Exporting tags to a CSV¶

scripts/export-tags.sh writes every paper's tags to a CSV with one row per paper per tag. Run it on the machine that hosts the linXiv-web container; it calls the server at http://127.0.0.1:8086, the port docker-compose.yml publishes.

Needs curl and jq.

Getting the script onto the server¶

Copy it next to your docker-compose.yml:

scp scripts/export-tags.sh server:linxiv-web/
ssh server 'chmod +x linxiv-web/export-tags.sh'

Usage¶

./export-tags.sh                     # writes ./paper-tags-<date>-<time>.csv
./export-tags.sh --out tags.csv      # writes tags.csv
./export-tags.sh --help

Output¶

source_id,tag
"2401.01234","RNA-seq"
"2401.01234","transcriptomics"

source_id is the key the tag endpoints take (/api/papers/{source_id}/tags), so you can use the file to put tags back. Papers without tags have no rows, and a tag repeated on one paper is written once. The script builds the CSV in a temp dir and moves it into place at the end, so a failed run leaves no partial file. When it finishes it prints the row count, paper count and output path to stderr.

Password¶

When the server has auth off, the script does not log in. When it has a password, the script reads it from the file named in LINXIV_WEB_PASSWORD_FILE, or asks for it on the terminal:

LINXIV_WEB_PASSWORD_FILE=/path/to/password.txt ./export-tags.sh

Without a terminal and without LINXIV_WEB_PASSWORD_FILE, the script stops. It also stops if first-run setup is not done; set the password in the web UI first.

The script sends the session cookies as headers, so it works over plain HTTP even with LINXIV_WEB_COOKIE_SECURE=true. If the session is lost during a run (a container restart, for example), it logs in again once and retries.

Exit codes¶

• 0: CSV written.
• 2: bad argument, missing curl or jq, server unreachable, login failed, or a paper list request failed. The message on stderr gives the reason.