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Simple tests for the main function of learn.

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leandrohw 2017-07-09 17:18:02 -06:00
parent d6a68795c0
commit fde211c4a9
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learn/src/test/java/edu/utah/ece/async/ibiosim/learn/LearnTests.java Normal file
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package edu.utah.ece.async.ibiosim.learn;
import static org.junit.Assert.*;
import java.io.File;
import org.junit.Before;
import org.junit.Test;
public class LearnTests {
private String root = "src" + File.separator + "test" + File.separator +
"resources" + File.separator;
@Test
public void test01() {
String directory = root + File.separator + "simpleDesign" + File.separator;
String filename = directory + "simpleDesign.xml";
Learn.main(new String[]{filename, directory});
//TODO: add check
}
@Test
public void test02() {
String directory = root + File.separator + "degradation" + File.separator;
String filename = directory + "degradation.xml";
Learn.main(new String[]{"-e", filename, directory});
//TODO: add check
}
}

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learn/src/test/resources/degradation/degradation.xml Normal file
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<?xml version='1.0' encoding='UTF-8' standalone='no'?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" fbc:required="false" level="3" version="1" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2">
<model fbc:strict="false" id="degradation" metaid="iBioSim3" name="Created by iBioSim flatten routine">
<listOfCompartments>
<compartment constant="true" id="Cell" size="1" spatialDimensions="3"/>
</listOfCompartments>
<listOfSpecies>
<species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="S0" initialAmount="100" metaid="iBioSim1"/>
</listOfSpecies>
<listOfParameters>
<parameter constant="true" id="kd" metaid="iBioSim2" name="Degradation rate" value="0.0075"/>
</listOfParameters>
<listOfReactions>
<reaction compartment="Cell" fast="false" id="Degradation_S0" metaid="iBioSim4" reversible="false" sboTerm="SBO:0000179">
<listOfReactants>
<speciesReference constant="true" species="S0" stoichiometry="1"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> kd </ci>
<ci> S0 </ci>
</apply>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>

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learn/src/test/resources/degradation/run-1.tsd Normal file
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(("time","S0"),(0, 100),(1, 95),(2, 95),(3, 94),(4, 94),(5, 94),(6, 92),(7, 92),(8, 91),(9, 91),(10, 91),(11, 90),(12, 90),(13, 89),(14, 86),(15, 86),(16, 86),(17, 84),(18, 84),(19, 82),(20, 81),(21, 81),(22, 81),(23, 80),(24, 80),(25, 79),(26, 79),(27, 79),(28, 79),(29, 79),(30, 78),(31, 78),(32, 78),(33, 77),(34, 77),(35, 74),(36, 73),(37, 72),(38, 72),(39, 72),(40, 70),(41, 70),(42, 69),(43, 69),(44, 69),(45, 68),(46, 68),(47, 67),(48, 67),(49, 67),(50, 67),(51, 67),(52, 66),(53, 65),(54, 65),(55, 65),(56, 65),(57, 65),(58, 64),(59, 64),(60, 64),(61, 64),(62, 64),(63, 64),(64, 64),(65, 63),(66, 62),(67, 62),(68, 62),(69, 62),(70, 62),(71, 62),(72, 62),(73, 61),(74, 61),(75, 60),(76, 59),(77, 59),(78, 59),(79, 59),(80, 59),(81, 59),(82, 59),(83, 59),(84, 59),(85, 59),(86, 58),(87, 58),(88, 58),(89, 58),(90, 58),(91, 58),(92, 57),(93, 56),(94, 56),(95, 56),(96, 56),(97, 56),(98, 55),(99, 55),(100, 54))

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learn/src/test/resources/degradation/run-2.tsd Normal file
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(("time","S0"),(0, 100),(1, 98),(2, 98),(3, 97),(4, 95),(5, 94),(6, 94),(7, 93),(8, 93),(9, 93),(10, 92),(11, 92),(12, 91),(13, 91),(14, 91),(15, 90),(16, 88),(17, 87),(18, 86),(19, 85),(20, 84),(21, 84),(22, 83),(23, 83),(24, 83),(25, 81),(26, 79),(27, 78),(28, 77),(29, 76),(30, 75),(31, 75),(32, 74),(33, 73),(34, 73),(35, 73),(36, 73),(37, 73),(38, 73),(39, 72),(40, 71),(41, 70),(42, 69),(43, 69),(44, 69),(45, 69),(46, 68),(47, 68),(48, 68),(49, 67),(50, 67),(51, 66),(52, 66),(53, 66),(54, 64),(55, 64),(56, 64),(57, 64),(58, 63),(59, 63),(60, 63),(61, 63),(62, 62),(63, 62),(64, 62),(65, 61),(66, 61),(67, 61),(68, 60),(69, 60),(70, 59),(71, 58),(72, 58),(73, 58),(74, 58),(75, 58),(76, 57),(77, 55),(78, 55),(79, 54),(80, 54),(81, 54),(82, 52),(83, 52),(84, 52),(85, 51),(86, 51),(87, 51),(88, 50),(89, 49),(90, 49),(91, 48),(92, 48),(93, 48),(94, 48),(95, 47),(96, 45),(97, 42),(98, 42),(99, 41),(100, 41))

