diff --git a/config/server/dataviews/wtsi-phenotyping/views/skin_screen_details.erubis b/config/server/dataviews/wtsi-phenotyping/views/skin_screen_details.erubis
new file mode 100644
index 0000000..bcf841c
--- /dev/null
+++ b/config/server/dataviews/wtsi-phenotyping/views/skin_screen_details.erubis
@@ -0,0 +1,101 @@
+
diff --git a/config/server/dataviews/wtsi-phenotyping/views/test_details.erubis b/config/server/dataviews/wtsi-phenotyping/views/test_details.erubis
index cc6d4b5..ead2979 100644
--- a/config/server/dataviews/wtsi-phenotyping/views/test_details.erubis
+++ b/config/server/dataviews/wtsi-phenotyping/views/test_details.erubis
@@ -1,16 +1,19 @@
<%= @test_name %> Data for <%= @marker_symbol %> (<%= @colony_prefix %>)
-
-
Overview
-
- <%= @test_desc %>
+ <% @data.each do |protocol_desc,images| %>
+ <% next if [:marker_symbol,:heatmap_group].include?(protocol_desc) %>
+
+
Overview
+
+ <%= protocol_desc %>
+
-
-
-
- <% @data.each do |img| %>
-
![<%= img[:test] %>](<%= img[:url] %>)
- <% end %>
-
+
+
+ <% images.each do |img| %>
+
+ <% end %>
+
+ <% end %>
diff --git a/lib/martsearch.rb b/lib/martsearch.rb
index 65420fd..a28b25b 100644
--- a/lib/martsearch.rb
+++ b/lib/martsearch.rb
@@ -1,10 +1,10 @@
+require 'rubygems'
+require 'bundler/setup'
+
require 'singleton'
require 'logger'
require 'date'
-require 'rubygems'
-require 'bundler/setup'
-
require 'biomart'
require 'sinatra/base'
require 'erubis'
@@ -23,7 +23,7 @@
require 'mongo'
require 'mongo_store'
-require 'ap'
+require 'awesome_print'
MARTSEARCH_PATH = "#{File.expand_path(File.dirname(__FILE__))}/.."
@@ -42,6 +42,9 @@ module MartSearch
# Error class raised when there is an error with the supplied configuration files.
class InvalidConfigError < StandardError; end
+ # MongoDB based cache class. This is entirely ActiveSupport::Cache::MongoStore, but
+ # we have to ovveride it here as we're not running in a Rails environment, and we
+ # need to include some Rails3 mixins for it to work correctly.
class MongoCache < ActiveSupport::Cache::MongoStore
include ::MongoStore::Cache::Rails3
end
@@ -59,11 +62,12 @@ class MongoCache < ActiveSupport::Cache::MongoStore
require "#{MARTSEARCH_PATH}/lib/martsearch/controller_utils"
require "#{MARTSEARCH_PATH}/lib/martsearch/controller"
require "#{MARTSEARCH_PATH}/lib/martsearch/ontology_term"
+require "#{MARTSEARCH_PATH}/lib/martsearch/ontology_term_cache"
require "#{MARTSEARCH_PATH}/lib/martsearch/index_builder_utils"
require "#{MARTSEARCH_PATH}/lib/martsearch/index_builder"
-require "#{MARTSEARCH_PATH}/lib/martsearch/project_utils"
require "#{MARTSEARCH_PATH}/lib/martsearch/server_utils"
require "#{MARTSEARCH_PATH}/lib/martsearch/server_view_helpers"
+require "#{MARTSEARCH_PATH}/lib/martsearch/project_utils"
require "#{MARTSEARCH_PATH}/lib/martsearch/server"
diff --git a/lib/martsearch/array.rb b/lib/martsearch/array.rb
index d9a285b..82b60fb 100644
--- a/lib/martsearch/array.rb
+++ b/lib/martsearch/array.rb
@@ -12,7 +12,7 @@ class Array
# "[1,2,3,4,5,6,7,8,9,10,11,12].chunk(5)" => "[[1,2,3,4,5],[6,7,8,9,10],[11,12]]"
def chunk( length )
chunks = []
- each_with_index do |element,index|
+ self.each_with_index do |element,index|
chunks << [] if index % length == 0
chunks.last << element
end
@@ -23,11 +23,7 @@ def chunk( length )
# @see http://snippets.dzone.com/posts/show/12019
def recursively_symbolize_keys!
self.each do |item|
- if item.is_a?(Hash)
- item.recursively_symbolize_keys!
- elsif item.is_a? Array
- item.recursively_symbolize_keys!
- end
+ item.recursively_symbolize_keys! if item.respond_to?(:recursively_symbolize_keys!)
end
end
@@ -35,11 +31,7 @@ def recursively_symbolize_keys!
# @see http://snippets.dzone.com/posts/show/12019
def recursively_stringify_keys!
self.each do |item|
- if item.is_a?(Hash)
- item.recursively_stringify_keys!
- elsif item.is_a? Array
- item.recursively_stringify_keys!
- end
+ item.recursively_stringify_keys! if item.respond_to?(:recursively_stringify_keys!)
end
end
@@ -56,7 +48,7 @@ def randomly_pick( number )
sort_by{ rand }.slice( 0...number )
end
- # Helper function for {Hash#clean_hashes} - this just call .clean_hashes
+ # Helper function for {Hash#clean_hashes} - just call .clean_hashes
# if one of the elements of the array is an instance of Hash (or one of its children).
def clean_hashes
self.map do |item|
diff --git a/lib/martsearch/index_builder.rb b/lib/martsearch/index_builder.rb
index caed44d..322b7aa 100644
--- a/lib/martsearch/index_builder.rb
+++ b/lib/martsearch/index_builder.rb
@@ -298,6 +298,11 @@ def process_dataset( ds )
if ds_index_conf[:ontology_terms]
index_ontology_terms( ds_index_conf[:ontology_terms], doc, data_row_obj, map_data, @ontology_cache )
end
+
+ # Any concatenated ontology term fields...
