Bug detected in loadDatabases

[Yu-sysbio]

trafficstars

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

* Operating System: macOS version 12.6.1 * Python version: * Matlab version: 2019b

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

[edkerk]

UniProt has indeed changed their API, @johan-gson solved this in #180, has not been reviewed yet.

[ae-tafur]

urlread function works for uniprot