GECKO
GECKO copied to clipboard
Bug detected in loadDatabases
Description of the bug:
Not able to retrieve data from UniProt via API
Expected behavior:
Download UniProt data
Current behavior:
Error using matlab.internal.webservices.HTTPConnector/copyContentToByteArray (line 396) The server returned the status 500 with message "Internal Server Error" in response to the request to URL https://rest.uniprot.org/uniprotkb/query=taxonomy:9606&format=tab&compress=no&columns=id,genes(OLN),genes(PREFERRED),ec,database(GeneID),database(RefSeq),mass,sequence.
Error in readContentFromWebService (line 46) byteArray = copyContentToByteArray(connection);
Error in webread (line 125) [varargout{1:nargout}] = readContentFromWebService(connection, options);
Reproducing these results:
% If you worked on matlab, paste your code here
taxonID = '9606'; url = ['https://www.uniprot.org/uniprot/?query=taxonomy:' taxonID ... '&format=tab&compress=no&columns=id,genes(OLN),genes(PREFERRED),ec,database(GeneID),database(RefSeq),mass,sequence']; uniprotDL = webread(url);
# If you worked on python, paste your code here
Context
I hereby confirm that I have:
- [x] Tested my code with all requirements for running GECKO
- [ ] Done this analysis in the
master
branch of the repository - [x] Checked that a similar issue does not exist already
UniProt has indeed changed their API, @johan-gson solved this in #180, has not been reviewed yet.
urlread function works for uniprot