+ if ds_index_conf[:concatenated_ontology_terms]
+ index_concatenated_ontology_terms( ds_index_conf[:concatenated_ontology_terms], doc, data_row_obj, map_data, @ontology_cache )
+ end
# Finally - save the document to the cache
doc_primary_key = doc[@index_config[:schema][:unique_key].to_sym][0]
diff --git a/lib/martsearch/index_builder_utils.rb b/lib/martsearch/index_builder_utils.rb
index e5e6498..f3ed13e 100644
--- a/lib/martsearch/index_builder_utils.rb
+++ b/lib/martsearch/index_builder_utils.rb
@@ -213,8 +213,8 @@ def index_ontology_terms( ontology_term_conf, doc, data_row_obj, map_data, cache
ontology_term_conf.each do |term_conf|
attribute = term_conf[:attr]
value_to_index = extract_value_to_index( attribute, map_data[:attribute_map], { attribute => data_row_obj[attribute] } )
-
- if value_to_index and !value_to_index.gsub(" ","").empty?
+
+ if value_to_index && !value_to_index.gsub(" ","").empty?
cached_data = cache[value_to_index]
if cached_data != nil
index_ontology_terms_from_cache( doc, term_conf, cached_data )
@@ -225,6 +225,40 @@ def index_ontology_terms( ontology_term_conf, doc, data_row_obj, map_data, cache
end
end
+
+ def index_concatenated_ontology_terms( concat_ont_term_conf, doc, data_row_obj, map_data, cache )
+ attribute = concat_ont_term_conf[:attr]
+ split_delimiter = concat_ont_term_conf[:split_on] || ", "
+ value_to_index = extract_value_to_index( attribute, map_data[:attribute_map], { attribute => data_row_obj[attribute] } )
+
+ if value_to_index && !value_to_index.gsub(" ","").empty?
+ terms_to_test = value_to_index.split(split_delimiter)
+ terms_to_test.each do |test_term|
+ concat_ont_term_conf[:ontologies].each do |ontology_matcher,ontology_conf|
+ regexp = Regexp.new(ontology_matcher.to_s)
+
+ unless test_term.match(regexp).nil?
+ cached_data = cache[test_term]
+ term_conf = {
+ :attr => attribute,
+ :idx => {
+ :term => ontology_conf[:term],
+ :term_name => ontology_conf[:term_name],
+ :breadcrumb => ontology_conf[:breadcrumb]
+ }
+ }
+
+ if cached_data != nil
+ index_ontology_terms_from_cache( doc, term_conf, cached_data )
+ else
+ index_ontology_terms_from_fresh( doc, term_conf, test_term, cache )
+ end
+ end
+ end
+ end
+ end
+ end
+
# Utility function to create the actual XML markup for a collection
# of solr document constructs.
#
diff --git a/lib/martsearch/ontology_term.rb b/lib/martsearch/ontology_term.rb
index 0ce1052..90a7575 100644
--- a/lib/martsearch/ontology_term.rb
+++ b/lib/martsearch/ontology_term.rb
@@ -340,7 +340,7 @@ def get_term_details
@leaf_node = true if subject[:is_leaf].to_i == 1
end
end
-
+
# Helper function to try to find an ontology term via a synonym.
def get_term_from_synonym
sql = <<-SQL
@@ -366,7 +366,7 @@ def get_term_from_synonym
@root_term = true if subject[:is_root_term].to_i == 1
@leaf_node = true if subject[:is_leaf].to_i == 1
end
-
+
# Helper function to produce the flat lists of all the child
# terms and names.
def get_all_child_lists
@@ -390,161 +390,4 @@ def get_all_child_lists
end
- class OntologyTermCache
-
- def initialize()
- create_table = <<-SQL
- CREATE TABLE martsearch_cache (
- term varchar(255) NOT NULL PRIMARY KEY,
- compressed_json longblob NOT NULL
- ) ENGINE=MyISAM DEFAULT CHARSET=utf8
- SQL
-
- unless MartSearch::OLS_DB.table_exists?( :martsearch_cache )
- MartSearch::OLS_DB.run create_table
- end
-
- @dataset = MartSearch::OLS_DB[:martsearch_cache]
- end
-
- # Looks up a given term in the cache. If not found, it creates it
- # before saving it.
- #
- # @param [String] term The ontology term (id) i.e. GO:00032
- # @return [OntologyTerm] The OntologyTerm object
- def fetch( term )
- obj = nil
- select_obj = @dataset.first( :term => term )
- select_par = @dataset.first( :term => "#{term}-parents" )
-
- if select_obj.nil?
- obj = MartSearch::OntologyTerm.new(term)
- else
- obj = JSON.parse( Zlib::Inflate.inflate(select_obj[:compressed_json]), :max_nesting => false )
-
- unless select_par.nil?
- parents = JSON.parse( Zlib::Inflate.inflate(select_par[:compressed_json]), :max_nesting => false )
- obj.already_fetched_parents = true
-
- target = obj
- parent = parents.pop
- while parent
- parent.already_fetched_parents = true
- target.parent = parent
- target = parent
- parent = parents.pop
- end
- end
- end
-
- return obj
- end
-
- # Builds an OntologyTerm object for the given term and appeneds the
- # parent terms to it from the cache. - useful if you're not interested in
- # the children of a given term.
- #
- # @param [String] term The ontology term (id) i.e. GO:00032
- # @return [OntologyTerm] The OntologyTerm object
- def fetch_just_parents( term )
- obj = MartSearch::OntologyTerm.new(term)
- select_par = @dataset.first( :term => "#{term}-parents" )
-
- unless select_par.nil?
- parents = JSON.parse( Zlib::Inflate.inflate(select_par[:compressed_json]), :max_nesting => false )
- obj.already_fetched_parents = true
-
- target = obj
- parent = parents.pop
- while parent
- parent.already_fetched_parents = true
- target.parent = parent
- target = parent
- parent = parents.pop
- end
- else
- obj.get_parents
- end
-
- return obj
- end
-
- # Save a cache entry for a given term. First creates the OntologyTerm
- # object, then saves it to the cache.
