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2018-03-26Skip automatic use of EXPLAIN_TEMPLATE_LOADING.Pjotr Prins
2018-03-26Refactor startup config for gunicorn and werkzeugPjotr Prins
2018-03-26FixPjotr Prins
2018-03-26Authentication: some mods around defaultsPjotr Prins
2018-03-26- Disabled PYTHONPATH injection - fix Guix instead, see ↵Pjotr Prins
https://github.com/pjotrp/genenetwork2/commit/63a5c8a42ad02e9126bb207465ff5eca98f6515d - Renamed WQFLASK_SETTINGS to GN2_SETTINGS
2018-03-26Fixing authentication stuff so it uses parameters properly. Also no ↵Pjotr Prins
PYTHONPATH needed as it is now in the Guix build.
2018-03-26Update module to make it more testableMuriithi Frederick Muriuki
* Update functions to make them more testable. * Update code using updated functions.
2018-03-26Check elasticsearch at point of useMuriithi 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.
2018-03-26Add check for elasticsearchMuriithi Frederick Muriuki
* Add some extra checks to ensure that elasticsearch is running before presenting the UI to the user.
2018-03-26Refactor 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
2018-03-26Add SMTP configuration variablesMuriithi Frederick Muriuki
* Add configuration variables to enable the system connect to the configured SMTP server to send out emails.
2018-03-26Fail safely if elasticsearch is down or unconfiguredMuriithi 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.
2018-03-26Set to None if no value providedMuriithi 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.
2018-03-26Update configurationsMuriithi Frederick Muriuki
* Have the authorisation URLs build up from the client id and client secret values.
2018-03-26Delay after save for indexingMuriithi Frederick Muriuki
* Elasticsearch need a short delay after adding document for it to index the document for subsequent access.
2018-03-26Add more configuration variables.Muriithi Frederick Muriuki
* Add configurations for elasticsearch and github.
2018-03-26Add save_user() functionMuriithi 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.
2018-03-26Add elasticsearch_tools moduleMuriithi Frederick Muriuki
* Collect variables and functions for using the elasticsearch system in a separate module.
2018-03-26Add client_id and client_secret configurationsMuriithi Frederick Muriuki
* Provide the OAuth2 client_id and client_secret values in configuration variables.
2018-03-26Add configuration variables for external servicesMuriithi Frederick Muriuki
* Add configuration variables for GitHub and ORCID which will be used by the system to allow users to login.
2018-02-10Fixed finding PATHs - one return statement!Pjotr Prins
2018-02-10Check for bimbam path and bail out if it is missingPjotr Prins
2017-12-20tools: find path for JS and gemma_wrapperPjotr Prins
2017-12-20Bring in some earlier work - mostly documentation and startup handlingPjotr Prins
2017-09-04gemma-wrapper: find binary in profilePjotr Prins
2017-06-12Fix binary paths for GEMMA_COMMAND, PYLMM_COMMAND and PLINK_COMMANDPjotr Prins
2017-06-02settings: do not enforce JS pathsPjotr Prins
2017-05-31JS_GUIX_PATH may not be therePjotr Prins
2017-05-31JS module handlingPjotr Prins
2017-05-21Merge 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
2017-02-06Fixed 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
2017-01-26GEMMA 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
2016-10-11Merge branch 'pjotr-gn2' into testingPjotr Prins
2016-10-09Add version informationPjotr Prins
2016-10-07Make sure JS path existsPjotr Prins
2016-10-07Changed error outputPjotr Prins
2016-10-07Saner handling of TMPDIR and TEMPDIRPjotr Prins
Throw error when TMPDIRs are not writable
2016-10-06Logger: add more granular debug messagesPjotr Prins
2016-10-05print statements should be loggerPjotr Prins
2016-10-03Config: supporting JSON OVERRIDESPjotr Prins
2016-10-03Debug: sanitize some outputPjotr Prins
2016-10-02Errors: added time stamps in UTCPjotr Prins
2016-09-25Make sure MAPPING_PATH existsPjotr Prins
2016-09-25tools: export GENENETWORK_FILES and move cache into TMPDIR/gn2Pjotr Prins
2016-09-10Support 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
2016-08-16Users 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).
2016-06-26gn_server: introduced one new query to fetch a dataset record and force ↵Pjotr Prins
fetch1 to return a tuple
2016-06-24Log: and document SQL callsPjotr Prins
2016-06-23Log: SQL queriesPjotr Prins
2016-06-23Logger: improved loggingPjotr Prins
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