Replace YARD documentation with Tomdoc ...

These changes use the YARD gem, but in the lighter Tomdoc format.

You can read more about Tomdoc here: https://tomdoc.org

Refactored model code for better readability

Add extra validations for all models ...

- Includes specs using the Shoulda gem
- Includes a refactoring of update_numbers to a "sortable" abstraction

Add annotate gem for models and Gemfile

Remove Rails 3 attr accessible from models (#1691)

fix typo

fixes 1293 and one other reported issue

bugfixes/tweaks

init changes

update bug in answer.rb, fixes for rda_metadata.js

init changes

migration to add complete flag to plans. #154 ...

Integrate pre-fetching plan and phase from 25e2669

after_save callback for answer model with tests. #154

rake task to update completed plans. #154

statistics#completed_plans action done. #154

HTML view for completed plans and tweaks to JS file associated. #154

switched to use plan edit date ...

added plan.touch to answer as a callback

added nil check to callback to allow controller to catch and handle RecordNotFound exceptions

removed after_create callback for answers since no longer is needed after introducing transactions. DMPRoadmap/roadmap#893 ...

unit test for answer#is_valid?. DMPRoadmap/roadmap#893

answer#update based on current_user. input text for answer based on either answer.text or question.default_text. DMPRoadmap/roadmap#893

renamed answers#update to answers#create_or_update and added new tests. DMPRoadmap/roadmap#893

guidances_notes layout according to bootstrap. DMPRoadmap/roadmap#562 ...

new notes view according to bootstrap. Display logic for each view at JS. DMPRoadmap/roadmap#562

new notes working without js.erb templates. Fixed functional test broken. TODO update number of comments view. DMPRoadmap/roadmap#562

$.ajax attributes url and method extracted from closest form action and method attributes respectively. DMPRoadmap/roadmap#562

number of comments template and includes method at answer for abstracting logic. DMPRoadmap/roadmap#562

added question_options to answer's deep copy method and added a unit test for it. Updated several views to use .length instead of .count

fixed typo introduced during merge conflict resolution

resolved merge conflicts from merging development 2016-06-09 into CDL-MVP

Added method to validate answer according to each question format. Partial view for section progress. Eager loading of resources needed to calculate plan and section progress. Refactoring of code for progress plan. DMPRoadmap/roadmap#382 ...

Fixed merge conflict. DMPRoadmap/roadmap#382

onChange event for tinymce at plan answers. Removed unnecessary options passed to tinymce. DMPRoadmap/roadmap#382

Plan duplication functionality. ...

Ability to Create a Plan copy

removing guidances being copied over since they requrie omly references

Plan deep copy method to duplicate plans (associated answers and guidance_groups)

Append 'Copy of' to the title of a duplicated plan

Checkbox using rails FormHelper. Helper method at answer model for determining if an option should be selected. DMPRoadmap/roadmap#354

updates to locking mechanism because it ActiveRecord does not catch 2 creates DMPRoadmap/roadmap#241

Optimistic Locking ...

- add bit field to question_format so we don't have to test strings to determine format

- add isOptionBased to question so we dn't have to do multiple string comps for this - there was a boolean already in the DB not being used

- add migration to add bit field

- add migration to add lock_version field to answer

- change answers_controller to do optimistic locking

- change answers controller not to redirect to plans/phase/edit as it wasn't doing anything

- introduced answers/update.js.erb to handle the return from /answers/update.

- to do the conflict resolution you need the old answer and new answer objects. Tried using clone but it doesn't work because it only does a shallow copy. So adopted a "nuclear-option" deep copy but it's a bit much. A compromise would be better.

fixes post merge

merge in changes from origin

first port of plan creation and editing to new data model

finished up answer and note unit tests

unit tests for notes and answers. addded new validator to check whether the question's template matches the plans template

updated some of the plan.rb model to deal with outdated calls to dmptemplate. fixed up answer unit tests and added some validations to Answer

Moved orcid_id from users table to user_identifiers. Added option_based flag to question_formats. switched Object.const_defined to table_exists checks in db migrations because rails loads references to classes on demand so the objects are likely not defined when the migrations run. safer to check for the underlying table's existence