Commit Graph

423 Commits

Author SHA1 Message Date
Helge Rausch
9c2b66ee5b Fix Authlogic logic 2018-04-08 16:28:47 +02:00
Katrin Leinweber
1085647703 Hyperlink DOIs against preferred resolver (#487) 2018-02-21 11:10:05 +01:00
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
6d98c7e724 Remove superfluous respond_to calls 2017-12-31 13:02:34 +01:00
Helge Rausch
ae6caa7cf8 Refactor recommendations (#463)
* Refactor recommendations

* Hound happiness 🐶

* Use `find`

* Remove unreachable code

* Add a newline

* Load comments through association

* Add spaces

* Make recommendation lookup instance methods

* Woof! 🐶

* Move things around
2017-12-28 11:01:05 -08:00
Helge Rausch
22cf00be1c Fix Fixnum deprecation warning (#461)
* Fix Fixnum warning

* Fix Fixnum deprecation warning in PhenotypesController

* Who's a good boy? 🐶

* Fix fix

* Add test
2017-12-28 10:10:45 -08:00
Philipp Bayer
3b361c63f2 Cleans up download button - should also fix issue #436 (#451)
* Nicer words in data dump link

* Correct information in footer, tiny guy disappeared long ago, fare well!

* Fixes issue #436 on my end

* Fix test

* Satisfy hound
2017-12-11 23:00:57 +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
Bastian Greshake Tzovaras
54a89e79ee remove cruft (#434)
The params deletes that accidentally came back with #443 are gone.
2017-09-06 11:39:26 +01:00
Bastian Greshake Tzovaras
cdf80bc66a Update snps_controller.rb
🐶
2017-09-05 16:36:59 +01:00
Bastian Greshake Tzovaras
b20323f34e Update snps_controller.rb
quickly fixed my own code review to get the ball rolling. :)
2017-09-05 16:34:51 +01:00
Philipp Bayer
9e9ec11f6f Satisfy hound 2017-09-05 22:50:53 +08:00
Philipp Bayer
11ed2cf985 VERY hacky way of getting rid of unwanted params 2017-09-05 22:49:20 +08:00
Bastian Greshake
f29752b550 [MRG] fixed message deleting + added tests, closes #391 (#394)
* fixed message deleting + added tests

* hound, codeclimate, travis…
2017-06-08 10:19:30 +02:00
Philipp Bayer
41a8da6912 Get the user # not by counting all users, but by subtracting from the total count once 2017-06-03 14:26:29 +08:00
Philipp Bayer
328da2ab5f Replaces sorting by created_at by sorting by ID, faster 2017-06-03 13:15:45 +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
Bastian Greshake
e49bb51814 removed unnecessary helpers (#347) 2017-02-06 14:59:04 +01:00
Philipp Bayer
21f19c2e14 Merge pull request #330 from philippbayer/snp_update_feed
Snp update feed
2017-02-06 11:42:54 +08:00
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
Philipp Bayer
a5d780bef2 Fix minor bug with user ID not being given to service at all 2016-09-18 21:58:35 +08:00
Philipp Bayer
3021a4399a Fix double @ 2016-09-18 21:24:13 +08:00
Philipp Bayer
41260b955b Changes more easy to understand name - also fixes forgotten variable in users/show 2016-09-18 21:23:31 +08:00
Philipp Bayer
c7471494aa Implements Helge's suggestions 2016-09-18 21:18:00 +08:00
Philipp Bayer
a7ffa74fef Gets newest updates the other way around 2016-08-13 15:19:57 +08:00
Philipp Bayer
1055023f78 Works for now - adding tests next 2016-08-12 21:06:57 +08:00
Helge Rausch
ca667b0998 Prefer single quoted strings 2016-08-08 14:08:43 +02:00
Helge Rausch
c9400bacd1 Refactor PhenotypesController#create 2016-08-08 14:08:43 +02:00
Helge Rausch
38df04a6de Add notification email to phenotype entering test 2016-08-08 14:07:35 +02:00
Helge Rausch
5425422c3e Add test for not-yet-entered variations 2016-08-08 14:07:35 +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
Austin Richardson
40988cdaab reduces calls to DB for indexing genotypes (#324)
- pre-fetch users
- remove call to `Genotype.all` in index view which was causing `n_row` calls to `Genotype.all`. Do you really need the `#` column? If so, I can use `#each_with_index` or something instead.
2016-07-18 09:04:12 +02:00
Austin Richardson
2b8a8381c3 decreases calls to DB when vieweing phenotypes index (#318)
Indexing phenotypes is slow. I believe this is due to looping over the entire table at least once to build a JSON object which I don't think is even being used by the html or xml views.

- Moved the JSON generating code within the json block so it doesn't run when rendering HTML
- Changed the `each` loop to a `find_each` loop used in generating the JSON. This causes phenotypes to be fetched in batches.
- Eager load `user_phenotypes` to reduce DB calls.
2016-07-17 22:17:00 +02:00
Helge Rausch
1ac7d6729d Refactor and schedule recommender worker (#317) 2016-07-08 10:15:04 -04:00
Helge Rausch
1576611701 Obey the cop 2016-06-26 13:29:39 +02:00
Helge Rausch
04187e64b3 Fix SNP comments 2016-06-26 13:09:20 +02:00
Helge Rausch
79e2c698af Fix indentation in SnpCommentsController 2016-06-26 13:07:35 +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
Bastian Greshake
4879eebe1d fix fitbit emails, close #310 (#311)
* fix fitbit emails, close #310

* pleasing the hound and helge

* tab fixed?
2016-06-20 13:00:49 +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
Philipp Bayer
30684bed1a Fixes problem with user phenotype updates 2016-05-27 23:03:17 +08:00
Helge Rausch
7f3649797f Just destroy the genotype in DeleteGenotype worker 2016-04-12 08:52:49 +02:00
Helge Rausch
6d0c6348cd Update gems 2016-02-06 14:02:59 +01:00
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
Helge Rausch
8aec988fbf Move configuration into environment 2015-10-31 12:08:31 +01:00
Calvyn82
1d30bf5a33 Removed deprecated file_link model and instance variables in controllers 2015-10-05 22:26:52 -05:00
Helge Rausch
5b8e119b32 Add default scopes, excluding HSTORE columns 2015-07-20 08:50:48 +02:00
Bastian Greshake
dba6b477d9 added some style changes hound recommended 2015-06-11 22:10:31 +02:00
Bastian Greshake
b3398299aa fixed? tests, again 2015-06-11 13:38:49 +02:00