Merge branch 'master' into build_integration_algorithms

Conflicts:
	frontend/assembly.xml
	frontend/pom.xml

.gitignore

@@ -5,3 +5,4 @@
 release.properties
 /.idea
 *.iml
+/target

.travis.yml

@@ -8,9 +8,6 @@ env:
         - secure: "cw80AZWTn5/TnqeRy0CMWvKiktVe84GGgK5DISFLJ9MhYdXYZwn+2r8rQk6TCguZ4GzvztStlXAzsvOIJzqOmS6bL4ZO9iT08LCsaNUb2K8vJFsTyqf9SYVHv/0Go9WTiAOIWZjvQG455FecFUdMdZxWcGgfDuScvFFx5gEmuzY="
         - secure: "mWWbU2L21JPD9zIZqgiwnLZNnNcEP73firR7DQtwfYgQO2ajfEuOikjUwO6BBds4jTxi0VagHsowEC24/CEet1YJDxryYDXfkGIZZbz5oKbCv2JJDpSbGmK5lcW0BIYl5UFObGs9K6LJ7vEQAGxoo7MS8h6G0a8u53cIsVhvnJs="
 
-install:
-  - sudo apt-get install texlive
-
 script: "mvn -q clean verify"
 
 after_success:

algorithm_integration/pom.xml

@@ -14,7 +14,7 @@
   ~ limitations under the License.
   -->
 
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+<project xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://maven.apache.org/POM/4.0.0"
          xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
     <modelVersion>4.0.0</modelVersion>
 

algorithm_integration/src/main/java/de/uni_potsdam/hpi/metanome/algorithm_integration/algorithm_execution/FileGenerator.java

@@ -21,17 +21,16 @@
 
 /**
  * Generates temporary files.
- * 
+ *
  * @author Jakob Zwiener
  */
 public interface FileGenerator extends Closeable {
 
-	/**
-	 * Returns a temporary file that will be deleted on close.
-	 * 
-	 * @return temporary file
-	 *
+    /**
+     * Returns a temporary file that will be deleted on close.
+     *
+     * @return temporary file
      * @throws FileCreationException if the file cannot be created
      */
-	File getTemporaryFile() throws FileCreationException;
+    File getTemporaryFile() throws FileCreationException;
 }

algorithm_integration/src/main/java/de/uni_potsdam/hpi/metanome/algorithm_integration/algorithm_types/SqlInputParameterAlgorithm.java

@@ -22,18 +22,18 @@
 
 /**
  * An {@link Algorithm} that takes {@link SQLInputGenerator} configuration values.
- * 
+ *
  * @author Jakob Zwiener
  */
 public interface SqlInputParameterAlgorithm extends Algorithm {
 
-	/**
-	 * Sets a SQLInputGenerator configuration value on the algorithm.
-	 * 
-	 * @param identifier the parameter's identifier
-	 * @param values one or multiple SQLInputGenerator values
+    /**
+     * Sets a SQLInputGenerator configuration value on the algorithm.
+     *
+     * @param identifier the parameter's identifier
+     * @param values     one or multiple SQLInputGenerator values
      * @throws de.uni_potsdam.hpi.metanome.algorithm_integration.AlgorithmConfigurationException if the algorithm cannot be correctly configured using the received configuration values
      */
-	void setConfigurationValue(String identifier, SQLInputGenerator... values) throws AlgorithmConfigurationException;
-	
+    void setConfigurationValue(String identifier, SQLInputGenerator... values) throws AlgorithmConfigurationException;
+
 }

algorithm_integration/src/main/java/de/uni_potsdam/hpi/metanome/algorithm_integration/configuration/ConfigurationSettingBoolean.java

@@ -16,12 +16,18 @@
 
 package de.uni_potsdam.hpi.metanome.algorithm_integration.configuration;
 
+import java.io.Serializable;
+
 /**
  * @author Jakob Zwiener
  */
-public class ConfigurationSettingBoolean {
+public class ConfigurationSettingBoolean implements Serializable {
+    private static final long serialVersionUID = 3374302400843066557L;
+
+    public boolean value;
 
