visualization : Two ravens url cant open the file.

Shiva Shankar

unread,

Jan 23, 2017, 1:24:27 PM1/23/17

to Dataverse Users Community

when I click on the explore button ,the two ravens window says an error.

Leonid Andreev

unread,

Jan 23, 2017, 5:09:20 PM1/23/17

to Dataverse Users Community

Hi,

I just looked at the discussion of this on IRC.
It appears that you set your tworavens url to this:

curl -X PUT -d http://drtc1.isibang.ac.in http://localhost/api/admin/settings/:TwoRavensUrl

- but "http://drtc1.isibang.ac.in" is not your tworavens url; it's your main dataverse url. So that's why the explore button is sending you back to the dataverse page...
As Don said, your tworavens url is http://drtc1.isibang.ac.in/dataexplore/gui.html.

So the proper setting command would be the one Don suggested:

curl -X PUT -d http://drtc1.isibang.ac.in/dataexplore/gui.html http://localhost:8080/admin/settings/:TwoRavensUrl

Shiva Shankar

unread,

Jan 23, 2017, 5:21:51 PM1/23/17

to Dataverse Users Community

I run as u suggested and the link explore button is redirecting [ http://drtc1.isibang.ac.in/dataset.xhtml?persistentId=doi:10.5072/FK2/5CKITW# ]

Shiva Shankar

unread,

Jan 23, 2017, 5:23:48 PM1/23/17

to Dataverse Users Community

[root@dv dataexplore]# curl -X PUT -d http://drtc1.isibang.ac.in/dataexplore/gui.html http://localhost:8080/admin/settings/:TwoRavensUrl

<?xml version='1.0' encoding='UTF-8' ?>

<!DOCTYPE html>

<title>403 Not Authorized - DRTC Dataverse</title>

//<![CDATA[

if(window.PrimeFaces){}

//]]>

</script>

//<![CDATA[

// Break out of iframe

if (window !== top) top.location = window.location;

//]]>

</script></head><body>

<a href="#content" class="sr-only">Skip to main content</a>

<nav role="navigation" id="navbarFixed" class="navbar navbar-default navbar-fixed-top">

<span class="sr-only">Toggle navigation</span>

</button>

<span class="navbar-brand"><i id="icon-dataverse" class="icon-dataverse"></i> Dataverse</span>

</a>

</div>

<li>

</a>

</li>

<label class="sr-only" for="navbarsearch">Search</label>

</div>

<span class="glyphicon glyphicon-search"></span> Find

</button>

</form>

About

</a>

</li>

Guides <b class="caret"></b>

</span>

User Guide

</a>

</li>

<li><a href="http://guides.dataverse.org/en/latest/developers" target="_blank">Developer Guide</a>

</li>

<li><a href="http://guides.dataverse.org/en/latest/installation" target="_blank">Installation Guide</a>

</li>

<li><a href="http://guides.dataverse.org/en/4.5.1/api" target="_blank">API Guide</a>

</li>

</ul>

</li>

<a id="j_idt38:j_idt39" href="#" class="ui-commandlink ui-widget" onclick="PrimeFaces.ab({s:"j_idt38:j_idt39",u:"contactDialog",onco:function(xhr,status,args){PF('contactForm').show();}});return false;">Support</a><input type="hidden" name="javax.faces.ViewState" id="j_id1:javax.faces.ViewState:0" value="7830019526540638133:-2718459585008793885" autocomplete="off" />

</form>

Sign Up

</a>

</li>

Log In

</a>

</li>

</ul>

</div>

</div></nav>

<div id="messagePanel">

</div></div>

</div>

<strong>Not Authorized</strong> - You are not authorized to view this page. If you believe this is an error, please contact <a id="j_idt152:j_idt156" href="#" class="ui-commandlink ui-widget" onclick="PrimeFaces.ab({s:"j_idt152:j_idt156",u:"contactDialog",onco:function(xhr,status,args){PF('contactForm').show();}});return false;">Dataverse Support</a> for assistance.<input type="hidden" name="javax.faces.ViewState" id="j_id1:javax.faces.ViewState:0" value="7830019526540638133:-2718459585008793885" autocomplete="off" />

