Commit Graph

211 Commits

Author SHA1 Message Date
Helge Rausch
0d66e20918 Encrypt message body and subject (#500) 2018-06-14 11:33:39 +02:00
Bastian Greshake Tzovaras
44184dda33 remove all of fitbit (#482)
* remove all of fitbit

* try fixing migration

* add new structure sql

* 🐶

* add first test for das

* 🐶

* fix structure.sql
2018-01-19 11:29:07 -08:00
Helge Rausch
3ff2a59ac4 Setup sentry.io for exception tracking (#465)
* Setup sentry.io for exception tracking

* Hound happiness 🐶

* Set user context

* Hound happiness 🐶
2017-12-30 12:38:50 -08:00
Bastian Greshake Tzovaras
7d0382b93c Integrate Open Humans, remove Fitbit (closes #392)
* adds Open Humans connection (incl. at least some tests)
* removes the capability to add fitbit data (was broken in any case)
* display current fitbit data is still included, will be removed after grace period (needs to be announced to users)
2017-11-21 09:32:45 -08:00
Philipp Bayer
cf25d77185 Mateus' PR (#365), closes #264 #333
* Renaming '.env.example' to '.env'

* Removing bootstrap gem

* Adding newest version of Bootstrap(3.3.6) and setting it up

* Renamed 'database.yml.example' to 'database.yml'

* Deleted common.css.scss

* Deleting active_admin/application requirement

* Adding style file that import all style partials and adding javascript file

* Updating application.html.erb and includes(footer and navbar)

* Removing from news all the updates(new users, new pheno...) and putting on updates page

* Updating user views

* Updating phenotype views

* Updating index page

* Updating FAQ and Stats pages

* Updating genotype views

* Updating messages views

* Updating snps views and signin page

* Updating fitbit and picture_phenotype views

* Updating warning

* Adding base style and variable of style

* Adding style of index, faq and stats page

* Adding style for user views

* Adding style for footer and navbar

* Adding modules of style

* Adding style for fitbit, genotype, phenotype and message views

* Adding style for snps and updates views

* Updating serverscript

* Adding new logo and RSS new image

* Adding style files for: comments, password reset, picture phenotypes, achievements and search results

* Removing !important and updating some styles

* Updating view from achievements

* Updating views from fitbit profiles

* Updating genotypes views

* Updating navbar view

* Updating password reset view

* Updating phenotype comments views

* Updating phenotypes views

* Updating views: search result, snps, user phenotypes and users

* Updating views: updates and picture phenotypes

* Adding updates page's routes

* Modify flash messages and change number of fitbit profiles and genotypes per page(20 -> 15)

* Replace will_paginate to a version that works with bootstraps

* Change serverscript to make Sidekiq work propely

* Updates user's views

* Updates script to run only when page is fully loaded

* Moves script tags to head and updates flash messages' views

* Updates and add style for: picture_phenotypes, snps, userpages, press, warnings

* Updates views for: genotypes, messages, fitbit_profiles, phenotype comments, phenotypes

* Updates views for: picture phenotype, picture phenotype comments, warnings and errors, snps, snps comments

* Updates views for: press, picture phenotype user, user session and snps user

* Updates views from: user, updates, press and stats

* Updates views from: snps, picture phenotypes, phenotypes, genotypes

* Updates views from: fitbit profiles, navbar, application, messages and news

* Updates script file

* Updates style files

* Changes modal views

* Renaming '.env.example' to '.env'

* Removing bootstrap gem

* Adding newest version of Bootstrap(3.3.6) and setting it up

* Renamed 'database.yml.example' to 'database.yml'

* Deleted common.css.scss

* Deleting active_admin/application requirement

* Adding style file that import all style partials and adding javascript file

* Updating application.html.erb and includes(footer and navbar)

* Removing from news all the updates(new users, new pheno...) and putting on updates page

* Updating user views

* Updating phenotype views

* Updating index page

* Updating FAQ and Stats pages

* Updating genotype views

* Updating messages views

* Updating snps views and signin page

* Updating fitbit and picture_phenotype views

* Updating warning

* Adding base style and variable of style

* Adding style of index, faq and stats page

* Adding style for user views

* Adding style for footer and navbar

* Adding modules of style

* Adding style for fitbit, genotype, phenotype and message views

* Adding style for snps and updates views

* Updating serverscript

* Adding new logo and RSS new image

* Adding style files for: comments, password reset, picture phenotypes, achievements and search results

* Removing !important and updating some styles

* Updating view from achievements

* Updating views from fitbit profiles

* Updating genotypes views

* Updating navbar view

* Updating password reset view

* Updating phenotype comments views

* Updating phenotypes views

* Updating views: search result, snps, user phenotypes and users

* Updating views: updates and picture phenotypes

* Adding updates page's routes

* Modify flash messages and change number of fitbit profiles and genotypes per page(20 -> 15)

* Replace will_paginate to a version that works with bootstraps

* Change serverscript to make Sidekiq work propely

* Updates user's views

* Updates script to run only when page is fully loaded

* Moves script tags to head and updates flash messages' views

* Updates and add style for: picture_phenotypes, snps, userpages, press, warnings