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learn/src/test/resources/degradation/run-3.tsd Normal file
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learn/src/test/resources/degradation/run-4.tsd Normal file
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(("time","S0"),(0, 100),(1, 100),(2, 98),(3, 96),(4, 95),(5, 94),(6, 94),(7, 94),(8, 92),(9, 91),(10, 88),(11, 87),(12, 86),(13, 83),(14, 82),(15, 81),(16, 80),(17, 78),(18, 77),(19, 77),(20, 77),(21, 76),(22, 76),(23, 74),(24, 74),(25, 74),(26, 74),(27, 74),(28, 73),(29, 73),(30, 72),(31, 71),(32, 71),(33, 71),(34, 70),(35, 70),(36, 69),(37, 67),(38, 66),(39, 66),(40, 66),(41, 66),(42, 66),(43, 65),(44, 64),(45, 64),(46, 63),(47, 62),(48, 62),(49, 62),(50, 62),(51, 62),(52, 62),(53, 61),(54, 61),(55, 58),(56, 58),(57, 57),(58, 56),(59, 56),(60, 56),(61, 56),(62, 56),(63, 56),(64, 55),(65, 55),(66, 55),(67, 55),(68, 55),(69, 55),(70, 55),(71, 55),(72, 54),(73, 54),(74, 53),(75, 53),(76, 53),(77, 52),(78, 52),(79, 52),(80, 51),(81, 50),(82, 50),(83, 50),(84, 49),(85, 49),(86, 49),(87, 49),(88, 49),(89, 48),(90, 48),(91, 48),(92, 47),(93, 47),(94, 47),(95, 46),(96, 45),(97, 45),(98, 45),(99, 45),(100, 45))

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learn/src/test/resources/degradation/run-5.tsd Normal file
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(("time","S0"),(0, 100),(1, 100),(2, 99),(3, 99),(4, 98),(5, 98),(6, 98),(7, 98),(8, 98),(9, 98),(10, 96),(11, 96),(12, 95),(13, 94),(14, 94),(15, 93),(16, 92),(17, 90),(18, 90),(19, 89),(20, 89),(21, 89),(22, 89),(23, 89),(24, 89),(25, 88),(26, 87),(27, 87),(28, 86),(29, 86),(30, 85),(31, 85),(32, 85),(33, 84),(34, 82),(35, 81),(36, 81),(37, 81),(38, 79),(39, 77),(40, 76),(41, 76),(42, 76),(43, 76),(44, 75),(45, 75),(46, 75),(47, 75),(48, 74),(49, 74),(50, 73),(51, 71),(52, 71),(53, 71),(54, 71),(55, 70),(56, 70),(57, 70),(58, 70),(59, 70),(60, 69),(61, 69),(62, 67),(63, 66),(64, 65),(65, 64),(66, 64),(67, 64),(68, 63),(69, 61),(70, 61),(71, 61),(72, 61),(73, 61),(74, 61),(75, 61),(76, 61),(77, 60),(78, 60),(79, 60),(80, 60),(81, 60),(82, 60),(83, 60),(84, 58),(85, 58),(86, 58),(87, 58),(88, 57),(89, 57),(90, 57),(91, 56),(92, 55),(93, 55),(94, 55),(95, 55),(96, 55),(97, 55),(98, 55),(99, 55),(100, 55))

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learn/src/test/resources/simpleDesign/method.dot Normal file
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digraph G {
s1 [shape=ellipse,color=black,label="S0"];
s2 [shape=ellipse,color=black,label="S1"];
s3 [shape=ellipse,color=black,label="S2"];
s4 [shape=ellipse,color=black,label="P0"];
s5 [shape=ellipse,color=black,label="P1"];
s1 -> s2 [color="firebrick4",arrowhead=tee]
s3 -> s2 [color="firebrick4",arrowhead=tee]
}

