cidc-cli 0.10.1

A command-line interface for interacting with the CIDC.

Branch	Status	License
Master

CIDC-CLI

Command line tool for interfacing with the CIDC API.

Setup

Install the CIDC-CLI

pip3 install cidc-cli

Run the CIDC-CLI

To display the help message for the CLI, run:

cidc

To authenticate with the CIDC API, run:

cidc login [token]

Development

For local development, first install the development dependencies:

pip install -r requirements.dev.txt

Then, install and configure the pre-commit hooks:

pre-commit install

JIRA Integration

To set-up the git hook for JIRA integration, run:

ln -s ../../.githooks/commit-msg .git/hooks/commit-msg
chmod +x .git/hooks/commit-msg
rm .git/hooks/commit-msg.sample

This symbolic link is necessary to correctly link files in .githooks to .git/hooks. Note that setting the core.hooksPath configuration variable would lead to pre-commit failing. The commit-msg hook runs after the pre-commit hook, hence the two are de-coupled in this workflow.

To associate a commit with an issue, you will need to reference the JIRA Issue key (For eg 'CIDC-1111') in the corresponding commit message.

Admin functions

Under the (hidden) admin are several functions meant for CIDC administators / engineers.

CSMS

cidc admin test-csms

A simple API hit for a test of CSMS connection. Hits API endpoint /admin/test_csms which in turn gets CSMS's /docs. This tests that the API is able to successfully make connection with the CSMS, as the /docs endpoint requires authorization. As the API endpoint is protected, only users with role cidc-admin can make this request.

dbedit suite

A set of commands to list / remove data from the database, including shipments, clinical data, and assay/analysis data. It directly uses Google's cloud SDK to make a direct connection to the postgres cloud sql database, so it requires the user has cloudsql.instances.connect IAM permission.

Authentication

Authentication uses Application Default Credentials (ADC). Log-in is done via:

gcloud auth application-default login

Configuration

Configuration of the environment ie staging versus production is done as above using:

cidc config get-env
cidc config set-env ENV

Configuration of the database username is done via a pair of functions:

cidc admin get-username
cidc admin set-username USERNAME

The password is requested every time you issue a command so as to not store it.

Listing data

Under the list subcommand of cidc admin, you can get descriptions of the data available in the database.

• cidc admin list clinical TRIAL_ID

  • prints a table describing all shipments for the given trial
  • with the following columns:
    • object_url, filename, num_participants, created, comment

• cidc admin list misc-data TRIAL_ID

  • prints a table describing all misc_data files for the given trial
  • with the following columns:
    • batch_id, object_url, filename, created, description

• cidc admin list shipments TRIAL_ID

  • prints a table describing all shipments for the given trial
  • with the following columns:
    • upload_type, manifest_id, num_samples, created

• cidc admin list assay TRIAL_ID ASSAY_OR_ANALYSIS

  • prints a table listing all samples for the given assay/analysis and trial
  • any of the following values are allowed:
    • clinical_data, same as cidc admin list clinical TRIAL_ID
    • misc_data, same as cidc admin list misc-data TRIAL_ID
    • analyses: atacseq_analysis, ctdna_analysis, cytof_analysis, microbiome_analysis, rna_level1_analysis, tcr_analysis, wes_analysis, wes_analysis_old, wes_tumor_only_analysis, wes_tumor_only_analysis_old
    • assays: atacseq, ctdna, cytof, hande, ihc, elisa, microbiome, mif, nanostring, olink, rna, tcr, wes

Removing data

Under the remove subcommand of cidc admin, you can remove a wide variety of data from the JSON blobs.

• cidc admin remove clinical TRIAL_ID TARGET_ID

  • removes a given clinical data file from a given trial's metadata as well as the file itself from the portal
  • TARGET_ID is the filename of the clinical data to remove, as from cidc admin list clinical TRIAL_ID
    • special value '*' for all files for this trial

• cidc admin remove shipment TRIAL_ID TARGET_ID

  • removes a given shipment from a given trial's metadata
  • TARGET_ID is the manifest_id of the shipment to remove, as from cidc admin list shipments TRIAL_ID

• cidc admin remove assay TRIAL_ID ASSAY_OR_ANALYSIS TARGET_ID

  • removes a given clinical data file from a given trial's metadata as well as the associated files themselves from the portal
  • for ASSAY_OR_ANALYSIS=clinical_data, same as cidc admin remove clinical TRIAL_ID TARGET_ID
  • TARGET_ID is a tuple of the ids to find the data to remove, as from cidc admin list assay TRIAL_ID ASSAY_OR_ANALYSIS.
    • It cannot go past where is divisible in the data, but can end early to remove the whole section.
    • Namely:
      • elisa: requires only assay_run_id
      • misc_data, olink: require batch_id with an optional filename
      • nanostring: requires batch_id and optional run_id
      • rna_level1_analysis, wes_tumor_only_analysis, wes_tumor_only_analysis_old: requires only cimac_id
      • wes_analysis, wes_analysis_old: requires only run_id
      • otherwise: requires batch_id and optional cimac_id