Merge pull request #22 from SBRG/refactoring

Refactoring

.travis.yml

@@ -11,11 +11,11 @@ before_install:
 - cd scripts && ./configureSQLiteDB.sh && cd ..
 - mkdir out
 install:
-- travis_retry mvn clean compile verify -B && zip -d target/ModelPolisher-1.5.jar log4j2.xml > /dev/null 
+- travis_retry mvn clean compile package -B && zip -d target/ModelPolisher-1.6.jar log4j2.xml > /dev/null 
 script:
-- travis_wait java -jar target/ModelPolisher-1.5.jar --input=bigg_models_data/models/RECON1.xml --output=out/RECON1.xml --annotate-with-bigg=true --log-level=SEVERE
-- travis_wait java -jar target/ModelPolisher-1.5.jar --input=bigg_models_data/models/ecoli_core_model.xml --output=out/ecoli_core_model.xml --annotate-with-bigg=true --log-level=SEVERE
-- travis_wait java -jar target/ModelPolisher-1.5.jar --input=bigg_models_data/models/yeast_7.00.xml --output=out/yeast_7.00.xml --annotate-with-bigg=true --log-level=SEVERE
+- travis_wait java -jar target/ModelPolisher-1.6.jar --input=bigg_models_data/models/RECON1.xml --output=out/RECON1.xml --annotate-with-bigg=true --log-level=SEVERE
+- travis_wait java -jar target/ModelPolisher-1.6.jar --input=bigg_models_data/models/ecoli_core_model.xml --output=out/ecoli_core_model.xml --annotate-with-bigg=true --log-level=SEVERE
+- travis_wait java -jar target/ModelPolisher-1.6.jar --input=bigg_models_data/models/yeast_7.00.xml --output=out/yeast_7.00.xml --annotate-with-bigg=true --log-level=SEVERE
 - ls -lish out
 git:
   depth: 10

README.md

@@ -15,3 +15,8 @@ ModelPolisher is essentially a command-line based tool. You can run it locally u
 The online version of ModelPolisher is described in this article: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0149263
 
 The article http://nar.oxfordjournals.org/content/44/D1/D515 describes BiGG Models knowledge-base including ModelPolisher, http://nar.oxfordjournals.org/content/44/D1/D515
+
+# Licenses
+
+ModelPolisher is distributed under the MIT License (see LICENSE).
+An Overview of all dependencies is provided in THIRD-PARTY.txt, their respective licenses can be found in the licenses folder.

