Logging and dependency mgmt polishing.

- made slf4j providers/bindings optional, test scope again, etc. - also fixed SCM URLs for submodules (for maven-site)
BioPAX · Feb 10, 2024 · 412bd0b · 412bd0b
1 parent afbf0e1
commit 412bd0b
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diff --git a/gsea-converter/pom.xml b/gsea-converter/pom.xml
@@ -7,15 +7,11 @@
   <modelVersion>4.0.0</modelVersion>
 
   <artifactId>gsea-converter</artifactId>
-  <name>BioPAX to GSEA (.gmt) Converter</name>
-  <description>Converts data to the GESA (.gmt) format.</description>
+  <name>BioPAX to GSEA/GMT</name>
+  <description>Converts BioPAX model/data to the GESA/GMT (.gmt) format</description>
 
   <url>https://biopax.github.io/Paxtools</url>
 
-  <scm><url>https://github.com/BioPAX/Paxtools</url>
-      <tag>HEAD</tag>
-  </scm>
-
   <dependencies>
    	<dependency>
     	<groupId>org.biopax.paxtools</groupId>

diff --git a/gsea-converter/src/test/resources/logback-test.xml b/gsea-converter/src/test/resources/logback-test.xml
@@ -5,6 +5,9 @@
     <resetJUL>true</resetJUL>
   </contextListener>
 
+  <!-- To enable JMX Management (also prints additional logback initializing info)-->
+<!--  <jmxConfigurator/>-->
+
   <appender name="console" class="ch.qos.logback.core.ConsoleAppender">
     <encoder>
       <pattern>%d %-5level [%thread] %logger{25} - %msg%n</pattern>

diff --git a/json-converter/pom.xml b/json-converter/pom.xml
@@ -6,15 +6,11 @@
 		<version>6.0.0-SNAPSHOT</version>
 	</parent>
 	<artifactId>json-converter</artifactId>
-	<name>BioPAX to/from JSON Converter</name>
-	<description>BioPAX to/from JSON Converters</description>
+	<name>BioPAX JSON-LD</name>
+	<description>Converts BioPAX model/file to or from JSON-LD format</description>
 
 	<url>https://biopax.github.io/Paxtools</url>
 
-	<scm><url>https://github.com/BioPAX/Paxtools</url>
-		<tag>HEAD</tag>
-	</scm>
-
 	<dependencies>
 		<dependency>
 			<groupId>org.apache.jena</groupId>

diff --git a/json-converter/src/test/resources/logback-test.xml b/json-converter/src/test/resources/logback-test.xml
@@ -5,6 +5,9 @@
     <resetJUL>true</resetJUL>
   </contextListener>
 
+  <!-- To enable JMX Management (also prints additional logback initializing info)-->
+<!--  <jmxConfigurator/>-->
+
   <appender name="console" class="ch.qos.logback.core.ConsoleAppender">
     <encoder>
       <pattern>%d %-5level [%thread] %logger{25} - %msg%n</pattern>

diff --git a/normalizer/pom.xml b/normalizer/pom.xml
@@ -3,9 +3,9 @@
 	<modelVersion>4.0.0</modelVersion>
 
 	<artifactId>normalizer</artifactId>
-	<name>BioPAX Normalizer and Resolver</name>
-	<description>A BioPAX Normalizer and Bio ID Resolver</description>
-	<inceptionYear>2009-2015</inceptionYear>
+	<name>BioPAX Normalizer</name>
+	<description>BioPAX Model/URIs Normalizer and BIO Identifiers Resolver</description>
+	<inceptionYear>2009</inceptionYear>
 	<parent>
 		<artifactId>paxtools</artifactId>
 		<groupId>org.biopax.paxtools</groupId>

diff --git a/normalizer/src/test/resources/logback-test.xml b/normalizer/src/test/resources/logback-test.xml
@@ -4,7 +4,7 @@
   <contextListener class="ch.qos.logback.classic.jul.LevelChangePropagator">
     <resetJUL>true</resetJUL>
   </contextListener>
- 
+
   <!-- To enable JMX Management (also prints additional logback initializing info)-->
 <!--  <jmxConfigurator/>-->
 

