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@ -0,0 +1,757 @@
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From c5fbad8093ca27deebf1b5fd5ffd39e1877c533d Mon Sep 17 00:00:00 2001
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From: antleb <antleb@di.uoa.gr>
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Date: Thu, 4 Mar 2021 00:42:21 +0200
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Subject: [PATCH 1/8] Contexts are now downloaded instead of using the
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stats_ext db
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---
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.../dhp/oa/graph/stats/oozie_app/contexts.sh | 33 +++++++++++++++++++
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.../graph/stats/oozie_app/scripts/step10.sql | 13 --------
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.../dhp/oa/graph/stats/oozie_app/workflow.xml | 17 ++++++++++
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3 files changed, 50 insertions(+), 13 deletions(-)
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create mode 100644 dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/contexts.sh
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diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/contexts.sh b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/contexts.sh
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new file mode 100644
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index 00000000..f06a43bb
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--- /dev/null
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+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/contexts.sh
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@@ -0,0 +1,33 @@
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+#!/usr/bin/env bash
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+
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+CONTEXT_API=$1
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+TARGET_DB=$2
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+
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+TMP=/tmp/stats-update-`tr -dc A-Za-z0-9 </dev/urandom | head -c 6`
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+
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+echo "Downloading context data"
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+curl ${CONTEXT_API}/contexts?all=true -H "accept: application/json" | /usr/local/sbin/jq -r '.[] | "\(.id),\(.label)"' > contexts.csv
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+cat contexts.csv | cut -d , -f1 | xargs -I {} curl ${CONTEXT_API}/context/{}/?all=true | /usr/local/sbin/jq -r '.[]|"\(.id|split(":")[0]),\(.id),\(.label)"' > categories.csv
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+cat categories.csv | cut -d , -f2 | sed 's/:/%3A/g'| xargs -I {} curl ${CONTEXT_API}/context/category/{}/?all=true | /usr/local/sbin/jq -r '.[]|"\(.id|split("::")[0])::\(.id|split("::")[1]),\(.id),\(.label)"' > concepts.csv
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+cat contexts.csv | cut -f1 -d, | sed 's/\(.*\)/\1,\1::other,other/' >> categories.csv
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+cat categories.csv | cut -d, -f2 | sed 's/\(.*\)/\1,\1::other,other/' >> concepts.csv
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+
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+echo "uploading context data to hdfs"
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+hdfs dfs -mkdir ${TMP}
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+hdfs dfs -copyFromLocal contexts.csv ${TMP}
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+hdfs dfs -copyFromLocal categories.csv ${TMP}
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+hdfs dfs -copyFromLocal concepts.csv ${TMP}
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+hdfs dfs -chmod -R 777 ${TMP}
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+
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+echo "Creating and populating impala tables"
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+impala-shell -c "create table ${TARGET_DB}.context (id string, name string) row format delimited fields terminated by ',';"
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+impala-shell -c "create table ${TARGET_DB}.category (context string, id string, name string) row format delimited fields terminated by ',';"
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+impala-shell -c "create table ${TARGET_DB}.concept (category string, id string, name string) row format delimited fields terminated by ',';"
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+impala-shell -c "load data inpath '${TMP}/contexts.csv' into table ${TARGET_DB}.context;"
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+impala-shell -c "load data inpath '${TMP}/categories.csv' into table ${TARGET_DB}.category;"
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+impala-shell -c "load data inpath '${TMP}/concepts.csv' into table ${TARGET_DB}.concept;"
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+
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+echo "Cleaning up"
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+hdfs dfs -rm -f -r -skipTrash ${TMP}
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+
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+echo "Finito!"
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\ No newline at end of file
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diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql
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index 6c96317e..77fbd3b1 100644
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--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql
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+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql
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@@ -23,19 +23,6 @@ CREATE OR REPLACE VIEW ${stats_db_name}.rndexpediture AS
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SELECT *
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FROM ${external_stats_db_name}.rndexpediture;
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-CREATE OR REPLACE VIEW ${stats_db_name}.context AS
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-SELECT *
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-FROM ${external_stats_db_name}.context;
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-
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-CREATE OR REPLACE VIEW ${stats_db_name}.category AS
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-SELECT *
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-FROM ${external_stats_db_name}.category;
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-
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-CREATE OR REPLACE VIEW ${stats_db_name}.concept AS
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-SELECT *
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-FROM ${external_stats_db_name}.concept;
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-
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-
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------------------------------------------------------------------------------------------------
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------------------------------------------------------------------------------------------------
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-- Creation date of the database
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diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml
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index 9c16f149..afb10c41 100644
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--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml
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+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml
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@@ -41,6 +41,10 @@
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<name>hive_timeout</name>
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<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>
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</property>
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+ <property>
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+ <name>context_api_url</name>
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+ <description>the base url of the context api (https://services.openaire.eu/openaire)</description>
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+ </property>
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</parameters>
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<global>
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@@ -263,6 +267,19 @@
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<ok to="Step19"/>
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<error to="Kill"/>
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</action>
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+
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+ <action name="Step17">
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+ <shell xmlns="uri:oozie:shell-action:0.1">
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+ <job-tracker>${jobTracker}</job-tracker>
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+ <name-node>${nameNode}</name-node>
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+ <exec>contexts.sh</exec>
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+ <argument>${context_api_url}</argument>
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+ <argument>${stats_db_name}</argument>
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+ <file>contexts.sh</file>
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+ </shell>
