Merge pull request #20 from unipept/upgrade_db_scripts

cleanup database upgrade scripts
unipept · Jun 8, 2021 · 9b81b21 · 9b81b21
2 parents 48e24fe + 8c51db0
commit 9b81b21
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Showing 15 changed files with 426 additions and 35 deletions.
diff --git a/database/data.sql → database/misc/data.sql b/database/data.sql → database/misc/data.sql
@@ -8,4 +8,3 @@ INSERT INTO `unipept`.`users` (`id`, `username`, `admin`) VALUES (2, 'pdawyndt',
 INSERT INTO `unipept`.`users` (`id`, `username`, `admin`) VALUES (3, 'guest', 0);
 
 COMMIT;
-
diff --git a/database/db_model.mwb → database/misc/db_model.mwb b/database/db_model.mwb → database/misc/db_model.mwb
diff --git a/database/headers.md → database/misc/headers.md b/database/headers.md → database/misc/headers.md
diff --git a/database/load_compress.sh → database/misc/load_compress.sh b/database/load_compress.sh → database/misc/load_compress.sh
diff --git a/database/sample_data.sql → database/misc/sample_data.sql b/database/sample_data.sql → database/misc/sample_data.sql
diff --git a/database/structure_index_only.sql → database/misc/structure_index_only.sql b/database/structure_index_only.sql → database/misc/structure_index_only.sql
diff --git a/database/structure_no_index.sql → database/misc/structure_no_index.sql b/database/structure_no_index.sql → database/misc/structure_no_index.sql
diff --git a/database/structure_no_index_compress.sql → ...base/misc/structure_no_index_compress.sql b/database/structure_no_index_compress.sql → ...base/misc/structure_no_index_compress.sql
diff --git a/database/swap_databases.sql b/database/swap_databases.sql
diff --git a/database/upgrade/README.md b/database/upgrade/README.md
@@ -0,0 +1,3 @@
+This file contains all scripts, completely preconfigured, to upgrade the database on our Unipept production server. See
+the main [Unipept wiki](https://github.com/unipept/unipept/wiki/Update-Unipept-database) for more information on how 
+to do this.
diff --git a/database/index.sh → database/upgrade/index.sh b/database/index.sh → database/upgrade/index.sh
@@ -17,7 +17,7 @@ function print {
 function doCmd {
     echo -n "-> "
     print "$1"
-    echo $1 | mysql -u unipept -punipept unipept 2>&1 | sed "s/^/   /" | grep -v "Using a password on the command line interface can be insecure" | tee -a $logfile
+    echo $1 | mysql -u unipept -punipept unipept2 2>&1 | sed "s/^/   /" | grep -v "Using a password on the command line interface can be insecure" | tee -a $logfile
 }
 
 

diff --git a/database/load.sh → database/upgrade/load.sh b/database/load.sh → database/upgrade/load.sh
@@ -2,12 +2,15 @@
 # extracts all .tsv.gz files, imports them into the unipept database
 # and removes the files
 
-db=unipept
+# Directory from which the .tsv.gz files should be read and parsed (= first argument to this script).
+dir="$1"
+db=unipept2
 
 function print {
     echo $(date -u) $1
 }
 
+cd "$dir"
 
 for file in *.tsv.gz
 do
@@ -17,3 +20,5 @@ do
     zcat $file | mysql  --local-infile=1 -uunipept -punipept $db -e "LOAD DATA LOCAL INFILE '/dev/stdin' INTO TABLE $tbl;SHOW WARNINGS" 2>&1
 done
 print "done"
+
+cd -
diff --git a/database/structure.sql → database/upgrade/structure.sql b/database/structure.sql → database/upgrade/structure.sql
Original file line number	Diff line number	Diff line change
Expand Up		@@ -8,4 +8,3 @@ INSERT INTO `unipept`.`users` (`id`, `username`, `admin`) VALUES (2, 'pdawyndt',
		INSERT INTO `unipept`.`users` (`id`, `username`, `admin`) VALUES (3, 'guest', 0);

		COMMIT;