Update nokogiri (#1807) * Update nokogiri * Use up-to-date travis config from branch add_repository_premium_flag_and_lots_of_fixes * Remove sinatra group restriction

Update gems (#1743) * Update gem: simplecov to 0.12.0 * Update gem: elasticsearch to 2.0.0. * Update gem: kaminari to 1.17.0. * Update gem: rdf to 2.0.2. * Update gem: rdf-rdfxml to 2.0.0. * Update gem: rdf-n3 to 2.0.0. * Update gem: rest-client to 2.0.0. * Update gem: secure_headers to 3.4.0. * Update gem: d3_rails to 4.1.1. * Update gem: poltergeist to 1.10.0. * Update gem: webmock to 2.1.0. * Update gem: yard to 0.9.5. * Add comment about exception_notification requirements. * Add comment about active_model_serializers requirements. * Bundle update. * Obey Hound.

Remove profiler gem. (#1740)

Add puma_worker_killer gem

Fix deadlocks caused by semaphore. (#1732)

Update gem: Nokogiri to 1.6.8. (#1722)

982 error this iri is already being processed (#1697) * Add expiration parameter to Semaphore After the expiration, the semaphore is unlocked. This allows dead processes (e.g. by kill -9) to release the lock again. * Namespace the redis semaphore at ontohub:semaphore. * Code style. * Code style: use class << self block. * Add concurrency testing gem. * Completely revamp Semaphore * Put it into the same redis-namespace as sidekiq. * Add method to check if a lock is closed. * Namespace semaphores even deeper. Checking if a lock is closed is not an atomic operation. To make it atomic, we put the check into a mutexed part. In order to really exclude the locking and unlocking from this mutexed check, these two operations must be mutexed as well with the same key (LOCK_ACTION_KEY). Unfortunately, using many threads/processes in an example makes the test suite hang. This is because of celluloid. Maybe we can unskip the example after upgrading to sidekiq 4 and dropping sidetiq. * Add settings keys for Redis. * Use redis namespace setting for Semaphore. * Share redis connections between Sidekiq and Semaphore When all connections are in use, any Redis call will block until a connection is freed. Sidekiq is now namespaced deeper in order to prevent conflicts with the semaphore. * Fix locked? and perform_exclusively signatures. * Add lock and unlock methods. * Use separate redis namespaces for our environments. * Use Semaphore only if not testing * Use Semaphore when parsing an Ontology * Remove not needed method perform_async_on_queue. * Refactor all the Worker classes for parsing Now, all comes down to the new OntologyParsingWorker. It performs on a queue of triples containing the version id, options for the version and the try_count (number of the next parsing attempt). If parsing a version fails, it is put back to the queue (at the end), with an incremented try_count. If this happens too often for the same version, it is given to the SequentialOntologyParsingWorker that only parses one OntologyVersion at a time. The OntologyParsingPriorityWorker is a more elegant way to use the priotitized queue. All the background parsing is now performed via the OntologyParsingWorker or its subclasses. * Be explicit about the namespace. * Obey Hound.

