.indi_funded_result_with_fundref stored as parquet as select * from SOURCE.indi_funded_result_with_fundref orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.indi_funded_result_with_fundref COMPUTE STATISTICS;
|
||||
create view TARGET.indi_result_org_collab as select * from SOURCE.indi_result_org_collab;
|
||||
create view TARGET.indi_result_org_country_collab as select * from SOURCE.indi_result_org_country_collab;
|
||||
create view TARGET.indi_project_collab_org as select * from SOURCE.indi_project_collab_org;
|
||||
create view TARGET.indi_project_collab_org_country as select * from SOURCE.indi_project_collab_org_country;
|
||||
create view TARGET.indi_funder_country_collab as select * from SOURCE.indi_funder_country_collab;
|
||||
create view TARGET.indi_result_country_collab as select * from SOURCE.indi_result_country_collab;
|
||||
---- Sprint 4 ----
|
||||
create table TARGET.indi_pub_diamond stored as parquet as select * from SOURCE.indi_pub_diamond orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.indi_pub_diamond COMPUTE STATISTICS;
|
||||
create table TARGET.indi_pub_in_transformative stored as parquet as select * from SOURCE.indi_pub_in_transformative orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.indi_pub_in_transformative COMPUTE STATISTICS;
|
||||
create table TARGET.indi_pub_closed_other_open stored as parquet as select * from SOURCE.indi_pub_closed_other_open orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.indi_pub_closed_other_open COMPUTE STATISTICS;
|
||||
---- Sprint 5 ----
|
||||
create table TARGET.indi_result_no_of_copies stored as parquet as select * from SOURCE.indi_result_no_of_copies orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.indi_result_no_of_copies COMPUTE STATISTICS;
|
||||
---- Sprint 6 ----
|
||||
create table TARGET.indi_pub_hybrid_oa_with_cc stored as parquet as select * from SOURCE.indi_pub_hybrid_oa_with_cc orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.indi_pub_hybrid_oa_with_cc COMPUTE STATISTICS;
|
||||
create table TARGET.indi_pub_bronze_oa stored as parquet as select * from SOURCE.indi_pub_bronze_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.indi_pub_bronze_oa COMPUTE STATISTICS;
|
||||
create table TARGET.indi_pub_downloads stored as parquet as select * from SOURCE.indi_pub_downloads orig where exists (select 1 from TARGET.result r where r.id=orig.result_id);
|
||||
--ANALYZE TABLE TARGET.indi_pub_downloads COMPUTE STATISTICS;
|
||||
create table TARGET.indi_pub_downloads_datasource stored as parquet as select * from SOURCE.indi_pub_downloads_datasource orig where exists (select 1 from TARGET.result r where r.id=orig.result_id);
|
||||
--ANALYZE TABLE TARGET.indi_pub_downloads_datasource COMPUTE STATISTICS;
|
||||
create table TARGET.indi_pub_downloads_year stored as parquet as select * from SOURCE.indi_pub_downloads_year orig where exists (select 1 from TARGET.result r where r.id=orig.result_id);
|
||||
--ANALYZE TABLE TARGET.indi_pub_downloads_year COMPUTE STATISTICS;
|
||||
create table TARGET.indi_pub_downloads_datasource_year stored as parquet as select * from SOURCE.indi_pub_downloads_datasource_year orig where exists (select 1 from TARGET.result r where r.id=orig.result_id);
|
||||
--ANALYZE TABLE TARGET.indi_pub_downloads_datasource_year COMPUTE STATISTICS;
|
||||
---- Sprint 7 ----
|
||||
create table TARGET.indi_pub_gold_oa stored as parquet as select * from SOURCE.indi_pub_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.indi_pub_gold_oa COMPUTE STATISTICS;
|
||||
create table TARGET.indi_pub_hybrid stored as parquet as select * from SOURCE.indi_pub_hybrid orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.indi_pub_hybrid COMPUTE STATISTICS;
|
||||
create view TARGET.indi_org_fairness as select * from SOURCE.indi_org_fairness;
|
||||
create view TARGET.indi_org_fairness_pub_pr as select * from SOURCE.indi_org_fairness_pub_pr;
|
||||
create view TARGET.indi_org_fairness_pub_year as select * from SOURCE.indi_org_fairness_pub_year;
|
||||
create view TARGET.indi_org_fairness_pub as select * from SOURCE.indi_org_fairness_pub;
|
||||
create view TARGET.indi_org_fairness_year as select * from SOURCE.indi_org_fairness_year;
|
||||
create view TARGET.indi_org_findable_year as select * from SOURCE.indi_org_findable_year;
|
||||
create view TARGET.indi_org_findable as select * from SOURCE.indi_org_findable;
|
||||
create view TARGET.indi_org_openess as select * from SOURCE.indi_org_openess;
|
||||
create view TARGET.indi_org_openess_year as select * from SOURCE.indi_org_openess_year;
|
||||
create table TARGET.indi_pub_has_preprint stored as parquet as select * from SOURCE.indi_pub_has_preprint orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.indi_pub_has_preprint COMPUTE STATISTICS;
|
||||
create table TARGET.indi_pub_in_subscribed stored as parquet as select * from SOURCE.indi_pub_in_subscribed orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.indi_pub_in_subscribed COMPUTE STATISTICS;
|
||||
create table TARGET.indi_result_with_pid stored as parquet as select * from SOURCE.indi_result_with_pid orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.indi_result_with_pid COMPUTE STATISTICS;
|
||||
create table TARGET.indi_impact_measures stored as parquet as select * from SOURCE.indi_impact_measures orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.indi_impact_measures COMPUTE STATISTICS;
|
||||
create table TARGET.indi_pub_interdisciplinarity stored as parquet as select * from SOURCE.indi_pub_interdisciplinarity orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.indi_pub_interdisciplinarity COMPUTE STATISTICS;
|
||||
create table TARGET.result_apc_affiliations stored as parquet as select * from SOURCE.result_apc_affiliations orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_apc_affiliations COMPUTE STATISTICS;
|
||||
create table TARGET.indi_is_project_result_after stored as parquet as select * from SOURCE.indi_is_project_result_after orig where exists (select 1 from TARGET.result r where r.id=orig.result_id);
|
||||
create table TARGET.indi_is_funder_plan_s stored as parquet as select * from SOURCE.indi_is_funder_plan_s orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
|
@ -0,0 +1,297 @@
|
|||
drop database if exists TARGET cascade;
|
||||
create database if not exists TARGET;
|
||||
|
||||
create view if not exists TARGET.category as select * from SOURCE.category;
|
||||
create view if not exists TARGET.concept as select * from SOURCE.concept;
|
||||
create view if not exists TARGET.context as select * from SOURCE.context;
|
||||
create view if not exists TARGET.country as select * from SOURCE.country;
|
||||
create view if not exists TARGET.countrygdp as select * from SOURCE.countrygdp;
|
||||
create view if not exists TARGET.creation_date as select * from SOURCE.creation_date;
|
||||
create view if not exists TARGET.funder as select * from SOURCE.funder;
|
||||
create view if not exists TARGET.fundref as select * from SOURCE.fundref;
|
||||
create view if not exists TARGET.rndexpenditure as select * from SOURCE.rndexpediture;
|
||||
create view if not exists TARGET.rndgdpexpenditure as select * from SOURCE.rndgdpexpenditure;
|
||||
create view if not exists TARGET.doctoratestudents as select * from SOURCE.doctoratestudents;
|
||||
create view if not exists TARGET.totalresearchers as select * from SOURCE.totalresearchers;
|
||||
create view if not exists TARGET.totalresearchersft as select * from SOURCE.totalresearchersft;
|
||||
create view if not exists TARGET.hrrst as select * from SOURCE.hrrst;
|
||||
--create view if not exists TARGET.graduatedoctorates as select * from SOURCE.graduatedoctorates;
|
||||
|
||||
create table TARGET.result stored as parquet as
|
||||
select distinct * from (
|
||||
select * from SOURCE.result r where exists (select 1 from SOURCE.result_projects rp join SOURCE.project p on rp.project=p.id where rp.id=r.id)
|
||||
union all
|
||||
select * from SOURCE.result r where exists (select 1 from SOURCE.result_concepts rc where rc.id=r.id)
|
||||
union all
|
||||
select * from SOURCE.result r where exists (select 1 from SOURCE.result_organization ro where ro.id=r.id and ro.organization in (
|
||||
'openorgs____::b84450f9864182c67b8611b5593f4250', --"Athena Research and Innovation Center In Information Communication & Knowledge Technologies', --ARC"
|
||||
'openorgs____::d41cf6bd4ab1b1362a44397e0b95c975', --National Research Council
|
||||
'openorgs____::d2a09b9d5eabb10c95f9470e172d05d2', --??? Not exists ??
|
||||
'openorgs____::d169c7407dd417152596908d48c11460', --Masaryk University
|
||||
'openorgs____::1ec924b1759bb16d0a02f2dad8689b21', --University of Belgrade
|
||||
'openorgs____::0ae431b820e4c33db8967fbb2b919150', --University of Helsinki
|
||||
'openorgs____::759d59f05d77188faee99b7493b46805', --University of Minho
|
||||
'openorgs____::cad284878801b9465fa51a95b1d779db', --Universidad Politécnica de Madrid
|
||||
'openorgs____::eadc8da90a546e98c03f896661a2e4d4', --University of Göttingen
|
||||
'openorgs____::c0286313e36479eff8676dba9b724b40', --National and Kapodistrian University of Athens
|
||||
-- 'openorgs____::c80a8243a5e5c620d7931c88d93bf17a', --Université Paris Diderot
|
||||
'openorgs____::c08634f0a6b0081c3dc6e6c93a4314f3', --Bielefeld University
|
||||
'openorgs____::6fc85e4a8f7ecaf4b0c738d010e967ea', --University of Southern Denmark
|
||||
'openorgs____::3d6122f87f9a97a99d8f6e3d73313720', --Humboldt-Universität zu Berlin
|
||||
'openorgs____::16720ada63d0fa8ca41601feae7d1aa5', --TU Darmstadt
|
||||
'openorgs____::ccc0a066b56d2cfaf90c2ae369df16f5', --KU Leuven
|
||||
'openorgs____::4c6f119632adf789746f0a057ed73e90', --University of the Western Cape
|
||||
'openorgs____::ec3665affa01aeafa28b7852c4176dbd', --Rudjer Boskovic Institute
|
||||
'openorgs____::5f31346d444a7f06a28c880fb170b0f6', --Ghent University
|
||||
'openorgs____::2dbe47117fd5409f9c61620813456632', --University of Luxembourg
|
||||
'openorgs____::6445d7758d3a40c4d997953b6632a368', --National Institute of Informatics (NII)
|
||||
'openorgs____::b77c01aa15de3675da34277d48de2ec1', -- Valencia Catholic University Saint Vincent Martyr
|
||||
'openorgs____::7fe2f66cdc43983c6b24816bfe9cf6a0', -- Unviersity of Warsaw
|
||||
'openorgs____::15e7921fc50d9aa1229a82a84429419e', -- University Of Thessaly
|
||||
'openorgs____::11f7919dadc8f8a7251af54bba60c956', -- Technical University of Crete
|
||||
'openorgs____::84f0c5f5dbb6daf42748485924efde4b', -- University of Piraeus
|
||||
'openorgs____::4ac562f0376fce3539504567649cb373', -- University of Patras
|
||||
'openorgs____::3e8d1f8c3f6cd7f418b09f1f58b4873b', -- Aristotle University of Thessaloniki
|
||||
'openorgs____::3fcef6e1c469c10f2a84b281372c9814', -- World Bank
|
||||
'openorgs____::1698a2eb1885ef8adb5a4a969e745ad3', -- École des Ponts ParisTech
|
||||
'openorgs____::e15adb13c4dadd49de4d35c39b5da93a', -- Nanyang Technological University
|
||||
'openorgs____::4b34103bde246228fcd837f5f1bf4212', -- Autonomous University of Barcelona
|
||||
'openorgs____::72ec75fcfc4e0df1a76dc4c49007fceb', -- McMaster University
|
||||
'openorgs____::51c7fc556e46381734a25a6fbc3fd398', -- University of Modena and Reggio Emilia
|
||||
'openorgs____::235d7f9ad18ecd7e6dc62ea4990cb9db', -- Bilkent University
|
||||
'openorgs____::31f2fa9e05b49d4cf40a19c3fed8eb06', -- Saints Cyril and Methodius University of Skopje
|
||||
'openorgs____::db7686f30f22cbe73a4fde872ce812a6', -- University of Milan
|
||||
'openorgs____::b8b8ca674452579f3f593d9f5e557483', -- University College Cork
|
||||
'openorgs____::38d7097854736583dde879d12dacafca', -- Brown University
|
||||
'openorgs____::57784c9e047e826fefdb1ef816120d92', --Arts et Métiers ParisTech
|
||||
'openorgs____::2530baca8a15936ba2e3297f2bce2e7e', -- University of Cape Town
|
||||
'openorgs____::d11f981828c485cd23d93f7f24f24db1', -- Technological University Dublin
|
||||
'openorgs____::5e6bf8962665cdd040341171e5c631d8', -- Delft University of Technology
|
||||
'openorgs____::846cb428d3f52a445f7275561a7beb5d', -- University of Manitoba
|
||||
'openorgs____::eb391317ed0dc684aa81ac16265de041', -- Universitat Rovira i Virgili
|
||||
'openorgs____::66aa9fc2fceb271423dfabcc38752dc0', -- Lund University
|
||||
'openorgs____::3cff625a4370d51e08624cc586138b2f', -- IMT Atlantique
|
||||
'openorgs____::c0b262bd6eab819e4c994914f9c010e2', -- National Institute of Geophysics and Volcanology
|
||||
'openorgs____::1624ff7c01bb641b91f4518539a0c28a', -- Vrije Universiteit Amsterdam
|
||||
'openorgs____::4d4051b56708688235252f1d8fddb8c1', -- Iscte - Instituto Universitário de Lisboa
|
||||
'openorgs____::ab4ac74c35fa5dada770cf08e5110fab', -- Universidade Católica Portuguesa
|
||||
'openorgs____::4d4051b56708688235252f1d8fddb8c1', -- Iscte - Instituto Universitário de Lisboa
|
||||
'openorgs____::5d55fb216b14691cf68218daf5d78cd9', -- Munster Technological University
|
||||
'openorgs____::0fccc7640f0cb44d5cd1b06b312a06b9', -- Cardiff University
|
||||
'openorgs____::8839b55dae0c84d56fd533f52d5d483a', -- Leibniz Institute of Ecological Urban and Regional Development
|
||||
'openorgs____::526468206bca24c1c90da6a312295cf4', -- Cyprus University of Technology
|
||||
'openorgs____::b5ca9d4340e26454e367e2908ef3872f', -- Alma Mater Studiorum University of Bologna
|
||||
'openorgs____::a6340e6ecf60f6bba163659df985b0f2' -- TU Dresden
|
||||
))) foo;
|
||||
|
||||
--ANALYZE TABLE TARGET.result COMPUTE STATISTICS;
|
||||
|
||||
create view if not exists TARGET.category as select * from SOURCE.category;
|
||||
create view if not exists TARGET.concept as select * from SOURCE.concept;
|
||||
create view if not exists TARGET.context as select * from SOURCE.context;
|
||||
create view if not exists TARGET.country as select * from SOURCE.country;
|
||||
create view if not exists TARGET.countrygdp as select * from SOURCE.countrygdp;
|
||||
create view if not exists TARGET.creation_date as select * from SOURCE.creation_date;
|
||||
create view if not exists TARGET.funder as select * from SOURCE.funder;
|
||||
create view if not exists TARGET.fundref as select * from SOURCE.fundref;
|
||||
create view if not exists TARGET.rndexpenditure as select * from SOURCE.rndexpediture;
|
||||
create view if not exists TARGET.rndgdpexpenditure as select * from SOURCE.rndgdpexpenditure;
|
||||
create view if not exists TARGET.doctoratestudents as select * from SOURCE.doctoratestudents;
|
||||
create view if not exists TARGET.totalresearchers as select * from SOURCE.totalresearchers;
|
||||
create view if not exists TARGET.totalresearchersft as select * from SOURCE.totalresearchersft;
|
||||
create view if not exists TARGET.hrrst as select * from SOURCE.hrrst;
|
||||
--create view if not exists TARGET.graduatedoctorates as select * from SOURCE.graduatedoctorates;
|
||||
|
||||
