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rampage extended
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@Schmoho
Schmoho committed Aug 15, 2024
1 parent 8829f61 commit 1b8a125
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12 changes: 11 additions & 1 deletion build.gradle
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Expand Up @@ -105,7 +105,10 @@ dependencies {
// reading, writing, and manipulating SBML files
implementation("org.sbml.jsbml:jsbml:1.6.1") {
exclude group: "org.apache.logging.log4j", module: "log4j-core"
exclude group: "org.apache.logging.log4j", module: "log4j-api"
exclude group: "org.apache.logging.log4j", module: "log4j-1.2-api "
exclude group: "org.apache.logging.log4j", module: "log4j-slf4j-impl"
exclude group: "org.apache.commons", module: "logging"
}
// ontology support within BioJava
implementation "org.biojava:biojava-ontology:7.1.1"
Expand All @@ -120,7 +123,7 @@ dependencies {
implementation group: 'commons-io', name: 'commons-io', version: '2.16.1'
// https://mvnrepository.com/artifact/org.apache.commons/commons-lang3
implementation group: 'org.apache.commons', name: 'commons-lang3', version: '3.15.0'
// JSON processor
// JSON processor
implementation "com.fasterxml.jackson.core:jackson-core:${jacksonVersion}"
// data binding for Jackson
implementation "com.fasterxml.jackson.core:jackson-databind:${jacksonVersion}"
Expand All @@ -141,7 +144,14 @@ dependencies {
// runtime engine for executing tests with JUnit 5
testRuntimeOnly 'org.junit.platform:junit-platform-launcher:1.10.2'
testRuntimeOnly "org.junit.jupiter:junit-jupiter-engine:${jupiterVersion}"
}

configurations {
runtime.exclude group: "org.apache.logging.log4j", module: "log4j-core"
runtime.exclude group: "org.apache.logging.log4j", module: "log4j-api"
runtime.exclude group: "org.apache.logging.log4j", module: "log4j-1.2-api"
runtime.exclude group: "org.apache.logging.log4j", module: "log4j-slf4j-impl"
runtime.exclude group: "org.apache.commons", module: "logging"
}

/** === Configuration for pre-existing Tasks === **/
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187 changes: 115 additions & 72 deletions docs/allclasses-index.html
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36 changes: 24 additions & 12 deletions docs/allpackages-index.html
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Expand Up @@ -71,29 +71,41 @@ <h1 title="All&amp;nbsp;Packages" class="title">All&nbsp;Packages</h1>
<div class="col-last odd-row-color">&nbsp;</div>
<div class="col-first even-row-color"><a href="edu/ucsd/sbrg/eco/package-summary.html">edu.ucsd.sbrg.eco</a></div>
<div class="col-last even-row-color">&nbsp;</div>
<div class="col-first odd-row-color"><a href="edu/ucsd/sbrg/io/package-summary.html">edu.ucsd.sbrg.io</a></div>
<div class="col-first odd-row-color"><a href="edu/ucsd/sbrg/fixing/package-summary.html">edu.ucsd.sbrg.fixing</a></div>
<div class="col-last odd-row-color">&nbsp;</div>
<div class="col-first even-row-color"><a href="edu/ucsd/sbrg/io/parsers/cobra/package-summary.html">edu.ucsd.sbrg.io.parsers.cobra</a></div>
<div class="col-first even-row-color"><a href="edu/ucsd/sbrg/fixing/ext/fbc/package-summary.html">edu.ucsd.sbrg.fixing.ext.fbc</a></div>
<div class="col-last even-row-color">&nbsp;</div>
<div class="col-first odd-row-color"><a href="edu/ucsd/sbrg/io/parsers/json/package-summary.html">edu.ucsd.sbrg.io.parsers.json</a></div>
<div class="col-first odd-row-color"><a href="edu/ucsd/sbrg/fixing/ext/groups/package-summary.html">edu.ucsd.sbrg.fixing.ext.groups</a></div>
<div class="col-last odd-row-color">&nbsp;</div>
<div class="col-first even-row-color"><a href="edu/ucsd/sbrg/io/parsers/json/mapping/package-summary.html">edu.ucsd.sbrg.io.parsers.json.mapping</a></div>
<div class="col-first even-row-color"><a href="edu/ucsd/sbrg/io/package-summary.html">edu.ucsd.sbrg.io</a></div>
<div class="col-last even-row-color">&nbsp;</div>
<div class="col-first odd-row-color"><a href="edu/ucsd/sbrg/parameters/package-summary.html">edu.ucsd.sbrg.parameters</a></div>
<div class="col-first odd-row-color"><a href="edu/ucsd/sbrg/io/parsers/cobra/package-summary.html">edu.ucsd.sbrg.io.parsers.cobra</a></div>
<div class="col-last odd-row-color">&nbsp;</div>
<div class="col-first even-row-color"><a href="edu/ucsd/sbrg/polishing/package-summary.html">edu.ucsd.sbrg.polishing</a></div>
