lazar-gui 1.4.0 → 1.4.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: ad561aa97606a3fea005b3093d9b8bdd0ccb7246564f1124f5f70cbd3f9a5a67
-  data.tar.gz: 736f17abe8d0c6df86e256f37dffdffddd4e367adbb5db322aa8cfad5463db11
+  metadata.gz: a0ca50134ea890caa141bbe3d1e24c1c0df610a34164157640a50912c2897806
+  data.tar.gz: 624a704eabec8c163847bdc2bda698f1554c7764572c28aec9ed43d7728e4a05
 SHA512:
-  metadata.gz: 3c918b6a66502ef6c9652a7fa40fa99abf6a5c12d51752cb36feea1cc58b267b37171cf4965d5074b9f9bf896d04ad69a1ee295b87ee8e7326622195b9b42c45
-  data.tar.gz: 96343339b9ed6326fb0bc525ea860ff07d184d39d9aadafea3916ea00106657b052828f674efad23b6c8ab29102ca8ed577d3552eb4c7b32832f84e7f5513507
+  metadata.gz: 7ec258039ef43e623613e13398ce20d1c8899a112f9f3dc54576f2b934c5234c17dea91fdf285685a46833dfff9db76c1752d248be09eca8aac7839b9572e0d2
+  data.tar.gz: e0f152007ba1a716425b9e17b034ab26998a95a914fa03f8a991c6ca203f026050731b184a1da1fbb1700370cc353de3e52e3c3e1c560f30a272086d94d6aba1

data/FAQ.md

@@ -1,6 +1,23 @@
 ## *lazar* Frequently Asked Questions
 
-#### The *lazar* program's interface has changed, and I am not sure how to use the information given with regard to its confidence. In the former version, I would consider a confidence value higher than 0.025 as reliable. But now, there is no such parameter in the prediction results. How can I consider a prediction as presenting high or low confidence?
+### I find multiple entries with different values for the same compound in the list of neighbors. Where do they come from and what is their impact on the prediction?
+
+Multiple entries for the same structure originate from different biological
+experiments. `lazar` can use the information from multiple experiments to
+improve predictions, by considering each measurement as a separate example.
+This has the effect, that the impact of a neighbor on the prediction is
+increased, if repeated measurements give the same (classification) or very
+similar (regression) values, and decreased if the measurements differ a lot.
+
+### I get different values, if I repeat a prediction for the same compound and endpoint. Why?
+
+This may happen for regression predictions only. `lazar` uses the random forest
+algorithm from R's Caret package to build local QSAR models. This algorithm
+uses *random* internal training set splits for parameter optimisations. This
+randomness can lead to models with slightly different parameters (and thus
+predictions) for the same set of neighbors. 
+
+### The *lazar* program's interface has changed, and I am not sure how to use the information given with regard to its confidence. In the former version I would consider a confidence value higher than 0.025 as reliable, but now there is no such parameter in the prediction results. 
 
 In the past many users had problems to interpret the confidence level,
 for this reason we provide now the probabilities that the prediction
@@ -17,7 +34,8 @@ Probabilities are calculated from the activities and similarities of
 neighbors, please make sure to inspect the neighbors list for any
 inconsistencies that might affect the prediction.
 
-#### How can I use *lazar* locally on my computer
+### How can I use *lazar* locally on my computer
+
 If you are familiar with docker, you can use one of our docker images to run lazar locally:
 
 [lazar docker image](https://hub.docker.com/r/insilicotox/lazar)
@@ -26,13 +44,13 @@ If you are familiar with docker, you can use one of our docker images to run laz
 
 If you want to install lazar/nano-lazar without docker you should know how to use UNIX/Linux and the Ruby programming language. Source code and brief installation instructions for the GUIs is available at:
 
-[lazar gui source code](https://github.com/opentox/lazar-gui)
+[lazar gui source code](https://git.in-silico.ch/lazar-gui)
 
-[nano-lazar gui source code](https://github.com/opentox/nano-lazar)
+[nano-lazar gui source code](https://git.in-silico.ch/nano-lazar)
 
 You can also use just the libraries from the command line:
 
-[lazar|nano-lazar lib](https://github.com/opentox/lazar)
+[lazar|nano-lazar lib](https://git.in-silico.ch/lazar)
 
 Documentation is available at:
 

data/VERSION

@@ -1 +1 @@
-1.4.0
+1.4.1

data/application.rb

@@ -18,10 +18,15 @@ PUBCHEM_CID_URI = PUBCHEM_URI.split("/")[0..-3].join("/")+"/compound/"
   "validation.rb"
 ].each{ |f| require_relative "./lib/#{f}" }
 
-configure :production, :development do
+configure :production do
   STDOUT.sync = true  
   $logger = Logger.new(STDOUT)
-  #$logger.level = Logger::DEBUG
+end
+
+configure :development do
+  STDOUT.sync = true  
+  $logger = Logger.new(STDOUT)
+  $logger.level = Logger::DEBUG
 end
 
 before do

data/bin/lazar-start.sh

@@ -1,9 +1,10 @@
 #!/bin/bash
 sudo mongod &
 R CMD Rserve --vanilla &
-LAZARPATH=$(gem path lazar-gui)
-cd $LAZARPATH
-cd $(gem which "lazar-gui"|sed 's#/lib/lazar-gui.rb/##')
+#LAZARPATH=$(gem path lazar-gui)
+#cd $LAZARPATH
+#cd $(gem which "lazar-gui"|sed 's#/lib/lazar-gui.rb/##')
+cd `ls -d $(gem environment gemdir)/gems/lazar-gui-*`
 unicorn -c unicorn.rb -E production
 
 exit 0

data/config.ru

@@ -1,4 +1,4 @@
-ENV["BATCH_MODE"] = "true"
+ENV["BATCH_MODE"] = "false"
 ENV["LAZAR_ENV"] = "production"
 require "lazar"
 require "qsar-report"

data/docker/Dockerfile

@@ -24,9 +24,7 @@ RUN         pacman -Scc --noconfirm
 RUN         R -e "install.packages('Rserve', repos='http://rforge.net/')"
 RUN         pip install xlsx2csv
 