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learn/src/test/resources/simpleDesign/method.gcm Normal file
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digraph G {
s1 [shape=ellipse,color=black,label="S0"];
s2 [shape=ellipse,color=black,label="S1"];
s3 [shape=ellipse,color=black,label="S2"];
s4 [shape=ellipse,color=black,label="P0"];
s5 [shape=ellipse,color=black,label="P1"];
s1 -> s2 [color="firebrick4",arrowhead=tee]
s3 -> s2 [color="firebrick4",arrowhead=tee]
}

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learn/src/test/resources/simpleDesign/run-1.tsd Normal file
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(("time","S0","S1","S2","P0","P1"),(0, 10, 100, 0, 2, 2),(10, 9, 91, 0, 2, 2),(20, 8, 82, 0, 2, 2),(30, 8, 79, 0, 2, 2),(40, 8, 70, 0, 2, 2),(50, 8, 67, 10, 2, 2),(60, 8, 65, 10, 2, 2),(70, 8, 62, 9, 2, 2),(80, 8, 59, 9, 2, 2),(90, 8, 55, 8, 2, 2),(100, 6, 51, 8, 2, 2),(110, 4, 49, 7, 2, 2),(120, 4, 47, 15, 2, 2),(130, 3, 44, 14, 2, 2),(140, 3, 38, 13, 2, 2),(150, 3, 36, 11, 2, 2),(160, 3, 32, 10, 2, 2),(170, 3, 30, 9, 2, 2),(180, 3, 28, 8, 2, 2),(190, 3, 28, 7, 2, 2),(200, 3, 28, 6, 2, 2),(210, 2, 26, 5, 2, 2),(220, 2, 24, 5, 2, 2),(230, 2, 20, 4, 2, 2),(240, 2, 18, 3, 2, 2),(250, 2, 16, 3, 2, 2),(260, 2, 15, 3, 2, 2),(270, 1, 13, 3, 2, 2),(280, 1, 21, 3, 2, 2),(290, 1, 18, 3, 2, 2),(300, 1, 17, 2, 2, 2))

1
learn/src/test/resources/simpleDesign/run-10.tsd Normal file
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(("time","S0","S1","S2","P0","P1"),(0, 10, 100, 0, 2, 2),(10, 9, 94, 0, 2, 2),(20, 7, 84, 0, 2, 2),(30, 6, 78, 0, 2, 2),(40, 5, 74, 0, 2, 2),(50, 5, 64, 0, 2, 2),(60, 4, 58, 0, 2, 2),(70, 4, 55, 0, 2, 2),(80, 4, 54, 0, 2, 2),(90, 4, 52, 0, 2, 2),(100, 4, 45, 0, 2, 2),(110, 4, 51, 0, 2, 2),(120, 4, 54, 0, 2, 2),(130, 4, 48, 0, 2, 2),(140, 4, 64, 0, 2, 2),(150, 4, 59, 0, 2, 2),(160, 4, 54, 0, 2, 2),(170, 3, 49, 0, 2, 2),(180, 2, 48, 0, 2, 2),(190, 2, 58, 0, 2, 2),(200, 2, 54, 0, 2, 2),(210, 2, 54, 0, 2, 2),(220, 2, 60, 0, 2, 2),(230, 1, 58, 0, 2, 2),(240, 1, 56, 0, 2, 2),(250, 1, 50, 0, 2, 2),(260, 1, 68, 0, 2, 2),(270, 1, 73, 0, 2, 2),(280, 1, 65, 0, 2, 2),(290, 1, 61, 0, 2, 2),(300, 1, 73, 0, 2, 2))

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learn/src/test/resources/simpleDesign/run-2.tsd Normal file
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(("time","S0","S1","S2","P0","P1"),(0, 10, 100, 0, 2, 2),(10, 10, 92, 0, 2, 2),(20, 7, 86, 0, 2, 2),(30, 5, 78, 0, 2, 2),(40, 4, 75, 0, 2, 2),(50, 4, 69, 0, 2, 2),(60, 4, 65, 0, 2, 2),(70, 4, 59, 0, 2, 2),(80, 3, 55, 0, 2, 2),(90, 1, 49, 0, 2, 2),(100, 1, 46, 0, 2, 2),(110, 1, 45, 0, 2, 2),(120, 1, 41, 0, 2, 2),(130, 1, 51, 0, 2, 2),(140, 1, 60, 0, 2, 2),(150, 1, 54, 0, 2, 2),(160, 1, 50, 0, 2, 2),(170, 1, 48, 0, 2, 2),(180, 1, 53, 0, 2, 2),(190, 1, 51, 0, 2, 2),(200, 1, 57, 0, 2, 2),(210, 1, 50, 0, 2, 2),(220, 1, 54, 0, 2, 2),(230, 0, 58, 0, 2, 2),(240, 0, 65, 0, 2, 2),(250, 0, 79, 0, 2, 2),(260, 0, 81, 0, 2, 2),(270, 0, 77, 0, 2, 2),(280, 0, 78, 0, 2, 2),(290, 0, 73, 0, 2, 2),(300, 0, 96, 0, 2, 2))