- #
- # @param [String] term The ontology term (id) i.e. GO:00032
- # @param [Boolean] build Build the full OntologyTerm tree before save
- # @return [OntologyTerm] The OntologyTerm object
- def cache_term( term, build=false )
- obj = MartSearch::OntologyTerm.new(term)
-
- if build
- obj.build_tree
- obj.all_child_terms
- else
- obj.get_parents
- obj.get_children
- end
-
- cache_obj( obj )
- return obj
- end
-
- # Save an existing OntologyTerm object into the cache.
- #
- # @param [OntologyTerm] obj The OntologyTerm object to be stored
- # @return [OntologyTerm] The OntologyTerm object
- def cache_obj( obj )
- MartSearch::OLS_DB.transaction do
- @dataset.filter( :term => obj.term ).delete
- @dataset.filter( :term => "#{obj.term}-parents" ).delete
-
- @dataset.insert(
- :term => obj.term,
- :compressed_json => Zlib::Deflate.deflate( JSON.generate( obj, :max_nesting => false ) )
- )
-
- if obj.parentage and !obj.parentage.empty?
- @dataset.insert(
- :term => "#{obj.term}-parents",
- :compressed_json => Zlib::Deflate.deflate( JSON.generate( obj.parentage, :max_nesting => false ) )
- )
- end
- end
-
- return obj
- end
-
- # Helper function to cache all the possible entries of an ontology tree.
- #
- # @param [String] term The ROOT ontology term (id) - i.e. EMAP:0
- # @param [Boolean] cache_full_tree Whether to build and store the full ontology tree (good for small ontologies - not so good for big ones)
- def prepare_full_cache( term, cache_full_tree=true )
- obj = cache_term( term, cache_full_tree )
- puts " - caching #{obj.term}"
- recursively_cache_children( obj, cache_full_tree )
- end
-
- private
-
- # Helper function to recursively cache the children of an OntologyTerm.
- #
- # @param [OntologyTerm] obj The OntologyTerm object to be processed
- # @param [Boolean] cache_full_tree Whether to build and store the full ontology tree of the child terms (good for small ontologies - not so good for big ones)
- def recursively_cache_children( obj, cache_full_tree=true )
- obj.children.each do |child|
- if cache_full_tree
- child.all_child_terms
- else
- child.get_children
- end
-
- cache_obj( child )
- puts " - caching #{child.term}"
- recursively_cache_children( child, cache_full_tree ) if child.has_children?
- end
- end
-
- end
-
end
diff --git a/lib/martsearch/ontology_term_cache.rb b/lib/martsearch/ontology_term_cache.rb
new file mode 100644
index 0000000..3314a8c
--- /dev/null
+++ b/lib/martsearch/ontology_term_cache.rb
@@ -0,0 +1,162 @@
+module MartSearch
+
+ # Class for handling the caching of MartSearch::OntologyTerm objects.
+ # Creates a small cache table within the OLS database schema and handles
+ # all of the serialisation/de-serialisation to store and fetch the objects.
+ #
+ # @author Darren Oakley
+ class OntologyTermCache
+
+ def initialize()
+ unless MartSearch::OLS_DB.table_exists?( :martsearch_cache )
+ MartSearch::OLS_DB.run <<-SQL
+ CREATE TABLE martsearch_cache (
+ term varchar(255) NOT NULL PRIMARY KEY,
+ compressed_json longblob NOT NULL
+ ) ENGINE=MyISAM DEFAULT CHARSET=utf8
+ SQL
+ end
+
+ @dataset = MartSearch::OLS_DB[:martsearch_cache]
+ end
+
+ # Looks up a given term in the cache. If not found, it creates it.
+ #
+ # @param [String] term The ontology term (id) i.e. GO:00032
+ # @return [OntologyTerm] The OntologyTerm object
+ def fetch( term )
+ obj = nil
+ select_obj = @dataset.first( :term => term )
+ select_par = @dataset.first( :term => "#{term}-parents" )
+
+ if select_obj.nil?
+ obj = MartSearch::OntologyTerm.new(term)
+ else
+ obj = JSON.parse( Zlib::Inflate.inflate(select_obj[:compressed_json]), :max_nesting => false )
+
+ unless select_par.nil?
+ parents = JSON.parse( Zlib::Inflate.inflate(select_par[:compressed_json]), :max_nesting => false )
+ obj.already_fetched_parents = true
+
+ target = obj
+ parent = parents.pop
+ while parent
+ parent.already_fetched_parents = true
+ target.parent = parent
+ target = parent
+ parent = parents.pop
+ end
+ end
+ end
+
+ return obj
+ end
+
+ # Builds an OntologyTerm object for the given term and appeneds the
+ # parent terms to it from the cache. - useful if you're not interested in
+ # the children of a given term.
+ #
+ # @param [String] term The ontology term (id) i.e. GO:00032
+ # @return [OntologyTerm] The OntologyTerm object
+ def fetch_just_parents( term )
+ obj = MartSearch::OntologyTerm.new(term)
+ select_par = @dataset.first( :term => "#{term}-parents" )
+
+ unless select_par.nil?
+ parents = JSON.parse( Zlib::Inflate.inflate(select_par[:compressed_json]), :max_nesting => false )
+ obj.already_fetched_parents = true
+
+ target = obj
+ parent = parents.pop
+ while parent
+ parent.already_fetched_parents = true
+ target.parent = parent
+ target = parent
+ parent = parents.pop
+ end
+ else
+ obj.get_parents
+ end
+
+ return obj
+ end
+
+ # Save a cache entry for a given term. First creates the OntologyTerm
+ # object, then saves it to the cache.
