From 20bf64b8e9391d16fe569529f365cccff99a8e50 Mon Sep 17 00:00:00 2001
From: John van Breda <john.vanbreda@biodiverseit.co.uk>
Date: Fri, 25 Oct 2019 14:48:55 +0100
Subject: [PATCH] Adds taxonomic data to ES output reports

Used when a taxon cannot be looked up in taxa.yml (e.g. non-standard taxonomy).
---
 reports/library/occurrences/list_for_elastic.xml    | 13 +++++++++++++
 .../library/occurrences/list_for_elastic_all.xml    | 13 +++++++++++++
 .../occurrences/list_for_elastic_sensitive.xml      | 13 +++++++++++++
 .../occurrences/list_for_elastic_sensitive_all.xml  | 13 +++++++++++++
 4 files changed, 52 insertions(+)

diff --git a/reports/library/occurrences/list_for_elastic.xml b/reports/library/occurrences/list_for_elastic.xml
index 17f5d51812..a2305f4ebf 100644
--- a/reports/library/occurrences/list_for_elastic.xml
+++ b/reports/library/occurrences/list_for_elastic.xml
@@ -24,6 +24,7 @@
     JOIN cache_samples_nonfunctional snf ON snf.id=o.sample_id
     JOIN taxa_taxon_lists ttl ON ttl.id=o.taxa_taxon_list_id
     JOIN taxa t ON t.id=ttl.taxon_id
+    LEFT JOIN cache_taxa_taxon_lists cttl ON cttl.id=o.taxa_taxon_list_id
     LEFT JOIN locations l on l.id=o.location_id AND l.deleted=false
     LEFT JOIN samples sp on sp.id=o.parent_sample_id AND sp.deleted=false
     LEFT JOIN locations lp on lp.id=sp.location_id AND lp.deleted=false
@@ -178,5 +179,17 @@
     <column name="occurrence_attrs_json" sql="onf.attrs_json" datatype="text" />
     <column name="tracking" sql="o.tracking" datatype="integer" />
     <column name="input_form" sql="o.input_form" datatype="text" />
+    <!-- Taxon info should get overwritten by master list data, but obtain default values to use just in case not
+      properly mapped -->
+    <column name="taxon_name" sql="cttl.taxon" datatype="text" />
+    <column name="taxon_authority" sql="cttl.authority" datatype="text" />
+    <column name="taxon_group_id" sql="cttl.taxon_group_id" datatype="integer" />
+    <column name="taxon_group" sql="cttl.taxon_group" datatype="text" />
+    <column name="common_name" sql="cttl.default_common_name" datatype="text" />
+    <column name="taxon_rank" sql="cttl.taxon_rank" datatype="text" />
+    <column name="taxon_rank_sort_order" sql="cttl.taxon_rank_sort_order" datatype="integer" />
+    <column name="taxon_kingdom" sql="cttl.kingdom_taxon" datatype="integer" />
+    <column name="taxon_order" sql="cttl.order_taxon" datatype="integer" />
+    <column name="taxon_family" sql="cttl.order_taxon" datatype="integer" />
   </columns>
 </report>
\ No newline at end of file
diff --git a/reports/library/occurrences/list_for_elastic_all.xml b/reports/library/occurrences/list_for_elastic_all.xml
index 3fbf5cb9be..10210a9449 100644
--- a/reports/library/occurrences/list_for_elastic_all.xml
+++ b/reports/library/occurrences/list_for_elastic_all.xml
@@ -23,6 +23,7 @@
     JOIN cache_samples_nonfunctional snf ON snf.id=o.sample_id
     JOIN taxa_taxon_lists ttl ON ttl.id=o.taxa_taxon_list_id
     JOIN taxa t ON t.id=ttl.taxon_id
+    LEFT JOIN cache_taxa_taxon_lists cttl ON cttl.id=o.taxa_taxon_list_id
     LEFT JOIN locations l on l.id=o.location_id AND l.deleted=false
     LEFT JOIN samples sp on sp.id=o.parent_sample_id AND sp.deleted=false
     LEFT JOIN locations lp on lp.id=sp.location_id AND lp.deleted=false
@@ -177,5 +178,17 @@
     <column name="occurrence_attrs_json" sql="onf.attrs_json" datatype="text" />
     <column name="tracking" sql="o.tracking" datatype="integer" />
     <column name="input_form" sql="o.input_form" datatype="text" />
+    <!-- Taxon info should get overwritten by master list data, but obtain default values to use just in case not
+      properly mapped -->
+    <column name="taxon_name" sql="cttl.taxon" datatype="text" />
+    <column name="taxon_authority" sql="cttl.authority" datatype="text" />
+    <column name="taxon_group_id" sql="cttl.taxon_group_id" datatype="integer" />
+    <column name="taxon_group" sql="cttl.taxon_group" datatype="text" />
+    <column name="common_name" sql="cttl.default_common_name" datatype="text" />
+    <column name="taxon_rank" sql="cttl.taxon_rank" datatype="text" />
+    <column name="taxon_rank_sort_order" sql="cttl.taxon_rank_sort_order" datatype="integer" />
