merge sbml test models

Squashed commit of the following: commit 8fd60d7e2c799070dd499d97c9804dd43326b32e Author: 0u812 <[email protected]> Date: Wed Nov 18 21:31:17 2015 -0800 copy test files to build dir commit 086c2f913db0f982f13707d6a7f5b8d7c17dfcd7 Author: 0u812 <[email protected]> Date: Wed Nov 18 21:17:28 2015 -0800 sbml test models: remove l2v3 files commit f588c7ffdf95df55b089d2f164aeac0429027a45 Author: 0u812 <[email protected]> Date: Wed Nov 18 21:17:13 2015 -0800 sbml test models: remove l2v2 files commit 0b1f649d08cca723701efec3aec58843eda86d8e Author: 0u812 <[email protected]> Date: Wed Nov 18 21:16:49 2015 -0800 sbml test models: remove l2v1 files commit 51570b18eb483a860c574ab48e0b67f2b7aaf39a Author: 0u812 <[email protected]> Date: Wed Nov 18 21:16:21 2015 -0800 sbml test models: remove plot images commit b11068ef05a2f52b1b0057a05dcf29d6a77b9e17 Author: 0u812 <[email protected]> Date: Wed Nov 18 21:08:49 2015 -0800 sbml test suite: use num failures as exit code commit 35fd894a4821c9be204bbd24e1f2b5c113f01ae6 Author: 0u812 <[email protected]> Date: Wed Nov 18 21:08:01 2015 -0800 third_party: add method to get test results from runner (already exists in UnitTest++ 1.5 commit e972c0465e3503f670e9ea4ff2931b4f7ef908b8 Author: 0u812 <[email protected]> Date: Tue Nov 17 21:46:44 2015 -0800 sbml test suite: remove html files commit f9b28c4e13652bcfb1ce89ec654e74ff859ee127 Author: 0u812 <[email protected]> Date: Tue Nov 17 21:46:30 2015 -0800 sbml test suite: remove matlab files commit 164be60690ef01b14ada8a5fd00b0286c9671b8e Author: 0u812 <[email protected]> Date: Tue Nov 17 21:46:04 2015 -0800 sbml test suite: remove sedml files commit 01b0d1020cc9ddfac399d9dfbf500ab3db04f723 Author: 0u812 <[email protected]> Date: Tue Nov 17 21:44:36 2015 -0800 add compiled tests
sys-bio · Nov 19, 2015 · 3bb3b79 · 3bb3b79
1 parent fcc5b5f
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diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -305,6 +305,7 @@ add_subdirectory(wrappers)
 
 if(BUILD_TESTS AND BUILD_TEST_TOOLS)
     message(STATUS "building tests")
+    file( COPY testing DESTINATION ${CMAKE_CURRENT_BINARY_DIR} )
     add_subdirectory(testing)
     add_subdirectory(autotest)
 else()

diff --git a/autotest/CMakeLists.txt b/autotest/CMakeLists.txt
@@ -7,8 +7,13 @@
 # @author JKM(0u812)
 # @date 07/01/2015
 # @copyright Apache License, Version 2.0
-# @brief Automated unit tests
+# @brief Unit tests
+# @details Tests can be run via ctest -VV
 
+# compiled test suite, including SBML benchmark
+add_subdirectory(compiled-test-suite)
+
+# performance benchmark (adapted from published benchmark in bioinformatics, 2015)
 if(BUILD_PYTHON)
   file(COPY python-benchmark-bioinf DESTINATION .)