</form>

</div>

<p>Developed at the <a href="http://www.iq.harvard.edu/" title="Institute for Quantitative Social Science" target="_blank">Institute for Quantitative Social Science</a> | Dataverse Project on <a href="https://twitter.com/dataverseorg" target="_blank" title="Dataverse Project on Twitter"><span class="socicon socicon-twitter" title="Dataverse Project on Twitter"></span></a> | Code available at <a href="https://github.com/IQSS/dataverse" target="_blank" title="Dataverse On GitHub"><span class="socicon socicon-github" title="Dataverse On GitHub"></span></a>

</p>

</p></div>

<span>Powered by</span>

<a href="http://dataverse.org/" title="The Dataverse Project" target="_blank"><img src="/resources/images/dataverseproject_logo.jpg" alt="The Dataverse Project" /></a><span class="version">v. 4.5.1 build 49-7e5e8c9</span>

</div>

</div><div id="ajaxStatusPanel"><div id="ajaxStatusPanel_start" style="display:none"><img src="/resources/images/ajax-loading.gif;jsessionid=d6731f47c5dd7824589c0b0cc124" alt="Loading" /></div><div id="ajaxStatusPanel_complete" style="display:none">

</div></div><script id="ajaxStatusPanel_s" type="text/javascript">

//<![CDATA[

$(function(){PrimeFaces.cw("AjaxStatus","widget_ajaxStatusPanel",{id:"ajaxStatusPanel"});});

//]]>

</script>

<div id="contactDialog" class="ui-dialog ui-widget ui-widget-content ui-corner-all ui-shadow ui-hidden-container"><div class="ui-dialog-titlebar ui-widget-header ui-helper-clearfix ui-corner-top"><span id="contactDialog_title" class="ui-dialog-title">Contact Dataverse Support</span><a href="#" class="ui-dialog-titlebar-icon ui-dialog-titlebar-close ui-corner-all"><span class="ui-icon ui-icon-closethick"></span></a></div><div class="ui-dialog-content ui-widget-content"><div id="j_idt185">

<p id="messageTo" class="form-control-static">Dataverse Support</p>

</div>

//<![CDATA[

PrimeFaces.cw("InputText","widget_emailForm_userEmail",{id:"emailForm:userEmail"});

//]]>

</script>

</div>

<label for="messageSubject" class="col-sm-3 control-label">Subject <span class="glyphicon glyphicon-asterisk text-danger" title="Required field"></span></label>

//<![CDATA[

PrimeFaces.cw("InputText","widget_emailForm_messageSubject",{id:"emailForm:messageSubject"});

//]]>

</script>

</div>

<label for="userMessage" class="col-sm-3 control-label">Message <span class="glyphicon glyphicon-asterisk text-danger" title="Required field"></span></label>

//<![CDATA[

$(function(){PrimeFaces.cw("InputTextarea","widget_emailForm_userMessage",{id:"emailForm:userMessage",autoResize:false});});

//]]>

</script>

</div>

<p><span class="highlightBold">Please fill this out to prove you are not a robot.</span> <span class="glyphicon glyphicon-asterisk text-danger" title="Required field"></span>

</p> + = <input id="emailForm:messageSum" name="emailForm:messageSum" type="text" size="4" class="ui-inputfield ui-inputtext ui-widget ui-state-default ui-corner-all" /><script id="emailForm:messageSum_s" type="text/javascript">

//<![CDATA[

PrimeFaces.cw("InputText","widget_emailForm_messageSum",{id:"emailForm:messageSum"});

//]]>

</script>

</div>

<div class="button-block"><a id="emailForm:j_idt203" href="#" class="ui-commandlink ui-widget btn btn-default" onclick="PrimeFaces.ab({s:"emailForm:j_idt203",u:"emailForm",onco:function(xhr,status,args){if (args && !args.validationFailed) PF('contactForm').hide();;},pa:[{name:"DO_VALIDATION",value:"true"}],fi:"j_idt185"});return false;">Send Message</a>

