Test Get Data tools

[tothuhien]

This issue is to keep track of testing all the tools in Get Data session.

• EGA Download Client : ConnectionRefusedError: [Errno 111] Connection refused. Tried to reconnect several times forever ...
• NCBI Accession Download: failed
• UniProt: failed
• NCBI Datasets Genomes: Just re-direct to ncbi page and does not run on usegalaxy.no
• Download and Extract Reads in FASTA/Q: ok
• Download and Extract Reads in BAM: ok
• IEDB: failed Error connecting to IEDB server <urlopen error [Errno -2] Name or service not known>
• NCBI ECitMatch: failed Name or service not known
• NCBI EFetch: failed Name or service not known
• UniProt: failed Name or service not known
• Unipept: failed HTTP Error <urlopen error [Errno -2] Name or service not known>
• Get sequences by Ensembl ID: failed Failed to establish a new connection: [Errno -2] Name or service not known',))
• Search ENA data: failed AttributeError: 'ConnectionError' object has no attribute 'encode'
• Retrieve ENA taxon data: failed AttributeError: 'ConnectionError' object has no attribute 'encode'
• Retrieve an analysis report: failed AttributeError: 'ConnectionError' object has no attribute 'encode'
• EBI Search: failed urllib2.URLError: <urlopen error [Errno -2] Name or service not known>
• Download run data from EBI Metagenomics database: failed urllib2.URLError: <urlopen error [Errno -2] Name or service not known>
• Protein Database Downloader: job is waiting for run forever
• UCSC Main table browser : OK
• UCSC Archaea table browser: OK
• EBI SRA ENA SRA: OK, just re-direct to ena browser
• modENCODE flye server: failed, the opening page is not responding
• InterMine server: OK, just re-direct to intermine page
• Flymine server: OK, just re-direct to Flymine page
• modENCODE modemine server: failed, the re-directing page is not responding
• Mousemine server: OK, just re-direct to Mousemine page
• Ratmine server: failed, the re-directing page is not responding
• Yeastmine server: OK, just re-direct to Yeastmine page
• modENCODE worm server: failed, the re-directing page is not responding
• WormBase server: the re-directing page : The server is temporarily unable to service your request due to maintenance downtime or capacity problems
• ZebrafishMine server: the re-directing page: 404 not found
• EuPathdb server: the re-directing page: page not found
• HbVar: failed, the re-directing page is not responding

[kjetilkl]

• EGA Download Client : ConnectionRefusedError: [Errno 111] Connection refused. => Removed v3.4.0, which had a non-functional container. However, the tool still requires special configuration under User->Preferences, which has not been added
• NCBI Accession Download: failed => FIXED!
• UniProt: failed => FIXED!
• NCBI Datasets Genomes: Just re-direct to ncbi page and does not run on usegalaxy.no => Does not work on EU either. The tool has been removed from Main. There is also another tool with identical name
• IEDB: failed Error connecting to IEDB server <urlopen error [Errno -2] Name or service not known> => FIXED! Updated the container
• NCBI ECitMatch: failed Name or service not known => Uninstalled older versions, but have not been able to build new functional container for recent version. The container at BioContainers also fails
• NCBI EFetch: failed Name or service not known => Same container as the tool above (Python3 + BioPython 1.70)
• UniProt: failed Name or service not known => The tool fails on Galaxy Main and Europe also, so there seems to be an issue with the tool itself
• Unipept: failed HTTP Error <urlopen error [Errno -2] Name or service not known> => FIXED! Deleted container Python:3 and symlinked the name to => **Python:3.7--1 instead
• Get sequences by Ensembl ID: failed Failed to establish a new connection: [Errno -2] Name or service not known',)) => FIXED! Rebuilt container with Planemo
• Search ENA data: failed AttributeError: 'ConnectionError' object has no attribute 'encode'
• Retrieve ENA taxon data: failed AttributeError: 'ConnectionError' object has no attribute 'encode'
• Retrieve an analysis report: failed AttributeError: 'ConnectionError' object has no attribute 'encode'
• EBI Search: failed urllib2.URLError: <urlopen error [Errno -2] Name or service not known> => Unable to build functional container