+ #
+ # @param [String] term The ontology term (id) i.e. GO:00032
+ # @param [Boolean] build Build the full OntologyTerm tree before save
+ # @return [OntologyTerm] The OntologyTerm object
+ def cache_term( term, build=false )
+ obj = MartSearch::OntologyTerm.new(term)
+
+ if build
+ obj.build_tree
+ obj.all_child_terms
+ else
+ obj.get_parents
+ obj.get_children
+ end
+
+ cache_obj( obj )
+ return obj
+ end
+
+ # Save an existing OntologyTerm object into the cache.
+ #
+ # @param [OntologyTerm] obj The OntologyTerm object to be stored
+ # @return [OntologyTerm] The OntologyTerm object
+ def cache_obj( obj )
+ MartSearch::OLS_DB.transaction do
+ @dataset.filter( :term => obj.term ).delete
+ @dataset.filter( :term => "#{obj.term}-parents" ).delete
+
+ @dataset.insert(
+ :term => obj.term,
+ :compressed_json => Zlib::Deflate.deflate( JSON.generate( obj, :max_nesting => false ) )
+ )
+
+ if obj.parentage and !obj.parentage.empty?
+ @dataset.insert(
+ :term => "#{obj.term}-parents",
+ :compressed_json => Zlib::Deflate.deflate( JSON.generate( obj.parentage, :max_nesting => false ) )
+ )
+ end
+ end
+
+ return obj
+ end
+
+ # Helper function to cache all the possible entries of an ontology tree.
+ #
+ # @param [String] term The ROOT ontology term (id) - i.e. EMAP:0
+ # @param [Boolean] cache_full_tree Whether to build and store the full ontology tree (good for small ontologies - not so good for big ones)
+ def prepare_full_cache( term, cache_full_tree=true )
+ obj = cache_term( term, cache_full_tree )
+ puts " - caching #{obj.term}"
+ recursively_cache_children( obj, cache_full_tree )
+ end
+
+ private
+
+ # Helper function to recursively cache the children of an OntologyTerm.
+ #
+ # @param [OntologyTerm] obj The OntologyTerm object to be processed
+ # @param [Boolean] cache_full_tree Whether to build and store the full ontology tree of the child terms (good for small ontologies - not so good for big ones)
+ def recursively_cache_children( obj, cache_full_tree=true )
+ obj.children.each do |child|
+ if cache_full_tree
+ child.all_child_terms
+ else
+ child.get_children
+ end
+
+ cache_obj( child )
+ puts " - caching #{child.term}"
+ recursively_cache_children( child, cache_full_tree ) if child.has_children?
+ end
+ end
+
+ end
+
+end
\ No newline at end of file
diff --git a/lib/martsearch/project_utils.rb b/lib/martsearch/project_utils.rb
index d396717..a4361b7 100644
--- a/lib/martsearch/project_utils.rb
+++ b/lib/martsearch/project_utils.rb
@@ -9,6 +9,7 @@ module MartSearch
module ProjectUtils
include MartSearch::Utils
+ include MartSearch::ServerViewHelpers
# Wrapper function to collate all of the data for a given IKMC project.
#
@@ -44,19 +45,19 @@ def get_ikmc_project_page_data( project_id )
[ :"targeted non-conditional", :conditional ].each do |symbol|
es_cell_names.push( data[:es_cells][symbol][:cells] ) unless data[:es_cells][symbol].nil?
end
- es_cell_names.flatten!
- es_cell_names.map! { |es_cell| es_cell[:name] }
+
+ es_cell_names.flatten!.map! { |es_cell| es_cell[:name] }
unless es_cell_names.empty?
mice = get_mice( datasources, es_cell_names )
data.merge!( mice[:data] ) unless mice[:data].empty?
errors.push( mice[:error] ) unless mice[:error].empty?
end
-
- mouse_data = nil
- mouse_data = data[:mice][:genotype_confirmed] if data[:mice] and data[:mice][:genotype_confirmed]
# Ammend the es cells data to say which cells have been made into a mouse, then sort the cells as
# we do in the current code (by mice, followed by qc count).
+ mouse_data = nil
+ mouse_data = data[:mice][:genotype_confirmed] if data[:mice] and data[:mice][:genotype_confirmed]
+
unless mouse_data.nil?
mouse_data.each do |mouse|
[ :"targeted non-conditional", :conditional ].each do |symbol|
@@ -79,21 +80,56 @@ def get_ikmc_project_page_data( project_id )
end
# Add the mutagenesis predictions
- mutagenesis_predictions = get_mutagenesis_predictions( project_id )
- data[:mutagenesis_predictions] = mutagenesis_predictions[:data]
- unless mutagenesis_predictions[:error].empty?
- errors.push( mutagenesis_predictions[:error] )
+ unless ['KOMP-Regeneron','mirKO'].include?(data[:ikmc_project])
+ mutagenesis_predictions = get_mutagenesis_predictions( project_id )
+ data[:mutagenesis_predictions] = mutagenesis_predictions[:data]
+ errors.push( mutagenesis_predictions[:error] ) unless mutagenesis_predictions[:error].empty?
end
+ # Add the conf for the floxed exon display
+ data.merge!( floxed_exon_display_conf( data ) )
+
# Finally, categorize the stage of the pipeline that we are in
data.merge!( get_pipeline_stage( data[:status]) ) if data[:status]
end
-
+
return { :data => data, :errors => errors }
end
-
+
private
-
+
+ # Helper function to setup links to the floxed/deleted exons and all the config
+ # needed for these activities in the templates.
+ #
+ # @param [Hash] data The current project page data hash
+ # @return [Hash] The additional data required for the floxed exon display
+ def floxed_exon_display_conf( data )
+ new_data = {}
+
+ # Calculate the links to the Floxed/Deleted exons...
+ exon_links = []
+ unless data[:floxed_start_exon].nil?