create table TARGET.result_citations stored as parquet as select * from SOURCE.result_citations orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_citations COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_references_oc stored as parquet as select * from SOURCE.result_references_oc orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_references_oc COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_citations_oc stored as parquet as select * from SOURCE.result_citations_oc orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_citations_oc COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_classifications stored as parquet as select * from SOURCE.result_classifications orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_classifications COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_apc stored as parquet as select * from SOURCE.result_apc orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_apc COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_concepts stored as parquet as select * from SOURCE.result_concepts orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_concepts COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_datasources stored as parquet as select * from SOURCE.result_datasources orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_datasources COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_fundercount stored as parquet as select * from SOURCE.result_fundercount orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_fundercount COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_gold stored as parquet as select * from SOURCE.result_gold orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_gold COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_greenoa stored as parquet as select * from SOURCE.result_greenoa orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_greenoa COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_languages stored as parquet as select * from SOURCE.result_languages orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_languages COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_licenses stored as parquet as select * from SOURCE.result_licenses orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_licenses COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.licenses_normalized STORED AS PARQUET as select * from SOURCE.licenses_normalized;
|
||||
--ANALYZE TABLE TARGET.licenses_normalized COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_oids stored as parquet as select * from SOURCE.result_oids orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_oids COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_organization stored as parquet as select * from SOURCE.result_organization orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_organization COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_peerreviewed stored as parquet as select * from SOURCE.result_peerreviewed orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_peerreviewed COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_pids stored as parquet as select * from SOURCE.result_pids orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_pids COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_projectcount stored as parquet as select * from SOURCE.result_projectcount orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_projectcount COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_projects stored as parquet as select * from SOURCE.result_projects orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_projects COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_refereed stored as parquet as select * from SOURCE.result_refereed orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_refereed COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_sources stored as parquet as select * from SOURCE.result_sources orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_sources COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_topics stored as parquet as select * from SOURCE.result_topics orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_topics COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_fos stored as parquet as select * from SOURCE.result_fos orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_fos COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_accessroute stored as parquet as select * from SOURCE.result_accessroute orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_accessroute COMPUTE STATISTICS;
|
||||
|
||||
create table TARGET.result_instance stored as parquet as select * from SOURCE.result_instance orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
create table TARGET.result_orcid stored as parquet as select * from SOURCE.result_orcid orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
|
||||
create view TARGET.foo1 as select * from SOURCE.result_result rr where rr.source in (select id from TARGET.result);
|
||||
create view TARGET.foo2 as select * from SOURCE.result_result rr where rr.target in (select id from TARGET.result);
|
||||
create table TARGET.result_result STORED AS PARQUET as select distinct * from (select * from TARGET.foo1 union all select * from TARGET.foo2) foufou;
|
||||
drop view TARGET.foo1;
|
||||
drop view TARGET.foo2;
|
||||
--ANALYZE TABLE TARGET.result_result COMPUTE STATISTICS;
|
||||
|
||||
-- datasources
|
||||
create view if not exists TARGET.datasource as select * from SOURCE.datasource;
|
||||
create view if not exists TARGET.datasource_oids as select * from SOURCE.datasource_oids;
|
||||
create view if not exists TARGET.datasource_organizations as select * from SOURCE.datasource_organizations;
|
||||
create view if not exists TARGET.datasource_sources as select * from SOURCE.datasource_sources;
|
||||
|
||||
create table TARGET.datasource_results stored as parquet as select id as result, datasource as id from TARGET.result_datasources;
|
||||
--ANALYZE TABLE TARGET.datasource_results COMPUTE STATISTICS;
|
||||
|
||||
-- organizations
|
||||
create view if not exists TARGET.organization as select * from SOURCE.organization;
|
||||
create view if not exists TARGET.organization_datasources as select * from SOURCE.organization_datasources;
|
||||
create view if not exists TARGET.organization_pids as select * from SOURCE.organization_pids;
|
||||
create view if not exists TARGET.organization_projects as select * from SOURCE.organization_projects;
|
||||
create view if not exists TARGET.organization_sources as select * from SOURCE.organization_sources;
|
||||
|
||||
-- projects
|
||||
create view if not exists TARGET.project as select * from SOURCE.project;
|
||||
create view if not exists TARGET.project_oids as select * from SOURCE.project_oids;
|
||||
create view if not exists TARGET.project_organizations as select * from SOURCE.project_organizations;
|
||||
create view if not exists TARGET.project_resultcount as select * from SOURCE.project_resultcount;
|
||||
create view if not exists TARGET.project_classification as select * from SOURCE.project_classification;
|
||||
create view if not exists TARGET.project_organization_contribution as select * from SOURCE.project_organization_contribution;
|
||||
|
||||
create table TARGET.project_results stored as parquet as select id as result, project as id from TARGET.result_projects;
|
||||
--ANALYZE TABLE TARGET.project_results COMPUTE STATISTICS;
|
||||
|
||||
-- indicators
|
||||
-- Sprint 1 ----
|
||||
create table TARGET.indi_pub_green_oa stored as parquet as select * from SOURCE.indi_pub_green_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.indi_pub_green_oa COMPUTE STATISTICS;
|
||||
create table TARGET.indi_pub_grey_lit stored as parquet as select * from SOURCE.indi_pub_grey_lit orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.indi_pub_grey_lit COMPUTE STATISTICS;
|
||||
create table TARGET.indi_pub_doi_from_crossref stored as parquet as select * from SOURCE.indi_pub_doi_from_crossref orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.indi_pub_doi_from_crossref COMPUTE STATISTICS;
|
||||
-- Sprint 2 ----
|
||||
create table TARGET.indi_result_has_cc_licence stored as parquet as select * from SOURCE.indi_result_has_cc_licence orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.indi_result_has_cc_licence COMPUTE STATISTICS;
|
||||
create table TARGET.indi_result_has_cc_licence_url stored as parquet as select * from SOURCE.indi_result_has_cc_licence_url orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.indi_result_has_cc_licence_url COMPUTE STATISTICS;
|
||||
create table TARGET.indi_pub_has_abstract stored as parquet as select * from SOURCE.indi_pub_has_abstract orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.indi_pub_has_abstract COMPUTE STATISTICS;
|
||||
create table TARGET.indi_result_with_orcid stored as parquet as select * from SOURCE.indi_result_with_orcid orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.indi_result_with_orcid COMPUTE STATISTICS;
|
||||
---- Sprint 3 ----
|
||||
create table TARGET.indi_funded_result_with_fundref stored as parquet as select * from SOURCE.indi_funded_result_with_fundref orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.indi_funded_result_with_fundref COMPUTE STATISTICS;
|
||||
create view TARGET.indi_result_org_collab as select * from SOURCE.indi_result_org_collab;
|
||||
create view TARGET.indi_result_org_country_collab as select * from SOURCE.indi_result_org_country_collab;
|
||||
create view TARGET.indi_project_collab_org as select * from SOURCE.indi_project_collab_org;
|
||||
create view TARGET.indi_project_collab_org_country as select * from SOURCE.indi_project_collab_org_country;
|
||||
create view TARGET.indi_funder_country_collab as select * from SOURCE.indi_funder_country_collab;
|
||||
create view TARGET.indi_result_country_collab as select * from SOURCE.indi_result_country_collab;
|
||||
---- Sprint 4 ----
|
||||
create table TARGET.indi_pub_diamond stored as parquet as select * from SOURCE.indi_pub_diamond orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.indi_pub_diamond COMPUTE STATISTICS;
|
||||
create table TARGET.indi_pub_in_transformative stored as parquet as select * from SOURCE.indi_pub_in_transformative orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.indi_pub_in_transformative COMPUTE STATISTICS;
|
||||
create table TARGET.indi_pub_closed_other_open stored as parquet as select * from SOURCE.indi_pub_closed_other_open orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.indi_pub_closed_other_open COMPUTE STATISTICS;
|
||||
---- Sprint 5 ----
|
||||
create table TARGET.indi_result_no_of_copies stored as parquet as select * from SOURCE.indi_result_no_of_copies orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.indi_result_no_of_copies COMPUTE STATISTICS;
|
||||
---- Sprint 6 ----
|
||||
create table TARGET.indi_pub_hybrid_oa_with_cc stored as parquet as select * from SOURCE.indi_pub_hybrid_oa_with_cc orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.indi_pub_hybrid_oa_with_cc COMPUTE STATISTICS;
|
||||
create table TARGET.indi_pub_bronze_oa stored as parquet as select * from SOURCE.indi_pub_bronze_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.indi_pub_bronze_oa COMPUTE STATISTICS;
|
||||
create table TARGET.indi_pub_downloads stored as parquet as select * from SOURCE.indi_pub_downloads orig where exists (select 1 from TARGET.result r where r.id=orig.result_id);
|
||||
--ANALYZE TABLE TARGET.indi_pub_downloads COMPUTE STATISTICS;
|
||||
create table TARGET.indi_pub_downloads_datasource stored as parquet as select * from SOURCE.indi_pub_downloads_datasource orig where exists (select 1 from TARGET.result r where r.id=orig.result_id);
|
||||
--ANALYZE TABLE TARGET.indi_pub_downloads_datasource COMPUTE STATISTICS;
|
||||
create table TARGET.indi_pub_downloads_year stored as parquet as select * from SOURCE.indi_pub_downloads_year orig where exists (select 1 from TARGET.result r where r.id=orig.result_id);
|
||||
--ANALYZE TABLE TARGET.indi_pub_downloads_year COMPUTE STATISTICS;
|
||||
create table TARGET.indi_pub_downloads_datasource_year stored as parquet as select * from SOURCE.indi_pub_downloads_datasource_year orig where exists (select 1 from TARGET.result r where r.id=orig.result_id);
|
||||
--ANALYZE TABLE TARGET.indi_pub_downloads_datasource_year COMPUTE STATISTICS;
|
||||
---- Sprint 7 ----
|
||||
create table TARGET.indi_pub_gold_oa stored as parquet as select * from SOURCE.indi_pub_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.indi_pub_gold_oa COMPUTE STATISTICS;
|
||||
create table TARGET.indi_pub_hybrid stored as parquet as select * from SOURCE.indi_pub_hybrid orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.indi_pub_hybrid COMPUTE STATISTICS;
|
||||
create view TARGET.indi_org_fairness as select * from SOURCE.indi_org_fairness;
|
||||
create view TARGET.indi_org_fairness_pub_pr as select * from SOURCE.indi_org_fairness_pub_pr;
|
||||
create view TARGET.indi_org_fairness_pub_year as select * from SOURCE.indi_org_fairness_pub_year;
|
||||
create view TARGET.indi_org_fairness_pub as select * from SOURCE.indi_org_fairness_pub;
|
||||
create view TARGET.indi_org_fairness_year as select * from SOURCE.indi_org_fairness_year;
|
||||
create view TARGET.indi_org_findable_year as select * from SOURCE.indi_org_findable_year;
|
||||
create view TARGET.indi_org_findable as select * from SOURCE.indi_org_findable;
|
||||
create view TARGET.indi_org_openess as select * from SOURCE.indi_org_openess;
|
||||
create view TARGET.indi_org_openess_year as select * from SOURCE.indi_org_openess_year;
|
||||
create table TARGET.indi_pub_has_preprint stored as parquet as select * from SOURCE.indi_pub_has_preprint orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.indi_pub_has_preprint COMPUTE STATISTICS;
|
||||
create table TARGET.indi_pub_in_subscribed stored as parquet as select * from SOURCE.indi_pub_in_subscribed orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.indi_pub_in_subscribed COMPUTE STATISTICS;
|
||||
create table TARGET.indi_result_with_pid stored as parquet as select * from SOURCE.indi_result_with_pid orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.indi_result_with_pid COMPUTE STATISTICS;
|
||||
create table TARGET.indi_impact_measures stored as parquet as select * from SOURCE.indi_impact_measures orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.indi_impact_measures COMPUTE STATISTICS;
|
||||
create table TARGET.indi_pub_interdisciplinarity stored as parquet as select * from SOURCE.indi_pub_interdisciplinarity orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.indi_pub_interdisciplinarity COMPUTE STATISTICS;
|
||||
create table TARGET.result_apc_affiliations stored as parquet as select * from SOURCE.result_apc_affiliations orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--ANALYZE TABLE TARGET.result_apc_affiliations COMPUTE STATISTICS;
|
||||
--create table TARGET.indi_is_project_result_after stored as parquet as select * from SOURCE.indi_is_project_result_after orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--create table TARGET.indi_is_funder_plan_s stored as parquet as select * from SOURCE.indi_is_funder_plan_s orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--create view TARGET.indi_funder_fairness as select * from SOURCE.indi_funder_fairness;
|
||||
--create view TARGET.indi_funder_openess as select * from SOURCE.indi_funder_openess;
|
||||
--create view TARGET.indi_funder_findable as select * from SOURCE.indi_funder_findable;
|
||||
--create view TARGET.indi_ris_fairness as select * from SOURCE.indi_ris_fairness;
|
||||
--create view TARGET.indi_ris_openess as select * from SOURCE.indi_ris_openess;
|
||||
--create view TARGET.indi_ris_findable as select * from SOURCE.indi_ris_findable;
|
||||
|
|
@ -0,0 +1,67 @@
|
|||
drop database if exists TARGET cascade;
|
||||
create database if not exists TARGET;
|
||||
|
||||
create table TARGET.result stored as parquet as
|
||||
select distinct * from (
|
||||
select * from SOURCE.result r where exists (select 1 from SOURCE.result_organization ro where ro.id=r.id and ro.organization in (
|
||||
'openorgs____::b84450f9864182c67b8611b5593f4250', --"Athena Research and Innovation Center In Information Communication & Knowledge Technologies', --ARC"
|
||||
'openorgs____::d41cf6bd4ab1b1362a44397e0b95c975', --National Research Council
|
||||
'openorgs____::d2a09b9d5eabb10c95f9470e172d05d2', --??? Not exists ??
