service-tests for public repo

7 files changed, 379 insertions, 0 deletions

diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..5093a29
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1 @@
+scripts/
diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..9bedbe5
--- /dev/null
+++ b/Dockerfile
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+FROM        insilicotox/lazar-dev
+MAINTAINER  in-silico toxicology GmbH
+
+RUN         sudo pacman-db-upgrade
+RUN         sudo pacman -Syyu --noconfirm
+RUN         sudo pacman -S --noconfirm msmtp msmtp-mta
+RUN         sudo pacman -Scc --noconfirm
+
+RUN         cd lazar && \
+            git checkout "master"
+
+RUN         mkdir -p /home/ist/log
+
+COPY        service-tests /home/ist/service-tests
+RUN         sudo chown -R ist:ist service-tests
+
+COPY        test.sh /home/ist/test.sh
+RUN         sudo chmod +x /home/ist/test.sh
+
+COPY        start.sh /home/ist/start.sh
+RUN         sudo chmod +x /home/ist/start.sh
+
+ENTRYPOINT  ["/home/ist/start.sh"]
diff --git a/service-tests/service-tests.rb b/service-tests/service-tests.rb
new file mode 100644
index 0000000..f0897af
--- /dev/null
+++ b/service-tests/service-tests.rb
@@ -0,0 +1,277 @@
+# Make updates and copy to container
+# docker cp service-tests.rb service-tests:/home/ist/service-tests/service-tests.rb
+# even if container is stopped !
+
+require 'minitest/autorun'
+require 'rest-client'
+require 'nokogiri'
+require 'csv'
+
+class WebServiceTests < Minitest::Test
+
+  def get_models
+    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
+  end
+
+  def test_virtuoso
+    puts "\nhttps://virtuoso.in-silico.ch"
+    assert_raises RestClient::NotFound do
+      response = RestClient.get "https://virtuoso.in-silico.ch"
+    end
+  end
+  
+  def test_insilico_website
+    puts "\nhttps://in-silico.ch"
+    response = RestClient.get "https://in-silico.ch"
+    assert_equal response.code, 200
+    xml = Nokogiri::HTML.parse(response.body)
+    value = xml.at('li.active').text.strip
+    assert_equal "Software and services", value
+  end
+  
+  def test_predictive_toxicology
+    puts "\nhttps://predictive-toxicology.org/"
+    response = RestClient.get "https://predictive-toxicology.org/"
+    assert_equal response.code, 200
+    xml = Nokogiri::HTML.parse(response.body)
+    value = xml.at('title').text
+    assert_equal "Predictive Toxicology", value
+  end
+  
+  def test_lazar_batch
+    puts "\nhttps://lazar-batch.in-silico.ch"
+    require '../batch-login.rb'
+    assert_raises RestClient::Unauthorized do
+      response = RestClient.get "https://lazar-batch.in-silico.ch"
+    end
+    assert_raises RestClient::Unauthorized do
+      response = RestClient::Request.execute method: :get, url: "https://lazar-batch.in-silico.ch", user: $user+"f", password: $passwd
+    end
+    assert_raises RestClient::Unauthorized do
+      response = RestClient::Request.execute method: :get, url: "https://lazar-batch.in-silico.ch", user: $user, password: $passwd+"f"
+    end
+    response = RestClient::Request.execute method: :get, url: "https://lazar-batch.in-silico.ch", user: $user, password: $passwd
+    xml = Nokogiri::HTML.parse(response.body)
+    assert_match xml.at('h1').text.gsub(/\n/,"").strip, "lazar toxicity predictions"