-    boolean value;
+    public ConfigurationSettingBoolean() {
+    }
 
     public ConfigurationSettingBoolean(boolean value) {
         this.value = value;

algorithm_integration/src/main/java/de/uni_potsdam/hpi/metanome/algorithm_integration/configuration/ConfigurationSettingCsvFile.java

@@ -0,0 +1,117 @@
+/*
+ * Copyright 2014 by the Metanome project
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package de.uni_potsdam.hpi.metanome.algorithm_integration.configuration;
+
+
+/**
+ * @author Jakob Zwiener
+ */
+public class ConfigurationSettingCsvFile extends ConfigurationSettingDataSource {
+    private static final long serialVersionUID = -770650561337139324L;
+
+    private String fileName;
+    private boolean advanced;
+    private char separatorChar;
+    private char quoteChar;
+    private char escapeChar;
+    private boolean strictQuotes;
+    private boolean ignoreLeadingWhiteSpace;
+    private int line;
+
+    public ConfigurationSettingCsvFile() {
+    }
+
+    public ConfigurationSettingCsvFile(String fileName, boolean advanced, char separator, char quote,
+                                       char escape, boolean strictQuotes, boolean ignoreLeadingWhiteSpace, int line) {
+        this.fileName = fileName;
+        this.advanced = advanced;
+        this.separatorChar = separator;
+        this.quoteChar = quote;
+        this.escapeChar = escape;
+        this.strictQuotes = strictQuotes;
+        this.ignoreLeadingWhiteSpace = ignoreLeadingWhiteSpace;
+        this.line = line;
+    }
+
+    public String getFileName() {
+        return fileName;
+    }
+
+    public void setFileName(String value) {
+        this.fileName = value;
+    }
+
+    public boolean isAdvanced() {
+        return advanced;
+    }
+
+    public void setAdvanced(boolean value) {
+        this.advanced = value;
+    }
+
+    public char getSeparatorChar() {
+        return separatorChar;
+    }
+
+    public void setSeparatorChar(char value) {
+        this.separatorChar = value;
+    }
+
+    public char getQuoteChar() {
+        return quoteChar;
+    }
+
+    public void setQuoteChar(char value) {
+        this.quoteChar = value;
+    }
+
+    public char getEscapeChar() {
+        return escapeChar;
+    }
+
+    public void setEscapeChar(char value) {
+        this.escapeChar = value;
+    }
+
+    public boolean isStrictQuotes() {
+        return strictQuotes;
+    }
+
+    public void setStrictQuotes(boolean value) {
+        this.strictQuotes = value;
+    }
+
+    public boolean isIgnoreLeadingWhiteSpace() {
+        return ignoreLeadingWhiteSpace;
+    }
+
+    public void setIgnoreLeadingWhiteSpace(boolean value) {
+        this.ignoreLeadingWhiteSpace = value;
+    }
+
+    public int getLine() {
+        return line;
+    }
+
+    public void setLine(int value) {
+        this.line = value;
+    }
+
+    public String getValueAsString() {
+        return fileName;
+    }
+}

algorithm_integration/src/main/java/de/uni_potsdam/hpi/metanome/algorithm_integration/configuration/ConfigurationSettingDataSource.java

@@ -0,0 +1,34 @@
+/*
+ * Copyright 2014 by the Metanome project
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package de.uni_potsdam.hpi.metanome.algorithm_integration.configuration;
+
+import java.io.Serializable;
+
+
+/**
+ * InputParameters correspond to a ConfigurationSpecification and ConfigurationValue type.
+ * It is used for frontend input of the configuration value, so generally, a ConfigurationSpecification
+ * will be converted to an InputParameter, which is used to get the user's value input, and then converted
+ * to the ConfigurationValue handed back to the algorithm.
+ *
+ * @author Claudia
+ */
+public abstract class ConfigurationSettingDataSource implements Serializable {
+    private static final long serialVersionUID = 8344875059579539858L;
+
+    public abstract String getValueAsString();
+}

algorithm_integration/src/main/java/de/uni_potsdam/hpi/metanome/algorithm_integration/configuration/ConfigurationSettingSQLIterator.java