|
||||
'openorgs____::d169c7407dd417152596908d48c11460', --Masaryk University
|
||||
'openorgs____::1ec924b1759bb16d0a02f2dad8689b21', --University of Belgrade
|
||||
'openorgs____::0ae431b820e4c33db8967fbb2b919150', --University of Helsinki
|
||||
'openorgs____::759d59f05d77188faee99b7493b46805', --University of Minho
|
||||
'openorgs____::cad284878801b9465fa51a95b1d779db', --Universidad Politécnica de Madrid
|
||||
'openorgs____::eadc8da90a546e98c03f896661a2e4d4', --University of Göttingen
|
||||
'openorgs____::c0286313e36479eff8676dba9b724b40', --National and Kapodistrian University of Athens
|
||||
-- 'openorgs____::c80a8243a5e5c620d7931c88d93bf17a', --Université Paris Diderot
|
||||
'openorgs____::c08634f0a6b0081c3dc6e6c93a4314f3', --Bielefeld University
|
||||
'openorgs____::6fc85e4a8f7ecaf4b0c738d010e967ea', --University of Southern Denmark
|
||||
'openorgs____::3d6122f87f9a97a99d8f6e3d73313720', --Humboldt-Universität zu Berlin
|
||||
'openorgs____::16720ada63d0fa8ca41601feae7d1aa5', --TU Darmstadt
|
||||
'openorgs____::ccc0a066b56d2cfaf90c2ae369df16f5', --KU Leuven
|
||||
'openorgs____::4c6f119632adf789746f0a057ed73e90', --University of the Western Cape
|
||||
'openorgs____::ec3665affa01aeafa28b7852c4176dbd', --Rudjer Boskovic Institute
|
||||
'openorgs____::5f31346d444a7f06a28c880fb170b0f6', --Ghent University
|
||||
'openorgs____::2dbe47117fd5409f9c61620813456632', --University of Luxembourg
|
||||
'openorgs____::6445d7758d3a40c4d997953b6632a368', --National Institute of Informatics (NII)
|
||||
'openorgs____::b77c01aa15de3675da34277d48de2ec1', -- Valencia Catholic University Saint Vincent Martyr
|
||||
'openorgs____::7fe2f66cdc43983c6b24816bfe9cf6a0', -- Unviersity of Warsaw
|
||||
'openorgs____::15e7921fc50d9aa1229a82a84429419e', -- University Of Thessaly
|
||||
'openorgs____::11f7919dadc8f8a7251af54bba60c956', -- Technical University of Crete
|
||||
'openorgs____::84f0c5f5dbb6daf42748485924efde4b', -- University of Piraeus
|
||||
'openorgs____::4ac562f0376fce3539504567649cb373', -- University of Patras
|
||||
'openorgs____::3e8d1f8c3f6cd7f418b09f1f58b4873b', -- Aristotle University of Thessaloniki
|
||||
'openorgs____::3fcef6e1c469c10f2a84b281372c9814', -- World Bank
|
||||
'openorgs____::1698a2eb1885ef8adb5a4a969e745ad3', -- École des Ponts ParisTech
|
||||
'openorgs____::e15adb13c4dadd49de4d35c39b5da93a', -- Nanyang Technological University
|
||||
'openorgs____::4b34103bde246228fcd837f5f1bf4212', -- Autonomous University of Barcelona
|
||||
'openorgs____::72ec75fcfc4e0df1a76dc4c49007fceb', -- McMaster University
|
||||
'openorgs____::51c7fc556e46381734a25a6fbc3fd398', -- University of Modena and Reggio Emilia
|
||||
'openorgs____::235d7f9ad18ecd7e6dc62ea4990cb9db', -- Bilkent University
|
||||
'openorgs____::31f2fa9e05b49d4cf40a19c3fed8eb06', -- Saints Cyril and Methodius University of Skopje
|
||||
'openorgs____::db7686f30f22cbe73a4fde872ce812a6', -- University of Milan
|
||||
'openorgs____::b8b8ca674452579f3f593d9f5e557483', -- University College Cork
|
||||
'openorgs____::38d7097854736583dde879d12dacafca', -- Brown University
|
||||
'openorgs____::57784c9e047e826fefdb1ef816120d92', --Arts et Métiers ParisTech
|
||||
'openorgs____::2530baca8a15936ba2e3297f2bce2e7e', -- University of Cape Town
|
||||
'openorgs____::d11f981828c485cd23d93f7f24f24db1', -- Technological University Dublin
|
||||
'openorgs____::5e6bf8962665cdd040341171e5c631d8', -- Delft University of Technology
|
||||
'openorgs____::846cb428d3f52a445f7275561a7beb5d', -- University of Manitoba
|
||||
'openorgs____::eb391317ed0dc684aa81ac16265de041', -- Universitat Rovira i Virgili
|
||||
'openorgs____::66aa9fc2fceb271423dfabcc38752dc0', -- Lund University
|
||||
'openorgs____::3cff625a4370d51e08624cc586138b2f', -- IMT Atlantique
|
||||
'openorgs____::c0b262bd6eab819e4c994914f9c010e2', -- National Institute of Geophysics and Volcanology
|
||||
'openorgs____::1624ff7c01bb641b91f4518539a0c28a', -- Vrije Universiteit Amsterdam
|
||||
'openorgs____::4d4051b56708688235252f1d8fddb8c1', --Iscte - Instituto Universitário de Lisboa
|
||||
'openorgs____::ab4ac74c35fa5dada770cf08e5110fab', -- Universidade Católica Portuguesa
|
||||
'openorgs____::4d4051b56708688235252f1d8fddb8c1', -- Iscte - Instituto Universitário de Lisboa
|
||||
'openorgs____::5d55fb216b14691cf68218daf5d78cd9', -- Munster Technological University
|
||||
'openorgs____::0fccc7640f0cb44d5cd1b06b312a06b9', -- Cardiff University
|
||||
'openorgs____::8839b55dae0c84d56fd533f52d5d483a', -- Leibniz Institute of Ecological Urban and Regional Development
|
||||
'openorgs____::526468206bca24c1c90da6a312295cf4', -- Cyprus University of Technology
|
||||
'openorgs____::b5ca9d4340e26454e367e2908ef3872f', -- Alma Mater Studiorum University of Bologna
|
||||
'openorgs____::a6340e6ecf60f6bba163659df985b0f2' -- TU Dresden
|
||||
))) foo;
|
||||
|
||||
--ANALYZE TABLE TARGET.result COMPUTE STATISTICS;
|
||||
|
|
@ -0,0 +1,111 @@
|
|||
<workflow-app name="Stats Monitor Update" xmlns="uri:oozie:workflow:0.5">
|
||||
<parameters>
|
||||
<property>
|
||||
<name>stats_db_name</name>
|
||||
<description>the target stats database name</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>monitor_db_name</name>
|
||||
<description>the target monitor db name</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>monitor_db_shadow_name</name>
|
||||
<description>the name of the shadow monitor db</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>hive_metastore_uris</name>
|
||||
<description>hive server metastore URIs</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>hive_jdbc_url</name>
|
||||
<description>hive server jdbc url</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>hive_timeout</name>
|
||||
<description>the time period, in seconds, after which Hive fails a transaction if a Hive client has not sent a hearbeat. The default value is 300 seconds.</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>hadoop_user_name</name>
|
||||
<description>user name of the wf owner</description>
|
||||
</property>
|
||||
</parameters>
|
||||
|
||||
<global>
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<configuration>
|
||||
<property>
|
||||
<name>hive.metastore.uris</name>
|
||||
<value>${hive_metastore_uris}</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>hive.txn.timeout</name>
|
||||
<value>${hive_timeout}</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>mapred.job.queue.name</name>
|
||||
<value>analytics</value>
|
||||
</property>
|
||||
</configuration>
|
||||
</global>
|
||||
|
||||
<start to="resume_from"/>
|
||||
<decision name="resume_from">
|
||||
<switch>
|
||||
<case to="Step1-updateMonitorDB">${wf:conf('resumeFrom') eq 'Step1-updateMonitorDB'}</case>
|
||||
<case to="Step2-copyDataToImpalaCluster">${wf:conf('resumeFrom') eq 'Step2-copyDataToImpalaCluster'}</case>
|
||||
<case to="Step3-finalizeImpalaCluster">${wf:conf('resumeFrom') eq 'Step3-finalizeImpalaCluster'}</case>
|
||||
<default to="Step1-updateMonitorDB"/>
|
||||
</switch>
|
||||
</decision>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
<action name="Step1-updateMonitorDB">
|
||||
<shell xmlns="uri:oozie:shell-action:0.1">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<exec>monitor.sh</exec>
|
||||
<argument>${stats_db_name}</argument>
|
||||
<argument>${monitor_db_name}</argument>
|
||||
<argument>${monitor_db_shadow_name}</argument>
|
||||
<argument>${wf:appPath()}/scripts/updateMonitorDB_institutions.sql</argument>
|
||||
<argument>${wf:appPath()}/scripts/updateMonitorDB.sql</argument>
|
||||
<argument>${wf:appPath()}/scripts/updateMonitorDBAll.sql</argument>
|
||||
<file>monitor.sh</file>
|
||||
</shell>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="Step2-copyDataToImpalaCluster">
|
||||
<shell xmlns="uri:oozie:shell-action:0.1">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<exec>copyDataToImpalaCluster.sh</exec>
|
||||
<argument>${monitor_db_name}</argument>
|
||||
<argument>${hadoop_user_name}</argument>
|
||||
<file>copyDataToImpalaCluster.sh</file>
|
||||
</shell>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="Step3-finalizeImpalaCluster">
|
||||
<shell xmlns="uri:oozie:shell-action:0.1">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<exec>finalizeImpalaCluster.sh</exec>
|
||||
<argument>${monitor_db_name}</argument>
|
||||
<argument>${monitor_db_prod_name}</argument>
|
||||
<argument>${monitor_db_shadow_name}</argument>
|
||||
<file>finalizeImpalaCluster.sh</file>
|
||||
</shell>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
||||
|
|
@ -35,12 +35,20 @@ export HADOOP_USER="oozie"
|
|||
export HADOOP_USER_NAME="oozie"
|
||||
|
||||
echo "Creating and populating impala tables"
|
||||
hive $HIVE_OPTS -e "create table ${TARGET_DB}.context (id string, name string) row format delimited fields terminated by ','"
|
||||
hive $HIVE_OPTS -e "create table ${TARGET_DB}.category (context string, id string, name string) row format delimited fields terminated by ','"
|
||||
hive $HIVE_OPTS -e "create table ${TARGET_DB}.concept (category string, id string, name string) row format delimited fields terminated by ','"
|
||||
hive $HIVE_OPTS -e "load data inpath '${TMP}/contexts.csv' into table ${TARGET_DB}.context"
|
||||
hive $HIVE_OPTS -e "load data inpath '${TMP}/categories.csv' into table ${TARGET_DB}.category"
|
||||
hive $HIVE_OPTS -e "load data inpath '${TMP}/concepts.csv' into table ${TARGET_DB}.concept"
|
||||
hive $HIVE_OPTS -e "create table ${TARGET_DB}.context_csv (id string, name string) row format delimited fields terminated by ','"
|
||||
hive $HIVE_OPTS -e "load data inpath '${TMP}/contexts.csv' into table ${TARGET_DB}.context_csv"
|
||||
hive $HIVE_OPTS -e "create table ${TARGET_DB}.context stored as parquet as select * from ${TARGET_DB}.context_csv"
|
||||
hive $HIVE_OPTS -e "drop table ${TARGET_DB}.context_csv purge"
|
||||
|
||||
hive $HIVE_OPTS -e "create table ${TARGET_DB}.category_csv (context string, id string, name string) row format delimited fields terminated by ','"
|
||||
hive $HIVE_OPTS -e "load data inpath '${TMP}/categories.csv' into table ${TARGET_DB}.category_csv"
|
||||
hive $HIVE_OPTS -e "create table ${TARGET_DB}.category stored as parquet as select * from ${TARGET_DB}.category_csv"
|
||||
hive $HIVE_OPTS -e "drop table ${TARGET_DB}.category_csv purge"
|
||||
|
||||
hive $HIVE_OPTS -e "create table ${TARGET_DB}.concept_csv (category string, id string, name string) row format delimited fields terminated by ','"
|
||||
hive $HIVE_OPTS -e "load data inpath '${TMP}/concepts.csv' into table ${TARGET_DB}.concept_csv"
|
||||
hive $HIVE_OPTS -e "create table ${TARGET_DB}.concept stored as parquet as select * from ${TARGET_DB}.concept_csv"
|
||||
hive $HIVE_OPTS -e "drop table ${TARGET_DB}.concept_csv purge"
|
||||
|
||||
echo "Cleaning up"
|
||||
rm concepts.csv
|
||||
|
|
|
|||
|
|
@ -6,68 +6,215 @@ then
|
|||
ln -sfn ${PYTHON_EGG_CACHE}${link_folder} ${link_folder}
|
||||
fi
|
||||
|
||||
|
||||
# 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}"
|
||||
|
||||
IMPALA_HDFS_NODE=''
|
||||
COUNTER=0
|
||||
while [ $COUNTER -lt 3 ]; do
|
||||
if hdfs dfs -test -e hdfs://impala-cluster-mn1.openaire.eu/tmp >/dev/null 2>&1; then
|
||||
IMPALA_HDFS_NODE='hdfs://impala-cluster-mn1.openaire.eu:8020'
|
||||
break
|
||||
elif hdfs dfs -test -e hdfs://impala-cluster-mn2.openaire.eu/tmp >/dev/null 2>&1; then
|
||||
IMPALA_HDFS_NODE='hdfs://impala-cluster-mn2.openaire.eu:8020'
|
||||
break
|
||||
else
|
||||
IMPALA_HDFS_NODE=''
|
||||
sleep 1
|
||||
fi
|
||||
((COUNTER++))
|
||||
done
|
||||
if [ -z "$IMPALA_HDFS_NODE" ]; then
|
||||
echo -e "\n\nERROR: PROBLEM WHEN SETTING THE HDFS-NODE FOR IMPALA CLUSTER! | AFTER ${COUNTER} RETRIES.\n\n"
|
||||
exit 1
|
||||
fi
|
||||
echo -e "Active IMPALA HDFS Node: ${IMPALA_HDFS_NODE} , after ${COUNTER} retries.\n\n"
|
||||
|
||||
IMPALA_HOSTNAME='impala-cluster-dn1.openaire.eu'
|
||||
IMPALA_CONFIG_FILE='/etc/impala_cluster/hdfs-site.xml'
|
||||
|
||||
IMPALA_HDFS_DB_BASE_PATH="${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'
|
||||
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 copydb() {
|
||||
db=$1
|
||||
FILE=("hive_wf_tmp_"$RANDOM)
|
||||
hdfs dfs -mkdir hdfs://impala-cluster-mn1.openaire.eu:8020/tmp/$FILE/
|
||||
# copy the databases from ocean to impala
|
||||
echo -e "\nStart processing db: '${db}'..\n"
|
||||
|
||||
echo "copying $db"
|
||||
hadoop distcp -Dmapreduce.map.memory.mb=6144 -pb hdfs://nameservice1/user/hive/warehouse/${db}.db hdfs://impala-cluster-mn1.openaire.eu:8020/tmp/$FILE/
|
||||
# Delete the old DB from Impala cluster (if exists).
|
||||
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "drop database if exists ${db} cascade" |& tee error.log # impala-shell prints all logs in stderr, so wee need to capture them and put them in a file, in order to perform "grep" on them later
|
||||
log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
|
||||
if [ -n "$log_errors" ]; then
|
||||
echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN DROPPING THE OLD DATABASE! EXITING...\n\n"
|
||||
rm -f error.log
|
||||
return 1
|
||||
fi
|
||||
|
||||
# change ownership to impala
|
||||
hdfs dfs -conf /etc/impala_cluster/hdfs-site.xml -chmod -R 777 /tmp/$FILE/${db}.db
|
||||
# Make Impala aware of the deletion of the old DB immediately.
|
||||
sleep 1
|
||||
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
|
||||
|
||||
# drop tables from db
|
||||
for i in `impala-shell --user $HADOOP_USER_NAME -i impala-cluster-dn1.openaire.eu -d ${db} --delimited -q "show tables"`;
|
||||
do
|
||||
`impala-shell -i impala-cluster-dn1.openaire.eu -d ${db} -q "drop table $i;"`;
|
||||
done
|
||||
echo -e "\n\nCopying files of '${db}', from Ocean to Impala cluster..\n"
|
||||
# Using max-bandwidth of: 50 * 100 Mb/s = 5 Gb/s
|
||||
# Using max memory of: 50 * 6144 = 300 Gb
|
||||
# Using 1MB as a buffer-size.
|
||||
# The " -Ddistcp.dynamic.recordsPerChunk=50" arg is not available in our version of hadoop
|
||||
# The "ug" args cannot be used as we get a "User does not belong to hive" error.
|
||||
# The "p" argument cannot be used, as it blocks the files from being used, giving a "sticky bit"-error, even after applying chmod and chown onm the files.
