source stringclasses 1
value | repo stringlengths 5 63 | repo_url stringlengths 24 82 | path stringlengths 5 167 | language stringclasses 1
value | license stringclasses 5
values | stars int64 10 51.4k | ref stringclasses 23
values | size_bytes int64 200 258k | text stringlengths 137 258k |
|---|---|---|---|---|---|---|---|---|---|
github | PecanProject/bety | https://github.com/PecanProject/bety | app/helpers/bulk_upload_helper.rb | Ruby | bsd-3-clause | 19 | develop | 4,825 | module BulkUploadHelper
MAXIMUM_ERRORS_TO_DISPLAY_PER_TYPE = 10
# maps data reference errors to appropriate page for finding or
# adding referents
ERROR_REMEDY_MAP = {
unresolvable_citation_reference: { link_url: :citations, link_text: "Search for or add citation" },
unresolvable_site_reference: { lin... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/helpers/application_helper.rb | Ruby | bsd-3-clause | 19 | develop | 9,570 | # Methods added to this helper will be available to all templates in the application.
module ApplicationHelper
DATA_ACCESS_LEVELS = [ ["1. Restricted", 1], ["2. Internal & Collaborators", 2], ["3. External Researcher", 3], ["4. Public", 4] ]
ABBREVIATED_DATA_ACCESS_LEVELS = [ ["1. Restricted", 1], ["2. Internal", ... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/helpers/users_helper.rb | Ruby | bsd-3-clause | 19 | develop | 3,825 | module UsersHelper
#
# Use this to wrap view elements that the user can't access.
# !! Note: this is an *interface*, not *security* feature !!
# You need to do all access control at the controller level.
#
# Example:
# <%= if_authorized?(:index, User) do link_to('List all users', users_path) end %> ... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/helpers/formats_helper.rb | Ruby | bsd-3-clause | 19 | develop | 9,207 | module FormatsHelper
# $mime_types = ["applicaiton/x-bytecode.python", "application/acad", "application/arj", "application/base64", "application/binhex", "application/binhex4", "application/book", "application/cdf", "application/clariscad", "application/commonground", "application/drafting", "application/dsptype", "a... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/lib/api/csv_handler.rb | Ruby | bsd-3-clause | 19 | develop | 8,561 | require 'memoist'
module Api::CsvHandler
extend Memoist
class BadHeading < Exception
end
STAT_HEADING_NAMES = ["SE", "n"]
CITATION_HEADING_NAMES = ["citation_doi", "citation_author",
"citation_title", "citation_year"]
CHILD_ELEMENT_HEADING_NAMES = ["site", "species", "treatme... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/lib/api/trait_creation_support.rb | Ruby | bsd-3-clause | 19 | develop | 17,370 | module Api::TraitCreationSupport
include JsonHandler, CsvHandler
private
# Exception to signal document didn't validate against schema or had other
# structural problems not captured by the schema constraints.
class InvalidDocument < StandardError
end
# Exception used for various data errors that prev... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/lib/api/json_handler.rb | Ruby | bsd-3-clause | 19 | develop | 1,159 | module Api::JsonHandler
private
##### JSON HANDLING #####
def json_2_xml(json_string)
doc_as_hash = Yajl::Parser.parse(json_string)
doc = Nokogiri::XML::Document.new
def create_element(doc, hash)
if hash.keys.size != 1
raise "Unexpected hash size"
end
element_name = has... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/lib/utilities/sql_comments.rb | Ruby | bsd-3-clause | 19 | develop | 750 | module Utilities::SQLComments
def self.get_column_comment(table_name, column_name)
query = <<-QUERY
SELECT d.description FROM pg_description d
JOIN information_schema.columns c
ON (c.table_schema = current_schema
AND (current_schema || '.' || c.table_name)::regclass =
... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/formats_controller.rb | Ruby | bsd-3-clause | 19 | develop | 5,088 | class FormatsController < ApplicationController
before_action :login_required
helper_method :sort_column, :sort_direction
def rem_formats_variables
formats_variable = FormatsVariable.find(params[:id])
@format = formats_variable.format
formats_variable.destroy
respond_to do |format|
format... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/workflows_controller.rb | Ruby | bsd-3-clause | 19 | develop | 1,604 | class WorkflowsController < ApplicationController
before_action :login_required, :except => [ :show ]
helper_method :sort_column, :sort_direction
require 'csv'
# GET /workflows
# GET /workflows.xml
def index
if params[:format].nil? or params[:format] == 'html'
@iteration = params[:iteration][/\d... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/inputs_runs_controller.rb | Ruby | bsd-3-clause | 19 | develop | 1,753 | class InputsRunsController < ApplicationController
before_action :login_required, :except => [ :show ]
require 'csv'
# GET /inputsruns
# GET /inputsruns.xml
def index
params[:format] = 'xml' if params[:format].nil?
