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dnet-hadoop/100.patch

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From c5fbad8093ca27deebf1b5fd5ffd39e1877c533d Mon Sep 17 00:00:00 2001
From: antleb <antleb@di.uoa.gr>
Date: Thu, 4 Mar 2021 00:42:21 +0200
Subject: [PATCH 1/8] Contexts are now downloaded instead of using the
stats_ext db
---
.../dhp/oa/graph/stats/oozie_app/contexts.sh | 33 +++++++++++++++++++
.../graph/stats/oozie_app/scripts/step10.sql | 13 --------
.../dhp/oa/graph/stats/oozie_app/workflow.xml | 17 ++++++++++
3 files changed, 50 insertions(+), 13 deletions(-)
create mode 100644 dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/contexts.sh
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
new file mode 100644
index 00000000..f06a43bb
--- /dev/null
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/contexts.sh
@@ -0,0 +1,33 @@
+#!/usr/bin/env bash
+
+CONTEXT_API=$1
+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
+cat contexts.csv | cut -f1 -d, | sed 's/\(.*\)/\1,\1::other,other/' >> categories.csv
+cat categories.csv | cut -d, -f2 | sed 's/\(.*\)/\1,\1::other,other/' >> concepts.csv
+
+echo "uploading context data to hdfs"
+hdfs dfs -mkdir ${TMP}
+hdfs dfs -copyFromLocal contexts.csv ${TMP}
+hdfs dfs -copyFromLocal categories.csv ${TMP}
+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;"
+
+echo "Cleaning up"
+hdfs dfs -rm -f -r -skipTrash ${TMP}
+
+echo "Finito!"
\ 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/scripts/step10.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql
index 6c96317e..77fbd3b1 100644
--- 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
@@ -23,19 +23,6 @@ CREATE OR REPLACE VIEW ${stats_db_name}.rndexpediture AS
SELECT *
FROM ${external_stats_db_name}.rndexpediture;
-CREATE OR REPLACE VIEW ${stats_db_name}.context AS
-SELECT *
-FROM ${external_stats_db_name}.context;
-
-CREATE OR REPLACE VIEW ${stats_db_name}.category AS
-SELECT *
-FROM ${external_stats_db_name}.category;
-
-CREATE OR REPLACE VIEW ${stats_db_name}.concept AS
-SELECT *
-FROM ${external_stats_db_name}.concept;
-
-
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
-- Creation date of the database
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml
index 9c16f149..afb10c41 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml
@@ -41,6 +41,10 @@
<name>hive_timeout</name>
<description>the time period, in seconds, after which Hive fails a transaction if a Hive client has not sent a hearbeat. The default value is 300 seconds.</description>
</property>
+ <property>
+ <name>context_api_url</name>
+ <description>the base url of the context api (https://services.openaire.eu/openaire)</description>
+ </property>
</parameters>
<global>
@@ -263,6 +267,19 @@
<ok to="Step19"/>
<error to="Kill"/>
</action>
+
+ <action name="Step17">
+ <shell xmlns="uri:oozie:shell-action:0.1">
+ <job-tracker>${jobTracker}</job-tracker>
+ <name-node>${nameNode}</name-node>
+ <exec>contexts.sh</exec>
+ <argument>${context_api_url}</argument>
+ <argument>${stats_db_name}</argument>
+ <file>contexts.sh</file>
+ </shell>
+ <ok to="step20-createMonitorDB"/>
+ <error to="Kill"/>
+ </action>
<action name="Step19">
<shell xmlns="uri:oozie:shell-action:0.1">
--
2.17.1
From 6147ee495053634436abe822aaf9ba909813d8c4 Mon Sep 17 00:00:00 2001
From: antleb <antleb@di.uoa.gr>
Date: Fri, 5 Mar 2021 14:12:18 +0200
Subject: [PATCH 2/8] assigning correctly hive contexts to concepts
---
.../eu/dnetlib/dhp/oa/graph/stats/oozie_app/contexts.sh | 7 +++++--
.../dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql | 5 ++++-
.../dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql | 5 ++++-
.../dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql | 5 ++++-
.../dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql | 5 ++++-
5 files changed, 21 insertions(+), 6 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 f06a43bb..6788f88b 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
@@ -9,8 +9,8 @@ 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
-cat contexts.csv | cut -f1 -d, | sed 's/\(.*\)/\1,\1::other,other/' >> categories.csv
-cat categories.csv | cut -d, -f2 | sed 's/\(.*\)/\1,\1::other,other/' >> 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
echo "uploading context data to hdfs"
hdfs dfs -mkdir ${TMP}
@@ -29,5 +29,8 @@ impala-shell -c "load data inpath '${TMP}/concepts.csv' into table ${TARGET_DB}.
