| Age | Commit message (Expand) | Author |
|---|
| 2022-02-28 | Fix fulltext search for certain searches...Hyphens in fulltext searches were causing problems, but a recent commit
I made to fix the issue apparently had some side effects for other types
of searches, in addition to make such searches someewhat slower
Apparently the issue wasn't just the hyphens, but also the text to
either side of the hyphen being lower than the minimum word length
(which is either 2 or 3 for us, can't remember). To try and address
this, I did a regular expression check for a pattern with text of <3
legnth to either side of a hyphen, and when that's the case I add quotes
from the search term plus an asterisk, which seeems to be necessary to
get it to not treat the hyphen as a delimiter and to correctly detect
the search term
| zsloan |
| 2022-02-28 | Add distinct to fix issue where GeneRIF search returns duplicates | zsloan |
| 2022-02-26 | Remove CSS from partial_correlations.css...This CSS is overwritten by CSS from trait_list.css and show_trait.css
| zsloan |
| 2022-02-26 | Add container div | zsloan |
| 2022-02-26 | Add checkbox and index columns | zsloan |
| 2022-02-26 | Include DataTables imports and necessary CSS | zsloan |
| 2022-02-26 | Add JS initializing DataTables | zsloan |
| 2022-02-24 | Fix ProbeSet query for aliases...ProbeSet queries previously weren't dealing with aliases correctly,
because it was doing a MATCH/AGAINST against the ProbeSet.alias field,
but that field usually contains a list of gene symbols separated by
semi-colons (so it wouldn't detect the alias unless there was only a
single alias.
To fix this, I added some LIKE conditions, searching for the possible
variations. This is a little awkward, because I needed to make sure to
avoid a situation where, for example, an alias like 'LPD-1' matches a
search for 'PD-1'. I don't think the way it currently works is
efficient, but I don't know of any good alternative without changing the
way we store aliases in the database.
| zsloan |
| 2022-02-24 | Fix alias query | zsloan |
| 2022-02-24 | Change parser.py to also detect hyphen in search terms | zsloan |
| 2022-02-23 | Fix Heatmap GN3 URL | zsloan |
| 2022-02-23 | Improve Heatmap options' appearance...Moved the Heatmap display area above the table selection options (since
it didn't make sense to have it below those)
Added a button for clearing the Heatmap area and hiding the Heatmap
options
Added some margins to the Heatmap options
| zsloan |
| 2022-02-23 | Show heatmap options when heatmap is run...Heatmap options are now shown after the user clicks the button
I also reordered the Heatmap and Partial Correlation buttons, since it's
awkward to get the Heatmap options to display well if its button is
second. We'll probably completely rework this later, but for now this
looks a little less ugly.
| zsloan |
| 2022-02-23 | Reposition Partial Correlations and Heatmap buttons...Moved Partial Correlations and Generate Heatmap buttons to be lined up
below the other buttons and hide the Heatmap orientation selection (JS
will be added to show it after Heatmap is run)
| zsloan |
| 2022-02-23 | Add top margin to Partial Correlations button...Later this button should just be included with the other function buttons.
There's no need for it to be in a separate form, since it should be able
to take the same trait list input as all the other collection page
functions (with just the action url for the form changing)
| zsloan |
| 2022-02-21 | Fix incorrect dataset trait data caching...Trait data caching wasn't working correctly because it didn't account
for the samplelist, causing caching to work incorrect in any situation
where the target dataset's samplelist wasn't the same as that of the
trait being correlated against. Trait data is stored as a dictionary
where the keys are trait IDs and values are *lists* of sample values.
This means that the caching needs to account for the exact same set of
samples; otherwise you'll end up with samples being mismatched (since
"the third sample with a value" for one dataset's trait might not be the
same as "the third sample with a value" for another dataset's trait).
To fix this, I added the samplelist to the functions that generate and
fetch the hash file. This will require more cache files, though, so this
should probably be reexamined later to make the code work with only a
single cache file for each dataset.
| zsloan |
| 2022-02-18 | wqflask: Remove python pre-2.2 checks....These checks are only relevant for python pre-2.2.
* wqflask/utility/svg.py: Remove python pre-2.2 checks.
| Arun Isaac |
| 2022-02-14 | Add search text for cis/transLRS/LOD searches...There wasn't any search text for cis/trans searches including both
chromosome and exclusion zone, so I added somee
| zsloan |
| 2022-02-14 | Fix CisTrans search bug...', Geno' was being added to the FROM clause, which is wrong becausee
Geno is included in the query via a JOIN (and caused an error making
those searches not work)
| zsloan |
| 2022-02-09 | variable naming and docstrings fix | Alexander Kabui |
| 2022-02-09 | handle exceptions | Alexander Kabui |
| 2022-02-09 | autopep8 formatting | Alexander Kabui |
| 2022-02-09 | delete unused js packages | Alexander Kabui |
| 2022-02-09 | autopep8 formatting | Alexander Kabui |
| 2022-02-09 | fix for performing parametric analysis | Alexander Kabui |
| 2022-02-09 | minor template fixes | Alexander Kabui |
| 2022-02-09 | add trait lists and links to ctl plot | Alexander Kabui |
| 2022-02-09 | disabble autoslide | Alexander Kabui |
| 2022-02-09 | fix for ctl ui page | Alexander Kabui |
| 2022-02-09 | endpoint to download network files | Alexander Kabui |
| 2022-02-09 | btn download for network sif and node file | Alexander Kabui |
| 2022-02-09 | modify ctl endpoint | Alexander Kabui |
| 2022-02-09 | minor fixes for images | Alexander Kabui |
| 2022-02-09 | fix for dcor and LOD rounding | Alexander Kabui |
| 2022-02-09 | styling for carousel | Alexander Kabui |
| 2022-02-09 | add carousel for plots | Alexander Kabui |
| 2022-02-09 | ui form modifications | Alexander Kabui |
| 2022-02-09 | minor refactoring to destruct objects | Alexander Kabui |
| 2022-02-09 | template file cleanup | Alexander Kabui |
| 2022-02-09 | rename template file | Alexander Kabui |
| 2022-02-09 | minor bug fixes | Alexander Kabui |
| 2022-02-09 | process significant table results | Alexander Kabui |
| 2022-02-09 | delete class initiliazation object | Alexander Kabui |
| 2022-02-09 | minor refactoring | Alexander Kabui |
| 2022-02-09 | pep8 formatting | Alexander Kabui |
| 2022-02-09 | fetch pheno input data | Alexander Kabui |
| 2022-02-09 | parse geno input data | Alexander Kabui |
| 2022-02-09 | parse input data | Alexander Kabui |
| 2022-02-09 | init py file:call gn3 ctl api | Alexander Kabui |
| 2022-02-09 | add ui template for ctl | Alexander Kabui |
