Merge main

distros/clariah/jupyter-semantics.yaml

@@ -0,0 +1 @@
+../../services-available/jupyter/jupyter-semantics.yaml

distros/clariah/rmlmappingapi.yaml

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+../../services-available/semantics/rmlmappingapi.yaml

distros/clariah/semantic-bot.yaml

@@ -0,0 +1 @@
+../../services-available/semantics/semantic-bot.yaml

distros/dataverse-jdk11/.env

@@ -1,18 +1,30 @@
-COMPOSE_PROJECT_NAME=dataverse.org.ua
+COMPOSE_PROJECT_NAME=datasetscoronawhyorg
 
 # traefik settings
-traefikhost=dataverse.org.ua
+traefikhost=datasets.coronawhy.org
+useremail=[email protected]
 
 # local postgres settings
 LC_ALL=C.UTF-8
-POSTGRES_DB=dvndb
-POSTGRES_USER=dvnuser
-POSTGRES_PASSWORD=dvnsecret
-POSTGRES_PORT=5432
+#POSTGRES_DB=dvndb
+#POSTGRES_USER=dvnuser
+#POSTGRES_PASSWORD=dvnsecret
+#POSTGRES_PORT=5432
 
-# local dataverse settings
-DATAVERSE_URL=https://dataverse.s3.coronawhy.org
-POSTGRES_SERVER=postgres
-POSTGRES_DATABASE=postgres
-PGPASSWORD=dvnsecret
+# Dataverse database settings
+DATAVERSE_DB_HOST=postgres
+DATAVERSE_DB_USER=dataverse
+DATAVERSE_DB_PASSWORD=changeme
+DATAVERSE_DB_NAME=dataverse
+
+SOLR_SERVICE_HOST=solr
+SOLR_SERVICE_PORT=8983
+DATAVERSE_URL=localhost:8080
+DATAVERSE_SERVICE_HOST=localhost
 
+# Postgres settings
+POSTGRES_USER=dataverse
+POSTGRES_PASSWORD=changeme
+POSTGRES_SERVER=postgres
+POSTGRES_DATABASE=dataverse
+#PGPASSWORD=dvnsecret

distros/dataverse-jdk11/README.!!!!!!!!!!!!!!!

@@ -0,0 +1,5 @@
+# IDEA: remap uid https://docs.docker.com/engine/security/userns-remap/
+mkdir -p var/solr
+sudo chown 8983:8983 var/solr
+sudo chmod g+w var/solr
+

distros/dataverse-jdk11/dataverse-5.5.yaml

@@ -0,0 +1 @@
+../../services-available/dataverse/dataverse-5.5.yaml

distros/dataverse-jdk11/secrets

@@ -0,0 +1 @@
+../../services-available/dataverse/secrets

images/solr-coronawhy/Dockerfile

@@ -0,0 +1,3 @@
+FROM ekoindarto/solr-cvm:latest
+COPY entrypoint.sh /tmp
+COPY solr-var-init.tar.gz /tmp

images/solr-coronawhy/Makefile

@@ -0,0 +1,2 @@
+build:
+	@docker build -t coronawhy/solr:latest .

images/solr-coronawhy/bak/entrypoint.sh.orig

@@ -0,0 +1,27 @@
+#!/bin/bash
+# Fail on any error
+#set -e
+
+solr start -v
+echo "Starting Solr...."
+if [ -f /tmp/updateSchemaMDB.sh ]; then
+    sleep 25;
+    solr stop -v
+    unzip -o -qq /tmp/collection1.zip -d /var/solr/data/
+    solr start -v
+    echo "Checking Dataverse....";
+    sleep 10;
+    until curl -sS -f "http://dataverse:8080/robots.txt" -m 2 2>&1 > /dev/null;
+    do echo ">>>>>>>> Waiting for Dataverse...."; echo "---- Dataverse is not ready...."; sleep 20; done;
+    echo "Dataverse is running...";
+    echo "Trying to update scheme...";
+    echo "Updating";
+    /tmp/updateSchemaMDB.sh -d http://dataverse:8080 -t /var/solr/data//collection1/conf
+    sleep 5;
+    echo "-----Scheme updated------";
+    rm /tmp/updateSchemaMDB.sh
+else
+    echo ":) :) :)"
+fi
+
+tail -f /dev/null

