Thanks for the report Alexander. Carl has fixed this problem in dev with https://github.com/galaxyproject/galaxy/pull/431. Thanks Carl! -John On Thu, Jun 25, 2015 at 7:11 PM, John Chilton <jmchilton@gmail.com> wrote:
Conversation in IRC. tl;dr - it looks like it might be a GUI related problem since the API does contain all of the datasets. Carl - any chance you have an idea of what is going on here?
21:20 < jmchilton> avowinkel: is it possible there were duplicated identifiers (has your discover_datasets pattern changed from earlier) 21:21 < jmchilton> I'm leaning toward saying it is likely a backend problem - since explicit output collections are pretty new and you are the first person I can think of really exercising them strenuously 21:21 < jmchilton> One way to verify though is to check the API - if you just open localhost:<port>/api/histories in your browser - find the history id 21:21 < jmchilton> then open /api/histories/<history_id>/contents and then find the collection 21:22 < jmchilton> you should be able to open something like 21:22 < jmchilton> /api/histories/<history_id>/contents/collections/<collection_id> - which should show the individual datasets 21:23 < avowinkel> there are defenitely no duplicate designations - if thats the same like identifiers 21:23 < avowinkel> It's still <discover_datasets pattern="__name_and_ext__" directory="splits" /> 21:27 < jmchilton> My next question would be (if you can verify it is a backend thing) - are the elements in the dataset - the hidden elements less than a certain HID - or are they random. 21:28 < avowinkel> via the api all 96 entries are in the collection 21:29 < avowinkel> with element_index's 0 to 95, in total 96 21:29 < avowinkel> in both lists 21:31 < avowinkel> biggest hid is 202 21:32 < avowinkel> the parent's list hid is always smaller than the containing element's hids 22:26 < jmchilton> so you are sure every element_index from 0 to 95 is represented? This being a GUI problem is really odd - but it seems like it probably is. I wonder if someone a div id is generated from the identifiers in such a way that one is duplicated. Seems unlikely 22:26 < jmchilton> Can you open your JavaScript console and see if there are any JavaScript errors/ 22:27 < avowinkel> well. I did grep element_index, I saw index 0 on the top, Index 95 on the bottom. and wc -l gives 96 - so yes. very sure 22:28 < avowinkel> and when I scan loosely through the list of greps, I don't see anything odd 22:29 < avowinkel> don't want to count from 0 to 95 ^^ 22:29 < jmchilton> :) 22:29 < avowinkel> for all the tests 22:30 < jmchilton> does that API response have a hidden field for the datasets? 22:31 < avowinkel> there is nothing in that file that matches "hidden" 22:31 < avowinkel> (in the history they are all hidden) 22:32 < jmchilton> I would open your web browser and check for javascript errors next 22:34 < avowinkel> nop. nothing (Firefox 34 - ubuntu biolinux) 22:34 < jmchilton> can you send me a screenshot of the expanded collection? 22:35 < avowinkel> the newest run has 69 entries in the history 22:36 < avowinkel> what part do you want screenshotted? 22:38 < jmchilton> "When I open the list, I just can see 64 items." The opened list in the history panel 22:40 < avowinkel> http://snag.gy/2knoI.jpg 22:43 < jmchilton> are you hand counting these lists in the browswer then? 22:47 < avowinkel> yes, hand counting 22:50 < jmchilton> I'll ping carl about this - he is the GUI mastermind - he might have some clue 22:59 < avowinkel> jmchilton: http://pastebin.com/DcpF1QAU 22:59 < mrscribe> Title: [YAML] galaxy dataset_collection contents - Pastebin.com (at pastebin.com) 23:00 < avowinkel> don't get confused: On the picture is a different dataset. It doesn't have "sample_" in the name 23:04 < jmchilton> yeah - that response looks perfectly fine - really odd
-John
On Thu, Jun 25, 2015 at 4:58 PM, Alexander Vowinkel <vowinkel.alexander@gmail.com> wrote:
Hi Team,
my tool creates dynamically 96 datasets bundled into a list. In the history I can see the number 96 in the top as hidden datasets (6 shown, 96 hidden)
When I open the list, I just can see 64 items.
Now I run the job again and I have 96 more hidden items. I open the new list and can see 66 items in that new list.
What is going on here? Is that "just" a visual bug? Or are my datasets affected?
Thanks, Alexander
PS: I use postgres
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