 

diff --git a/autotest/compiled-test-suite/CMakeLists.txt b/autotest/compiled-test-suite/CMakeLists.txt
@@ -0,0 +1,19 @@
+# == PREAMBLE ================================================
+# * Licensed under the Apache License, Version 2.0; see README
+
+# == FILEDOC =================================================
+
+# @file autotest/CMakeLists.txt
+# @author JKM(0u812)
+# @date 11/17/2015
+# @copyright Apache License, Version 2.0
+# @brief Compiled unit tests
+
+if(WIN32)
+  set(RUN_TEST_SUITE_EXE_NAME "run_test_suite.exe")
+else()
+  set(RUN_TEST_SUITE_EXE_NAME "run_test_suite")
+endif()
+
+add_test(NAME CompiledTestSuite
+  COMMAND ${CMAKE_BINARY_DIR}/bin/${RUN_TEST_SUITE_EXE_NAME} -c llvm -m ${CMAKE_SOURCE_DIR}/models/sbml-test-suite -r results.xml >log 2>&1)
diff --git a/models/sbml-test-suite/cases/semantic/.cases-archive-date b/models/sbml-test-suite/cases/semantic/.cases-archive-date
@@ -0,0 +1 @@
+2014-10-22
diff --git a/models/sbml-test-suite/cases/semantic/.cases-tags-map b/models/sbml-test-suite/cases/semantic/.cases-tags-map
diff --git a/models/sbml-test-suite/cases/semantic/00001/00001-results.csv b/models/sbml-test-suite/cases/semantic/00001/00001-results.csv
@@ -0,0 +1,52 @@
+time,S1,S2
+0,0.00015,0
+0.1,0.0001357256127053939,1.427438729460607e-005
+0.2,0.0001228096129616973,2.719038703830272e-005
+0.3,0.0001111227331022577,3.887726689774233e-005
+0.4,0.0001005480069053459,4.945199309465411e-005
+0.5,9.097959895689501e-005,5.902040104310499e-005
+0.6,8.232174541410396e-005,6.767825458589604e-005
+0.7,7.448779556871142e-005,7.551220443128858e-005
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+1,5.518191617571635e-005,9.481808382428365e-005
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+2.7,1.008082691096246e-005,0.0001399191730890375
+2.8,9.121509393782692e-006,0.0001408784906062173
+2.9,8.253483008461082e-006,0.0001417465169915389
+3,7.468060255179591e-006,0.0001425319397448204
+3.1,6.757380359033671e-006,0.0001432426196409663
+3.2,6.114330596754931e-006,0.0001438856694032451
+3.3,5.532475110186e-006,0.000144467524889814
+3.4,5.00599049404891e-006,0.0001449940095059511
+3.5,4.529607513347775e-006,0.0001454703924866522
+3.6,4.098558367093884e-006,0.0001459014416329061
+3.7,3.708528970550908e-006,0.0001462914710294491
+3.8,3.355615778424839e-006,0.0001466443842215752
+3.9,3.036286716870657e-006,0.0001469637132831294
+4,2.747345833310127e-006,0.0001472526541666899
+4.1,2.485901310264186e-006,0.0001475140986897358
+4.2,2.249336523071655e-006,0.0001477506634769283
+4.3,2.03528385183014e-006,0.0001479647161481699
+4.4,1.841600985460266e-006,0.0001481583990145397
+4.5,1.666349480736346e-006,0.0001483336505192637
+4.6,1.507775361695036e-006,0.000148492224638305
+4.7,1.364291565254372e-006,0.0001486357084347456
+4.8,1.234462057353003e-006,0.000148765537942647
+4.9,1.116987460638651e-006,0.0001488830125393614
+5,1.01069204986282e-006,0.0001489893079501372
diff --git a/models/sbml-test-suite/cases/semantic/00001/00001-sbml-l1v2.xml b/models/sbml-test-suite/cases/semantic/00001/00001-sbml-l1v2.xml
@@ -0,0 +1,26 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level1" level="1" version="2">
+  <model name="case00001">
+    <listOfCompartments>
+      <compartment name="compartment" volume="1" units="volume"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species name="S1" compartment="compartment" initialAmount="0.00015" units="substance"/>
+      <species name="S2" compartment="compartment" initialAmount="0" units="substance"/>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter name="k1" value="1"/>
+    </listOfParameters>
+    <listOfReactions>
+      <reaction name="reaction1" reversible="false">
+        <listOfReactants>
+          <speciesReference species="S1"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="S2"/>
+        </listOfProducts>
+        <kineticLaw formula="compartment * k1 * S1"/>
+      </reaction>
+    </listOfReactions>
+  </model>
+</sbml>
diff --git a/models/sbml-test-suite/cases/semantic/00001/00001-sbml-l2v4.xml b/models/sbml-test-suite/cases/semantic/00001/00001-sbml-l2v4.xml