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+ <ok to="step20-createMonitorDB"/>
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+ <error to="Kill"/>
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+ </action>
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<action name="Step19">
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<shell xmlns="uri:oozie:shell-action:0.1">
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--
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2.17.1
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From 6147ee495053634436abe822aaf9ba909813d8c4 Mon Sep 17 00:00:00 2001
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From: antleb <antleb@di.uoa.gr>
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Date: Fri, 5 Mar 2021 14:12:18 +0200
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Subject: [PATCH 2/8] assigning correctly hive contexts to concepts
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---
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.../eu/dnetlib/dhp/oa/graph/stats/oozie_app/contexts.sh | 7 +++++--
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.../dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql | 5 ++++-
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.../dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql | 5 ++++-
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.../dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql | 5 ++++-
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.../dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql | 5 ++++-
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5 files changed, 21 insertions(+), 6 deletions(-)
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diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/contexts.sh b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/contexts.sh
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index f06a43bb..6788f88b 100644
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--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/contexts.sh
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+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/contexts.sh
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@@ -9,8 +9,8 @@ echo "Downloading context data"
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curl ${CONTEXT_API}/contexts?all=true -H "accept: application/json" | /usr/local/sbin/jq -r '.[] | "\(.id),\(.label)"' > contexts.csv
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cat contexts.csv | cut -d , -f1 | xargs -I {} curl ${CONTEXT_API}/context/{}/?all=true | /usr/local/sbin/jq -r '.[]|"\(.id|split(":")[0]),\(.id),\(.label)"' > categories.csv
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cat categories.csv | cut -d , -f2 | sed 's/:/%3A/g'| xargs -I {} curl ${CONTEXT_API}/context/category/{}/?all=true | /usr/local/sbin/jq -r '.[]|"\(.id|split("::")[0])::\(.id|split("::")[1]),\(.id),\(.label)"' > concepts.csv
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-cat contexts.csv | cut -f1 -d, | sed 's/\(.*\)/\1,\1::other,other/' >> categories.csv
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-cat categories.csv | cut -d, -f2 | sed 's/\(.*\)/\1,\1::other,other/' >> concepts.csv
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+cat contexts.csv | sed 's/^\(.*\),\(.*\)/\1,\1::other,\2/' >> categories.csv
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+cat categories.csv | grep -v ::other | sed 's/^.*,\(.*\),\(.*\)/\1,\1::other,\2/' >> concepts.csv
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echo "uploading context data to hdfs"
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hdfs dfs -mkdir ${TMP}
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@@ -29,5 +29,8 @@ impala-shell -c "load data inpath '${TMP}/concepts.csv' into table ${TARGET_DB}.
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echo "Cleaning up"
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hdfs dfs -rm -f -r -skipTrash ${TMP}
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+rm concepts.csv
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+rm categories.csv
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+rm contexts.csv
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echo "Finito!"
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\ No newline at end of file
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diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql
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index 62a15856..75b24b18 100644
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--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql
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+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql
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@@ -47,7 +47,10 @@ from ${openaire_db_name}.publication p
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where p.datainfo.deletedbyinference = false;
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CREATE TABLE ${stats_db_name}.publication_concepts AS
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-SELECT substr(p.id, 4) as id, contexts.context.id as concept
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+SELECT substr(p.id, 4) as id, case
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+ when contexts.context.id RLIKE '^[^::]+::[^::]+::.+$' then contexts.context.id
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+ when contexts.context.id RLIKE '^[^::]+::[^::]+$' then concat(contexts.context.id, '::other')
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+ when contexts.context.id RLIKE '^[^::]+$' then concat(contexts.context.id, '::other::other') END as concept
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from ${openaire_db_name}.publication p
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LATERAL VIEW explode(p.context) contexts as context
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where p.datainfo.deletedbyinference = false;
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diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql
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index dcd5ad85..540cc03a 100644
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--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql
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+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql
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@@ -54,7 +54,10 @@ FROM ${openaire_db_name}.dataset p
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where p.datainfo.deletedbyinference = false;
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CREATE TABLE ${stats_db_name}.dataset_concepts AS
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-SELECT substr(p.id, 4) as id, contexts.context.id as concept
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+SELECT substr(p.id, 4) as id, case
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+ when contexts.context.id RLIKE '^[^::]+::[^::]+::.+$' then contexts.context.id
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+ when contexts.context.id RLIKE '^[^::]+::[^::]+$' then concat(contexts.context.id, '::other')
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+ when contexts.context.id RLIKE '^[^::]+$' then concat(contexts.context.id, '::other::other') END as concept
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from ${openaire_db_name}.dataset p
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LATERAL VIEW explode(p.context) contexts as context
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where p.datainfo.deletedbyinference = false;
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diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql
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index fd5390e6..54345e07 100644
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--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql
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+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql
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@@ -54,7 +54,10 @@ FROM ${openaire_db_name}.software p
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where p.datainfo.deletedbyinference = false;
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CREATE TABLE ${stats_db_name}.software_concepts AS
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-SELECT substr(p.id, 4) AS id, contexts.context.id AS concept
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+SELECT substr(p.id, 4) as id, case
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+ when contexts.context.id RLIKE '^[^::]+::[^::]+::.+$' then contexts.context.id
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+ when contexts.context.id RLIKE '^[^::]+::[^::]+$' then concat(contexts.context.id, '::other')
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+ when contexts.context.id RLIKE '^[^::]+$' then concat(contexts.context.id, '::other::other') END as concept
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FROM ${openaire_db_name}.software p
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LATERAL VIEW explode(p.context) contexts AS context
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where p.datainfo.deletedbyinference = false;
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diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql
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index b359b596..36ad5d92 100644
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--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql
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+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql
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@@ -52,7 +52,10 @@ FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.instance.