Improve locId (#1618) * introduce new model to ontohub * introduce new locid behavior * adding try to prevent undefined method for nil * generate the locids by object creation * introduce method to simulate an attribute * generate Locids correctly for ontologies * correct creation of child_ontology locids * remove old uniqueness validation for ontology locid * use better names vor locidportion * correct behaviour for locid creation * generate loc_id correctly for ontology * use correct class for inherritanc * remove locids on deletion of objects * rename the base model * introduce data-migration to move the locids * remove double naming in the cat ontology * obey hound * correct behaviour of external repository for locid * change factory behaviour for locid * fix missing comma * begin to fix test * change ontology factory to new locid * change factories for new LocId Model * remove unneeded test * Use proper class retrieval in factories. * Always use to_s on the class call in LocIdBaseModel. * Always use .class.to_s instead of .class when used for the database. * Fix external repository. * Be clean and unstub again. * Fix sentence factory. * Quick fix the destruction of locids. * Fix code style. * Generate locids during create process: Base class. * Generate locids during create process: Mapping. * Generate locids during create process: Sentence. * Generate locids during create process: Symbol. * Generate locids during create process: ProofAttempt. * Generate locids during create process: ProverOutput. * Generate locids during create process: Ontology #1. * Generate locids during create process: Ontology #2. * Generate locids during create process: Ontology #3. * Generate locids during create process: Factories. * Fix seeds errors. * Fix ontology spec on error while parsing The ontology needs to be reloaded because sidekiq does so as well. It always fetches a fresh record from the database. The test failed before because `NodeEvaluationHelper#clean_ontology` called destroy on all the ontology's symbols which existed in the object, but were not really persisted because of an aborted transaction. * Remove redundant space. * Move comment to the correct line. * Fix worker_spec In the production code, the locid is never set before saving the ontology. * Add gems pry-stack_explorer, awesome_print for debugging purposes. * Only start hets if there was a hets error and rollback the changes. * Destroy dependent prover output. * Fix ProofAttempt factory. * Rename assorted_object to specific and fix migration. * Fix migration code style. * Reanalyze ontologies with duplicate locids. * Fix code style. * Remove redundancies. * Remove useless association. * Obey Hound. * Directly query in the LocIdBaseModel. * Add locid routing feature. * Cache LocId query results This should speed up the routing in a great extent. For each matching `specified_get`, the LocIdRouterConstraint fetched the element once from the database. This resulted in 8 times the same SQL query for a ProofAttempt. The implemented cache reduces this to a single query. * Clear the elements cache periodically to prevent memory leaks. * Add missing dependent: :destroy. * Add Recreating repository feature. * Combine if statements. * Change Given to When. * Catch ambiguous locid error. * Fix i18n key usage. * Fix code style. * Comment on error suppression. * Add spec for Syntax Error. * Use single-quoted strings. * Fix error message check: language. * Keep parameter assignment DRY. * Rename RecreatingRepository feature to Repository. * Use local_variable_get instead of eval. * Change locid column type to text. * Implement (implicit) down-migration. * Implement (explicit) down migration. * Add migration to create missing locids. * Fix nil error. * Really fix nil error. * Fix migration. * Fix sentence migration accessing association. * Force old Mappings to have a name. * Add missing locids to symbols.

Bundle update.

Retry ontology parsing when no hets instance available

Add test unit to Gemfile.

Bundle update.

Bundle update.

Security-update Rails to 3.2.22.2 This fixes * CVE-2016-2097 Possible Information Leak Vulnerability in Action View * CVE-2016-2098 Possible remote code execution vulnerability in Action Pack

Update rails.

Update gem nokogiri to 1.6.7.2.

Update gem devise to 3.5.5.

Bundle update.

Bundle update.

Bundle update.

Bundle update.

Bundle update.

Update puma.

Replace gem god by eye.

Update gems: Sidekiq, Sidetiq Celluloid 17.2 is needed for eye.

include rack-mini-profiler

Bundle update.

Update Sidekiq Fixes security issues - OSVDB-125678 - SIDEKIQ GEM FOR RUBY WEB/VIEWS/QUEUE.ERB MSG.DISPLAY_CLASS ELEMENT XSS - OSVDB-125676 - SIDEKIQ CROSS-SITE SCRIPTING(XSS) IN QUEUES PAGE - OSVDB-125675 - SIDEKIQ GEM FOR RUBY MULTIPLE UNSPECIFIED CSRF

Add redis semaphore.

Add redis semaphore.

Overwrite arrays in config The previous rails_config version didn't properly overwrite arrays. This version does overwrite them.

Add models: [Manual]AxiomSelection There will be more subclasses of AxiomSelection each with different attributes. To avoid creating many NULL values in the database, we use multiple table inheritance with the gem 'acts_as_relation'. This gem mimicks actual class inheritance of ruby with the method `acts_as`. The migration changes the has_and_belongs_to_many association between Axioms and ProofAttemptConfigurations to be between Axioms and AxiomSelections.

Add puma to production gems We don't specify a version because we don't expect any incompatibilities with puma and Ontohub.

Bundle update.

Use eugenk's rails_config version It seems like hnakamur's fork has been rebased and does not contain the desired commit any more. Until rails_config fixes the merging issue, we stay on eugenk's fork.

Update gems: rails-erd, ruby-graphviz.

Update gem: secure_headers.

Update gem: jquery-ui-rails.

Security update for redcarpet The new version fixes CVE-2015-5147

Update gem: rugged.

