[dspace-tech] DSpace 5.5 issues - some pages not working

2017-10-06 Thread Paul Huddleston 


I have a DSpace 5.5 server

 

Running Windows 2012 R2

Tomcat 8

Apache 2.4

XMLUI – Mirage 2

Postgre SQL

 

 

I am running into quite a few problems with the stability of the server.  I 
did not build the server, but a colleague of mine and I somewhat inherited 
it in its current location.  She was able to customize it, but it has never 
been very reliable.  Windows never shows erorrs in the logs … all of the 
issues seem to be with either Tomcat or Apache, etc.  It will run fine some 
of the time, then it will give a ‘page cannot be displayed’ in the content 
pane of the main DSpace page … the header and sidebar will continue to show 
properly.  If I click ‘about the repository’, it will show that static 
page.  Many of the items that list research communities or colleges and 
talk to the database will also not work and show a page cannot be displayed 
error, as well.

 

Apache is used as a passthrough, so we can use a shibboleth login mechanism 
so that people can login with campus accounts.

 

If I go the port 8080 on the server, it will serve the page via tomcat and 
it works properly.  When I use port 80, I have the issues I mentioned above.

 

Stack Trace of that page:

*Java stacktrace: *org.apache.cocoon.ResourceNotFoundException: Page cannot 
be found

at 
org.dspace.app.xmlui.aspect.general.PageNotFoundTransformer.addBody(PageNotFoundTransformer.java:170)

at 
org.dspace.app.xmlui.wing.AbstractWingTransformer.startElement(AbstractWingTransformer.java:223)

at 
org.dspace.app.xmlui.aspect.general.PageNotFoundTransformer.sendEvent(PageNotFoundTransformer.java:243)

at 
org.dspace.app.xmlui.aspect.general.PageNotFoundTransformer.endElement(PageNotFoundTransformer.java:147)

at sun.reflect.GeneratedMethodAccessor113.invoke(Unknown 
Source)

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

at java.lang.reflect.Method.invoke(Method.java:483)

at 
org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)

at com.sun.proxy.$Proxy59.endElement(Unknown Source)

at 
org.apache.cocoon.environment.internal.EnvironmentChanger.endElement(EnvironmentStack.java:147)

at 
org.apache.cocoon.environment.internal.EnvironmentChanger.endElement(EnvironmentStack.java:147)

at 
org.apache.cocoon.environment.internal.EnvironmentChanger.endElement(EnvironmentStack.java:147)

at 
org.apache.cocoon.environment.internal.EnvironmentChanger.endElement(EnvironmentStack.java:147)

at 
org.apache.cocoon.xml.AbstractXMLPipe.endElement(AbstractXMLPipe.java:111)

at 
org.dspace.app.xmlui.wing.AbstractWingTransformer.endElement(AbstractWingTransformer.java:283)

at sun.reflect.GeneratedMethodAccessor113.invoke(Unknown 
Source)

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

at java.lang.reflect.Method.invoke(Method.java:483)

at 
org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)

at com.sun.proxy.$Proxy59.endElement(Unknown Source)

at 
org.apache.cocoon.components.sax.XMLTeePipe.endElement(XMLTeePipe.java:93)

at 
org.apache.cocoon.environment.internal.EnvironmentChanger.endElement(EnvironmentStack.java:147)

at 
org.apache.cocoon.components.sax.XMLTeePipe.endElement(XMLTeePipe.java:93)

at 
org.apache.cocoon.components.sax.AbstractXMLByteStreamInterpreter.parse(AbstractXMLByteStreamInterpreter.java:120)

at 
org.apache.cocoon.components.sax.XMLByteStreamInterpreter.deserialize(XMLByteStreamInterpreter.java:44)

at 
org.apache.cocoon.components.pipeline.impl.AbstractCachingProcessingPipeline.processXMLPipeline(AbstractCachingProcessingPipeline.java:324)

at 
org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.process(AbstractProcessingPipeline.java:750)

at sun.reflect.GeneratedMethodAccessor159.invoke(Unknown 
Source)

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

at java.lang.reflect.Method.invoke(Method.java:483)

at 
org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)

at com.sun.proxy.$Proxy52.process(Unknown Source)

at 
org.apache.cocoon.components.source.impl.SitemapSource.toSAX(SitemapSource.java:362)

at 
org.apache.cocoon.components.source.util.SourceUtil.toSAX(SourceUtil.java:111)

at 
org.apache.cocoon.components.source.util.SourceUtil.parse(SourceUtil.java:294)

RE: [dspace-tech] RE: submissions time out but still work

2017-10-06 Thread Graham Faulkner 
Hi Tim et al,

A further point of clarification: the PostgreSQL database and Solr index have 
the same number of items. (Used the technique suggested by Tom Desair in 
https://groups.google.com/forum/#!topic/dspace-tech/hF0NTZJpqlU).

So, Solr appears to index everything correctly, but our XMLUI Mirage 2’s 
‘author browse’ function does not work for newly ingested (after 5.8 migration) 
items.

