Skip to content

Commit

Permalink
Logging and dependency mgmt polishing.
Browse files Browse the repository at this point in the history 
 - made slf4j providers/bindings optional, test scope again, etc.
 - also fixed SCM URLs for submodules (for maven-site)
  • Loading branch information
@IgorRodchenkov
IgorRodchenkov committed Feb 10, 2024
1 parent afbf0e1 commit 412bd0b
Show file tree
Hide file tree
Showing 19 changed files with 118 additions and 89 deletions.
8 changes: 2 additions & 6 deletions gsea-converter/pom.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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>
Expand Down
3 changes: 3 additions & 0 deletions gsea-converter/src/test/resources/logback-test.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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>
Expand Down
8 changes: 2 additions & 6 deletions json-converter/pom.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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>
Expand Down
3 changes: 3 additions & 0 deletions json-converter/src/test/resources/logback-test.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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>
Expand Down
6 changes: 3 additions & 3 deletions normalizer/pom.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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>
Expand Down
2 changes: 1 addition & 1 deletion normalizer/src/test/resources/logback-test.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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/>-->

Expand Down
8 changes: 2 additions & 6 deletions pattern/pom.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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>
Expand Down
3 changes: 3 additions & 0 deletions pattern/src/test/resources/logback-test.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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>
Expand Down
36 changes: 21 additions & 15 deletions paxtools-console/pom.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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>
Expand Down Expand Up @@ -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>

Expand Down
8 changes: 2 additions & 6 deletions paxtools-core/pom.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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 -->
Expand Down
7 changes: 0 additions & 7 deletions paxtools-core/src/test/resources/log4j.properties
View file

This file was deleted.

3 changes: 3 additions & 0 deletions paxtools-core/src/test/resources/logback-test.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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>
Expand Down
6 changes: 1 addition & 5 deletions paxtools-query/pom.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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>
Expand Down
3 changes: 3 additions & 0 deletions paxtools-query/src/test/resources/logback-test.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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>
Expand Down
69 changes: 55 additions & 14 deletions pom.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -182,7 +182,7 @@
<scm>
<connection>scm:git:git://github.com/BioPAX/Paxtools.git</connection>
<developerConnection>scm:git:[email protected]:BioPAX/Paxtools.git</developerConnection>
<url>https://github.com/BioPAX/Paxtools</url>
<url>https://github.com/BioPAX/Paxtools/tree/master</url>
<tag>HEAD</tag>
</scm>

Expand Down Expand Up @@ -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>
Expand All @@ -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>
Expand All @@ -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>

Expand All @@ -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>
Expand Down
13 changes: 4 additions & 9 deletions psimi-converter/pom.xml
View file
Original file line number Diff line number Diff line change
@@ -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>
Expand Down
Loading

0 comments on commit 412bd0b

Please sign in to comment.