+ url = ensembl_link_url_from_exon( :mouse, data[:floxed_start_exon] )
+ url = vega_link_url_from_exon( :mouse, data[:floxed_start_exon] ) if data[:floxed_start_exon] =~ /OTT/
+ exon_links.push( '
'+data[:floxed_start_exon]+'' )
+ end
+
+ if !data[:floxed_end_exon].nil? && ( data[:floxed_start_exon] != data[:floxed_end_exon] )
+ url = ensembl_link_url_from_exon( :mouse, data[:floxed_end_exon] )
+ url = vega_link_url_from_exon( :mouse, data[:floxed_end_exon] ) if data[:floxed_end_exon] =~ /OTT/
+ exon_links.push( '
'+data[:floxed_end_exon]+'' )
+ end
+
+ new_data[:floxed_exon_count] = exon_links.size
+ new_data[:floxed_exon_link] = exon_links.join(" - ")
+
+ # Also, extablish id these are "Floxed" or "Deleted" exons...
+ new_data[:deletion] = false
+ new_data[:deletion] = true if data[:design_type].include?('Deletion')
+
+ return new_data
+ end
+
# Wrapper function to handle Biomart::BiomartErrors
#
# @param [String] data_source - the biomart data source name
@@ -461,6 +497,8 @@ def get_pipeline_stage( status )
"Regeneron Selected" => { :stage => "pre", :stage_type => "normal" },
"Design Finished/Oligos Ordered" => { :stage => "designs", :stage_type => "normal" },
"Parental BAC Obtained" => { :stage => "vectors", :stage_type => "normal" },
+ "BAC QC Failure" => { :stage => "vectors", :stage_type => "error" },
+ "Targeting Vector Unsuccessful" => { :stage => "vectors", :stage_type => "error" },
"Targeting Vector QC Completed" => { :stage => "vectors", :stage_type => "normal" },
"Vector Electroporated into ES Cells" => { :stage => "vectors", :stage_type => "normal" },
"ES cell colonies picked" => { :stage => "cells", :stage_type => "normal" },
diff --git a/lib/martsearch/server/views/project_report.erubis b/lib/martsearch/server/views/project_report.erubis
index 9c80442..f7d7a4a 100644
--- a/lib/martsearch/server/views/project_report.erubis
+++ b/lib/martsearch/server/views/project_report.erubis
@@ -57,29 +57,6 @@
<% end %>
<% end %>
- <%
- # Calculate the links to the Floxed/Deleted exons...
- exon_links = []
- unless @data[:floxed_start_exon].nil?
- url = ensembl_link_url_from_exon( :mouse, @data[:floxed_start_exon] )
- url = vega_link_url_from_exon( :mouse, @data[:floxed_start_exon] ) if @data[:floxed_start_exon] =~ /OTT/
- exon_links.push( '
'+@data[:floxed_start_exon]+'' )
- end
-
- if !@data[:floxed_end_exon].nil? && @data[:floxed_start_exon] != @data[:floxed_end_exon]
- url = ensembl_link_url_from_exon( :mouse, @data[:floxed_end_exon] )
- url = vega_link_url_from_exon( :mouse, @data[:floxed_end_exon] ) if @data[:floxed_end_exon] =~ /OTT/
- exon_links.push( '
'+@data[:floxed_end_exon]+'' )
- end
-
- @data[:floxed_exon_count] = exon_links.size
- @data[:floxed_exon_link] = exon_links.join(" - ")
-
- # Also, extablish id these are "Floxed" or "Deleted" exons...
- @data[:deletion] = false
- @data[:deletion] = true if @data[:design_type].include?('Deletion')
- -%>
-
<% unless @data[:es_cells].nil? %>
<% unless @data[:es_cells][:conditional][:cells].empty? %>
diff --git a/public/css/screen.css b/public/css/screen.css
index 9252156..69cc415 100644
--- a/public/css/screen.css
+++ b/public/css/screen.css
@@ -469,7 +469,7 @@ tr.odd td {
background: none !important;
}
-.noborder, .noborder th, .noborder td {
+.noborder, .noborder th, .noborder td, td.noborder {
border: none !important;
}
@@ -478,7 +478,7 @@ tr.odd td {
padding-bottom: 2px;
}
-.border, .border th, .border td {
+.border, .border th, .border td, td.border {
border: 1px solid #999 !important;
}
diff --git a/public/images/diagonal_line.png b/public/images/diagonal_line.png
new file mode 100644
index 0000000..67620f5
Binary files /dev/null and b/public/images/diagonal_line.png differ
diff --git a/public/js/martsearch-base.js b/public/js/martsearch-base.js
index d85b7ce..0b5b20d 100644
--- a/public/js/martsearch-base.js
+++ b/public/js/martsearch-base.js
@@ -19,7 +19,7 @@ jQuery(document).ready(function() {
overwrite: false,
style: {
tip: "topRight",
- classes: "ui-tooltip-light ui-tooltip-shadow"
+ classes: "ui-tooltip-light ui-tooltip-rounded ui-tooltip-shadow"
},
position: {
at: "bottom left",
diff --git a/script/wtsi_phenotyping_spreadsheet.pl b/script/wtsi_phenotyping_spreadsheet.pl
index 484d0ca..1a2baa5 100644
--- a/script/wtsi_phenotyping_spreadsheet.pl
+++ b/script/wtsi_phenotyping_spreadsheet.pl
@@ -121,20 +121,19 @@ sub _xls_setup_result_formats {
my $xls_formats = {
completed_data_available => { bg => 'navy', col => 'white' },