+    # batch
+    get_models
+    response = RestClient::Request.execute method: :post, 
+      url:  "https://lazar-batch.in-silico.ch/predict", 
+      user: $user,
+      password: $passwd,
+      payload: {
+        multipart: true,
+        fileselect: File.new('./test.csv', 'rb'),
+        selection: {$r_model => ""}
+      }
+    assert_equal response.code, 200
+    xml = Nokogiri::HTML.parse(response.body)
+    value = xml.css('h5').text
+    assert_equal "Lowest observed adverse effect level (LOAEL) (Rat)", value
+    value = xml.at_css('a#detailsbutton_0').text.strip
+    assert_equal "Details", value
+  end
+  
+  def test_dump
+    puts "\nhttps://dump.in-silico.ch"
+    response = RestClient.get "https://dump.in-silico.ch"
+    assert_equal response.code, 200
+    xml = Nokogiri::HTML.parse(response.body)
+    dumpsize = xml.at('pre').text.split.last.to_i 
+    response = RestClient.get "https://dump.in-silico.ch/dump.tar.gz"
+    assert_equal response.body.size.to_i, dumpsize
+  end
+  
+  def test_lazar
+    puts "\nhttps://lazar.in-silico.ch"
+    get_models
+    response = RestClient.get "https://lazar.in-silico.ch"
+    assert_equal response.code, 200
+    xml = Nokogiri::HTML.parse(response.body)
+    assert_match xml.at('h1').text.gsub(/\n/,"").strip, "lazar toxicity predictions"
+    puts "\npredict regression: https://lazar.in-silico.ch/predict"
+    # regression
+    response = RestClient.post "https://lazar.in-silico.ch/predict", {identifier: "O=[N+]([O-])c1ccccc1", selection: {$r_model=>""}}
+    xml = Nokogiri::HTML.parse(response.body)
+    value = xml.css('td')[1].css('p')[2].text.split[1].to_f
+    assert value.between?(0.06,0.09)
+    puts "\npredict classification: https://lazar.in-silico.ch/predict"
+    # classification
+    response = RestClient.post "https://lazar.in-silico.ch/predict", {identifier: "O=[N+]([O-])c1ccccc1", selection: {$c_model=>""}}
+    xml = Nokogiri::HTML.parse(response.body)
+    value = xml.css('td')[1].css('p')[4].text.split.last
+    assert_equal "mutagenic", value
+    # regression
+    puts "\nmodel details regression: https://lazar.in-silico.ch/predict/modeldetails/#{$r_model}"
+    response = RestClient.get "https://lazar.in-silico.ch/predict/modeldetails/#{$r_model}"
+    xml = Nokogiri::HTML.parse(response.body)
+    puts "check metadata\n"
+    links = xml.css('a')
+    assert_equal "https://github.com/opentox/loael-paper/blob/revision/data/training_log10.csv", links[0].children.text.strip
+    assert_equal "training_log10", links[1].children.text.strip
+    assert_equal "Algorithm::Similarity.tanimoto", links[2].children.text.strip
+    assert_equal "Algorithm::Caret.rf", links[3].children.text.strip
+    text = xml.css('div.panel-body')[0]
+    a,b = text.children[4].text.strip.split("\n")
+    assert_equal "Type:", a.strip
+    assert_equal "Regression", b.strip
+    a,b = text.children[6].text.strip.split("\n")
+    assert_equal "Training compounds:", a.strip
+    assert_equal "671", b.strip
+    text = xml.css('div.panel-body')[1]
+    a,b,c = text.children[8].text.strip.split
+    assert_equal "Descriptors:", a.strip
+    assert_equal "fingerprint,", b.strip
+    assert_equal "MP2D", c.strip
+    # classification
