This script is intended to convert the NCBI tsv file format into xml format, and submit it through an ftp upload.

https://www.ncbi.nlm.nih.gov/viewvc/v1/trunk/submit/public-docs/common/docs/UI-lessSubmissionProtocol.docx?revision=71197

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Script Prerequisites

Before running the script, you will need to do the following steps:

1. Run `npm install`
2. Modify the "src/config.js" file to enter your: A. FTP connection information B. Organization information C. Submitter information
3. Move the TSV files you would like converted into the "files" folder

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How to Use

Example

node main.js -i=sample.tsv -c="this is a comment" --uploadFolder=folder
node main.js -i=sample.tsv --runTestMode --debug --force
node main.js --uploadFiles=sample.tsv,submission.xml -poll=1
node main.js --uploadFiles=sample.tsv,submission.xml -poll=disabled

Parameter	flag	Required	Type	Default Value	Description
help	-h				print help table
submissionType			string	BioSample	'BioSample' or 'SRA'
submissionDataType			'autodetect-xml', 'generic-data' , 'phenotype-table' , ... (to see full list, run without specifying value) , default is 'generic-data'	generic-data	If uploading a file, what type of content does the file contain
submissionFileLoc			string		if a filename column exists in the tsv file, prepend this string to the filename provided (for indicating folder or path or source of file, ex: 'gs://example_paper_sra/')
bioproject			string		bioproject reference ID default value if tsv file does not contain a row with this information.
inputFilename	-i	(required)	string		filename for the tsv file to be uploaded
uploadFiles	-f	(required)	string		(Either input filename or uploadFiles is required, but not both) comma separated list of files to upload
outputFilename	-o		string		filename to write the generated xml file to. Default value will use inputFilename
uploadFolder	-u		string		if provided, the generated xml file will be uploaded through ftp to the specified folder
uploadComment	-c		string		description or comment about this submission
uploaded				false	Poll and check reports for a request that has already been uploaded
poll			'(number)' | 'all' | 'disabled'	all	Poll until either this report number is hit or poll until all requests have been completed
processReport	-r		string		filename for report to convert to tsv - If upload folder is included, it will be downloaded from the FTP, otherwise, the script will look in the local files
releaseDate	-d		datestring		All data in this submission is requested to be publicly released on or after this date; example: '2017-01-01'
runTestMode					Run the script in test mode (aka: skip ftp upload)
debug					Show verbose logging details
force					Force upload and processing, even when validation fails

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Going through the flow:

1. drop your file into the "/files".
2. from the root, run node src/main.js -i=sample.tsv -c="this is a comment" --uploadFolder=folder --runTestMode=true
3. The script will now generate "sample-submission.xml" from your sample.tsv file, and save it in /files.
4. If you choose an upload folder, the script will also generate a "sample-attributes.tsv" file from the "sample-report.xml" file

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Example Usages

• Generate a biosample submission:
  • Generate a sample-submission.xml file from biosample-example.tsv
  • Upload to ftp:/path/to/folder/submission.xml
  • Poll until submission processing has been completed
  • node main.js -i=sample.tsv --uploadFolder=ftp:/path/to/folder
• Generate a genbank submission:
  • Upload content.tsv and submission.xml to /path/to/folder
  • content.zip and submission.xml should be locally at ./files
  • Poll until report.1.xml is generated
  • node main.js --uploadFiles=content.zip,submission.xml --uploadFolder=ftp:/path/to/folder -poll=1
• Generate an SRA submission:
  • Generate a sample-submission.xml file from sra-example.tsv
  • node src/main.js -i=tests/sra-example.tsv --submissionType=sra --bioproject=PRJNA535086 --submissionFileLoc=gs://sdf -uploadFolder=/submit/Test/sra-test
• Generate a tsv file from a report.xml file
  • convert report.5.xml file into report-attributes.tsv
  • report.5.xml should be located in ./reports
  • node main.js --inputFilename=sample.tsv --processReport=report.5.xml