significant_difference => { bg => 'red' },
- no_significant_difference => { bg => 44 }, # light blue
early_indication => { bg => 'yellow' },
+ no_significant_difference => { bg => 44 }, # light blue
not_applicable => { bg => 'silver' },
- test_pending => { bg => 'white' }
+ test_pending => { bg => 'white' },
+ test_abandoned => { bg => 'white', fg => 'silver', pattern => 14 }
};
foreach my $result ( keys %{$xls_formats} ) {
my $format = $workbook->add_format( %{$default_props} );
- if ( defined $xls_formats->{$result}->{bg} ) {
- $format->set_bg_color( $xls_formats->{$result}->{bg} );
- }
- if ( defined $xls_formats->{$result}->{col} ) {
- $format->set_color( $xls_formats->{$result}->{col} );
- }
+ if ( defined $xls_formats->{$result}->{bg} ) { $format->set_bg_color( $xls_formats->{$result}->{bg} ); }
+ if ( defined $xls_formats->{$result}->{fg} ) { $format->set_fg_color( $xls_formats->{$result}->{fg} ); }
+ if ( defined $xls_formats->{$result}->{pattern} ) { $format->set_pattern( $xls_formats->{$result}->{pattern} ); }
+ if ( defined $xls_formats->{$result}->{col} ) { $format->set_color( $xls_formats->{$result}->{col} ); }
$xls_formats->{$result} = $format;
}
@@ -153,6 +152,7 @@ sub _xls_test_result_format {
elsif ( $result eq "Test complete but not considered interesting" ) { $form = $tf->{no_significant_difference}; }
elsif ( $result eq "Early indication of possible phenotype" ) { $form = $tf->{early_indication}; }
elsif ( $result =~ /^Test not performed or applicable/i ) { $form = $tf->{not_applicable}; }
+ elsif ( $result eq "Test abandoned" ) { $form = $tf->{test_abandoned}; }
else { $form = $tf->{test_pending}; }
return $form;
@@ -163,10 +163,11 @@ sub sorted_results_test_codes {
my $test_mapping = {
completed_data_available => 1,
significant_difference => 2,
- no_significant_difference => 3,
- early_indication => 4,
+ early_indication => 3,
+ no_significant_difference => 4,
not_applicable => 5,
- test_pending => 6
+ test_abandoned => 6,
+ test_pending => 7
};
return $test_mapping;
}
@@ -179,20 +180,22 @@ sub write_unsorted_legend {
my $linked_formats = $formats->{linked_tests};
$worksheet->write( 2, $number_of_columns+2, "LEGEND" );
- $worksheet->write( 4, $number_of_columns+3, "Test complete and data/resources available" );
+ $worksheet->write( 4, $number_of_columns+3, "Test complete and data/resources are available" );
$worksheet->write( 4, $number_of_columns+2, "", $unlinked_formats->{completed_data_available} );
- $worksheet->write( 5, $number_of_columns+3, "Test complete and considered interesting" );
+ $worksheet->write( 5, $number_of_columns+3, "Test is complete and the data are considered interesting" );
$worksheet->write( 5, $number_of_columns+2, "", $unlinked_formats->{significant_difference} );
- $worksheet->write( 6, $number_of_columns+3, "Test complete but not considered interesting" );
- $worksheet->write( 6, $number_of_columns+2, "", $unlinked_formats->{no_significant_difference} );
- $worksheet->write( 7, $number_of_columns+3, "Early indication of possible phenotype" );
- $worksheet->write( 7, $number_of_columns+2, "", $unlinked_formats->{early_indication} );
+ $worksheet->write( 6, $number_of_columns+3, "Preliminary indication of an interesting phenotype" );
+ $worksheet->write( 6, $number_of_columns+2, "", $unlinked_formats->{early_indication} );
+ $worksheet->write( 7, $number_of_columns+3, "Test is complete but the data are not considered interesting" );
+ $worksheet->write( 7, $number_of_columns+2, "", $unlinked_formats->{no_significant_difference} );
$worksheet->write( 8, $number_of_columns+3, "Test not performed or applicable e.g. no lacZ reporter therefore no expression" );
$worksheet->write( 8, $number_of_columns+2, "", $unlinked_formats->{not_applicable} );
$worksheet->write( 9, $number_of_columns+3, "Test pending" );
$worksheet->write( 9, $number_of_columns+2, "", $unlinked_formats->{test_pending} );
- $worksheet->write( 10, $number_of_columns+3, "Link to a phenotyping test report page" );
- $worksheet->write( 10, $number_of_columns+2, ">", $linked_formats->{test_pending} );
+ $worksheet->write( 10, $number_of_columns+3, "Test abandoned" );
+ $worksheet->write( 10, $number_of_columns+2, "", $unlinked_formats->{test_abandoned} );
+ $worksheet->write( 11, $number_of_columns+3, "Link to a phenotyping test report page" );
+ $worksheet->write( 11, $number_of_columns+2, ">", $linked_formats->{test_pending} );
}
# Helper function to write the cells for the sortable heatmap.
@@ -204,20 +207,22 @@ sub write_sorted_legend {
my $test_code = sorted_results_test_codes();
$worksheet->write( 2, $number_of_columns+2, "LEGEND" );
- $worksheet->write( 4, $number_of_columns+3, "Test complete and data/resources available" );
+ $worksheet->write( 4, $number_of_columns+3, "Test complete and data/resources are available" );
$worksheet->write( 4, $number_of_columns+2, $test_code->{completed_data_available}, $test_formats->{completed_data_available} );
- $worksheet->write( 5, $number_of_columns+3, "Test complete and considered interesting" );
+ $worksheet->write( 5, $number_of_columns+3, "Test is complete and the data are considered interesting" );
$worksheet->write( 5, $number_of_columns+2, $test_code->{significant_difference}, $test_formats->{significant_difference} );
- $worksheet->write( 6, $number_of_columns+3, "Test complete but not considered interesting" );
- $worksheet->write( 6, $number_of_columns+2, $test_code->{no_significant_difference}, $test_formats->{no_significant_difference} );
- $worksheet->write( 7, $number_of_columns+3, "Early indication of possible phenotype" );
- $worksheet->write( 7, $number_of_columns+2, $test_code->{early_indication}, $test_formats->{early_indication} );
+ $worksheet->write( 6, $number_of_columns+3, "Preliminary indication of an interesting phenotype" );
+ $worksheet->write( 6, $number_of_columns+2, $test_code->{early_indication}, $test_formats->{early_indication} );
+ $worksheet->write( 7, $number_of_columns+3, "Test is complete but the data are not considered interesting" );
+ $worksheet->write( 7, $number_of_columns+2, $test_code->{no_significant_difference}, $test_formats->{no_significant_difference} );
$worksheet->write( 8, $number_of_columns+3, "Test not performed or applicable e.g. no lacZ reporter therefore no expression" );
$worksheet->write( 8, $number_of_columns+2, $test_code->{not_applicable}, $test_formats->{not_applicable} );
$worksheet->write( 9, $number_of_columns+3, "Test pending" );
$worksheet->write( 9, $number_of_columns+2, $test_code->{test_pending}, $test_formats->{test_pending} );
- $worksheet->write( 10, $number_of_columns+3, "Link to a phenotyping test report page" );
- $worksheet->write( 10, $number_of_columns+2, "x", $linked_formats->{test_pending} );
+ $worksheet->write( 10, $number_of_columns+3, "Test pending" );
+ $worksheet->write( 10, $number_of_columns+2, $test_code->{test_abandoned}, $test_formats->{test_abandoned} );
+ $worksheet->write( 11, $number_of_columns+3, "Link to a phenotyping test report page" );
+ $worksheet->write( 11, $number_of_columns+2, ">", $linked_formats->{test_pending} );
}
@@ -268,7 +273,7 @@ sub write_test_results {
if ( $worksheet->get_name() =~ /Sort/ ) {
$worksheet->write_url( $row, $col, $pheno_details_url, _xls_test_result_format( $sorted_test_mapping, $result ), _xls_test_result_format( $formats->{linked_tests}, $result ) );
} else {
- $worksheet->write_url( $row, $col, $pheno_details_url, "x", _xls_test_result_format( $formats->{linked_tests}, $result ) );
+ $worksheet->write_url( $row, $col, $pheno_details_url, ">", _xls_test_result_format( $formats->{linked_tests}, $result ) );
}
}
else {
diff --git a/tasks/metric_fu.task b/tasks/metric_fu.task
deleted file mode 100644
index b4d576d..0000000
--- a/tasks/metric_fu.task
+++ /dev/null
@@ -1,21 +0,0 @@
-begin
- require 'rubygems'
- require 'metric_fu'
-
- unless Object.respond_to?(:to_json!)
- # Rails 3 fixes
- require 'active_support/core_ext/object/to_json'
- require 'active_support/core_ext/object/blank'
- end
-
- MetricFu::Configuration.run do |config|
- config.metrics = [:churn, :saikuro, :flog, :flay, :reek, :roodi]
- config.graphs = [:flog, :flay, :reek, :roodi]
- config.flog = { :dirs_to_flog => ['lib'] }
- config.flay = { :dirs_to_flay => ['lib'] }
- config.reek = { :dirs_to_reek => ['lib'] }
- config.roodi = { :dirs_to_roodi => ['lib'] }
- end
-rescue LoadError
- puts "[ERROR] Unable to load 'metric_fu' tasks - please run 'bundle install'"
-end
\ No newline at end of file
diff --git a/test/test_helper.rb b/test/test_helper.rb
index 995ce5f..d3b7a9f 100644
--- a/test/test_helper.rb
+++ b/test/test_helper.rb
@@ -1,3 +1,6 @@
+# Add the lib directory to the search path
+$:.unshift( "#{File.expand_path(File.dirname(__FILE__))}/../lib" )
+
require 'rubygems'
# Set-up SimpleCov (code coverage tool for Ruby 1.9)
@@ -15,14 +18,10 @@
end
end
-# Add the lib directory to the search path
-$:.unshift( "#{File.expand_path(File.dirname(__FILE__))}/../lib" )
-
-require 'ap'
+require 'martsearch'
require 'test/unit'
require 'vcr'
require 'shoulda'
-require 'martsearch'
# Set-up VCR for mocking up web requests.
VCR.config do |c|
diff --git a/test/test_index_builder_utils.rb b/test/test_index_builder_utils.rb
index d3e0184..b25a9d0 100644
--- a/test/test_index_builder_utils.rb
+++ b/test/test_index_builder_utils.rb
@@ -248,4 +248,75 @@ def test_index_ontology_terms
assert( doc3[:mp_ontology].empty? )
end
+ def test_concatenated_ontology_terms
+ ontology_cache = {}
+ doc = new_document()
+ attr_map = [
+ { :attr => 'colony_prefix', :idx => 'colony_prefix', :use_to_map => true },
+ { :attr => 'annotations', :idx => 'ignore_me' }
+ ]
+ concatenated_ontology_term_conf = {
+ :attr => 'annotations',
+ :split_on => '; ',
+ :ontologies => {
+ :"^MA\\:\\d+$" => { :term => 'ma_id', :term_name => 'ma_term', :breadcrumb => 'ma_ontology' },
+ :"^MP\\:\\d+$" => { :term => 'mp_id', :term_name => 'mp_term', :breadcrumb => 'mp_ontology' }
+ }
+ }
+ data_row_obj = {
+ 'colony_prefix' => 'MAMM',
+ 'annotations' => 'MA:0000053; MP:0003866'
+ }
+
+ # Perform the search from fresh...
+ index_concatenated_ontology_terms( concatenated_ontology_term_conf, doc, data_row_obj, process_attribute_map(attr_map), ontology_cache )
+
+ assert_equal( 6, doc[:ma_id].size )
+ assert_equal( 5, doc[:ma_term].size )
+ assert( doc[:ma_id].include?('MA:0000005') )
+ assert( doc[:ma_id].include?('MA:0000001') )
+ assert( doc[:ma_term].include?('body cavity or lining') )
+ assert( doc[:ma_term].include?('adult mouse') )
+ assert( doc[:ma_ontology].include?('MA:0000001 | MA:0002405 | MA:0002433 | MA:0000005 | MA:0002447 | MA:0000053') )
+
+ assert_equal( 4, doc[:mp_id].size )
+ assert_equal( 3, doc[:mp_term].size )
+ assert( doc[:mp_id].include?('MP:0001663') )
+ assert( doc[:mp_id].include?('MP:0000001') )
+ assert( doc[:mp_term].include?('abnormal defecation') )
+ assert( doc[:mp_term].include?('digestive/alimentary phenotype') )
+ assert( doc[:mp_ontology].include?('MP:0000001 | MP:0005381 | MP:0001663 | MP:0003866') )
+
+ # Perform the search from cache...