Temporarily set libv8 to a previous version The current version is not installable on several Linux clients.

Update the complete bundle.

Update the bundle for security fixes. rails 3.2.22 fixes CVE-2015-3227. jquery-rails 3.1.3 fixes CVE-2015-1840.

Use rails_config fork adding only overwrite_array When loading the hets.yml last, we don't need the patch to prepend sources. The only additional feature we need in rails_config is overwrite_array.

Downgrade gem again: inherited_resources It breaks out combinations feature. See #1340.

Update gem: capistrano.

Update gem: webmock.

Update gem: simplecov.

Update gem: secure_headers.

Update gem: rest-client.

Update gem: pry-byebug.

Update gem: momentjs-rails.

Update gem: i18n-tasks.

Update gem: exception_notification.

Update gem: yard.

Update gem: webmock.

Update gem: vcr.

Update gem: underscore-rails.

Update gem: simplecov.

Update gem: redcarpet.

Update gem: quiet_assets.

Update gem: pry-byebug.

Update gem: momentjs-rails.

Update gem: launchy.

Update gem: jquery-ui-rails Version 5.0.0 lead to problems with DELETE requests, but this seems to be fixed in 5.0.3. See db8fb18.

Update gem: jquery-rails.

Update gem: i18n-tasks.

Update gem: handlebars_assets As soon as #1253 is fixed, this needs to be tested: Visit an ontology graphs page and click on a node. If the Symbols are displayed correctly, this is okay.

Update gem: factory_girl.

Update gem: database_cleaner.

Update gem: d3_rails.

Update gem: compass Also removes blueprint because it is not used at all.

Update gem: capybara.

Replace gem: font_awesome by font-awesome-sass This gives us the current version of font-awesome. There were some breaking changes, but this commit adjusts the views as well.

Update gems: bootstrap-sass, bootstrap-select-rails.

Update gem: better_errors.

Update gems: sidekiq, sidetiq.

Update gem: secure_headers.

Update gem: rails-erd The new version only adds functionality according to the project's changelog.

Update gems: rdf, rdf-rdfxml, rdf-n3.

Update gem: nokogiri.

Update gem: inherited_resources.

Update gem: pg.

Update gem: foreigner.

Update gem: devise.

Update gem: acts_as_tree The new version only adds functionality according to the project's commit messages.

Update gem (critical): rugged.

Update gem (critical): rest-client.

Update the bundle.

Remove puma from Gemfile again.

Include Gemfile.lock.

add rspec-its to prevent deprecation.

add rspec-activemodel-mocks to prevent deprecation.

Load hets.yml before the others This allows to overwrite the hets settings in `*.local.*` files.

Update rails_config to allow overwriting arrays The old rails_config always merged arrays. The new version allows arrays to be overwritten. For example settings.yml could define some_array: - foo - bar and settings.local.yml could define: some_array: - baz The new version reads ['baz'] while the old one reads ['foo', 'bar', 'baz']. We need this new behaviour for a secure production configuration. Also the Rails dependency is removed so that we can use it in our light environment.

Add json-stream gem.

upgrade specroutes This is for the newly implemented reroutes feature, which allows rerouting to a different controller based on mime-type. Additionally this gets us the allstar feature and a breaking reversal of standard allstar handling (it is deactivated by default).

add the json-schema gem to test.

switch rabl for activemodel serializers ActiveModel::Serializers seems the way to go since it uses POROs instead of its own external language for defining serializations.

Use gem poltergeist for integration tests.

Update invoker.

upgrade specroutes to current version.

Add repository undelete functionality.

Add data_migrate gem.

add specroutes to Gemfile, upgrade rails to 3.2.21 This also upgrades rails as this is necessary via the dependency entry for specroutes. Additionally it also makes sense to use the latest bugfixes.

added indefinite article gem

Fix view for searchbar so it looks equal The searchbar looked weird in firefox, the bootstrap select gem should make it look equal in every browser.

Deleted leftovers of solr in the Gemfile.

