| Age | Commit message (Expand) | Author |
|---|
| 2018-03-15 | Changed appearance of mapping and correlation options on trait page...Fixed issue where changed sample values were not passed to qtlreaper mapping ("Interval Mapping")
Loading factors and their plot are hidden in situations where there's some error with calculating principal components
Added GEMMA description and changed order of descriptions for mapping options on trait page
| zsloan |
| 2018-03-05 | rename draw_corr_scatterplot-2.js to draw_corr_scatterplot.js | Lei Yan |
| 2018-03-05 | update Correlation Scatterplot | Lei Yan |
| 2018-03-02 | Added option to display selected covariates for GEMMA mapping...Changed layout/appearance of mapping options
Partially fixed issue with deleting collections
Changes to correlation table still in progress; having trouble getting tabulator to load JSON
| zsloan |
| 2018-02-26 | Merge /home/lei/gene into testing | zsloan |
| 2018-02-26 | Committing some in-progress changes related to loading correlation page from ... | zsloan |
| 2018-02-23 | Provide connections to elasticsearch...* Provide connections to elasticsearch at various points in the code.
These oversight was caught while running tests.
| Muriithi Frederick Muriuki |
| 2018-02-23 | update corr scatterplot interface | Lei Yan |
| 2018-02-21 | Fix assumption of existing collection...* When logging in, if a user selects "Import existing collections", the
system would throw an exception, since Redis would return a NoneType,
which would then be accessed by json.loads(), which doesn't seem to
know how to process that.
This fixes that, by providing a string representing an empty json
array ("[]"), in place of the NoneType.
| Muriithi Frederick Muriuki |
| 2018-02-19 | Add more login tests. | Muriithi Frederick Muriuki |
| 2018-02-15 | Added unittest example | Pjotr Prins |
| 2018-02-15 | Fixing authentication stuff so it uses parameters properly. Also no PYTHONPAT......it is now in the Guix build.
| Pjotr Prins |
| 2018-02-15 | Fix conflict | Pjotr Prins |
| 2018-02-14 | Added empty collection error page to git, since it wasn't on production | zsloan |
| 2018-02-13 | Resolved conflict | zsloan |
| 2018-02-13 | Just committing very minor change to correlation table so I can pull other ch... | zsloan |
| 2018-02-13 | Add tests for Registration process. | Muriithi Frederick Muriuki |
| 2018-02-13 | Update module to make it more testable...* Update functions to make them more testable.
* Update code using updated functions.
| Muriithi Frederick Muriuki |
| 2018-02-13 | @zsloan: we should introduce full parameter checking and sensible defaults fo......work on. It will help bug tracking.
Probably fixes #279
| Pjotr Prins |
| 2018-02-12 | Changed code parsing GEMMA output to fix issue where it wasn't getting the co... | zsloan |
| 2018-02-12 | Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing | zsloan |
| 2018-02-12 | Quick parallel correlation should work, though I'm not sure why the code sudd......Switched correlation table to tabulator
| zsloan |
| 2018-02-10 | Fixing GEMMA LOCO | Pjotr Prins |
| 2018-02-10 | Fixed finding PATHs - one return statement! | Pjotr Prins |
| 2018-02-10 | Check for bimbam path and bail out if it is missing | Pjotr Prins |
| 2018-02-09 | Check elasticsearch at point of use...* Instead of checking for the state of elasticsearch at startup, check
the state at the moment the user requests a feature that depends on
elasticsearch.
This reduces the chances that the user is dropped onto an exception
page when elasticsearch server goes down.
| Muriithi Frederick Muriuki |
| 2018-02-09 | Add check for elasticsearch...* Add some extra checks to ensure that elasticsearch is running before
presenting the UI to the user.
| Muriithi Frederick Muriuki |
| 2018-02-05 | Add code to allow user to change password...* After the email is sent to the user, there is need to provide a way
for the user to actually change their password, and have the results
saved.
| Muriithi Frederick Muriuki |
| 2018-02-05 | Refactor common items to more generic methods....* Refactor code that can be used in more than one place to a more
generic method/function that's called by other methods
| Muriithi Frederick Muriuki |
| 2018-02-05 | Send emails for forgotten passwords...* Update the code so that it sends out emails for the "forgot password"
feature.
| Muriithi Frederick Muriuki |
| 2018-02-05 | Add SMTP configuration variables...* Add configuration variables to enable the system connect to the
configured SMTP server to send out emails.
| Muriithi Frederick Muriuki |
| 2018-02-05 | Merge remote-tracking branch 'origin/testing' into testing | Muriithi Frederick Muriuki |
| 2018-01-30 | gunicorn dev and prod modes added | Pjotr Prins |
| 2018-01-30 | Fail safely if elasticsearch is down or unconfigured...* If elasticsearch server is down, or the configuration variables are
not provided at startup or in a configuration file, then do not allow
the system to simply crash, but instead, inform the user that they
cannot use the services that depend on elasticsearch to be running.
| Muriithi Frederick Muriuki |
| 2018-01-30 | Set to None if no value provided...* Add a method to set the configuration variables to None if the
configuration values are not provided at startup or in the
configuration files.
The system already checks for these values, and if they are absent, it
simply fails to display the OAuth service as available for use to
login.
| Muriithi Frederick Muriuki |
| 2018-01-29 | Gunicorn works | Pjotr Prins |
| 2018-01-29 | startup script: adapting for gunicorn | Pjotr Prins |
| 2018-01-24 | Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing | zsloan |
| 2018-01-24 | Added links for markers in mapping results table when genotypes exist in DB...Added more info to trait details for phenotype traits
Changed order of mapping methods
Fixed layout of mapping loading screen to hopefully be centered on different screen sizes
Improved layout of some elements in mapping results page
| zsloan |
| 2018-01-19 | Use elasticsearch rather than mysql for local accounts...* Register local accounts onto elasticsearch rather than mysql.
* Login from the accounts on elasticsearch
* Harmonise local and oauth2 logins to use the same code.
| Muriithi Frederick Muriuki |
| 2018-01-19 | Add OAuth2 login code for ORCID...* Add code to handle the login via ORCID
| Muriithi Frederick Muriuki |
| 2018-01-19 | Update configurations...* Have the authorisation URLs build up from the client id and client
secret values.
| Muriithi Frederick Muriuki |
| 2018-01-19 | Add code to enable OAuth2 login...* Add some code to handle the login if the user chooses to login via
GitHub or ORCID.
| Muriithi Frederick Muriuki |
| 2018-01-19 | Delay after save for indexing...* Elasticsearch need a short delay after adding document for it to index
the document for subsequent access.
| Muriithi Frederick Muriuki |
| 2018-01-19 | Add more configuration variables....* Add configurations for elasticsearch and github.
| Muriithi Frederick Muriuki |
| 2018-01-19 | Add save_user() function...* On successful login via OAuth2, save the details of the user in
elasticsearch store, to avoid hitting the external provider for the
basic details.
| Muriithi Frederick Muriuki |
| 2018-01-12 | Add functions to help handle github login...* Add functions to help with the github OAuth2 login process
| Muriithi Frederick Muriuki |
| 2018-01-12 | Add elasticsearch_tools module...* Collect variables and functions for using the elasticsearch system in
a separate module.
| Muriithi Frederick Muriuki |
| 2018-01-12 | Add client_id and client_secret configurations...* Provide the OAuth2 client_id and client_secret values in configuration
variables.
| Muriithi Frederick Muriuki |
| 2018-01-10 | Add template elements for OAuth login...* Add html elements that will be used to prompt users to login with
either GitHub or ORCID.
| Muriithi Frederick Muriuki |
