pc-lazar.rb and shell tests removed

9 files changed, 0 insertions, 129 deletions

diff --git a/test/pc-lazar.rb b/test/pc-lazar.rb
deleted file mode 100644
index 033e7cc..0000000
--- a/test/pc-lazar.rb
+++ /dev/null
@@ -1,52 +0,0 @@
-=begin
-  * File: pc-lazar.rb
-  * Purpose: pc-lazar tests
-  * Author: Andreas Maunz <andreas@maunz.de>
-  * Date: 10/2012
-=end
-
-TEST_DIR = File.expand_path(File.dirname(__FILE__))
-require_relative "setup.rb"
-#require File.join(TEST_DIR,"setup.rb")
-#require File.join(TEST_DIR,"helper.rb")
-#SHELL_DIR = File.join(TEST_DIR,"shell")
-DATA_DIR = File.join(TEST_DIR,"data")
-
-class PcLazarTest < MiniTest::Test
-  i_suck_and_my_tests_are_order_dependent!
-
-  def test_01_upload
-    @@dataset = OpenTox::Dataset.new nil, SUBJECTID
-    @@dataset.upload File.join(DATA_DIR,"hamster_carcinogenicity.csv")
-    assert_equal @@dataset.uri.uri?, true
-  end
-
-  def test_02_pc_fds
-    #task_uri = OpenTox::RestClientWrapper.post File.join(@@dataset.uri, "pc"), {:pc_type => "geometrical"}
-    #puts task_uri
-    #@pc = wait_for_task(task_uri)
-    #puts @pc.uri
-    #assert_equal @pc.uri.uri?, true
-    #mkvar(`bash #{SHELL_DIR}/pc_fds.sh`)
-    #puts "pc_fds: '#{ENV['pc_fds']}'"
-    #assert_equal ENV['pc_fds'].uri?, true
-  end
-
-  def test_02_lazar_pc_model
-    lazar = OpenTox::Algorithm.new File.join($algorithm[:uri],"lazar"), SUBJECTID
-    @@model = lazar.run :dataset_uri => @@dataset.uri, :feature_generation_uri => File.join($algorithm[:uri],"pc-descriptors"), :pc_type => "geometrical"
-    assert_equal @@model.uri.uri?, true
-    puts @@model.uri
-  end
-
-  def test_03_lazar_pc_prediction
-    prediction_uri = @@model.run :compound_uri => "#{$compound[:uri]}/InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H"
-    prediction = OpenTox::Dataset.new prediction_uri, SUBJECTID
-    assert_equal prediction.uri.uri?, true
-    puts prediction.uri
-    #mkvar(`bash #{SHELL_DIR}/lazar_p_pc.sh`)
-    #puts "lazar_p_pc: '#{ENV['lazar_p_pc']}'"
-    #assert_equal ENV['lazar_p_pc'].uri?, true
-  end
-
-end
diff --git a/test/shell/lazar_ds_bbrc.sh b/test/shell/lazar_ds_bbrc.sh
deleted file mode 100755
index 5ca62d5..0000000
--- a/test/shell/lazar_ds_bbrc.sh
+++ /dev/null
@@ -1,13 +0,0 @@
-dir=`dirname -z "$0"`
-. $dir/setup.sh
-
-# make a dataset prediction
-task=`curl -X POST \
--F "file=@$dir/../data/EPAFHM.mini.csv;type=text/csv" \
-$DATASET`
-mini=`get_result $task`
-task=`curl -X POST \
---data-urlencode "dataset_uri=$mini" \
-$lazar_m_bbrc`
-lazar_ds_bbrc=`get_result "$task"`
-echo "lazar_ds_bbrc: $lazar_ds_bbrc"
diff --git a/test/shell/lazar_m_bbrc.sh b/test/shell/lazar_m_bbrc.sh
deleted file mode 100755
index 952f9c9..0000000
--- a/test/shell/lazar_m_bbrc.sh
+++ /dev/null
@@ -1,9 +0,0 @@
