BIAD/nci-match-workflow-api

Name: nci-match-workflow-api

Owner: NCI CBIIT Development Sandbox

Owner: Biomedical Informatics Applications Development

Description: This repository contains the Matchbox workflow rest services.

Created: 2015-10-22 20:56:37.0

Updated: 2018-02-27 16:55:03.0

Pushed: 2018-03-02 18:59:59.0

Homepage: null

Size: 304

Language: Ruby

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README

NCI-MATCHBox Workflow API

This repository contains the codebase for the following functionalities.

• Storing change request documents.
• Handling trial rejoin request.
• Generating bai file.
• Migrating files from NFS to S3.

To start the Workflow API service, run 'bundle exec rackup'.

Change request example usage

• Upload file:

• curl -v -F “data=@/Users/smithj/git/nci-match-workflow-api/test.txt” http://localhost:9292/changerequest/123

• File list per patient:

• curl https://localhost:9292/changerequest/123

• Download file:

• curl https://localhost:9292/changerequest/123/test.txt

The rejoin scanner script example usage:

• Print out the usage statement for the scanner script.

• ruby patient_rejoin_matchbox_scanner.rb –help

• Run the scanner script to find patients that are eligible to rejoin the trial and print them out.

• ruby patient_rejoin_matchbox_scanner.rb -c ../config/scanner.yml -e development|prodtest|production –print

• Run the scanner script to find patients that are eligible to rejoin the trial and send them to ECOG.

• ruby patient_rejoin_matchbox_scanner.rb -c ../config/scanner.yml -e development|prodtest|production

• Run the scanner sender script to look for the most recent rejoin requested trigger and send them to ECOG for the given patients.

• ruby patient_rejoin_list_sender.rb -c ../config/scanner.yml -e development|prodtest|production

The bai file scanner script example usage:

• Run the bai file scanner script to look for bai files that are missing and call the ion reporter api to create it.
• ruby bai_file_scanner.rb -c ../config/scanner.yml -e development|prodtest|production

The document file transfer scanner script usage:

• Run the document transfer script to analyze the NFS for patient documents and copy the files to S3.
• ruby doc_file_transfer_scanner.rb -c ../config/scanner.yml

The sequencing file transfer scanner script usage:

• Run the file transfer script to analyze the database for all patients that have files stored in NFS, copy the files to S3, and update the patient document to point to S3.

• ruby sequencing_file_transfer_scanner.rb -c ../config/scanner.yml -a -t -u

• Run the file transfer script to analyze the database for all patients that have files stored in NFS

• ruby sequencing_file_transfer_scanner.rb -c ../config/scanner.yml -a

• Run the file transfer script to copy the files for patient 10010 to S3 and update the patient document to point to S3.

• ruby sequencing_file_transfer_scanner.rb -c ../config/scanner.yml -t -u -p 10010

The control file transfer scanner script usage:

• Run the file transfer script to analyze the database for all sample controls that have files stored in NFS, copy the files to S3, and update the sample control document to point to S3.

• ruby control_file_transfer_scanner.rb -c ../config/scanner.yml -a -t -u

• Run the file transfer script to analyze the database for all sample controls that have files stored in NFS

• ruby control_file_transfer_scanner.rb -c ../config/scanner.yml -a

• Run the file transfer script to copy the files for sample control SampleControl_MDACC_1 to S3 and update the sample control document to point to S3.

• ruby control_file_transfer_scanner.rb -c ../config/scanner.yml -t -u -m SampleControl_MDACC_1