Cancel

</button>

</div><input type="hidden" name="javax.faces.ViewState" id="j_id1:javax.faces.ViewState:0" value="7830019526540638133:-2718459585008793885" autocomplete="off" />

</form></div></div></div><script id="contactDialog_s" type="text/javascript">

//<![CDATA[

$(function(){PrimeFaces.cw("Dialog","contactForm",{id:"contactDialog",modal:true});});

//]]>

</script><div id="statusInfo" class="ui-dialog ui-widget ui-widget-content ui-corner-all ui-shadow ui-hidden-container"><div class="ui-dialog-titlebar ui-widget-header ui-helper-clearfix ui-corner-top"><span id="statusInfo_title" class="ui-dialog-title"></span><a href="#" class="ui-dialog-titlebar-icon ui-dialog-titlebar-close ui-corner-all"><span class="ui-icon ui-icon-closethick"></span></a></div><div class="ui-dialog-content ui-widget-content">

<p></p>

Close

</button>

</div></div></div><script id="statusInfo_s" type="text/javascript">

//<![CDATA[

$(function(){PrimeFaces.cw("Dialog","statusInfo",{id:"statusInfo",modal:true});});

//]]>

</script>

//<![CDATA[

$(document).ready(function () {

// Navbar Search Toggle

$(document).on('click', '#navbar-search-toggle', function (e) {

$(this).parent("li").hide();

$("form.navbar-form[role='search']").show();

});

$('body').click(function (e) {

if (!$(e.target).closest("form.navbar-form[role='search']").length) {

$("form.navbar-form[role='search']").hide();

$("#navbar-search-toggle").parent("li").show();

}

;

});

// Rebind bootstrap UI components

bind_bsui_components();

});

/*

* Custom Popover with HTML code snippet

*/

function popoverHTML() {

var popoverTemplateHTML = ['<div class="popover">',

'<div class="arrow"></div>',

'<h3 class="popover-title"></h3>',

'<div class="popover-content">',

'</div>',

'</div>'].join('');

var popoverContentHTML = ['<code>',

'<a>, <b>, <blockquote>, <br>, <code>, <del>, <dd>, <dl>, <dt>, <em>, <hr>, <h1>-<h3>, <i>, <img>, <kbd>, <li>, <ol>, <p>, <pre>, <s>, <sup>, <sub>, <strong>, <strike>, <ul>',

'</code>'].join('');

$('body').popover({

selector: 'span.popoverHTML',

title: 'Allowed HTML Tags',

trigger: 'hover',

content: popoverContentHTML,

template: popoverTemplateHTML,

placement: "bottom",

container: "#content",

html: true

});

}

//]]>

</script>

//<![CDATA[

//]]>

</script></body>

</html>

Shiva Shankar

unread,

Jan 23, 2017, 5:35:57 PM1/23/17

to Dataverse Users Community

and the page it is opening is http://drtc1.isibang.ac.in/?dfId=49&key=7aa3cc6b-a621-42cd-8571-3c295416b870

Leonid Andreev

unread,

Jan 23, 2017, 6:10:40 PM1/23/17

to Dataverse Users Community

It looks like you are missing the "/api" part in the "/api/admin/settings/:TwoRavensUrl :

# curl -X PUT -d http://drtc1.isibang.ac.in/dataexplore/gui.html http://localhost:8080/admin/settings/:TwoRavensUrl

Leonid Andreev

unread,

Jan 23, 2017, 6:12:20 PM1/23/17

to Dataverse Users Community

(looks like it was missing in the url that I sent you; sorry - I just copy and pasted it from the IRC discussion)

Leonid Andreev

unread,

Jan 23, 2017, 6:14:56 PM1/23/17

to Dataverse Users Community

I'm assuming that this page is opening because the :TwoRavensUrl is still set to your main dataverse url.
So please reset it to the proper .../dataexplore/gui.html location; if you are still getting any error messages after that, please send them to us.

