d3b-cds-manifest-prep

Installation

Install latest release

pip install git+https://github.com/d3b-center/d3b-cds-manifest-prep.git@latest-release

Install Most Recent Development Version

pip install git+https://github.com/d3b-center/d3b-cds-manifest-prep.git

Data

The most recently generated manifest can be found here.

For development, the unzipped manifest can be found at data/submission_packet

Usage

Generate CDS Submission Manifest

n.b. cds generate --help to get detailed descriptions of options

Generate a submission packet

cds -c $DATABASE_URL generate

This uses the environment variable $DATABASE_URL. This is expected to be a postgres connection url to kidsfirst postgres dataservice.

By default, the file-sample-participant mapping bundled in this package here is used to generate the manifests.

Generate a submission packet using a specific file-sample-participant map

The -f option specifies the seed file-sample-participant map to use.

cds -c $DATABASE_URL generate -f path/to/file_sample_participant_map.csv

generate only a specific manifest in the submission packet

cds -c $DATABASE_URL generate -g sample

This will generate only the sample manifest.

generate specific manifests in the submission packet

cds -c $DATABASE_URL generate -g sample -g participant

This will generate both the sample and participant manifests.

QC a submission manifest

cds -c $DATABASE_URL -d data/submission_packet/ qc

Generate the histologies file

cds -c $D3BWAREHOUSE_URL gen_histologies -o openpedcan_histologies.csv