images/solr-coronawhy/bak/log4j2.xml

@@ -0,0 +1,144 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+  Licensed to the Apache Software Foundation (ASF) under one or more
+  contributor license agreements.  See the NOTICE file distributed with
+  this work for additional information regarding copyright ownership.
+  The ASF licenses this file to You under the Apache License, Version 2.0
+  (the "License"); you may not use this file except in compliance with
+  the License.  You may obtain a copy of the License at
+
+      http://www.apache.org/licenses/LICENSE-2.0
+
+  Unless required by applicable law or agreed to in writing, software
+  distributed under the License is distributed on an "AS IS" BASIS,
+  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+  See the License for the specific language governing permissions and
+  limitations under the License.
+  -->
+
+<!-- Configuration for asynchronous logging -->
+<Configuration status="WARN">
+  <Appenders>
+
+    <Console name="STDOUT" target="SYSTEM_OUT">
+      <PatternLayout>
+        <Pattern>
+          %maxLen{%d{yyyy-MM-dd HH:mm:ss.SSS} %-5p (%t) [%X{collection} %X{shard} %X{replica} %X{core}] %c{1.} %m%notEmpty{ =>%ex{short}}}{10240}%n
+        </Pattern>
+      </PatternLayout>
+    </Console>
+
+    <RollingRandomAccessFile
+        name="MainLogFile"
+        fileName="${sys:solr.log.dir}/solr.log"
+        filePattern="${sys:solr.log.dir}/solr.log.%i" >
+      <PatternLayout>
+        <Pattern>
+          %maxLen{%d{yyyy-MM-dd HH:mm:ss.SSS} %-5p (%t) [%X{collection} %X{shard} %X{replica} %X{core}] %c{1.} %m%notEmpty{ =>%ex{short}}}{10240}%n
+        </Pattern>
+      </PatternLayout>
+      <Policies>
+        <OnStartupTriggeringPolicy />
+        <SizeBasedTriggeringPolicy size="32 MB"/>
+      </Policies>
+      <DefaultRolloverStrategy max="10"/>
+    </RollingRandomAccessFile>
+
+    <RollingRandomAccessFile
+        name="SlowLogFile"
+        fileName="${sys:solr.log.dir}/solr_slow_requests.log"
+        filePattern="${sys:solr.log.dir}/solr_slow_requests.log.%i" >
+      <PatternLayout>
+        <Pattern>
+          %maxLen{%d{yyyy-MM-dd HH:mm:ss.SSS} %-5p (%t) [%X{collection} %X{shard} %X{replica} %X{core}] %c{1.} %m%notEmpty{ =>%ex{short}}}{10240}%n
+        </Pattern>
+      </PatternLayout>
+      <Policies>
+        <OnStartupTriggeringPolicy />
+        <SizeBasedTriggeringPolicy size="32 MB"/>
+      </Policies>
+      <DefaultRolloverStrategy max="10"/>
+    </RollingRandomAccessFile>
+
+  </Appenders>
+  <Loggers>
+	  <Root level="info">
+	    <AsyncLogger name="org.apache.hadoop" level="warn"/>
+	    <AsyncLogger name="org.apache.solr.update.LoggingInfoStream" level="off"/>
+	    <AsyncLogger name="org.apache.zookeeper" level="warn"/>
+	    <AsyncLogger name="org.apache.solr.core.SolrCore.SlowRequest" level="info" additivity="false">
+	      <AppenderRef ref="SlowLogFile"/>
+	    </AsyncLogger>
+
+	    <AsyncRoot level="info">
+	      <AppenderRef ref="MainLogFile"/>
+	      <AppenderRef ref="STDOUT"/>
+	    </AsyncRoot>
+    </Root>
+  </Loggers>
+</Configuration>
+
+<!-- Configuration for synchronous logging
+     there _may_ be a very small window where log messages will not be flushed
+     to the log file on abnormal shutdown. If even this risk is unacceptable, use
+     the configuration below
+-->
+<!--Configuration>
+  <Appenders>
+
+    <Console name="STDOUT" target="SYSTEM_OUT">
+      <PatternLayout>
+        <Pattern>
+          %d{yyyy-MM-dd HH:mm:ss.SSS} %-5p (%t) [%X{collection} %X{shard} %X{replica} %X{core}] %c{1.} %m%n
+        </Pattern>
+      </PatternLayout>
+    </Console>
+
+    <RollingFile
+        name="RollingFile"
+        fileName="${sys:solr.log.dir}/solr.log"
+        filePattern="${sys:solr.log.dir}/solr.log.%i" >
+      <PatternLayout>
+        <Pattern>
+          %d{yyyy-MM-dd HH:mm:ss.SSS} %-5p (%t) [%X{collection} %X{shard} %X{replica} %X{core}] %c{1.} %m%n
+        </Pattern>
+      </PatternLayout>
+      <Policies>
+        <OnStartupTriggeringPolicy />
+        <SizeBasedTriggeringPolicy size="32 MB"/>
+      </Policies>
+      <DefaultRolloverStrategy max="10"/>
+    </RollingFile>
+
+    <RollingFile
+        name="SlowFile"
+        fileName="${sys:solr.log.dir}/solr_slow_requests.log"
+        filePattern="${sys:solr.log.dir}/solr_slow_requests.log.%i" >
+      <PatternLayout>
+        <Pattern>
+          %d{yyyy-MM-dd HH:mm:ss.SSS} %-5p (%t) [%X{collection} %X{shard} %X{replica} %X{core}] %c{1.} %m%n
+        </Pattern>
+      </PatternLayout>
+      <Policies>
+        <OnStartupTriggeringPolicy />
+        <SizeBasedTriggeringPolicy size="32 MB"/>
+      </Policies>
+      <DefaultRolloverStrategy max="10"/>
+    </RollingFile>
+
+  </Appenders>
+  <Loggers>
+    <Logger name="org.apache.hadoop" level="warn"/>
+    <Logger name="org.apache.solr.update.LoggingInfoStream" level="off"/>
+    <Logger name="org.apache.zookeeper" level="warn"/>
+    <Logger name="org.apache.solr.core.SolrCore.SlowRequest" level="info" additivity="false">
+      <AppenderRef ref="SlowFile"/>
+    </Logger>
+
+    <Root level="info">
+      <AppenderRef ref="RollingFile"/>
+      <AppenderRef ref="STDOUT"/>
+    </Root>
+  </Loggers>
+</Configuration-->
+