| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 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 | Add SMTP configuration variables | Muriithi Frederick Muriuki | |
| * Add configuration variables to enable the system connect to the configured SMTP server to send out emails. | |||
| 2018-01-30 | 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. | |||
| 2018-01-19 | Update configurations | Muriithi Frederick Muriuki | |
| * Have the authorisation URLs build up from the client id and client secret values. | |||
| 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. | |||
| 2018-01-12 | 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 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. | |||
| 2017-12-20 | tools: find path for JS and gemma_wrapper | Pjotr Prins | |
| 2017-12-20 | Bring in some earlier work - mostly documentation and startup handling | Pjotr Prins | |
| 2017-09-04 | gemma-wrapper: find binary in profile | Pjotr Prins | |
| 2017-06-12 | Fix binary paths for GEMMA_COMMAND, PYLMM_COMMAND and PLINK_COMMAND | Pjotr Prins | |
| 2017-06-02 | settings: do not enforce JS paths | Pjotr Prins | |
| 2017-05-31 | JS_GUIX_PATH may not be there | Pjotr Prins | |
| 2017-05-31 | JS module handling | Pjotr Prins | |
| 2017-05-21 | Merge from the diet branch. | Pjotr Prins | |
| * refactored ./bin/genenetwork2 and /etc/default_settings - better detection of Guix - removed unused parameters, such as GEMMA_RESULT_PATH and TEMP_TRAITS - removing some default settings, such as PYLMM_COMMAND - rename some settings, such as SQL_URI and LOG_SQL_ALCHEMY - added GUIX_JS_PATH for JS modules * Added documentation on installing binary GN2 * Updated Twitter board to latest version in Guix - it had broken * Updated many tools in the latest Guix profile | |||
| 2017-02-06 | Fixed appearance of several tables (search, mapping results, sample data) | zsloan | |
| Temporarily removed second sample table for CFW traits Fixed location of global search bar to work with wider screens | |||
| 2017-01-26 | GEMMA now works with CFW data (had to update where it looks for the input ↵ | zsloan | |
| files and how it writes the phenotype file) Y-axis for GEMMA now says -log(p) Updated the style of the trait sample data table in the trait page Updated dataset_select_menu_orig.js to also build just the Species and Group drop-downs for the trait input page (as opposed to all 4 drop-downs) Updated dataset menu json file Added option to show and hide columns to regular search page using colVis Changed regular and global search result table styles/column widths Began work on user trait submission code (not working yet though) Began work on static loading page for mapping results | |||
| 2016-10-11 | Merge branch 'pjotr-gn2' into testing | Pjotr Prins | |
| 2016-10-09 | Add version information | Pjotr Prins | |
| 2016-10-07 | Make sure JS path exists | Pjotr Prins | |
| 2016-10-07 | Changed error output | Pjotr Prins | |
| 2016-10-07 | Saner handling of TMPDIR and TEMPDIR | Pjotr Prins | |
| Throw error when TMPDIRs are not writable | |||
| 2016-10-06 | Logger: add more granular debug messages | Pjotr Prins | |
| 2016-10-05 | print statements should be logger | Pjotr Prins | |
| 2016-10-03 | Config: supporting JSON OVERRIDES | Pjotr Prins | |
| 2016-10-03 | Debug: sanitize some output | Pjotr Prins | |
| 2016-10-02 | Errors: added time stamps in UTC | Pjotr Prins | |
| 2016-09-25 | Make sure MAPPING_PATH exists | Pjotr Prins | |
| 2016-09-25 | tools: export GENENETWORK_FILES and move cache into TMPDIR/gn2 | Pjotr Prins | |
| 2016-09-10 | Support for running maintenance scripts so they can pick up all webserver ↵ | Pjotr Prins | |
| settings Run with ./bin/genenetwork2 ~/my_settings.py -c ./wqflask/maintenance/gen_select_dataset.py | |||
| 2016-08-16 | Users can now select specific traits from collection when using collection ↵ | zsloan | |
| tools (correlation matrix, wgcna, etc) To do the above, changed the way form submission worked for those features; previously each feature had its own form, but that was dumb so instead I wrote a javascript function that just changed a single form's target url Duplicate traits can no longer by added to collections Fixed the digits for a few table columns in collection (additive effect, etc). | |||
| 2016-06-26 | gn_server: introduced one new query to fetch a dataset record and force ↵ | Pjotr Prins | |
| fetch1 to return a tuple | |||
| 2016-06-24 | Log: and document SQL calls | Pjotr Prins | |
| 2016-06-23 | Log: SQL queries | Pjotr Prins | |
| 2016-06-23 | Logger: improved logging | Pjotr Prins | |
| 2016-06-23 | Logger: prettify | Pjotr Prins | |
| 2016-06-23 | Settings: add GN_SERVER_URL | Pjotr Prins | |
| 2016-06-23 | Add warnings for adding MySQLdb cursor | Pjotr Prins | |
| 2016-06-21 | log: replace print statements | Pjotr Prins | |
| 2016-06-21 | logger: add format field (reserve) | Pjotr Prins | |
| 2016-06-21 | Use logger also for benchmarking | Pjotr Prins | |
| 2016-06-21 | Logger: switch for logging SQLALCHEMY | Pjotr Prins | |
| 2016-06-21 | Benchmarking: allow output select with LOG_BENCH | Pjotr Prins | |
| 2016-06-21 | Logger: SQL | Pjotr Prins | |
| 2016-06-19 | gn_server: Species info can be fetched from gn_server | Pjotr Prins | |
| 2016-06-19 | gn_server: SQL handling | Pjotr Prins | |
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index : genenetwork2 | |
| GeneNetwork (2nd generation) |
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