<div class="col-first even-row-color"><a href="edu/ucsd/sbrg/io/parsers/json/package-summary.html">edu.ucsd.sbrg.io.parsers.json</a></div>
<div class="col-last even-row-color">&nbsp;</div>
<div class="col-first odd-row-color"><a href="edu/ucsd/sbrg/polishing/fbc/package-summary.html">edu.ucsd.sbrg.polishing.fbc</a></div>
<div class="col-first odd-row-color"><a href="edu/ucsd/sbrg/io/parsers/json/mapping/package-summary.html">edu.ucsd.sbrg.io.parsers.json.mapping</a></div>
<div class="col-last odd-row-color">&nbsp;</div>
<div class="col-first even-row-color"><a href="edu/ucsd/sbrg/reporting/package-summary.html">edu.ucsd.sbrg.reporting</a></div>
<div class="col-first even-row-color"><a href="edu/ucsd/sbrg/parameters/package-summary.html">edu.ucsd.sbrg.parameters</a></div>
<div class="col-last even-row-color">&nbsp;</div>
<div class="col-first odd-row-color"><a href="edu/ucsd/sbrg/resolver/package-summary.html">edu.ucsd.sbrg.resolver</a></div>
<div class="col-first odd-row-color"><a href="edu/ucsd/sbrg/polishing/package-summary.html">edu.ucsd.sbrg.polishing</a></div>
<div class="col-last odd-row-color">&nbsp;</div>
<div class="col-first even-row-color"><a href="edu/ucsd/sbrg/resolver/identifiersorg/package-summary.html">edu.ucsd.sbrg.resolver.identifiersorg</a></div>
<div class="col-first even-row-color"><a href="edu/ucsd/sbrg/polishing/fbc/package-summary.html">edu.ucsd.sbrg.polishing.fbc</a></div>
<div class="col-last even-row-color">&nbsp;</div>
<div class="col-first odd-row-color"><a href="edu/ucsd/sbrg/resolver/identifiersorg/mapping/package-summary.html">edu.ucsd.sbrg.resolver.identifiersorg.mapping</a></div>
<div class="col-first odd-row-color"><a href="edu/ucsd/sbrg/reporting/package-summary.html">edu.ucsd.sbrg.reporting</a></div>
<div class="col-last odd-row-color">&nbsp;</div>
<div class="col-first even-row-color"><a href="edu/ucsd/sbrg/util/package-summary.html">edu.ucsd.sbrg.util</a></div>
<div class="col-first even-row-color"><a href="edu/ucsd/sbrg/resolver/package-summary.html">edu.ucsd.sbrg.resolver</a></div>
<div class="col-last even-row-color">&nbsp;</div>
<div class="col-first odd-row-color"><a href="edu/ucsd/sbrg/resolver/identifiersorg/package-summary.html">edu.ucsd.sbrg.resolver.identifiersorg</a></div>
<div class="col-last odd-row-color">&nbsp;</div>
<div class="col-first even-row-color"><a href="edu/ucsd/sbrg/resolver/identifiersorg/mapping/package-summary.html">edu.ucsd.sbrg.resolver.identifiersorg.mapping</a></div>
<div class="col-last even-row-color">&nbsp;</div>
<div class="col-first odd-row-color"><a href="edu/ucsd/sbrg/util/package-summary.html">edu.ucsd.sbrg.util</a></div>
<div class="col-last odd-row-color">&nbsp;</div>
<div class="col-first even-row-color"><a href="edu/ucsd/sbrg/util/ext/fbc/package-summary.html">edu.ucsd.sbrg.util.ext.fbc</a></div>
<div class="col-last even-row-color">&nbsp;</div>
<div class="col-first odd-row-color"><a href="edu/ucsd/sbrg/util/ext/groups/package-summary.html">edu.ucsd.sbrg.util.ext.groups</a></div>
<div class="col-last odd-row-color">&nbsp;</div>
<div class="col-first even-row-color"><a href="edu/ucsd/sbrg/validation/package-summary.html">edu.ucsd.sbrg.validation</a></div>
<div class="col-last even-row-color">&nbsp;</div>
</div>
</main>
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6 changes: 3 additions & 3 deletions docs/constant-values.html
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Expand Up @@ -195,13 +195,13 @@ <h2 title="edu.ucsd">edu.ucsd.*</h2>
</ul>
<ul class="block-list">
<li>
<div class="caption"><span>edu.ucsd.sbrg.util.<a href="edu/ucsd/sbrg/util/SBMLUtils.html" title="class in edu.ucsd.sbrg.util">SBMLUtils</a></span></div>
<div class="caption"><span>edu.ucsd.sbrg.util.ext.groups.<a href="edu/ucsd/sbrg/util/ext/groups/GroupsUtils.html" title="class in edu.ucsd.sbrg.util.ext.groups">GroupsUtils</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="edu.ucsd.sbrg.util.SBMLUtils.SUBSYSTEM_LINK">public&nbsp;static&nbsp;final&nbsp;<a href="https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/lang/String.html" title="class or interface in java.lang" class="external-link">String</a></code></div>
<div class="col-second even-row-color"><code><a href="edu/ucsd/sbrg/util/SBMLUtils.html#SUBSYSTEM_LINK">SUBSYSTEM_LINK</a></code></div>
<div class="col-first even-row-color"><code id="edu.ucsd.sbrg.util.ext.groups.GroupsUtils.SUBSYSTEM_LINK">public&nbsp;static&nbsp;final&nbsp;<a href="https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/lang/String.html" title="class or interface in java.lang" class="external-link">String</a></code></div>