echo "Cleaning up"
hdfs dfs -rm -f -r -skipTrash ${TMP}
+rm concepts.csv
+rm categories.csv
+rm contexts.csv
echo "Finito!"
\ 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/scripts/step2.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql
index 62a15856..75b24b18 100644
--- 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
@@ -47,7 +47,10 @@ from ${openaire_db_name}.publication p
where p.datainfo.deletedbyinference = false;
CREATE TABLE ${stats_db_name}.publication_concepts AS
-SELECT substr(p.id, 4) as id, contexts.context.id as concept
+SELECT substr(p.id, 4) as id, case
+ when contexts.context.id RLIKE '^[^::]+::[^::]+::.+$' then contexts.context.id
+ 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}.publication p
LATERAL VIEW explode(p.context) contexts as context
where p.datainfo.deletedbyinference = false;
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
index dcd5ad85..540cc03a 100644
--- 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
@@ -54,7 +54,10 @@ FROM ${openaire_db_name}.dataset p
where p.datainfo.deletedbyinference = false;
CREATE TABLE ${stats_db_name}.dataset_concepts AS
-SELECT substr(p.id, 4) as id, contexts.context.id as concept
+SELECT substr(p.id, 4) as id, case
+ when contexts.context.id RLIKE '^[^::]+::[^::]+::.+$' then contexts.context.id
+ 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}.dataset p
LATERAL VIEW explode(p.context) contexts as context
where p.datainfo.deletedbyinference = false;
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
index fd5390e6..54345e07 100644
--- 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
@@ -54,7 +54,10 @@ FROM ${openaire_db_name}.software p
where p.datainfo.deletedbyinference = false;
CREATE TABLE ${stats_db_name}.software_concepts AS
-SELECT substr(p.id, 4) AS id, contexts.context.id AS concept
+SELECT substr(p.id, 4) as id, case
+ when contexts.context.id RLIKE '^[^::]+::[^::]+::.+$' then contexts.context.id
+ 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}.software p
LATERAL VIEW explode(p.context) contexts AS context
where p.datainfo.deletedbyinference = false;
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
index b359b596..36ad5d92 100644
--- 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
@@ -52,7 +52,10 @@ FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.instance.
where p.datainfo.deletedbyinference = false;
CREATE TABLE ${stats_db_name}.otherresearchproduct_concepts AS
-SELECT substr(p.id, 4) AS id, contexts.context.id AS concept
+SELECT substr(p.id, 4) as id, case
+ when contexts.context.id RLIKE '^[^::]+::[^::]+::.+$' then contexts.context.id
+ 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
deleted file mode 100644
index 48f8d58f..00000000
--- a/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/updateProductionViews.sql
+++ /dev/null
@@ -1,207 +0,0 @@
-------------------------------------------------------
-------------------------------------------------------
--- Shadow schema table exchange
-------------------------------------------------------
-------------------------------------------------------
-
--- Dropping old views
-DROP VIEW IF EXISTS ${stats_db_production_name}.category;
-DROP VIEW IF EXISTS ${stats_db_production_name}.concept;
-DROP VIEW IF EXISTS ${stats_db_production_name}.context;
-DROP VIEW IF EXISTS ${stats_db_production_name}.country;
-DROP VIEW IF EXISTS ${stats_db_production_name}.countrygdp;
-DROP VIEW IF EXISTS ${stats_db_production_name}.creation_date;
-DROP VIEW IF EXISTS ${stats_db_production_name}.dataset;
-DROP VIEW IF EXISTS ${stats_db_production_name}.dataset_citations;
-DROP VIEW IF EXISTS ${stats_db_production_name}.dataset_classifications;
-DROP VIEW IF EXISTS ${stats_db_production_name}.dataset_concepts;
-DROP VIEW IF EXISTS ${stats_db_production_name}.dataset_datasources;
-DROP VIEW IF EXISTS ${stats_db_production_name}.dataset_languages;
-DROP VIEW IF EXISTS ${stats_db_production_name}.dataset_licenses;
-DROP VIEW IF EXISTS ${stats_db_production_name}.dataset_oids;
-DROP VIEW IF EXISTS ${stats_db_production_name}.dataset_pids;
-DROP VIEW IF EXISTS ${stats_db_production_name}.dataset_refereed;
-DROP VIEW IF EXISTS ${stats_db_production_name}.dataset_sources;
-DROP VIEW IF EXISTS ${stats_db_production_name}.dataset_topics;
-DROP VIEW IF EXISTS ${stats_db_production_name}.datasource;
-DROP VIEW IF EXISTS ${stats_db_production_name}.datasource_languages;
-DROP VIEW IF EXISTS ${stats_db_production_name}.datasource_oids;
-DROP VIEW IF EXISTS ${stats_db_production_name}.datasource_organizations;
-DROP VIEW IF EXISTS ${stats_db_production_name}.datasource_results;