# We have a lot of params and they or may not have to be
# passed as conditions ... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/pfts_species_controller.rb | Ruby | bsd-3-clause | 19 | develop | 1,782 | class PftsSpeciesController < ApplicationController
before_action :login_required, :except => [ :show ]
require 'csv'
# GET /pftsspecies
# GET /pftsspecies.xml
def index
params[:format] = 'xml' if params[:format].nil?
# We have a lot of params and they or may not have to be
# passed as conditio... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/yields_controller.rb | Ruby | bsd-3-clause | 19 | develop | 7,443 | class YieldsController < ApplicationController
before_action :login_required, :except => [ :show ]
helper_method :sort_column, :sort_direction
require 'csv'
def checked
id = params[:id]
y = Yield.all_limited(current_user).find(id)
if y
y.checked = params[:y][:checked]
end
@element_... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/priors_controller.rb | Ruby | bsd-3-clause | 19 | develop | 6,398 | class PriorsController < ApplicationController
before_action :login_required
helper_method :sort_column, :sort_direction
require 'csv'
require 'open3'
def search_pfts
@prior = Prior.find(params[:id])
# the "sorted_order" call is mainly so "search" has the joins it needs
@pfts = Pft.sorted_order... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/models_controller.rb | Ruby | bsd-3-clause | 19 | develop | 5,168 | class ModelsController < ApplicationController
before_action :login_required
helper_method :sort_column, :sort_direction
def edit_models_files
@model = Model.find(params[:id])
file = params[:file]
if @model and file
_file = DBFile.find(file)
# If relationship exists we must want to remo... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/cultivars_controller.rb | Ruby | bsd-3-clause | 19 | develop | 4,968 | class CultivarsController < ApplicationController
before_action :login_required, :except => [ :show ]
helper_method :sort_column, :sort_direction
require 'csv'
# autocompletion for bulk upload wizard
def bu_autocomplete
search_term = params[:term]
species_id = Specie.find_by_scientificname(params[:... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/pfts_controller.rb | Ruby | bsd-3-clause | 19 | develop | 7,085 | class PftsController < ApplicationController
before_action :login_required
helper_method :sort_column, :sort_direction
require 'csv'
# restful-authentication override
def access_denied
flash[:notice] = 'You have insufficient permissions to create new PFTs'
redirect_to root_path
end
def searc... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/traits_controller.rb | Ruby | bsd-3-clause | 19 | develop | 8,536 | class TraitsController < ApplicationController
before_action :login_required, :except => [ :show ]
helper_method :sort_column, :sort_direction
require 'csv'
require 'timeout'
def trait_search
@query = params[:symbol] || nil
if !params[:symbol].nil? and !params[:cont].nil? and params[:symbol].length ... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/application_controller.rb | Ruby | bsd-3-clause | 19 | develop | 7,810 | # Filters added to this controller apply to all controllers in the application.
# Likewise, all the methods added will be available for all controllers.
class ApplicationController < ActionController::Base
rescue_from ActiveRecord::InvalidForeignKey do |e|
case e.message
# deletion of sites
when /fk... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/posteriors_controller.rb | Ruby | bsd-3-clause | 19 | develop | 1,540 | class PosteriorsController < ApplicationController
before_action :login_required
helper_method :sort_column, :sort_direction
# GET /posteriors
# GET /posteriors.xml
def index
if params[:format].nil? or params[:format] == 'html'
@iteration = params[:iteration][/\d+/] rescue 1
@posteriors = Po... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/yieldsviews_controller.rb | Ruby | bsd-3-clause | 19 | develop | 1,010 | class YieldsviewsController < ApplicationController
before_action :login_required
require 'csv'
# GET /yields/1
# GET /yields/1.xml
def show
@yield = Yieldsview.all_limited(current_user).find_by_yield_id(params[:id])
if !logged_in? or @yield.nil?
@yield = nil if @yield.nil? or !@yield.checked... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/variables_controller.rb | Ruby | bsd-3-clause | 19 | develop | 4,076 | class VariablesController < ApplicationController
before_action :login_required
helper_method :sort_column, :sort_direction
require 'csv'
# general autocompletion
def autocomplete
variables = search_model(Variable.order(:description), %w( name units ), params[:term])
variables = variables.to_a.map ... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/managements_treatments_controller.rb | Ruby | bsd-3-clause | 19 | develop | 2,063 | class ManagementsTreatmentsController < ApplicationController
before_action :login_required, :except => [ :show ]
require 'csv'
# GET /managementstreatments
# GET /managementstreatments.xml
def index
params[:format] = 'xml' if params[:format].nil?
