Please cite this repository in AMP® SCZ papers as:
Billah T, Cho KIK, Nicholas S, Ennis M, Eichi HR, Bouix S, Baker JT, Accelerating Medicines Partnership® Schizophrenia (AMP® SCZ) Data Processing and Submission Software, https://github.com/AMP-SCZ/utility, 2022, DOI: 10.5281/zenodo.7849718
This repository is the storehouse of all DPdash utility scripts. Currently, it consists of scripts that make DPdash importable files.
Prerequisites are only Python libraries. Install them against Python 3 as:
pip install -r requirements.txt
https://github.com/AMP-SCZ/dpimport and https://github.com/NDAR/nda-tools are two packages used by several programs in this repository. They are put in the requirements.txt too.
Most scripts' usage can be obtained by ./script.* --help.
Some scripts' usage can be obtained by cat ./script.*.
Only outstanding ones are noted below:
remove_collections.js
/data/predict/utility/gen_hash.py /path/to/YA_metadata.csv mriqc > /tmp/mriqc_hashes.txt
mongo --tls --tlsCAFile $state/ssl/ca/cacert.pem --tlsCertificateKeyFile $state/ssl/mongo_client.pem mongodb://dpdash:$MONGO_PASS@`hostname`:27017/dpdata?authSource=admin --eval "hash_script=\"/tmp/mriqc_hashes.txt\"" /data/predict/utility/remove_collections.js
(The back slashes are important: \"/tmp/mriqc_hashes.txt\"
remove_studies.js
mongo --tls --tlsCAFile $state/ssl/ca/cacert.pem --tlsCertificateKeyFile $state/ssl/mongo_client.pem mongodb://dpdash:$MONGO_PASS@`hostname`:27017/dpdata?authSource=admin /data/predict/utility/remove_studies.js
The mechanism for downloading configuration item at server backend is described in this wiki.
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