unhelpful links in Log from "open formats" command

[Elaine Meng]

If in the daily build you use command “open formats” and then try to use the links in the format description columns, some of them (e.g. for HTML, STL, STORM) do nothing but give "TypeError: Cannot read property 'getItem' of null", some of them make the Log blank (e.g. Gromacs), and several (Collada, PDB, etc.) render a web page in the Log. Either the blanking-our or rendering some other web page blot out the Log contents which you can't get back unless you think to enter another command that is logged.

Personally, I don’t think we need to overload the Log with a lot of links that are merely informational, especially if they are this annoying and antifunctional. People can use the full documentation if they want all those details/links.

[Greg Couch]

The links are supposed to work. Will add code to have any html link in the log window be opened in the help viewer.

[Elaine Meng]

I don’t think we should load up the Log with all kinds of external links “just because we can.”  Maybe there should be some evaluation of   usefulness in this context.  

In my opinion it is much more important to leverage the HTML capabilities for ChimeraX-specific advantages, like helping people make tutorials by allowing them to save the Log and/or Command History as HTML with ChimeraX-executable links, ticket #312  (automatically including the javascript for non-ChimeraX browsers as per #342).

Also, opening up external web pages in the Help viewer is extremely annoying when it makes the Back button no longer work, ticket #370, so unless somebody is planning to implement tabs to fix that one, these new links will just make it more likely to annoy the user. 

[Conrad Huang]

On 6/20/2017 8:55 AM, Elaine Meng wrote:

In this case I disagree.  When I see the log, I don't have an urge to 
click on every hyperlink on the page.  If I actually want to know the 
details of a format, having the link helps; otherwise, I just ignore 
them.  Obviously, my perspective is as a developer.  I would imagine 
that there are few others who really care about format details.  On the 
other hand, making the *databases* into hyperlinks would help "real" 
users because it can provide information about the location, terms and 
capability of a service.


We have not added executable links yet, but including Javascript when 
saving log as HTML is done (#342 is closed).  I don't know about saving 
Command History as HTML.


The intent is to make it go into a new tab in the Help Viewer, although 
that is open to discussion.  Erasing history when opening a new document 
in the same viewer/tab seems like a bug to me, i.e., very 
counter-intuitive because web browsers don't do that.

But once again, I think we have a different view of what a hyperlink on 
a page suggests.  It doesn't bother me to have lots of links since I 
don't intend to click on any of them, so "loading up" is fine with me.

Conrad

[Conrad Huang]

The http links in Log are now displayed in Help Viewer, and history is *not* wiped, so you can still get to previous pages.

Tabs in Help Viewer and executable ChimeraX links in Log are still not implemented yet.

[Elaine Meng]

In my opinion I have much better URLs for ChimeraX command file, session, IHM, STL (because we use the binary format only, not the ASCII), STORM etc. in the "open" manpage than what is used for this formats table. I also prefer what I had for PDB and VTK (the latter in the formats page goes to a PDF file). I guess whoever did this tried to look up things from scratch rather than to use the work I've already done. The STORM link doesn't even work.

[pett]

I'd say either update the links or nuke them.

--Eric

[Elaine Meng]

STORM link doesn’t work

IHM link is wrong (goes to Salilab) recommend https://pdb-dev.wwpdb.org/about/

STL link should go to binary section of page https://en.wikipedia.org/wiki/STL_%28file_format%29#Binary_STL

Chimera commands recommend  http://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-files

Chimera sessions recommend  http://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html

PDB link OK, but alternative is  http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.html 

[Greg Couch]

Used help:user/commands/... links to link to internal documentation.