From 16f32b5e8a016dafd2cd09314a63506916f4fe1d Mon Sep 17 00:00:00 2001
From: EL KARCHI Jad <jad.el-karchi@inria.fr>
Date: Fri, 21 Mar 2025 10:41:24 +0100
Subject: [PATCH] remove add, remove, status commands, testing file push, fetch
on rlabkey
---
.gitlab-ci.yml | 9 +++++----
bash/rlabkey | 55 +-------------------------------------------------
2 files changed, 6 insertions(+), 58 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 8047c8a..dd6b164 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -6,8 +6,8 @@ stages :
variables:
PACKAGE_REGISTRY_PROJECT_ID: $CI_PROJECT_ID
PACKAGE_REGISTRY_URL: "$CI_API_V4_URL/projects/$PACKAGE_REGISTRY_PROJECT_ID/packages/generic"
- LATEST_TAG : git describe --tags | head -n 1 | cut -d'-' -f1
- ARCHIVE_PATH : ../rlabkey-cli_1.0.0.tar.gz
+ LATEST_TAG : 1.0.0
+ ARCHIVE_PATH : ../rlabkey-cli_$LATEST_TAG.tar.gz
upload_to_registry:
stage: publish
@@ -17,8 +17,9 @@ upload_to_registry:
- echo "Starting upload & archiving of project files to the GitLab Package Registry..."
- echo $LATEST_TAG
- rm -rf ./.git/ .git* ./docs
- - mkdir -p rlabkey-cli && cp -r ./* ./rlabkey-cli/
- - tar -czvf $ARCHIVE_PATH ./rlabkey-cli/
+ - mkdir -p rlabkey-cli_$LATEST_TAG
+ - mv ./* ./rlabkey-cli_$LATEST_TAG/
+ - tar -czvf $ARCHIVE_PATH ./rlabkey-cli_$LATEST_TAG/
- |
filename=$(basename "$ARCHIVE_PATH" .tar.gz);
base_name=$(echo "$filename" | cut -d'_' -f1)
diff --git a/bash/rlabkey b/bash/rlabkey
index b42e933..1366585 100644
--- a/bash/rlabkey
+++ b/bash/rlabkey
@@ -76,8 +76,6 @@ init_config() {
mkdir -p "$RLABKEY_DIR/config/" || error "Failed to create config directory."
echo "_webdav folder created."
mkdir -p "$RLABKEY_DIR/_webdav/" || error "Failed to create Files directory."
- echo "target folder created."
- mkdir -p "$RLABKEY_DIR/target/" || error "Failed to create Target directory."
touch "$CONFIG_FILE" || error "Failed to create config file."
echo "Configuration initialized at $CONFIG_FILE"
}
@@ -181,15 +179,8 @@ case "$1" in
word="ASSAY"
fi
- echo "Uploading available files as $word to project $PROJECT:"
- echo
- ls $RLABKEY_DIR/target/
- echo
- echo -n "Are you sure you want to upload ? (Y/n): "
- read -r response
-
if [[ "$response" =~ ^([yY][eE][sS]|[yY])$ ]]; then
- for file in "$RLABKEY_DIR/target"/*; do
+ for file in "$DIR"/*; do
echo "Uploading $(basename "$file") as $word ..."
Rscript $RLABKEY_DIR/R/push.R "$PROJECT" "$file" $(basename "$file") "$ASSAY" "$DATASET" || error "Failed to push file: $file"
done
@@ -199,20 +190,6 @@ case "$1" in
fi
fi
;;
- status)
- shift
- # Check for status-specific help
- if [[ "$1" == "--help" || "$1" == "-h" ]]; then
- show_status_help
- exit 0
- fi
- echo "Ready to push datasets :"
- echo
- ls $RLABKEY_DIR/target/
- echo
-
- Rscript $RLABKEY_DIR/R/status.R || error "Failed to execute status command."
- ;;
init)
# Check for init-specific help
@@ -232,36 +209,6 @@ case "$1" in
echo "RLabKey CLI - Version $VERSION"
;;
- add)
- shift
- FILE=""
-
- while [[ $# -gt 0 ]]; do
- case "$1" in
- --file)
- FILE="$2"
- shift 2
- ;;
- *)
- error "Unknown option: $1"
- ;;
- esac
- done
-
- cp $FILE $RLABKEY_DIR/target/ && echo "$FILE copied to target."
- ;;
-
- remove)
- shift
- FILE=""
-
- if [[ -n $1 ]]; then
- FILE=$1
- fi
-
- rm "$RLABKEY_DIR/target/$FILE" && echo "$1 removed from target."
- ;;
-
*)
if [[ -z "$1" ]]; then
show_help
--
GitLab