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APE is a command line tool and an API for the automated exploration of possible computational pipelines (workflows) from large collections of computational tools.
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package nl.uu.cs.ape.configuration;
import org.json.JSONArray;
import org.json.JSONException;
import org.json.JSONObject;
import lombok.Getter;
import nl.uu.cs.ape.configuration.tags.APEConfigDependentTag;
import nl.uu.cs.ape.configuration.tags.APEConfigTag;
import nl.uu.cs.ape.configuration.tags.APEConfigTagFactory;
import nl.uu.cs.ape.configuration.tags.APEConfigTags;
import nl.uu.cs.ape.configuration.tags.APEConfigTagFactory.TAGS.*;
import nl.uu.cs.ape.configuration.tags.validation.ValidationResults;
import nl.uu.cs.ape.domain.APEDomainSetup;
import nl.uu.cs.ape.models.Range;
import nl.uu.cs.ape.models.Type;
import nl.uu.cs.ape.models.enums.ConfigEnum;
import nl.uu.cs.ape.models.enums.SolverType;
import java.io.IOException;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.Collections;
import java.util.List;
/**
* The {@link APERunConfig} class is used to define the run configuration
* variables, required for the proper execution of the synthesis process.
*
* @author Vedran Kasalica
*/
public class APERunConfig {
/**
* Path to the file with all workflow constraints.
*/
private final APEConfigTag CONSTRAINTS_FILE = new APEConfigTagFactory.TAGS.CONSTRAINTS_FILE();
/**
* Content of workflow constraints.
*/
private final APEConfigTag CONSTRAINTS_CONTENT = new APEConfigTagFactory.TAGS.CONSTRAINTS_CONTENT();
/**
* Path to the directory that will contain all the solutions to the problem.
*/
private final APEConfigTag SOLUTION_DIR_PATH = new APEConfigTagFactory.TAGS.SOLUTION_DIR_PATH();
/**
* Min and Max possible length of the solutions (length of the automaton). For
* no upper limit, max length should be set to 0.
*/
private final APEConfigTag SOLUTION_LENGTH_RANGE = new APEConfigTagFactory.TAGS.SOLUTION_LENGTH_RANGE();
/**
* Number of solution that the solver should return.
*/
private final APEConfigTag NO_SOLUTIONS = new NO_SOLUTIONS();
/**
* Number of the workflow scripts that should be generated from candidate
* workflows. Default is 0.
*/
private final APEConfigTag NO_EXECUTIONS = new APEConfigTagFactory.TAGS.NO_EXECUTIONS();
/**
* Number of the solution graphs that should be generated from candidate
* workflows. Default is 0.
*/
private final APEConfigTag NO_GRAPHS = new APEConfigTagFactory.TAGS.NO_GRAPHS();
/**
* Number of CWL files that should be generated from candidate workflows.
* Default is 0.
*/
private final APEConfigTag NO_CWL = new APEConfigTagFactory.TAGS.NO_CWL();
/**
* Determines the required usage for the data instances that are given as
* workflow input:
* {@link ConfigEnum#ALL} if all the workflow inputs have to be used,
* {@link ConfigEnum#ONE} if one of the workflow inputs should be used or
* {@link ConfigEnum#NONE} if none of the workflow inputs has to be used
*/
private final APEConfigTag USE_WORKFLOW_INPUT = new APEConfigTagFactory.TAGS.USE_WORKFLOW_INPUT();
/**
* Determines the required usage for the generated data instances:
* {@link ConfigEnum#ALL} if all the generated data has to be used,
* {@link ConfigEnum#ONE} if one of the data instances that are generated as
* output, per tool, has to be used or
* {@link ConfigEnum#NONE} if none of the data instances is obligatory to use.
*/
private final APEConfigTag USE_ALL_GENERATED_DATA = new APEConfigTagFactory.TAGS.USE_ALL_GENERATED_DATA();
/**
* Mode is true if debug mode is turned on.
*/
private final APEConfigTag DEBUG_MODE = new APEConfigTagFactory.TAGS.DEBUG_MODE();
/**
* Synthesis timeout in seconds.