# We have a lot of params and they or may not have ... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/ensembles_controller.rb | Ruby | bsd-3-clause | 19 | develop | 1,290 | class EnsemblesController < ApplicationController
before_action :login_required
helper_method :sort_column, :sort_direction
# GET /ensembles
# GET /ensembles.xml
def index
if params[:format].nil? or params[:format] == 'html'
@iteration = params[:iteration][/\d+/] rescue 1
@ensembles = Ensemb... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/maps_controller.rb | Ruby | bsd-3-clause | 19 | develop | 8,081 | if Rails.env == "production"
require "#{Rails.root}/lib/mercator"
include Mercator
end
require 'will_paginate/array'
class MapsController < ApplicationController
layout 'application'
def location_yields_lookup
location = County.where('state like ? and name like ?',params[:state],params[:county]).first
... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/methods_controller.rb | Ruby | bsd-3-clause | 19 | develop | 3,930 | # coding: utf-8
class MethodsController < ApplicationController
before_action :login_required
helper_method :sort_column, :sort_direction
# This action acts as a _source_ for the jQuery UI autocompletion widgets on
# the Bulk Upload "Specify Upload Options and Global Values" page. It
# responds by sending ... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/dbfiles_controller.rb | Ruby | bsd-3-clause | 19 | develop | 4,863 | class DbfilesController < ApplicationController
before_action :login_required
helper_method :sort_column, :sort_direction
require 'csv'
def download
file = DBFile.find(params[:id]) rescue nil
# Need to make sure someone cannot create a link to other files on forecast
# by modifying the file_path... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/sites_controller.rb | Ruby | bsd-3-clause | 19 | develop | 8,543 | class SitesController < ApplicationController
before_action :login_required, :except => [ :show ]
helper_method :sort_column, :sort_direction
layout 'application', :except => [ :map ]
require 'csv'
#AJAX Calls
def linked
@citation = Citation.find(session["citation"])
@site = Site.find(params[:id]... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/users_controller.rb | Ruby | bsd-3-clause | 19 | develop | 4,324 | class UsersController < ApplicationController
before_action :login_required, :except => [:create,:new]
helper_method :sort_column, :sort_direction
def index
@iteration = params[:iteration][/\d+/] rescue 1
if current_user.page_access_level == 1
@users = User.sorted_order("#{sort_column('users', 'c... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/citations_sites_controller.rb | Ruby | bsd-3-clause | 19 | develop | 1,827 | class CitationsSitesController < ApplicationController
before_action :login_required, :except => [ :show ]
require 'csv'
# GET /sites
# GET /sites.xml
def index
params[:format] = 'xml' if params[:format].nil?
# We have a lot of params and they or may not have to be
# passed as conditions this i... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/trait_covariate_associations_controller.rb | Ruby | bsd-3-clause | 19 | develop | 202 | class TraitCovariateAssociationsController < ApplicationController
def index
@recognized_traits = TraitCovariateAssociation.all.map { |tca| Variable.find(tca.trait_variable_id) }.uniq
end
end |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/feedback_controller.rb | Ruby | bsd-3-clause | 19 | develop | 231 | class FeedbackController < ApplicationController
def feedback_email
ContactMailer::feedback_email(params[:feedback_email]).deliver
respond_to do |format|
format.js {render :layout =>false}
end
end
end |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/entities_controller.rb | Ruby | bsd-3-clause | 19 | develop | 3,060 | class EntitiesController < ApplicationController
require 'will_paginate/array'
before_action :login_required
# GET /entitys
# GET /entitys.xml
def index
# @entities = Entity.all
@entities = Entity.order('created_at DESC').page(params[:page])
respond_to do |format|
format.html # index.html... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/sessions_controller.rb | Ruby | bsd-3-clause | 19 | develop | 3,031 | # This controller handles the login/logout function of the site.
include AuthenticatedSystem
class SessionsController < ApplicationController
# This should be used on opening the home page ... before a user logs in
# On attempting to login from this page ... feed it to the create method in this controller
def ne... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/contacts_controller.rb | Ruby | bsd-3-clause | 19 | develop | 342 | class ContactsController < ApplicationController
def index
respond_to do |format|
format.html # index.html.erb
end
end
def send_mail
ContactMailer::contact_email(params[:email]).deliver
flash[:notice] = "Thank you for your email."
respond_to do |format|
format.html # index.html.e... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/bulk_upload_controller.rb | Ruby | bsd-3-clause | 19 | develop | 18,942 | #