|
||||
hadoop distcp -Dmapreduce.map.memory.mb=6144 -m 70 -bandwidth 150 \
|
||||
-numListstatusThreads 40 \
|
||||
-copybuffersize 1048576 \
|
||||
-strategy dynamic \
|
||||
-pb \
|
||||
${OCEAN_HDFS_NODE}/user/hive/warehouse/${db}.db ${IMPALA_HDFS_DB_BASE_PATH}
|
||||
|
||||
# drop views from db
|
||||
for i in `impala-shell --user $HADOOP_USER_NAME -i impala-cluster-dn1.openaire.eu -d ${db} --delimited -q "show tables"`;
|
||||
do
|
||||
`impala-shell -i impala-cluster-dn1.openaire.eu -d ${db} -q "drop view $i;"`;
|
||||
done
|
||||
# Check the exit status of the "hadoop distcp" command.
|
||||
if [ $? -eq 0 ]; then
|
||||
echo -e "\nSuccessfully copied the files of '${db}'.\n"
|
||||
else
|
||||
echo -e "\n\nERROR: FAILED TO TRANSFER THE FILES OF '${db}', WITH 'hadoop distcp'. GOT WITH EXIT STATUS: $?\n\n"
|
||||
rm -f error.log
|
||||
return 2
|
||||
fi
|
||||
|
||||
# delete the database
|
||||
impala-shell --user $HADOOP_USER_NAME -i impala-cluster-dn1.openaire.eu -q "drop database if exists ${db} cascade";
|
||||
# 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
|
||||
|
||||
# create the databases
|
||||
impala-shell --user $HADOOP_USER_NAME -i impala-cluster-dn1.openaire.eu -q "create database ${db}";
|
||||
echo -e "\nCreating schema for db: '${db}'\n"
|
||||
|
||||
impala-shell --user $HADOOP_USER_NAME -q "INVALIDATE METADATA"
|
||||
echo "creating schema for ${db}"
|
||||
for (( k = 0; k < 5; k ++ )); do
|
||||
for i in `impala-shell --user $HADOOP_USER_NAME -d ${db} --delimited -q "show tables"`;
|
||||
do
|
||||
impala-shell --user $HADOOP_USER_NAME -d ${db} --delimited -q "show create table $i";
|
||||
done | sed 's/"$/;/' | sed 's/^"//' | sed 's/[[:space:]]\date[[:space:]]/`date`/g' | impala-shell --user $HADOOP_USER_NAME -i impala-cluster-dn1.openaire.eu -c -f -
|
||||
# create the new database (with the same name)
|
||||
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create database ${db}"
|
||||
|
||||
# Make Impala aware of the creation of the new DB immediately.
|
||||
sleep 1
|
||||
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
|
||||
sleep 1
|
||||
# Because "Hive" and "Impala" do not have compatible schemas, we cannot use the "show create table <name>" output from hive to create the exact same table in impala.
|
||||
# So, we have to find at least one parquet file (check if it's there) from the table in the ocean cluster for impala to use it to extract the table-schema itself from that file.
|
||||
|
||||
all_create_view_statements=()
|
||||
|
||||
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.
|
||||
# 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_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' \
|
||||
| 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"
|
||||
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"
|
||||
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"
|
||||
fi
|
||||
fi
|
||||
fi
|
||||
done
|
||||
|
||||
# for i in `impala-shell --user $HADOOP_USER_NAME -d ${db} --delimited -q "show tables"`;
|
||||
# do
|
||||
# impala-shell --user $HADOOP_USER_NAME -d ${db} --delimited -q "show create table $i";
|
||||
# done | sed 's/"$/;/' | sed 's/^"//' | sed 's/[[:space:]]\date[[:space:]]/`date`/g' | impala-shell --user $HADOOP_USER_NAME -i impala-cluster-dn1.openaire.eu -c -f -
|
||||
#
|
||||
# # run the same command twice because we may have failures in the first run (due to views pointing to the same db)
|
||||
# for i in `impala-shell --user $HADOOP_USER_NAME -d ${db} --delimited -q "show tables"`;
|
||||
# do
|
||||
# impala-shell --user $HADOOP_USER_NAME -d ${db} --delimited -q "show create table $i";
|
||||
# done | sed 's/"$/;/' | sed 's/^"//' | sed 's/[[:space:]]\date[[:space:]]/`date`/g' | impala-shell --user $HADOOP_USER_NAME -i impala-cluster-dn1.openaire.eu -c -f -
|
||||
echo -e "\nAll tables have been created, going to create the views..\n"
|
||||
|
||||
# load the data from /tmp in the respective tables
|
||||
echo "copying data in tables and computing stats"
|
||||
for i in `impala-shell --user $HADOOP_USER_NAME -i impala-cluster-dn1.openaire.eu -d ${db} --delimited -q "show tables"`;
|
||||
do
|
||||
impala-shell --user $HADOOP_USER_NAME -i impala-cluster-dn1.openaire.eu -d ${db} -q "load data inpath '/tmp/$FILE/${db}.db/$i' into table $i";
|
||||
impala-shell --user $HADOOP_USER_NAME -i impala-cluster-dn1.openaire.eu -d ${db} -q "compute stats $i";
|
||||
done
|
||||
# Time to loop through the views and create them.
|
||||
# At this point all table-schemas should have been created.
|
||||
|
||||
# deleting the remaining directory from hdfs
|
||||
hdfs dfs -conf /etc/impala_cluster/hdfs-site.xml -rm -R /tmp/$FILE/${db}.db
|
||||
previous_num_of_views_to_retry=${#all_create_view_statements}
|
||||
if [[ $previous_num_of_views_to_retry -gt 0 ]]; then
|
||||
echo -e "\nAll_create_view_statements:\n\n${all_create_view_statements[@]}\n" # DEBUG
|
||||
# Make Impala aware of the new tables, so it knows them when creating the views.
|
||||
sleep 1
|
||||
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
|
||||
sleep 1
|
||||
else
|
||||
echo -e "\nDB '${db}' does not contain any views.\n"
|
||||
fi
|
||||
|
||||
level_counter=0
|
||||
while [[ ${#all_create_view_statements[@]} -gt 0 ]]; do
|
||||
((level_counter++))
|
||||
# The only accepted reason for a view to not be created, is if it depends on another view, which has not been created yet.
|
||||
# In this case, we should retry creating this particular view again.
|
||||
should_retry_create_view_statements=()
|
||||
|
||||
for create_view_statement in "${all_create_view_statements[@]}"; do # Here we use double quotes, as the elements are phrases, instead of single-words.
|
||||
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "${create_view_statement}" |& tee error.log # impala-shell prints all logs in stderr, so wee need to capture them and put them in a file, in order to perform "grep" on them later
|
||||
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 "CREATE VIEW " | sed 's/CREATE VIEW //g' | sed 's/ as select .*//g')' failed to be created, possibly because it depends on another view.\n"
|
||||
should_retry_create_view_statements+=("$create_view_statement")
|
||||
else
|
||||
sleep 1 # Wait a bit for Impala to register that the view was created, before possibly referencing it by another view.
|
||||
fi
|
||||
done
|
||||
|
||||
new_num_of_views_to_retry=${#should_retry_create_view_statements}
|
||||
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"
|
||||
return 3
|
||||
elif [[ $new_num_of_views_to_retry -gt 0 ]]; then
|
||||
echo -e "\nTo be retried \"create_view_statements\":\n\n${should_retry_create_view_statements[@]}\n"
|
||||
previous_num_of_views_to_retry=$new_num_of_views_to_retry
|
||||
else
|
||||
echo -e "\nFinished creating views, for db: '${db}', in level-${level_counter}.\n"
|
||||
fi
|
||||
all_create_view_statements=("${should_retry_create_view_statement[@]}") # This is needed in any case to either move forward with the rest of the views or stop at 0 remaining views.
|
||||
done
|
||||
|
||||
sleep 1
|
||||
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
|
||||
sleep 1
|
||||
|
||||
echo -e "\nComputing stats for tables..\n"
|
||||
entities_on_impala=`impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} --delimited -q "show tables in ${db}"`
|
||||
for i in ${entities_on_impala[@]}; do # Use un-quoted values, as the elemetns are single-words.
|
||||
# Taking the create table statement from the Ocean cluster, just to check if its a view, as the output is easier than using impala-shell from Impala cluster.
|
||||
create_view_statement=`hive -e "show create table ${db}.${i};" | grep "CREATE VIEW"` # This grep works here, as we do not want to match multiple-lines.
|
||||
if [ -z "$create_view_statement" ]; then # If it's a table, then go load the data to it.
|
||||
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "compute stats ${db}.${i}";
|
||||
fi
|
||||
done
|
||||
|
||||
if [ "${entities_on_impala[@]}" == "${entities_on_ocean[@]}" ]; then
|
||||
echo -e "\nAll entities have been copied to Impala cluster.\n"
|
||||
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
|
||||
return 4
|
||||
fi
|
||||
|
||||
rm -f error.log
|
||||
echo -e "\n\nFinished processing db: ${db}\n\n"
|
||||
}
|
||||
|
||||
STATS_DB=$1
|
||||
|
|
|
|||
|
|
@ -85,12 +85,12 @@ hive $HIVE_OPTS --database ${2}_funded -e "show tables" | grep -v WARN | sed "s/
|
|||
hive -f foo
|
||||
echo "Updated shadow monitor funded database"
|
||||
|
||||
echo "Updating shadow monitor insitutions database"
|
||||
echo "Updating shadow monitor institutions database"
|
||||
hive -e "drop database if exists ${SHADOW}_institutions cascade"
|
||||
hive -e "create database if not exists ${SHADOW}_institutions"
|
||||
hive $HIVE_OPTS --database ${2}_institutions -e "show tables" | grep -v WARN | sed "s/\(.*\)/create view ${SHADOW}_institutions.\1 as select * from ${2}_institutions.\1;/" > foo
|
||||
hive -f foo
|
||||
echo "Shadow db monitor insitutions ready!"
|
||||
echo "Shadow db monitor institutions ready!"
|
||||
|
||||
echo "Updating shadow monitor RIs database"
|
||||
for i in $contexts
|
||||
|
|
|
|||
|
|
@ -69,7 +69,7 @@ SELECT * FROM ${stats_db_name}.otherresearchproduct_sources;
|
|||
DROP TABLE IF EXISTS ${stats_db_name}.result_orcid purge;
|
||||
|
||||
CREATE TABLE IF NOT EXISTS ${stats_db_name}.result_orcid STORED AS PARQUET as
|
||||
select distinct res.id, regexp_replace(res.orcid, 'http://orcid.org/' ,'') as orcid
|
||||
select distinct res.id, upper(regexp_replace(res.orcid, 'http://orcid.org/' ,'')) as orcid
|
||||
from (
|
||||
SELECT substr(res.id, 4) as id, auth_pid.value as orcid
|
||||
FROM ${openaire_db_name}.result res
|
||||
|
|
|
|||
|
|
@ -7,32 +7,76 @@
|
|||
------------------------------------------------------
|
||||
|
||||
DROP TABLE IF EXISTS ${stats_db_name}.publication_refereed purge;
|
||||
|
||||
CREATE TABLE IF NOT EXISTS ${stats_db_name}.publication_refereed STORED AS PARQUET as
|
||||
select substr(r.id, 4) as id, inst.refereed.classname as refereed
|
||||
from ${openaire_db_name}.publication r lateral view explode(r.instance) instances as inst
|
||||
where r.datainfo.deletedbyinference=false and r.datainfo.invisible = FALSE;
|
||||
with peer_reviewed as (
|
||||
select distinct substr(r.id, 4) as id, inst.refereed.classname as refereed
|
||||
from ${openaire_db_name}.publication r lateral view explode(r.instance) instances as inst
|
||||
where r.datainfo.deletedbyinference=false and r.datainfo.invisible = FALSE and inst.refereed.classname='peerReviewed'),
|
||||
non_peer_reviewed as (
|
||||
select distinct substr(r.id, 4) as id, inst.refereed.classname as refereed
|
||||
from ${openaire_db_name}.publication r lateral view explode(r.instance) instances as inst
|
||||
where r.datainfo.deletedbyinference=false and r.datainfo.invisible = FALSE and inst.refereed.classname='nonPeerReviewed')
|
||||
select distinct *
|
||||
from (
|
||||
select peer_reviewed.* from peer_reviewed
|
||||
union all
|
||||
select non_peer_reviewed.* from non_peer_reviewed
|
||||
left join peer_reviewed on peer_reviewed.id=non_peer_reviewed.id
|
||||
where peer_reviewed.id is null) pr;
|
||||
|
||||
DROP TABLE IF EXISTS ${stats_db_name}.dataset_refereed purge;
|
||||
|
||||
CREATE TABLE IF NOT EXISTS ${stats_db_name}.dataset_refereed STORED AS PARQUET as
|
||||
select substr(r.id, 4) as id, inst.refereed.classname as refereed
|
||||
from ${openaire_db_name}.dataset r lateral view explode(r.instance) instances as inst
|
||||
where r.datainfo.deletedbyinference=false and r.datainfo.invisible = FALSE;
|
||||
with peer_reviewed as (
|
||||
select distinct substr(r.id, 4) as id, inst.refereed.classname as refereed
|
||||
from ${openaire_db_name}.dataset r lateral view explode(r.instance) instances as inst
|
||||
where r.datainfo.deletedbyinference=false and r.datainfo.invisible = FALSE and inst.refereed.classname='peerReviewed'),
|
||||
non_peer_reviewed as (
|
||||
select distinct substr(r.id, 4) as id, inst.refereed.classname as refereed
|
||||
from ${openaire_db_name}.dataset r lateral view explode(r.instance) instances as inst
|
||||
where r.datainfo.deletedbyinference=false and r.datainfo.invisible = FALSE and inst.refereed.classname='nonPeerReviewed')
|
||||
select distinct *
|
||||
from (
|
||||
select peer_reviewed.* from peer_reviewed
|
||||
union all
|
||||
select non_peer_reviewed.* from non_peer_reviewed
|
||||
left join peer_reviewed on peer_reviewed.id=non_peer_reviewed.id
|
||||
where peer_reviewed.id is null) pr;
|
||||
|
||||
DROP TABLE IF EXISTS ${stats_db_name}.software_refereed purge;
|
||||
|
||||
CREATE TABLE IF NOT EXISTS ${stats_db_name}.software_refereed STORED AS PARQUET as
|
||||
select substr(r.id, 4) as id, inst.refereed.classname as refereed
|
||||
from ${openaire_db_name}.software r lateral view explode(r.instance) instances as inst
|
||||
where r.datainfo.deletedbyinference=false and r.datainfo.invisible = FALSE;
|
||||
with peer_reviewed as (
|
||||
select distinct substr(r.id, 4) as id, inst.refereed.classname as refereed
|
||||
from ${openaire_db_name}.software r lateral view explode(r.instance) instances as inst
|
||||
where r.datainfo.deletedbyinference=false and r.datainfo.invisible = FALSE and inst.refereed.classname='peerReviewed'),
|
||||
non_peer_reviewed as (
|
||||
select distinct substr(r.id, 4) as id, inst.refereed.classname as refereed
|
||||