*/
public final APEConfigTag TIMEOUT_SEC = new APEConfigTagFactory.TAGS.TIMEOUT_SEC();
/**
* false iff the provided solutions should be distinguished based on the tool
* sequences alone, i.e. tool sequences cannot repeat, ignoring the types in the
* solutions.
*/
private final APEConfigTag TOOL_SEQ_REPEAT = new APEConfigTagFactory.TAGS.TOOL_SEQ_REPEAT();
/**
* Input types of the workflow.
*/
private final APEConfigDependentTag.One, APEDomainSetup> PROGRAM_INPUTS = new APEConfigTagFactory.TAGS.PROGRAM_INPUTS(
this::getApeDomainSetup);
/**
* Output types of the workflow.
*/
private final APEConfigDependentTag.One, APEDomainSetup> PROGRAM_OUTPUTS = new APEConfigTagFactory.TAGS.PROGRAM_OUTPUTS(
this::getApeDomainSetup);
/**
* All the Tags specified in this class. Should be in correct order of
* dependencies.
*/
private final APEConfigTag[] all_tags = new APEConfigTag[] {
this.CONSTRAINTS_FILE,
this.CONSTRAINTS_CONTENT,
this.SOLUTION_DIR_PATH,
this.SOLUTION_LENGTH_RANGE,
this.NO_SOLUTIONS,
this.NO_EXECUTIONS,
this.NO_GRAPHS,
this.NO_CWL,
this.USE_WORKFLOW_INPUT,
this.USE_ALL_GENERATED_DATA,
this.DEBUG_MODE,
this.TIMEOUT_SEC,
this.TOOL_SEQ_REPEAT,
this.PROGRAM_OUTPUTS,
this.PROGRAM_INPUTS
};
/**
* Static versions of the Tags specified in this class. Should be in correct
* order for the Web API.
*/
public static final APEConfigTags TAGS = new APEConfigTags(
new CONSTRAINTS_FILE(),
new CONSTRAINTS_CONTENT(),
new SOLUTION_DIR_PATH(),
new SOLUTION_LENGTH_RANGE(),
new NO_SOLUTIONS(),
new NO_EXECUTIONS(),
new NO_GRAPHS(),
new NO_CWL(),
new USE_WORKFLOW_INPUT(),
new USE_ALL_GENERATED_DATA(),
new DEBUG_MODE(),
new TIMEOUT_SEC(),
new TOOL_SEQ_REPEAT(),
new PROGRAM_OUTPUTS(null),
new PROGRAM_INPUTS(null));
/**
* Object containing domain information needed for the execution.
*/
@Getter
private APEDomainSetup apeDomainSetup;
/** Solver type that should be used (SAT). */
private SolverType solverType = SolverType.SAT;
/**
* Constructor used to implement the Builder Pattern.
*
* @param builder Builder object
*/
private APERunConfig(Builder builder) {
if (builder.apeDomainSetup == null) {
throw new APEConfigException("Domain setup provided cannot have null value.");
}
this.apeDomainSetup = builder.apeDomainSetup;
setConstraintsJSON(builder.constraintsJSON);
setSolutionLength(builder.solutionMinLength, builder.solutionMaxLength);
setMaxNoSolutions(builder.maxNoSolutions);
setToolSeqRepeat(builder.toolSeqRepeat);
setSolutionPath(builder.solutionDirPath);
setNoExecutions(builder.noExecutions);
setNoGraphs(builder.noGraphs);
setNoCWL(builder.noCWL);
setUseWorkflowInput(builder.useWorkflowInput);
setUseAllGeneratedData(builder.useAllGeneratedData);
setDebugMode(builder.debugMode);
setTimeoutSec(builder.timeoutSec);
setProgramInputs(builder.programInputs);
setProgramOutputs(builder.programOutputs);
}
/**
* Private constructor used by
* {@link APERunConfig#validate(JSONObject config, APEDomainSetup setup)}
* to create an empty instance.