-Leonid

Shiva Shankar

unread,

Jan 23, 2017, 6:19:09 PM1/23/17

to Dataverse Users Community

Hey thank you ..its looks like working... :)

danny...@g.harvard.edu

unread,

Jan 23, 2017, 6:30:48 PM1/23/17

to Dataverse Users Community

Awesome! Thanks Leonid!

Shiva Shankar

unread,

Jan 23, 2017, 6:39:31 PM1/23/17

to Dataverse Users Community

Two ravens window is opening. The new problem is the file[.tab] variables are not appearing for visualisation..

Leonid Andreev

unread,

Jan 23, 2017, 6:58:29 PM1/23/17

to Dataverse Users Community

What about that "file not found" message, are you still seeing it in the logs?

Also, please send us the top portion (the first 60 lines) of your .../dataexplore/app_ddi.js file.
We'll figure it all out tomorrow.

Shiva Shankar

unread,

Jan 24, 2017, 1:30:52 AM1/24/17

to Dataverse Users Community

file ...../dataexplore/app_ddi.js

var production=true;

var private=false;

if(production && fileid=="") {

alert("Error: No fileid has been provided.");

throw new Error("Error: No fileid has been provided.");

}

var dataverseurl="";

if (hostname) {

dataverseurl="https://"+hostname;

} else {

if (production) {

dataverseurl="http://192.168.0.155:80";

} else {

dataverseurl="http://localhost:80";

}

if (fileid && !dataurl) {

// file id supplied; we are going to assume that we are dealing with

// a dataverse and cook a standard dataverse data access url,

// with the fileid supplied and the hostname we have

// either supplied or configured:

dataurl = dataverseurl+"/api/access/datafile/"+fileid;

dataurl = dataurl+"?key="+apikey;

// (it is also possible to supply dataurl to the script directly,

// as an argument -- L.A.)

}

if (!production) {

// base URL for the R apps:

var rappURL = "http://0.0.0.0:8000/custom/";

} else {

var rappURL = "https://beta.dataverse.org/custom/"; //this will change when/if the production host changes

}

// space index

var myspace = 0;

var svg = d3.select("#main.left div.carousel-inner").attr('id', 'innercarousel')

.append('div').attr('class', 'item active').attr('id', 'm0').append('svg').attr('id', 'whitespace');

var logArray = [];

//.attr('width', width)

//.attr('height', height);

var tempWidth = d3.select("#main.left").style("width")

var width = tempWidth.substring(0,(tempWidth.length-2));

/*var tempHeight = d3.select("#main.left").style("height")

var height = tempHeight.substring(0,(tempHeight.length-2));*/

var height = $(window).height() -120; // Hard coding for header and footer and bottom margin.

var forcetoggle=["true"];

var estimated=false;

var estimateLadda = Ladda.create(document.getElementById("btnEstimate"));

var selectLadda = Ladda.create(document.getElementById("btnSelect"));

var rightClickLast = false;

var colorTime=false;

var timeColor = '#2d6ca2';

var colorCS=false;

var csColor = '#419641';

var depVar=false;

var dvColor = '#28a4c9';

var nomColor = '#ff6600';

var subsetdiv=false;

var setxdiv=false;

var varColor = '#f0f8ff'; //d3.rgb("aliceblue");

var selVarColor = '#fa8072'; //d3.rgb("salmon");

var taggedColor = '#f5f5f5'; //d3.rgb("whitesmoke");

var d3Color = '#1f77b4'; // d3's default blue

var grayColor = '#c0c0c0';

var lefttab = "tab1"; //global for current tab in left panel

var righttab = "btnModels"; // global for current tab in right panel

var zparams = { zdata:[], zedges:[], ztime:[], znom:[], zcross:[], zmodel:"", zvars:[], zdv:[], zdataurl:"", zsubset:[], zsetx:[], zmodelcount:0, zplot:[], zsessionid:"", zdatacite:""};

// Radius of circle

var allR = 40;

//Width and height for histgrams

var barwidth = 1.3*allR;

var barheight = 0.5*allR;

Shiva Shankar

unread,

Jan 24, 2017, 1:34:57 AM1/24/17

to Dataverse Users Community

when I am clicking the explore button...the new tab of two ravens looks blank.. (screen shot below) :

Shiva Shankar

unread,

Jan 24, 2017, 1:13:26 PM1/24/17

to Dataverse Users Community

There was no "file not found" message .