# Controller for the Bulk Upload wizard. The steps of the wizard are
#
# 1. {start_upload}
#
# The user is presented with a form for choosing a file to upload.
#
# 1. {choose_global_citation}
#
# The user is presented with a form for choosing a global (dataset-wide)
# citation. This page is skipped if... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/species_controller.rb | Ruby | bsd-3-clause | 19 | develop | 7,003 | # encoding: utf-8
# RAILS3 added above encoding (actually this is needed with Ruby 1.9.2)
class SpeciesController < ApplicationController
before_action :login_required, :except => [ :show ]
helper_method :sort_column, :sort_direction
require 'csv'
# autocompletion for bulk upload wizard
def bu_autocomplete... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/citations_controller.rb | Ruby | bsd-3-clause | 19 | develop | 6,577 | class CitationsController < ApplicationController
before_action :login_required
helper_method :sort_column, :sort_direction
require 'csv'
# General autocompletion
# @calls {search_model}
def autocomplete
citations = search_model(Citation.order('author'), %w( author title ), params[:term])
citati... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/likelihoods_controller.rb | Ruby | bsd-3-clause | 19 | develop | 3,666 | class LikelihoodsController < ApplicationController
before_action :login_required
helper_method :sort_column, :sort_direction
# GET /likelihoods
# GET /likelihoods.xml
def index
if params[:format].nil? or params[:format] == 'html'
@iteration = params[:iteration][/\d+/] rescue 1
@likelihoods ... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/managements_controller.rb | Ruby | bsd-3-clause | 19 | develop | 6,122 | class ManagementsController < ApplicationController
before_action :login_required
helper_method :sort_column, :sort_direction
require 'csv'
def search_treatments
@management = Management.find(params[:id])
# the "sorted_order" call is mainly so "search" has the joins it needs
@treatments = Treatme... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/mimetypes_controller.rb | Ruby | bsd-3-clause | 19 | develop | 384 | class MimetypesController < ApplicationController
def autocomplete
mimetypes = search_model(Mimetype.order(:type_string), %w( type_string ), params[:term])
mimetypes = mimetypes.to_a.map do |item|
{
label: item.type_string,
value: item.id
}
end
respond_to do |format|
... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/runs_controller.rb | Ruby | bsd-3-clause | 19 | develop | 1,402 | class RunsController < ApplicationController
before_action :login_required
helper_method :sort_column, :sort_direction
# GET /runs
# GET /runs.xml
def index
if params[:format].nil? or params[:format] == 'html'
@iteration = params[:iteration][/\d+/] rescue 1
@runs = Run.sorted_order("#{sort_c... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/experiments_controller.rb | Ruby | bsd-3-clause | 19 | develop | 3,478 | class ExperimentsController < ApplicationController
before_action :login_required
helper_method :sort_column, :sort_direction
# GET /experiments
# GET /experiments.xml
def index
if params[:format].nil? or params[:format] == 'html'
@iteration = params[:iteration][/\d+/] rescue 1
@experiments ... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/sitegroups_controller.rb | Ruby | bsd-3-clause | 19 | develop | 5,567 | class SitegroupsController < ApplicationController
before_action :login_required
helper_method :sort_column, :sort_direction
def edit_sitegroups_sites
@sitegroup = Sitegroup.access(current_user).find(params[:id])
site = params[:site]
if @sitegroup and site
_site = Site.find(site)
# If r... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/pfts_priors_controller.rb | Ruby | bsd-3-clause | 19 | develop | 1,753 | class PftsPriorsController < ApplicationController
before_action :login_required, :except => [ :show ]
require 'csv'
# GET /pftspriors
# GET /pftspriors.xml
def index
params[:format] = 'xml' if params[:format].nil?
# We have a lot of params and they or may not have to be
# passed as conditions ... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/schemas_controller.rb | Ruby | bsd-3-clause | 19 | develop | 241 | class SchemasController < ApplicationController
def index
@partial='index_table'
if params[:partial].present?
@partial=params[:partial].strip
end
respond_to do |format|
format.html # index.html.erb
end
end
end |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/machines_controller.rb | Ruby | bsd-3-clause | 19 | develop | 2,502 | class MachinesController < ApplicationController
before_action :login_required
helper_method :sort_column, :sort_direction
# GET /machines
# GET /machines.xml
def index
if params[:format].nil? or params[:format] == 'html'
@iteration = params[:iteration][/\d+/] rescue 1
@machines = Machine.so... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/inputs_controller.rb | Ruby | bsd-3-clause | 19 | develop | 5,721 | class InputsController < ApplicationController
before_action :login_required
helper_method :sort_direction, :sort_column
# general autocompletion
def autocomplete
inputs = search_model(Input.joins(:site), %w( name sitename), params[:term])
inputs = inputs.to_a.map do |item|
{
# show inp... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/modeltypes_controller.rb | Ruby | bsd-3-clause | 19 | develop | 4,811 | class ModeltypesController < ApplicationController
before_action :login_required
helper_method :sort_column, :sort_direction
def remove_modeltypes_format
@modeltypes_format = ModeltypesFormat.find(params[:id])
@modeltype = @modeltypes_format.modeltype
@modeltypes_format.destroy
respond_to do |... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/covariates_controller.rb | Ruby | bsd-3-clause | 19 | develop | 4,595 | class CovariatesController < ApplicationController
before_action :login_required
helper_method :sort_column, :sort_direction
# GET /covariates
# GET /covariates.xml
def index
if params[:format].nil? or params[:format] == 'html'
@iteration = params[:iteration][/\d+/] rescue 1
@covariates = Cov... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/search_controller.rb | Ruby | bsd-3-clause | 19 | develop | 6,020 | # This controller handles searches.
include AuthenticatedSystem
class SearchController < ApplicationController
helper_method :sort_column, :sort_direction
CREDITS = ActionController::Base.helpers.strip_tags(CONFIG[:citation_license_copyright_markup])
CONTACT_EMAIL = CONFIG[:admin_email]
# Possible paramate... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/citations_treatments_controller.rb | Ruby | bsd-3-clause | 19 | develop | 2,006 | class CitationsTreatmentsController < ApplicationController
before_action :login_required, :except => [ :show ]
require 'csv'
# GET /citationstreatments
# GET /citationstreatments.xml
def index
params[:format] = 'xml' if params[:format].nil?