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where p.datainfo.deletedbyinference = false;
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CREATE TABLE ${stats_db_name}.otherresearchproduct_concepts AS
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-SELECT substr(p.id, 4) AS id, contexts.context.id AS concept
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+SELECT substr(p.id, 4) as id, case
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+ when contexts.context.id RLIKE '^[^::]+::[^::]+::.+$' then contexts.context.id
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|
|
+ when contexts.context.id RLIKE '^[^::]+::[^::]+$' then concat(contexts.context.id, '::other')
|
|
|
|
|
+ when contexts.context.id RLIKE '^[^::]+$' then concat(contexts.context.id, '::other::other') END as concept
|
|
|
|
|
FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.context) contexts AS context
|
|
|
|
|
where p.datainfo.deletedbyinference = false;
|
|
|
|
|
|
|
|
|
|
--
|
|
|
|
|
2.17.1
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
From f40c150a0d549e2dbcfd42ecf81e17ad4b505391 Mon Sep 17 00:00:00 2001
|
|
|
|
|
From: antleb <antleb@di.uoa.gr>
|
|
|
|
|
Date: Sat, 6 Mar 2021 00:35:57 +0200
|
|
|
|
|
Subject: [PATCH 3/8] fixed steps...
|
|
|
|
|
|
|
|
|
|
---
|
|
|
|
|
.../eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml | 4 ++--
|
|
|
|
|
1 file changed, 2 insertions(+), 2 deletions(-)
|
|
|
|
|
|
|
|
|
|
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml
|
|
|
|
|
index afb10c41..2184cb8a 100644
|
|
|
|
|
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml
|
|
|
|
|
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml
|
|
|
|
|
@@ -264,7 +264,7 @@
|
|
|
|
|
<param>stats_db_name=${stats_db_name}</param>
|
|
|
|
|
<param>openaire_db_name=${openaire_db_name}</param>
|
|
|
|
|
</hive2>
|
|
|
|
|
- <ok to="Step19"/>
|
|
|
|
|
+ <ok to="Step17"/>
|
|
|
|
|
<error to="Kill"/>
|
|
|
|
|
</action>
|
|
|
|
|
|
|
|
|
|
@@ -277,7 +277,7 @@
|
|
|
|
|
<argument>${stats_db_name}</argument>
|
|
|
|
|
<file>contexts.sh</file>
|
|
|
|
|
</shell>
|
|
|
|
|
- <ok to="step20-createMonitorDB"/>
|
|
|
|
|
+ <ok to="step19"/>
|
|
|
|
|
<error to="Kill"/>
|
|
|
|
|
</action>
|
|
|
|
|
|
|
|
|
|
--
|
|
|
|
|
2.17.1
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
From fa1ec5b5e9b6038b3b565422af5c6406f21220d3 Mon Sep 17 00:00:00 2001
|
|
|
|
|
From: antleb <antleb@di.uoa.gr>
|
|
|
|
|
Date: Wed, 10 Mar 2021 14:05:58 +0200
|
|
|
|
|
Subject: [PATCH 4/8] fixed typo...
|
|
|
|
|
|
|
|
|
|
---
|
|
|
|
|
.../eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml | 2 +-
|
|
|
|
|
1 file changed, 1 insertion(+), 1 deletion(-)
|
|
|
|
|
|
|
|
|
|
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml
|
|
|
|
|
index 2184cb8a..321500e2 100644
|
|
|
|
|
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml
|
|
|
|
|
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml
|
|
|
|
|
@@ -277,7 +277,7 @@
|
|
|
|
|
<argument>${stats_db_name}</argument>
|
|
|
|
|
<file>contexts.sh</file>
|
|
|
|
|
</shell>
|
|
|
|
|
- <ok to="step19"/>
|
|
|
|
|
+ <ok to="Step19"/>
|
|
|
|
|
<error to="Kill"/>
|
|
|
|
|
</action>
|
|
|
|
|
|
|
|
|
|
--
|
|
|
|
|
2.17.1
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
From 3c75a050443942b632cf8469b5af16a8c61e7569 Mon Sep 17 00:00:00 2001
|
|
|
|
|
From: antleb <antleb@di.uoa.gr>
|
|
|
|
|
Date: Fri, 12 Mar 2021 13:47:04 +0200
|
|
|
|
|
Subject: [PATCH 5/8] fixed a ton of typos
|
|
|
|
|
|
|
|
|
|
---
|
|
|
|
|
.../scripts/computeProductionStats.sql | 8 -------
|
|
|
|
|
.../stats/oozie_app/updateProductionViews.sh | 18 ++++++++++++++++
|
|
|
|
|
.../dhp/oa/graph/stats/oozie_app/contexts.sh | 21 ++++++++++++-------
|
|
|
|
|
3 files changed, 32 insertions(+), 15 deletions(-)
|
|
|
|
|
delete mode 100644 dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/computeProductionStats.sql
|
|
|
|
|
create mode 100644 dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/updateProductionViews.sh
|
|
|
|
|
|
|
|
|
|
diff --git a/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/computeProductionStats.sql b/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/computeProductionStats.sql
|
|
|
|
|
deleted file mode 100644
|
|
|
|
|
index 34e48a18..00000000
|
|
|
|
|
--- a/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/computeProductionStats.sql
|
|
|
|
|
+++ /dev/null
|
|
|
|
|
@@ -1,8 +0,0 @@
|
|
|
|
|
-------------------------------------------------------
|
|
|
|
|
-------------------------------------------------------
|
|
|
|
|
--- Impala table statistics - Needed to make the tables
|
|
|
|
|
--- visible for impala
|
|
|
|
|
-------------------------------------------------------
|
|
|
|
|
-------------------------------------------------------
|
|
|
|
|
-
|
|
|
|
|
-INVALIDATE METADATA ${stats_db_name};
|
|
|
|
|
diff --git a/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/updateProductionViews.sh b/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/updateProductionViews.sh
|
|
|
|
|
new file mode 100644
|
|
|
|
|
index 00000000..57acb2ee
|
|
|
|
|
--- /dev/null
|
|
|
|
|
+++ b/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/updateProductionViews.sh
|
|
|
|
|
@@ -0,0 +1,18 @@
|
|
|
|
|
+export PYTHON_EGG_CACHE=/home/$(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 SHADOW=$2
|
|
|
|
|
+
|
|
|
|
|
+echo "Updating shadow database"
|
|
|
|
|
+impala-shell -d ${SOURCE} -q "invalidate metadata"
|
|
|
|
|
+impala-shell -d ${SOURCE} -q "show tables" --delimited | sed "s/^\(.*\)/compute stats ${SOURCE}.\1;/" | impala-shell -c -f -
|
|
|
|
|
+impala-shell -q "create database if not exists ${SHADOW}"
|
|
|
|
|
+impala-shell -d ${SHADOW} -q "show tables" --delimited | sed "s/^/drop view if exists ${SHADOW}./" | sed "s/$/;/" | impala-shell -c -f -
|
|
|
|
|
+impala-shell -d ${SOURCE} -q "show tables" --delimited | sed "s/\(.*\)/create view ${SHADOW}.\1 as select * from ${SOURCE}.\1;/" | impala-shell -c -f -
|
|
|
|
|
+echo "Shadow db ready!"
|
|
|
|
|
\ No newline at end of file
|
|
|
|
|
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/contexts.sh b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/contexts.sh
|
|
|
|
|
index 6788f88b..c28be50d 100644
|
|
|
|
|
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/contexts.sh
|
|
|
|
|
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/contexts.sh
|
|
|
|
|
@@ -1,4 +1,10 @@
|
|
|
|
|
-#!/usr/bin/env bash
|
|
|
|
|
+export PYTHON_EGG_CACHE=/home/$(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
|
|
|
|
|
|
|
|
|
|
CONTEXT_API=$1
|
|
|
|
|
TARGET_DB=$2
|
|
|
|
|
@@ -20,12 +26,13 @@ hdfs dfs -copyFromLocal concepts.csv ${TMP}
|
|
|
|
|
hdfs dfs -chmod -R 777 ${TMP}
|
|
|
|
|
|
|
|
|
|
echo "Creating and populating impala tables"
|
|
|
|
|
-impala-shell -c "create table ${TARGET_DB}.context (id string, name string) row format delimited fields terminated by ',';"
|
|
|
|
|
-impala-shell -c "create table ${TARGET_DB}.category (context string, id string, name string) row format delimited fields terminated by ',';"
|
|
|
|
|
-impala-shell -c "create table ${TARGET_DB}.concept (category string, id string, name string) row format delimited fields terminated by ',';"