*/
private APERunConfig(APEDomainSetup setup) {
this.apeDomainSetup = setup;
}
/**
* Validate the JSONObject for each RUN tag.
* If {@link ValidationResults#success()} ()} returns true,
* the configuration object can be safely used to create
* an APERunConfig object.
*
* @param json the configuration file
* @param setup the domain setup
* @return the validation results
*/
public static ValidationResults validate(JSONObject json, APEDomainSetup setup) {
APERunConfig dummy = new APERunConfig(setup);
ValidationResults results = new ValidationResults();
for (APEConfigTag tag : dummy.all_tags) {
results.add(tag.validateConfig(json));
if (results.hasFails()) {
return results;
} else {
tag.setValueFromConfig(json); // for dependencies
}
}
return results;
}
/**
* Setup the configuration for the current run of the synthesis.
*
* @param runConfiguration The APE configuration {@link JSONObject}.
* @param apeDomainSetup The ape domain setup
* @throws IOException Error in reading the configuration file.
* @throws JSONException Error in parsing the configuration file.
* @throws APEConfigException Error in setting up the the configuration.
*/
public APERunConfig(JSONObject runConfiguration, APEDomainSetup apeDomainSetup)
throws IOException, JSONException, APEConfigException {
/* JSONObject must have been parsed correctly. */
if (runConfiguration == null) {
throw new APEConfigException(
"Cannot set up the run configuration, because the JSONObject is initialized to NULL. The configuration file might not have been parsed correctly.");
}
if (apeDomainSetup == null) {
throw new APEConfigException("Domain setup provided cannot have null value.");
}
this.apeDomainSetup = apeDomainSetup;
// set the apeDomain BEFORE setting the tags
for (APEConfigTag tag : all_tags) {
tag.setValueFromConfig(runConfiguration);
}
}
/**
* Creates builder to build {@link APERunConfig}.
*
* @return created builder
*/
public static ISolutionMinLengthStage builder() {
return new Builder();
}
/**
* Gets constraints as a JSONArray, represented as either
* {@link #CONSTRAINTS_CONTENT} or {@link #CONSTRAINTS_FILE}.
*
* @return the constraints as a JSONArray.
*/
public JSONArray getConstraintsJSON() {
return CONSTRAINTS_CONTENT.getValue() != null ? CONSTRAINTS_CONTENT.getValue()
: CONSTRAINTS_FILE.getValue();
}
/**
* Set the constrains.
*
* @param constraintsJSON JSON object that contains the constraints
*/
public void setConstraintsJSON(JSONArray constraintsJSON) {
CONSTRAINTS_CONTENT.setValue(constraintsJSON);
}
/**
* Returns false if the provided solutions should be distinguished based on the
* tool sequences alone, i.e. tool sequences cannot repeat, ignoring the types
* in the solutions.
*
* @return {@code false} if tool sequences cannot repeat, ignoring the types in
* the
* solutions, or {@code true} in case that the tool sequences can repeat
* as
* long as the corresponding types differ.
*/
public boolean getAllowToolSeqRepeat() {
return TOOL_SEQ_REPEAT.getValue();
}
/**
* @param toolSeqRepeat the toolSeqRepeat to set
*/
public void setToolSeqRepeat(boolean toolSeqRepeat) {
TOOL_SEQ_REPEAT.setValue(toolSeqRepeat);
}
/**
* Gets solution path.
*
* @return the value of {@link #SOLUTION_DIR_PATH}
*/
public Path getSolutionDirPath() {
return SOLUTION_DIR_PATH.getValue();
}
/**
* Get the path of the relative path in solution_dir_path.
*
* @param relativePath the relative path
*
* @return absolute path of the relative path in solution_dir_path
*/
public Path getSolutionDirPath2(String relativePath) {
// relative paths should not start with '/' or '\'
if (relativePath.startsWith("/") || relativePath.startsWith("\\")) {
return getSolutionDirPath().resolve(relativePath.substring(1));
}
return getSolutionDirPath().resolve(relativePath);
}
/** Tag value. */
public static final String EXECUTABLES_FOLDER_NAME = "Executables";
/**
* Get the path to the directory where the executable scripts corresponding to
* the given solutions should be stored.