# We have a lot of params and they or may not have to be
... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/treatments_controller.rb | Ruby | bsd-3-clause | 19 | develop | 9,842 | require 'will_paginate/array'
class TreatmentsController < ApplicationController
before_action :login_required, :except => [ :show ]
helper_method :sort_column, :sort_direction
require 'csv'
# autocompletion for bulk upload wizard
def bu_autocomplete
search_term = params[:term]
# filter treatment... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/api/base_controller.rb | Ruby | bsd-3-clause | 19 | develop | 4,839 | class Api::BaseController < ActionController::Base
# Not sure why or even if these eight lines are needed. Just copied them from
# article at https://labs.kollegorna.se/blog/2015/04/build-an-api-now/
# Presumably we'll change things around here when we decide what sort of
# authentication and authorization we... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/api/v1/base_controller.rb | Ruby | bsd-3-clause | 19 | develop | 5,363 | require 'utilities/sql_comments.rb'
class Api::V1::BaseController < Api::BaseController
include ApiAuthenticationSystem
before_action :set_content_type # IMPORTANT: Run this filter first!
before_action :login_required
NO_CONSTRAINT = lambda { |value| true }
# Set the response content type based on the "f... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/controllers/api/v1/traits_controller.rb | Ruby | bsd-3-clause | 19 | develop | 2,240 | require 'yajl'
class Api::V1::TraitsController < Api::V1::BaseController
include Api::TraitCreationSupport
define_actions(Trait)
api!
description <<-DESC
Create new traits from the data specified in the posted data. Data about
traits to be inserted can be supplied in either JSON (the default), CSV... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/models/managements_treatments.rb | Ruby | bsd-3-clause | 19 | develop | 298 | class ManagementsTreatments < ActiveRecord::Base
self.primary_key = "id"
validates_presence_of :management_id
validates_presence_of :treatment_id
belongs_to :management
belongs_to :treatment
comma do
treatment_id
management_id
created_at
updated_at
end
end |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/models/posteriors_ensembles.rb | Ruby | bsd-3-clause | 19 | develop | 264 | class PosteriorsEnsembles < ActiveRecord::Base
belongs_to :ensemble
belongs_to :posterior
validates_presence_of :posterior_id
validates_presence_of :ensemble_id
comma do
posterior_id
ensemble_id
created_at
updated_at
end
end |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/models/treatment.rb | Ruby | bsd-3-clause | 19 | develop | 2,335 | class Treatment < ActiveRecord::Base
attr_protected []
include Overrides
extend SimpleSearch
SEARCH_INCLUDES = %w{ }
SEARCH_FIELDS = %w{ name definition }
has_many :traits
has_many :yields
has_many :managements_treatments, :class_name => "ManagementsTreatments"
has_many :managements, :through => :... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/models/modeltypes_format.rb | Ruby | bsd-3-clause | 19 | develop | 379 | class ModeltypesFormat < ActiveRecord::Base
attr_protected []
validates :tag,
presence: { message: "tag can't be blank" },
format: { with: /\A[a-z]+\z/,
message: 'A tag must be a non-empty sequence of lowercase letters.' }
validates_uniqueness_of :tag, scope: :modeltype_id
belongs... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/models/prior.rb | Ruby | bsd-3-clause | 19 | develop | 1,760 | class Prior < ActiveRecord::Base
attr_protected []
include Overrides
extend SimpleSearch
SEARCH_INCLUDES = %w{ citation variable }
SEARCH_FIELDS = %w{ citations.author variables.name priors.phylogeny priors.distn priors.parama priors.paramb priors.n priors.notes }
has_many :pfts_priors, :class_name => "P... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/models/yieldsview.rb | Ruby | bsd-3-clause | 19 | develop | 988 | class Yieldsview < ActiveRecord::Base
self.table_name = 'yieldsview'
scope :all_limited, lambda { |current_user|
if !current_user.nil?
if current_user.page_access_level == 1
checked = -1
access_level = 1
elsif current_user.page_access_level <= 2
checked = -1
access_l... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/models/pfts_species.rb | Ruby | bsd-3-clause | 19 | develop | 258 | class PftsSpecies < ActiveRecord::Base
self.primary_key = "id"
belongs_to :pft
belongs_to :specie
validates_presence_of :pft_id
validates_presence_of :specie_id
comma do
pft_id
specie_id
created_at
updated_at
end
end |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/models/bulk_upload_data_set.rb | Ruby | bsd-3-clause | 19 | develop | 82,522 | require 'memoist'