-DROP VIEW IF EXISTS ${stats_db_production_name}.datasource_sources;
-DROP VIEW IF EXISTS ${stats_db_production_name}.funder;
-DROP VIEW IF EXISTS ${stats_db_production_name}.fundref;
-DROP VIEW IF EXISTS ${stats_db_production_name}.numbers_country;
-DROP VIEW IF EXISTS ${stats_db_production_name}.organization;
-DROP VIEW IF EXISTS ${stats_db_production_name}.organization_datasources;
-DROP VIEW IF EXISTS ${stats_db_production_name}.organization_pids;
-DROP VIEW IF EXISTS ${stats_db_production_name}.organization_projects;
-DROP VIEW IF EXISTS ${stats_db_production_name}.organization_sources;
-DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct;
-DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct_citations;
-DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct_classifications;
-DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct_concepts;
-DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct_datasources;
-DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct_languages;
-DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct_licenses;
-DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct_oids;
-DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct_pids;
-DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct_refereed;
-DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct_sources;
-DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct_topics;
-DROP VIEW IF EXISTS ${stats_db_production_name}.project;
-DROP VIEW IF EXISTS ${stats_db_production_name}.project_oids;
-DROP VIEW IF EXISTS ${stats_db_production_name}.project_organizations;
-DROP VIEW IF EXISTS ${stats_db_production_name}.project_results;
-DROP VIEW IF EXISTS ${stats_db_production_name}.project_resultcount;
-DROP VIEW IF EXISTS ${stats_db_production_name}.project_results_publication;
-DROP VIEW IF EXISTS ${stats_db_production_name}.publication;
-DROP VIEW IF EXISTS ${stats_db_production_name}.publication_citations;
-DROP VIEW IF EXISTS ${stats_db_production_name}.publication_classifications;
-DROP VIEW IF EXISTS ${stats_db_production_name}.publication_concepts;
-DROP VIEW IF EXISTS ${stats_db_production_name}.publication_datasources;
-DROP VIEW IF EXISTS ${stats_db_production_name}.publication_languages;
-DROP VIEW IF EXISTS ${stats_db_production_name}.publication_licenses;
-DROP VIEW IF EXISTS ${stats_db_production_name}.publication_oids;
-DROP VIEW IF EXISTS ${stats_db_production_name}.publication_pids;
-DROP VIEW IF EXISTS ${stats_db_production_name}.publication_refereed;
-DROP VIEW IF EXISTS ${stats_db_production_name}.publication_sources;
-DROP VIEW IF EXISTS ${stats_db_production_name}.publication_topics;
-DROP VIEW IF EXISTS ${stats_db_production_name}.result;
-DROP VIEW IF EXISTS ${stats_db_production_name}.result_affiliated_country;
-DROP VIEW IF EXISTS ${stats_db_production_name}.result_citations;
-DROP VIEW IF EXISTS ${stats_db_production_name}.result_classifications;
-DROP VIEW IF EXISTS ${stats_db_production_name}.result_concepts;
-DROP VIEW IF EXISTS ${stats_db_production_name}.result_datasources;
-DROP VIEW IF EXISTS ${stats_db_production_name}.result_deposited_country;
-DROP VIEW IF EXISTS ${stats_db_production_name}.result_fundercount;
-DROP VIEW IF EXISTS ${stats_db_production_name}.result_gold;
-DROP VIEW IF EXISTS ${stats_db_production_name}.result_greenoa;
-DROP VIEW IF EXISTS ${stats_db_production_name}.result_languages;
-DROP VIEW IF EXISTS ${stats_db_production_name}.result_licenses;
-DROP VIEW IF EXISTS ${stats_db_production_name}.result_oids;
-DROP VIEW IF EXISTS ${stats_db_production_name}.result_organization;
-DROP VIEW IF EXISTS ${stats_db_production_name}.result_peerreviewed;
-DROP VIEW IF EXISTS ${stats_db_production_name}.result_pids;
-DROP VIEW IF EXISTS ${stats_db_production_name}.result_projectcount;
-DROP VIEW IF EXISTS ${stats_db_production_name}.result_projects;
-DROP VIEW IF EXISTS ${stats_db_production_name}.result_refereed;
-DROP VIEW IF EXISTS ${stats_db_production_name}.result_sources;
-DROP VIEW IF EXISTS ${stats_db_production_name}.result_topics;
-DROP VIEW IF EXISTS ${stats_db_production_name}.rndexpediture;
-DROP VIEW IF EXISTS ${stats_db_production_name}.roarmap;
-DROP VIEW IF EXISTS ${stats_db_production_name}.software;
-DROP VIEW IF EXISTS ${stats_db_production_name}.software_citations;
-DROP VIEW IF EXISTS ${stats_db_production_name}.software_classifications;
-DROP VIEW IF EXISTS ${stats_db_production_name}.software_concepts;
-DROP VIEW IF EXISTS ${stats_db_production_name}.software_datasources;
-DROP VIEW IF EXISTS ${stats_db_production_name}.software_languages;