@@ -0,0 +1,35 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
+  <model metaid="_case00001" id="case00001" name="case00001">
+    <listOfCompartments>
+      <compartment id="compartment" name="compartment" size="1" units="volume"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species id="S1" name="S1" compartment="compartment" initialAmount="0.00015" substanceUnits="substance"/>
+      <species id="S2" name="S2" compartment="compartment" initialAmount="0" substanceUnits="substance"/>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter id="k1" name="k1" value="1"/>
+    </listOfParameters>
+    <listOfReactions>
+      <reaction id="reaction1" name="reaction1" reversible="false" fast="false">
+        <listOfReactants>
+          <speciesReference species="S1"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="S2"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> compartment </ci>
+              <ci> k1 </ci>
+              <ci> S1 </ci>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+    </listOfReactions>
+  </model>
+</sbml>
diff --git a/models/sbml-test-suite/cases/semantic/00001/00001-sbml-l3v1.xml b/models/sbml-test-suite/cases/semantic/00001/00001-sbml-l3v1.xml
@@ -0,0 +1,52 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+  <model metaid="_case00001" id="case00001" name="case00001" timeUnits="time">
+    <listOfUnitDefinitions>
+      <unitDefinition id="volume">
+        <listOfUnits>
+          <unit kind="litre" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="substance">
+        <listOfUnits>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="time">
+        <listOfUnits>
+          <unit kind="second" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+    </listOfUnitDefinitions>
+    <listOfCompartments>
+      <compartment id="compartment" name="compartment" spatialDimensions="3" size="1" units="volume" constant="true"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species id="S1" name="S1" compartment="compartment" initialAmount="0.00015" substanceUnits="substance" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+      <species id="S2" name="S2" compartment="compartment" initialAmount="0" substanceUnits="substance" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter id="k1" name="k1" value="1" constant="true"/>
+    </listOfParameters>
+    <listOfReactions>
+      <reaction id="reaction1" name="reaction1" reversible="false" fast="false">
+        <listOfReactants>
+          <speciesReference species="S1" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="S2" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> compartment </ci>
+              <ci> k1 </ci>
+              <ci> S1 </ci>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+    </listOfReactions>
+  </model>
+</sbml>
diff --git a/models/sbml-test-suite/cases/semantic/00001/00001-settings.txt b/models/sbml-test-suite/cases/semantic/00001/00001-settings.txt
@@ -0,0 +1,9 @@
+start: 0
+duration: 5
+steps: 50
+variables: S1, S2
+absolute: 1.000000e-007
+relative: 0.0001
+amount: S1, S2
+concentration:
+
diff --git a/models/sbml-test-suite/cases/semantic/00002/00002-results.csv b/models/sbml-test-suite/cases/semantic/00002/00002-results.csv
@@ -0,0 +1,52 @@
+time,S1,S2
+0,0.0015,0
+0.1,0.001357256127053939,0.0001427438729460607
+0.2,0.001228096129616973,0.0002719038703830273
+0.3,0.001111227331022577,0.0003887726689774233
+0.4,0.001005480069053459,0.0004945199309465411
+0.5,0.0009097959895689501,0.0005902040104310499
+0.6,0.0008232174541410396,0.0006767825458589605
+0.7,0.0007448779556871142,0.0007551220443128858
+0.8,0.0006739934461758324,0.0008260065538241676
+0.9,0.0006098544896108987,0.0008901455103891014
+1,0.0005518191617571635,0.0009481808382428365
+1.1,0.0004993066255471192,0.001000693374452881
+1.2,0.0004517913178683031,0.001048208682131697
+1.3,0.0004087976895510189,0.001091202310448981
+1.4,0.0003698954459124097,0.00113010455408759
+1.5,0.0003346952402226448,0.001165304759777355
+1.6,0.0003028447769919831,0.001197155223008017
+1.7,0.0002740252860791019,0.001225974713920898