+    puts "\nmodel details classification: https://lazar.in-silico.ch/predict/modeldetails/#{$c_model}"
+    response = RestClient.get "https://lazar.in-silico.ch/predict/modeldetails/#{$c_model}"
+    xml = Nokogiri::HTML.parse(response.body)
+    puts "check metadata\n"
+    links = xml.css('a')
+    assert_equal "http://cheminformatics.org/datasets/", links[0].children.text.strip
+    assert_equal "kazius", links[1].children.text.strip
+    assert_equal "Algorithm::Similarity.tanimoto", links[2].children.text.strip
+    assert_equal "Algorithm::Classification.weighted_majority_vote", links[3].children.text.strip
+    text = xml.css('div.panel-body')[0]
+    a,b = text.children[4].text.strip.split("\n")
+    assert_equal "Type:", a.strip
+    assert_equal "Classification", b.strip
+    a,b = text.children[6].text.strip.split("\n")
+    assert_equal "Training compounds:", a.strip
+    assert_equal "4069", b.strip
+    text = xml.css('div.panel-body')[1]
+    a,b,c = text.children[8].text.strip.split
+    assert_equal "Descriptors:", a.strip
+    assert_equal "fingerprint,", b.strip
+    assert_equal "MP2D", c.strip
+  end
+
+  def test_nano_lazar
+    puts "\nhttps://nano-lazar.in-silico.ch"
+    response = RestClient.get "https://nano-lazar.in-silico.ch"
+    assert_equal response.code, 200
+    xml = Nokogiri::HTML.parse(response.body)
+    assert_match xml.at('h1').text.gsub(/\n/,"").strip, "nano-lazar toxicity predictions"
+    
+    params = {example_coating_0: "N-(2-Mercaptopropionyl)glycine",
+              example_core:	"Au",
+              example_id:	"5878a6097b6c9b003a862710",
+              example_pc:	"{}",
+              input_coating_0: "N-(2-Mercaptopropionyl)glycine",
+              input_core:	"Au",
+              prediction_model:	"5878aa1d7b6c9b003a8629b1",
+              type:	"fingerprint"
+    }
+    puts "\npredict example: https://nano-lazar.in-silico.ch/predict"
+    response = RestClient.post "https://nano-lazar.in-silico.ch/predict", params
+    xml = Nokogiri::HTML.parse(response.body)
+    value = xml.css('tbody').css('tr')[1].css('td')[0].css('a').text.gsub(/\n/,"").strip
+    assert_equal value, "G15.AC"
+  end
+
+  def test_aop
+    puts "\nhttps://aop.in-silico.ch"
+    response = RestClient.get "https://aop.in-silico.ch"
+    assert_equal response.code, 200
+    xml = Nokogiri::HTML.parse(response.body)
+    assert_match xml.at('h1').text.gsub(/\n/,"").strip, "PubChem read across"
+    puts "\nhttps://aop.in-silico.ch/cid/31703"
+    response = RestClient.get "https://aop.in-silico.ch/cid/31703"
+    assert_equal response.code, 200
+    xml = Nokogiri::HTML.parse(response.body)
+    value =  xml.at('th').text.split.first.strip
+    assert_equal "(7S,9S)-7-[(2R,4S,5S,6S)-4-amino-5-hydroxy-6-methyloxan-2-yl]oxy-6,9,11-trihydroxy-9-(2-hydroxyacetyl)-4-methoxy-8,10-dihydro-7H-tetracene-5,12-dione", value
+  end
+
+  def test_dg2_Elena
+    puts "\nhttps://dg2.in-silico.ch"
+    response = RestClient.get "https://dg2.in-silico.ch"
+    assert_equal response.code, 200
+    xml = Nokogiri::HTML.parse(response.body)
+    batch_file_id = xml.search("label")[4].attributes["for"].value.gsub(/existing|\[|\]/,"")
+    batch_file_name = xml.search("label")[4].text.strip
+    assert_match xml.at('h1').text.gsub(/\n/,"").strip, "lazar toxicity predictions"
