<commit_before>#!/bin/sh
logdir="/shared/data/download_logs/"
if [ ! -d $logdir ]
then
	mkdir -p $logdir
fi
tempname="temp_log.txt"
tempfile=$logdir/$tempname
shared_data="/shared/data"
config_file="./resources/get_scripts.config"
rm $tempfile
echo "==========================================================="
echo "Getting Fly Anatomy Ontology"
./get_fly_anatomy_ontology $logdir $tempname $shared_data
echo "==========================================================="
echo
echo "==========================================================="
echo "Getting FlyAtlas"
./get_flyatlas $logdir $tempname $shared_data
echo "==========================================================="
echo
echo "==========================================================="
echo "Getting go annotation"
./get_go-annotation $logdir $tempname $shared_data $config_file
echo "==========================================================="
echo
echo "==========================================================="
echo "Getting intact data"
./get_intact $logdir $tempname $shared_data $config_file
echo "==========================================================="
echo
echo "==========================================================="
echo "Getting KEGG data"
./get_kegg $logdir $tempname $shared_data
echo "==========================================================="
echo
echo "==========================================================="
echo "Getting wormbase identifiers"
./get_wormbase_identifiers $logdir $tempname $shared_data
echo "==========================================================="
echo
echo "==========================================================="
echo "Getting wormbase rnai"
./get_wormbase_rnai $logdir $tempname $shared_data
echo "==========================================================="
echo
echo "==========================================================="
echo "Getting pubmed data"
./get_ncbi_pubmed $logdir $tempname $shared_data $config_file
echo "==========================================================="
echo 
echo "==========================================================="<commit_msg>removed worm RNAi from get_all script.<commit_after>#!/bin/sh
logdir="/shared/data/download_logs/"
if [ ! -d $logdir ]
then
	mkdir -p $logdir
fi
tempname="temp_log.txt"
tempfile=$logdir/$tempname
shared_data="/shared/data"
config_file="./resources/get_scripts.config"
rm $tempfile
echo "==========================================================="
echo "Getting Fly Anatomy Ontology"
./get_fly_anatomy_ontology $logdir $tempname $shared_data
echo "==========================================================="
echo
echo "==========================================================="
echo "Getting FlyAtlas"
./get_flyatlas $logdir $tempname $shared_data
echo "==========================================================="
echo
echo "==========================================================="
echo "Getting go annotation"
./get_go-annotation $logdir $tempname $shared_data $config_file
echo "==========================================================="
echo
echo "==========================================================="
echo "Getting intact data"
./get_intact $logdir $tempname $shared_data $config_file
echo "==========================================================="
echo
echo "==========================================================="
echo "Getting KEGG data"
./get_kegg $logdir $tempname $shared_data
echo "==========================================================="
echo
echo "==========================================================="
echo "Getting wormbase identifiers"
./get_wormbase_identifiers $logdir $tempname $shared_data
echo "==========================================================="
echo
echo "==========================================================="
echo "Getting pubmed data"
./get_ncbi_pubmed $logdir $tempname $shared_data $config_file
echo "==========================================================="
echo 
echo "==========================================================="
{'fraction_non_alphanumeric': 0.5350920856147336, 'fraction_numerical': 0.0, 'mean_word_length': 11.718354430379748, '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': 2, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6473729', 'n_tokens_mistral': 968, 'n_tokens_neox': 832, 'n_words': 210}