module ValidationResult
extend Memoist
# A symbol representing the result of data validation.
attr :result
# The message to use as the title attribute of the table cell containing the
# data item.
attr :message
# The message to put in the validation summary. This is also used as the ke... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/models/specie.rb | Ruby | bsd-3-clause | 19 | develop | 3,126 | # -*- coding: utf-8 -*-
class Specie < ActiveRecord::Base
attr_protected []
require "comma"
include Overrides
def as_json(options = {})
options[:except] = self.class.column_names.select { |nam| nam =~ /[A-Z]/ && nam != "AcceptedSymbol" }
super(options)
end
def to_xml(options = {})
options[:ex... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/models/citations_sites.rb | Ruby | bsd-3-clause | 19 | develop | 270 | class CitationsSites < ActiveRecord::Base
self.primary_key = "id"
validates_presence_of :citation_id
validates_presence_of :site_id
belongs_to :citation
belongs_to :site
comma do
citation_id
site_id
created_at
updated_at
end
end |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/models/db_file.rb | Ruby | bsd-3-clause | 19 | develop | 3,497 | class DBFile < ActiveRecord::Base
attr_protected []
self.table_name = 'dbfiles'
include Overrides
extend SimpleSearch
SEARCH_INCLUDES = %w{ machine }
SEARCH_FIELDS = %w{ dbfiles.file_name dbfiles.file_path dbfiles.md5 machines.hostname }
validates :file_name,
format: /\A[^\/]*\z/,
unique... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/models/pfts_priors.rb | Ruby | bsd-3-clause | 19 | develop | 254 | class PftsPriors < ActiveRecord::Base
self.primary_key = "id"
belongs_to :pft
belongs_to :prior
validates_presence_of :pft_id
validates_presence_of :prior_id
comma do
pft_id
prior_id
created_at
updated_at
end
end |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/models/input.rb | Ruby | bsd-3-clause | 19 | develop | 1,560 | class Input < ActiveRecord::Base
attr_protected []
include Overrides
extend SimpleSearch
SEARCH_INCLUDES = %w{ site }
SEARCH_FIELDS = %w{ sites.sitename inputs.name inputs.start_date inputs.end_date inputs.notes inputs.created_at inputs.updated_at }
has_and_belongs_to_many :runs
has_many :likelihoods
... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/models/posterior_samples.rb | Ruby | bsd-3-clause | 19 | develop | 316 | class PosteriorSamples < ActiveRecord::Base
validates_presence_of :posterior_id
validates_presence_of :variable_id
validates_presence_of :pft_id
validates_presence_of :parent_id
comma do
posterior_id
variable_id
pft_id
parent_id
created_at
updated_at
end
end |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/models/trait.rb | Ruby | bsd-3-clause | 19 | develop | 4,841 | class Trait < ActiveRecord::Base
attr_protected []
# Passed from controller for validation of ability
attr_accessor :current_user
include Overrides
extend DataAccess # provides all_limited
extend SimpleSearch
SEARCH_INCLUDES = %w{ citation variable specie site treatment }
SEARCH_FIELDS = %w{ traits.... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/models/management.rb | Ruby | bsd-3-clause | 19 | develop | 1,901 | class Management < ActiveRecord::Base
attr_protected []
include Overrides
extend SimpleSearch
SEARCH_INCLUDES = %w{ citation }
SEARCH_FIELDS = %w{ citations.author managements.date managements.mgmttype managements.level managements.units managements.notes }
has_many :managements_treatments, :class_name =... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/models/format.rb | Ruby | bsd-3-clause | 19 | develop | 1,223 | class Format < ActiveRecord::Base
attr_protected []
include Overrides
extend SimpleSearch
SEARCH_INCLUDES = %w{ mimetype }
SEARCH_FIELDS = %w{ formats.name mimetypes.type_string formats.notes formats.skip formats.header }
has_many :inputs
has_many :formats_variables
has_many :variables, :through => :... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/models/sitegroups_sites.rb | Ruby | bsd-3-clause | 19 | develop | 275 | class SitegroupsSites < ActiveRecord::Base
self.primary_key = "id"
belongs_to :sitegroup
belongs_to :site
validates_presence_of :sitegroup_id
validates_presence_of :site_id
comma do
sitegroup_id
site_id
created_at
updated_at
end
end |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/models/entity.rb | Ruby | bsd-3-clause | 19 | develop | 547 | class Entity < ActiveRecord::Base
attr_protected []
include Overrides
belongs_to :parent, :class_name => "Entity"
has_many :children, :foreign_key => "parent_id", :class_name => "Entity"
has_many :traits
# Validation callbacks
before_validation WhitespaceNormalizer.new([:name])
