diff --git a/gsea-converter/pom.xml b/gsea-converter/pom.xml
index 096e63d0..d5351160 100644
--- a/gsea-converter/pom.xml
+++ b/gsea-converter/pom.xml
@@ -7,15 +7,11 @@
4.0.0
gsea-converter
- BioPAX to GSEA (.gmt) Converter
- Converts data to the GESA (.gmt) format.
+ BioPAX to GSEA/GMT
+ Converts BioPAX model/data to the GESA/GMT (.gmt) format
https://biopax.github.io/Paxtools
- https://github.com/BioPAX/Paxtools
- HEAD
-
-
org.biopax.paxtools
diff --git a/gsea-converter/src/test/resources/logback-test.xml b/gsea-converter/src/test/resources/logback-test.xml
index 72639f95..5262308b 100644
--- a/gsea-converter/src/test/resources/logback-test.xml
+++ b/gsea-converter/src/test/resources/logback-test.xml
@@ -5,6 +5,9 @@
true
+
+
+
%d %-5level [%thread] %logger{25} - %msg%n
diff --git a/json-converter/pom.xml b/json-converter/pom.xml
index 58a99ff3..ca975400 100644
--- a/json-converter/pom.xml
+++ b/json-converter/pom.xml
@@ -6,15 +6,11 @@
6.0.0-SNAPSHOT
json-converter
- BioPAX to/from JSON Converter
- BioPAX to/from JSON Converters
+ BioPAX JSON-LD
+ Converts BioPAX model/file to or from JSON-LD format
https://biopax.github.io/Paxtools
- https://github.com/BioPAX/Paxtools
- HEAD
-
-
org.apache.jena
diff --git a/json-converter/src/test/resources/logback-test.xml b/json-converter/src/test/resources/logback-test.xml
index e7dd5e34..5caf8599 100644
--- a/json-converter/src/test/resources/logback-test.xml
+++ b/json-converter/src/test/resources/logback-test.xml
@@ -5,6 +5,9 @@
true
+
+
+
%d %-5level [%thread] %logger{25} - %msg%n
diff --git a/normalizer/pom.xml b/normalizer/pom.xml
index d674bcdf..d8a0710a 100644
--- a/normalizer/pom.xml
+++ b/normalizer/pom.xml
@@ -3,9 +3,9 @@
4.0.0
normalizer
- BioPAX Normalizer and Resolver
- A BioPAX Normalizer and Bio ID Resolver
- 2009-2015
+ BioPAX Normalizer
+ BioPAX Model/URIs Normalizer and BIO Identifiers Resolver
+ 2009
paxtools
org.biopax.paxtools
diff --git a/normalizer/src/test/resources/logback-test.xml b/normalizer/src/test/resources/logback-test.xml
index b3bfef52..ecd2028a 100644
--- a/normalizer/src/test/resources/logback-test.xml
+++ b/normalizer/src/test/resources/logback-test.xml
@@ -4,7 +4,7 @@
true
-
+
diff --git a/pattern/pom.xml b/pattern/pom.xml
index cbcb73c2..8c5c05db 100644
--- a/pattern/pom.xml
+++ b/pattern/pom.xml
@@ -9,17 +9,13 @@
pattern
- BioPAX Pattern Search
+ BioPAX Pattern
- 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.