+    <column name="taxon_kingdom" sql="cttl.kingdom_taxon" datatype="integer" />
+    <column name="taxon_order" sql="cttl.order_taxon" datatype="integer" />
+    <column name="taxon_family" sql="cttl.order_taxon" datatype="integer" />
   </columns>
 </report>
\ No newline at end of file
diff --git a/reports/library/occurrences/list_for_elastic_sensitive.xml b/reports/library/occurrences/list_for_elastic_sensitive.xml
index 3f5c7995c8..202b99840e 100644
--- a/reports/library/occurrences/list_for_elastic_sensitive.xml
+++ b/reports/library/occurrences/list_for_elastic_sensitive.xml
@@ -26,6 +26,7 @@
     JOIN cache_samples_nonfunctional snf ON snf.id=o.sample_id
     JOIN taxa_taxon_lists ttl ON ttl.id=o.taxa_taxon_list_id
     JOIN taxa t ON t.id=ttl.taxon_id
+    LEFT JOIN cache_taxa_taxon_lists cttl ON cttl.id=o.taxa_taxon_list_id
     JOIN samples s on s.id=o.sample_id AND s.deleted=false
     LEFT JOIN locations l ON l.id=s.location_id AND l.deleted=false
     LEFT JOIN samples sp ON sp.id=s.parent_id AND sp.deleted=false
@@ -175,5 +176,17 @@
     <column name="occurrence_attrs_json" sql="onf.attrs_json" datatype="text" />
     <column name="tracking" sql="o.tracking" datatype="integer" />
     <column name="input_form" sql="o.input_form" datatype="text" />
+    <!-- Taxon info should get overwritten by master list data, but obtain default values to use just in case not
+      properly mapped -->
+    <column name="taxon_name" sql="cttl.taxon" datatype="text" />
+    <column name="taxon_authority" sql="cttl.authority" datatype="text" />
+    <column name="taxon_group_id" sql="cttl.taxon_group_id" datatype="integer" />
+    <column name="taxon_group" sql="cttl.taxon_group" datatype="text" />
+    <column name="common_name" sql="cttl.default_common_name" datatype="text" />
+    <column name="taxon_rank" sql="cttl.taxon_rank" datatype="text" />
+    <column name="taxon_rank_sort_order" sql="cttl.taxon_rank_sort_order" datatype="integer" />
+    <column name="taxon_kingdom" sql="cttl.kingdom_taxon" datatype="integer" />
+    <column name="taxon_order" sql="cttl.order_taxon" datatype="integer" />
+    <column name="taxon_family" sql="cttl.order_taxon" datatype="integer" />
   </columns>
 </report>
\ No newline at end of file
diff --git a/reports/library/occurrences/list_for_elastic_sensitive_all.xml b/reports/library/occurrences/list_for_elastic_sensitive_all.xml
index 330fdddfec..2ffbb585d6 100644
--- a/reports/library/occurrences/list_for_elastic_sensitive_all.xml
+++ b/reports/library/occurrences/list_for_elastic_sensitive_all.xml
@@ -25,6 +25,7 @@
     JOIN cache_samples_nonfunctional snf ON snf.id=o.sample_id
     JOIN taxa_taxon_lists ttl ON ttl.id=o.taxa_taxon_list_id
     JOIN taxa t ON t.id=ttl.taxon_id
+    LEFT JOIN cache_taxa_taxon_lists cttl ON cttl.id=o.taxa_taxon_list_id
     JOIN samples s on s.id=o.sample_id AND s.deleted=false
     LEFT JOIN locations l ON l.id=s.location_id AND l.deleted=false
     LEFT JOIN samples sp ON sp.id=s.parent_id AND sp.deleted=false
@@ -174,5 +175,17 @@
     <column name="occurrence_attrs_json" sql="onf.attrs_json" datatype="text" />
     <column name="tracking" sql="o.tracking" datatype="integer" />
     <column name="input_form" sql="o.input_form" datatype="text" />
+    <!-- Taxon info should get overwritten by master list data, but obtain default values to use just in case not
+      properly mapped -->
+    <column name="taxon_name" sql="cttl.taxon" datatype="text" />
+    <column name="taxon_authority" sql="cttl.authority" datatype="text" />
+    <column name="taxon_group_id" sql="cttl.taxon_group_id" datatype="integer" />
+    <column name="taxon_group" sql="cttl.taxon_group" datatype="text" />
+    <column name="common_name" sql="cttl.default_common_name" datatype="text" />
+    <column name="taxon_rank" sql="cttl.taxon_rank" datatype="text" />
+    <column name="taxon_rank_sort_order" sql="cttl.taxon_rank_sort_order" datatype="integer" />
+    <column name="taxon_kingdom" sql="cttl.kingdom_taxon" datatype="integer" />
+    <column name="taxon_order" sql="cttl.order_taxon" datatype="integer" />
+    <column name="taxon_family" sql="cttl.order_taxon" datatype="integer" />
   </columns>
 </report>
\ No newline at end of file