Add pry-byebug gem. This allows us to navigate through the code with the debugger.

introduce i18n-tasks gem with thoughtbot config

revert jquery-ui-rails gem to version 4 With version 5.0.0, delete links created by link_to did result in a GET request. With version 4.2.1 they correctly created a DELETE request.

remove coveralls from project.

remove unused gems diffy, byebug and pry-byebug were removed as gem-dependencies as we do not currently use them or plan to use them in the near future.

be safe through twiddle-wakka version operator The twiddle-wakka version operator in the Gemfile should keep us safe of unexpected major version upgrades. See http://robots.thoughtbot.com/rubys-pessimistic-operator for more twiddle-wakka information.

Update assorted gems Here is a list produced by bundle update: Updating git://github.com/tristanm/jstree-rails.git Updating git://github.com/digineo/sunspot.git Updating git://github.com/llwt/codemirror-rails.git Updating git://github.com/0robustus1/ontology-united.git Installing coffee-script-source 1.7.1 (was 1.7.0) Installing i18n 0.6.11 (was 0.6.9) Installing tzinfo 0.3.40 (was 0.3.39) Installing execjs 2.2.1 (was 2.2.0) Installing netrc 0.7.7 Installing diffy 3.0.6 (was 3.0.4) Installing ice_cube 0.12.1 (was 0.12.0) Installing slop 3.6.0 (was 3.5.0) Installing rdf 1.1.4.3 (was 1.1.4) Installing redis 3.1.0 (was 3.0.7) Installing rspec-core 2.99.1 (was 2.99.0) Installing rspec-mocks 2.99.2 (was 2.99.1) Installing faker 1.4.2 (was 1.3.0) Installing simplecov 0.9.0 (was 0.8.2) Installing compass 0.12.7 (was 0.12.6) Installing rspec-expectations 2.99.2 (was 2.99.0) Installing coffee-script 2.3.0 (was 2.2.0) Installing uglifier 2.5.3 (was 2.5.1) Installing rubydns 0.8.5 (was 0.8.4) Installing rest-client 1.7.2 (was 1.6.7) Installing redis-namespace 1.5.1 (was 1.4.1) Installing cucumber 1.3.16 (was 1.3.15) Installing shoulda-matchers 2.6.2 (was 2.6.1) Installing pry-byebug 1.3.3 (was 1.3.2) Installing sidekiq 3.2.1 (was 3.1.4) Installing capistrano-bundler 1.1.3 (was 1.1.2) Installing acts_as_tree 2.0.0 (was 1.6.1) Installing sidekiq-failures 0.4.3 (was 0.4.2) Installing d3_rails 3.4.10 (was 3.4.8) Installing jquery-rails 3.1.1 (was 3.1.0) Installing jquery-ui-rails 5.0.0 (was 4.2.1) Installing momentjs-rails 2.8.1 (was 2.7.0) Installing quiet_assets 1.0.3 (was 1.0.2) Installing nokogiri 1.6.3.1 (was 1.6.2.1) Installing capybara 2.4.1 (was 2.3.0) The 'using' lines were removed.

update usage of ontology-united with vars.

bump rugged to 0.21.0

updatet rails to 3.2.19

add invoker to Gemfile.

add new bounds for rails_config Versions greater than 0.3 (0.4 series and up) won't work for us, as they require to be loaded inside a rails environment.

upgrade every bundled gem in bounds.

upgrade sidekiq to 3.1 and sidekiq dependents Additionally upgrade sidetiq and sidekiq-failures.

bump rugged to current development version

adding cucumber-rails gem

add underscore.js dependency.

Rails update.

require ontology-united This gem should allow us to write ontologies for testing purposes in a small dsl.

Fixed wrong git URL for codemirror.

use codemirror for displaying file contents

Gems updated

Gems updated

Updated rails to 3.2.17.

Sidekiq and Faker updated

Coveralls added

SimpleCov added SimpleCov is a code coverage analysis tool that generates awesome reports after running our test suite.

Gems updated

Capistrano updated

Upgrade to Devise 3 solves #564

Migration to Capistrano 3

More gem updates.

Updated some gems.

add sidekiq-failures for more detailed infos.

pry-byebug added

Rails updated

Sidekiq and Sidetiq updated

Tests can be started again.

generating necessarily controllers

Categories javascript should work now on production too

New gemfile

fix text of paths_starting_with

bootstrap-sass updated

Added better_errors and binding_of_caller.