|
|
|
|
|
-impala-shell -c "load data inpath '${TMP}/contexts.csv' into table ${TARGET_DB}.context;"
|
|
|
|
|
-impala-shell -c "load data inpath '${TMP}/categories.csv' into table ${TARGET_DB}.category;"
|
|
|
|
|
-impala-shell -c "load data inpath '${TMP}/concepts.csv' into table ${TARGET_DB}.concept;"
|
|
|
|
|
+impala-shell -q "create table ${TARGET_DB}.context (id string, name string) row format delimited fields terminated by ','"
|
|
|
|
|
+impala-shell -q "create table ${TARGET_DB}.category (context string, id string, name string) row format delimited fields terminated by ','"
|
|
|
|
|
+impala-shell -q "create table ${TARGET_DB}.concept (category string, id string, name string) row format delimited fields terminated by ','"
|
|
|
|
|
+impala-shell -d ${TARGET_DB} -q "invalidate metadata"
|
|
|
|
|
+impala-shell -q "load data inpath '${TMP}/contexts.csv' into table ${TARGET_DB}.context"
|
|
|
|
|
+impala-shell -q "load data inpath '${TMP}/categories.csv' into table ${TARGET_DB}.category"
|
|
|
|
|
+impala-shell -q "load data inpath '${TMP}/concepts.csv' into table ${TARGET_DB}.concept"
|
|
|
|
|
|
|
|
|
|
echo "Cleaning up"
|
|
|
|
|
hdfs dfs -rm -f -r -skipTrash ${TMP}
|
|
|
|
|
--
|
|
|
|
|
2.17.1
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
From 236435b47010ea1ab94c3f018dcf278f5d2c44aa Mon Sep 17 00:00:00 2001
|
|
|
|
|
From: antleb <antleb@di.uoa.gr>
|
|
|
|
|
Date: Fri, 12 Mar 2021 14:11:21 +0200
|
|
|
|
|
Subject: [PATCH 6/8] following redirects
|
|
|
|
|
|
|
|
|
|
---
|
|
|
|
|
.../eu/dnetlib/dhp/oa/graph/stats/oozie_app/contexts.sh | 6 +++---
|
|
|
|
|
1 file changed, 3 insertions(+), 3 deletions(-)
|
|
|
|
|
|
|
|
|
|
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/contexts.sh b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/contexts.sh
|
|
|
|
|
index c28be50d..29b225e3 100644
|
|
|
|
|
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/contexts.sh
|
|
|
|
|
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/contexts.sh
|
|
|
|
|
@@ -12,9 +12,9 @@ TARGET_DB=$2
|
|
|
|
|
TMP=/tmp/stats-update-`tr -dc A-Za-z0-9 </dev/urandom | head -c 6`
|
|
|
|
|
|
|
|
|
|
echo "Downloading context data"
|
|
|
|
|
-curl ${CONTEXT_API}/contexts?all=true -H "accept: application/json" | /usr/local/sbin/jq -r '.[] | "\(.id),\(.label)"' > contexts.csv
|
|
|
|
|
-cat contexts.csv | cut -d , -f1 | xargs -I {} curl ${CONTEXT_API}/context/{}/?all=true | /usr/local/sbin/jq -r '.[]|"\(.id|split(":")[0]),\(.id),\(.label)"' > categories.csv
|
|
|
|
|
-cat categories.csv | cut -d , -f2 | sed 's/:/%3A/g'| xargs -I {} curl ${CONTEXT_API}/context/category/{}/?all=true | /usr/local/sbin/jq -r '.[]|"\(.id|split("::")[0])::\(.id|split("::")[1]),\(.id),\(.label)"' > concepts.csv
|
|
|
|
|
+curl -L ${CONTEXT_API}/contexts?all=true -H "accept: application/json" | /usr/local/sbin/jq -r '.[] | "\(.id),\(.label)"' > contexts.csv
|
|
|
|
|
+cat contexts.csv | cut -d , -f1 | xargs -I {} curl -L ${CONTEXT_API}/context/{}/?all=true | /usr/local/sbin/jq -r '.[]|"\(.id|split(":")[0]),\(.id),\(.label)"' > categories.csv
|
|
|
|
|
+cat categories.csv | cut -d , -f2 | sed 's/:/%3A/g'| xargs -I {} curl -L ${CONTEXT_API}/context/category/{}/?all=true | /usr/local/sbin/jq -r '.[]|"\(.id|split("::")[0])::\(.id|split("::")[1]),\(.id),\(.label)"' > concepts.csv
|
|
|
|
|
cat contexts.csv | sed 's/^\(.*\),\(.*\)/\1,\1::other,\2/' >> categories.csv
|
|
|
|
|
cat categories.csv | grep -v ::other | sed 's/^.*,\(.*\),\(.*\)/\1,\1::other,\2/' >> concepts.csv
|
|
|
|
|
|
|
|
|
|
--
|
|
|
|
|
2.17.1
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
From 60ebdf2dbe704733809f401df70bffcf49cede29 Mon Sep 17 00:00:00 2001
|
|
|
|
|
From: antleb <antleb@di.uoa.gr>
|
|
|
|
|
Date: Fri, 12 Mar 2021 16:34:53 +0200
|
|
|
|
|
Subject: [PATCH 7/8] update promote wf to support monitor&production
|
|
|
|
|
|
|
|
|
|
---
|
|
|
|
|
.../oa/graph/stats/oozie_app/impala-shell.sh | 18 --
|
|
|
|
|
.../scripts/updateProductionViews.sql | 207 ------------------
|
|
|
|
|
2 files changed, 225 deletions(-)
|
|
|
|
|
delete mode 100644 dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/impala-shell.sh
|
|
|
|
|
delete mode 100644 dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/updateProductionViews.sql
|
|
|
|
|
|
|
|
|
|
diff --git a/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/impala-shell.sh b/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/impala-shell.sh
|
|
|
|
|
deleted file mode 100644
|
|
|
|
|
index 70112dc7..00000000
|
|
|
|
|
--- a/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/impala-shell.sh
|
|
|
|
|
+++ /dev/null
|
|
|
|
|
@@ -1,18 +0,0 @@
|
|
|
|
|
-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
|
|
|
|
|
-
|
|
|
|
|
-echo "Getting file from " $3
|
|
|
|
|
-hdfs dfs -copyToLocal $3
|
|
|
|
|
-
|
|
|
|
|
-echo "Running impala shell make the new database visible"
|
|
|
|
|
-impala-shell -q "INVALIDATE METADATA;"
|
|
|
|
|
-
|
|
|
|
|
-echo "Running impala shell to compute new table stats"
|
|
|
|
|
-impala-shell -d $1 -f $2
|
|
|
|
|
-echo "Impala shell finished"
|
|
|
|
|
-rm $2
|
|
|
|
|
diff --git a/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/updateProductionViews.sql b/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/updateProductionViews.sql
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deleted file mode 100644
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index 48f8d58f..00000000
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--- a/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/updateProductionViews.sql
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+++ /dev/null
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@@ -1,207 +0,0 @@
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-------------------------------------------------------
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-------------------------------------------------------
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--- Shadow schema table exchange
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-------------------------------------------------------
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-------------------------------------------------------
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-
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--- Dropping old views