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learn/src/test/resources/simpleDesign/run-3.tsd Normal file
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learn/src/test/resources/simpleDesign/run-4.tsd Normal file
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(("time","S0","S1","S2","P0","P1"),(0, 10, 100, 0, 2, 2),(10, 10, 95, 0, 2, 2),(20, 10, 89, 0, 2, 2),(30, 8, 85, 10, 2, 2),(40, 6, 80, 10, 2, 2),(50, 5, 76, 9, 2, 2),(60, 5, 69, 8, 2, 2),(70, 5, 66, 8, 2, 2),(80, 5, 62, 8, 2, 2),(90, 5, 58, 6, 2, 2),(100, 4, 52, 6, 2, 2),(110, 4, 46, 3, 2, 2),(120, 4, 45, 3, 2, 2),(130, 4, 42, 1, 2, 2),(140, 4, 52, 1, 2, 2),(150, 4, 47, 1, 2, 2),(160, 3, 43, 1, 2, 2),(170, 3, 41, 1, 2, 2),(180, 3, 40, 1, 2, 2),(190, 3, 37, 1, 2, 2),(200, 2, 35, 1, 2, 2),(210, 2, 43, 1, 2, 2),(220, 2, 42, 1, 2, 2),(230, 2, 38, 1, 2, 2),(240, 0, 46, 1, 2, 2),(250, 0, 44, 1, 2, 2),(260, 0, 40, 1, 2, 2),(270, 0, 49, 1, 2, 2),(280, 0, 43, 1, 2, 2),(290, 0, 49, 1, 2, 2),(300, 0, 45, 1, 2, 2))