+    puts "\nsingle prediction Mazzatorta: https://dg2.in-silico.ch/predict"
+    response = RestClient.post "https://dg2.in-silico.ch/predict", {identifier: "O=[N+]([O-])c1ccccc1", selection: {"Mazzatorta"=>""}}
+    xml = Nokogiri::HTML.parse(response.body)
+    value = xml.css('td')[1].css('p')[0].text.split[1].to_f
+    assert value, 0.384
+    puts "\nsingle prediction lazar LOAEL: https://dg2.in-silico.ch/predict"
+    response = RestClient.post "https://dg2.in-silico.ch/predict", {identifier: "O=[N+]([O-])c1ccccc1", selection: {"5ba4e38b5e110b01688fa0ca"=>""}}
+    xml = Nokogiri::HTML.parse(response.body)
+    value = xml.css('td')[1].css('p')[2].text.split[1].to_f
+    assert value, 0.0807
+    
+    puts "\nbatch prediction with first dataset in existing list\n"
+    response = RestClient.post "https://dg2.in-silico.ch/predict", {existing: {batch_file_id=>""}, selection: {"5ba4e38b5e110b01688fa0ca"=>""}}
+    assert_equal response.code, 200
+    xml = Nokogiri::HTML.parse(response.body)
+    title = xml.search("h3").text
+    assert_equal title, "Batch Prediction Results:RHC_input"
+    sleep 3
+    href = xml.search("a#downbutton_0")[0]["href"]
+    puts "\ndownload csv batch results\n"
+    response = RestClient.get href
+    csv = CSV.new(response.body)
+    header = csv.first
+    ["ID", "Original ID", "Input", "Endpoint"].each do |h|
+      assert_includes header, h
+    end
+    
+    puts "\nmodel details lazar LOAEL: https://dg2.in-silico.ch/predict/modeldetails/5ba4e38b5e110b01688fa0ca"
+    response = RestClient.get "https://dg2.in-silico.ch/predict/modeldetails/5ba4e38b5e110b01688fa0ca"
+    xml = Nokogiri::HTML.parse(response.body)
+    puts "check metadata\n"
+    links = xml.css('a')
+    assert_equal "https://github.com/opentox/loael-paper/blob/revision/data/training_log10.csv", links[0].children.text.strip
+    assert_equal "training_log10", links[1].children.text.strip
+    assert_equal "Algorithm::Similarity.tanimoto", links[2].children.text.strip
+    assert_equal "Algorithm::Caret.rf", links[3].children.text.strip
+    text = xml.css('div.panel-body')[0]
+    a,b = text.children[4].text.strip.split("\n")
+    assert_equal "Type:", a.strip
+    assert_equal "Regression", b.strip
+    a,b = text.children[6].text.strip.split("\n")
+    assert_equal "Training compounds:", a.strip
+    assert_equal "671", b.strip
+    text = xml.css('div.panel-body')[1]
+    a,b,c = text.children[8].text.strip.split
+    assert_equal "Descriptors:", a.strip
+    assert_equal "fingerprint,", b.strip
+    assert_equal "MP2D", c.strip
+  end
+
+  def test_dg3_Elena
+    puts "\nhttps://dg3.in-silico.ch"
+    response = RestClient.get "https://dg3.in-silico.ch"
+    assert_equal response.code, 200
+    xml = Nokogiri::HTML.parse(response.body)
+    assert_match xml.at('h1').text.gsub(/\n/,"").strip, "lazar toxicity predictions"
+  end
+
+  def test_test1_Elena
+    puts "\nhttps://test1.in-silico.ch"
+    response = RestClient.get "https://test1.in-silico.ch"
+    assert_equal response.code, 200
+    xml = Nokogiri::HTML.parse(response.body)
+    assert_match xml.at('h1').text.gsub(/\n/,"").strip, "Nestec Toxicity Predictions"
+  end
+
+  #def test_git_server