Leonid Andreev

unread,

Jan 24, 2017, 4:20:05 PM1/24/17

to Dataverse Users Community

Hello,

I am seeing multiple problems with your TwoRavens installation.

First of all, this line in your app_ddi.js file:

var rappURL = "https://beta.dataverse.org/custom/";

needs to be changed to

var rappURL = "http://drtc1.isibang.ac.in/custom/";

(or "http://192.168.0.155/custom", similarly to how your dataverseurl is configured?)

This may be due to a problem with our installer script; we'll investigate.
But this is the least of your problems really.
I don't think the R and RApache components are installed on your system properly.

is Rserve currently running?
Has RApache been installed?

If I try to download one of your tabular files, like this:

http://drtc1.isibang.ac.in/api/access/datafile/23

- this works.
However, if I try to download the pre-processed statistics fragment for this file:

http://drtc1.isibang.ac.in/api/access/datafile/23?format=prep

- this gives me a 500 error. This likely means that either Rserve isn't running, or the R libraries that it needs haven't been installed.
TwoRavens needs this in order to initialize itself.

Another thing, if I attempt to access one of the R apps that should be running on your system under rApache, for example:

http://drtc1.isibang.ac.in/custom/zeligapp

- I get a "file not found".
This most likely means that the rApache installation didn't succeed on this system.

Message has been deleted

Shiva Shankar

unread,

Jan 25, 2017, 12:48:16 PM1/25/17

to Dataverse Users Community

I have followed all the steps given in the installation guides...Is there any other way through which I can solve my problem. plz help..

On Monday, January 23, 2017 at 11:54:27 PM UTC+5:30, Shiva Shankar wrote:

Leonid Andreev

unread,

Jan 26, 2017, 4:56:45 PM1/26/17

to Dataverse Users Community

We'll have to work with you testing and diagnosing each of the R and rApache components.
We'll figure it out eventually. But this is fairly time consuming; and I may not have time to look into this seriously until next week.

But let's start with Rserve.
Please check if it's running; by something like

ps awux | grep -i rserve

If it is running, you'll see something like

rserve 7889 0.0 0.0 277612 292 ? SNs 2016 7:26 /usr/lib64/R/bin/Rserve

if it's NOT running, please try to start it (as root):

service rserve start

If you see any errors at this point, please let us know.
If it starts, please test this url again:

http://drtc1.isibang.ac.in/api/access/datafile/23?format=prep

- and see if you get any output.

Also, we will likely need your Apache log files to investigate this.
The files are /var/log/error_log and /var/log/ssl_error_log (if present).
You can either attach the files here or email them to me directly.

Shiva Shankar

unread,

Jan 30, 2017, 2:49:47 PM1/30/17

to Dataverse Users Community

Thanx Andreev ..thank you very much. As it is becoming difficult for me to start two ravens. I followed the steps and these are the outputs :--