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learn/src/test/resources/simpleDesign/run-6.tsd Normal file
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learn/src/test/resources/simpleDesign/run-7.tsd Normal file
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learn/src/test/resources/simpleDesign/run-8.tsd Normal file
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learn/src/test/resources/simpleDesign/run-9.tsd Normal file
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<?xml version='1.0' encoding='UTF-8' standalone='no'?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" arrays:required="true" comp:required="true" fbc:required="false" layout:required="false" level="3" version="1" xmlns:arrays="http://www.sbml.org/sbml/level3/version1/arrays/version1" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
<model fbc:strict="false" id="simpleDesign" metaid="iBioSim4">
<listOfCompartments>
<compartment constant="true" id="Cell" size="1" spatialDimensions="3"/>
</listOfCompartments>
<listOfSpecies>
<species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="S0" initialAmount="10" metaid="iBioSim1"/>
<species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="S1" initialAmount="100" metaid="iBioSim3"/>
<species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="S2" initialAmount="0" metaid="iBioSim5"/>
<species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="P0" initialAmount="2" metaid="iBioSim6" sboTerm="SBO:0000590"/>
<species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="P1" initialAmount="2" metaid="iBioSim9" sboTerm="SBO:0000590"/>
</listOfSpecies>
<listOfParameters>
<parameter constant="true" id="kr_f" name="Forward repression binding rate" value="0.5"/>
<parameter constant="true" id="kr_r" name="Reverse repression binding rate" value="1"/>
<parameter constant="true" id="ka_f" name="Forward activation binding rate" value="0.0033"/>
<parameter constant="true" id="ka_r" name="Reverse activation binding rate" value="1"/>
<parameter constant="true" id="ko_f" name="Forward RNAP binding rate" value="0.033"/>
<parameter constant="true" id="ko_r" name="Reverse RNAP binding rate" value="1"/>
<parameter constant="true" id="kao_f" name="Forward activated RNAP binding rate" value="1"/>
<parameter constant="true" id="kao_r" name="Reverse activated RNAP binding rate" value="1"/>
<parameter constant="true" id="nc" name="Stoichiometry of binding" value="2"/>
<parameter constant="true" id="nr" name="Initial RNAP count" value="30"/>
<parameter constant="true" id="ko" name="Open complex production rate" value="0.05"/>
<parameter constant="true" id="kb" name="Basal production rate" value="0.0001"/>
<parameter constant="true" id="ng" name="Initial promoter count" value="2"/>
<parameter constant="true" id="np" name="Stoichiometry of production" value="10"/>
<parameter constant="true" id="ka" name="Activated production rate" value="0.25"/>
<parameter constant="true" id="kd" name="Degradation rate" value="0.0075"/>
</listOfParameters>
<listOfReactions>
<reaction compartment="Cell" fast="false" id="Production_P0" metaid="iBioSim8" reversible="false" sboTerm="SBO:0000589">
<listOfProducts>
<speciesReference constant="true" species="S2" stoichiometry="10"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference sboTerm="SBO:0000598" species="P0"/>
<modifierSpeciesReference sboTerm="SBO:0000459" species="S0"/>
</listOfModifiers>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<apply>
<times/>
<ci> P0 </ci>
<apply>
<plus/>
<apply>
<times/>
<apply>
<times/>
<ci> kb </ci>
<apply>
<divide/>
<ci> ko_f </ci>
<ci> ko_r </ci>
</apply>
</apply>
<ci> nr </ci>
</apply>
<apply>
<times/>
<apply>
<times/>
<apply>
<times/>
<ci> ka </ci>
<apply>
<divide/>
<ci> kao_f </ci>
<ci> kao_r </ci>
</apply>
</apply>
<ci> nr </ci>
</apply>
<apply>
<power/>
<apply>
<times/>
<apply>
<divide/>
<ci> ka_f </ci>
<ci> ka_r </ci>
</apply>
<ci> S0 </ci>
</apply>
<ci> nc </ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<plus/>
<apply>
<plus/>
<cn type="integer"> 1 </cn>
<apply>
<times/>
<apply>
<divide/>
<ci> ko_f </ci>
<ci> ko_r </ci>
</apply>
<ci> nr </ci>
</apply>
</apply>
<apply>
<times/>
<apply>
<times/>
<apply>
<divide/>
<ci> kao_f </ci>
<ci> kao_r </ci>
</apply>
<ci> nr </ci>
</apply>
<apply>
<power/>
<apply>
<times/>
<apply>
<divide/>
<ci> ka_f </ci>
<ci> ka_r </ci>
</apply>
<ci> S0 </ci>
</apply>
<ci> nc </ci>
</apply>
</apply>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction compartment="Cell" fast="false" id="Production_P1" metaid="iBioSim11" reversible="false" sboTerm="SBO:0000589">
<listOfProducts>
<speciesReference constant="true" species="S1" stoichiometry="10"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference sboTerm="SBO:0000598" species="P1"/>
<modifierSpeciesReference sboTerm="SBO:0000020" species="S0"/>
</listOfModifiers>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<apply>
<times/>
<apply>
<times/>
<apply>
<times/>
<ci> P1 </ci>
<ci> ko </ci>
</apply>
<apply>
<divide/>
<ci> ko_f </ci>
<ci> ko_r </ci>
</apply>
</apply>
<ci> nr </ci>
</apply>
<apply>
<plus/>
<apply>
<plus/>
<cn type="integer"> 1 </cn>
<apply>
<times/>
<apply>
<divide/>
<ci> ko_f </ci>
<ci> ko_r </ci>
</apply>
<ci> nr </ci>
</apply>
</apply>
<apply>
<power/>
<apply>
<times/>
<apply>
<divide/>
<ci> kr_f </ci>
<ci> kr_r </ci>
</apply>
<ci> S0 </ci>
</apply>
<ci> nc </ci>
</apply>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction compartment="Cell" fast="false" id="Degradation_S1" reversible="false" sboTerm="SBO:0000179">
<listOfReactants>
<speciesReference constant="true" species="S1" stoichiometry="1"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> kd </ci>
<ci> S1 </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction compartment="Cell" fast="false" id="Degradation_S2" reversible="false" sboTerm="SBO:0000179">
<listOfReactants>
<speciesReference constant="true" species="S2" stoichiometry="1"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> kd </ci>
<ci> S2 </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction compartment="Cell" fast="false" id="Degradation_S0" reversible="false" sboTerm="SBO:0000179">
<listOfReactants>
<speciesReference constant="true" species="S0" stoichiometry="1"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> kd </ci>
<ci> S0 </ci>
</apply>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>