-. $(cd "$(dirname "$0")"; pwd)/setup.sh
-
-# create lazar m w/ bbrc
-task=`curl -X POST \
-  --data-urlencode "dataset_uri=$ds" \
-  --data-urlencode "feature_generation_uri=$ALGORITHM/fminer/bbrc" \
-  $ALGORITHM/lazar`
-lazar_m_bbrc=`get_result "$task"`
-echo "lazar_m_bbrc: $lazar_m_bbrc"
diff --git a/test/shell/lazar_m_pc.sh b/test/shell/lazar_m_pc.sh
deleted file mode 100755
index 3c3b870..0000000
--- a/test/shell/lazar_m_pc.sh
+++ /dev/null
@@ -1,11 +0,0 @@
-dir=`dirname -z "$0"`
-. $dir/setup.sh
-
-# create lazar m w/ bbrc
-task=`curl -X POST \
---data-urlencode "dataset_uri=$ds" \
---data-urlencode "feature_dataset_uri=$pc_fds" \
---data-urlencode "feature_generation_uri=$ds/pc" \
-$ALGORITHM/lazar`
-lazar_m_pc=`get_result "$task"`
-echo "lazar_m_pc: $lazar_m_pc"
diff --git a/test/shell/lazar_p_bbrc.sh b/test/shell/lazar_p_bbrc.sh
deleted file mode 100755
index 62fba5e..0000000
--- a/test/shell/lazar_p_bbrc.sh
+++ /dev/null
@@ -1,8 +0,0 @@
-. $(cd "$(dirname "$0")"; pwd)/setup.sh
-
-# make benzene prediction w/ lazar m w/ bbrc
-task=`curl -X POST \
-  --data-urlencode "compound_uri=$COMPOUND/InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H" \
-  $lazar_m_bbrc`
-lazar_p_bbrc=`get_result "$task"`
-echo "lazar_p_bbrc: $lazar_p_bbrc" 
diff --git a/test/shell/lazar_p_pc.sh b/test/shell/lazar_p_pc.sh
deleted file mode 100755
index 2c5c3a9..0000000
--- a/test/shell/lazar_p_pc.sh
+++ /dev/null
@@ -1,9 +0,0 @@
-dir=`dirname -z "$0"`
-. $dir/setup.sh
-
-# make benzene prediction w/ lazar m w/ pc
-task=`curl -X POST \
---data-urlencode "compound_uri=$COMPOUND/InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H" \
-$lazar_m_pc`
-lazar_p_pc=`get_result "$task"`
-echo "lazar_p_pc: $lazar_p_pc" 
diff --git a/test/shell/pc_fds.sh b/test/shell/pc_fds.sh
deleted file mode 100755
index 746b73b..0000000
--- a/test/shell/pc_fds.sh
+++ /dev/null
@@ -1,9 +0,0 @@
-dir=`dirname -z "$0"`
-. $dir/setup.sh
-
-task=`curl \
---data-urlencode "pc_type=geometrical"  \
--X POST $ds/pc`
-echo $task
-pc_fds=`get_result "$task"`
-echo "pc_fds: $pc_fds"
diff --git a/test/shell/setup.sh b/test/shell/setup.sh
deleted file mode 100755
index d670e68..0000000
--- a/test/shell/setup.sh
+++ /dev/null
@@ -1,9 +0,0 @@
-# util 
-function get_result {
-  task=$1
-  while [ 1 ]; do
-    result=`curl -H "accept:text/uri-list" $task 2>/dev/null`
-    [ $result == $task ] && sleep 1 || break
-  done
-  echo $result
-}
diff --git a/test/shell/upload.sh b/test/shell/upload.sh
deleted file mode 100755
index d903889..0000000
--- a/test/shell/upload.sh
+++ /dev/null
@@ -1,9 +0,0 @@
-dir=`dirname -z "$0"`
-. $dir/setup.sh
-
-# load ds
-task=`curl -X POST \
--F "file=@$dir/../data/hamster_carcinogenicity.csv;type=text/csv" \
-$DATASET`
-ds=`get_result "$task"`
-echo "ds: $ds"