From c5fbad8093ca27deebf1b5fd5ffd39e1877c533d Mon Sep 17 00:00:00 2001 From: antleb 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 000000000..f06a43bb4 --- /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 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 6c96317e6..77fbd3b18 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 9c16f149d..afb10c419 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 @@ hive_timeout 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. + + context_api_url + the base url of the context api (https://services.openaire.eu/openaire) + @@ -263,6 +267,19 @@ + + + + ${jobTracker} + ${nameNode} + contexts.sh + ${context_api_url} + ${stats_db_name} + contexts.sh + + + + From 6147ee495053634436abe822aaf9ba909813d8c4 Mon Sep 17 00:00:00 2001 From: antleb 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 f06a43bb4..6788f88bf 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 62a158560..75b24b189 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 dcd5ad858..540cc03a5 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 fd5390e66..54345e074 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 b359b596f..36ad5d92a 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 ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.context) contexts AS context where p.datainfo.deletedbyinference = false; From f40c150a0d549e2dbcfd42ecf81e17ad4b505391 Mon Sep 17 00:00:00 2001 From: antleb Date: Sat, 6 Mar 2021 00:35:57 +0200 Subject: [PATCH 3/8] fixed steps... --- .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml index afb10c419..2184cb8a5 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml @@ -264,7 +264,7 @@ stats_db_name=${stats_db_name} openaire_db_name=${openaire_db_name} - + @@ -277,7 +277,7 @@ ${stats_db_name} contexts.sh - + From fa1ec5b5e9b6038b3b565422af5c6406f21220d3 Mon Sep 17 00:00:00 2001 From: antleb 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 2184cb8a5..321500e2c 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 @@ ${stats_db_name} contexts.sh - + From 3c75a050443942b632cf8469b5af16a8c61e7569 Mon Sep 17 00:00:00 2001 From: antleb 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 34e48a18a..000000000 --- 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 ${stats_db_name}; diff --git a/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/updateProductionViews.sh b/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/updateProductionViews.sh new file mode 100644 index 000000000..57acb2ee7 --- /dev/null +++ b/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/updateProductionViews.sh @@ -0,0 +1,18 @@ +export PYTHON_EGG_CACHE=/home/$(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 ${SOURCE}.\1;/" | impala-shell -c -f - +echo "Shadow db ready!" \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/contexts.sh b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/contexts.sh index 6788f88bf..c28be50db 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/contexts.sh +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/contexts.sh @@ -1,4 +1,10 @@ -#!/usr/bin/env bash +export PYTHON_EGG_CACHE=/home/$(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} From 236435b47010ea1ab94c3f018dcf278f5d2c44aa Mon Sep 17 00:00:00 2001 From: antleb 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 c28be50db..29b225e3c 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 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 From 60ebdf2dbe704733809f401df70bffcf49cede29 Mon Sep 17 00:00:00 2001 From: antleb 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 70112dc7b..000000000 --- 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 48f8d58fd..000000000 --- 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; From 0ba0a6b9dac25f5ec73e8eafefbf7f91442ad1c5 Mon Sep 17 00:00:00 2001 From: antleb 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 | 41 +++++++++++-------- 2 files changed, 31 insertions(+), 24 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 57acb2ee7..3e510e87e 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 d744f18da..0d8ff7ee3 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 @@ stats_db_production_name - the name of the production schema + the name of the public production schema + + + monitor_db_name + the monitor database name + + + monitor_db_production_name + the name of the monitor public database stats_tool_api_url @@ -48,25 +56,26 @@ - - ${hive_jdbc_url} - - stats_db_name=${stats_db_name} - stats_db_production_name=${stats_db_production_name} - - - - - - ${jobTracker} ${nameNode} - impala-shell.sh + updateProductionViews.sh + ${stats_db_name} ${stats_db_production_name} - computeProductionStats.sql - ${wf:appPath()}/scripts/computeProductionStats.sql - impala-shell.sh + updateProductionViews.sh + + + + + + + + ${jobTracker} + ${nameNode} + updateProductionViews.sh + ${monitor_db_name} + ${monitor_db_production_name} + updateProductionViews.sh