Merge pull request #79 from dig-team/code-clean

Code clean provided by Weichen

.gitignore

@@ -4,5 +4,6 @@
 .project
 .settings/
 .vscode/
+.idea/
 bin/
 kb/nb-configuration.xml

Parameters.txt

@@ -0,0 +1,147 @@
+Command line parameters documentation
+
+Basic command: 
+java -jar amie3.jar [TSV file]
+
+Parameters:
+
+#  -mins <number>                     “min-support"
+   Minimum absolute support. The number of positive examples.
+   Default value: 100 
+
+#  -minis <number>                    "min-initial-support"
+   Minimum size of the relations to be considered as head relations. The number of  facts or entities depending on the bias.
+   Default value: 100
+
+#  -minhc <number>                    "min-head-coverage"
+   Minimum head coverage. 
+   Default value: 0.01
+
+#  -pm <support|headcoverage>         "pruning-metric"
+   Metric used for pruning of intermediate queries.
+   Default value: headcoverage
+
+#  -oute                              "output-at-end"
+   Print the rules at the end and not while they are discovered.
+   Default: False
+
+#  -datalog                           "datalog-output"
+   Print rules using the datalog notation.
+   Default: False
+
+#  -bexr <relations>                  "body-excluded-relations"
+   Do not use these relations as atoms in the body of rules.
+   Example: java -jar amie3.jar -bexr bornIn
+
+#  -hexr <relations>                  "head-excluded-relations"
+   Do not use these relations as atoms in the head of rules. (Incompatible with head-target-relations)
+   Example: java -jar amie3.jar -hexr bornIn
+
+#  -iexr <relations>                  "instantiation-excluded-relations"
+   Do not instantiate these relations. Should be used with -fconst or -const. (incompatible with instantiation-target-relations). 
+   Example: java -jar amie3.jar -iexr bornIn
+
+#  -htr <relations>                   "head-target-relations"
+   Mine only rules with these relations in the head. Provide a list of relation names separated by commas. (incompatible with head-excluded-relations)
+   Example: java -jar amie3.jar -htr bornIn
+
+#  -btr <relations>                   "body-target-relations"
+   Allow only these relations in the body. Provide a list of relation names separated by commas (incompatible with body-excluded-relations)
+   Example: java -jar amie3.jar -btr bornIn
+
+#  -itr <relations>                   "instantiation-target-relations"
+   Allow only these relations to be instantiated. Should be used with -fconst or -const. Provide a list of relation names separated by commas(incompatible with instantiation-excluded-relations).
+   Example: java -jar amie3.jar -itr bornIn
+
+#  -maxad <number>                    "max-depth"
+   Maximum number of atoms in the antecedent and succedent of rules.
+   Default value: 3
+
+#  -minpca <number>                   "min-pca-confidence"
+   Minimum PCA confidence threshold.This value is not used for pruning, only for filtering of the results.
+   Defalut value: 0.0
+
+#  -const                             "allow-constants"
+   Enable rules with constants.
+   Default value: false
+
+#  -fconst                            "only-constants"
+   Enforce constants in all atoms.
+   Default: false
+
+#  -bias <oneVar|default|lazy|lazit|[Path to a subclass of amie.mining.assistant.MiningAssistant]>            "e-name"
+   Syntatic/semantic bias
+   Default: default (defines support and confidence in terms of 2 head variables given an order, cf -vo)
+
+#  -caos                              "count-always-on-subject"
+   If a single variable bias is used (oneVar),force to count support always on the subject position.
+
+#  -nc <number>                       "n-threads"
+   Preferred number of cores. Round down to the actual number of cores in the system if a higher value is provided.
+
+#  -minc <number>                     "min-std-confidence"
+   Minimum standard confidence threshold. This value is not used for pruning, only for filtering of the results. 
+   Default: 0.0.
+
+#  -optimcb                           "optim-confidence-bounds"
+   Enable the calculation of confidence upper bounds to prune rules.
+
+#  -optimfh                           "optim-func-heuristic"
+   Enable functionality heuristic to identify potential low confident rules for pruning.
+
+#  -verbose                           "verbose"
+   Maximal verbosity.
+
+#  -rl                                "recursivity-limit"
+   Recursivity limit
+
+#  -auta                              "avoid-unbound-type-atoms"
+   Avoid unbound type atoms, e.g., type(x, y), i.e., bind always 'y' to a type.
+
+#  -deml                              "do-not-exploit-max-length"
+   Do not exploit max length for speedup(requested by the reviewers of AMIE+). 
+   Defalut value: False
+
+#  -dqrw                              "disable-query-rewriting"
+   Disable query rewriting and caching.
+
+#  -dpr                               "disable-perfect-rules"
+   Disable perfect rules.
+
+#  -oout                              "only-output"
+   If enabled, it activates only the output enhacements, that is, the confidence approximation and upper bounds. It overrides any other configuration that is incompatible.
+
+#  -full                              "full"
+   It enables all enhancements: lossless heuristics and confidence approximation and upper bounds. It overrides any other configuration that is incompatible.
+
+#  -noHeuristics                      "noHeuristics"
+   Disable functionality heuristic, should be used with the -full option.
+
+#  -noKbRewrite                       "noKbRewrite"
+   Prevent the KB to rewrite query when counting pairs.
+
+#  -noKbExistsDetection               "noKbExistsDetection"
+   Prevent the KB to detect existential variable on-the-fly and to optimize the query.
+
+#  -noSkyline                         "noSkyline"
+   Disable Skyline pruning of results.
+
+#  -vo                                "variableOrder"
+   Define the order of the variable in counting query among: app, fun (default), ifun.
+
+#  -ef                                "extraFile"
+   An additional text file whose interpretation depends on the selected mining assistant (bias).
+
+#  -ostd                              "ommit-std-conf"
+   Do not calculate standard confidence.
+
+#  -optimai                           "adaptive-instantiations"
+   Prune instantiated rules that decrease too much the support of their parent rule (ratio 0.2).
+
+#  -mlg                               "multilingual"
+   Parse labels language as new facts
+
+#  -d <A SEPARATOR>                    "delimiter"
+   Separator in input files. 
+   Default separator: TAB
+