[root@dv ~]# ps awux|grep -i rserve

root 2677 0.6 11.0 5363080 1328264 ? Sl Jan24 29:24 /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.111-1.b15.el7_2.x86_64/bin/java -cp /usr/local/glassfish4/glassfish/modules/glassfish.jar -XX:+UnlockDiagnosticVMOptions -XX:NewRatio=2 -XX:MaxPermSize=512m -XX:PermSize=256m -Xmx1394m -javaagent:/usr/local/glassfish4/glassfish/lib/monitor/flashlight-agent.jar -Djavax.xml.accessExternalSchema=all -Djavax.net.ssl.trustStore=/usr/local/glassfish4/glassfish/domains/domain1/config/cacerts.jks -Ddataverse.timerServer=true -Djdk.corba.allowOutputStreamSubclass=true -Dfelix.fileinstall.dir=/usr/local/glassfish4/glassfish/modules/autostart/ -Djavax.xml.parsers.SAXParserFactory=com.sun.org.apache.xerces.internal.jaxp.SAXParserFactoryImpl -Ddoi.password=apitest -Dorg.glassfish.additionalOSGiBundlesToStart=org.apache.felix.shell,org.apache.felix.gogo.runtime,org.apache.felix.gogo.shell,org.apache.felix.gogo.command,org.apache.felix.shell.remote,org.apache.felix.fileinstall -Dcom.sun.aas.installRoot=/usr/local/glassfish4/glassfish -Dfelix.fileinstall.poll=5000 -Djava.endorsed.dirs=/usr/local/glassfish4/glassfish/modules/endorsed:/usr/local/glassfish4/glassfish/lib/endorsed -Djava.security.policy=/usr/local/glassfish4/glassfish/domains/domain1/config/server.policy -Ddataverse.rserve.host=localhost -Dosgi.shell.telnet.maxconn=1 -Dfelix.fileinstall.bundles.startTransient=true -Dcom.sun.enterprise.config.config_environment_factory_class=com.sun.enterprise.config.serverbeans.AppserverConfigEnvironmentFactory -Dfelix.fileinstall.log.level=2 -Ddataverse.fqdn=192.168.0.155 -Ddataverse.auth.password-reset-timeout-in-minutes=60 -Ddataverse.rserve.password=rserve -Djavax.net.ssl.keyStore=/usr/local/glassfish4/glassfish/domains/domain1/config/keystore.jks -Djava.security.auth.login.config=/usr/local/glassfish4/glassfish/domains/domain1/config/login.conf -Dfelix.fileinstall.disableConfigSave=false -Ddoi.username=apitest -Ddataverse.rserve.port=6311 -Dfelix.fileinstall.bundles.new.start=true -Dcom.sun.aas.instanceRoot=/usr/local/glassfish4/glassfish/domains/domain1 -Dosgi.shell.telnet.port=6666 -Dgosh.args=--nointeractive -Dcom.sun.enterprise.security.httpsOutboundKeyAlias=s1as -Dosgi.shell.telnet.ip=127.0.0.1 -Ddataverse.files.directory=/usr/local/glassfish4/glassfish/domains/domain1/files -Ddataverse.rserve.user=rserve -DANTLR_USE_DIRECT_CLASS_LOADING=true -Djava.awt.headless=true -Dcom.ctc.wstx.returnNullForDefaultNamespace=true -Djava.ext.dirs=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.111-1.b15.el7_2.x86_64/lib/ext:/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.111-1.b15.el7_2.x86_64/jre/lib/ext:/usr/local/glassfish4/glassfish/domains/domain1/lib/ext -Ddoi.baseurlstring=https://ezid.cdlib.org -Djdbc.drivers=org.apache.derby.jdbc.ClientDriver -Djava.library.path=/usr/local/glassfish4/glassfish/lib:/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib com.sun.enterprise.glassfish.bootstrap.ASMain -upgrade false -domaindir /usr/local/glassfish4/glassfish/domains/domain1 -read-stdin true -asadmin-args --host,,,localhost,,,--port,,,4848,,,--secure=false,,,--terse=false,,,--echo=false,,,--interactive=false,,,start-domain,,,--verbose=false,,,--watchdog=false,,,--debug=false,,,--domaindir,,,/usr/local/glassfish4/glassfish/domains,,,domain1 -domainname domain1 -instancename server -type DAS -verbose false -asadmin-classpath /usr/local/glassfish4/glassfish/lib/client/appserver-cli.jar -debug false -asadmin-classname com.sun.enterprise.admin.cli.AdminMain

root 19570 0.0 0.0 112652 980 pts/0 R+ 10:32 0:00 grep --color=auto -i rserve

[root@dv ~]# service rserve start

Starting rserve (via systemctl): [ OK ]

error_log file is in /var/log/httpd/error_log instead of /var/log/error_log and the ssl_error_log not present........and the output is :----------

[Sun Jan 29 03:37:07.324894 2017] [auth_digest:notice] [pid 22519] AH01757: generating secret for digest authentication ...

