From d81a8c332ddf31901648e0d55a0b17aed8e52053 Mon Sep 17 00:00:00 2001
From: Jover Lee <joverlee521@gmail.com>
Date: Fri, 18 Oct 2024 13:47:27 -0700
Subject: [PATCH] Remove `gisaid_epi_isl` from auspice_config JSONs
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Temporarily dropping `gisaid_epi_isl` after discussion on Slack¹
about the duplicate accessions we are seeing with cell/egg passaged
sequences. Once we update the data model to accurately link virus
record and sequence record, we can add it back.

¹ <https://bedfordlab.slack.com/archives/C03KWDET9/p1729271930916079>
---
 config/h1n1pdm/auspice_config.json      | 1 -
 config/h1n1pdm/ha/auspice_config.json   | 1 -
 config/h1n1pdm/na/auspice_config.json   | 1 -
 config/h3n2/auspice_config.json         | 1 -
 config/h3n2/auspice_config_fitness.json | 1 -
 config/h3n2/ha/auspice_config.json      | 1 -
 config/h3n2/na/auspice_config.json      | 1 -
 config/vic/auspice_config.json          | 1 -
 config/vic/ha/auspice_config.json       | 1 -
 config/vic/na/auspice_config.json       | 1 -
 config/yam/auspice_config.json          | 1 -
 11 files changed, 11 deletions(-)

diff --git a/config/h1n1pdm/auspice_config.json b/config/h1n1pdm/auspice_config.json
index 64a2b033..2c049bef 100644
--- a/config/h1n1pdm/auspice_config.json
+++ b/config/h1n1pdm/auspice_config.json
@@ -156,7 +156,6 @@
     "frequencies"
   ],
   "metadata_columns": [
-    "gisaid_epi_isl",
     "accession_ha",
     "accession_na"
   ]
diff --git a/config/h1n1pdm/ha/auspice_config.json b/config/h1n1pdm/ha/auspice_config.json
index 405816da..1ec49fb2 100644
--- a/config/h1n1pdm/ha/auspice_config.json
+++ b/config/h1n1pdm/ha/auspice_config.json
@@ -231,7 +231,6 @@
     "frequencies"
   ],
   "metadata_columns": [
-    "gisaid_epi_isl",
     "accession_ha",
     "accession_na"
   ]
diff --git a/config/h1n1pdm/na/auspice_config.json b/config/h1n1pdm/na/auspice_config.json
index 562344b1..2722f25d 100644
--- a/config/h1n1pdm/na/auspice_config.json
+++ b/config/h1n1pdm/na/auspice_config.json
@@ -196,7 +196,6 @@
     "frequencies"
   ],
   "metadata_columns": [
-    "gisaid_epi_isl",
     "accession_ha",
     "accession_na"
   ]
diff --git a/config/h3n2/auspice_config.json b/config/h3n2/auspice_config.json
index 18dda4d8..0f4016f1 100644
--- a/config/h3n2/auspice_config.json
+++ b/config/h3n2/auspice_config.json
@@ -166,7 +166,6 @@
     "frequencies"
   ],
   "metadata_columns": [
-    "gisaid_epi_isl",
     "accession_ha",
     "accession_na"
   ]
diff --git a/config/h3n2/auspice_config_fitness.json b/config/h3n2/auspice_config_fitness.json
index a9c9793c..e8f568f6 100644
--- a/config/h3n2/auspice_config_fitness.json
+++ b/config/h3n2/auspice_config_fitness.json
@@ -154,7 +154,6 @@
     "frequencies"
   ],
   "metadata_columns": [
-    "gisaid_epi_isl",
     "accession_ha",
     "accession_na"
   ]
diff --git a/config/h3n2/ha/auspice_config.json b/config/h3n2/ha/auspice_config.json
index 1f2c138f..190cadb1 100644
--- a/config/h3n2/ha/auspice_config.json
+++ b/config/h3n2/ha/auspice_config.json
@@ -248,7 +248,6 @@
     "frequencies"
   ],
   "metadata_columns": [
-    "gisaid_epi_isl",
     "accession_ha",
     "accession_na"
   ]
diff --git a/config/h3n2/na/auspice_config.json b/config/h3n2/na/auspice_config.json
index c27f605c..bb551d80 100644
--- a/config/h3n2/na/auspice_config.json
+++ b/config/h3n2/na/auspice_config.json
@@ -181,7 +181,6 @@
     "frequencies"
   ],
   "metadata_columns": [
-    "gisaid_epi_isl",
     "accession_ha",
     "accession_na"
   ]
diff --git a/config/vic/auspice_config.json b/config/vic/auspice_config.json
index 601f4bbd..f86f95f4 100644
--- a/config/vic/auspice_config.json
+++ b/config/vic/auspice_config.json
@@ -141,7 +141,6 @@
     "frequencies"
   ],
   "metadata_columns": [
-    "gisaid_epi_isl",
     "accession_ha",
     "accession_na"
   ]
diff --git a/config/vic/ha/auspice_config.json b/config/vic/ha/auspice_config.json
index 4dd55ace..49039be1 100644
--- a/config/vic/ha/auspice_config.json
+++ b/config/vic/ha/auspice_config.json
@@ -188,7 +188,6 @@
     "frequencies"
   ],
   "metadata_columns": [
-    "gisaid_epi_isl",
     "accession_ha",
     "accession_na"
   ]
diff --git a/config/vic/na/auspice_config.json b/config/vic/na/auspice_config.json
index d925076b..102b7926 100644
--- a/config/vic/na/auspice_config.json
+++ b/config/vic/na/auspice_config.json
@@ -181,7 +181,6 @@
     "frequencies"
   ],
   "metadata_columns": [
-    "gisaid_epi_isl",
     "accession_ha",
     "accession_na"
   ]
diff --git a/config/yam/auspice_config.json b/config/yam/auspice_config.json
index 41439858..4a0d4765 100644
--- a/config/yam/auspice_config.json
+++ b/config/yam/auspice_config.json
@@ -119,7 +119,6 @@
     "frequencies"
   ],
   "metadata_columns": [
-    "gisaid_epi_isl",
     "accession_ha",
     "accession_na"
   ]