Adds taxonomic data to ES output reports

Used when a taxon cannot be looked up in taxa.yml (e.g. non-standard taxonomy).
Indicia-Team · Oct 25, 2019 · 20bf64b · 20bf64b
1 parent 2f19aac
commit 20bf64b
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diff --git 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>
diff --git 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>
diff --git 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>
diff --git 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>