<div class="col-second even-row-color"><code><a href="edu/ucsd/sbrg/util/ext/groups/GroupsUtils.html#SUBSYSTEM_LINK">SUBSYSTEM_LINK</a></code></div>
<div class="col-last even-row-color"><code>"SUBSYSTEM_LINK"</code></div>
</div>
</li>
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56 changes: 35 additions & 21 deletions docs/edu/ucsd/sbrg/eco/ECOparser.html → docs/edu/ucsd/sbrg/ECOParserCLILauncher.html
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Expand Up @@ -2,24 +2,24 @@
<html lang="en">
<head>
<!-- Generated by javadoc (17) -->
<title>ECOparser (ModelPolisher 2.1 API)</title>
<title>ECOParserCLILauncher (ModelPolisher 2.1 API)</title>
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<meta name="description" content="declaration: package: edu.ucsd.sbrg.eco, class: ECOparser">
<meta name="description" content="declaration: package: edu.ucsd.sbrg, class: ECOParserCLILauncher">
<meta name="generator" content="javadoc/ClassWriterImpl">
<link rel="stylesheet" type="text/css" href="../../../../stylesheet.css" title="Style">
<link rel="stylesheet" type="text/css" href="../../../../script-dir/jquery-ui.min.css" title="Style">
<link rel="stylesheet" type="text/css" href="../../../../jquery-ui.overrides.css" title="Style">
<script type="text/javascript" src="../../../../script.js"></script>
<script type="text/javascript" src="../../../../script-dir/jquery-3.6.1.min.js"></script>
<script type="text/javascript" src="../../../../script-dir/jquery-ui.min.js"></script>
<link rel="stylesheet" type="text/css" href="../../../stylesheet.css" title="Style">
<link rel="stylesheet" type="text/css" href="../../../script-dir/jquery-ui.min.css" title="Style">
<link rel="stylesheet" type="text/css" href="../../../jquery-ui.overrides.css" title="Style">
<script type="text/javascript" src="../../../script.js"></script>
<script type="text/javascript" src="../../../script-dir/jquery-3.6.1.min.js"></script>
<script type="text/javascript" src="../../../script-dir/jquery-ui.min.js"></script>
</head>
<body class="class-declaration-page">
<script type="text/javascript">var evenRowColor = "even-row-color";
var oddRowColor = "odd-row-color";
var tableTab = "table-tab";
var activeTableTab = "active-table-tab";
var pathtoroot = "../../../../";
var pathtoroot = "../../../";
loadScripts(document, 'script');</script>
<noscript>
<div>JavaScript is disabled on your browser.</div>
Expand All @@ -31,12 +31,12 @@
<div class="top-nav" id="navbar-top">
<div class="skip-nav"><a href="#skip-navbar-top" title="Skip navigation links">Skip navigation links</a></div>
<ul id="navbar-top-firstrow" class="nav-list" title="Navigation">
<li><a href="../../../../index.html">Overview</a></li>
<li><a href="../../../index.html">Overview</a></li>
<li><a href="package-summary.html">Package</a></li>
<li class="nav-bar-cell1-rev">Class</li>
<li><a href="package-tree.html">Tree</a></li>
<li><a href="../../../../index-all.html">Index</a></li>
<li><a href="../../../../help-doc.html#class">Help</a></li>
<li><a href="../../../index-all.html">Index</a></li>
<li><a href="../../../help-doc.html#class">Help</a></li>
</ul>
</div>
<div class="sub-nav">
Expand Down Expand Up @@ -67,15 +67,15 @@
<main role="main">
<!-- ======== START OF CLASS DATA ======== -->
<div class="header">
<div class="sub-title"><span class="package-label-in-type">Package</span>&nbsp;<a href="package-summary.html">edu.ucsd.sbrg.eco</a></div>
<h1 title="Class ECOparser" class="title">Class ECOparser</h1>
<div class="sub-title"><span class="package-label-in-type">Package</span>&nbsp;<a href="package-summary.html">edu.ucsd.sbrg</a></div>
<h1 title="Class ECOParserCLILauncher" class="title">Class ECOParserCLILauncher</h1>
</div>
<div class="inheritance" title="Inheritance Tree"><a href="https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/lang/Object.html" title="class or interface in java.lang" class="external-link">java.lang.Object</a>
<div class="inheritance">edu.ucsd.sbrg.eco.ECOparser</div>
<div class="inheritance">edu.ucsd.sbrg.ECOParserCLILauncher</div>
</div>
<section class="class-description" id="class-description">
<hr>
<div class="type-signature"><span class="modifiers">public class </span><span class="element-name type-name-label">ECOparser</span>