from ${openaire_db_name}.software r lateral view explode(r.instance) instances as inst
|
||||
where r.datainfo.deletedbyinference=false and r.datainfo.invisible = FALSE and inst.refereed.classname='nonPeerReviewed')
|
||||
select distinct *
|
||||
from (
|
||||
select peer_reviewed.* from peer_reviewed
|
||||
union all
|
||||
select non_peer_reviewed.* from non_peer_reviewed
|
||||
left join peer_reviewed on peer_reviewed.id=non_peer_reviewed.id
|
||||
where peer_reviewed.id is null) pr;
|
||||
|
||||
DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_refereed purge;
|
||||
|
||||
CREATE TABLE IF NOT EXISTS ${stats_db_name}.otherresearchproduct_refereed STORED AS PARQUET as
|
||||
select substr(r.id, 4) as id, inst.refereed.classname as refereed
|
||||
from ${openaire_db_name}.otherresearchproduct r lateral view explode(r.instance) instances as inst
|
||||
where r.datainfo.deletedbyinference=false and r.datainfo.invisible = FALSE;
|
||||
with peer_reviewed as (
|
||||
select distinct substr(r.id, 4) as id, inst.refereed.classname as refereed
|
||||
from ${openaire_db_name}.otherresearchproduct r lateral view explode(r.instance) instances as inst
|
||||
where r.datainfo.deletedbyinference=false and r.datainfo.invisible = FALSE and inst.refereed.classname='peerReviewed'),
|
||||
non_peer_reviewed as (
|
||||
select distinct substr(r.id, 4) as id, inst.refereed.classname as refereed
|
||||
from ${openaire_db_name}.otherresearchproduct r lateral view explode(r.instance) instances as inst
|
||||
where r.datainfo.deletedbyinference=false and r.datainfo.invisible = FALSE and inst.refereed.classname='nonPeerReviewed')
|
||||
select distinct *
|
||||
from (
|
||||
select peer_reviewed.* from peer_reviewed
|
||||
union all
|
||||
select non_peer_reviewed.* from non_peer_reviewed
|
||||
left join peer_reviewed on peer_reviewed.id=non_peer_reviewed.id
|
||||
where peer_reviewed.id is null) pr;
|
||||
|
||||
CREATE VIEW IF NOT EXISTS ${stats_db_name}.result_refereed as
|
||||
select * from ${stats_db_name}.publication_refereed
|
||||
|
|
@ -60,4 +104,4 @@ rel.properties[1].value apc_currency
|
|||
from ${openaire_db_name}.relation rel
|
||||
join ${openaire_db_name}.organization o on o.id=rel.source
|
||||
join ${openaire_db_name}.result r on r.id=rel.target
|
||||
where rel.subreltype = 'affiliation' and rel.datainfo.deletedbyinference = false and size(rel.properties)>0;
|
||||
where rel.subreltype = 'affiliation' and rel.datainfo.deletedbyinference = false and size(rel.properties)>0;
|
||||
|
|
@ -50,13 +50,13 @@ select distinct r.*
|
|||
from (
|
||||
select substr(r.id, 4) as id, inst.accessright.classname as accessright, inst.accessright.openaccessroute as accessright_uw, substr(inst.collectedfrom.key, 4) as collectedfrom,
|
||||
substr(inst.hostedby.key, 4) as hostedby, inst.dateofacceptance.value as dateofacceptance, inst.license.value as license, p.qualifier.classname as pidtype, p.value as pid
|
||||
from ${openaire_db_name}.result r lateral view explode(r.instance) instances as inst lateral view explode(inst.pid) pids as p) r
|
||||
from ${openaire_db_name}.result r lateral view explode(r.instance) instances as inst lateral view outer explode(inst.pid) pids as p) r
|
||||
join ${stats_db_name}.result res on res.id=r.id;
|
||||
|
||||
DROP TABLE IF EXISTS ${stats_db_name}.result_apc purge;
|
||||
|
||||
create table if not exists ${stats_db_name}.result_apc STORED AS PARQUET as
|
||||
select r.id, r.amount, r.currency
|
||||
select distinct r.id, r.amount, r.currency
|
||||
from (
|
||||
select substr(r.id, 4) as id, cast(inst.processingchargeamount.value as float) as amount, inst.processingchargecurrency.value as currency
|
||||
from ${openaire_db_name}.result r lateral view explode(r.instance) instances as inst) r
|
||||
|
|
|
|||
|
|
@ -1,390 +1,255 @@
|
|||
-- Sprint 1 ----
|
||||
drop table if exists ${stats_db_name}.indi_pub_green_oa purge; /*EOS*/
|
||||
|
||||
--create table if not exists ${stats_db_name}.indi_pub_green_oa stored as parquet as
|
||||
--select distinct p.id, coalesce(green_oa, 0) as green_oa
|
||||
--from ${stats_db_name}.publication p
|
||||
-- left outer join (
|
||||
-- select p.id, 1 as green_oa
|
||||
-- from ${stats_db_name}.publication p
|
||||
-- join ${stats_db_name}.result_instance ri on ri.id = p.id
|
||||
-- join ${stats_db_name}.datasource on datasource.id = ri.hostedby
|
||||
-- where datasource.type like '%Repository%'
|
||||
-- and (ri.accessright = 'Open Access'
|
||||
-- or ri.accessright = 'Embargo' or ri.accessright = 'Open Source')) tmp
|
||||
-- on p.id= tmp.id;
|
||||
create table if not exists ${stats_db_name}.indi_pub_green_oa stored as parquet as
|
||||
select distinct p.id, coalesce(green_oa, 0) as green_oa
|
||||
from ${stats_db_name}.publication p
|
||||
left outer join (
|
||||
left outer join (
|
||||
select p.id, 1 as green_oa
|
||||
from ${stats_db_name}.publication p
|
||||
join ${stats_db_name}.result_instance ri on ri.id = p.id
|
||||
join ${stats_db_name}.datasource on datasource.id = ri.hostedby
|
||||
where datasource.type like '%Repository%'
|
||||
and (ri.accessright = 'Open Access'
|
||||
or ri.accessright = 'Embargo' or ri.accessright = 'Open Source') and datasource.name!='Other') tmp
|
||||
on p.id= tmp.id; /*EOS*/
|
||||
join ${stats_db_name}.result_instance ri on ri.id = p.id
|
||||
join ${stats_db_name}.datasource on datasource.id = ri.hostedby
|
||||
where datasource.type like '%Repository%' and (ri.accessright = 'Open Access' or ri.accessright = 'Embargo' or ri.accessright = 'Open Source') and datasource.name!='Other') tmp on p.id= tmp.id; /*EOS*/
|
||||
|
||||
drop table if exists ${stats_db_name}.indi_pub_grey_lit purge; /*EOS*/
|
||||
|
||||
create table if not exists ${stats_db_name}.indi_pub_grey_lit stored as parquet as
|
||||
select distinct p.id, coalesce(grey_lit, 0) as grey_lit
|
||||
from ${stats_db_name}.publication p
|
||||
left outer join (
|
||||
left outer join (
|
||||
select p.id, 1 as grey_lit
|
||||
from ${stats_db_name}.publication p
|
||||
join ${stats_db_name}.result_classifications rt on rt.id = p.id
|
||||
where rt.type not in ('Article','Part of book or chapter of book','Book','Doctoral thesis','Master thesis','Data Paper', 'Thesis', 'Bachelor thesis', 'Conference object') and
|
||||
not exists (select 1 from ${stats_db_name}.result_classifications rc where type ='Other literature type'
|
||||
and rc.id=p.id)) tmp on p.id=tmp.id; /*EOS*/
|
||||
join ${stats_db_name}.result_classifications rt on rt.id = p.id
|
||||
where rt.type not in ('Article','Part of book or chapter of book','Book','Doctoral thesis','Master thesis','Data Paper', 'Thesis', 'Bachelor thesis', 'Conference object')
|
||||
and not exists (select 1 from ${stats_db_name}.result_classifications rc where type ='Other literature type' and rc.id=p.id)) tmp on p.id=tmp.id; /*EOS*/
|
||||
|
||||
drop table if exists ${stats_db_name}.indi_pub_doi_from_crossref purge; /*EOS*/
|
||||
|
||||
create table if not exists ${stats_db_name}.indi_pub_doi_from_crossref stored as parquet as
|
||||
select distinct p.id, coalesce(doi_from_crossref, 0) as doi_from_crossref
|
||||
from ${stats_db_name}.publication p
|
||||
left outer join
|
||||
(select ri.id, 1 as doi_from_crossref from ${stats_db_name}.result_instance ri
|
||||
join ${stats_db_name}.datasource d on d.id = ri.collectedfrom
|
||||
where pidtype='Digital Object Identifier' and d.name ='Crossref') tmp
|
||||
on tmp.id=p.id; /*EOS*/
|
||||
left outer join (
|
||||
select ri.id, 1 as doi_from_crossref from ${stats_db_name}.result_instance ri
|
||||
join ${stats_db_name}.datasource d on d.id = ri.collectedfrom
|
||||
where pidtype='Digital Object Identifier' and d.name ='Crossref') tmp on tmp.id=p.id; /*EOS*/
|
||||
|
||||
-- Sprint 2 ----
|
||||
drop table if exists ${stats_db_name}.indi_result_has_cc_licence purge; /*EOS*/
|
||||
|
||||
create table if not exists ${stats_db_name}.indi_result_has_cc_licence stored as parquet as
|
||||
select distinct r.id, (case when lic='' or lic is null then 0 else 1 end) as has_cc_license
|
||||
from ${stats_db_name}.result r
|
||||
left outer join (select r.id, license.type as lic from ${stats_db_name}.result r
|
||||
join ${stats_db_name}.result_licenses as license on license.id = r.id
|
||||
where lower(license.type) LIKE '%creativecommons.org%' OR lower(license.type) LIKE '%cc-%') tmp
|
||||
on r.id= tmp.id; /*EOS*/
|
||||
left outer join (
|
||||
select r.id, license.type as lic from ${stats_db_name}.result r
|
||||
join ${stats_db_name}.result_licenses as license on license.id = r.id
|
||||
where lower(license.type) LIKE '%creativecommons.org%' OR lower(license.type) LIKE '%cc %') tmp on r.id= tmp.id; /*EOS*/
|
||||
|
||||
drop table if exists ${stats_db_name}.indi_result_has_cc_licence_url purge; /*EOS*/
|
||||
|
||||
create table if not exists ${stats_db_name}.indi_result_has_cc_licence_url stored as parquet as
|
||||
select distinct r.id, case when lic_host='' or lic_host is null then 0 else 1 end as has_cc_license_url
|
||||
from ${stats_db_name}.result r
|
||||
left outer join (select r.id, lower(parse_url(license.type, "HOST")) as lic_host
|
||||
from ${stats_db_name}.result r
|
||||
join ${stats_db_name}.result_licenses as license on license.id = r.id
|
||||
WHERE lower(parse_url(license.type, "HOST")) = "creativecommons.org") tmp
|
||||
on r.id= tmp.id; /*EOS*/
|
||||
left outer join (
|
||||
select r.id, lower(parse_url(license.type, "HOST")) as lic_host
|
||||
from ${stats_db_name}.result r
|
||||
join ${stats_db_name}.result_licenses as license on license.id = r.id
|
||||
WHERE lower(parse_url(license.type, "HOST")) = "creativecommons.org") tmp on r.id= tmp.id; /*EOS*/
|
||||
|
||||
drop table if exists ${stats_db_name}.indi_pub_has_abstract purge; /*EOS*/
|
||||
|
||||
create table if not exists ${stats_db_name}.indi_pub_has_abstract stored as parquet as
|
||||
select distinct publication.id, cast(coalesce(abstract, true) as int) has_abstract
|
||||
from ${stats_db_name}.publication; /*EOS*/
|
||||
|
||||
drop table if exists ${stats_db_name}.indi_result_with_orcid purge; /*EOS*/
|
||||
|
||||
create table if not exists ${stats_db_name}.indi_result_with_orcid stored as parquet as
|
||||
select distinct r.id, coalesce(has_orcid, 0) as has_orcid
|
||||
from ${stats_db_name}.result r
|
||||
left outer join (select id, 1 as has_orcid from ${stats_db_name}.result_orcid) tmp
|
||||
on r.id= tmp.id; /*EOS*/
|
||||
left outer join (
|
||||
select id, 1 as has_orcid from ${stats_db_name}.result_orcid) tmp on r.id= tmp.id; /*EOS*/
|
||||
|
||||
|
||||
---- Sprint 3 ----
|
||||
|
||||
drop table if exists ${stats_db_name}.indi_funded_result_with_fundref purge; /*EOS*/
|
||||
|
||||
create table if not exists ${stats_db_name}.indi_funded_result_with_fundref stored as parquet as
|
||||
select distinct r.result as id, coalesce(fundref, 0) as fundref
|
||||
from ${stats_db_name}.project_results r
|
||||
left outer join (select distinct result, 1 as fundref from ${stats_db_name}.project_results
|
||||
where provenance='Harvested') tmp
|
||||
on r.result= tmp.result; /*EOS*/
|
||||
|
||||
-- create table indi_result_org_collab stored as parquet as
|
||||
-- select o1.organization org1, o2.organization org2, count(distinct o1.id) as collaborations
|
||||
-- from result_organization as o1
|
||||
-- join result_organization as o2 on o1.id=o2.id and o1.organization!=o2.organization
|
||||
-- group by o1.organization, o2.organization;
|
||||
--
|
||||
-- compute stats indi_result_org_collab;
|
||||
--
|
||||
create TEMPORARY VIEW tmp AS SELECT ro.organization organization, ro.id, o.name from ${stats_db_name}.result_organization ro
|
||||
join ${stats_db_name}.organization o on o.id=ro.organization where o.name is not null; /*EOS*/
|
||||
left outer join (
|
||||
select distinct result, 1 as fundref from ${stats_db_name}.project_results where provenance='Harvested') tmp on r.result= tmp.result; /*EOS*/
|
||||
|
||||
drop table if exists ${stats_db_name}.indi_result_org_collab purge; /*EOS*/
|
||||
|
||||
create table if not exists ${stats_db_name}.indi_result_org_collab stored as parquet as
|
||||
select o1.organization org1, o1.name org1name1, o2.organization org2, o2.name org2name2, count(o1.id) as collaborations
|
||||
from tmp as o1
|
||||
join tmp as o2 where o1.id=o2.id and o1.organization!=o2.organization and o1.name!=o2.name
|
||||
group by o1.organization, o2.organization, o1.name, o2.name; /*EOS*/
|
||||
|
||||
DROP VIEW if exists tmp; /*EOS*/
|
||||
|
||||
create TEMPORARY VIEW tmp AS
|
||||
select distinct ro.organization organization, ro.id, o.name, o.country from ${stats_db_name}.result_organization ro
|
||||
join ${stats_db_name}.organization o on o.id=ro.organization where country <> 'UNKNOWN' and o.name is not null; /*EOS*/
|
||||
WITH tmp AS (
|
||||
SELECT ro.organization organization, ro.id, o.name
|
||||
from ${stats_db_name}.result_organization ro
|
||||
join ${stats_db_name}.organization o on o.id=ro.organization where o.name is not null)
|
||||
select o1.organization org1, o1.name org1name1, o2.organization org2, o2.name org2name2, count(o1.id) as collaborations
|
||||
from tmp as o1
|
||||
join tmp as o2 where o1.id=o2.id and o1.organization!=o2.organization and o1.name!=o2.name
|
||||
group by o1.organization, o2.organization, o1.name, o2.name; /*EOS*/
|
||||
|
||||
drop table if exists ${stats_db_name}.indi_result_org_country_collab purge; /*EOS*/
|
||||
|
||||
create table if not exists ${stats_db_name}.indi_result_org_country_collab stored as parquet as
