<commit_before>#!/usr/bin/env bash

set -euo pipefail
IFS=$'\n\t'

export NXF_OPTS='-Dnxf.pool.type=sync -Dnxf.pool.maxThreads=10000'
export SINGULARITY_TMPDIR='/scratch'

[ -d work/tmp] || mkdir -p work/tmp
[ ! -e local.config ] || rm local.config

when=$(date +'%Y-%m-%d')

ln -s local.config weekly-update/update.config

./nextflow -quiet run -with-report "$when-import.html" -profile prod import-data.nf
./nextflow -quiet run -with-report "$when-search.html" -profile prod search-export.nf
<commit_msg>Fixes to weekly update script<commit_after>#!/usr/bin/env bash

set -euo pipefail
IFS=$'\n\t'

export NXF_OPTS='-Dnxf.pool.type=sync -Dnxf.pool.maxThreads=10000'
export SINGULARITY_TMPDIR='/scratch'
export PATH="/nfs/software/singularity/3.5.0/bin:$HOME/.cargo/bin:$PATH"

[ -d work/tmp ] || mkdir -p work/tmp
[ ! -e local.config ] || rm local.config

when=$(date +'%Y-%m-%d')

ln -s weekly-update/update.config local.config 

make rust

./nextflow -quiet run -with-report "$when-import.html" -profile prod import-data.nf
./nextflow -quiet run -with-report "$when-precompute.html" -profile prod precompute.nf
./nextflow -quiet run -with-report "$when-search.html" -profile prod search-export.nf

{'fraction_non_alphanumeric': 0.1723563696919234, 'fraction_numerical': 0.010824313072439634, 'mean_word_length': 3.987551867219917, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '1163217', 'n_tokens_mistral': 476, 'n_tokens_neox': 454, 'n_words': 100}