Commit Graph

216 Commits

Author SHA1 Message Date
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
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
7745ac70c3 adds fake phenotypes for seeding development database (#319) 2016-07-19 10:13:00 +02:00
Helge Rausch
105515efa9 Move Frequency jobs to frequency queue
In order to not block the parsing jobs, move the frequency jobs to a
different queue.
2016-06-26 14:28:25 +02:00
Helge Rausch
2163baecdf Update structure.sql
I ran `rake db:structure:dump` on production, so we are up-to-date with
the production database after adding the foreign keys and removing old
tables.
2016-05-16 10:38:06 +02:00
Philipp Bayer
58b788730d Forgot the migration - fixes rollback - also adds another foreign key constraint on userachievements 2016-02-07 12:51:57 +08:00
Philipp Bayer
0b218a7a66 Adds foreign key restraints 2016-02-07 12:47:14 +08:00
Philipp Bayer
9ec897ba96 adds structure.sql 2015-11-19 16:07:48 +08:00
Philipp Bayer
552798dbe5 Minor style changes 2015-11-19 16:05:40 +08:00
Philipp Bayer
6dfc630ed9 Adds migration that removes possibly dangling DB entries 2015-11-19 15:57:09 +08:00
Philipp Bayer
521124460c Renames backup indexes, adds new ones for snp_references 2015-10-28 21:58:51 +08:00
Philipp Bayer
5389c4c17e Reintroduces lost index 2015-10-28 21:39:31 +08:00
Philipp Bayer
74a7a29e51 Adds missing structure for Travis 2015-10-28 21:14:25 +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
Helge Rausch
43a6bd2c56 Move user_snps importing SQL into database 2015-10-20 22:30:33 +02:00
Helge Rausch
a5f3ac8d37 Dump production schema 2015-07-14 08:59:09 +02:00
Bastian Greshake
d8610a6462 workaround for setting up new db 2015-06-11 22:57:15 +02:00
Philipp Bayer
f608b9c16f Reintroduces proper schema.rb 2014-09-01 11:59:01 +10:00
Philipp Bayer
60e3d59f2b Turns off commit after every model save, instead turning over to autocommit every 10s or 1000 new objects 2014-09-01 11:27:47 +10:00
Helge Rausch
86b7b4afce Rewrite seeds in SQL to prevent Solr from indexing 2014-08-30 15:12:06 +02:00
Helge Rausch
c713f40f59 Include Snp creation in genotype parsing 2014-08-30 15:12:06 +02:00
Helge Rausch
649c9bd5cd Update schema.rb with current production dump 2014-08-16 15:05:02 +02:00
Philipp Bayer
5558c569bd Fixes genome browser 2014-06-27 11:33:07 +10:00
Philipp Bayer
9eca0da0a5 Updates paperclip to 4.0, fixes tests 2014-05-15 15:17:29 +10:00
Philipp Bayer
1f8ea2ae43 Picture phenotypes' description now longer than 255 chars 2014-05-09 11:49:18 +10:00
Philipp Bayer
254f52515d Removes standard 0 from user_snps count 2014-02-27 21:16:25 +10:00
Helge Rausch
f0ed9d477e Speed up user_snps_count initialization in migration 2014-02-21 09:28:14 +01:00
Philipp Bayer
8499c6a912 Adds user_snps_count column to all SNPs 2014-02-21 16:48:04 +10:00
Philipp Bayer
ab57bfbcda Removes unnecessary index 2014-01-20 10:58:34 +10:00
Helge Rausch
3986370bfb Actually removing snp_id column from papers 2013-12-24 14:54:42 +01:00
Helge Rausch
a3db5692f8 Removing snp_id from PlosSearch worker 2013-12-24 14:17:21 +01:00
Helge Rausch
57e00f1729 renaming Reference to SnpReference
Turns out, 'reference' is a reserved word in PostgreSQL.
2013-12-01 14:36:29 +01:00
Helge Rausch
39506b1800 adding migration for references 2013-11-30 13:08:00 +01:00
Helge Rausch
7d439cc505 many-to-many association between snps and papers 2013-11-17 12:20:22 +01:00
Philipp Bayer
9e07fe7525 Fixes problems with uploading of some files (notably, AncestryDNA) 2013-10-28 15:56:18 +10:00
Philipp Bayer
de27297249 Updates gems and rails to remove 2 security vulnerabilities. Fiddles around with sunspot and devise config to get new versions to run. UPDATE YOUR app_config.yml 2013-10-28 15:45:18 +10:00
Helge Rausch
77b1521186 refactoring MendeleySearch
It now processes each page of results before proceeding to the next one.
This way we shouldn't have any issue with this job sucking up all the
memory anymore, when there are a lot of results.
2013-09-08 09:35:38 +02:00
Philipp Bayer
0c238d92a7 Do not create an admin by default 2013-09-04 16:06:29 +10:00
Philipp Bayer
2338031bc8 Implements basic ActiveAdmin installation. Next: Pages for users, phenotypes and eventually curated phenotypes. 2013-09-04 11:16:52 +10:00
Helge Rausch
d9b1389230 reverting drop_snp_name_from_user_snps 2013-09-03 10:23:31 +02:00
Philipp Bayer
46d9dd8d9d Added small note on opposite strand genotypes 2013-07-20 15:41:10 +10:00
Helge Rausch
f44e4936af dropping snp_name column from user_snps 2013-06-30 14:44:53 +02:00
Philipp Bayer
f5bf89de40 Added missing index on Mendeley_papers (based on snp_name) 2013-06-08 23:59:03 +10:00
drsnuggles
43540836c9 Updated gems. Installed extra-gem to assign only one worker per API-queue. Added config for that. 2013-03-19 10:03:02 +10:00
drsnuggles
02c96d96f9 Made workers independent from iconv for Ruby 2.0. SNPs-controller slightly faster in non-JSON. 2013-03-18 21:13:07 +10:00
drsnuggles
3d57b8a816 Added newest Rails, JSON-gem versions 2013-02-12 08:17:44 +10:00
Bastian Greshake
29b85530c8 fixed fitbit-display 2013-02-03 17:29:34 +01:00
drsnuggles
5a5a1618b3 Fixed Mendeley-parser to overwrite the data for existing papers that have empty titles with the information the API returns 2013-02-03 16:17:01 +10:00
drsnuggles
c0814d9496 Added minimal 23andme-testfile for annotation testing. Fixed SNPedia-parser to not include summaries for SNPs when SNPs are redirects. 2013-02-03 15:29:52 +10:00