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-DROP VIEW IF EXISTS ${stats_db_production_name}.category;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.concept;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.context;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.country;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.countrygdp;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.creation_date;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.dataset;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.dataset_citations;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.dataset_classifications;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.dataset_concepts;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.dataset_datasources;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.dataset_languages;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.dataset_licenses;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.dataset_oids;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.dataset_pids;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.dataset_refereed;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.dataset_sources;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.dataset_topics;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.datasource;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.datasource_languages;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.datasource_oids;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.datasource_organizations;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.datasource_results;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.datasource_sources;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.funder;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.fundref;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.numbers_country;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.organization;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.organization_datasources;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.organization_pids;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.organization_projects;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.organization_sources;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct_citations;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct_classifications;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct_concepts;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct_datasources;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct_languages;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct_licenses;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct_oids;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct_pids;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct_refereed;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct_sources;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct_topics;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.project;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.project_oids;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.project_organizations;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.project_results;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.project_resultcount;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.project_results_publication;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.publication;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.publication_citations;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.publication_classifications;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.publication_concepts;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.publication_datasources;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.publication_languages;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.publication_licenses;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.publication_oids;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.publication_pids;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.publication_refereed;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.publication_sources;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.publication_topics;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.result;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.result_affiliated_country;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.result_citations;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.result_classifications;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.result_concepts;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.result_datasources;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.result_deposited_country;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.result_fundercount;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.result_gold;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.result_greenoa;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.result_languages;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.result_licenses;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.result_oids;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.result_organization;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.result_peerreviewed;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.result_pids;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.result_projectcount;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.result_projects;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.result_refereed;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.result_sources;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.result_topics;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.rndexpediture;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.roarmap;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.software;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.software_citations;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.software_classifications;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.software_concepts;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.software_datasources;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.software_languages;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.software_licenses;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.software_oids;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.software_pids;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.software_refereed;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.software_sources;
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-DROP VIEW IF EXISTS ${stats_db_production_name}.software_topics;
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-
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-
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--- Creating the shadow database, in case it doesn't exist
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-CREATE database IF NOT EXISTS ${stats_db_production_name};
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-
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--- Creating new views