+  #TODO Net::HTTPBadResponse: wrong status line: "SSH-2.0-OpenSSH_7.8"
+  #  response = RestClient.get "https://git.in-silico.ch"
+  #end
+
+  def test_server_invalid_cert
+    puts "\ninvalid cert test4"
+    assert_raises RestClient::SSLCertificateNotVerified do
+      response = RestClient.get "https://test4.in-silico.ch"
+    end
+  end
+
+end
+
diff --git a/service-tests/test-batch-with-errors.csv b/service-tests/test-batch-with-errors.csv
new file mode 100644
index 0000000..2f5c2c1
--- /dev/null
+++ b/service-tests/test-batch-with-errors.csv
@@ -0,0 +1,5 @@
+SMILES
+"O=P(OCC)(SC(C)CC)SC(C)CC"
+O=C1CCC2(O1)C=C(C(=O)C(=C2)C(C)(C)C)C(C)(C)C
+O[C@@H]8[C@@H](O)[C@@H]1O[C@H](CO)[C@H]8O[C@H]7O[C@H](CO)[C@@H](O[C@H]6O[C@H](CO)[C@@H](O[C@H]5O[C@H](CO)[C@@H](O[C@H]4O[C@H](CO)[C@@H](O[C@H]3O[C@H](CO)[C@@H](O[C@H]2O[C@H](CO)[C@@H](O1)[C@H](O)[C@H]2O)[C@H](O)[C@H]3O)[C@H](O)[C@H]4O)[C@H](O)[C@H]5O)[C
+Toast
\ No newline at end of file
diff --git a/service-tests/test.csv b/service-tests/test.csv
new file mode 100644
index 0000000..7d074a3
--- /dev/null
+++ b/service-tests/test.csv
@@ -0,0 +1,2 @@
+SMILES
+O=[N+]([O-])c1ccccc1
diff --git a/start.sh b/start.sh
new file mode 100755
index 0000000..86bd54a
--- /dev/null
+++ b/start.sh
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+#!/bin/sh
+
+# start basic services
+sudo mongod &
+R CMD Rserve --vanilla &
+
+# fetch and load database content
+if [ ! -d "$HOME/dump" ]; then
+  wget https://dump.in-silico.ch/dump.tar.gz
+  tar xfvz dump.tar.gz
+  mongorestore
+fi
+
+ln -s "$HOME/scripts/batch-login.rb" "$HOME/batch-login.rb"
+sudo chown ist:ist ~/batch-login.rb
+ln -s "$HOME/scripts/.msmtprc" "$HOME/.msmtprc"
+sudo chown ist:ist ~/.msmtprc
+sudo chmod 600 ~/.msmtprc
+
+./test.sh
+
diff --git a/test.sh b/test.sh
new file mode 100755
index 0000000..ef0206c
--- /dev/null
+++ b/test.sh
@@ -0,0 +1,50 @@
+#!/bin/bash
+
+TITLE="Service Tests"
+HOME="/home/ist"
+TESTDIR="$HOME/service-tests"
+
+. $HOME/.bashrc
+
+DATE=`date +%y%m%d`
+separator="============================"
+
+LOGDIR="$HOME/log"
+ERRLOG="$LOGDIR/$DATE-err.log"
+LOG="$LOGDIR/$DATE.log"
+MSG="$HOME/msg.log"
+rm "$LOG" 2>/dev/null
+rm "$ERRLOG" 2>/dev/null
+rm "$MSG" 2>/dev/null
+
+touch $LOG
+touch $ERRLOG
+touch $MSG
+
+cd $TESTDIR
+tests=(service-tests.rb)
+for t in ${tests[@]}; do
+  echo $separator | tee -a $LOG $MSG
+  echo " "$t|tr [a-z] [A-Z] | tee -a $LOG $MSG
+  echo " "`date` | tee -a $LOG $MSG
+  echo $separator | tee -a $LOG $MSG
+  echo ruby $t | tee -a $LOG $MSG
+  # whole test output to logfile only
+  ruby $t >> $LOG
+  # take last occurrence of regex to end of the file
+  awk '/^Finished in/ { buf = "" } { buf = buf "\n" $0 } END { print buf }' $LOG >> $MSG
+  echo "" >> $LOG
+done
+
+# MAIL 
+file="$HOME/scripts/recipients"
+recipients=$(cat $file)
+if grep -q "Error:" $LOG; then ERRMSG=" ERROR (`grep -c ' Error:' $LOG`)"; else ERRMSG=" OK "; fi
+if grep -q "Failure:" $LOG; then FAILMSG=" FAIL (`grep -c ' Failure:' $LOG`)"; else FAILMSG=""; fi
+
+for p in ${recipients[@]}; do
+  #{ printf "To: $p\nSubject: [service tests] -$TITLE- $DATE $ERRMSG $FAILMSG\n"; cat $MSG; } | msmtp -a default $p
+  { printf "To: $p\nSubject: [service tests] -$TITLE- $DATE $ERRMSG $FAILMSG\n"; cat $LOG; } | msmtp -a default $p
+done
+
+exit 0