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Commit 62ca0537 authored by Davide Lagoa's avatar Davide Lagoa
Browse files

debug to run in server mode

parent e03bc30b
......@@ -57,7 +57,7 @@
<repository>
<id>nexus</id>
<name>Nexus BioSystems Server</name>
<url>http://193.137.11.210/nexus/content/groups/public/</url>
<url>https://www.bio.di.uminho.pt/nexus/content/groups/public/</url>
</repository>
<repository>
<id>ebi-repo</id>
......
......@@ -1039,3 +1039,1009 @@
2018-12-11 16:15:46,411 ERROR o.s.j.e.f.FBCSpeciesPlugin [main] Skipped invalid chemical formula: null
2018-12-11 16:15:47,060 ERROR o.s.j.e.f.FBCSpeciesPlugin [main] Skipped invalid chemical formula: null
2018-12-11 16:15:47,139 ERROR o.s.j.e.f.FBCSpeciesPlugin [main] Skipped invalid chemical formula: null
2019-01-29 10:42:34,201 ERROR o.s.j.v.SBMLValidator [main] There has been an error parsing the consistency check XML result.
2019-01-29 10:42:34,250 INFO o.s.j.v.SBMLValidator [main] Below is the String returned by the sbml.org validator REST API:
<style type='text/css'>
body {
font-family: Verdana, sans-serif;
font-size: 9pt;
line-height: 140%;
color: #444;
}
small { font-size: 75%; }
h1 { font-size: 140%; font-weight: bold; margin-bottom: 0; padding-top: 5pt; padding-bottom: 5pt;}
h2 { font-size: 120%; font-weight: bold; padding-top: 5pt; }
h3 { font-size: 100%; font-weight: bold; font-style: italic; line-height: 12pt; }
h3 { font-size: 100%; font-weight: bold; font-style: italic; line-height: 11pt; }
big { font-size: 120%; font-weight: bold; }
pre { font-size: 100%; }
b, h1, h2, h3, h4, strong { color: #595959; }
.small-font {
font-size: 8pt;
line-height: 120%;
}
a {
font-weight: bold;
color: #1e4487;
text-decoration: none;
}
a:visited {
color: #7790ba;
}
a:hover {
text-decoration: underline;
color: #000;
}
a.printable {
text-decoration: underline;
}
h1
{
margin-bottom: 0.5ex;
}
h3
{
text-align: center;
font-size: small;
margin-top: 2px;
margin-bottom: 1.5em;
}
#input-table {
padding-top: 1em;
width: 90%;
text-align: left;
}
#menu
{
font-size: 8pt;
border-bottom: 1px solid #ccc;
margin: 0;
padding-bottom: 19px;
padding-left: 10px;
margin-bottom: 10px;
}
#menu ul, #menu li
{
display: inline;
list-style-type: none;
margin: 0;
padding: 0;
}
#menu a:link, #menu a:visited
{
background: #e8ebf0;
border: 1px solid #cccccc;
color: #666666;
float: left;
font-weight: normal;
line-height: 14px;
margin-right: 8px;
padding: 2px 10px 2px 10px;
text-decoration: none;
}
#menu a:hover
{
color: red;
}
#menu li#selected a
{
background: white;
font-weight: bold;
border-bottom: 1px solid white;
color: black;
}
.example
{
font-size: 7pt;
color: gray;
}
h2.banner
{
background: #ffc;
border: 1px solid #ccc;
margin-top: 0em;
padding: .5em;
}
h2.valid, h2.invalid, h2.valid-warning
{
text-align: center;
margin: 0;
font-size-adjust: .53;
font-style: normal;
text-decoration: none;
word-spacing: normal;
letter-spacing: normal;
text-transform: none;
padding-top: .5em;
padding-bottom: .5em;
}
.valid
{
background: #55b05a;
color: white;
}
.invalid
{
background: #d23d24;
color: white;
}
.valid-warning
{
background-color: gold;
color: black;
}
.li
{
padding: 1em .5em;
}
.advisory
{
background-color: silver;
padding: .1em .5em;
color: white;
font-size: smaller
}
.warning
{
background-color: gold;
padding: .1em .5em;
color: black;
font-size: smaller
}
.error
{
background-color: #D23D24;
padding: .1em .5em;
color: white;
font-size: smaller