|
||||
select o1.organization org1,o1.name org1name1, o2.country country2, count(o1.id) as collaborations
|
||||
from tmp as o1 join tmp as o2 on o1.id=o2.id
|
||||
where o1.id=o2.id and o1.country!=o2.country
|
||||
group by o1.organization, o1.id, o1.name, o2.country; /*EOS*/
|
||||
|
||||
drop table if exists tmp purge; /*EOS*/
|
||||
|
||||
create TEMPORARY VIEW tmp AS
|
||||
select o.id organization, o.name, ro.project as project from ${stats_db_name}.organization o
|
||||
join ${stats_db_name}.organization_projects ro on o.id=ro.id where o.name is not null; /*EOS*/
|
||||
WITH tmp AS (
|
||||
select distinct ro.organization organization, ro.id, o.name, o.country
|
||||
from ${stats_db_name}.result_organization ro
|
||||
join ${stats_db_name}.organization o on o.id=ro.organization
|
||||
where country <> 'UNKNOWN' and o.name is not null)
|
||||
select o1.organization org1,o1.name org1name1, o2.country country2, count(o1.id) as collaborations
|
||||
from tmp as o1 join tmp as o2 on o1.id=o2.id
|
||||
where o1.id=o2.id and o1.country!=o2.country
|
||||
group by o1.organization, o1.id, o1.name, o2.country; /*EOS*/
|
||||
|
||||
drop table if exists ${stats_db_name}.indi_project_collab_org purge; /*EOS*/
|
||||
|
||||
create table if not exists ${stats_db_name}.indi_project_collab_org stored as parquet as
|
||||
select o1.organization org1,o1.name orgname1, o2.organization org2, o2.name orgname2, count(distinct o1.project) as collaborations
|
||||
from tmp as o1
|
||||
join tmp as o2 on o1.project=o2.project
|
||||
where o1.organization<>o2.organization and o1.name<>o2.name
|
||||
group by o1.name,o2.name, o1.organization, o2.organization; /*EOS*/
|
||||
|
||||
DROP VIEW if exists tmp; /*EOS*/
|
||||
|
||||
create TEMPORARY VIEW tmp AS
|
||||
select o.id organization, o.name, o.country , ro.project as project from ${stats_db_name}.organization o
|
||||
join ${stats_db_name}.organization_projects ro on o.id=ro.id
|
||||
and o.country <> 'UNKNOWN' and o.name is not null; /*EOS*/
|
||||
WITH tmp AS (
|
||||
select o.id organization, o.name, ro.project as project
|
||||
from ${stats_db_name}.organization o
|
||||
join ${stats_db_name}.organization_projects ro on o.id=ro.id where o.name is not null)
|
||||
select o1.organization org1,o1.name orgname1, o2.organization org2, o2.name orgname2, count(distinct o1.project) as collaborations
|
||||
from tmp as o1
|
||||
join tmp as o2 on o1.project=o2.project
|
||||
where o1.organization<>o2.organization and o1.name<>o2.name
|
||||
group by o1.name,o2.name, o1.organization, o2.organization; /*EOS*/
|
||||
|
||||
drop table if exists ${stats_db_name}.indi_project_collab_org_country purge; /*EOS*/
|
||||
|
||||
create table if not exists ${stats_db_name}.indi_project_collab_org_country stored as parquet as
|
||||
select o1.organization org1,o1.name org1name, o2.country country2, count(distinct o1.project) as collaborations
|
||||
from tmp as o1
|
||||
join tmp as o2 on o1.project=o2.project
|
||||
where o1.organization<>o2.organization and o1.country<>o2.country
|
||||
group by o1.organization, o2.country, o1.name; /*EOS*/
|
||||
|
||||
DROP VIEW if exists tmp; /*EOS*/
|
||||
WITH tmp AS (
|
||||
select o.id organization, o.name, o.country , ro.project as project
|
||||
from ${stats_db_name}.organization o
|
||||
join ${stats_db_name}.organization_projects ro on o.id=ro.id and o.country <> 'UNKNOWN' and o.name is not null)
|
||||
select o1.organization org1,o1.name org1name, o2.country country2, count(distinct o1.project) as collaborations
|
||||
from tmp as o1
|
||||
join tmp as o2 on o1.project=o2.project
|
||||
where o1.organization<>o2.organization and o1.country<>o2.country
|
||||
group by o1.organization, o2.country, o1.name; /*EOS*/
|
||||
|
||||
drop table if exists ${stats_db_name}.indi_funder_country_collab purge; /*EOS*/
|
||||
|
||||
create table if not exists ${stats_db_name}.indi_funder_country_collab stored as parquet as
|
||||
with tmp as (select funder, project, country from ${stats_db_name}.organization_projects op
|
||||
join ${stats_db_name}.organization o on o.id=op.id
|
||||
join ${stats_db_name}.project p on p.id=op.project
|
||||
where country <> 'UNKNOWN')
|
||||
select f1.funder, f1.country as country1, f2.country as country2, count(distinct f1.project) as collaborations
|
||||
from tmp as f1
|
||||
join tmp as f2 on f1.project=f2.project
|
||||
where f1.country<>f2.country
|
||||
group by f1.funder, f2.country, f1.country; /*EOS*/
|
||||
|
||||
create TEMPORARY VIEW tmp AS
|
||||
select distinct country, ro.id as result from ${stats_db_name}.organization o
|
||||
join ${stats_db_name}.result_organization ro on o.id=ro.organization
|
||||
where country <> 'UNKNOWN' and o.name is not null; /*EOS*/
|
||||
select f1.funder, f1.country as country1, f2.country as country2, count(distinct f1.project) as collaborations
|
||||
from tmp as f1
|
||||
join tmp as f2 on f1.project=f2.project
|
||||
where f1.country<>f2.country
|
||||
group by f1.funder, f2.country, f1.country; /*EOS*/
|
||||
|
||||
drop table if exists ${stats_db_name}.indi_result_country_collab purge; /*EOS*/
|
||||
|
||||
create table if not exists ${stats_db_name}.indi_result_country_collab stored as parquet as
|
||||
select o1.country country1, o2.country country2, count(o1.result) as collaborations
|
||||
from tmp as o1
|
||||
join tmp as o2 on o1.result=o2.result
|
||||
where o1.country<>o2.country
|
||||
group by o1.country, o2.country; /*EOS*/
|
||||
WITH tmp AS (
|
||||
select distinct country, ro.id as result from ${stats_db_name}.organization o
|
||||
join ${stats_db_name}.result_organization ro on o.id=ro.organization
|
||||
where country <> 'UNKNOWN' and o.name is not null)
|
||||
select o1.country country1, o2.country country2, count(o1.result) as collaborations
|
||||
from tmp as o1
|
||||
join tmp as o2 on o1.result=o2.result
|
||||
where o1.country<>o2.country
|
||||
group by o1.country, o2.country; /*EOS*/
|
||||
|
||||
DROP VIEW if exists tmp; /*EOS*/
|
||||
|
||||
---- Sprint 4 ----
|
||||
drop table if exists ${stats_db_name}.indi_pub_diamond purge; /*EOS*/
|
||||
|
||||
--create table if not exists ${stats_db_name}.indi_pub_diamond stored as parquet as
|
||||
--select distinct pd.id, coalesce(in_diamond_journal, 0) as in_diamond_journal
|
||||
--from ${stats_db_name}.publication_datasources pd
|
||||
-- left outer join (
|
||||
-- select pd.id, 1 as in_diamond_journal from ${stats_db_name}.publication_datasources pd
|
||||
-- join ${stats_db_name}.datasource d on d.id=pd.datasource
|
||||
-- join STATS_EXT.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_online=d.issn_online)
|
||||
-- and (ps.journal_is_in_doaj=true or ps.journal_is_oa=true) and ps.has_apc=false) tmp
|
||||
-- on pd.id=tmp.id;
|
||||
|
||||
create table if not exists ${stats_db_name}.indi_pub_diamond stored as parquet as
|
||||
select distinct pd.id, coalesce(in_diamond_journal, 0) as in_diamond_journal
|
||||
from ${stats_db_name}.publication_datasources pd
|
||||
left outer join (select pd.id, 1 as in_diamond_journal from ${stats_db_name}.publication_datasources pd
|
||||
join ${stats_db_name}.datasource d on d.id=pd.datasource
|
||||
join STATS_EXT.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_online=d.issn_online)
|
||||
and (ps.journal_is_in_doaj=true or ps.journal_is_oa=true) and ps.has_apc=false) tmp
|
||||
on pd.id=tmp.id; /*EOS*/
|
||||
select distinct pd.id, coalesce(in_diamond_journal, 0) as in_diamond_journal
|
||||
from ${stats_db_name}.publication_datasources pd
|
||||
left outer join (
|
||||
select pd.id, 1 as in_diamond_journal
|
||||
from ${stats_db_name}.publication_datasources pd
|
||||
join ${stats_db_name}.datasource d on d.id=pd.datasource
|
||||
join STATS_EXT.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_online=d.issn_online)
|
||||
and (ps.journal_is_in_doaj=true or ps.journal_is_oa=true) and ps.has_apc=false) tmp on pd.id=tmp.id; /*EOS*/
|
||||
|
||||
drop table if exists ${stats_db_name}.indi_pub_in_transformative purge; /*EOS*/
|
||||
|
||||
create table if not exists ${stats_db_name}.indi_pub_in_transformative stored as parquet as
|
||||
select distinct pd.id, coalesce(is_transformative, 0) as is_transformative
|
||||
from ${stats_db_name}.publication pd
|
||||
left outer join (
|
||||
select pd.id, 1 as is_transformative from ${stats_db_name}.publication_datasources pd
|
||||
join ${stats_db_name}.datasource d on d.id=pd.datasource
|
||||
join STATS_EXT.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_online=d.issn_online)
|
||||
and ps.is_transformative_journal=true) tmp
|
||||
on pd.id=tmp.id; /*EOS*/
|
||||
select distinct pd.id, coalesce(is_transformative, 0) as is_transformative
|
||||
from ${stats_db_name}.publication pd
|
||||
left outer join (
|
||||
select pd.id, 1 as is_transformative
|
||||
from ${stats_db_name}.publication_datasources pd
|
||||
join ${stats_db_name}.datasource d on d.id=pd.datasource
|
||||
join STATS_EXT.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_online=d.issn_online)
|
||||
and ps.is_transformative_journal=true) tmp on pd.id=tmp.id; /*EOS*/
|
||||
|
||||
drop table if exists ${stats_db_name}.indi_pub_closed_other_open purge; /*EOS*/
|
||||
|
||||
create table if not exists ${stats_db_name}.indi_pub_closed_other_open stored as parquet as
|
||||
select distinct ri.id, coalesce(pub_closed_other_open, 0) as pub_closed_other_open from ${stats_db_name}.result_instance ri
|
||||
left outer join
|
||||
(select ri.id, 1 as pub_closed_other_open from ${stats_db_name}.result_instance ri
|
||||
join ${stats_db_name}.publication p on p.id=ri.id
|
||||
join ${stats_db_name}.datasource d on ri.hostedby=d.id
|
||||
where d.type like '%Journal%' and ri.accessright='Closed Access' and
|
||||
(p.bestlicence='Open Access' or p.bestlicence='Open Source')) tmp
|
||||
on tmp.id=ri.id; /*EOS*/
|
||||
select distinct ri.id, coalesce(pub_closed_other_open, 0) as pub_closed_other_open
|
||||
from ${stats_db_name}.result_instance ri
|
||||
left outer join (
|
||||
select ri.id, 1 as pub_closed_other_open
|
||||
from ${stats_db_name}.result_instance ri
|
||||
join ${stats_db_name}.publication p on p.id=ri.id
|
||||
join ${stats_db_name}.datasource d on ri.hostedby=d.id
|
||||
where d.type like '%Journal%' and ri.accessright='Closed Access' and
|
||||
(p.bestlicence='Open Access' or p.bestlicence='Open Source')) tmp on tmp.id=ri.id; /*EOS*/
|
||||
|
||||
|
||||
---- Sprint 5 ----
|
||||
drop table if exists ${stats_db_name}.indi_result_no_of_copies purge; /*EOS*/
|
||||
|
||||
create table if not exists ${stats_db_name}.indi_result_no_of_copies stored as parquet as
|
||||
select id, count(id) as number_of_copies from ${stats_db_name}.result_instance group by id; /*EOS*/
|
||||
select id, count(id) as number_of_copies
|
||||
from ${stats_db_name}.result_instance
|
||||
group by id; /*EOS*/
|
||||
|
||||
---- Sprint 6 ----
|
||||
drop table if exists ${stats_db_name}.indi_pub_downloads purge; /*EOS*/
|
||||
|
||||
create table if not exists ${stats_db_name}.indi_pub_downloads stored as parquet as
|
||||
SELECT result_id, sum(downloads) no_downloads from openaire_prod_usage_stats.usage_stats
|
||||
join ${stats_db_name}.publication on result_id=id
|
||||
where downloads>0
|
||||
GROUP BY result_id
|
||||
order by no_downloads desc; /*EOS*/
|
||||
|
||||
--ANALYZE TABLE ${stats_db_name}.indi_pub_downloads COMPUTE STATISTICS;
|
||||
SELECT result_id, sum(downloads) no_downloads
|
||||
from openaire_prod_usage_stats.usage_stats
|
||||
join ${stats_db_name}.publication on result_id=id
|
||||
where downloads>0
|
||||
GROUP BY result_id; /*EOS*/
|
||||
|
||||
drop table if exists ${stats_db_name}.indi_pub_downloads_datasource purge; /*EOS*/
|
||||
|
||||
create table if not exists ${stats_db_name}.indi_pub_downloads_datasource stored as parquet as
|
||||
SELECT result_id, repository_id, sum(downloads) no_downloads from openaire_prod_usage_stats.usage_stats
|
||||
join ${stats_db_name}.publication on result_id=id
|
||||
where downloads>0
|
||||
GROUP BY result_id, repository_id
|
||||
order by result_id; /*EOS*/
|
||||
SELECT result_id, repository_id, sum(downloads) no_downloads
|
||||
from openaire_prod_usage_stats.usage_stats
|
||||
join ${stats_db_name}.publication on result_id=id
|
||||
where downloads>0
|
||||
GROUP BY result_id, repository_id; /*EOS*/
|
||||
|
||||
drop table if exists ${stats_db_name}.indi_pub_downloads_year purge; /*EOS*/
|
||||
|
||||
create table if not exists ${stats_db_name}.indi_pub_downloads_year stored as parquet as
|
||||
SELECT result_id, cast(substring(us.`date`, 1,4) as int) as `year`, sum(downloads) no_downloads
|
||||
from openaire_prod_usage_stats.usage_stats us
|
||||
join ${stats_db_name}.publication on result_id=id where downloads>0
|
||||
GROUP BY result_id, substring(us.`date`, 1,4); /*EOS*/
|
||||
SELECT result_id, cast(substring(us.`date`, 1,4) as int) as `year`, sum(downloads) no_downloads
|
||||
from openaire_prod_usage_stats.usage_stats us
|
||||
join ${stats_db_name}.publication on result_id=id where downloads>0
|
||||
GROUP BY result_id, substring(us.`date`, 1,4); /*EOS*/
|
||||
|
||||
drop table if exists ${stats_db_name}.indi_pub_downloads_datasource_year purge; /*EOS*/
|
||||
|
||||
create table if not exists ${stats_db_name}.indi_pub_downloads_datasource_year stored as parquet as
|
||||
SELECT result_id, cast(substring(us.`date`, 1,4) as int) as `year`, repository_id, sum(downloads) no_downloads from openaire_prod_usage_stats.usage_stats us
|
||||