[Sun Jan 29 03:37:07.325380 2017] [lbmethod_heartbeat:notice] [pid 22519] AH02282: No slotmem from mod_heartmonitor

[Sun Jan 29 03:37:07.325422 2017] [mpm_prefork:notice] [pid 22519] AH00163: Apache/2.4.6 (CentOS) mod_R/1.2.7 R/3.3.0 mod_apreq2-20090110/2.8.0 configured -- resuming normal operations

[Sun Jan 29 03:37:07.325426 2017] [core:notice] [pid 22519] AH00094: Command line: '/usr/sbin/httpd -D FOREGROUND'

[1] "system time at source: "

[1] "2017-01-29 03:37:07 IST"

[1] "system time at source: "

[1] "2017-01-29 03:37:07 IST"

[1] "system time at source: "

[1] "2017-01-29 03:37:07 IST"

[1] "system time at source: "

[1] "2017-01-29 03:37:07 IST"

Attaching package: 'jsonlite'

The following objects are masked from 'package:rjson':

fromJSON, toJSON

Attaching package: 'jsonlite'

The following objects are masked from 'package:rjson':

fromJSON, toJSON

Attaching package: 'jsonlite'

The following objects are masked from 'package:rjson':

fromJSON, toJSON

Attaching package: 'jsonlite'

The following objects are masked from 'package:rjson':

fromJSON, toJSON

Attaching package: 'jsonlite'

The following objects are masked from 'package:rjson':

fromJSON, toJSON

Attaching package: 'Zelig'

The following objects are masked from 'package:DescTools':

Median, Mode

The following object is masked from 'package:base':

mode

Loading required package: stats4

Loading required package: splines

Attaching package: 'Zelig'

The following objects are masked from 'package:DescTools':

Median, Mode

The following object is masked from 'package:base':

mode

Loading required package: stats4

Loading required package: splines

Attaching package: 'Zelig'

The following objects are masked from 'package:DescTools':

Median, Mode

The following object is masked from 'package:base':

mode

Loading required package: stats4

Attaching package: 'Zelig'

The following objects are masked from 'package:DescTools':

Median, Mode

The following object is masked from 'package:base':

mode

Loading required package: splines

Loading required package: stats4

Loading required package: splines

Attaching package: 'Zelig'

The following objects are masked from 'package:DescTools':

Median, Mode

The following object is masked from 'package:base':

mode

Loading required package: stats4

he following object is masked from 'package:base':

mode

Loading required package: stats4

Loading required package: splines

[1] "system time at source: "

[1] "2017-01-30 15:51:47 IST"

Attaching package: 'jsonlite'

The following objects are masked from 'package:rjson':

fromJSON, toJSON

[1] "system time at source: "

[1] "2017-01-30 15:51:48 IST"

Attaching package: 'jsonlite'

The following objects are masked from 'package:rjson':

Attaching package: 'Zelig'

The following objects are masked from 'package:DescTools':

Median, Mode

The following object is masked from 'package:base':

mode

Loading required package: stats4

Loading required package: splines

Attaching package: 'Zelig'

The following objects are masked from 'package:DescTools':

Median, Mode

The following object is masked from 'package:base':

mode

thanx..

Shiva Shankar

unread,

Jan 30, 2017, 2:51:51 PM1/30/17

to Dataverse Users Community

and when I click http://drtc1.isibang.ac.in/api/access/datafile/23?format=prep Internal Server Error - An unexpected error was encountered, no more information is available.

errors come.

On Friday, January 27, 2017 at 3:26:45 AM UTC+5:30, Leonid Andreev wrote:

Leonid Andreev

unread,

Jan 31, 2017, 7:33:38 PM1/31/17

to Dataverse Users Community

After you started rserve, could you check again, if it's actually running:

ps awux | grep Rserv

If it's running, please check if it's accepting network connections on port 6311:

telnet localhost 6311

And also, try to access http://drtc1.isibang.ac.in/api/access/datafile/23?format=prep again. It will fail again with the "internal server error", but please see if any errors appear in the Glassfish server log file: /usr/local/glassfish4/glassfish/domains/domain1/logs/server.log

Shiva Shankar

unread,

Feb 2, 2017, 3:34:59 AM2/2/17

to Dataverse Users Community

sir,here is what I get...

