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Wormbase Build Pipeline
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WS280 32: XML file does not validate #153

Closed MagdalenaZZ closed 3 years ago

MagdalenaZZ commented 3 years ago

Running the script upload_empc_links.pl the final files do not validate as valid XML files.

/nfs/production/panda/ensemblgenomes/wormbase/BUILD/autoace/acefiles/Wormbase_links.xml.gz

/nfs/production/panda/ensemblgenomes/wormbase/BUILD/autoace/acefiles/Wormbase_provider.xml.gz

With the same script, we also cannot connect to the ftp server using the credentials in ebi_resources/EPMCFTP.s

noah-login-02[wormbase]5019: ftp labslink.ebi.ac.uk Connected to labslink.ebi.ac.uk (193.62.194.179). 220-Private FTP 220 Name (labslink.ebi.ac.uk:wormbase): elinks 421 Service not available, remote server has closed connection Login failed. No control connection for command: Transport endpoint is not connected

Documentation: http://europepmc.org/LabsLink

Action: Check Europe PMC the format and submission guidelines what they need. Re-write the script to give them what they want. Test: by submitting WS280 data.

markquintontulloch commented 3 years ago

There was a bug meaning that the Tablemaker query was not getting printed to the .def file. As such an empty XML template was being generated, which did not validate as at least one entry is required. The bug was fixed and validation reimplemented with commit f8e3561. WS280 data was successfully submitted.