+1.8,0.0002479483323323798,0.00125205166766762
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+2,0.000203002924854919,0.001296997075145081
+2.1,0.0001836846423794728,0.001316315357620527
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+3,7.468060255179592e-005,0.001425319397448204
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+3.5,4.529607513347775e-005,0.001454703924866522
+3.6,4.098558367093884e-005,0.001459014416329061
+3.7,3.708528970550908e-005,0.001462914710294491
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+3.9,3.036286716870657e-005,0.001469637132831294
+4,2.747345833310127e-005,0.001472526541666899
+4.1,2.485901310264186e-005,0.001475140986897358
+4.2,2.249336523071656e-005,0.001477506634769284
+4.3,2.03528385183014e-005,0.001479647161481699
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+4.5,1.666349480736346e-005,0.001483336505192637
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+4.8,1.234462057353003e-005,0.00148765537942647
+4.9,1.116987460638651e-005,0.001488830125393614
+5,1.01069204986282e-005,0.001489893079501372
diff --git a/models/sbml-test-suite/cases/semantic/00002/00002-sbml-l1v2.xml b/models/sbml-test-suite/cases/semantic/00002/00002-sbml-l1v2.xml
@@ -0,0 +1,36 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level1" level="1" version="2">
+  <model name="case00002">
+    <listOfCompartments>
+      <compartment name="compartment" volume="1" units="volume"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species name="S1" compartment="compartment" initialAmount="0.0015" units="substance"/>
+      <species name="S2" compartment="compartment" initialAmount="0" units="substance"/>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter name="k1" value="1"/>
+      <parameter name="k2" value="0"/>
+    </listOfParameters>
+    <listOfReactions>
+      <reaction name="reaction1" reversible="false">
+        <listOfReactants>
+          <speciesReference species="S1"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="S2"/>
+        </listOfProducts>
+        <kineticLaw formula="compartment * k1 * S1"/>
+      </reaction>
+      <reaction name="reaction2" reversible="false">
+        <listOfReactants>
+          <speciesReference species="S2"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="S1"/>
+        </listOfProducts>
+        <kineticLaw formula="compartment * k2 * S2"/>
+      </reaction>
+    </listOfReactions>
+  </model>
+</sbml>
diff --git a/models/sbml-test-suite/cases/semantic/00002/00002-sbml-l2v4.xml b/models/sbml-test-suite/cases/semantic/00002/00002-sbml-l2v4.xml
@@ -0,0 +1,54 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
+  <model metaid="_case00002" id="case00002" name="case00002">
+    <listOfCompartments>
+      <compartment id="compartment" name="compartment" size="1" units="volume"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species id="S1" name="S1" compartment="compartment" initialAmount="0.0015" substanceUnits="substance"/>
+      <species id="S2" name="S2" compartment="compartment" initialAmount="0" substanceUnits="substance"/>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter id="k1" name="k1" value="1"/>
+      <parameter id="k2" name="k2" value="0"/>
+    </listOfParameters>
+    <listOfReactions>
+      <reaction id="reaction1" name="reaction1" reversible="false" fast="false">
+        <listOfReactants>
+          <speciesReference species="S1"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="S2"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> compartment </ci>
+              <ci> k1 </ci>
+              <ci> S1 </ci>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+      <reaction id="reaction2" name="reaction2" reversible="false" fast="false">
+        <listOfReactants>
+          <speciesReference species="S2"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="S1"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> compartment </ci>
+              <ci> k2 </ci>
+              <ci> S2 </ci>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+    </listOfReactions>
+  </model>
+</sbml>