metadata-sub

Modify sample metadata XML files from ENA, then resubmit them.

Developed for the VRE crosswords project ('GSC MIxS human associated' metadata schema).

Prerequisites

• Python3
• Python3 library lxml
• curl

Workflow

1. retriever.sh
2. modifier.sh
3. concatenator.sh
4. submitter.sh

Usage

1. retreiver.sh

./retriever.sh input_file.tsv filter_file.tsv

2. modifier.sh

(Assumes sample XML files are in folder 'xml/samples' ./modifier.sh metadata_file.tsv

1. concatenator.sh

./concatenator.sh xml/modified_samples xml

1. submitter.sh

First validate your XML file for submission:

./submitter.sh xml/sample.xml xml/validate.xml

If submission is successful (i.e. if 'success="true"' in line 3 of 'xml/receipt.xml'), then you can do the real submission:

./submitter.sh xml/sample.xml xml/submission.xml