cidc-cli

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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

Release files for cidc-cli 0.10.2

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for cidc-cli 0.10.2
File	Size	Uploaded
cidc_cli-0.10.2.tar.gz	41.6 kB	Oct 27, 2022	Details

Built distribution (wheel)

Table of built distributions (wheels) for cidc-cli 0.10.2
File	Interpreter	ABI	Platform	Reset
cidc_cli-0.10.2-py3-none-any.whl 50.8 kB Oct 27, 2022	Python 3	none	any	Details

Total release size: 92.4 kB

Release files / cidc_cli-0.10.2.tar.gz

Download URL	cidc_cli-0.10.2.tar.gz
Size	41.6 kB
Tags	Source
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Upload date	Oct 27, 2022
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.1 CPython/3.9.15`

Release files / cidc_cli-0.10.2-py3-none-any.whl

Download URL	cidc_cli-0.10.2-py3-none-any.whl
Size	50.8 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`5172a7e568cad89a7cbbfcbbfc73e55679db57a70f91aa2a3b314975db3a05f2`
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Upload date	Oct 27, 2022
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.1 CPython/3.9.15`