https://biopax.github.io/Paxtools
- https://github.com/BioPAX/Paxtools
- HEAD
-
-
${project.groupId}
diff --git a/pattern/src/test/resources/logback-test.xml b/pattern/src/test/resources/logback-test.xml
index f6b7ff4e..b1f0fb91 100644
--- a/pattern/src/test/resources/logback-test.xml
+++ b/pattern/src/test/resources/logback-test.xml
@@ -5,6 +5,9 @@
true
+
+
+
%d %-5level [%thread] %logger{25} - %msg%n
diff --git a/paxtools-console/pom.xml b/paxtools-console/pom.xml
index 4695fa2d..6a8ea6e0 100644
--- a/paxtools-console/pom.xml
+++ b/paxtools-console/pom.xml
@@ -7,16 +7,11 @@
paxtools-console
jar
- Paxtools Console Application
+ Paxtools CLI
Paxtools Console Application and Examples
https://biopax.github.io/Paxtools
-
- https://github.com/BioPAX/Paxtools
- HEAD
-
-
@@ -90,23 +85,34 @@
org.apache.httpcomponents
fluent-hc
- 4.5.14
-
-
- commons-logging
- commons-logging
-
-
org.apache.httpcomponents
httpmime
- 4.5.14
com.googlecode.json-simple
json-simple
- 1.1.1
+
+
+ org.slf4j
+ jcl-over-slf4j
+ runtime
+
+
+ org.slf4j
+ jul-to-slf4j
+ runtime
+
+
+ org.slf4j
+ log4j-over-slf4j
+ runtime
+
+
+ ch.qos.logback
+ logback-classic
+ runtime
diff --git a/paxtools-core/pom.xml b/paxtools-core/pom.xml
index 410c6b5c..b7b3e702 100644
--- a/paxtools-core/pom.xml
+++ b/paxtools-core/pom.xml
@@ -9,18 +9,14 @@
paxtools-core
jar
- Paxtools Core (BioPAX object model, I/O API, implementation and extras)
+ Paxtools Core
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.
https://biopax.github.io/Paxtools
- https://github.com/BioPAX/Paxtools
- HEAD
-
-
diff --git a/paxtools-core/src/test/resources/log4j.properties b/paxtools-core/src/test/resources/log4j.properties
deleted file mode 100644
index a32ad7c7..00000000
--- a/paxtools-core/src/test/resources/log4j.properties
+++ /dev/null
@@ -1,7 +0,0 @@
-log4j.threshold=ALL
-log4j.rootLogger=ALL, InfoAppender
-
-log4j.appender.InfoAppender=org.apache.log4j.ConsoleAppender
-log4j.appender.InfoAppender.layout=org.apache.log4j.PatternLayout
-log4j.appender.InfoAppender.layout.ConversionPattern=%-4r [%t] %-5p %c %x - %m%n
-log4j.appender.InfoAppender.Threshold=INFO
diff --git a/paxtools-core/src/test/resources/logback-test.xml b/paxtools-core/src/test/resources/logback-test.xml
index 1fbd0c36..6a6223bf 100644
--- a/paxtools-core/src/test/resources/logback-test.xml
+++ b/paxtools-core/src/test/resources/logback-test.xml
@@ -5,6 +5,9 @@
true
+
+
+
%d %-5level [%thread] %logger{25} - %msg%n
diff --git a/paxtools-query/pom.xml b/paxtools-query/pom.xml
index 6d4579f2..cee8b827 100644
--- a/paxtools-query/pom.xml
+++ b/paxtools-query/pom.xml
@@ -9,17 +9,13 @@
paxtools-query
jar
- Graph-Theoretic Querying
+ BioPAX Query
BioPAX graph-theoretic querying - for finding paths between molecules,
or identifying molecules that are reachable through specific paths, using the BioPAX pathway data model.