*
* @return the path to the directory where the executable scripts corresponding
* to the given solutions should be stored
*/
public Path getSolutionDirPath2Executables() {
return getSolutionDirPath2(EXECUTABLES_FOLDER_NAME);
}
/** Tag value. */
public static final String FIGURES_FOLDER_NAME = "Figures";
/**
* Get the path to the directory where the graphs representation of the
* solutions should be stored.
*
* @return the path to the directory where the graphs representation of the
* solutions should be stored
*/
public Path getSolutionDirPath2Figures() {
return getSolutionDirPath2(FIGURES_FOLDER_NAME);
}
/** Tag value. */
public static final String CWL_FOLDER_NAME = "CWL";
/**
* Get the path to the directory where the CWL scripts corresponding the given
* solutions should be stored.
*
* @return the path to the directory where the CWL scripts corresponding to the
* given solutions should be stored
*/
public Path getSolutionDirPath2CWL() {
return getSolutionDirPath2(CWL_FOLDER_NAME);
}
/** Tag value. */
public static final String EXECUTABLE_CWL_FOLDER_NAME = "CWL_executables";
/**
* Get the path to the directory where the executable CWL scripts corresponding
* the given solutions should be stored.
*
* @return the path to the directory where the executable CWL scripts
* corresponding to the given solutions should be stored
*/
public Path getSolutionDirPath2ExecutableCWL() {
return getSolutionDirPath2(EXECUTABLE_CWL_FOLDER_NAME);
}
/**
* @param solutionPath the solutionPath to set
*/
public void setSolutionPath(String solutionPath) {
SOLUTION_DIR_PATH.setValue(Paths.get(solutionPath));
}
/**
* Gets solution min and max length.
*
* @return the value of {@link #SOLUTION_LENGTH_RANGE}
*/
public Range getSolutionLength() {
return SOLUTION_LENGTH_RANGE.getValue();
}
/**
* Gets max no solutions.
*
* @return the value of {@link #NO_SOLUTIONS}
*/
public int getMaxNoSolutions() {
return NO_SOLUTIONS.getValue();
}
/**
* @param maxNoSolutions the maxNoSolutions to set
*/
public void setMaxNoSolutions(int maxNoSolutions) {
NO_SOLUTIONS.setValue(maxNoSolutions);
}
/**
* Gets no executions.
*
* @return the value of {@link #NO_EXECUTIONS}
*/
public int getNoExecutions() {
return NO_EXECUTIONS.getValue();
}
/**
* @param noExecutions the noExecutions to set
*/
public void setNoExecutions(int noExecutions) {
NO_EXECUTIONS.setValue(noExecutions);
}
/**
* Gets no graphs.
*
* @return the value of {@link #NO_GRAPHS}
*/
public int getNoGraphs() {
return NO_GRAPHS.getValue();
}
/**
* @param noGraphs the noGraphs to set
*/
public void setNoGraphs(int noGraphs) {
NO_GRAPHS.setValue(noGraphs);
}
/**
* Gets number of CWL files.
*
* @return The value of {@link #NO_CWL}
*/
public int getNoCWL() {
return NO_CWL.getValue();
}
/**
* Set the number of CWL files.
*
* @param noCWL The number to set.
*/
public void setNoCWL(int noCWL) {
NO_CWL.setValue(noCWL);
}
/**
* Gets program inputs.
*
* @return the value of {@link #PROGRAM_INPUTS}
*/
public List getProgramInputs() {
return PROGRAM_INPUTS.getValue();
}
/**
* @param programInputs the programInputs to set
*/
public void setProgramInputs(List programInputs) {
PROGRAM_INPUTS.setValue(programInputs);
}
/**
* Gets program outputs.
