Create solr8 docker instance for testing

Use namematching service for name lookup on conservation lists and vernacular lists #346 Handle duplicate common names in lists Handle aliases for common name status
AtlasOfLivingAustralia · charvolant · Jun 2, 2022 · May 23, 2022 · May 26, 2022 · May 26, 2022
commit 9f543aa7eca6bd5faa9eb712af4140c1dc24f02e
diff --git a/build.gradle b/build.gradle
@@ -11,7 +11,7 @@ buildscript {
  }
 }
 
-version "1.6-SNAPSHOT"
+version "1.7-SNAPSHOT"
 group "au.org.ala"
 
 apply plugin:"eclipse"

diff --git a/docker/README.md b/docker/README.md
@@ -6,17 +6,31 @@ debugging
 ## Solr
 
 The solr image contains a solr server with pre-configred `bie` and `bie-offline` cores.
-To build a solr6 image for use with the bie-index run, from this directory
+To build a solr8 image for use with the bie-index run, from this directory
 
 ```shell
-docker build solr6 -t bie-solr:v1
+docker build solr8 -t bie-solr:v2
 ```
 
 To run the resulting image in a fresh container, use
 
 ```shell
-docker run -p 8983:8983 bie-solr:v1
+docker run -p 8983:8983 bie-solr:v2
 ```
 