https://biopax.github.io/Paxtools
- https://github.com/BioPAX/Paxtools
- HEAD
-
-
org.biopax.paxtools
diff --git a/paxtools-query/src/test/resources/logback-test.xml b/paxtools-query/src/test/resources/logback-test.xml
index f6835890..95b842e6 100644
--- a/paxtools-query/src/test/resources/logback-test.xml
+++ b/paxtools-query/src/test/resources/logback-test.xml
@@ -5,6 +5,9 @@
true
+
+
+
%d %-5level [%thread] %logger{25} - %msg%n
diff --git a/pom.xml b/pom.xml
index eafde23e..261092d9 100644
--- a/pom.xml
+++ b/pom.xml
@@ -182,7 +182,7 @@
scm:git:git://github.com/BioPAX/Paxtools.git
scm:git:git@github.com:BioPAX/Paxtools.git
- https://github.com/BioPAX/Paxtools
+ https://github.com/BioPAX/Paxtools/tree/master
HEAD
@@ -380,11 +380,6 @@
commons-lang3
3.8.1
-
- com.hp.hpl.jena
- jena
- 2.6.4
-
org.slf4j
slf4j-api
@@ -394,24 +389,24 @@
org.slf4j
jcl-over-slf4j
2.0.11
- runtime
+ true
org.slf4j
jul-to-slf4j
2.0.11
- runtime
+ true
org.slf4j
log4j-over-slf4j
2.0.11
+ true
ch.qos.logback
logback-classic
- 1.4.12
- runtime
+ 1.4.14
true
@@ -429,6 +424,52 @@
lombok
1.18.24
+
+ commons-codec
+ commons-codec
+ 1.16.1
+
+
+ commons-logging
+ commons-logging
+ 1.3.0
+
+
+ org.apache.httpcomponents
+ fluent-hc
+ 4.5.14
+
+
+ org.apache.httpcomponents
+ httpmime
+ 4.5.14
+
+
+ com.googlecode.json-simple
+ json-simple
+ 1.1.1
+
+
+ junit
+ junit
+
+
+
+
+ org.apache.commons
+ commons-compress
+ 1.25.0
+
+
+ com.sun.xml.bind
+ jaxb-impl
+ 2.3.9
+
+
+ javax.xml.bind
+ jaxb-api
+ 2.3.1
+
@@ -440,22 +481,22 @@
org.slf4j
jcl-over-slf4j
- runtime
+ test
org.slf4j
jul-to-slf4j
- runtime
+ test
org.slf4j
log4j-over-slf4j
- runtime
+ test
ch.qos.logback
logback-classic
- runtime
+ test
org.junit.jupiter
diff --git a/psimi-converter/pom.xml b/psimi-converter/pom.xml
index 7a4db223..957536bc 100644
--- a/psimi-converter/pom.xml
+++ b/psimi-converter/pom.xml
@@ -1,22 +1,17 @@
+ 4.0.0
org.biopax.paxtools
paxtools
6.0.0-SNAPSHOT
-
- 4.0.0
psimi-converter
- PSI-MI/MITAB to BioPAX Converter
- To Convert PSI-MI or MITAB v2.5 files to BioPAX.
- https://biopax.github.io/Paxtools
+ PSIMI/MITAB to BioPAX
+ Converts PSI-MI or PCI-MITAB v2.5 files to BioPAX
-
- https://github.com/BioPAX/Paxtools
- HEAD
-
+ https://biopax.github.io/Paxtools
diff --git a/psimi-converter/src/test/resources/logback-test.xml b/psimi-converter/src/test/resources/logback-test.xml
index c86dc6ab..c38d73a8 100644
--- a/psimi-converter/src/test/resources/logback-test.xml
+++ b/psimi-converter/src/test/resources/logback-test.xml
@@ -5,6 +5,9 @@
true
+
+
+
%d %-5level [%thread] %logger{25} - %msg%n
diff --git a/sbgn-converter/pom.xml b/sbgn-converter/pom.xml
index 26618a8d..f2d3bd98 100644
--- a/sbgn-converter/pom.xml
+++ b/sbgn-converter/pom.xml
@@ -1,24 +1,19 @@
+ 4.0.0
+
paxtools
org.biopax.paxtools
6.0.0-SNAPSHOT
- 4.0.0
-
sbgn-converter
-
jar
- BioPAX to SBGN-ML Converter
+ BioPAX to SBGN-ML
+ Converts a BioPAX Model to SBGN-ML (SBGN PD)
https://biopax.github.io/Paxtools
-
- https://github.com/BioPAX/Paxtools
- HEAD
-
-
org.biopax.paxtools
@@ -36,6 +31,4 @@
3.1.0
-
- To convert a BioPAX L3 model to SBGN-ML (SBGN PD), and optionally align.
\ No newline at end of file
diff --git a/sbgn-converter/src/test/resources/logback-test.xml b/sbgn-converter/src/test/resources/logback-test.xml
index 7f9a618e..47a80640 100644
--- a/sbgn-converter/src/test/resources/logback-test.xml
+++ b/sbgn-converter/src/test/resources/logback-test.xml
@@ -5,6 +5,9 @@
true
+
+
+
%d %-5level [%thread] %logger{25} - %msg%n