-# install lazar-gui gem
 RUN         echo 'gem: --no-document' > /etc/gemrc
-RUN         gem install lazar-gui
 
 RUN         useradd -ms /bin/bash ist
 
@@ -53,11 +51,20 @@ COPY        start.sh /home/ist/start.sh
 USER        root
 RUN         pacman -U --noconfirm /home/ist/src/mongodb-bin/mongodb-bin*.pkg.tar.xz 
 
-# swagger links
-RUN         ln -s /home/ist/swagger-ui/dist/swagger-ui-bundle.js $(gem which "lazar-gui"|sed 's#/lib/lazar-gui.rb/##')/public/swagger-ui-bundle.js
-RUN         ln -s /home/ist/swagger-ui/dist/swagger-ui-standalone-preset.js $(gem which "lazar-gui"|sed 's#/lib/lazar-gui.rb/##')/public/swagger-ui-standalone-preset.js
-RUN         ln -s /home/ist/swagger-ui/dist/swagger-ui.css $(gem which "lazar-gui"|sed 's#/lib/lazar-gui.rb/##')/public/swagger-ui.css
+# install lazar-gui gem
+# lazar gem (required from lazar-gui) needs mongodb
+RUN         gem install lazar-gui 
+
+# change owners (temporary workaround)
+RUN         chown ist `ls -d $(gem environment gemdir)/gems/lazar-gui-*`/public
+RUN         chown ist `ls -d $(gem environment gemdir)/gems/lazar-gui-*`/tmp
+RUN         chown ist `ls -d $(gem environment gemdir)/gems/lazar-gui-*`/api/api.json
 
 USER        ist
 RUN         rm -r /home/ist/src
+# swagger links
+RUN         ln -s /home/ist/swagger-ui/dist/swagger-ui-bundle.js `ls -d $(gem environment gemdir)/gems/lazar-gui-*`/public/swagger-ui-bundle.js
+RUN         ln -s /home/ist/swagger-ui/dist/swagger-ui-standalone-preset.js `ls -d $(gem environment gemdir)/gems/lazar-gui-*`/public/swagger-ui-standalone-preset.js
+RUN         ln -s /home/ist/swagger-ui/dist/swagger-ui.css `ls -d $(gem environment gemdir)/gems/lazar-gui-*`/public/swagger-ui.css
+
 ENTRYPOINT  ["/home/ist/start.sh"]

data/docker/start.sh

@@ -8,5 +8,5 @@ R CMD Rserve --vanilla &
 ruby -e "require 'lazar'; include OpenTox; Import.public_data if Model::Validation.all.empty?" 
 
 # start lazar service
-cd $(gem which lazar-gui|sed 's#/lib/lazar-gui.rb/##')
+cd `ls -d $(gem environment gemdir)/gems/lazar-gui-*`
 unicorn -p 8088 -E production

data/test/service-test.rb

@@ -0,0 +1,41 @@
+require 'minitest/autorun'
+require 'rest-client'
+require 'nokogiri'
+require '~/lazar/lib/lazar.rb'
+$models = OpenTox::Model::Validation.all
+$r_model = $models.select{|m| m if m.model.name == "LOAEL (training_log10)"}[0].id.to_s
+$c_model = $models.select{|m| m if m.model.name == "Mutagenicity (kazius)"}[0].id.to_s
+
+class WebServiceTests < Minitest::Test
+
+  def test_prediction
+
+    # regression
+    response = RestClient.post "http://localhost:8088/predict", {identifier: "O=[N+]([O-])c1ccccc1", selection: {$r_model=>""}}
+    xml = Nokogiri::HTML.parse(response.body)
+    value = xml.css('td')[1].css('p')[2].text.split[1].to_f
+    assert value.between?(0.06,0.09)
+
+    # classification
+    response = RestClient.post "http://localhost:8088/predict", {identifier: "O=[N+]([O-])c1ccccc1", selection: {$c_model=>""}}
+    xml = Nokogiri::HTML.parse(response.body)
+    value = xml.css('td')[1].css('p')[4].text.split.last
+    assert_equal "mutagenic", value
+  end
+
+  def test_validation
+
+		# regression
+    response = RestClient.get "http://localhost:8088/predict/modeldetails/#{$r_model}"
+    xml = Nokogiri::HTML.parse(response.body)
+    links = xml.css('a')
+    assert_equal "Algorithm::Caret.rf", links[3].children.text.strip
+
+		# classification
+    response = RestClient.get "http://localhost:8088/predict/modeldetails/#{$c_model}"
+    xml = Nokogiri::HTML.parse(response.body)
+    links = xml.css('a')
+    assert_equal "Algorithm::Classification.weighted_majority_vote", links[3].children.text.strip
+  end
+
+end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: lazar-gui
 version: !ruby/object:Gem::Version
-  version: 1.4.0
+  version: 1.4.1
 platform: ruby
 authors:
 - Christoph Helma
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-09-03 00:00:00.000000000 Z
+date: 2019-09-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: lazar
@@ -360,6 +360,7 @@ files:
 - public/stylesheets/pagination.css
 - qmrf_report.rb
 - task.rb
+- test/service-test.rb
 - tmp/.gitignore
 - unicorn.rb
 - views/batch.haml