def to_s
name
... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/models/model.rb | Ruby | bsd-3-clause | 19 | develop | 1,310 | class Model < ActiveRecord::Base
attr_protected []
include Overrides
extend SimpleSearch
SEARCH_INCLUDES = %w{ modeltype }
SEARCH_FIELDS = %w{ models.model_name models.revision modeltypes.name }
has_many :files, :as => :container, :class_name => 'DBFile'
has_many :runs
belongs_to :modeltype
has_man... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/models/workflow.rb | Ruby | bsd-3-clause | 19 | develop | 1,026 | class Workflow < ActiveRecord::Base
include Overrides
extend SimpleSearch
SEARCH_INCLUDES = %w{ }
SEARCH_FIELDS = %w{ workflows.folder workflows.started_at workflows.finished_at workflows.created_at workflows.updated_at }
has_many :ensembles
belongs_to :model
belongs_to :site
belongs_to :user
sco... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/models/user.rb | Ruby | bsd-3-clause | 19 | develop | 3,318 | require 'digest/sha1'
class User < ActiveRecord::Base
require 'authentication'
require 'authentication/by_password'
require 'authentication/by_cookie_token'
include Authentication
include Authentication::ByPassword
include Authentication::ByCookieToken
extend SimpleSearch
SEARCH_INCLUDES = %w{ }
SE... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/models/covariate.rb | Ruby | bsd-3-clause | 19 | develop | 1,358 | class Covariate < ActiveRecord::Base
attr_protected []
include Overrides
extend SimpleSearch
SEARCH_INCLUDES = %w{ variable }
SEARCH_FIELDS = %w{ variables.name covariates.level covariates.n covariates.stat covariates.statname }
# Validations
## Validation methods
def level_in_range
v = Varia... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/models/variable.rb | Ruby | bsd-3-clause | 19 | develop | 1,666 | class Variable < ActiveRecord::Base
# Using "attr_protected []" doesn't remove protection for the "type" column,
# so we have to whitelist accessible columns instead:
attr_accessible :description, :units, :notes, :name, :standard_name, :standard_units, :label, :type
# rename inheritance column from "type" so w... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/models/posterior.rb | Ruby | bsd-3-clause | 19 | develop | 1,055 | class Posterior < ActiveRecord::Base
include Overrides
extend SimpleSearch
SEARCH_INCLUDES = %w{ pft }
SEARCH_FIELDS = %w{ pfts.name }
has_many :posteriors_ensembles, :class_name => "PosteriorsEnsembles"
has_many :ensembles, :through => :posteriors_ensembles
has_many :posterior_samples, :class_name =>... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/models/citations_treatments.rb | Ruby | bsd-3-clause | 19 | develop | 290 | class CitationsTreatments < ActiveRecord::Base
self.primary_key = "id"
validates_presence_of :citation_id
validates_presence_of :treatment_id
belongs_to :citation
belongs_to :treatment
comma do
citation_id
treatment_id
created_at
updated_at
end
end |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/models/whitespace_normalizer.rb | Ruby | bsd-3-clause | 19 | develop | 252 | class WhitespaceNormalizer
def initialize(attrs_to_normalize)
@attrs_to_normalize = attrs_to_normalize
end
def before_validation(model)
@attrs_to_normalize.each do |attr|
model[attr].nil? || model[attr].squish!
end
end
end |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/models/modeltype.rb | Ruby | bsd-3-clause | 19 | develop | 894 | class Modeltype < ActiveRecord::Base
attr_protected []
include Overrides
extend SimpleSearch
SEARCH_INCLUDES = %w{ }
SEARCH_FIELDS = %w{ modeltypes.name }
has_many :modeltypes_formats
has_many :models
has_many :pfts
belongs_to :user
# Validations
validates_uniqueness_of :name
validates_form... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/models/inputs_variables.rb | Ruby | bsd-3-clause | 19 | develop | 202 | class InputsVariables < ActiveRecord::Base
validates_presence_of :input_id
validates_presence_of :variable_id
comma do
input_id
variable_id
created_at
updated_at
end
end |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/models/ensemble.rb | Ruby | bsd-3-clause | 19 | develop | 974 | class Ensemble < ActiveRecord::Base
include Overrides
extend SimpleSearch
SEARCH_INCLUDES = %w{ }
SEARCH_FIELDS = %w{ ensembles.runtype ensembles.notes ensembles.created_at ensembles.updated_at }
RUNTYPETYPES = ["ENS","SA"]
has_many :runs
has_many :posteriors_ensembles, :class_name => "PosteriorsEnsem... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/models/traits_and_yields_view.rb | Ruby | bsd-3-clause | 19 | develop | 2,751 | # This overrides the to_comma method in the "comma" gem, replacing the
