np-upload-validation

np-upload-validation

AWS upload validation

Usage

Install

pip install np-upload-validation

Python

import np_upload_validation

Command-line

np-upload-validation --help

Deployment

Due to limitations on user accounts for the onprem HPC, this package needs to be installed into a singularity container that is then used by a "Job" submitted to the onprem HPC. A docker container would have been preferable but required more permissions than were available at the time of writing this document (11-20-24).

Deploying to hpc

Requires the following environment variables to be present:

• HPC_SIF_LOCATION
• HPC_JOBS_DIR
• HPC_JOB_LOGS_DIR
• OUTPUT_DIR

From the build machine.

make deploy-hpc

If host and build machines are configured you also do it remotely (ssh)

make remote-deploy-hpc

Deploying to windows task scheduler

Automated deployment to windows task scheduler (may require admin access).

• create a directory at: NP_UPLOAD_VALIDATION_WORKING_DIR
• create a directory at: NP_UPLOAD_VALIDATION_OUTPUT_DIR for validation outputs and logs
• validates against directory: NP_UPLOAD_VALIDATION_TARGET_DIR

Default values are

• NP_UPLOAD_VALIDATION_WORKING_DIR: "%USERPROFILE%\Desktop\np-upload-validation"
• NP_UPLOAD_VALIDATION_OUTPUT_DIR: "//allen/programs/mindscope/workgroups/dynamicrouting/PilotEphys/np-upload-validation/"
• NP_UPLOAD_VALIDATION_TARGET_DIR: "//allen/programs/mindscope/workgroups/dynamicrouting/PilotEphys/Task 2 pilot/"

Requires the following variables used by npc-lims, npc-sessions to be present in a .env file in NP_UPLOAD_VALIDATION_WORKING_DIR

• CODE_OCEAN_API_TOKEN
• CODE_OCEAN_DOMAIN (https://codeocean.allenneuraldynamics.org)
• AWS_ACCESS_KEY_ID
• AWS_SECRET_ACCESS_KEY
• AWS_DEFAULT_REGION (us-west-2)

init && init-scheduled

Testing

Unit tests

make test

Onprem integration tests

make test-onprem

Development

See instructions in https://github.com/AllenInstitute/np-upload-validation/CONTRIBUTING.md and the original template: https://github.com/AllenInstitute/copier-pdm-npc/blob/main/README.md

Debugging version divergences

pdm bumpver