From d5107ad03322a3bbcdbba7e89988260ccbd4a7c2 Mon Sep 17 00:00:00 2001
From: Kori Kuzma <korikuzma@gmail.com>
Date: Tue, 16 Jul 2024 12:41:03 -0400
Subject: [PATCH] chore: update seqrepo version to 2024-02-20 (#385)

* update docs + elastic beanstalk extensions
---
 .ebextensions/01_app_config.config | 50 +++++++++---------------------
 docs/source/install.rst            |  2 +-
 2 files changed, 15 insertions(+), 37 deletions(-)

diff --git a/.ebextensions/01_app_config.config b/.ebextensions/01_app_config.config
index e1358921..8ee01fd2 100644
--- a/.ebextensions/01_app_config.config
+++ b/.ebextensions/01_app_config.config
@@ -3,46 +3,24 @@ commands:
         command: "yum install -y python-devel postgresql-devel"
     02_install_aws_cli:
         command: "yum install -y awscli"
-    03_install_p7zip:
-        command: "yum install -y p7zip"
-    04_eb_packages:
+    03_eb_packages:
        command: "/var/app/venv/staging-LQM1lest/bin/pip install uvloop websockets httptools typing-extensions"
-    05_export_eb_env_var:
+    04_export_eb_env_var:
         command: "export $(cat /opt/elasticbeanstalk/deployment/env | xargs)"
 
 container_commands:
-    01_cool_seq_tool_permissions:
-        test: test -d "/var/app/venv/staging-LQM1lest/lib/python3.11/site-packages/cool_seq_tool"
-        command: "chmod -R 777 /var/app/venv/staging-LQM1lest/lib/python3.11/site-packages/cool_seq_tool/data"
+    01_s3_download:
+        test: test ! -d "/usr/local/share/seqrepo/2024-02-20"
+        command: "aws s3 cp s3://${AWS_BUCKET_NAME}/${AWS_SEQREPO_OBJECT} /usr/local/share/seqrepo.tar.gz --region us-east-2"
 
-    02_s3_download:
-        test: test ! -d "/usr/local/share/seqrepo"
-        command: "aws s3 cp s3://${AWS_BUCKET_NAME}/${AWS_SEQREPO_OBJECT} /usr/local/share/seqrepo.zip --region us-east-2"
+    02_extract_seqrepo:
+        test: test -f "/usr/local/share/seqrepo.tar.gz"
+        command: "mkdir -p /usr/local/share/seqrepo/2024-02-20 && tar -xzvf /usr/local/share/seqrepo.tar.gz -C /usr/local/share/seqrepo/2024-02-20"
 
-    03_p7zip_seqrepo:
-        test: test -f "/usr/local/share/seqrepo.zip"
-        command: "7za x /usr/local/share/seqrepo.zip -o/usr/local/share -y"
+    03_seqrepo_zip_permission:
+        test: test -f "/usr/local/share/seqrepo.tar.gz"
+        command: "chmod +wr /usr/local/share/seqrepo.tar.gz"
 
-    04_seqrepo_permission:
-        test: test -d "/usr/local/share/seqrepo"
-        command: "chmod -R 777 /usr/local/share/seqrepo"
-
-    05_macosx_permission:
-        test: test -d "/usr/local/share/__MACOSX"
-        command: "chmod -R +wr /usr/local/share/__MACOSX"
-
-    06_seqrepo_zip_permission:
-        test: test -f "/usr/local/share/seqrepo.zip"
-        command: "chmod +wr /usr/local/share/seqrepo.zip"
-
-    07_remove_macosx:
-        test: test -d "/usr/local/share/__MACOSX"
-        command: "rm -R /usr/local/share/__MACOSX"
-
-    08_remove_seqrepo_zip:
-        test: test -f "/usr/local/share/seqrepo.zip"
-        command: "rm /usr/local/share/seqrepo.zip"
-
-    9_data_permission:
-        test: test -d "/usr/local/share/seqrepo"
-        command: "chmod -R +wrx /usr/local/share/seqrepo"
+    04_remove_seqrepo_zip:
+        test: test -f "/usr/local/share/seqrepo.tar.gz"
+        command: "rm /usr/local/share/seqrepo.tar.gz"
diff --git a/docs/source/install.rst b/docs/source/install.rst
index b9978156..5058308d 100644
--- a/docs/source/install.rst
+++ b/docs/source/install.rst
@@ -65,7 +65,7 @@ If you encounter a permission error similar to the one below:
 
 .. code-block::
 
-   PermissionError: [Error 13] Permission denied: '/usr/local/share/seqrepo/2021-01-29._fkuefgd' -> '/usr/local/share/seqrepo/2021-01-29'
+   PermissionError: [Error 13] Permission denied: '/usr/local/share/seqrepo/2024-02-20._fkuefgd' -> '/usr/local/share/seqrepo/2024-02-20'
 
 Try moving data manually with ``sudo``: