From d3a4c309d48b794f2f60f44bb9a3d94f402cc82f Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Wed, 16 Sep 2015 13:11:45 +0200
Subject: repeated crossvalidations, improved experiment reports

---
 lib/dataset.rb | 1 +
 1 file changed, 1 insertion(+)

(limited to 'lib/dataset.rb')

diff --git a/lib/dataset.rb b/lib/dataset.rb
index 851fabd..d884716 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -47,6 +47,7 @@ module OpenTox
           @data_entries = Marshal.load(data_entry_file.data)
           bad_request_error "Data entries (#{data_entries_id}) are not a 2D-Array" unless @data_entries.is_a? Array and @data_entries.first.is_a? Array
           bad_request_error "Data entries (#{data_entries_id}) have #{@data_entries.size} rows, but dataset (#{id}) has #{compound_ids.size} compounds" unless @data_entries.size == compound_ids.size
+          # TODO: data_entries can be empty, poorly reproducible, mongo problem?
           bad_request_error "Data entries (#{data_entries_id}) have #{@data_entries.first.size} columns, but dataset (#{id}) has #{feature_ids.size} features" unless @data_entries.first.size == feature_ids.size
           #$logger.debug "Retrieving data: #{Time.now-t}"
         end
-- 
cgit v1.2.3


From 6ac119c32cef094d4f1c2fb5c2daa4e274401f70 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Thu, 17 Sep 2015 14:56:25 +0200
Subject: neighbor calculation moved to Compound class

---
 lib/dataset.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'lib/dataset.rb')

diff --git a/lib/dataset.rb b/lib/dataset.rb
index d884716..7d889f8 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -152,7 +152,7 @@ module OpenTox
       name = File.basename(file,".*")
       dataset = self.find_by(:source => source, :name => name)
       if dataset
-        $logger.debug "Skipping #{file}, it is already in the database (id: #{dataset.id})."
+        $logger.debug "Skipping import of #{file}, it is already in the database (id: #{dataset.id})."
       else
         $logger.debug "Parsing #{file}."
         table = CSV.read file, :skip_blanks => true
-- 
cgit v1.2.3


From 33989261450bba279b4e002e5e4ea0475d742abb Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Fri, 18 Sep 2015 13:01:59 +0200
Subject: fix for empty values

---
 lib/dataset.rb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'lib/dataset.rb')

diff --git a/lib/dataset.rb b/lib/dataset.rb
index 7d889f8..00e2bc3 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -203,7 +203,7 @@ module OpenTox
             feature = NominalFeature.find_or_create_by(metadata)
           end
         end
-        feature_ids << feature.id
+        feature_ids << feature.id if feature
       end
       
       $logger.debug "Feature values: #{Time.now-time}"
@@ -245,7 +245,7 @@ module OpenTox
         end
 
         compound_ids << compound.id
-        @data_entries << Array.new(table.first.size-1)
+        @data_entries << Array.new(table.first.size-1) if (table.first.size-1) > 0
         
         vals.each_with_index do |v,j|
           if v.blank?
-- 
cgit v1.2.3