@@ -0,0 +1,64 @@
+/*
+ * Copyright 2014 by the Metanome project
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package de.uni_potsdam.hpi.metanome.algorithm_integration.configuration;
+
+
+public class ConfigurationSettingSQLIterator extends ConfigurationSettingDataSource {
+    private static final long serialVersionUID = 3242593091096735218L;
+
+    private String dbUrl;
+    private String username;
+    private String password;
+
+    public ConfigurationSettingSQLIterator() {
+    }
+
+    public ConfigurationSettingSQLIterator(String dbUrl, String username, String password) {
+        this.dbUrl = dbUrl;
+        this.username = username;
+        this.password = password;
+    }
+
+    public String getDbUrl() {
+        return dbUrl;
+    }
+
+    public void setDbUrl(String dbUrl) {
+        this.dbUrl = dbUrl;
+    }
+
+    public String getUsername() {
+        return username;
+    }
+
+    public void setUsername(String username) {
+        this.username = username;
+    }
+
+    public String getPassword() {
+        return password;
+    }
+
+    public void setPassword(String password) {
+        this.password = password;
+    }
+
+    @Override
+    public String getValueAsString() {
+        return this.dbUrl + ";" + this.username + ";" + this.password;
+    }
+}

frontend/src/main/java/de/uni_potsdam/hpi/metanome/frontend/client/parameter/InputParameterInteger.java → algorithm_integration/src/main/java/de/uni_potsdam/hpi/metanome/algorithm_integration/configuration/ConfigurationSettingString.java

@@ -14,31 +14,23 @@
  * limitations under the License.
  */
 
-package de.uni_potsdam.hpi.metanome.frontend.client.parameter;
+package de.uni_potsdam.hpi.metanome.algorithm_integration.configuration;
 
+import java.io.Serializable;
 
-public class InputParameterInteger extends InputParameter {
-	private static final long serialVersionUID = 5161219640594711634L;
-
-	private int value;
-
-	public InputParameterInteger(){}
+/**
+ * @author Jakob Zwiener
+ */
+public class ConfigurationSettingString implements Serializable {
+    private static final long serialVersionUID = 1753877522641977576L;
 
-	public InputParameterInteger(String identifier) {
-		super(identifier);
-	}
+    public String value;
 
-	// **** GETTERS & SETTERS ****
-	public Integer getValue() {
-		return value;
-	}
 
-	public void setValue(int value) {
-		this.value = value;
-	}
+    public ConfigurationSettingString() {
+    }
 
-	@Override
-	public InputParameterWidget createWrappingWidget() {
-		return new InputParameterIntegerWidget(this);
-	}
+    public ConfigurationSettingString(String value) {
+        this.value = value;
+    }
 }

algorithm_integration/src/main/java/de/uni_potsdam/hpi/metanome/algorithm_integration/configuration/ConfigurationSpecification.java

@@ -18,6 +18,8 @@
 
 import de.uni_potsdam.hpi.metanome.algorithm_integration.Algorithm;
 
+import java.io.Serializable;
+
 /**
  * Represents a configuration parameter an {@link Algorithm} needs to be properly configured.
  * The ConfigurationSpecification is then used to construct a configuration value that
@@ -27,12 +29,17 @@
  *
  * @author Jakob Zwiener
  */
-public abstract class ConfigurationSpecification {
-
+public abstract class ConfigurationSpecification implements Serializable {
     public static final int ARBITRARY_NUMBER_OF_VALUES = -1;
+    private static final long serialVersionUID = 4312752686730530733L;
+    protected String identifier;
+    /**
+     * would be good to make this final, but then it would not be serialized and thus be reset to 1 in frontend
+     */
+    protected int numberOfValues;
 
-    protected final String identifier;
-    protected final int numberOfValues;
+    public ConfigurationSpecification() {
+    }
 
     /**
      * Construct a configuration specification.
@@ -75,4 +82,7 @@ public int getNumberOfValues() {
         return numberOfValues;
     }
 
+    //TODO use sth more specific than object
+    public abstract Object[] getSettings();
+
 }