| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2020-06-20 | Added some admin functionality and fixed issue with temp traits | zsloan | |
| 2020-06-17 | Adding all the authentication stuff | zsloan | |
| 2020-06-05 | Commiting other current group/resource management code, plus the new files | zsloan | |
| 2020-06-04 | Added back in trait info queries for situations where the proxy isn't running | zsloan | |
| 2020-06-04 | Really should have split this into many more commits: | zsloan | |
| - Now use proxy to pull trait data and hide traits/results that the user doesn't have view permission for - Created a factory method for creating trait ob so it can return None when user doesn't have view permissions (this is why such a large number of files are changed) - Added metadata to permutation export - Added current group management code - Added fixed password verification e-mail code | |||
| 2020-05-28 | Added lines calling proxy for publish datasets + added some resource redis ↵ | zsloan | |
| queries and a missing import for the hmac functions | |||
| 2020-05-21 | Made search result table width variable again and fixed row highlighting, ↵ | zsloan | |
| though later I need to go through and redo a bunch of CSS stuff | |||
| 2020-05-07 | Fixed blatseq issue and geno correlation issueblatseq_fix | zsloan | |
| 2020-05-07 | Committing current progress on group manager + a minor fix in dataset.py | zsloan | |
| 2020-04-27 | Added timeout for when/if it does the REST API query, so it doesn't hang ↵ | zsloan | |
| indefinitely | |||
| 2020-04-27 | Made change that should allow dataset structure to be loaded from Redis ↵ | zsloan | |
| instead of the JSON file without breaking things | |||
| 2020-04-26 | Removed the code that was still writing the database menu JSON | zsloan | |
| 2020-04-24 | Replaced hard-coded instances of GN2 urls with ones pulled from settings file | zsloan | |
| 2020-04-24 | Made a fix that should prevent the issue where new datasets cause an error ↵ | zsloan | |
| when they're in search results | |||
| 2020-04-06 | Added Mean column for phenotype traits in search and global search result tables | zsloan | |
| 2020-03-27 | Fixed issue where GEMMA wasn't showing up for certain groups | zsloan | |
| 2020-03-27 | Added integration for using RData files with R/qtl, plus some other changes ↵ | zsloan | |
| to how it decides which mapping methods to display on the trait page | |||
| 2020-03-09 | I think this should complete consolidating all the collections code. | zsloan | |
| 2020-03-03 | Forgot to replace code referring to hmac function user_manager | zsloan | |
| 2020-02-07 | Users can now add and do mapping on genotype files that only include a ↵ | zsloan | |
| subset of samples/strains Also filtered the results used by Christian's genome browser, so now it should have an easier time loading when dealing with larger numbers of markers | |||
| 2020-02-06 | Fixed encoding issue | zsloan | |
| 2020-01-22 | Fixed issue that caused submitting temp traits to not work | zsloan | |
| 2020-01-08 | Made change that I think should fix the unicode stuff once and for all | zsloan | |
| 2019-12-17 | Added RGD link to trait page and removed Genotation link since it isn't working | zsloan | |
| 2019-12-04 | Added M to the possible non-number 'chromosome' names | zsloan | |
| 2019-12-04 | Fixed error that sometimes occurs if there's no mean expression and changed ↵ | zsloan | |
| index page header style a little | |||
| 2019-11-21 | Use updated phenotype display IDs for all phenotypes with codes now, not ↵ | zsloan | |
| just unpublished ones | |||
| 2019-11-21 | Added 3-letter codes to unpublished phenotype traits and fixed issue with ↵ | zsloan | |
| ordering phenotype results from searches | |||
| 2019-11-14 | Changed code to rebuild dataset list each time you view the trait page to ↵ | zsloan | |
| avoid having to restart each time a new dataset is added. Will need to keep an eye out for any issues, but doesn't seem to affect speed much Fixed logic for UniProt link to use UniProtId instead of protein ID | |||
| 2019-11-05 | Fixed issue with ordering items in correlation dataset select dropdown | zsloan | |
| 2019-10-24 | Changed logic for generating drop-downs such that it shows the correct ↵ | zsloan | |
| Phenotypes name when there's no accession ID | |||
| 2019-10-18 | Added UniProt link and fixed issue that caused sample lists to not be formed ↵ | zsloan | |
| correctly in certain situations | |||