}
.fatal
{
background-color: #D23D24;
padding: .1em .5em;
color: white;
font-size: smaller
}
.message
{
font-weight: bold;
}
code.excerpt
{
border: 1px solid #eee;
color: #333;
background: #f4f8fb;
font: normal 98%/110% Courier, monospace;
margin: 0;
overflow: auto;
padding: 0px 5px 0px 45px;
}
code.excerpt em
{
color: red;
padding-left: .5ex;
padding-right: .5ex;
font-weight: bolder;
}
/* XML source code listing */
ol.code
{
border: 1px solid #eee;
color: #333;
font: normal 98%/110% Courier, monospace;
margin: 0;
overflow: auto;
padding: 5px 5px 5px 65px;
}
ol.code li
{
background-color: #f4f8fb;
margin: 0;
padding: 0 5px;
}
ol.code li:hover
{
background-color: #ffffbb;
color: #000000;
}
ol.code li.source
{
background-color: #fff;
list-style-type: none;
padding: 5px;
text-align: center;
}
ol.code li+li, ul.code li+li
{
margin-top: 2px;
}
ol.code li.tab0 { padding-left: 0px; }
ol.code li.tab1 { padding-left: 15px; }
ol.code li.tab2 { padding-left: 30px; }
ol.code li.tab3 { padding-left: 45px; }
ol.code li.tab4 { padding-left: 60px; }
ol.code li.tab5 { padding-left: 75px; }
ol.code li.tab6 { padding-left: 90px; }
ol.code li.tab7 { padding-left: 105px; }
ol.code li.tab8 { padding-left: 120px; }
ol.code li.tab9 { padding-left: 135px; }
ol.code li.tab10 { padding-left: 150px; }
ol.code li.tab11 { padding-left: 165px; }
ol.code li.tab12 { padding-left: 180px; }
ol.code li.tab13 { padding-left: 195px; }
ol.code li.tab14 { padding-left: 210px; }
ol.code li.tab15 { padding-left: 225px; }
ol.code li code
{
color: #333;
}
ol.code li span
{
color: #ff4444;
}
div.test-files
{
display: block;
width: 100%;
padding-top: 0px;
margin-top: 0px;
}
.test-files h2
{
margin-top: 0px;
padding-top: 10px;
clear: left;
}
.test-files ul
{
float: left;
list-style-type: none;
padding: 0px;
margin: 0 1em 0 0;
}
.test-files li
{
font: normal 100% Courier, monospace;
}
.test-files a:visited
{
color: #0140a0;
}
.footnote
{
margin-top: 1em;
font-size: smaller;
color: gray
}
div.api h1
{
text-align: left;
color: #0155a5;
}
div.api h2
{
color: #000;
border-bottom: 3px solid #fc0;
padding: 2px 0;
margin: 25px 0 0 0;
}
div.api .example
{
border: 1px solid #ccc;
color: #000;
background: #ffc;
font: normal 98%/110% Courier, monospace;
margin: 5px 10px 5px 10px;
padding: 10px 25px 10px 25px;
}
div.api .example em
{
font-style: normal;
color: red;
}
div.api .example.pre
{
white-space: pre;
}
div.api .example.output
{
background: #cfc;
margin: 5px 10px 5px 20px;
}
div.api .example.warning
{
background-color: gold;
margin: 5px 10px 5px 20px;
}
div.api .example.error
{
background: #fcc;
margin: 5px 10px 5px 20px;
}
div.recent .meta
{
margin: 0;
color: gray;
font-size: smaller;
}
div.recent .status
{
margin: 0 10px 0 0;
padding: .5em;
border: 1px solid #ccc;
font-size: larger;
text-align: center;
float: left;
width: 100px;
}
div.recent .file
{
margin-top: 0;
margin-left: 120px;
padding: .5em;
background: #ffc;
border: 1px solid #ccc;
font-size: larger;
clear: right;
}
#ccheck-title
{
display: block;
margin-top: 10px;
font-size: 9pt;
}
div.ccheck-options,
div.ccheck-options table
{
margin: 3px;
padding: .2em;
/* border: 1px dotted #ccc; */
font-size: 8pt;
text-align: left;
}
div.ccheck-options p,
div.ccheck-options input,
div.ccheck-options td
{
margin: 1px;
padding: 0;
}
div.ccheck-disabled
{
margin-top: 2px;
margin-bottom: 2px;
padding: .2em;
border: 1px solid #ccc;
font-size: smaller;
text-align: left;
}
.notice
