submit-cgap 0.8.0

Support for uploading file submissions to the Clinical Genomics Analysis Platform (CGAP).

A file submission tool for CGAP

Description

This is a tool for uploading certain kinds of files to CGAP.

Current support is for “metadata bundles” and “gene lists”. “Metadata bundles” are Excel files (.xlsx) accompanied by other files (such as .fastq.gz files). “Gene lists” are either Excel files (.xlsx) or plain text (.txt) files.

About Metadata Bundles

“Metadata bundles” are Excel files (.xlsx) accompanied by other files (such as .fastq.gz files).

Note: The format of the Excel files that are used as “metadata bundles” is not yet documented. For now you should begin by obtaining a template file from your contact on the CGAP Team and then customize that as appropriate.

Installation

Installing this system involves these steps:

1. Create, install, and activate a virtual environment.

2. Install poetry

3. Only if you are a developer, select the source repository. Others will not have a source repository to select, so should skip this step.

4. If you are an end user, do “pip install submit_cgap”. Otherwise, do “make build”.

5. Set up a ~/.cgap-keys.json credentials file.

For detailed information about these installation steps, see Installing SubmitCGAP.

Testing

To run unit tests, do:

$ make test

Additional notes on testing these scripts for release can be found in Testing SubmitCGAP.

Getting Started

Once poetry has finished installing this library into your virtual environment, you should have access to the submit-metadata-bundle and the submit-genelist commands.

Metadata Bundles

For help about arguments, do:

submit-metadata-bundle --help

However, it should suffice for many cases to specify the bundle file you want to upload and either a site or a CGAP beanstalk environment. For example:

submit-metadata-bundle mymetadata.xls

This command should do everything, including upload referenced files if they are in the same directory. (It will ask for confirmation.)

To invoke it for validation only, without submitting anything, do:

submit-metadata-bundle mymetadata.xls --validate_only

You can resume execution with the upload part by doing:

resume-uploads <uuid> --env <env>

or:

resume-uploads <uuid> --server <server>

You can upload individual files separately by doing:

upload-item-data <filename> --uuid <item-uuid> --env <env>

or:

upload-item-data <filename> --uuid <item-uuid> --server <server>

where the <item-uuid> is the uuid for the individual item, not the metadata bundle.

Gene Lists

The submit-genelist command shares similar features with submit-metadata-bundle. For help about arguments, do:

submit-genelist --help

and to submit a gene list for validation only, do:

submit-genelist --validate-only

For most situations, simply specify the gene list you want to upload, e.g.:

submit-genelist mygenelist.xlsx