<div class="type-signature"><span class="modifiers">public class </span><span class="element-name type-name-label">ECOParserCLILauncher</span>
<span class="extends-implements">extends <a href="https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/lang/Object.html" title="class or interface in java.lang" class="external-link">Object</a></span></div>
</section>
<section class="summary">
Expand All @@ -88,7 +88,7 @@ <h2>Constructor Summary</h2>
<div class="summary-table two-column-summary">
<div class="table-header col-first">Constructor</div>
<div class="table-header col-last">Description</div>
<div class="col-constructor-name even-row-color"><code><a href="#%3Cinit%3E()" class="member-name-link">ECOparser</a>()</code></div>
<div class="col-constructor-name even-row-color"><code><a href="#%3Cinit%3E()" class="member-name-link">ECOParserCLILauncher</a>()</code></div>
<div class="col-last even-row-color">&nbsp;</div>
</div>
</section>
Expand Down Expand Up @@ -138,8 +138,8 @@ <h2>Constructor Details</h2>
<ul class="member-list">
<li>
<section class="detail" id="&lt;init&gt;()">
<h3>ECOparser</h3>
<div class="member-signature"><span class="modifiers">public</span>&nbsp;<span class="element-name">ECOparser</span>()</div>
<h3>ECOParserCLILauncher</h3>
<div class="member-signature"><span class="modifiers">public</span>&nbsp;<span class="element-name">ECOParserCLILauncher</span>()</div>
</section>
</li>
</ul>
Expand All @@ -153,7 +153,14 @@ <h2>Method Details</h2>
<li>
<section class="detail" id="main(java.lang.String[])">
<h3>main</h3>
<div class="member-signature"><span class="modifiers">public static</span>&nbsp;<span class="return-type">void</span>&nbsp;<span class="element-name">main</span><wbr><span class="parameters">(<a href="https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/lang/String.html" title="class or interface in java.lang" class="external-link">String</a>[]&nbsp;args)</span></div>
<div class="member-signature"><span class="modifiers">public static</span>&nbsp;<span class="return-type">void</span>&nbsp;<span class="element-name">main</span><wbr><span class="parameters">(<a href="https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/lang/String.html" title="class or interface in java.lang" class="external-link">String</a>[]&nbsp;args)</span>
throws <span class="exceptions"><a href="https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/io/IOException.html" title="class or interface in java.io" class="external-link">IOException</a>,
<a href="https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/text/ParseException.html" title="class or interface in java.text" class="external-link">ParseException</a></span></div>
<dl class="notes">
<dt>Throws:</dt>
<dd><code><a href="https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/io/IOException.html" title="class or interface in java.io" class="external-link">IOException</a></code></dd>
<dd><code><a href="https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/text/ParseException.html" title="class or interface in java.text" class="external-link">ParseException</a></code></dd>
</dl>
</section>
</li>
<li>
Expand All @@ -171,7 +178,14 @@ <h3>getConfidenceScoreForTerm</h3>
<li>
<section class="detail" id="parseECO()">
<h3>parseECO</h3>
<div class="member-signature"><span class="modifiers">public static</span>&nbsp;<span class="return-type">void</span>&nbsp;<span class="element-name">parseECO</span>()</div>
<div class="member-signature"><span class="modifiers">public static</span>&nbsp;<span class="return-type">void</span>&nbsp;<span class="element-name">parseECO</span>()
throws <span class="exceptions"><a href="https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/io/IOException.html" title="class or interface in java.io" class="external-link">IOException</a>,
<a href="https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/text/ParseException.html" title="class or interface in java.text" class="external-link">ParseException</a></span></div>
<dl class="notes">
<dt>Throws:</dt>
<dd><code><a href="https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/io/IOException.html" title="class or interface in java.io" class="external-link">IOException</a></code></dd>
<dd><code><a href="https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/text/ParseException.html" title="class or interface in java.text" class="external-link">ParseException</a></code></dd>
</dl>
</section>
</li>
<li>
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