Simple REST API for listing/updating Repositories and Ontologies

bundle update

Periodic updating of remote repositories implemented.

carrierwave removed not used any more

Categorys view working with dagnabit

ExceptionNotification updated

Rails updated

Migrated from resque to sidekiq Sidekiq has some great features and offers multithreading.

close #281

Repaired inclusion of bootstrap3.

Tests fixed

RSpec added Conflicts: Gemfile.lock

dagnabit gem

Updated gems (and testing github-merge-hook deployment).

Add top navbar

add cloning feature to backend two tests fail because a shallow clone has a faulty parents-reference in the oldest cloned commit

Add commit information in files view

prepare for codemirror

Gems updated

Debugger added

Debugger added

new Gemfile.lock

use pry instead of irb for rails console.

add hamlbars gem for 'hb'-helper support.

add handlebars as gem dependency.

Parser EntityMapping in Links

Bundle Update

update bundled gems.

remove jit from application.

add category framework

Updated rugged

Gems updated

add necessary hets paths - also remove mysql - and remove some mocha deprecation warnings.

add d3 support via Gemfile.

remove mysql-gem from Gemfile - We actually use PostgreSQL now, so we don't need the mysql-gem anymore.

secure_headers added

Attachments with carrier_wave removed, commit_oid for Git commits added.

font_awesome and bootstrap-sass updated

Create (untested) git lib

Add gemfile lock

localice supports, fixes #123

shoulda_update

Ooops parser is able to parse responses.

OOPS client and tests added.

font_awesome added

Switched to a bootstrap fork with javascript fixes.

use thejit as gem and add context-menu

Revert "Capistrano removed, will be restored in the deployment branch." This reverts commit 53cacd694ed31d42ea292fffef8cbf3c56eeb2ba.

Capistrano removed, will be restored in the deployment branch.

rails_config and exception_notification added

Gems updated

Using latest version of inherited_resources

Had to add rack-protections manually.

Other gems updated

Rails updated

fix registry-import if iris are already existing

add serializations Bug #83

Using inherited_resources from Git to get compatibility with Ruby 2.0.

Gems updated

Ruby p392. Updated gems capybara and capybara-webkit.

Migrated from formtastic to simple_form, it has great bootstrap support.

jQuery updated

Bootstrap updated

Capistrano updated

Integration test written with capybara-webkit to test adding permissions.

Rails updated

Some gems updated

Devise updated

Read logics from registry ontology WARNING: there are logic iris which are malformed iris

p374 as default, documentation dependencies and link in README.md, therubyracer update.

Add example languages to the seeds

Rails updated... again :-(

Rails updated

gems updated

Capistrano upgraded

Rails upgraded

Switched to postgresql again

quiet_assets added

Import of distributed ontologies works

Added rails-erd gem to Gemfile. Use "rake erd" to generate a ERD of the current model.

Rails updated

Merge branch 'master' into bootstrap Conflicts: Gemfile.lock

gems updated

Remove PostgreSQL dependency

redis namespace added

deployment to staging.ontohub.org

newrelic removed

rvm-capistrano added

Gems updated

formtastic-plus-bootstrap added

Add first integration test

Add progress bar

Deprecation Warnings removed

Updated Rails to 3.2.5

Bootstrap Integration improved

Replaced relatizeDate by moment.js

Update database Change database system

Navigation, Tooltips, Pagination and Tables styled

Migration to Boostrap started

Gemfile updated

compass updated

use my fork of sunspot

We don't need no Barbosa..

Changes to language model and file name generation for ontologyversion download.

bundle updated

Desperate trial of carrierwave from git to validate file upload size correctly with passenger.

bundle update

[#26337061] Entity search implemented with sunspot+solr

newrelic integrated

haml replaced by haml-rails

built in mocha

jquery-ui-rails integrated

CanCan integrated

A god to monitor resque.

Asynchronous parsing by hets.

OntologyUploader with carrierwave and OntologyVersion factory.

strip_attributes added

#[26147381] Pagination for Ontologies, Entities, Axioms and Users

more tests

Written some fancy CSS styles and rewritten the devise views with formtastic.

Admin::Users-Controller and Views created

Session-Views and User tests created.

Models: Logic, Ontology, OntologyVersion

capistrano

Devise integrated

SAX Parser for XML including symbols implemented

rails skeleton