* Updates views for: genotypes, messages, fitbit_profiles, phenotype comments, phenotypes

* Updates views for: picture phenotype, picture phenotype comments, warnings and errors, snps, snps comments

* Updates views for: press, picture phenotype user, user session and snps user

* Updates views from: user, updates, press and stats

* Updates views from: snps, picture phenotypes, phenotypes, genotypes

* Updates views from: fitbit profiles, navbar, application, messages and news

* Updates script file

* Updates style files

* Changes modal views

* Updates script file

* Add style file for modal

* Updates views from: snp comments, user phenotypes, modal and picture phenotypes

* Removes empty style files

* Moves comments style to modules directory

* Creates a more general class for containers and titles

* Removing more specific classes for containers and titles

* Changes load order, now variables are loaded before base styles

* Replaces all containers and titles classes with the more general class for them

* Corrects styles order and organization

* Updates minimum height for content container

* Organizes and refactors script file

* Updates views for fitbit and user

* Removes 'test-' from all classes and updates some views

* Updates settings view

* Updates gitignore

* Changes config files

* Removes some file from .gitignore

* Readds the example files

* Changes all unnecessary double-quotes to single-quotes

* Corrects script file

* Updates hound file to ignore JS files

* Hopefully merged both

* fixes typos, gem installation

* Adds missing pagination gem

* Deletes Vagrantfile

* Automatically replaced all pre Ruby 1.9 hashes with new style to satisfy Hound

* More changes for Hound, triggered by me automatically changing the hash syntax

* More hound changes

* Fully satisfy the hound

* Fix some more style issues, delete some old Vagrant stuff

* Fix usermailer complaints

* Changed some stuff in fitbit notification worker - prob. needs bigger refactor, long lines, cannot change

* Two more borked tests

* Get rid of useless asset pipeline errors

* Skipping search test for now.

* added about us here

* disclaimer now also for genotypes

* working a bit on the hound

* fixed FAQ language
2017-06-01 14:47:00 +02:00
Helge Rausch
906eef5403 Update gems (#338)
* Passwords now need to be 8 characters long (new default in authlogic).
* To login to the Sidekiq web interface, log in to opensnp.org, if you
  have the `admin` flag set, you will find it at the usual place.
* I finally found out why Rubocop didn't complain about the frozen string literal pragma missing and added all of them.
* Rubocop complained about keyword arguments, which is only relevant for Rails 5, so I disabled the cop.
* I removed the `inherit_from: .rubocop_todo.yml` from `.rubocop.yml`, so Hound does complain about **all** the issues. I also added a few tasks for running Rubocop.
2017-01-04 15:30:22 +01:00
Helge Rausch
8899a5f8d9 Fix with_number_of_users scope
Wrap the `with_number_of_users` scope in a `from()`, in order to not
break the `ActiveRecord` API.
2016-08-09 11:10:10 +02:00
Helge Rausch
cbdb713b73 Fix/move two tests 2016-08-08 14:08:43 +02:00
Helge Rausch
c9400bacd1 Refactor PhenotypesController#create 2016-08-08 14:08:43 +02:00
Helge Rausch
75cc203a93 Remove counter columns (#327)
* Remove counter columns

The equivalent operations take less then a millisecond, no need for
trying to keep counters up-to-date.

* Add `with_number_of_users` to Phenotype

* Use `number_of_users` instead of `user_phenotypes.length`

* Improve test
2016-08-07 19:07:10 +02:00
Philipp Bayer
b88242ad14 Cleanup cruft (#291)
* Removes broken html5.js from Google

* Replaces a few rocket-style links with modern Rails links. Replaces the dead Twitter feed on news page that used the dead Twitter APIv1 with a modern widget.

* Remove relic gem since it doesn't work at all ATM

* Forgot to run bundle install to remove from Gemfile.lock too

* Removes some overhang from Active Admin

* Bring back Snacks! No wait - bring back brackets!

* Removes one seventy seven URL since taken over by spam

* Update sign-in page with modern bootstrap, get rid of clearfix hacks

* Get rid of beautifier, no-one uses it. Remove some spans and labels from genotype upload form. form-stacked doesn't even exist anymore.

* Finally solves 2013 TODO about phenotype-arrays. Cleans up Phenotype-new form a bit.

* Minor cleanup of first-time user help header

* More terse form of helper method to satisfy hound

* Makes application help modal a bit more logical. FINALLY, after a thousand years, fixes that annoying 'missing tempplate' error message when closing help_one to help_three.

