feat(rr): add zenodo database uploader

libs/jump_rr/src/tools/upload_databases.sh

@@ -0,0 +1,87 @@
+# Find the latest version of the dataset
+ZENODO_ENDPOINT="https://zenodo.org"
+DEPOSITION_PREFIX="${ZENODO_ENDPOINT}/api/deposit/depositions"
+ORIGINAL_ID="12775236"
+DIR_TO_VERSION="src/jump_rr/databases"
+
+if [ -z "${ORIGINAL_ID}" ]; then # Only get latest id when provided an original one
+    echo "Creating new deposition"
+    DEPOSITION_ENDPOINT="${DEPOSITION_PREFIX}"
+else # Update existing dataset
+    echo "Creating new version"
+    LATEST_ID=$(curl "${ZENODO_ENDPOINT}/records/${ORIGINAL_ID}/latest" |
+		    grep records | sed 's/.*href=".*\.org\/records\/\(.*\)".*/\1/')
+    DEPOSITION_ENDPOINT="${DEPOSITION_PREFIX}/${LATEST_ID}/actions/newversion"
+fi
+
+
+if [ -z "${ZENODO_TOKEN}" ]; then # Check Zenodo Token
+    echo "Access token not available"
+    exit 1
+else
+    echo "Access token found."
+fi
+
+
+# Create new deposition
+DEPOSITION=$(curl -H "Content-Type: application/json" \
+		  -X POST\
+		  --data "{}" \
+		  "${DEPOSITION_ENDPOINT}?access_token=${ZENODO_TOKEN}"\
+		 | jq .id)
+echo "New deposition ID is ${DEPOSITION}"
+
+# Variables
+BUCKET_DATA=$(curl "${DEPOSITION_PREFIX}/$DEPOSITION?access_token=$ZENODO_TOKEN")
+BUCKET=$(echo "${BUCKET_DATA}" | jq --raw-output .links.bucket)
+
+if [ "${BUCKET}" = "null" ]; then
+    echo "Could not find URL for upload. Response from server:"
+    echo "${BUCKET_DATA}"
+    exit 1
+fi
+
+# Upload file
+echo "Uploading files to bucket ${BUCKET}"
+for FILE_TO_VERSION in $(find "${DIR_TO_VERSION}" -name '*.parquet'); do
+    echo "${FILE_TO_VERSION}"
+    curl --retry 5 \
+	 --retry-delay 5 \
+	 -o /dev/null \
+	 --upload-file ${FILE_TO_VERSION} \
+	 "${BUCKET}/${FILE_TO_VERSION##*/}?access_token=${ZENODO_TOKEN}"
+done
+
+
+# Upload Metadata
+echo -e '{"metadata": {
+    "title": "Processed JUMP Datasets: For Web and programmatic exploration.",
+    "creators": [
+        {
+            "name": "Alán F. Muñoz"
+        }
+    ],
+"description":"
+This dataset provides multiple tables for JUMP exploration:
+- Full datasets contain precomputed analysis: - significance - is the phenotypic activity of a given value (see broad.io/crispr_feature for a formal definition), while distance contains the cosine distance of all perturbations vs all other perturbations within a given dataset.
+- The 'features' and 'matches' files contain a selection of the raw precomputed analyses and are intended for consumption on a web browser through the Datasette tool (see broad.io/jump-explore for details).
+- Lastly, 'galleries' are for quick visualization of the images with all channels collapsed into one.",
+"upload_type": "dataset",
+"access_right": "open"
+}}' > metadata.json
+
+NEW_DEPOSITION_ENDPOINT="${DEPOSITION_PREFIX}/${DEPOSITION}"
+echo "Uploading file to ${NEW_DEPOSITION_ENDPOINT}"
+curl -H "Content-Type: application/json" \
+     -X PUT\
+     --data @metadata.json \
+     "${NEW_DEPOSITION_ENDPOINT}?access_token=${ZENODO_TOKEN}"
+
+# Publish
+echo "Publishing to ${NEW_DEPOSITION_ENDPOINT}"
+curl -H "Content-Type: application/json" \
+     -X POST\
+     --data "{}"\
+     "${NEW_DEPOSITION_ENDPOINT}/actions/publish?access_token=${ZENODO_TOKEN}"\
+    | jq .id
+