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authorgebele <gebele@in-silico.ch>2016-11-10 11:07:03 +0000
committergebele <gebele@in-silico.ch>2016-11-10 11:07:03 +0000
commit347ef2891876af871e101f9a9efc643e5f28da4c (patch)
tree508a3f0fcfeb4fa934f703adbdf9b0aee2954ece
parent295dcfc74e1375e495ec3d9c1e74a402eb4decd4 (diff)
parent7bd244b35d2e2059baf1fa535dca854999b5da75 (diff)
Merge branch 'development' of https://github.com/opentox/lazar into development
-rw-r--r--lib/crossvalidation.rb2
-rw-r--r--lib/validation-statistics.rb11
-rw-r--r--test/descriptor.rb4
-rw-r--r--test/validation-classification.rb6
-rw-r--r--test/validation-nanoparticle.rb1
5 files changed, 16 insertions, 8 deletions
diff --git a/lib/crossvalidation.rb b/lib/crossvalidation.rb
index 4f779a2..be680ae 100644
--- a/lib/crossvalidation.rb
+++ b/lib/crossvalidation.rb
@@ -95,7 +95,6 @@ module OpenTox
crossvalidation_ids.collect{|id| CrossValidation.find(id)}
end
-=begin
def correlation_plot format: "png"
#unless correlation_plot_id
feature = Feature.find(crossvalidations.first.model.prediction_feature)
@@ -129,7 +128,6 @@ module OpenTox
#end
$gridfs.find_one(_id: correlation_plot_id).data
end
-=end
end
end
diff --git a/lib/validation-statistics.rb b/lib/validation-statistics.rb
index b251bdb..b6f8a60 100644
--- a/lib/validation-statistics.rb
+++ b/lib/validation-statistics.rb
@@ -66,8 +66,13 @@ module OpenTox
end
def probability_plot format: "pdf"
- unless probability_plot_id
- tmpfile = "/tmp/#{id.to_s}_probability.#{format}"
+ #unless probability_plot_id
+
+ #tmpdir = File.join(ENV["HOME"], "tmp")
+ tmpdir = "/tmp"
+ #p tmpdir
+ FileUtils.mkdir_p tmpdir
+ tmpfile = File.join(tmpdir,"#{id.to_s}_probability.#{format}")
accuracies = []
probabilities = []
correct_predictions = 0
@@ -91,7 +96,7 @@ module OpenTox
file = Mongo::Grid::File.new(File.read(tmpfile), :filename => "#{self.id.to_s}_probability_plot.svg")
plot_id = $gridfs.insert_one(file)
update(:probability_plot_id => plot_id)
- end
+ #end
$gridfs.find_one(_id: probability_plot_id).data
end
end
diff --git a/test/descriptor.rb b/test/descriptor.rb
index e5d8ff9..42d4661 100644
--- a/test/descriptor.rb
+++ b/test/descriptor.rb
@@ -12,7 +12,9 @@ class DescriptorTest < MiniTest::Test
def test_smarts
c = OpenTox::Compound.from_smiles "N=C=C1CCC(=F=FO)C1"
- File.open("tmp.png","w+"){|f| f.puts c.png}
+ File.open("/tmp/tmp.png","w+"){|f| f.puts c.png}
+ assert_match /^PNG/,`file -b /tmp/tmp.png`
+ File.delete "/tmp/tmp.png"
s = Smarts.find_or_create_by(:smarts => "F=F")
result = c.smarts_match [s]
assert_equal [1], result
diff --git a/test/validation-classification.rb b/test/validation-classification.rb
index c93e71f..fb4c3e7 100644
--- a/test/validation-classification.rb
+++ b/test/validation-classification.rb
@@ -11,8 +11,10 @@ class ValidationClassificationTest < MiniTest::Test
cv = ClassificationCrossValidation.create model
assert cv.accuracy > 0.7, "Accuracy (#{cv.accuracy}) should be larger than 0.7, this may occur due to an unfavorable training/test set split"
assert cv.weighted_accuracy > cv.accuracy, "Weighted accuracy (#{cv.weighted_accuracy}) should be larger than accuracy (#{cv.accuracy})."
- #p cv
- #File.open("tmp.pdf","w+"){|f| f.puts cv.probability_plot}
+ File.open("/tmp/tmp.pdf","w+"){|f| f.puts cv.probability_plot(format:"pdf")}
+ p `file -b /tmp/tmp.pdf`
+ File.open("/tmp/tmp.png","w+"){|f| f.puts cv.probability_plot(format:"png")}
+ p `file -b /tmp/tmp.png`
end
# parameters
diff --git a/test/validation-nanoparticle.rb b/test/validation-nanoparticle.rb
index c0f2f92..1742ef2 100644
--- a/test/validation-nanoparticle.rb
+++ b/test/validation-nanoparticle.rb
@@ -15,6 +15,7 @@ class NanoparticleValidationTest < MiniTest::Test
def test_validate_default_nanoparticle_model
model = Model::Lazar.create training_dataset: @training_dataset, prediction_feature: @prediction_feature
cv = CrossValidation.create model
+ p cv
p cv.rmse
p cv.r_squared
#File.open("tmp.pdf","w+"){|f| f.puts cv.correlation_plot}