* Spruce up SNP comment form a little bit

* Get rid of empty or unused helpers

* Render nothing in a better concise way, cheers Helge
2016-06-22 17:48:14 +02:00
Helge Rausch
38c9da1e46 Schedule updating papers once a month 2016-06-19 11:36:55 +02:00
Helge Rausch
91645d4468 Fix genotype deletion 2016-06-11 10:10:15 +02:00
Vivek Rai
6d1faf8d14 Fix erroneous class name, Mendeley->MendeySearch
Signed-off-by: Vivek Rai <vivekrai.iitkgp@gmail.com>
2016-05-16 18:22:12 -07:00
Philipp Bayer
953e095569 Increase file limit to 400mb 2016-04-17 21:54:48 +08:00
Helge Rausch
7f3649797f Just destroy the genotype in DeleteGenotype worker 2016-04-12 08:52:49 +02:00
Helge Rausch
b81b826b99 Add dependent: :destroys to reflect foreign key constraints 2016-04-10 14:09:44 +02:00
Helge Rausch
20221e1b43 Remove IgnoreColumns concern 2015-12-31 12:40:37 +01:00
Philipp Bayer
f190afffad Makes {} nicer. Updates Gemfile a bit. Makes image RE nicer. 2015-11-06 18:08:39 +08:00
Philipp Bayer
0fd0903051 Fixes minor style problems 2015-11-06 14:09:48 +08:00
Philipp Bayer
92c096d076 Fixes bug with unreplaceable avatar. Removes obsolete rake tasks. Removes solr from serverscript. Slightly refactors edit page. 2015-11-06 14:02:42 +08:00
Philipp Bayer
fbf96424bd Dot beats rocket in the game of Ruby 2015-10-29 10:11:45 +08:00
Philipp Bayer
fb809a0abf Moves rake task into migration. Changes uniqueness constraint to stop the baying of the hounds. 2015-10-28 21:11:23 +08:00
Philipp Bayer
2d03669002 Adds uniqueness constraint on paper-SNP connection. Replaces rake task by SQL command. 2015-10-28 21:03:34 +08:00
Helge Rausch
43a6bd2c56 Move user_snps importing SQL into database 2015-10-20 22:30:33 +02:00
Calvyn82
1d30bf5a33 Removed deprecated file_link model and instance variables in controllers 2015-10-05 22:26:52 -05:00
Helge Rausch
c273a38a22 Move duplicate code into module 2015-07-20 09:03:22 +02:00
Helge Rausch
2ae8bac37d Add comments 2015-07-20 08:50:52 +02:00
Helge Rausch
5b8e119b32 Add default scopes, excluding HSTORE columns 2015-07-20 08:50:48 +02:00
Helge Rausch
4126d3afb7 Rename local_genotype to snp_variation SnpediaPaper 2015-07-08 08:39:53 +02:00
Helge Rausch
e6ac9c5210 Move list of SNPedia links to partial 2015-06-28 11:27:55 +02:00
Helge Rausch
472d719ebd Fix UserPhenotype search in Zipgenotypingfiles worker 2015-04-06 10:29:11 +02:00
Helge Rausch
cd9f1b9c8f Clean up a little... 2015-04-05 14:59:41 +02:00
Helge Rausch
518d91ba43 Get rid of deprecation warnings 2015-03-18 08:48:03 +01:00
Helge Rausch
280975e18e Get rid of most of the deprecation warnings 2015-03-15 19:05:51 +01:00
Helge Rausch
535ac823bf Fix tests 2015-03-15 14:34:32 +01:00
Helge Rausch
533b691dcf Use strong params 2015-03-15 11:29:45 +01:00
Philipp Bayer
d751a04b01 Merge pull request #139 from tsujigiri/pg_search
Ditch Solr for pg_search
2014-10-27 16:26:43 +01:00
Helge Rausch
4d898e06cd Change pg_search config's name to sth less generic 2014-10-27 09:52:30 +01:00
Helge Rausch
8d4ede024f Remove ActiveAdmin 2014-10-27 07:09:24 +01:00
Helge Rausch
17c0ff6165 Include all results in search feature test 2014-10-24 08:09:32 +02:00
Helge Rausch
632e9f3161 Match partial words in search 2014-10-23 14:35:25 +02:00
Helge Rausch
a7af758335 Ditch Solr for pg_search 2014-10-22 20:07:19 +02:00
Philipp Bayer
dd15c14af6 Turns off re-indexing in Solr when UserSNPs are added 2014-09-01 19:23:49 +10:00
Philipp Bayer
171f53dcec git pushMerge branch 'master' of github.com:gedankenstuecke/snpr 2014-09-01 10:50:03 +10:00
Philipp Bayer
0c5a693777 Prevents Solr reindexing of user on login. Users can now log in even if Solr is off. See http://stackoverflow.com/questions/6040493/sunspot-index-only-when-searchable-fields-change 2014-09-01 10:49:50 +10:00
Helge Rausch
ed55e1d900 Properly test genotype deletion 2014-08-30 15:12:06 +02:00
Helge Rausch
86b7b4afce Rewrite seeds in SQL to prevent Solr from indexing 2014-08-30 15:12:06 +02:00
Helge Rausch
22fb415630 Use update_column to prevent Solr from indexing 2014-08-22 09:16:25 +02:00
Helge Rausch
60967a0559 Associate User with UserSnp via Genotype 2014-08-09 09:11:52 +02:00