README.md

@@ -49,7 +49,7 @@ If you want to modify the code of AMIE, you need
 * Apache Maven >= 3.6.0
 * Java >= 8
 * Apache Commons >= 1.3.1
-* [Javatools](https://www.mpi-inf.mpg.de/departments/databases-and-information-systems/research/yago-naga/javatools/). This package can be found as Maven projects here: https://github.com/lajus/amie-utils. As this artifact is not yet uploaded into a central repository, please follow the installation procedure described in the previous link before trying to compile this project.
+* [Javatools](https://www.mpi-inf.mpg.de/departments/databases-and-information-systems/research/yago-naga/amie.data.javatools/). This package can be found as Maven projects here: https://github.com/lajus/amie-utils. As this artifact is not yet uploaded into a central repository, please follow the installation procedure described in the previous link before trying to compile this project.
 
 AMIE is managed with [Maven](https://maven.apache.org/), therefore to deploy you need:
 
@@ -88,4 +88,4 @@ The code resides in: typing/
 
 <a rel="license" href="http://creativecommons.org/licenses/by/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by/4.0/80x15.png" /></a>. AMIE is distributed under the terms of the <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a> by the [YAGO-NAGA team](https://www.mpi-inf.mpg.de/departments/databases-and-information-systems/research/yago-naga/amie/) and the [DIG team](https://dig.telecom-paris.fr/blog/).
 