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.category AS SELECT * FROM ${stats_db_name}.category;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.concept AS SELECT * FROM ${stats_db_name}.concept;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.context AS SELECT * FROM ${stats_db_name}.context;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.country AS SELECT * FROM ${stats_db_name}.country;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.countrygdp AS SELECT * FROM ${stats_db_name}.countrygdp;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.creation_date AS SELECT * FROM ${stats_db_name}.creation_date;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset AS SELECT * FROM ${stats_db_name}.dataset;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset_citations AS SELECT * FROM ${stats_db_name}.dataset_citations;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset_classifications AS SELECT * FROM ${stats_db_name}.dataset_classifications;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset_concepts AS SELECT * FROM ${stats_db_name}.dataset_concepts;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset_datasources AS SELECT * FROM ${stats_db_name}.dataset_datasources;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset_languages AS SELECT * FROM ${stats_db_name}.dataset_languages;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset_licenses AS SELECT * FROM ${stats_db_name}.dataset_licenses;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset_oids AS SELECT * FROM ${stats_db_name}.dataset_oids;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset_pids AS SELECT * FROM ${stats_db_name}.dataset_pids;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset_refereed AS SELECT * FROM ${stats_db_name}.dataset_refereed;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset_sources AS SELECT * FROM ${stats_db_name}.dataset_sources;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset_topics AS SELECT * FROM ${stats_db_name}.dataset_topics;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.datasource AS SELECT * FROM ${stats_db_name}.datasource;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.datasource_languages AS SELECT * FROM ${stats_db_name}.datasource_languages;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.datasource_oids AS SELECT * FROM ${stats_db_name}.datasource_oids;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.datasource_organizations AS SELECT * FROM ${stats_db_name}.datasource_organizations;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.datasource_results AS SELECT * FROM ${stats_db_name}.datasource_results;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.datasource_sources AS SELECT * FROM ${stats_db_name}.datasource_sources;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.funder AS SELECT * FROM ${stats_db_name}.funder;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.fundref AS SELECT * FROM ${stats_db_name}.fundref;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.numbers_country AS SELECT * FROM ${stats_db_name}.numbers_country;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.organization AS SELECT * FROM ${stats_db_name}.organization;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.organization_datasources AS SELECT * FROM ${stats_db_name}.organization_datasources;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.organization_pids AS SELECT * FROM ${stats_db_name}.organization_pids;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.organization_projects AS SELECT * FROM ${stats_db_name}.organization_projects;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.organization_sources AS SELECT * FROM ${stats_db_name}.organization_sources;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct AS SELECT * FROM ${stats_db_name}.otherresearchproduct;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct_citations AS SELECT * FROM ${stats_db_name}.otherresearchproduct_citations;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct_classifications AS SELECT * FROM ${stats_db_name}.otherresearchproduct_classifications;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct_concepts AS SELECT * FROM ${stats_db_name}.otherresearchproduct_concepts;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct_datasources AS SELECT * FROM ${stats_db_name}.otherresearchproduct_datasources;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct_languages AS SELECT * FROM ${stats_db_name}.otherresearchproduct_languages;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct_licenses AS SELECT * FROM ${stats_db_name}.otherresearchproduct_licenses;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct_oids AS SELECT * FROM ${stats_db_name}.otherresearchproduct_oids;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct_pids AS SELECT * FROM ${stats_db_name}.otherresearchproduct_pids;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct_refereed AS SELECT * FROM ${stats_db_name}.otherresearchproduct_refereed;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct_sources AS SELECT * FROM ${stats_db_name}.otherresearchproduct_sources;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct_topics AS SELECT * FROM ${stats_db_name}.otherresearchproduct_topics;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.project AS SELECT * FROM ${stats_db_name}.project;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.project_oids AS SELECT * FROM ${stats_db_name}.project_oids;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.project_organizations AS SELECT * FROM ${stats_db_name}.project_organizations;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.project_results AS SELECT * FROM ${stats_db_name}.project_results;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.project_resultcount AS SELECT * FROM ${stats_db_name}.project_resultcount;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.project_results_publication AS SELECT * FROM ${stats_db_name}.project_results_publication;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication AS SELECT * FROM ${stats_db_name}.publication;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication_citations AS SELECT * FROM ${stats_db_name}.publication_citations;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication_classifications AS SELECT * FROM ${stats_db_name}.publication_classifications;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication_concepts AS SELECT * FROM ${stats_db_name}.publication_concepts;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication_datasources AS SELECT * FROM ${stats_db_name}.publication_datasources;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication_languages AS SELECT * FROM ${stats_db_name}.publication_languages;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication_licenses AS SELECT * FROM ${stats_db_name}.publication_licenses;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication_oids AS SELECT * FROM ${stats_db_name}.publication_oids;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication_pids AS SELECT * FROM ${stats_db_name}.publication_pids;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication_refereed AS SELECT * FROM ${stats_db_name}.publication_refereed;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication_sources AS SELECT * FROM ${stats_db_name}.publication_sources;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication_topics AS SELECT * FROM ${stats_db_name}.publication_topics;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result AS SELECT * FROM ${stats_db_name}.result;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_affiliated_country AS SELECT * FROM ${stats_db_name}.result_affiliated_country;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_citations AS SELECT * FROM ${stats_db_name}.result_citations;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_classifications AS SELECT * FROM ${stats_db_name}.result_classifications;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_concepts AS SELECT * FROM ${stats_db_name}.result_concepts;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_datasources AS SELECT * FROM ${stats_db_name}.result_datasources;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_deposited_country AS SELECT * FROM ${stats_db_name}.result_deposited_country;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_fundercount AS SELECT * FROM ${stats_db_name}.result_fundercount;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_gold AS SELECT * FROM ${stats_db_name}.result_gold;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_greenoa AS SELECT * FROM ${stats_db_name}.result_greenoa;