+You will then need to add the cores.
+Go to http:https://localhost:8983 and choose the cores item.
+Click on add core and set the following:
+
+Parameter | Value (bie) | Value (bie-offline)
+--- | --- | ---
+name | bie | bie-offline
+instanceDir | /opt/solr/server/solr/bie | /opt/solr/server/solr/bie-offline
+dataDir | /opt/solr/server/solr/bie/data | /opt/solr/server/solr/bie-offline/data
+config | solrconfig.xml | solrconfig.xml 
+schema | schema.xml | schema.xml
+
+(You may need to do this twice; no idea why.)
+
 Set the solr connections in the configuration to
 `http:https://localhost:8983/solr/bie` and `http:https://localhost:8983/solr/bie-offline`
diff --git a/docker/solr8/Dockerfile b/docker/solr8/Dockerfile
@@ -0,0 +1,15 @@
+FROM solr:8.1
+USER solr:solr
+WORKDIR /var/solr/data
+COPY solr.xml solr.xml
+COPY zoo.cfg zoo.cfg
+#COPY --chown=solr:solr lib /opt/solr/server/solr-webapp/webapp/WEB-INF/lib/
+RUN mkdir -p bie bie/conf bie/data bie/suggest-infix
+COPY conf bie/conf
+COPY bie.core.properties bie/core.properties
+RUN mkdir -p bie-offline bie-offline/conf bie-offline/data bie-offline/suggest-infix
+COPY conf bie-offline/conf
+COPY bie-offline.core.properties bie-offline/core.properties
+COPY solr.in.sh /etc/default/solr.in.sh
+
+
diff --git a/docker/solr8/bie-offline.core.properties b/docker/solr8/bie-offline.core.properties
@@ -0,0 +1,4 @@
+config=solrconfig.xml
+name=bie-offline
+dataDir=data
+schema=schema.xml
diff --git a/docker/solr8/bie.core.properties b/docker/solr8/bie.core.properties
@@ -0,0 +1,4 @@
+config=solrconfig.xml
+name=bie
+dataDir=data
+schema=schema.xml
diff --git a/docker/solr8/conf/admin-extra.html b/docker/solr8/conf/admin-extra.html
@@ -0,0 +1,24 @@
+<!--
+ 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:https://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.
+-->
+
+<!-- The content of this page will be statically included into the top-
+right box of the cores overview page. Uncomment this as an example to 
+see there the content will show up.
+
+<img src="img/ico/construction.png"> This line will appear at the top-
+right box on collection1's Overview
+-->
diff --git a/docker/solr8/conf/admin-extra.menu-bottom.html b/docker/solr8/conf/admin-extra.menu-bottom.html
@@ -0,0 +1,25 @@
+<!--
+ 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:https://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.
+-->
+
+<!-- admin-extra.menu-bottom.html -->
+<!--
+<li>
+ <a href="#" style="background-image: url(img/ico/construction.png);">
+ LAST ITEM
+ </a>
+</li>
+-->
diff --git a/docker/solr8/conf/admin-extra.menu-top.html b/docker/solr8/conf/admin-extra.menu-top.html
@@ -0,0 +1,25 @@
+<!--
+ 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:https://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.
+-->
+
+<!-- admin-extra.menu-top.html -->
+<!--
+<li>
+ <a href="#" style="background-image: url(img/ico/construction.png);">
+ FIRST ITEM
+ </a>
+</li>
+-->
diff --git a/docker/solr8/conf/bie_stopwords.txt b/docker/solr8/conf/bie_stopwords.txt
diff --git a/docker/solr8/conf/data-config.xml b/docker/solr8/conf/data-config.xml
@@ -0,0 +1,68 @@
+<dataConfig>
+ <dataSource type="JdbcDataSource" driver="com.mysql.jdbc.Driver" url="jdbc:mysql:https://localhost/portal" user="root" password="" batchSize="-1"/>
+ <document>
+ <entity name="occurrence" query="SELECT oc.id, oc.data_provider_id, dp.name data_provider, oc.data_resource_id, dr.name data_resource,
+ oc.institution_code_id, ic.code institution_code, ic.name institution_code_name, ic.lsid institution_code_lsid,
+ oc.collection_code_id, cc.code collection_code, oc.catalogue_number_id, cn.code catalogue_number,
+ tc.guid taxon_concept_lsid, tn.canonical taxon_name, tn.author, tc.rank rank_id, rnk.name rank,
+ ror.scientific_name raw_taxon_name, ror.author raw_author, oc.iso_country_code country_code,
+ kdc.guid kingdom_lsid, kdn.canonical kingdom, phc.guid phylum_lsid, phn.canonical phylum,
+ clc.guid class_lsid, cln.canonical class, odc.guid order_lsid, odn.canonical `order`,
+ fmc.guid family_lsid, fmn.canonical family, gnc.guid genus_lsid, gnn.canonical genus, spc.guid species_lsid, spn.canonical species,
+ oc.latitude, oc.longitude, ror.lat_long_precision, CONCAT_WS(',', oc.latitude, oc.longitude) as lat_long,
+ oc.cell_id, oc.centi_cell_id, oc.tenmilli_cell_id,
+ oc.year, oc.month, DATE_FORMAT(oc.occurrence_date,'%Y-%m-%dT%H:%i:%sZ') occurrence_date,
+ oc.basis_of_record basis_of_record_id, bor.description basis_of_record, ror.basis_of_record raw_basis_of_record,
+ typ.type_status, lit.it_value identifier_type, idr.identifier identifier_value, ror.identifier_name,
+ DATE_FORMAT(ror.identification_date,'%Y-%m-%dT%H:%i:%sZ') identifier_date, ror.collector_name collector,
+ taxonomic_issue, geospatial_issue, other_issue, ror.created created_date, oc.modified modified_date
+ FROM occurrence_record oc
+ INNER JOIN raw_occurrence_record ror ON ror.id = oc.id
+ INNER JOIN data_provider dp ON dp.id = oc.data_provider_id
+ INNER JOIN data_resource dr ON dr.id = oc.data_resource_id
+ INNER JOIN institution_code ic ON ic.id = oc.institution_code_id
+ INNER JOIN collection_code cc ON cc.id = oc.collection_code_id
+ INNER JOIN catalogue_number cn ON cn.id = oc.catalogue_number_id
+ INNER JOIN basis_of_record bor ON bor.id = oc.basis_of_record
+ INNER JOIN taxon_name tn ON tn.id = oc.taxon_name_id
+ INNER JOIN taxon_concept tc ON tc.id = oc.nub_concept_id
+ INNER JOIN rank rnk ON rnk.id = tc.rank
+ LEFT JOIN taxon_concept kdc ON kdc.id = oc.kingdom_concept_id
+ LEFT JOIN taxon_name kdn ON kdn.id = kdc.taxon_name_id
+ LEFT JOIN taxon_concept phc ON phc.id = oc.phylum_concept_id
+ LEFT JOIN taxon_name phn ON phn.id = phc.taxon_name_id
+ LEFT JOIN taxon_concept clc ON clc.id = oc.class_concept_id
+ LEFT JOIN taxon_name cln ON cln.id = clc.taxon_name_id
+ LEFT JOIN taxon_concept odc ON odc.id = oc.order_concept_id
+ LEFT JOIN taxon_name odn ON odn.id = odc.taxon_name_id
+ LEFT JOIN taxon_concept fmc ON fmc.id = oc.family_concept_id
+ LEFT JOIN taxon_name fmn ON fmn.id = fmc.taxon_name_id
+ LEFT JOIN taxon_concept gnc ON gnc.id = oc.genus_concept_id
+ LEFT JOIN taxon_name gnn ON gnn.id = gnc.taxon_name_id
+ LEFT JOIN taxon_concept spc ON spc.id = oc.species_concept_id
+ LEFT JOIN taxon_name spn ON spn.id = spc.taxon_name_id
+ LEFT JOIN typification_record typ ON typ.occurrence_id = oc.id
+ LEFT JOIN identifier_record idr ON idr.occurrence_id = oc.id
+ LEFT JOIN lookup_identifier_type lit ON lit.it_key = idr.identifier_type
+ WHERE oc.data_resource_id = 56"> <!-- where data_resource_id = 71 -->
+ <entity name="state" query="select st.name
+ FROM geo_mapping gm
+ LEFT JOIN geo_region st ON st.id = gm.geo_region_id AND st.region_type &lt;= 2
+ WHERE gm.occurrence_id=${occurrence.id}">
+ <field column="name" name="state"/>
+ </entity>
+ <entity name="biogeographic_region" query="select bgr.name
+ FROM geo_mapping gm
+ LEFT JOIN geo_region bgr ON bgr.id = gm.geo_region_id AND bgr.region_type = 2000
+ WHERE gm.occurrence_id=${occurrence.id}">
+ <field column="name" name="biogeographic_region"/>
+ </entity>
+ <entity name="places" query="select plc.name
+ FROM geo_mapping gm
+ LEFT JOIN geo_region plc ON plc.id = gm.geo_region_id AND (plc.region_type &gt;= 3 AND plc.region_type &lt;= 11)
+ WHERE gm.occurrence_id=${occurrence.id}">
+ <field column="name" name="places"/>
+ </entity>
+ </entity>
+ </document>
+</dataConfig>
diff --git a/docker/solr8/conf/elevate.xml b/docker/solr8/conf/elevate.xml
@@ -0,0 +1,36 @@
+<?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:https://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.
+-->
+
+<!-- If this file is found in the config directory, it will only be
+ loaded once at startup. If it is found in Solr's data
+ directory, it will be re-loaded every commit.
+-->
+
+<elevate>
+ <query text="foo bar">
+ <doc id="1" />
+ <doc id="2" />
+ <doc id="3" />
+ </query>
+
+ <query text="ipod">
+ <doc id="MA147LL/A" /> <!-- put the actual ipod at the top -->
+ <doc id="IW-02" exclude="true" /> <!-- exclude this cable -->
+ </query>
+
+</elevate>