diff --git a/pattern/pom.xml b/pattern/pom.xml
@@ -9,17 +9,13 @@
 	</parent>
 
 	<artifactId>pattern</artifactId>
-	<name>BioPAX Pattern Search</name>
+	<name>BioPAX Pattern</name>
 	<description>
-		The BioPAX Pattern Search library; also, e.g., converts BioPAX model to SIF (simple binary interactions) text format.
+		BioPAX Pattern Search library. Also, converts BioPAX model to SIF (simple binary interactions) text format.
 	</description>
 
 	<url>https://biopax.github.io/Paxtools</url>
 
-	<scm><url>https://github.com/BioPAX/Paxtools</url>
-		<tag>HEAD</tag>
-	</scm>
-
 	<dependencies>
 		<dependency>
 			<groupId>${project.groupId}</groupId>

diff --git a/pattern/src/test/resources/logback-test.xml b/pattern/src/test/resources/logback-test.xml
@@ -5,6 +5,9 @@
     <resetJUL>true</resetJUL>
   </contextListener>
 
+  <!-- To enable JMX Management (also prints additional logback initializing info)-->
+<!--  <jmxConfigurator/>-->
+
   <appender name="console" class="ch.qos.logback.core.ConsoleAppender">
     <encoder>
       <pattern>%d %-5level [%thread] %logger{25} - %msg%n</pattern>

diff --git a/paxtools-console/pom.xml b/paxtools-console/pom.xml
@@ -7,16 +7,11 @@
 	</parent>
 	<artifactId>paxtools-console</artifactId>
 	<packaging>jar</packaging>
-	<name>Paxtools Console Application</name>
+	<name>Paxtools CLI</name>
 	<description>Paxtools Console Application and Examples</description>
 
 	<url>https://biopax.github.io/Paxtools</url>
 
-	<scm>
-		<url>https://github.com/BioPAX/Paxtools</url>
-		<tag>HEAD</tag>
-	</scm>
-
 	<build>
 		<plugins>
 			<plugin>
@@ -90,23 +85,34 @@
 		<dependency>
 			<groupId>org.apache.httpcomponents</groupId>
 			<artifactId>fluent-hc</artifactId>
-			<version>4.5.14</version>
-			<exclusions>
-				<exclusion>
-					<groupId>commons-logging</groupId>
-					<artifactId>commons-logging</artifactId>
-				</exclusion>
-			</exclusions>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.httpcomponents</groupId>
 			<artifactId>httpmime</artifactId>
-			<version>4.5.14</version>
 		</dependency>
 		<dependency>
 			<groupId>com.googlecode.json-simple</groupId>
 			<artifactId>json-simple</artifactId>
-			<version>1.1.1</version>
+		</dependency>
+		<dependency>
+			<groupId>org.slf4j</groupId>
+			<artifactId>jcl-over-slf4j</artifactId>
+			<scope>runtime</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.slf4j</groupId>
+			<artifactId>jul-to-slf4j</artifactId>
+			<scope>runtime</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.slf4j</groupId>
+			<artifactId>log4j-over-slf4j</artifactId>
+			<scope>runtime</scope>
+		</dependency>
+		<dependency>
+			<groupId>ch.qos.logback</groupId>
+			<artifactId>logback-classic</artifactId>
+			<scope>runtime</scope>
 		</dependency>
 	</dependencies>
 

diff --git a/paxtools-core/pom.xml b/paxtools-core/pom.xml
@@ -9,18 +9,14 @@
 
 	<artifactId>paxtools-core</artifactId>
 	<packaging>jar</packaging>
-	<name>Paxtools Core (BioPAX object model, I/O API, implementation and extras)</name>
+	<name>Paxtools Core</name>
 	<description>Paxtools core library includes the BioPAX object model and interfaces, the default implementation
 		and extras: reflection-based class factories and property editors/accessors, some inverse properties
-		(e.g., xrefOf, componentOf), traversal and file (I/O) utilities.
+		(e.g., xrefOf, componentOf), traversal, and file (I/O) utilities.
 	</description>
 
