Trackhubs #6
Trackhubs #6
Conversation
… or lists, fixed typos in trackhub_file and trackhub_list, added tests for trackhubs and headers and made tests.py indentation consistent, simplified utilities install by using precompiled binaries.
…lowed trackhub creation of all avaliable data, amended test file to account for new file names and fixed typo
…s were added to trackDb.txt, added more descriptive info for the track hub output
plotter/templates/profile_table.pt
Outdated
| </form> | ||
|
|
||
| <form method="get" action="/trackhub_init/${user}/"> | ||
| <button type="submit">Create Track Hub</button> |
There was a problem hiding this comment.
sorry for not mentioning this earlier but it is usually a bad idea to use a form if there are no fields/data to submit, as is the case above. in this case you could just use a standard link, a href instead, right?
and actualy i would suggest changing the URL scheme from /trackhub_*/${user}/ to simply /trackhub_*/ because anyways the user variable is stored in the session info
plotter/views.py
Outdated
| if linelist == ['']: | ||
| continue | ||
| if len(linelist) >= 2: | ||
| if linelist[0][3:] not in cl.keys(): |
There was a problem hiding this comment.
please add comments to clarify you intention in this new block of code.. it is not clear to me what you are doing here
plotter/views.py
Outdated
| '\nshortLabel ' + request.POST['short_label'] + datatype + '\nlongLabel ' + | ||
| request.POST['long_label'] + datatype + '\ntype bigBed\ncolor 0,253,0' + | ||
| '\nalwaysZero on\n\n') | ||
| trackdbtxt.write('track ' + x + '\nbigDataUrl ' + x + '.bigWig\nshortLabel ' + request.POST['short_label'] + |
There was a problem hiding this comment.
is there some way to remove repetition in these trackdbtxt.write lines?
also instead of using 'track ' + x + "_" you may consider using 'track %s_'.format(x) etc
tests/tests.py
Outdated
| submit_button.click() | ||
| sleep(10) | ||
| if ("Trackhub data for test1" in driver.page_source): | ||
| assert True |
There was a problem hiding this comment.
nice, glad to see that you added a test for the track hub functionality that you implemented
you may also want to check for the presence of the profile name, ES0004, on the web page
also it would be good test track hubs with multiple profiles (here there is only one profile in the track hub, right?)
|
thanks for the code contributions! nice to see that tests are passing. please address my comments the best you can and then we can merge with master |
…ents, userid usage, string formatting, and bug fix in multiple profile creation (with accompanying test) to trackhub code
|
I did correct everything you asked for except for removing the repetition. There was a lot of repetition (more than currently) to begin with, and the current loops are about as small as I can make it right now. |
plotter/views.py
Outdated
| for x in request.POST.getall('profile'): | ||
| trackdbtxt.write('track %s' % x + 'multiWig\ntype bigWig\ncontainer multiWig\naggregate transparentOverlay\n' + | ||
| 'shortLabel ' + request.POST['short_label'] + 'multiWig\nlongLabel ' + | ||
| request.POST['long_label'] + 'multiWig\nautoScale on\nnegativeValues on\nalwaysZero on\n\n') |
There was a problem hiding this comment.
sorry for not being clear earlier -- I meant to say that it would be good to replace all of the + with % (not just the first)
In fact I think it would be even easier to understand/read if you use triple quotes and % here, e.g.
trackdbtxt.write("""track %smultiWig
type bigWig
shortLabel %smultiWig
"""%(x, request.POST['short_label'])here i just show what it should look like with two variable substitutions in the text, but please use %s/etc (not +) for all variable substitutions
the only difference between single and triple quotes is that triple quotes allow line breaks in literal character strings... which is very useful from a readability perspective here
|
Thanks for the clarification/suggestion. Looks much better now. |
This pull request adds functionality for trackhubs in SegAnnDB.