-DROP VIEW IF EXISTS ${stats_db_production_name}.software_licenses;
-DROP VIEW IF EXISTS ${stats_db_production_name}.software_oids;
-DROP VIEW IF EXISTS ${stats_db_production_name}.software_pids;
-DROP VIEW IF EXISTS ${stats_db_production_name}.software_refereed;
-DROP VIEW IF EXISTS ${stats_db_production_name}.software_sources;
-DROP VIEW IF EXISTS ${stats_db_production_name}.software_topics;
-
-
--- Creating the shadow database, in case it doesn't exist
-CREATE database IF NOT EXISTS ${stats_db_production_name};
-
--- Creating new views
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.category AS SELECT * FROM ${stats_db_name}.category;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.concept AS SELECT * FROM ${stats_db_name}.concept;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.context AS SELECT * FROM ${stats_db_name}.context;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.country AS SELECT * FROM ${stats_db_name}.country;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.countrygdp AS SELECT * FROM ${stats_db_name}.countrygdp;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.creation_date AS SELECT * FROM ${stats_db_name}.creation_date;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset AS SELECT * FROM ${stats_db_name}.dataset;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset_citations AS SELECT * FROM ${stats_db_name}.dataset_citations;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset_classifications AS SELECT * FROM ${stats_db_name}.dataset_classifications;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset_concepts AS SELECT * FROM ${stats_db_name}.dataset_concepts;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset_datasources AS SELECT * FROM ${stats_db_name}.dataset_datasources;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset_languages AS SELECT * FROM ${stats_db_name}.dataset_languages;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset_licenses AS SELECT * FROM ${stats_db_name}.dataset_licenses;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset_oids AS SELECT * FROM ${stats_db_name}.dataset_oids;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset_pids AS SELECT * FROM ${stats_db_name}.dataset_pids;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset_refereed AS SELECT * FROM ${stats_db_name}.dataset_refereed;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset_sources AS SELECT * FROM ${stats_db_name}.dataset_sources;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset_topics AS SELECT * FROM ${stats_db_name}.dataset_topics;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.datasource AS SELECT * FROM ${stats_db_name}.datasource;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.datasource_languages AS SELECT * FROM ${stats_db_name}.datasource_languages;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.datasource_oids AS SELECT * FROM ${stats_db_name}.datasource_oids;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.datasource_organizations AS SELECT * FROM ${stats_db_name}.datasource_organizations;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.datasource_results AS SELECT * FROM ${stats_db_name}.datasource_results;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.datasource_sources AS SELECT * FROM ${stats_db_name}.datasource_sources;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.funder AS SELECT * FROM ${stats_db_name}.funder;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.fundref AS SELECT * FROM ${stats_db_name}.fundref;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.numbers_country AS SELECT * FROM ${stats_db_name}.numbers_country;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.organization AS SELECT * FROM ${stats_db_name}.organization;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.organization_datasources AS SELECT * FROM ${stats_db_name}.organization_datasources;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.organization_pids AS SELECT * FROM ${stats_db_name}.organization_pids;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.organization_projects AS SELECT * FROM ${stats_db_name}.organization_projects;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.organization_sources AS SELECT * FROM ${stats_db_name}.organization_sources;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct AS SELECT * FROM ${stats_db_name}.otherresearchproduct;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct_citations AS SELECT * FROM ${stats_db_name}.otherresearchproduct_citations;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct_classifications