[root@dv ~]# ps awux|grep Rserv

root 12417 0.0 0.0 112648 964 pts/4 S+ 14:01 0:00 grep --color=auto Rserv

root 26283 0.0 0.2 292264 28108 ? Ss 00:33 0:03 /usr/lib64/R/bin/Rserve

[root@dv ~]# telnet localhost 6311

Trying ::1...

telnet: connect to address ::1: Connection refused

Trying 127.0.0.1...

Connected to localhost.

Escape character is '^]'.

Rsrv0103QAP1

--------------

$vi /usr/local/glassfish4/glassfish/domains/domain1/logs/server.log

[2017-02-02T13:56:43.274+0530] [glassfish 4.1] [WARNING] [] [javax.enterprise.ejb.container] [tid: _ThreadID=138 _ThreadName=__ejb-thread-pool14] [timeMillis: 1486024003274] [levelValue: 900] [[

javax.ejb.EJBTransactionRolledbackException

at com.sun.ejb.containers.BaseContainer.mapLocal3xException(BaseContainer.java:2342)

at com.sun.ejb.containers.BaseContainer.postInvoke(BaseContainer.java:2123)

at com.sun.ejb.containers.BaseContainer.postInvoke(BaseContainer.java:2044)

at com.sun.ejb.containers.EJBLocalObjectInvocationHandler.invoke(EJBLocalObjectInvocationHandler.java:220)

at com.sun.ejb.containers.EJBLocalObjectInvocationHandlerDelegate.invoke(EJBLocalObjectInvocationHandlerDelegate.java:88)

at com.sun.proxy.$Proxy207.processOAIDCxml(Unknown Source)

at edu.harvard.iq.dataverse.api.imports.__EJB31_Generated__ImportGenericServiceBean__Intf____Bean__.processOAIDCxml(Unknown Source)

at edu.harvard.iq.dataverse.api.imports.ImportServiceBean.doImportHarvestedDataset(ImportServiceBean.java:240)

at sun.reflect.GeneratedMethodAccessor846.invoke(Unknown Source)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

at java.lang.reflect.Method.invoke(Method.java:498)

at org.glassfish.ejb.security.application.EJBSecurityManager.runMethod(EJBSecurityManager.java:1081)

at org.glassfish.ejb.security.application.EJBSecurityManager.invoke(EJBSecurityManager.java:1153)

at com.sun.ejb.containers.BaseContainer.invokeBeanMethod(BaseContainer.java:4786)

at com.sun.ejb.EjbInvocation.invokeBeanMethod(EjbInvocation.java:656)

at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)

at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:608)

at org.jboss.weld.ejb.AbstractEJBRequestScopeActivationInterceptor.aroundInvoke(AbstractEJBRequestScopeActivationInterceptor.java:64)

at org.jboss.weld.ejb.SessionBeanInterceptor.aroundInvoke(SessionBeanInterceptor.java:52)

at sun.reflect.GeneratedMethodAccessor96.invoke(Unknown Source)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

at java.lang.reflect.Method.invoke(Method.java:498)

at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:883)

at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)

Caused by: javax.ejb.TransactionRolledbackLocalException: Exception thrown from bean

at com.sun.ejb.containers.EJBContainerTransactionManager.checkExceptionClientTx(EJBContainerTransactionManager.java:662)

at com.sun.ejb.containers.EJBContainerTransactionManager.postInvokeTx(EJBContainerTransactionManager.java:507)

at com.sun.ejb.containers.BaseContainer.postInvokeTx(BaseContainer.java:4566)

at com.sun.ejb.containers.BaseContainer.postInvoke(BaseContainer.java:2074)

... 74 more

Caused by: javax.ejb.EJBException: Failed to find a global identifier in the OAI_DC XML record.

at edu.harvard.iq.dataverse.api.imports.ImportGenericServiceBean.processOAIDCxml(ImportGenericServiceBean.java:228)

at sun.reflect.GeneratedMethodAccessor847.invoke(Unknown Source)