join ${stats_db_name}.publication on result_id=id
|
||||
where downloads>0
|
||||
GROUP BY result_id, repository_id, substring(us.`date`, 1,4); /*EOS*/
|
||||
SELECT result_id, cast(substring(us.`date`, 1,4) as int) as `year`, repository_id, sum(downloads) no_downloads
|
||||
from openaire_prod_usage_stats.usage_stats us
|
||||
join ${stats_db_name}.publication on result_id=id
|
||||
where downloads>0
|
||||
GROUP BY result_id, repository_id, substring(us.`date`, 1,4); /*EOS*/
|
||||
|
||||
|
||||
---- Sprint 7 ----
|
||||
drop table if exists ${stats_db_name}.indi_pub_gold_oa purge; /*EOS*/
|
||||
|
||||
--create table if not exists ${stats_db_name}.indi_pub_gold_oa stored as parquet as
|
||||
-- WITH gold_oa AS ( SELECT
|
||||
-- issn_l,
|
||||
-- journal_is_in_doaj,
|
||||
-- journal_is_oa,
|
||||
-- issn_1 as issn
|
||||
-- FROM
|
||||
-- STATS_EXT.oa_journals
|
||||
-- WHERE
|
||||
-- issn_1 != ""
|
||||
-- UNION
|
||||
-- ALL SELECT
|
||||
-- issn_l,
|
||||
-- journal_is_in_doaj,
|
||||
-- journal_is_oa,
|
||||
-- issn_2 as issn
|
||||
-- FROM
|
||||
-- STATS_EXT.oa_journals
|
||||
-- WHERE
|
||||
-- issn_2 != "" ), issn AS ( SELECT
|
||||
-- *
|
||||
-- FROM
|
||||
--( SELECT
|
||||
-- id,
|
||||
-- issn_printed as issn
|
||||
-- FROM
|
||||
-- ${stats_db_name}.datasource
|
||||
-- WHERE
|
||||
-- issn_printed IS NOT NULL
|
||||
-- UNION ALL
|
||||
-- SELECT
|
||||
-- id,
|
||||
-- issn_online as issn
|
||||
-- FROM
|
||||
-- ${stats_db_name}.datasource
|
||||
-- WHERE
|
||||
-- issn_online IS NOT NULL or id like '%doajarticles%') as issn
|
||||
-- WHERE
|
||||
-- LENGTH(issn) > 7)
|
||||
--SELECT
|
||||
-- DISTINCT pd.id, coalesce(is_gold, 0) as is_gold
|
||||
--FROM
|
||||
-- ${stats_db_name}.publication_datasources pd
|
||||
-- left outer join(
|
||||
-- select pd.id, 1 as is_gold FROM ${stats_db_name}.publication_datasources pd
|
||||
-- JOIN issn on issn.id=pd.datasource
|
||||
-- JOIN gold_oa on issn.issn = gold_oa.issn) tmp
|
||||
-- on pd.id=tmp.id;
|
||||
|
||||
--create table if not exists ${stats_db_name}.indi_pub_gold_oa stored as parquet as
|
||||
--with gold_oa as (
|
||||
--SELECT issn,issn_l from stats_ext.issn_gold_oa_dataset_v5),
|
||||
--issn AS (SELECT * FROM
|
||||
--(SELECT id,issn_printed as issn FROM ${stats_db_name}.datasource
|
||||
--WHERE issn_printed IS NOT NULL
|
||||
--UNION ALL
|
||||
--SELECT id, issn_online as issn FROM ${stats_db_name}.datasource
|
||||
--WHERE issn_online IS NOT NULL or id like '%doajarticles%') as issn
|
||||
--WHERE LENGTH(issn) > 7),
|
||||
--alljournals AS(select issn, issn_l from stats_ext.alljournals
|
||||
--where journal_is_in_doaj=true or journal_is_oa=true)
|
||||
--SELECT DISTINCT pd.id, coalesce(is_gold, 0) as is_gold
|
||||
--FROM ${stats_db_name}.publication_datasources pd
|
||||
--left outer join (
|
||||
--select pd.id, 1 as is_gold FROM ${stats_db_name}.publication_datasources pd
|
||||
--JOIN issn on issn.id=pd.datasource
|
||||
--JOIN gold_oa on issn.issn = gold_oa.issn
|
||||
--join alljournals on issn.issn=alljournals.issn
|
||||
--left outer join ${stats_db_name}.result_instance ri on ri.id=pd.id
|
||||
--and ri.accessright!='Closed Access' and ri.accessright_uw='gold') tmp
|
||||
--on pd.id=tmp.id;
|
||||
create table if not exists ${stats_db_name}.indi_pub_gold_oa stored as parquet as
|
||||
with gold_oa as (
|
||||
select distinct issn from (
|
||||
SELECT issn_l as issn from stats_ext.issn_gold_oa_dataset_v5
|
||||
UNION ALL
|
||||
SELECT issn as issn from stats_ext.issn_gold_oa_dataset_v5
|
||||
UNION ALL
|
||||
select issn from stats_ext.alljournals where journal_is_in_doaj=true or journal_is_oa=true
|
||||
UNION ALL
|
||||
select issn_l as issn from stats_ext.alljournals where journal_is_in_doaj=true or journal_is_oa=true) foo),
|
||||
dd as (
|
||||
select distinct * from (
|
||||
select id, issn_printed as issn from ${stats_db_name}.datasource d where d.id like '%doajarticles%'
|
||||
UNION ALL
|
||||
select id, issn_online as issn from ${stats_db_name}.datasource d where d.id like '%doajarticles%'
|
||||
UNION ALL
|
||||
select id, issn_printed as issn from ${stats_db_name}.datasource d join gold_oa on gold_oa.issn=d.issn_printed
|
||||
UNION ALL
|
||||
select id, issn_online as issn from ${stats_db_name}.datasource d join gold_oa on gold_oa.issn=d.issn_online) foo
|
||||
)
|
||||
SELECT DISTINCT pd.id, coalesce(is_gold, 0) as is_gold
|
||||
FROM ${stats_db_name}.publication_datasources pd
|
||||
left outer join (
|
||||
select pd.id, 1 as is_gold
|
||||
FROM ${stats_db_name}.publication_datasources pd
|
||||
join dd on dd.id=pd.datasource
|
||||
left outer join ${stats_db_name}.result_accessroute ra on ra.id = pd.id where ra.accessroute = 'gold') tmp on tmp.id=pd.id; /*EOS*/
|
||||
with gold_oa as (
|
||||
select distinct issn from (
|
||||
SELECT issn_l as issn from stats_ext.issn_gold_oa_dataset_v5
|
||||
UNION ALL
|
||||
SELECT issn as issn from stats_ext.issn_gold_oa_dataset_v5
|
||||
UNION ALL
|
||||
select issn from stats_ext.alljournals where journal_is_in_doaj=true or journal_is_oa=true
|
||||
UNION ALL
|
||||
select issn_l as issn from stats_ext.alljournals where journal_is_in_doaj=true or journal_is_oa=true) foo),
|
||||
dd as (
|
||||
select distinct * from (
|
||||
select id, issn_printed as issn from ${stats_db_name}.datasource d where d.id like '%doajarticles%'
|
||||
UNION ALL
|
||||
select id, issn_online as issn from ${stats_db_name}.datasource d where d.id like '%doajarticles%'
|
||||
UNION ALL
|
||||
select id, issn_printed as issn from ${stats_db_name}.datasource d left semi join gold_oa on gold_oa.issn=d.issn_printed
|
||||
UNION ALL
|
||||
select id, issn_online as issn from ${stats_db_name}.datasource d left semi join gold_oa on gold_oa.issn=d.issn_online) foo
|
||||
)
|
||||
SELECT DISTINCT pd.id, coalesce(is_gold, 0) as is_gold
|
||||
FROM ${stats_db_name}.publication_datasources pd
|
||||
left outer join (
|
||||
select pd.id, 1 as is_gold
|
||||
FROM ${stats_db_name}.publication_datasources pd
|
||||
left semi join dd on dd.id=pd.datasource
|
||||
left outer join ${stats_db_name}.result_accessroute ra on ra.id = pd.id where ra.accessroute = 'gold') tmp on tmp.id=pd.id; /*EOS*/
|
||||
|
||||
drop table if exists ${stats_db_name}.indi_pub_hybrid_oa_with_cc purge; /*EOS*/
|
||||
|
||||
create table if not exists ${stats_db_name}.indi_pub_hybrid_oa_with_cc stored as parquet as
|
||||
WITH hybrid_oa AS (
|
||||
SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_print as issn
|
||||
|
|
@ -395,121 +260,57 @@ create table if not exists ${stats_db_name}.indi_pub_hybrid_oa_with_cc stored as
|
|||
FROM STATS_EXT.plan_s_jn
|
||||
WHERE issn_online != "" and (journal_is_in_doaj = FALSE OR journal_is_oa = FALSE)),
|
||||
issn AS (
|
||||
SELECT *
|
||||
FROM (
|
||||
SELECT id, issn_printed as issn
|
||||
FROM ${stats_db_name}.datasource
|
||||
WHERE issn_printed IS NOT NULL
|
||||
UNION ALL
|
||||
SELECT id,issn_online as issn
|
||||
FROM ${stats_db_name}.datasource
|
||||
WHERE issn_online IS NOT NULL ) as issn
|
||||
WHERE LENGTH(issn) > 7)
|
||||
SELECT DISTINCT pd.id, coalesce(is_hybrid_oa, 0) as is_hybrid_oa
|
||||
FROM ${stats_db_name}.publication_datasources pd
|
||||
LEFT OUTER JOIN (
|
||||
SELECT pd.id, 1 as is_hybrid_oa from ${stats_db_name}.publication_datasources pd
|
||||
JOIN ${stats_db_name}.datasource d on d.id=pd.datasource
|
||||
JOIN issn on issn.id=pd.datasource
|
||||
JOIN hybrid_oa ON issn.issn = hybrid_oa.issn
|
||||
JOIN ${stats_db_name}.indi_result_has_cc_licence cc on pd.id=cc.id
|
||||
JOIN ${stats_db_name}.indi_pub_gold_oa ga on pd.id=ga.id
|
||||
where cc.has_cc_license=1 and ga.is_gold=0) tmp on pd.id=tmp.id; /*EOS*/
|
||||
SELECT *
|
||||
FROM (
|
||||
SELECT id, issn_printed as issn
|
||||
FROM ${stats_db_name}.datasource
|
||||
WHERE issn_printed IS NOT NULL
|
||||
UNION ALL
|
||||
SELECT id,issn_online as issn
|
||||
FROM ${stats_db_name}.datasource
|
||||
WHERE issn_online IS NOT NULL ) as issn
|
||||
WHERE LENGTH(issn) > 7)
|
||||
SELECT DISTINCT pd.id, coalesce(is_hybrid_oa, 0) as is_hybrid_oa
|
||||
FROM ${stats_db_name}.publication_datasources pd
|
||||
LEFT OUTER JOIN (
|
||||
SELECT pd.id, 1 as is_hybrid_oa from ${stats_db_name}.publication_datasources pd
|
||||
JOIN ${stats_db_name}.datasource d on d.id=pd.datasource
|
||||
JOIN issn on issn.id=pd.datasource
|
||||
JOIN hybrid_oa ON issn.issn = hybrid_oa.issn
|
||||
JOIN ${stats_db_name}.indi_result_has_cc_licence cc on pd.id=cc.id
|
||||
JOIN ${stats_db_name}.indi_pub_gold_oa ga on pd.id=ga.id where cc.has_cc_license=1 and ga.is_gold=0) tmp on pd.id=tmp.id; /*EOS*/
|
||||
|
||||
drop table if exists ${stats_db_name}.indi_pub_hybrid purge; /*EOS*/
|
||||
|
||||
--create table if not exists ${stats_db_name}.indi_pub_hybrid stored as parquet as
|
||||
-- WITH gold_oa AS ( SELECT
|
||||
-- issn_l,
|
||||
-- journal_is_in_doaj,
|
||||
-- journal_is_oa,
|
||||
-- issn_1 as issn,
|
||||
-- has_apc
|
||||
-- FROM
|
||||
-- STATS_EXT.oa_journals
|
||||
-- WHERE
|
||||
-- issn_1 != ""
|
||||
-- UNION
|
||||
-- ALL SELECT
|
||||
-- issn_l,
|
||||
-- journal_is_in_doaj,
|
||||
-- journal_is_oa,
|
||||
-- issn_2 as issn,
|
||||
-- has_apc
|
||||
-- FROM
|
||||
-- STATS_EXT.oa_journals
|
||||
-- WHERE
|
||||
-- issn_2 != "" ), issn AS ( SELECT
|
||||
-- *
|
||||
-- FROM
|
||||
--( SELECT
|
||||
-- id,
|
||||
-- issn_printed as issn
|
||||
-- FROM
|
||||
-- ${stats_db_name}.datasource
|
||||
-- WHERE
|
||||
-- issn_printed IS NOT NULL
|
||||
-- UNION ALL
|
||||
-- SELECT
|
||||
-- id,
|
||||
-- issn_online as issn
|
||||
-- FROM
|
||||
-- ${stats_db_name}.datasource
|
||||
-- WHERE
|
||||
-- issn_online IS NOT NULL or id like '%doajarticles%') as issn
|
||||
-- WHERE
|
||||
-- LENGTH(issn) > 7)
|
||||
--select distinct pd.id, coalesce(is_hybrid, 0) as is_hybrid
|
||||
--from ${stats_db_name}.publication_datasources pd
|
||||
-- left outer join (
|
||||
-- select pd.id, 1 as is_hybrid from ${stats_db_name}.publication_datasources pd
|
||||
-- join ${stats_db_name}.datasource d on d.id=pd.datasource
|
||||
-- join issn on issn.id=pd.datasource
|
||||
-- join gold_oa on issn.issn=gold_oa.issn
|
||||
-- where (gold_oa.journal_is_in_doaj=false or gold_oa.journal_is_oa=false))tmp
|
||||
-- on pd.id=tmp.id;
|
||||
|
||||
--create table if not exists ${stats_db_name}.indi_pub_hybrid stored as parquet as
|
||||
--select distinct pd.id,coalesce(is_hybrid,0) is_hybrid from ${stats_db_name}.publication_datasources pd
|
||||
--left outer join (select pd.id, 1 as is_hybrid from ${stats_db_name}.publication_datasources pd
|
||||
--join ${stats_db_name}.datasource d on pd.datasource=d.id
|
||||
--join ${stats_db_name}.result_instance ri on ri.id=pd.id
|
||||
--join ${stats_db_name}.indi_pub_gold_oa indi_gold on indi_gold.id=pd.id
|
||||
--join ${stats_db_name}.result_accessroute ra on ra.id=pd.id
|
||||
--where d.type like '%Journal%' and ri.accessright!='Closed Access' and (ri.accessright_uw!='gold'
|
||||
--or indi_gold.is_gold=0) and (ra.accessroute='hybrid' or ri.license is not null)) tmp
|
||||
--on pd.id=tmp.id;
|
||||
|
||||
create table if not exists ${stats_db_name}.indi_pub_hybrid stored as parquet as
|
||||
select distinct pd.id,coalesce(is_hybrid,0) is_hybrid from ${stats_db_name}.publication pd
|
||||
left outer join (select pd.id, 1 as is_hybrid from ${stats_db_name}.publication pd
|
||||
join ${stats_db_name}.result_instance ri on ri.id=pd.id
|
||||
join ${stats_db_name}.indi_pub_gold_oa indi_gold on indi_gold.id=pd.id
|
||||
join ${stats_db_name}.result_accessroute ra on ra.id=pd.id
|
||||
join ${stats_db_name}.datasource d on d.id=ri.hostedby
|
||||
where indi_gold.is_gold=0 and ((d.type like '%Journal%' and ri.accessright!='Closed Access' and ri.accessright!='Restricted' and ri.license is not null) or
|
||||
ra.accessroute='hybrid'))tmp
|
||||
on pd.id=tmp.id; /*EOS*/
|
||||
left outer join (
|
||||
select pd.id, 1 as is_hybrid from ${stats_db_name}.publication pd
|
||||
join ${stats_db_name}.result_instance ri on ri.id=pd.id
|
||||
join ${stats_db_name}.indi_pub_gold_oa indi_gold on indi_gold.id=pd.id
|
||||
join ${stats_db_name}.result_accessroute ra on ra.id=pd.id
|
||||
join ${stats_db_name}.datasource d on d.id=ri.hostedby
|
||||
where indi_gold.is_gold=0 and ((d.type like '%Journal%' and ri.accessright!='Closed Access' and ri.accessright!='Restricted' and ri.license is not null) or ra.accessroute='hybrid')) tmp on pd.id=tmp.id; /*EOS*/
|
||||
|
||||
drop table if exists ${stats_db_name}.indi_org_fairness purge; /*EOS*/
|
||||
|
||||
create table if not exists ${stats_db_name}.indi_org_fairness stored as parquet as
|
||||
--return results with PIDs, and rich metadata group by organization
|
||||
with result_fair as
|
||||
(select ro.organization organization, count(distinct ro.id) no_result_fair from ${stats_db_name}.result_organization ro
|
||||
join ${stats_db_name}.result r on r.id=ro.id
|
||||
with result_fair as (
|
||||
select ro.organization organization, count(distinct ro.id) no_result_fair
|
||||
from ${stats_db_name}.result_organization ro
|
||||
join ${stats_db_name}.result r on r.id=ro.id
|
||||
--join result_pids rp on r.id=rp.id
|
||||
where (title is not null) and (publisher is not null) and (abstract=true) and (year is not null) and (authors>0) and cast(year as int)>2003
|
||||
group by ro.organization),
|
||||
where (title is not null) and (publisher is not null) and (abstract=true) and (year is not null) and (authors>0) and cast(year as int)>2003
|
||||