AS SELECT * FROM ${stats_db_name}.otherresearchproduct_classifications;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct_concepts AS SELECT * FROM ${stats_db_name}.otherresearchproduct_concepts;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct_datasources AS SELECT * FROM ${stats_db_name}.otherresearchproduct_datasources;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct_languages AS SELECT * FROM ${stats_db_name}.otherresearchproduct_languages;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct_licenses AS SELECT * FROM ${stats_db_name}.otherresearchproduct_licenses;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct_oids AS SELECT * FROM ${stats_db_name}.otherresearchproduct_oids;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct_pids AS SELECT * FROM ${stats_db_name}.otherresearchproduct_pids;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct_refereed AS SELECT * FROM ${stats_db_name}.otherresearchproduct_refereed;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct_sources AS SELECT * FROM ${stats_db_name}.otherresearchproduct_sources;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct_topics AS SELECT * FROM ${stats_db_name}.otherresearchproduct_topics;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.project AS SELECT * FROM ${stats_db_name}.project;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.project_oids AS SELECT * FROM ${stats_db_name}.project_oids;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.project_organizations AS SELECT * FROM ${stats_db_name}.project_organizations;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.project_results AS SELECT * FROM ${stats_db_name}.project_results;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.project_resultcount AS SELECT * FROM ${stats_db_name}.project_resultcount;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.project_results_publication AS SELECT * FROM ${stats_db_name}.project_results_publication;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication AS SELECT * FROM ${stats_db_name}.publication;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication_citations AS SELECT * FROM ${stats_db_name}.publication_citations;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication_classifications AS SELECT * FROM ${stats_db_name}.publication_classifications;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication_concepts AS SELECT * FROM ${stats_db_name}.publication_concepts;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication_datasources AS SELECT * FROM ${stats_db_name}.publication_datasources;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication_languages AS SELECT * FROM ${stats_db_name}.publication_languages;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication_licenses AS SELECT * FROM ${stats_db_name}.publication_licenses;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication_oids AS SELECT * FROM ${stats_db_name}.publication_oids;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication_pids AS SELECT * FROM ${stats_db_name}.publication_pids;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication_refereed AS SELECT * FROM ${stats_db_name}.publication_refereed;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication_sources AS SELECT * FROM ${stats_db_name}.publication_sources;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication_topics AS SELECT * FROM ${stats_db_name}.publication_topics;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result AS SELECT * FROM ${stats_db_name}.result;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_affiliated_country AS SELECT * FROM ${stats_db_name}.result_affiliated_country;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_citations AS SELECT * FROM ${stats_db_name}.result_citations;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_classifications AS SELECT * FROM ${stats_db_name}.result_classifications;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_concepts AS SELECT * FROM ${stats_db_name}.result_concepts;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_datasources AS SELECT * FROM ${stats_db_name}.result_datasources;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_deposited_country AS SELECT * FROM ${stats_db_name}.result_deposited_country;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_fundercount AS SELECT * FROM ${stats_db_name}.result_fundercount;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_gold AS SELECT * FROM ${stats_db_name}.result_gold;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_greenoa AS SELECT * FROM ${stats_db_name}.result_greenoa;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_languages AS SELECT * FROM ${stats_db_name}.result_languages;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_licenses AS SELECT * FROM ${stats_db_name}.result_licenses;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_oids AS SELECT * FROM ${stats_db_name}.result_oids;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_organization AS SELECT * FROM ${stats_db_name}.result_organization;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_peerreviewed AS SELECT * FROM ${stats_db_name}.result_peerreviewed;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_pids AS SELECT * FROM ${stats_db_name}.result_pids;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_projectcount AS SELECT * FROM ${stats_db_name}.result_projectcount;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_projects AS SELECT * FROM ${stats_db_name}.result_projects;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_refereed AS SELECT * FROM ${stats_db_name}.result_refereed;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_sources AS SELECT * FROM ${stats_db_name}.result_sources;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_topics AS SELECT * FROM ${stats_db_name}.result_topics;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.rndexpediture AS SELECT * FROM ${stats_db_name}.rndexpediture;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.roarmap AS SELECT * FROM ${stats_db_name}.roarmap;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software AS SELECT * FROM ${stats_db_name}.software;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software_citations AS SELECT * FROM ${stats_db_name}.software_citations;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software_classifications AS SELECT * FROM ${stats_db_name}.software_classifications;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software_concepts AS SELECT * FROM ${stats_db_name}.software_concepts;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software_datasources AS SELECT * FROM ${stats_db_name}.software_datasources;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software_languages AS SELECT * FROM ${stats_db_name}.software_languages;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software_licenses AS SELECT * FROM ${stats_db_name}.software_licenses;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software_oids AS SELECT * FROM ${stats_db_name}.software_oids;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software_pids AS SELECT * FROM ${stats_db_name}.software_pids;
-CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software_refereed AS SELECT * FROM ${stats_db_name}.software_refereed;
-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;
--
2.17.1
From 0ba0a6b9dac25f5ec73e8eafefbf7f91442ad1c5 Mon Sep 17 00:00:00 2001
From: antleb <antleb@di.uoa.gr>
Date: Fri, 12 Mar 2021 16:42:59 +0200
Subject: [PATCH 8/8] update promote wf to support monitor&production
---
.../stats/oozie_app/updateProductionViews.sh | 14 +++----
.../dhp/oa/graph/stats/oozie_app/workflow.xml | 37 ++++++++++++-------
2 files changed, 29 insertions(+), 22 deletions(-)
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
index 57acb2ee..3e510e87 100644
--- 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
@@ -7,12 +7,10 @@ then
fi
export SOURCE=$1
-export SHADOW=$2
+export PRODUCTION=$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
+echo "Updating ${PRODUCTION} database"
+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 ${SOURCE}.\1;/" | impala-shell -c -f -
+echo "Production db ready!"
\ No newline at end of file
diff --git a/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml b/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml
index d744f18d..0d8ff7ee 100644
--- a/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml
@@ -6,7 +6,15 @@
</property>
<property>
<name>stats_db_production_name</name>
- <description>the name of the production schema</description>
+ <description>the name of the public production schema</description>
+ </property>
+ <property>
+ <name>monitor_db_name</name>
+ <description>the monitor database name</description>
+ </property>
+ <property>
+ <name>monitor_db_production_name</name>
+ <description>the name of the monitor public database</description>
</property>
<property>
<name>stats_tool_api_url</name>
@@ -48,25 +56,26 @@
</kill>
<action name="updateProductionViews">
- <hive2 xmlns="uri:oozie:hive2-action:0.1">
- <jdbc-url>${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
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