First thanks for the great work on UGENE.

I have a problem accessing remote databases using:
in an open project File>Access Remote Databases
only fetching entries from NCBI works for me.  I have had this problem since I started using UGENE 1.9, now I have 1.9.5 and still get the same problem. UGENE is running, otherwise perfectly, a IBM T410 laptop. Originally i suspected a firewall problem but now I am not so sure.

An example of the log file is pasted below for swissprot and pdb:


[Tasks][DETAILS][09:13] Registering new task: Load remote document and open view
[Tasks][TRACE][09:13] promoting task {Load remote document and open view} to 'Prepared'
[Tasks][TRACE][09:13] promoting task {LoadRemoteDocument} to 'Prepared'
[Tasks][TRACE][09:13] promoting task {Copy Data Task} to 'Prepared'
[Tasks][TRACE][09:13] promoting task {Load remote document and open view} to 'Running'
[Tasks][TRACE][09:13] promoting task {LoadRemoteDocument} to 'Running'
[Tasks][TRACE][09:13] acquiring resource: 'Threads':1, state: 1/1000
[Tasks][TRACE][09:13] promoting task {Copy Data Task} to 'Running'
[Tasks][TRACE][09:13] releasing resource: 'Threads':1, state: 0/1000
[Tasks][TRACE][09:13] promoting task {Copy Data Task} to 'Finished', error 'IO adapter error'
[Tasks][TRACE][09:13] promoting task {LoadRemoteDocument} to 'Finished', error 'Cannot find P16152 in UniProtKB/Swiss-Prot database: IO adapter error'
[Tasks][TRACE][09:13] promoting task {Load remote document and open view} to 'Finished', error 'Cannot find P16152 in UniProtKB/Swiss-Prot database: IO adapter error'
[Tasks][ERROR][09:13] Task {Load remote document and open view} finished with error: Cannot find P16152 in UniProtKB/Swiss-Prot database: IO adapter error
[Tasks][TRACE][09:13] Unregistering task: Load remote document and open view
[Tasks][TRACE][09:13] Deleting task: Copy Data Task
[Tasks][TRACE][09:13] Deleting task: LoadRemoteDocument
[Tasks][TRACE][09:13] Deleting task: Load remote document and open view

or PDB

[Tasks][DETAILS][09:14] Registering new task: Load remote document and open view
[Tasks][TRACE][09:14] promoting task {Load remote document and open view} to 'Prepared'
[Tasks][TRACE][09:14] promoting task {LoadRemoteDocument} to 'Prepared'
[Tasks][TRACE][09:14] promoting task {Copy Data Task} to 'Prepared'
[Tasks][TRACE][09:14] promoting task {Load remote document and open view} to 'Running'
[Tasks][TRACE][09:14] promoting task {LoadRemoteDocument} to 'Running'
[Tasks][TRACE][09:14] acquiring resource: 'Threads':1, state: 1/1000
[Tasks][TRACE][09:14] promoting task {Copy Data Task} to 'Running'
[Tasks][TRACE][09:14] releasing resource: 'Threads':1, state: 0/1000
[Tasks][TRACE][09:14] promoting task {Copy Data Task} to 'Finished', error 'IO adapter error'
[Tasks][TRACE][09:14] promoting task {LoadRemoteDocument} to 'Finished', error 'Cannot find 3INS in PDB database: IO adapter error'
[Tasks][TRACE][09:14] promoting task {Load remote document and open view} to 'Finished', error 'Cannot find 3INS in PDB database: IO adapter error'
[Tasks][ERROR][09:14] Task {Load remote document and open view} finished with error: Cannot find 3INS in PDB database: IO adapter error
[Tasks][TRACE][09:14] Unregistering task: Load remote document and open view
[Tasks][TRACE][09:14] Deleting task: Copy Data Task
[Tasks][TRACE][09:14] Deleting task: LoadRemoteDocument
[Tasks][TRACE][09:14] Deleting task: Load remote document and open view

From the same machine I can access the same databases and pull out the entries with a webbrowser,

thanks for any help,

Euan

Hi Euan,
I've tested the feautre in 1.9.5, WinXP. Everything was fine: the files from PDB and Uniprot were downloaded correctly.

I suspect that your problem is somehow related to networking. Internally downloading from PDB and Uniprot is implemented differently from similar feature to access NCBI. More information is requried to understand what may causing the problem.

What OS are you using? Are you sitting behind the proxy? What are the firewall rules for HTTP connection and for UGENE?

What will happend if you put the following link into your browser:
http://www.rcsb.org/pdb/files/3INS.pdb?

thanks for the reply.

I am using Vista with 1.9.5, and I can now say that I have tested it in a different network, also with Vista and w7 and do not get any problems,  http://www.rcsb.org/pdb/files/3INS.pdb works fine in a browser but not in UGENE, so I guess as you pointed out it is indeed a network problem.
Have tried with and without using a proxy, and get the same results.

I also discovered today  that the 'Check for updates' also gives a similar response
[Tasks][TRACE][10:53] releasing resource: 'Threads':1, state: 0/1000
[Tasks][TRACE][10:53] promoting task {Check for updates} to 'Finished', error 'Connection error: Connection refused (or timed out)'
[Tasks][ERROR][10:53] Task {Check for updates} finished with error: Connection error: Connection refused (or timed out)
[Tasks][TRACE][10:53] Unregistering task: Check for updates
[Tasks][TRACE][10:53] Deleting task: Check for updates

so everything seems to point towards a net problem rather than a UGENE one, I will try to sort it out and post back when I get it fixed,

thanks for the help,

Euan