 	<url>https://biopax.github.io/Paxtools</url>
 
-	<scm><url>https://github.com/BioPAX/Paxtools</url>
-		<tag>HEAD</tag>
-	</scm>
-
 	<dependencies>
 		<dependency>
 			<!-- (collections15, composite) is used in the BioPAX Level2 and Path Accessors implementations -->

diff --git a/paxtools-core/src/test/resources/log4j.properties b/paxtools-core/src/test/resources/log4j.properties
diff --git a/paxtools-core/src/test/resources/logback-test.xml b/paxtools-core/src/test/resources/logback-test.xml
@@ -5,6 +5,9 @@
     <resetJUL>true</resetJUL>
   </contextListener>
 
+  <!-- To enable JMX Management (also prints additional logback initializing info)-->
+  <jmxConfigurator/>
+
   <appender name="console" class="ch.qos.logback.core.ConsoleAppender">
     <encoder>
       <pattern>%d %-5level [%thread] %logger{25} - %msg%n</pattern>

diff --git a/paxtools-query/pom.xml b/paxtools-query/pom.xml
@@ -9,17 +9,13 @@
     <artifactId>paxtools-query</artifactId>
     <packaging>jar</packaging>
 
-    <name>Graph-Theoretic Querying</name>
+    <name>BioPAX Query</name>
     <description>BioPAX graph-theoretic querying - for finding paths between molecules,
     or identifying molecules that are reachable through specific paths, using the BioPAX pathway data model.
     </description>
 
     <url>https://biopax.github.io/Paxtools</url>
 
-    <scm><url>https://github.com/BioPAX/Paxtools</url>
-        <tag>HEAD</tag>
-    </scm>
-
   <dependencies>
         <dependency>
             <groupId>org.biopax.paxtools</groupId>

diff --git a/paxtools-query/src/test/resources/logback-test.xml b/paxtools-query/src/test/resources/logback-test.xml
@@ -5,6 +5,9 @@
     <resetJUL>true</resetJUL>
   </contextListener>
 
+  <!-- To enable JMX Management (also prints additional logback initializing info)-->
+  <jmxConfigurator/>
+
   <appender name="console" class="ch.qos.logback.core.ConsoleAppender">
     <encoder>
       <pattern>%d %-5level [%thread] %logger{25} - %msg%n</pattern>

diff --git a/pom.xml b/pom.xml
@@ -182,7 +182,7 @@
   <scm>
     <connection>scm:git:git://github.com/BioPAX/Paxtools.git</connection>
     <developerConnection>scm:git:git@github.com:BioPAX/Paxtools.git</developerConnection>
-    <url>https://github.com/BioPAX/Paxtools</url>
+    <url>https://github.com/BioPAX/Paxtools/tree/master</url>
     <tag>HEAD</tag>
   </scm>
 