| 2019-10-04 | Fixed issue where there was an error if the REST API used for aliases was down | zsloan | |
| Added option to download as JPEG in addition to SVG for basic stats figures | |||
| 2019-08-22 | Changed header drop-down menu layout | zsloan | |
| Added a couple new third party links Added link to GN1 trait page in trait pages Fixed gene global search table appearance | |||
| 2019-08-01 | Updated aliases to get all species aliases and remove duplicates | zsloan | |
| 2019-08-01 | Added wikidata aliases | zsloan | |
| Fixed year to not be a hyperlink when no pubmed id Fixed first column width so it doesn't go onto two lines for trait details | |||
| 2019-08-01 | Made some more aesthetic changes to various pages and charts/figures | zsloan | |
| Added some information to the mapping loading page | |||
| 2019-07-23 | Added change to automatically update datasets list using rest api instead of ↵ | zsloan | |
| json file Removed option to edit certain html pages, like news, policies, etc | |||
| 2019-07-18 | Made change that should fix encoding issue, fingers crossed | zsloan | |
| 2019-07-03 | Fixed bug for creating one of the third party links on the trait page | zsloan | |
| Changed text in several pages (submit trait, mapping error) Changed header menu structure some | |||
| 2019-06-24 | Got non-LOCO GEMMA mapping working with gemma-wrapper (so caching should ↵ | zsloan | |
| work for that now) Fixed position digits and row highlighting on interval analyst table Updated default MAF to 0.05 Updated footer text | |||
| 2019-06-18 | Fixed issue with sorting involving 0's on trait page | zsloan | |
| Fixed links to dataset info pages in search results and correlation results pages | |||
| 2019-06-05 | Fixed issue that caused interval mapping to not work because the python ↵ | zsloan | |
| implementation of the reaper Dataset object doesn't include the addinterval method (so for those situations I still use reaper) Fixed issue where the last chromosome wasn't displayed for mapping results (though still need to fix issue where points are drawn too far to the right when a specific range is viewed) | |||
| 2019-06-04 | Added GeneMANIA link | zsloan | |
| Fixed issue that caused error when creating UCSC RefSeq link Fixed issue that sometimes caused an error for phenotype searches Changed some text on collections page | |||
| 2019-05-24 | Replaced qtlreaper Dataset object with python object | zsloan | |
| 2019-05-14 | Added all of the third party links from GN1 | zsloan | |
| Fixed issue with the script that generates the drop-down menus where phenotype/genotype datasets wouldn't show up for species without any mRNA assay datasets Added icon for smartphones/tablets Made error more informative for main search Added gene symbol column to collections (need to add something that removes the column if it's all empty) | |||
| 2019-05-06 | Removed some unused imports of htmlgen | zsloan | |
| Fixed a bug that sometimes occurred in search results Changed order of items on index page | |||
| 2019-03-18 | - Added PCA traits to correlation matrix. You can't change their names yet ↵ | zsloan | |
| or add them to a collection from the corr matrix page, but you can click them and access them from the trait page. I'll add the option to access them from the corr matrix page as well, but adding the option to change their names might be trickier since they're currently used as their Redis keys. I need some better way of passing the Redis key around so it can be stored in collections, but this is tricky without changing the structure in ElasticSearch - Fixed the way temp traits work so you can use them with various functions, like mapping, correlations, network graph, etc - Fixed some appearance issue where the network graph options were too wide if a trait name was too long | |||
| 2019-03-07 | Changed the way covariates are displayed when selected for mapping | zsloan | |
| Made the outlier notification appear for all mapping methods Removed some misleading text saying "Block samples" from the Transform and Filter Data section | |||
| 2019-02-22 | Fixed some appearance issues with several tables | zsloan | |
| Fixed issue where cofactor selection screens were broken Changed case attributes to be applied across groups, though need to discuss this with Rob since it shouldn't always be done this way Added new inversion transformation | |||
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index : genenetwork2 | |
| GeneNetwork (2nd generation) |
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