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

set -x

env

# init GCS Fuse directory
if [ "$DEPLOY_TO_PREFIX" = 'gcloud' ]
then
    mkdir -p /mounted-bucket/exomiser/exomiser-cli-8.0.0/data/phenix
fi

cd /matchbox_deployment/config/
wget https://storage.googleapis.com/matchbox-mounted-bucket/gene_symbol_to_ensembl_id_map.txt

cd /matchbox_deployment

java -jar \
    -Dallow.no-gene-in-common.matches=$ALLOW_NO_GENE_IN_COMMON_MATCHES \
    -Dexomiser.data-directory=$EXOMISER_DATA_DIR \
    -Dspring.data.mongodb.host=$MONGO_SERVICE_HOSTNAME \
    -Dspring.data.mongodb.port=$MONGO_SERVICE_PORT \
    -Dspring.data.mongodb.database=$MONGODB_DATABASE \
    matchbox-0.1.0.jar &

sleep 10000000000
<commit_msg>updated path of gene name file. Matchbox is now running!<commit_after>#!/usr/bin/env bash

set -x

env

# init GCS Fuse directory
if [ "$DEPLOY_TO_PREFIX" = 'gcloud' ]
then
    mkdir -p /mounted-bucket/exomiser/exomiser-cli-8.0.0/data/phenix
fi

cd /
wget https://storage.googleapis.com/matchbox-mounted-bucket/gene_symbol_to_ensembl_id_map.txt

cd /matchbox_deployment

java -jar \
    -Dallow.no-gene-in-common.matches=$ALLOW_NO_GENE_IN_COMMON_MATCHES \
    -Dexomiser.data-directory=$EXOMISER_DATA_DIR \
    -Dspring.data.mongodb.host=$MONGO_SERVICE_HOSTNAME \
    -Dspring.data.mongodb.port=$MONGO_SERVICE_PORT \
    -Dspring.data.mongodb.database=$MONGODB_DATABASE \
    -Dmatchbox.gene-symbol-to-id-mappings=/gene_symbol_to_ensembl_id_map.txt \
    matchbox-0.1.0.jar &

sleep 10000000000

{'fraction_non_alphanumeric': 0.12173913043478261, 'fraction_numerical': 0.02274247491638796, 'mean_word_length': 3.9536423841059603, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 2, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 2, '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': '7540464', 'n_tokens_mistral': 656, 'n_tokens_neox': 604, 'n_words': 75}