# iterator_method parameter value passed to the Comma::Generator#run
# method so that it uses "find_all" instead of "find_each".
# ("find_each" doesn't seem to work correctly with SQL views in rails
# 3.0.8.)
class ActiveRecord::Relation
def to_co... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/models/yield.rb | Ruby | bsd-3-clause | 19 | develop | 2,267 | class Yield < ActiveRecord::Base
attr_protected []
include Overrides
extend DataAccess # provides all_limited
extend SimpleSearch
SEARCH_INCLUDES = %w{ citation specie site treatment cultivar }
SEARCH_FIELDS = %w{ species.genus cultivars.name yields.mean yields.n yields.stat yields.statname citations.aut... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/models/sitegroup.rb | Ruby | bsd-3-clause | 19 | develop | 826 | class Sitegroup < ActiveRecord::Base
attr_protected []
include Overrides
extend SimpleSearch
SEARCH_INCLUDES = %w{ }
SEARCH_FIELDS = %w{ sitegroups.name }
before_validation WhitespaceNormalizer.new([:name])
validates_presence_of :name
scope :sorted_order, lambda { |order| order(order).includes(SEARC... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/models/experiment.rb | Ruby | bsd-3-clause | 19 | develop | 534 | class Experiment < ActiveRecord::Base
attr_protected []
extend SimpleSearch
SEARCH_INCLUDES = %w{ user }
SEARCH_FIELDS = %w{ experiments.name users.name }
before_validation WhitespaceNormalizer.new([:name])
validates_presence_of :name
has_many :experiments_sites
has_many :sites, :through => :experim... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/models/run.rb | Ruby | bsd-3-clause | 19 | develop | 1,534 | class Run < ActiveRecord::Base
include Overrides
extend SimpleSearch
SEARCH_INCLUDES = %w{ model site }
SEARCH_FIELDS = %w{ models.model_name sites.sitename runs.start_time runs.finish_time runs.started_at runs.finished_at runs.outdir runs.outprefix runs.setting runs.parameter_list }
validates_format_of :s... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/models/machine.rb | Ruby | bsd-3-clause | 19 | develop | 1,117 | class Machine < ActiveRecord::Base
attr_protected []
include Overrides
extend SimpleSearch
SEARCH_INCLUDES = %w{ }
SEARCH_FIELDS = %w{ machines.hostname }
validates :hostname,
presence: true,
uniqueness: true,
host: true
scope :sorted_order, lambda { |order| order(order).includes(SEA... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/models/citation.rb | Ruby | bsd-3-clause | 19 | develop | 3,191 | require 'whitespace_normalizer'
class Citation < ActiveRecord::Base
attr_protected []
include Overrides
extend SimpleSearch
SEARCH_INCLUDES = %w{ }
SEARCH_FIELDS = %w{ citations.author citations.year citations.title citations.journal citations.vol citations.pg citations.url citations.doi }
has_many :ci... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/models/pft.rb | Ruby | bsd-3-clause | 19 | develop | 1,512 | class Pft < ActiveRecord::Base
attr_protected []
include Overrides
extend SimpleSearch
SEARCH_INCLUDES = %w{ modeltype }
SEARCH_FIELDS = %w{ pfts.name pfts.definition modeltypes.name }
has_many :pfts_priors, :class_name => "PftsPriors"
has_many :priors, :through => :pfts_priors
has_many :pfts_specie... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/models/cultivar.rb | Ruby | bsd-3-clause | 19 | develop | 1,076 | class Cultivar < ActiveRecord::Base
attr_protected []
include Overrides
extend SimpleSearch
SEARCH_INCLUDES = %w{ specie }
SEARCH_FIELDS = %w{ species.scientificname cultivars.previous_id cultivars.name cultivars.ecotype cultivars.notes }
has_many :traits
has_many :yields
belongs_to :specie
valid... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/models/likelihood.rb | Ruby | bsd-3-clause | 19 | develop | 1,285 | class Likelihood < ActiveRecord::Base
attr_protected []
include Overrides
extend SimpleSearch
SEARCH_INCLUDES = %w{ input run variable }
SEARCH_FIELDS = %w{ variables.name likelihoods.loglikelihood likelihoods.n_eff likelihoods.weight likelihoods.residual }
belongs_to :run
belongs_to :variable
belon... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/models/site.rb | Ruby | bsd-3-clause | 19 | develop | 9,017 | class Site < ActiveRecord::Base
attr_protected []
#--
### Module Usage ###
include Overrides
extend CoordinateSearch # provides coordinate_search
extend SimpleSearch
SEARCH_INCLUDES = %w{ }
SEARCH_FIELDS = %w{ sites.sitename sites.city sites.state sites.country }
#--
### Associations ###
has... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/models/methods.rb | Ruby | bsd-3-clause | 19 | develop | 706 | class Methods < ActiveRecord::Base
attr_protected []
include Overrides
extend SimpleSearch
SEARCH_INCLUDES = %w{ citation }
SEARCH_FIELDS = %w{ methods.name methods.description citations.author }
belongs_to :citation
has_many :traits, foreign_key: :method_id
has_many :yields, foreign_key: :method_id
... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/assets/stylesheets/windows_js_1.3/helper/prototype_window_class_helper.rb | Ruby | bsd-3-clause | 19 | develop | 2,587 | # Prototype Window Class Helper (http://pwc-helper.xurdeonrails.com)
# by Jorge Díaz (http://xurde.info)
# thanks to Sebastien Gruhier for his Prototype Window Class (http://prototype-window.xilinus.com/)
#Quick use:
#Reference this helper in your rails applicaction adding -> helper :prototype_window_class in your app... |
github | PecanProject/bety | https://github.com/PecanProject/bety | app/services/api_authentication_system.rb | Ruby | bsd-3-clause | 19 | develop | 1,307 | # coding: utf-8
module ApiAuthenticationSystem
include AuthenticatedSystem
# Override default access_denied action.
def access_denied
if @errors
@errors = "authentication failed: " + @errors
else
@errors = "authentication failed"
end
render status: 401
end
# Override default perm... |
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