-AMIE uses Javatools, a library released under the [Creative Commons Attribution license v3.0](https://creativecommons.org/licenses/by/3.0/) by the [YAGO-NAGA team](https://www.mpi-inf.mpg.de/departments/databases-and-information-systems/research/yago-naga/javatools/).
+AMIE uses Javatools, a library released under the [Creative Commons Attribution license v3.0](https://creativecommons.org/licenses/by/3.0/) by the [YAGO-NAGA team](https://www.mpi-inf.mpg.de/departments/databases-and-information-systems/research/yago-naga/amie.data.javatools/).

kb/pom.xml

@@ -1,56 +1,74 @@
 <?xml version="1.0"?>
-<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd" xmlns="http://maven.apache.org/POM/4.0.0"
-    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-  <modelVersion>4.0.0</modelVersion>
-  <parent>
-    <groupId>fr.enst.dbweb</groupId>
-    <artifactId>amie</artifactId>
-    <version>2.0</version>
-  </parent>
-  <artifactId>kb</artifactId>
-  <version>1.0</version>
-  <name>kb</name>
-  <url>http://maven.apache.org</url>
-  <properties>
-    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-  </properties>
+<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"
+         xmlns="http://maven.apache.org/POM/4.0.0"
+         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+    <modelVersion>4.0.0</modelVersion>
+    <parent>
+        <groupId>fr.enst.dbweb</groupId>
+        <artifactId>amie</artifactId>
+        <version>2.0</version>
+    </parent>
+    <artifactId>kb</artifactId>
+    <version>1.0</version>
+    <name>kb</name>
+    <url>http://maven.apache.org</url>
+    <properties>
+        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+    </properties>
 
-  <build>
-  <plugins>
-  <plugin>
-    <groupId>org.apache.maven.plugins</groupId>
-    <artifactId>maven-compiler-plugin</artifactId>
-    <version>3.2</version>
-    <configuration>
-      <excludes>
-	<exclude>**/WikidataCleaner.java</exclude>
-      </excludes>
-    </configuration>
-  </plugin>
-  </plugins>
-  </build>
-
-  <dependencies>
-    <dependency>
-      <groupId>junit</groupId>
-      <artifactId>junit</artifactId>
-      <version>3.8.1</version>
-      <scope>test</scope>
-    </dependency>
-    <dependency>
-      <groupId>org.semanticweb.yars</groupId>
-      <artifactId>nxparser-parsers</artifactId>
-      <version>2.3.3</version>
-    </dependency>
-    <dependency>
-      <groupId>de.mpg.mpi-inf</groupId>
-      <artifactId>javatools</artifactId>
-      <version>1.0-SNAPSHOT</version>
-    </dependency>
-    <dependency>
-        <groupId>it.unimi.dsi</groupId>
-        <artifactId>fastutil</artifactId>
-        <version>8.3.0</version>
-    </dependency>
-  </dependencies>
+    <build>
+        <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-compiler-plugin</artifactId>
+                <version>3.2</version>
+                <configuration>
+                    <excludes>
+                        <exclude>**/WikidataCleaner.java</exclude>
+                    </excludes>
+                </configuration>
+            </plugin>
+        </plugins>
+    </build>
+
+    <dependencies>
+        <dependency>
+            <groupId>junit</groupId>
+            <artifactId>junit</artifactId>
+            <version>3.8.1</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.semanticweb.yars</groupId>
+            <artifactId>nxparser-parsers</artifactId>
+            <version>2.3.3</version>
+        </dependency>
+        <dependency>
+            <groupId>org.openjfx</groupId>
+            <artifactId>javafx-base</artifactId>
+            <version>11</version>
+        </dependency>
+        <dependency>
+            <groupId>org.eclipse.rdf4j</groupId>
+            <artifactId>rdf4j-storage</artifactId>
+            <version>4.3.2</version>
+            <type>pom</type>
+        </dependency>
+        <dependency>
+            <groupId>log4j</groupId>
+            <artifactId>log4j</artifactId>
+            <version>1.2.17</version>
+        </dependency>
+
+        <dependency>
+            <groupId>it.unimi.dsi</groupId>
+            <artifactId>fastutil</artifactId>
+            <version>8.3.0</version>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.jena</groupId>
+            <artifactId>jena-tdb</artifactId>
+            <version>0.9.0-incubating</version>
+        </dependency>
+    </dependencies>
 </project>