group by ro.organization),
|
||||
--return all results group by organization
|
||||
allresults as (select ro.organization, count(distinct ro.id) no_allresults from ${stats_db_name}.result_organization ro
|
||||
join ${stats_db_name}.result r on r.id=ro.id
|
||||
where cast(year as int)>2003
|
||||
group by ro.organization)
|
||||
allresults as (
|
||||
select ro.organization, count(distinct ro.id) no_allresults from ${stats_db_name}.result_organization ro
|
||||
join ${stats_db_name}.result r on r.id=ro.id
|
||||
where cast(year as int)>2003
|
||||
group by ro.organization)
|
||||
--return results_fair/all_results
|
||||
select allresults.organization, result_fair.no_result_fair/allresults.no_allresults org_fairness
|
||||
from allresults
|
||||
join result_fair on result_fair.organization=allresults.organization; /*EOS*/
|
||||
select allresults.organization, result_fair.no_result_fair/allresults.no_allresults org_fairness
|
||||
from allresults
|
||||
join result_fair on result_fair.organization=allresults.organization; /*EOS*/
|
||||
|
||||
CREATE TEMPORARY VIEW result_fair as
|
||||
select ro.organization organization, count(distinct ro.id) no_result_fair
|
||||
|
|
@ -859,19 +660,6 @@ drop view pub_fos_totals; /*EOS*/
|
|||
|
||||
drop table if exists ${stats_db_name}.indi_pub_bronze_oa purge; /*EOS*/
|
||||
|
||||
--create table if not exists ${stats_db_name}.indi_pub_bronze_oa stored as parquet as
|
||||
--select distinct p.id, coalesce(is_bronze_oa,0) as is_bronze_oa
|
||||
--from ${stats_db_name}.publication p
|
||||
--left outer join
|
||||
--(select p.id, 1 as is_bronze_oa from ${stats_db_name}.publication p
|
||||
--join ${stats_db_name}.indi_result_has_cc_licence cc on cc.id=p.id
|
||||
--join ${stats_db_name}.indi_pub_gold_oa ga on ga.id=p.id
|
||||
--join ${stats_db_name}.result_instance ri on ri.id=p.id
|
||||
--join ${stats_db_name}.datasource d on d.id=ri.hostedby
|
||||
--where cc.has_cc_license=0 and ga.is_gold=0
|
||||
--and (d.type='Journal' or d.type='Journal Aggregator/Publisher')
|
||||
--and ri.accessright='Open Access') tmp on tmp.id=p.id;
|
||||
|
||||
create table ${stats_db_name}.indi_pub_bronze_oa stored as parquet as
|
||||
select distinct pd.id,coalesce(is_bronze_oa,0) is_bronze_oa from ${stats_db_name}.publication pd
|
||||
left outer join (select pd.id, 1 as is_bronze_oa from ${stats_db_name}.publication pd
|
||||
|
|
@ -1189,7 +977,7 @@ union all
|
|||
select pf.name from stats_ext.insitutions_for_publicly_funded pf
|
||||
join ${stats_db_name}.project p on p.funder=pf.name
|
||||
union all
|
||||
select pf.name from stats_ext.insitutions_for_publicly_funded pf
|
||||
select op.name from stats_ext.insitutions_for_publicly_funded pf
|
||||
join org_names_pids op on (op.name=pf.name or op.pid=pf.ror)
|
||||
and pf.publicly_funded='yes') foo)
|
||||
select distinct p.id, coalesce(publicly_funded, 0) as publicly_funded
|
||||
|
|
@ -1199,3 +987,58 @@ select distinct ro.id, 1 as publicly_funded from ${stats_db_name}.result_organiz
|
|||
join ${stats_db_name}.organization o on o.id=ro.organization
|
||||
join publicly_funded_orgs pfo on o.name=pfo.name) tmp on p.id=tmp.id; /*EOS*/
|
||||
|
||||
drop table if exists ${stats_db_name}.indi_pub_green_with_license purge; /*EOS*/
|
||||
create table ${stats_db_name}.indi_pub_green_with_license stored as parquet as
|
||||
select distinct p.id, coalesce(green_with_license, 0) as green_with_license
|
||||
from ${stats_db_name}.publication p
|
||||
left outer join (
|
||||
select distinct p.id, 1 as green_with_license from ${stats_db_name}.publication p
|
||||
join ${stats_db_name}.result_instance ri on ri.id = p.id
|
||||
join ${stats_db_name}.datasource on datasource.id = ri.hostedby
|
||||
where ri.license is not null and datasource.type like '%Repository%' and datasource.name!='Other') tmp on p.id= tmp.id; /*EOS*/
|
||||
|
||||
drop table if exists ${stats_db_name}.result_country purge; /*EOS*/
|
||||
|
||||
create table ${stats_db_name}.result_country stored as parquet as
|
||||
select distinct *
|
||||
from (
|
||||
select ro.id, o.country
|
||||
from ${stats_db_name}.result_organization ro
|
||||
left outer join ${stats_db_name}.organization o on o.id=ro.organization
|
||||
union all
|
||||
select rp.id, f.country
|
||||
from ${stats_db_name}.result_projects
|
||||
left outer join ${stats_db_name}.project p on p.id=rp.project
|
||||
left outer join ${stats_db_name}.funder f on f.name=p.funder
|
||||
) rc
|
||||
where rc.country is not null; /*EOS*/
|
||||
|
||||
drop table if exists ${stats_db_name}.indi_result_oa_with_license purge; /*EOS*/
|
||||
create table ${stats_db_name}.indi_result_oa_with_license stored as parquet as
|
||||
select distinct r.id, coalesce(oa_with_license,0) as oa_with_license
|
||||
from ${stats_db_name}.result r
|
||||
left outer join (select distinct r.id, 1 as oa_with_license from ${stats_db_name}.result r
|
||||
join ${stats_db_name}.result_licenses rl on rl.id=r.id where r.bestlicence='Open Access') tmp on r.id=tmp.id; /*EOS*/
|
||||
|
||||
drop table if exists ${stats_db_name}.indi_result_oa_without_license purge; /*EOS*/
|
||||
create table ${stats_db_name}.indi_result_oa_without_license stored as parquet as
|
||||
with without_license as
|
||||
(select distinct id from ${stats_db_name}.indi_result_oa_with_license
|
||||
where oa_with_license=0)
|
||||
select distinct r.id, coalesce(oa_without_license,0) as oa_without_license
|
||||
from ${stats_db_name}.result r
|
||||
left outer join (select distinct r.id, 1 as oa_without_license
|
||||
from ${stats_db_name}.result r
|
||||
join without_license wl on wl.id=r.id
|
||||
where r.bestlicence='Open Access') tmp on r.id=tmp.id; /*EOS*/
|
||||
|
||||
drop table if exists ${stats_db_name}.indi_result_under_transformative purge; /*EOS*/
|
||||
create table ${stats_db_name}.indi_result_under_transformative stored as parquet as
|
||||
with transformative_dois as (
|
||||
select distinct doi from stats_ext.transformative_facts)
|
||||
select distinct r.id, coalesce(under_transformative,0) as under_transformative
|
||||
from ${stats_db_name}.result r
|
||||
left outer join (
|
||||
select distinct rp.id, 1 as under_transformative
|
||||
from ${stats_db_name}.result_pids rp join ${stats_db_name}.result r on r.id=rp.id
|
||||
join transformative_dois td on td.doi=rp.pid) tmp on r.id=tmp.id; /*EOS*/
|
||||
|
|
@ -180,4 +180,12 @@ create view TARGET.indi_funder_openess as select * from SOURCE.indi_funder_opene
|
|||
create view TARGET.indi_funder_findable as select * from SOURCE.indi_funder_findable;
|
||||
create view TARGET.indi_ris_fairness as select * from SOURCE.indi_ris_fairness;
|
||||
create view TARGET.indi_ris_openess as select * from SOURCE.indi_ris_openess;
|
||||
create view TARGET.indi_ris_findable as select * from SOURCE.indi_ris_findable;
|
||||
create view TARGET.indi_ris_findable as select * from SOURCE.indi_ris_findable;
|
||||
|
||||
create table TARGET.indi_pub_green_with_license stored as parquet as select * from SOURCE.indi_pub_green_with_license orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
create table TARGET.result_country stored as parquet as select * from SOURCE.result_country orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.indi_result_oa_with_license stored as parquet as select * from SOURCE.indi_result_oa_with_license orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
create table TARGET.indi_result_oa_without_license stored as parquet as select * from SOURCE.indi_result_oa_without_license orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.indi_result_under_transformative stored as parquet as select * from SOURCE.indi_result_under_transformative orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
|
|
|||
|
|
@ -80,8 +80,12 @@ create table TARGET.result stored as parquet as
|
|||
'openorgs____::0fccc7640f0cb44d5cd1b06b312a06b9', -- Cardiff University
|
||||
'openorgs____::8839b55dae0c84d56fd533f52d5d483a', -- Leibniz Institute of Ecological Urban and Regional Development
|
||||
'openorgs____::526468206bca24c1c90da6a312295cf4', -- Cyprus University of Technology
|
||||
'openorgs____::b5ca9d4340e26454e367e2908ef3872f' -- Alma Mater Studiorum University of Bologna
|
||||
|
||||
'openorgs____::b5ca9d4340e26454e367e2908ef3872f', -- Alma Mater Studiorum University of Bologna
|
||||
'openorgs____::a6340e6ecf60f6bba163659df985b0f2', -- TU Dresden
|
||||
'openorgs____::64badd35233ba2cd4946368ef2f4cf57', -- University of Vienna
|
||||
'openorgs____::7501d66d2297a963ebfb075c43fff88e', -- Royal Institute of Technology
|
||||
'openorgs____::d5eb679abdd31f70fcd4c8ba711148bf', -- Sorbonne University
|
||||
'openorgs____::b316f25380d106aac402f5ae8653910d' -- Centre for Research on Ecology and Forestry Applications
|
||||
) )) foo;
|
||||
|
||||
create view if not exists TARGET.category as select * from SOURCE.category;
|
||||
|
|
@ -264,4 +268,11 @@ create view TARGET.indi_ris_fairness as select * from SOURCE.indi_ris_fairness;
|
|||
create view TARGET.indi_ris_openess as select * from SOURCE.indi_ris_openess;
|
||||
create view TARGET.indi_ris_findable as select * from SOURCE.indi_ris_findable;
|
||||
|
||||
create table TARGET.indi_pub_green_with_license stored as parquet as select * from SOURCE.indi_pub_green_with_license orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
create table TARGET.result_country stored as parquet as select * from SOURCE.result_country orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.indi_result_oa_with_license stored as parquet as select * from SOURCE.indi_result_oa_with_license orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
create table TARGET.indi_result_oa_without_license stored as parquet as select * from SOURCE.indi_result_oa_without_license orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
create table TARGET.indi_result_under_transformative stored as parquet as select * from SOURCE.indi_result_under_transformative orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
|
||||
|
|
|
|||
|
|
@ -60,5 +60,10 @@ create table TARGET.result stored as parquet as
|
|||
'openorgs____::0fccc7640f0cb44d5cd1b06b312a06b9', -- Cardiff University
|
||||
'openorgs____::8839b55dae0c84d56fd533f52d5d483a', -- Leibniz Institute of Ecological Urban and Regional Development
|
||||
'openorgs____::526468206bca24c1c90da6a312295cf4', -- Cyprus University of Technology
|
||||
'openorgs____::b5ca9d4340e26454e367e2908ef3872f' -- Alma Mater Studiorum University of Bologna
|
||||
'openorgs____::b5ca9d4340e26454e367e2908ef3872f', -- Alma Mater Studiorum University of Bologna
|
||||
'openorgs____::a6340e6ecf60f6bba163659df985b0f2', -- TU Dresden
|
||||
'openorgs____::64badd35233ba2cd4946368ef2f4cf57', -- University of Vienna
|
||||
'openorgs____::7501d66d2297a963ebfb075c43fff88e', -- Royal Institute of Technology
|
||||
'openorgs____::d5eb679abdd31f70fcd4c8ba711148bf', -- Sorbonne University
|
||||
'openorgs____::b316f25380d106aac402f5ae8653910d' -- Centre for Research on Ecology and Forestry Applications
|
||||
))) foo;
|
||||
|
|
@ -2,9 +2,8 @@ create table ${observatory_db_name}.result_cc_licence stored as parquet as
|
|||
select r.id, coalesce(rln.count, 0) > 0 as cc_licence
|
||||
from ${stats_db_name}.result r
|
||||
left outer join (
|
||||
select rl.id, sum(case when lower(rln.normalized) like 'cc-%' then 1 else 0 end) as count
|
||||
select rl.id, sum(case when rl.type like 'CC%' then 1 else 0 end) as count
|
||||
from ${stats_db_name}.result_licenses rl
|
||||
left outer join ${stats_db_name}.licenses_normalized rln on rl.type=rln.license
|
||||
group by rl.id
|
||||
) rln on rln.id=r.id;
|
||||
|
||||
|
|
|
|||
|
|
@ -95,7 +95,8 @@ DROP TABLE IF EXISTS ${stats_db_name}.funder purge;
|
|||
create table ${stats_db_name}.funder STORED AS PARQUET as
|
||||
select distinct xpath_string(fund, '//funder/id') as id,
|
||||
xpath_string(fund, '//funder/name') as name,
|
||||
xpath_string(fund, '//funder/shortname') as shortname
|
||||
xpath_string(fund, '//funder/shortname') as shortname,
|
||||
xpath_string(fundingtree[0].value, '//funder/jurisdiction') as country
|
||||
from ${openaire_db_name}.project p lateral view explode(p.fundingtree.value) fundingtree as fund;
|
||||
|
||||
DROP TABLE IF EXISTS ${stats_db_name}.project_organization_contribution purge;
|
||||
|
|
|
|||
|
|
@ -345,6 +345,17 @@
|
|||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<!-- <action name="Step16-createIndicatorsTables">-->
|
||||
<!-- <hive2 xmlns="uri:oozie:hive2-action:0.1">-->
|
||||
<!-- <jdbc-url>${hive_jdbc_url}</jdbc-url>-->
|
||||
<!-- <script>scripts/step16-createIndicatorsTables.sql</script>-->
|
||||
<!-- <param>stats_db_name=${stats_db_name}</param>-->
|
||||
<!-- <param>external_stats_db_name=${external_stats_db_name}</param>-->
|
||||
<!-- </hive2>-->
|
||||
<!-- <ok to="Step16_1-definitions"/>-->
|
||||
<!-- <error to="Kill"/>-->
|
||||
<!-- </action>-->
|
||||
|
||||
<action name="Step16-createIndicatorsTables">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
|
|
|
|||
|
|
@ -31,6 +31,10 @@
|
|||
<module>dhp-enrichment</module>
|
||||
<module>dhp-graph-provision</module>
|
||||
<module>dhp-blacklist</module>
|
||||
<module>dhp-stats-actionsets</module>
|
||||
<module>dhp-stats-hist-snaps</module>
|
||||
<module>dhp-stats-monitor-irish</module>
|
||||
<module>dhp-stats-monitor-update</module>
|
||||
<module>dhp-stats-update</module>
|
||||
<module>dhp-stats-promote</module>
|
||||
<module>dhp-usage-stats-build</module>
|
||||
|
|
|
|||
Loading…
Reference in New Issue