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|
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_languages AS SELECT * FROM ${stats_db_name}.result_languages;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_licenses AS SELECT * FROM ${stats_db_name}.result_licenses;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_oids AS SELECT * FROM ${stats_db_name}.result_oids;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_organization AS SELECT * FROM ${stats_db_name}.result_organization;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_peerreviewed AS SELECT * FROM ${stats_db_name}.result_peerreviewed;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_pids AS SELECT * FROM ${stats_db_name}.result_pids;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_projectcount AS SELECT * FROM ${stats_db_name}.result_projectcount;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_projects AS SELECT * FROM ${stats_db_name}.result_projects;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_refereed AS SELECT * FROM ${stats_db_name}.result_refereed;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_sources AS SELECT * FROM ${stats_db_name}.result_sources;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_topics AS SELECT * FROM ${stats_db_name}.result_topics;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.rndexpediture AS SELECT * FROM ${stats_db_name}.rndexpediture;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.roarmap AS SELECT * FROM ${stats_db_name}.roarmap;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software AS SELECT * FROM ${stats_db_name}.software;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software_citations AS SELECT * FROM ${stats_db_name}.software_citations;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software_classifications AS SELECT * FROM ${stats_db_name}.software_classifications;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software_concepts AS SELECT * FROM ${stats_db_name}.software_concepts;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software_datasources AS SELECT * FROM ${stats_db_name}.software_datasources;
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-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software_languages AS SELECT * FROM ${stats_db_name}.software_languages;
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|
|
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software_licenses AS SELECT * FROM ${stats_db_name}.software_licenses;
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|
|
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software_oids AS SELECT * FROM ${stats_db_name}.software_oids;
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|
|
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software_pids AS SELECT * FROM ${stats_db_name}.software_pids;
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|
|
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software_refereed AS SELECT * FROM ${stats_db_name}.software_refereed;
|
|
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|
|
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software_sources AS SELECT * FROM ${stats_db_name}.software_sources;
|
|
|
|
|
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software_topics AS SELECT * FROM ${stats_db_name}.software_topics;
|
|
|
|
|
--
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|
2.17.1
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|
From 0ba0a6b9dac25f5ec73e8eafefbf7f91442ad1c5 Mon Sep 17 00:00:00 2001
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|
|
From: antleb <antleb@di.uoa.gr>
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|
|
Date: Fri, 12 Mar 2021 16:42:59 +0200
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|
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Subject: [PATCH 8/8] update promote wf to support monitor&production
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|
|
---
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|
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|
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.../stats/oozie_app/updateProductionViews.sh | 14 +++----
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|
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.../dhp/oa/graph/stats/oozie_app/workflow.xml | 37 ++++++++++++-------
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|
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2 files changed, 29 insertions(+), 22 deletions(-)
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diff --git a/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/updateProductionViews.sh b/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/updateProductionViews.sh
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index 57acb2ee..3e510e87 100644
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|
|
--- a/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/updateProductionViews.sh
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|
|
+++ b/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/updateProductionViews.sh
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|
|
@@ -7,12 +7,10 @@ then
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fi
|
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|
|
export SOURCE=$1
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|
|
-export SHADOW=$2
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|
|
+export PRODUCTION=$2
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|
|
-echo "Updating shadow database"
|
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|
|
-impala-shell -d ${SOURCE} -q "invalidate metadata"
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|
|
-impala-shell -d ${SOURCE} -q "show tables" --delimited | sed "s/^\(.*\)/compute stats ${SOURCE}.\1;/" | impala-shell -c -f -
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|
|
-impala-shell -q "create database if not exists ${SHADOW}"
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|
|
-impala-shell -d ${SHADOW} -q "show tables" --delimited | sed "s/^/drop view if exists ${SHADOW}./" | sed "s/$/;/" | impala-shell -c -f -
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|
-impala-shell -d ${SOURCE} -q "show tables" --delimited | sed "s/\(.*\)/create view ${SHADOW}.\1 as select * from ${SOURCE}.\1;/" | impala-shell -c -f -
|
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|
|
-echo "Shadow db ready!"