{
background: #eee;
border: 2px solid #0155a5;
width: 75%;
padding: 1em;
text-align: left;
}
.disclaimer
{
width: 90%;
border: 1px dotted gray;
margin-top: 1em;
margin-bottom: 2em;
padding: 2px;
color: #777;
font-size: smaller;
text-align: left;
line-height: 9pt;
}
.example b {
color: #1e4487;
}
#validator-output-info
{
margin-top: 2em;
border: 1px solid #ccc;
width: 740px;
text-align: left;
}
#validator-output-info p
{
margin: 1px 0px 1px 0px;
}
</style>
<center>
<div id='validator-output-info'>
<p><b>File</b>: null</p>
<p><b>Options</b>:
<ol>
<li>Units consistency checking: on</li>
<li>Identifier consistency checking: on</li>
<li>MathML consistency checking: on</li>
<li>SBO consistency checking: on</li>
<li>Overdetermined model checking: on</li>
<li>Modeling practices checking: on</li>
<li>Overall SBML consistency checking: on</li>
<li>Remove unrecognized packages: on</li>
</ol>
</p>
</div>
</center>
<h1> Results: </h1>
<h2 xmlns="http://www.w3.org/1999/xhtml" class="invalid">No model was given, or it could not be resolved.</h2>
2019-01-29 10:42:34,261 INFO o.s.j.v.SBMLValidator [main] There is probably an issue with the sbml.org validator API, please contact the SBML team on [sbml-team at googlegroups.com].
2019-01-29 10:42:48,320 ERROR o.s.j.v.SBMLValidator [main] There has been an error parsing the consistency check XML result.
2019-01-29 10:42:48,321 INFO o.s.j.v.SBMLValidator [main] Below is the String returned by the sbml.org validator REST API:
<style type='text/css'>
body {
font-family: Verdana, sans-serif;
font-size: 9pt;
line-height: 140%;
color: #444;
}
small { font-size: 75%; }
h1 { font-size: 140%; font-weight: bold; margin-bottom: 0; padding-top: 5pt; padding-bottom: 5pt;}
h2 { font-size: 120%; font-weight: bold; padding-top: 5pt; }
h3 { font-size: 100%; font-weight: bold; font-style: italic; line-height: 12pt; }
h3 { font-size: 100%; font-weight: bold; font-style: italic; line-height: 11pt; }
big { font-size: 120%; font-weight: bold; }
pre { font-size: 100%; }
b, h1, h2, h3, h4, strong { color: #595959; }
.small-font {
font-size: 8pt;
line-height: 120%;
}
a {
font-weight: bold;
color: #1e4487;
text-decoration: none;
}
a:visited {
color: #7790ba;
}
a:hover {
text-decoration: underline;
color: #000;
}
a.printable {
text-decoration: underline;
}
h1
{
margin-bottom: 0.5ex;
}
h3
{
text-align: center;
font-size: small;
margin-top: 2px;
margin-bottom: 1.5em;
}
#input-table {
padding-top: 1em;
width: 90%;
text-align: left;
}
#menu
{
font-size: 8pt;
border-bottom: 1px solid #ccc;
margin: 0;
padding-bottom: 19px;
padding-left: 10px;
margin-bottom: 10px;
}
#menu ul, #menu li
{
display: inline;
list-style-type: none;
margin: 0;
padding: 0;
}
#menu a:link, #menu a:visited
{
background: #e8ebf0;
border: 1px solid #cccccc;
color: #666666;
float: left;
font-weight: normal;
line-height: 14px;
margin-right: 8px;
padding: 2px 10px 2px 10px;
text-decoration: none;
}
#menu a:hover
{
color: red;
}
#menu li#selected a
{
background: white;
font-weight: bold;
border-bottom: 1px solid white;
color: black;
}
.example
{
font-size: 7pt;
color: gray;
}
h2.banner
{
background: #ffc;
border: 1px solid #ccc;
margin-top: 0em;
padding: .5em;
}
h2.valid, h2.invalid, h2.valid-warning
{
text-align: center;
margin: 0;
font-size-adjust: .53;
font-style: normal;
text-decoration: none;
word-spacing: normal;
letter-spacing: normal;
text-transform: none;
padding-top: .5em;
padding-bottom: .5em;
}