+ doc2 = new_document()
+
+ index_concatenated_ontology_terms( concatenated_ontology_term_conf, doc2, data_row_obj, process_attribute_map(attr_map), ontology_cache )
+
+ assert_equal( 6, doc2[:ma_id].size )
+ assert_equal( 5, doc2[:ma_term].size )
+ assert( doc2[:ma_id].include?('MA:0000005') )
+ assert( doc2[:ma_id].include?('MA:0000001') )
+
+ assert_equal( 4, doc2[:mp_id].size )
+ assert_equal( 3, doc2[:mp_term].size )
+ assert( doc2[:mp_id].include?('MP:0001663') )
+ assert( doc2[:mp_id].include?('MP:0000001') )
+
+ # Make sure a bad ontology term doesn't blow stuff up...
+ doc3 = new_document()
+ data_row_obj2 = {
+ 'colony_prefix' => 'MAMM',
+ 'annotations' => 'FLIBBLE:5',
+ }
+
+ index_concatenated_ontology_terms( concatenated_ontology_term_conf, doc3, data_row_obj2, process_attribute_map(attr_map), ontology_cache )
+
+ assert( doc3[:ma_id].empty? )
+ assert( doc3[:ma_term].empty? )
+ assert( doc3[:ma_ontology].empty? )
+ assert( doc3[:mp_id].empty? )
+ assert( doc3[:mp_term].empty? )
+ assert( doc3[:mp_ontology].empty? )
+ end
+
end
\ No newline at end of file
diff --git a/test/test_project_utils.rb b/test/test_project_utils.rb
index 234f1cc..03d6fe5 100644
--- a/test/test_project_utils.rb
+++ b/test/test_project_utils.rb
@@ -1,5 +1,4 @@
require "test_helper"
-require "json"
class TestMartSearchProjectUtils < Test::Unit::TestCase
include MartSearch::ProjectUtils
@@ -910,9 +909,11 @@ class TestMartSearchProjectUtils < Test::Unit::TestCase
end
should "not throw any exceptions with no mice" do
- assert_nothing_raised do
- get_ikmc_project_page_data( 42474 )
- end
+ project_id = 42474
+ data = nil
+ assert_nothing_raised { data = get_ikmc_project_page_data( project_id ) }
+ assert( !data.nil? )
+ assert( data[:mice].nil?, "We're trying to test for exception handling for projects with no mice - but this project 'project_id' has mouse data!")
end
should "return the correct data with more than one mouse" do
diff --git a/test/test_server.rb b/test/test_server.rb
index 73dcbd6..239f1ea 100644
--- a/test/test_server.rb
+++ b/test/test_server.rb
@@ -100,8 +100,8 @@ def setup
should "render IKMC project pages" do
VCR.use_cassette('test_server_project_page') do
- project_ids_to_test = ['35505','27042','42474','82403','23242']
-
+ project_ids_to_test = ['35505','27042','42474','82403','23242','VG12252','VG11490']
+
project_ids_to_test.each do |project_id|
visit "/project/#{project_id}"
assert_equal( "/project/#{project_id}", current_path )
@@ -145,11 +145,13 @@ def setup
when 'embryo-expression' then 'Embryo Expression'
when 'homozygote-viability' then 'Homozygote Viability'
when 'fertility' then 'Fertility'
+ when 'skin-screen' then 'Skin Screen'
else
- test_data[0][:heatmap_group]
+ test_data[:heatmap_group]
end
urls_to_hit.push({
+ :test => test_url,
:url => "/phenotyping/#{colony_prefix}/#{test_url}/",
:title => test_title
})
@@ -162,6 +164,13 @@ def setup
visit test_conf[:url]
assert_equal( "#{test_conf[:url]}", current_path, "WTSI Phenotyping - can't visit '#{test_conf[:url]}'!" )
assert( page.has_content?(test_conf[:title]) )
+
+ if test_conf[:test] == 'abr'
+ assert( page.has_css?('#abr-thresholds') )
+ href = page.first(:css, "#abr-thresholds a[rel='prettyPhoto']")[:href]
+ visit "#{test_conf[:url]}#{href}"
+ visit "#{test_conf[:url]}foobarweewar.png"
+ end
end
end
end
@@ -225,15 +234,15 @@ def setup
should 'render IKMC project pages as JSON...' do
VCR.use_cassette('test_server_project_page') do
- project_ids_to_test = ['35505','27042','42474','82403','23242']
-
+ project_ids_to_test = ['35505','27042','42474','82403','23242','VG12252','VG11490']
+
project_ids_to_test.each do |project_id|
@browser.get "/project/#{project_id}?wt=json"
assert( @browser.last_response.ok?, "A request to '/project/#{project_id}?wt=json' failed!" )
json = JSON.parse( @browser.last_response.body )
assert( json.is_a?(Hash) )
end
-
+
@browser.get "/project/foobar"
assert_equal( 404, @browser.last_response.status )
end
@@ -300,7 +309,7 @@ def setup
skip("Skipping WTSI Phenotyping report tests as the DataView is not active.")
else
VCR.use_cassette('test_server_wtsi_phenotyping_report_pages') do
- tests_to_test = ['abr','homozygote-viability','fertility','adult-expression','embryo-expression','dexa','hot-plate']
+ tests_to_test = ['abr','homozygote-viability','fertility','adult-expression','embryo-expression','dexa','hot-plate','skin-screen']
colonies_to_test = ['FOOO','BAAR','BAAZ','ARRR']
colonies_to_test.each do |colony_prefix|