THIRD-PARTY.txt

@@ -0,0 +1,41 @@
+
+Lists of 39 third-party dependencies.
+     (New BSD License) matfilerw (com.diffplug.matsim:matfilerw:2.1.0 - https://github.com/diffplug/matfilerw)
+     (The Apache Software License, Version 2.0) Jackson-annotations (com.fasterxml.jackson.core:jackson-annotations:2.8.1 - http://github.com/FasterXML/jackson)
+     (The Apache Software License, Version 2.0) Jackson-core (com.fasterxml.jackson.core:jackson-core:2.8.1 - https://github.com/FasterXML/jackson-core)
+     (The Apache Software License, Version 2.0) jackson-databind (com.fasterxml.jackson.core:jackson-databind:2.8.1 - http://github.com/FasterXML/jackson)
+     (BSD) StaxMate (com.fasterxml.staxmate:staxmate:2.3.0 - http://staxmate.codehaus.org)
+     (The Apache License, Version 2.0) Woodstox (com.fasterxml.woodstox:woodstox-core:5.0.1 - https://github.com/FasterXML/woodstox)
+     (The Apache Software License, Version 2.0) JSON.simple (com.googlecode.json-simple:json-simple:1.1.1 - http://code.google.com/p/json-simple/)
+     (BSD style) XStream Core (com.thoughtworks.xstream:xstream:1.3.1 - no url defined)
+     (Unknown license) SysBio (de.zbit:SysBio:1390 - no url defined)
+     (Common Public License Version 1.0) JUnit (junit:junit:4.11 - http://junit.org)
+     (Java HTML Tidy License) JTidy (net.sf.jtidy:jtidy:r938 - http://jtidy.sourceforge.net)
+     (The Apache Software License, Version 2.0) Apache Log4j 1.x Compatibility API (org.apache.logging.log4j:log4j-1.2-api:2.3 - http://logging.apache.org/log4j/2.x/log4j-1.2-api/)
+     (The Apache Software License, Version 2.0) Apache Log4j API (org.apache.logging.log4j:log4j-api:2.3 - http://logging.apache.org/log4j/2.x/log4j-api/)
+     (The Apache Software License, Version 2.0) Apache Log4j Core (org.apache.logging.log4j:log4j-core:2.3 - http://logging.apache.org/log4j/2.x/log4j-core/)
+     (The Apache Software License, Version 2.0) Apache Log4j SLF4J Binding (org.apache.logging.log4j:log4j-slf4j-impl:2.1 - http://logging.apache.org/log4j/2.x/log4j-slf4j-impl/)
+     (GNU LGPL v2) biojava-ontology (org.biojava:biojava-ontology:4.0.0 - http://maven.apache.org)
+     (The BSD License) Stax2 API (org.codehaus.woodstox:stax2-api:3.1.4 - http://wiki.fasterxml.com/WoodstoxStax2)
+     (New BSD License) Hamcrest Core (org.hamcrest:hamcrest-core:1.3 - https://github.com/hamcrest/JavaHamcrest/hamcrest-core)
+     (GNU GPL v2) registry-lib (org.identifiers:registry-lib:1.1.1 - no url defined)
+     (The PostgreSQL License) PostgreSQL JDBC Driver (org.postgresql:postgresql:9.4-1202-jdbc41 - http://jdbc.postgresql.org)
+     (LGPL License) (Licensing and Distribution Terms for JSBML) JSBML (org.sbml.jsbml:jsbml:1.2 - http://www.sbml.org/Software/JSBML)
+     (LGPL License) (Licensing and Distribution Terms for JSBML) jsbml-core (org.sbml.jsbml:jsbml-core:1.2 - http://www.sbml.org/Software/JSBML/jsbml-core)
+     (LGPL License) (Licensing and Distribution Terms for JSBML) jsbml-arrays (org.sbml.jsbml.ext:jsbml-arrays:1.2 - http://www.sbml.org/Software/JSBML/ext/jsbml-arrays)
+     (LGPL License) (Licensing and Distribution Terms for JSBML) jsbml-comp (org.sbml.jsbml.ext:jsbml-comp:1.2 - http://www.sbml.org/Software/JSBML/ext/jsbml-comp)
+     (LGPL License) (Licensing and Distribution Terms for JSBML) jsbml-distrib (org.sbml.jsbml.ext:jsbml-distrib:1.2 - http://www.sbml.org/Software/JSBML/ext/jsbml-distrib)
+     (LGPL License) (Licensing and Distribution Terms for JSBML) jsbml-dyn (org.sbml.jsbml.ext:jsbml-dyn:1.2 - http://www.sbml.org/Software/JSBML/ext/jsbml-dyn)
+     (LGPL License) (Licensing and Distribution Terms for JSBML) jsbml-fbc (org.sbml.jsbml.ext:jsbml-fbc:1.2 - http://www.sbml.org/Software/JSBML/ext/jsbml-fbc)
+     (LGPL License) (Licensing and Distribution Terms for JSBML) jsbml-groups (org.sbml.jsbml.ext:jsbml-groups:1.2 - http://www.sbml.org/Software/JSBML/ext/jsbml-groups)
+     (LGPL License) (Licensing and Distribution Terms for JSBML) jsbml-layout (org.sbml.jsbml.ext:jsbml-layout:1.2 - http://www.sbml.org/Software/JSBML/ext/jsbml-layout)
+     (LGPL License) (Licensing and Distribution Terms for JSBML) jsbml-multi (org.sbml.jsbml.ext:jsbml-multi:1.2 - http://www.sbml.org/Software/JSBML/ext/jsbml-multi)
+     (LGPL License) (Licensing and Distribution Terms for JSBML) jsbml-qual (org.sbml.jsbml.ext:jsbml-qual:1.2 - http://www.sbml.org/Software/JSBML/ext/jsbml-qual)
+     (LGPL License) (Licensing and Distribution Terms for JSBML) jsbml-render (org.sbml.jsbml.ext:jsbml-render:1.2 - http://www.sbml.org/Software/JSBML/ext/jsbml-render)
+     (LGPL License) (Licensing and Distribution Terms for JSBML) jsbml-req (org.sbml.jsbml.ext:jsbml-req:1.2 - http://www.sbml.org/Software/JSBML/ext/jsbml-req)
+     (LGPL License) (Licensing and Distribution Terms for JSBML) jsbml-spatial (org.sbml.jsbml.ext:jsbml-spatial:1.2 - http://www.sbml.org/Software/JSBML/ext/jsbml-spatial)
+     (LGPL License) (Licensing and Distribution Terms for JSBML) jsbml-tidy (org.sbml.jsbml.modules:jsbml-tidy:1.2 - http://www.sbml.org/Software/JSBML/modules/jsbml-tidy)
+     (MIT License) SLF4J API Module (org.slf4j:slf4j-api:1.7.10 - http://www.slf4j.org)
+     (W3C Software License) W3C Jigsaw (org.w3c.jigsaw:jigsaw:2.2.6 - http://www.w3.org/Jigsaw/)
+     (The Apache Software License, Version 2.0) SQLite JDBC (org.xerial:sqlite-jdbc:3.8.7 - http://nexus.sonatype.org/oss-repository-hosting.html/sqlite-jdbc)
+     (Indiana University Extreme! Lab Software License, vesion 1.1.1) (Public Domain) MXP1: Xml Pull Parser 3rd Edition (XPP3) (xpp3:xpp3_min:1.1.4c - http://www.extreme.indiana.edu/xgws/xsoap/xpp/mxp1/)

assembly.xml

@@ -41,9 +41,9 @@
     <!-- Include scripts individually -->
     <fileSet>
       <directory>${project.build.scriptSourceDirectory}</directory>
-      <outputDirectory>./</outputDirectory>
+      <outputDirectory>./scripts</outputDirectory>
       <includes>
-        <include>*.sh</include>
+        <include>**/*</include>
       </includes>
       <filtered>true</filtered>
       <fileMode>0755</fileMode>
@@ -79,6 +79,12 @@
       <fileMode>0644</fileMode>
       <filtered>true</filtered>
     </file>
+    <file>
+      <outputDirectory>./</outputDirectory>
+      <source>THIRD-PARTY.txt</source>
+      <fileMode>0644</fileMode>
+      <filtered>true</filtered>
+    </file>
     <!-- Also include NOTICE, AUTHORS ... -->
   </files>