@@ -380,11 +380,6 @@
         <artifactId>commons-lang3</artifactId>
         <version>3.8.1</version>
       </dependency>
-      <dependency>
-        <groupId>com.hp.hpl.jena</groupId>
-        <artifactId>jena</artifactId>
-        <version>2.6.4</version>
-      </dependency>
       <dependency>
         <groupId>org.slf4j</groupId>
         <artifactId>slf4j-api</artifactId>
@@ -394,24 +389,24 @@
         <groupId>org.slf4j</groupId>
         <artifactId>jcl-over-slf4j</artifactId>
         <version>2.0.11</version>
-        <scope>runtime</scope>
+        <optional>true</optional>
       </dependency>
       <dependency>
         <groupId>org.slf4j</groupId>
         <artifactId>jul-to-slf4j</artifactId>
         <version>2.0.11</version>
-        <scope>runtime</scope>
+        <optional>true</optional>
       </dependency>
       <dependency>
         <groupId>org.slf4j</groupId>
         <artifactId>log4j-over-slf4j</artifactId>
         <version>2.0.11</version>
+        <optional>true</optional>
       </dependency>
       <dependency>
         <groupId>ch.qos.logback</groupId>
         <artifactId>logback-classic</artifactId>
-        <version>1.4.12</version>
-        <scope>runtime</scope>
+        <version>1.4.14</version>
         <optional>true</optional>
       </dependency>
       <dependency>
@@ -429,6 +424,52 @@
         <artifactId>lombok</artifactId>
         <version>1.18.24</version>
       </dependency>
+      <dependency>
+        <groupId>commons-codec</groupId>
+        <artifactId>commons-codec</artifactId>
+        <version>1.16.1</version>
+      </dependency>
+      <dependency>
+        <groupId>commons-logging</groupId>
+        <artifactId>commons-logging</artifactId>
+        <version>1.3.0</version>
+      </dependency>
+      <dependency>
+        <groupId>org.apache.httpcomponents</groupId>
+        <artifactId>fluent-hc</artifactId>
+        <version>4.5.14</version>
+      </dependency>
+      <dependency>
+        <groupId>org.apache.httpcomponents</groupId>
+        <artifactId>httpmime</artifactId>
+        <version>4.5.14</version>
+      </dependency>
+      <dependency>
+        <groupId>com.googlecode.json-simple</groupId>
+        <artifactId>json-simple</artifactId>
+        <version>1.1.1</version>
+        <exclusions>
+          <exclusion>
+            <groupId>junit</groupId>
+            <artifactId>junit</artifactId>
+          </exclusion>
+        </exclusions>
+      </dependency>
+      <dependency>
+        <groupId>org.apache.commons</groupId>
+        <artifactId>commons-compress</artifactId>
+        <version>1.25.0</version>
+      </dependency>
+      <dependency>
+        <groupId>com.sun.xml.bind</groupId>
+        <artifactId>jaxb-impl</artifactId>
+        <version>2.3.9</version>
+      </dependency>
+      <dependency>
+        <groupId>javax.xml.bind</groupId>
+        <artifactId>jaxb-api</artifactId>
+        <version>2.3.1</version>
+      </dependency>
     </dependencies>
   </dependencyManagement>
 
@@ -440,22 +481,22 @@
     <dependency>
       <groupId>org.slf4j</groupId>
       <artifactId>jcl-over-slf4j</artifactId>
-      <scope>runtime</scope>
+      <scope>test</scope>
     </dependency>
     <dependency>
       <groupId>org.slf4j</groupId>
       <artifactId>jul-to-slf4j</artifactId>
-      <scope>runtime</scope>
+      <scope>test</scope>
     </dependency>
     <dependency>
       <groupId>org.slf4j</groupId>
       <artifactId>log4j-over-slf4j</artifactId>
-      <scope>runtime</scope>
+      <scope>test</scope>
     </dependency>
     <dependency>
       <groupId>ch.qos.logback</groupId>
       <artifactId>logback-classic</artifactId>
-      <scope>runtime</scope>
+      <scope>test</scope>
     </dependency>
     <dependency>
       <groupId>org.junit.jupiter</groupId>

diff --git a/psimi-converter/pom.xml b/psimi-converter/pom.xml
@@ -1,22 +1,17 @@
 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+    <modelVersion>4.0.0</modelVersion>
 
     <parent>
         <groupId>org.biopax.paxtools</groupId>
         <artifactId>paxtools</artifactId>
         <version>6.0.0-SNAPSHOT</version>
     </parent>
-
-    <modelVersion>4.0.0</modelVersion>
     <artifactId>psimi-converter</artifactId>
-    <name>PSI-MI/MITAB to BioPAX Converter</name>
-    <description>To Convert PSI-MI or MITAB v2.5 files to BioPAX.</description>
 
-    <url>https://biopax.github.io/Paxtools</url>
+    <name>PSIMI/MITAB to BioPAX</name>
+    <description>Converts PSI-MI or PCI-MITAB v2.5 files to BioPAX</description>
 
-    <scm>
-        <url>https://github.com/BioPAX/Paxtools</url>
-        <tag>HEAD</tag>
-    </scm>
+    <url>https://biopax.github.io/Paxtools</url>
 
     <dependencies>
         <dependency>