add to group: colon in group name doesn't work

[mshukla1]

Adding genomes to a group, when use colon ":" in the group name and save, I get the notification that genomes were added to the workspace, however, the group never appear in the workspace. It looks like group creation fails without giving any error message to the user.

[olsonanl]

This is apparently a workspace issue:

JSONRPC error data:_ERROR_Object name file:name contains forbidden characters!ERROR

Chris - why is the workspace disallowing any characters from object names?

[olsonanl]

Additionally if we cannot fix that - what is the set of characters that is not allowed? We need to be able to trap those in the UI to give reasonable error messages.

[cshenry]

I do not want to allow characters that would break things if the workspace was cloned to your filesystem. ":" is not allowed in filenames on my filesystem at least. I think this is a reasonable position to take.

Right now, I think the name validation is something like this: if ($input =~ m/[:\/]/) { $self->_error("Object name ".$input." contains forbidden characters!"); }

So literally... you can use ANYTHING but ":" and "/". Is that okay?

[olsonanl]

I think windows is the only case where this is an issue; mac and linux are both fine.

mcswl174:~ olson$ date > foo:bar mcswl174:~ olson$ ls -l foo.bar -rw-r--r-- 1 olson staff 29 Jun 3 15:11 foo:bar

Do we support cloning the workspace to the filesystem?

Harry / Maulik - I suspect the correct solution here is to not name genome group files with the name of the group, but rather include the name of the group inside the data file; that way any bizarro quoted characters may be used in the group names. The filename can be a safely quoted version of the group name.

[olsonanl]

Chris comments that in Finder in the mac you can't do it either and I see that he is right. I'd make the same argument to Apple but I'll save my breath :-)

[olsonanl]

@cshenry do you know if workspace is clean with respect to full UTF 8 chars e.g. ∆

[cshenry]

We don't do any sort of escaping of workspace or object names. So if you try and use a character that can't be in a file name, it won't work....

I got to wonder why anyone would want to name an object something that you can't even type on a keyboard... It renders it very hard to use...

Sent from my iPhone

On Aug 19, 2015, at 2:34 PM, olsonanl notifications@github.com wrote:

@cshenry do you know if workspace is clean with respect to full UTF 8 chars e.g. ∆

— Reply to this email directly or view it on GitHub.

[olsonanl]

We had user-submitted job failures due to the delta (which is easy to type, Option J on a mac). It can be in a filename. I tested this with RAST and it works fine:

[cid:1790452A-AFBC-4680-9A89-15C185D07F5A@mcs.anl.gov]

gally2:~ olson$ cd √θθθ gally2:√θθθ olson$ pwd /Users/olson/√θθθ gally2:√θθθ olson$ ls -l total 752 -rw-r--r--@ 1 olson staff 381805 May 12 11:11 √θθθ.gb gally2:√θθθ olson$ head √θθθ.gb LOCUS NC_008512 159662 bp DNA circular BCT 16-MAR-2010 DEFINITION Candidatus Carsonella ruddii PV, complete genome. ACCESSION NC_008512 VERSION NC_008512.1 GI:116334902 DBLINK Project: 17977 KEYWORDS . SOURCE Candidatus Carsonella ruddii PV ORGANISM Candidatus Carsonella ruddii PV Bacteria; Proteobacteria; Gammaproteobacteria; Candidatus Carsonella.

On Aug 19, 2015, at 4:09 PM, cshenry notifications@github.com<mailto:notifications@github.com> wrote:

We don't do any sort of escaping of workspace or object names. So if you try and use a character that can't be in a file name, it won't work....

I got to wonder why anyone would want to name an object something that you can't even type on a keyboard... It renders it very hard to use...

Sent from my iPhone

On Aug 19, 2015, at 2:34 PM, olsonanl notifications@github.com<mailto:notifications@github.com> wrote:

@cshenry do you know if workspace is clean with respect to full UTF 8 chars e.g. ∆

— Reply to this email directly or view it on GitHub.

— Reply to this email directly or view it on GitHubhttps://github.com/PATRIC3/patric3_website/issues/210#issuecomment-132785305.

[olsonanl]

Picture didn't come through:

[cshenry]

OK. I have no idea why this would fail in the workspace. It will take some time to debug. Let�s make it an issue. I�m not personally going to have time to address this for a few weeks� just too much going on right now.

On Aug 20, 2015, at 8:28 AM, olsonanl notifications@github.com wrote:

Picture didn't come through:

� Reply to this email directly or view it on GitHub.

[hyoo]

the original problem, adding : in the group name is resolved by blocking from UI. I am closing this ticket.