*
* @return the value of {@link #PROGRAM_OUTPUTS}
*/
public List getProgramOutputs() {
return PROGRAM_OUTPUTS.getValue();
}
/**
* @param programOutputs the programOutputs to set
*/
public void setProgramOutputs(List programOutputs) {
PROGRAM_OUTPUTS.setValue(programOutputs);
}
/**
* Gets use workflow input.
*
* @return the value of {@link #USE_WORKFLOW_INPUT}
*/
public ConfigEnum getUseWorkflowInput() {
return USE_WORKFLOW_INPUT.getValue();
}
/**
* @param useWorkflowInput the useWorkflowInput to set
*/
public void setUseWorkflowInput(ConfigEnum useWorkflowInput) {
USE_WORKFLOW_INPUT.setValue(useWorkflowInput);
}
/**
* Gets all generated data.
*
* @return the value of {@link #USE_ALL_GENERATED_DATA}
*/
public ConfigEnum getUseAllGeneratedData() {
return USE_ALL_GENERATED_DATA.getValue();
}
/**
* @param useAllGeneratedData the useAllGeneratedData to set
*/
public void setUseAllGeneratedData(ConfigEnum useAllGeneratedData) {
USE_ALL_GENERATED_DATA.setValue(useAllGeneratedData);
}
/**
* Get timeout (in seconds) how long the execution should last.
*
* @return Timeout in seconds.
*/
public int getTimeoutSec() {
return TIMEOUT_SEC.getValue();
}
/**
* Get timeout (in ms) how long the execution should last.
*
* @return Timeout in seconds.
*/
public int getTimeoutMs() {
return TIMEOUT_SEC.getValue() * 1000;
}
/**
* Set the timeout in sec.
*
* @param timeoutSec Timeout in sec.
*/
public void setTimeoutSec(int timeoutSec) {
TIMEOUT_SEC.setValue(timeoutSec);
}
/**
* Gets debug mode.
*
* @return the value of {@link #DEBUG_MODE}
*/
public boolean getDebugMode() {
return DEBUG_MODE.getValue();
}
/**
* @param debugMode the debugMode to set
*/
public void setDebugMode(boolean debugMode) {
DEBUG_MODE.setValue(debugMode);
}
/**
* @param solutionMinLength the solutionMinLength to set
* @param solutionMaxLength the solutionMaxLength to set
*/
public void setSolutionLength(int solutionMinLength, int solutionMaxLength) {
this.SOLUTION_LENGTH_RANGE.setValue(Range.of(solutionMinLength, solutionMaxLength));
}
/**
* Gets the Solver type that should be used for solving.
*
* @return {@link SolverType} that corresponds to the solver type
*/
public SolverType getSolverType() {
return this.solverType;
}
/**
* @param solverType the solverType to set
*/
public void setSolverType(SolverType solverType) {
this.solverType = solverType;
}
/**
* Creates interface for the min length of {@link APERunConfig}.
*/
public interface ISolutionMinLengthStage {
ISolutionMaxLengthStage withSolutionMinLength(int solutionMinLength);
}
/**
* Creates interface for the max length of {@link APERunConfig}.
*/
public interface ISolutionMaxLengthStage {
/**
* Set Max length.
*
* @param solutionMaxLength
* @return
*/
IMaxNoSolutionsStage withSolutionMaxLength(int solutionMaxLength);
}
/**
* Creates interface for the max solution no of {@link APERunConfig}.
*/
public interface IMaxNoSolutionsStage {
IApeDomainSetupStage withMaxNoSolutions(int maxNoSolutions);
}
/**
* Creates interface to setup the domain of {@link APERunConfig}.
*/
public interface IApeDomainSetupStage {
IBuildStage withApeDomainSetup(APEDomainSetup apeDomainSetup);
}
/**
* Interface for the builder class.
