Updated the speleothem files for the SISAL work.

Author: SimonGoring

Proposals/publications/clean_offsets.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+uv run src/find_potential_dois.py --limit 30000 --output ./data/offset100.csv
+sed -i.bak '/^.*10\.2172\/6492710.*/d' ./data/offset100.csv

Proposals/speleothem_data/denormalize_sisal.sql

@@ -0,0 +1,56 @@
+SELECT DISTINCT
+    site.*,
+    notes.*,
+    entity.*,
+    entity_link_reference.*,
+    reference.*,
+    depths.*,
+    dating.*,
+    dating_lamina.*,
+    sample.*,
+    hiatus.*,
+    ba_ca.*,
+    mg_ca.*,
+    p_ca.*,
+    sr_ca.*,
+    u_ca.*,
+    sr_isotopes.*,
+    d18o.*,
+    d13c.*,
+    original_chronology.*,
+    sisal_chronology.*,
+    compe.*,
+    composite_link_entity.*,
+    single_ent.*
+FROM
+    site
+LEFT JOIN notes USING (site_id)
+LEFT JOIN entity USING (site_id)
+LEFT JOIN entity_link_reference ON entity.entity_id = entity_link_reference.entity_id
+LEFT JOIN reference USING (ref_id)
+LEFT JOIN (
+    SELECT depth_dating AS depth, entity_id FROM dating
+    UNION DISTINCT
+    SELECT depth_lam AS depth, entity_id FROM dating_lamina
+    UNION DISTINCT
+    SELECT depth_sample AS depth, entity_id FROM sample
+) AS depths ON depths.entity_id = entity.entity_id
+LEFT JOIN dating ON dating.entity_id = entity.entity_id AND dating.depth_dating = depths.depth
+LEFT JOIN dating_lamina ON dating_lamina.entity_id = entity.entity_id AND dating_lamina.depth_lam = depths.depth
+LEFT JOIN sample ON entity.entity_id = sample.entity_id AND sample.depth_sample = depths.depth
+LEFT JOIN hiatus USING (sample_id)
+LEFT JOIN ba_ca USING (sample_id)
+LEFT JOIN mg_ca USING (sample_id)
+LEFT JOIN p_ca USING (sample_id)
+LEFT JOIN sr_ca USING (sample_id)
+LEFT JOIN u_ca USING (sample_id)
+LEFT JOIN sr_isotopes USING (sample_id)
+LEFT JOIN d18o USING (sample_id)
+LEFT JOIN d13c USING (sample_id)
+LEFT JOIN original_chronology USING (sample_id)
+LEFT JOIN sisal_chronology USING (sample_id)
+LEFT JOIN entity compe ON entity.entity_id = compe.entity_id
+LEFT JOIN composite_link_entity ON compe.entity_id = composite_entity_id
+LEFT JOIN entity single_ent ON composite_link_entity.single_entity_id = single_ent.entity_id
+WHERE site.site_id = 316
+ORDER BY entity.entity_id, depths.depth;

Proposals/speleothem_data/speleothem_tables.qmd

@@ -37,7 +37,7 @@ con <- DBI::dbConnect(
   host = Sys.getenv('HOST'),
   port = Sys.getenv('PORT'),
   user = Sys.getenv('USER'),
-  password = Sys.getenv('PASSWORD') # insert your password here
+  password = Sys.getenv('PASSWORD')
 )
 ```