Rename repo, add script

README.md

-# dbnomics-gitlab
+# dbnomics-git-tools
 
-Various tools related to the GitLab installation of DBnomics
+Various tools related to the Git repositories of DBnomics
 
 ## Clone Git repo from static files
 

clone-or-update-storage.sh

+#! /bin/bash
+
+# Clone or update a DBnomics storage directory if it is a Git repository.
+#
+# If it is a "bare" repository and a series.jsonl file is detected, transform it in a normal repository,
+# because series.jsonl purpose is to be used with "fseek", which is not feasible with Git blobs.
+
+set -e
+
+JSON_DATA_BASE_DIR="$1"
+PROVIDER_SLUG="$2"
+
+if [ -z "${PROVIDER_SLUG}" -o -z "${JSON_DATA_BASE_DIR}" ]; then
+    echo "usage: $0 <json_data_dir> <provider_slug>"
+    exit -1
+fi
+
+if [ ! -d "${JSON_DATA_BASE_DIR}" ]; then
+    echo "${JSON_DATA_BASE_DIR} is not a directory"
+    exit -1
+fi
+
+JSON_DATA_BASE_DIR=$(realpath "$1")
+
+REPO_DIR="${JSON_DATA_BASE_DIR}/${PROVIDER_SLUG}-json-data"
+BARE_REPO_DIR="${REPO_DIR}.git"
+
+# By default prefer a bare repository than a normal one.
+if [ ! -d ${REPO_DIR} -a ! -d ${BARE_REPO_DIR} ]; then
+    cd $JSON_DATA_BASE_DIR
+    git clone --bare --quiet https://git.nomics.world/dbnomics-json-data/${PROVIDER_SLUG}-json-data.git
+fi
+
+if [ -d ${REPO_DIR} -a -d ${REPO_DIR}/.git ]; then
+    cd $REPO_DIR
+    time git pull --quiet
+elif [ -d ${BARE_REPO_DIR} ]; then
+    cd $BARE_REPO_DIR
+    time git fetch origin master:master
+fi
+
+if [ -d ${BARE_REPO_DIR} ]; then
+    # Detect if repository has at least one JSON lines file. In this case, re-clone it in normal (non-bare) mode.
+    cd $BARE_REPO_DIR
+    if $(git ls-tree master -r | grep --max-count=1 --quiet series.jsonl); then
+        echo "Bare repository with series.jsonl detected: transforming bare repository into normal one..."
+        cd $JSON_DATA_BASE_DIR
+        git clone ${PROVIDER_SLUG}-json-data.git
+        cd ${PROVIDER_SLUG}-json-data.git
+        ORIGIN_URL=$(git remote get-url origin)
+        cd ../${PROVIDER_SLUG}-json-data
+        git remote set-url origin $ORIGIN_URL
+        cd ..
+        rm -rf ${PROVIDER_SLUG}-json-data.git
+        echo "Repository is now normal: ${REPO_DIR}, bare repository (${BARE_REPO_DIR}) is deleted."
+    fi
+fi