*
* @author Vedran Kasalica
*
*/
public interface IBuildStage {
IBuildStage withConstraintsJSON(JSONArray constraintsJSON);
IBuildStage withToolSeqRepeat(boolean toolSeqRepeat);
IBuildStage withSolutionDirPath(String solutionPath);
IBuildStage withNoExecutions(int noExecutions);
IBuildStage withNoGraphs(int noGraphs);
IBuildStage withNoCWL(int noCWL);
IBuildStage withNoExecutableCWL(int noExecutableCWL);
IBuildStage withProgramInputs(List programInputs);
IBuildStage withProgramOutputs(List programOutputs);
IBuildStage withUseWorkflowInput(ConfigEnum useWorkflowInput);
IBuildStage withUseAllGeneratedData(ConfigEnum useAllGeneratedData);
IBuildStage withDebugMode(boolean debugMode);
IBuildStage withTimeoutSec(int timeoutSec);
APERunConfig build();
}
/**
* Builder to build {@link APERunConfig}.
*/
public static final class Builder implements ISolutionMinLengthStage, ISolutionMaxLengthStage, IMaxNoSolutionsStage,
IApeDomainSetupStage, IBuildStage {
private int solutionMinLength;
private int solutionMaxLength;
private int maxNoSolutions;
private APEDomainSetup apeDomainSetup;
private JSONArray constraintsJSON;
private boolean toolSeqRepeat;
private String solutionDirPath;
private int noExecutions;
private int noGraphs;
private int noCWL;
private int noExecutableCWL;
private List programInputs = Collections.emptyList();
private List programOutputs = Collections.emptyList();
private ConfigEnum useWorkflowInput;
private ConfigEnum useAllGeneratedData;
private boolean debugMode;
private int timeoutSec;
private Builder() {
}
@Override
public ISolutionMaxLengthStage withSolutionMinLength(int solutionMinLength) {
this.solutionMinLength = solutionMinLength;
return this;
}
@Override
public IMaxNoSolutionsStage withSolutionMaxLength(int solutionMaxLength) {
this.solutionMaxLength = solutionMaxLength;
return this;
}
@Override
public IApeDomainSetupStage withMaxNoSolutions(int maxNoSolutions) {
this.maxNoSolutions = maxNoSolutions;
return this;
}
@Override
public IBuildStage withApeDomainSetup(APEDomainSetup apeDomainSetup) {
this.apeDomainSetup = apeDomainSetup;
return this;
}
@Override
public IBuildStage withConstraintsJSON(JSONArray constraintsJSON) {
this.constraintsJSON = constraintsJSON;
return this;
}
@Override
public IBuildStage withToolSeqRepeat(boolean toolSeqRepeat) {
this.toolSeqRepeat = toolSeqRepeat;
return this;
}
@Override
public IBuildStage withSolutionDirPath(String solutionDirPath) {
this.solutionDirPath = solutionDirPath;
return this;
}
@Override
public IBuildStage withNoExecutions(int noExecutions) {
this.noExecutions = noExecutions;
return this;
}
@Override
public IBuildStage withNoGraphs(int noGraphs) {
this.noGraphs = noGraphs;
return this;
}
@Override
public IBuildStage withNoCWL(int noCWL) {
this.noCWL = noCWL;
return this;
}
@Override
public IBuildStage withNoExecutableCWL(int noExecutableCWL) {
this.noExecutableCWL = noExecutableCWL;
return this;
}
@Override
public IBuildStage withProgramInputs(List programInputs) {
this.programInputs = programInputs;
return this;
}
@Override
public IBuildStage withProgramOutputs(List programOutputs) {
this.programOutputs = programOutputs;
return this;
}
@Override
public IBuildStage withUseWorkflowInput(ConfigEnum useWorkflowInput) {
this.useWorkflowInput = useWorkflowInput;
return this;
}
@Override
public IBuildStage withUseAllGeneratedData(ConfigEnum useAllGeneratedData) {
this.useAllGeneratedData = useAllGeneratedData;
return this;
}
@Override
public IBuildStage withDebugMode(boolean debugMode) {
this.debugMode = debugMode;
return this;
}
@Override
public IBuildStage withTimeoutSec(int timeout) {
this.timeoutSec = timeout;
return this;
}
@Override
public APERunConfig build() {
return new APERunConfig(this);
}
}
}