| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2018-02-13 | @zsloan: we should introduce full parameter checking and sensible defaults ↵ | Pjotr Prins | |
| for every page we work on. It will help bug tracking. Probably fixes #279 | |||
| 2018-02-12 | Changed code parsing GEMMA output to fix issue where it wasn't getting the ↵ | zsloan | |
| correct p-values | |||
| 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 ↵ | zsloan | |
| suddenly decided to start running it when it wasn't in the past. Switched correlation table to tabulator | |||
| 2018-02-12 | Merge pull request #277 from pjotrp/gn-production | zsloan | |
| Gn production | |||
| 2018-02-11 | Added gunicorn pid so we can not run twice | Pjotr Prins | |
| 2018-02-11 | Using eventlet workers | zsloan | |
| 2018-02-10 | Fix env variable $GEMMA_WRAPPER_COMMAND | Pjotr Prins | |
| 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 | Muriithi Frederick Muriuki | |
| * 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. | |||
| 2018-02-09 | Add check for elasticsearch | Muriithi Frederick Muriuki | |
| * Add some extra checks to ensure that elasticsearch is running before presenting the UI to the user. | |||
| 2018-02-05 | Add code to allow user to change password | Muriithi Frederick Muriuki | |
| * 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. | |||
| 2018-02-05 | Refactor common items to more generic methods. | Muriithi Frederick Muriuki | |
| * Refactor code that can be used in more than one place to a more generic method/function that's called by other methods | |||
| 2018-02-05 | Send emails for forgotten passwords | Muriithi Frederick Muriuki | |
| * Update the code so that it sends out emails for the "forgot password" feature. | |||
| 2018-02-05 | Add SMTP configuration variables | Muriithi Frederick Muriuki | |
| * Add configuration variables to enable the system connect to the configured SMTP server to send out emails. | |||
| 2018-02-05 | Check each part of the PYTHONPATH | Muriithi Frederick Muriuki | |
| * PYTHONPATH may be composed of multiple locations in the filesystem, thus the need to test that each location exists and is a directory. | |||
| 2018-02-05 | Merge remote-tracking branch 'origin/testing' into testing | Muriithi Frederick Muriuki | |
| 2018-01-31 | Merge pull request #275 from pjotrp/pjotr | zsloan | |
| Added cli swith and set timeout to 3 minutes for gunicorn-dev mode | |||
| 2018-01-31 | Startup: longer timeout for gunicorn-dev mode | Pjotr Prins | |
| 2018-01-31 | Startup: added -cli option | Pjotr Prins | |
| 2018-01-30 | Merge pull request #274 from pjotrp/pjotr | zsloan | |
| Add gunicorn support | |||
| 2018-01-30 | gunicorn dev and prod modes added | Pjotr Prins | |
| 2018-01-30 | Fail safely if elasticsearch is down or unconfigured | Muriithi Frederick Muriuki | |
| * 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. | |||
| 2018-01-30 | Set to None if no value provided | Muriithi Frederick Muriuki | |
| * 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. | |||
| 2018-01-29 | Fixed gunicorn example | Pjotr Prins | |
| 2018-01-29 | Gunicorn works | Pjotr Prins | |
| 2018-01-29 | startup script: adapting for gunicorn | Pjotr Prins | |
| 2018-01-29 | Added checks in startup script, removed r-auwerx path | Pjotr Prins | |
| 2018-01-29 | Bumped version | 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 | zsloan | |
| 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 | |||
| 2018-01-19 | Use elasticsearch rather than mysql for local accounts | Muriithi Frederick Muriuki | |
| * Register local accounts onto elasticsearch rather than mysql. * Login from the accounts on elasticsearch * Harmonise local and oauth2 logins to use the same code. | |||
| 2018-01-19 | Add OAuth2 login code for ORCID | Muriithi Frederick Muriuki | |
| * Add code to handle the login via ORCID | |||
| 2018-01-19 | Update configurations | Muriithi Frederick Muriuki | |
| * Have the authorisation URLs build up from the client id and client secret values. | |||
| 2018-01-19 | Add code to enable OAuth2 login | Muriithi Frederick Muriuki | |
| * Add some code to handle the login if the user chooses to login via GitHub or ORCID. | |||
| 2018-01-19 | Delay after save for indexing | Muriithi Frederick Muriuki | |
| * Elasticsearch need a short delay after adding document for it to index the document for subsequent access. | |||
| 2018-01-19 | Add more configuration variables. | Muriithi Frederick Muriuki | |
| * Add configurations for elasticsearch and github. | |||
| 2018-01-19 | Add save_user() function | Muriithi Frederick Muriuki | |
| * On successful login via OAuth2, save the details of the user in elasticsearch store, to avoid hitting the external provider for the basic details. | |||
| 2018-01-19 | Add elasticsearch module to the path | Muriithi Frederick Muriuki | |
| * Add some code to set up the path for the python-elasticsearch module. | |||
| 2018-01-12 | Add functions to help handle github login | Muriithi Frederick Muriuki | |
| * Add functions to help with the github OAuth2 login process | |||
| 2018-01-12 | Add elasticsearch_tools module | Muriithi Frederick Muriuki | |
| * Collect variables and functions for using the elasticsearch system in a separate module. | |||
| 2018-01-12 | Add client_id and client_secret configurations | Muriithi Frederick Muriuki | |
| * Provide the OAuth2 client_id and client_secret values in configuration variables. | |||
| 2018-01-10 | Add template elements for OAuth login | Muriithi Frederick Muriuki | |
| * Add html elements that will be used to prompt users to login with either GitHub or ORCID. | |||
| 2018-01-10 | Add configuration variables for external services | Muriithi Frederick Muriuki | |
| * Add configuration variables for GitHub and ORCID which will be used by the system to allow users to login. | |||
| 2018-01-04 | Merge pull request #270 from pjotrp/testing | zsloan | |
| Merge some older commits | |||
| 2017-12-20 | Added submit_bnw even though it isn't working yet, just so views.py doesn't ↵ | zsloan | |
| throw an error | |||
| 2017-12-20 | Fixed issue that caused Mb ticks to get out of alignment for mapping figure | zsloan | |
| 2017-12-20 | Fixed the way PLINK outputs phenotype files (though there's still some ↵ | zsloan | |
| problem preventing it from working) Added some code related to new plotly probability plot, though it's commented out until it looks how I want it to Added some code for adding the BNW link to GN2, though it's not working yet Updated dataset menu structure JSON file | |||
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index : genenetwork2 | |
| GeneNetwork (2nd generation) |
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