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|
|
\ No newline at end of file
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|
|
+echo "Updating ${PRODUCTION} database"
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|
|
+impala-shell -q "create database if not exists ${PRODUCTION}"
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|
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|
|
+impala-shell -d ${PRODUCTION} -q "show tables" --delimited | sed "s/^/drop view if exists ${PRODUCTION}./" | sed "s/$/;/" | impala-shell -c -f -
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|
+impala-shell -d ${SOURCE} -q "show tables" --delimited | sed "s/\(.*\)/create view ${PRODUCTION}.\1 as select * from ${SOURCE}.\1;/" | impala-shell -c -f -
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|
|
+echo "Production db ready!"
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|
|
\ No newline at end of file
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|
|
diff --git a/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml b/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml
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index d744f18d..0d8ff7ee 100644
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|
--- a/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml
|
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|
|
|
+++ b/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml
|
|
|
|
|
@@ -6,7 +6,15 @@
|
|
|
|
|
</property>
|
|
|
|
|
<property>
|
|
|
|
|
<name>stats_db_production_name</name>
|
|
|
|
|
- <description>the name of the production schema</description>
|
|
|
|
|
+ <description>the name of the public production schema</description>
|
|
|
|
|
+ </property>
|
|
|
|
|
+ <property>
|
|
|
|
|
+ <name>monitor_db_name</name>
|
|
|
|
|
+ <description>the monitor database name</description>
|
|
|
|
|
+ </property>
|
|
|
|
|
+ <property>
|
|
|
|
|
+ <name>monitor_db_production_name</name>
|
|
|
|
|
+ <description>the name of the monitor public database</description>
|
|
|
|
|
</property>
|
|
|
|
|
<property>
|
|
|
|
|
<name>stats_tool_api_url</name>
|
|
|
|
|
@@ -48,25 +56,26 @@
|
|
|
|
|
</kill>
|
|
|
|
|
|
|
|
|
|
<action name="updateProductionViews">
|
|
|
|
|
- <hive2 xmlns="uri:oozie:hive2-action:0.1">
|
|
|
|
|
- <jdbc-url>${hive_jdbc_url}</jdbc-url>
|
|
|
|
|
- <script>scripts/updateProductionViews.sql</script>
|
|
|
|
|
- <param>stats_db_name=${stats_db_name}</param>
|
|
|
|
|
- <param>stats_db_production_name=${stats_db_production_name}</param>
|
|
|
|
|
- </hive2>
|
|
|
|
|
- <ok to="computeProductionStats"/>
|
|
|
|
|
+ <shell xmlns="uri:oozie:shell-action:0.1">
|
|
|
|
|
+ <job-tracker>${jobTracker}</job-tracker>
|
|
|
|
|
+ <name-node>${nameNode}</name-node>
|
|
|
|
|
+ <exec>updateProductionViews.sh</exec>
|
|
|
|
|
+ <argument>${stats_db_name}</argument>
|
|
|
|
|
+ <argument>${stats_db_production_name}</argument>
|
|
|
|
|
+ <file>updateProductionViews.sh</file>
|
|
|
|
|
+ </shell>
|
|
|
|
|
+ <ok to="updateMonitorViews"/>
|
|
|
|
|
<error to="Kill"/>
|
|
|
|
|
</action>
|
|
|
|
|
|
|
|
|
|
- <action name="computeProductionStats">
|
|
|
|
|
+ <action name="updateMonitorViews">
|
|
|
|
|
<shell xmlns="uri:oozie:shell-action:0.1">
|
|
|
|
|
<job-tracker>${jobTracker}</job-tracker>
|
|
|
|
|
<name-node>${nameNode}</name-node>
|
|
|
|
|
- <exec>impala-shell.sh</exec>
|
|
|
|
|
- <argument>${stats_db_production_name}</argument>
|
|
|
|
|
- <argument>computeProductionStats.sql</argument>
|
|
|
|
|
- <argument>${wf:appPath()}/scripts/computeProductionStats.sql</argument>
|
|
|
|
|
- <file>impala-shell.sh</file>
|
|
|
|
|
+ <exec>updateProductionViews.sh</exec>
|
|
|
|
|
+ <argument>${monitor_db_name}</argument>
|
|
|
|
|
+ <argument>${monitor_db_production_name}</argument>
|
|
|
|
|
+ <file>updateProductionViews.sh</file>
|
|
|
|
|
</shell>
|
|
|
|
|
<ok to="promoteCache"/>
|
|
|
|
|
<error to="Kill"/>
|
|
|
|
|
--
|
|
|
|
|
2.17.1
|
|
|
|
|
|