Cheers,

Graham

From: dspace-tech@googlegroups.com [mailto:dspace-tech@googlegroups.com] On 
Behalf Of Graham Faulkner
Sent: October 4, 2017 11:46 AM
To: Tim Donohue ; dspace-tech@googlegroups.com
Subject: RE: [dspace-tech] RE: submissions time out but still work

Hi Tim,

Thanks for the info.  FYI, we are running DSpace 5.8 on Ubuntu 14.04 LTS and 
PostgreSQL. We run Apache and Tomcat7.

I tried to view the logs while my colleague did a deposit through the UI.  The 
/dspace/log/solr.log file didn’t show any errors.

However, I did notice some errors/warnings in our 
/dspace/log/cocoon.log.2017-10-04 during the time frame of the deposit.

2017-10-04 10:39:32,176 WARN  cocoon.access  - 
org.apache.cocoon.ConnectionResetException: Connection reset by peer
   at  - jndi:/localhost/sitemap.xmap:256:68
   at  - 
jndi:/localhost/sitemap.xmap:255:88
   at  - jndi:/localhost/sitemap.xmap:254:70
2017-10-04 10:39:38,951 ERROR cocoon.handled  - Could not read resource 
cocoon://DRI/1/handle/10012/9972/workflow
   at  - 
jndi:/localhost/aspects/aspects.xmap:85:34
   at  - 
jndi:/localhost/aspects/aspects.xmap:84:43
   at  - jndi:/localhost/aspects/aspects.xmap:83:22
   at  - 
jndi:/localhost/themes/Mirage2/sitemap.xmap:198:56
   at  - 
jndi:/localhost/themes/Mirage2/sitemap.xmap:108:54
   at  - 
jndi:/localhost/themes/Mirage2/sitemap.xmap:102:44
   at  - jndi:/localhost/themes/Mirage2/sitemap.xmap:98:49
   at  - 
jndi:/localhost/themes/Mirage2/sitemap.xmap:85:51
   at  - jndi:/localhost/themes/Mirage2/sitemap.xmap:82:54
   at  - 
jndi:/localhost/themes/Mirage2/sitemap.xmap:190:67
   at  - jndi:/localhost/themes/Mirage2/sitemap.xmap:185:37
org.apache.cocoon.ProcessingException: Could not read resource 
cocoon://DRI/1/handle/10012/9972/workflow
   at  - 
jndi:/localhost/aspects/aspects.xmap:85:34
   at  - 
jndi:/localhost/aspects/aspects.xmap:84:43
   at  - jndi:/localhost/aspects/aspects.xmap:83:22
   at  - 
jndi:/localhost/themes/Mirage2/sitemap.xmap:198:56
   at  - 
jndi:/localhost/themes/Mirage2/sitemap.xmap:108:54
   at  - 
jndi:/localhost/themes/Mirage2/sitemap.xmap:102:44
   at  - jndi:/localhost/themes/Mirage2/sitemap.xmap:98:49
   at  - 
jndi:/localhost/themes/Mirage2/sitemap.xmap:85:51
   at  - jndi:/localhost/themes/Mirage2/sitemap.xmap:82:54
   at  - 
jndi:/localhost/themes/Mirage2/sitemap.xmap:190:67
   at  - jndi:/localhost/themes/Mirage2/sitemap.xmap:185:37
   at 
org.apache.cocoon.components.source.util.SourceUtil.handleSAXException(SourceUtil.java:409)
   at 
org.apache.cocoon.generation.FileGenerator.generate(FileGenerator.java:138)
   at sun.reflect.GeneratedMethodAccessor150.invoke(Unknown Source)
   at 
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
   at java.lang.reflect.Method.invoke(Method.java:606)
   at 
org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
   at com.sun.proxy.$Proxy92.generate(Unknown Source)
   at 
org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.processXMLPipeline(AbstractProcessingPipeline.java:544)
   at 
org.apache.cocoon.components.pipeline.impl.AbstractCachingProcessingPipeline.processXMLPipeline(AbstractCachingProcessingPipeline.java:273)
   at 
org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.process(AbstractProcessingPipeline.java:750)
   at sun.reflect.GeneratedMethodAccessor151.invoke(Unknown Source)
   at 
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
   at java.lang.reflect.Method.invoke(Method.java:606)
   at 
org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
   at com.sun.proxy.$Proxy91.process(Unknown Source)
   at 
org.apache.cocoon.components.source.impl.SitemapSource.toSAX(SitemapSource.java:362)
   at 
org.apache.cocoon.components.source.util.SourceUtil.toSAX(SourceUtil.java:111)
   at 
org.apache.cocoon.components.source.util.SourceUtil.parse(SourceUtil.java:294)
   at 
org.apache.cocoon.generation.FileGenerator.generate(FileGenerator.java:136)
   at sun.reflect.GeneratedMethodAccessor150.invoke(Unknown Source)
   at 
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
   at java.lang.reflect.Method.invoke(Method.java:606)
   at

Re: [dspace-tech] DSpace API

2017-10-06 Thread Terry Brady 
Ed,

What admin actions are you hoping to support?

The following repo describes some of the custom administration that we have
developed at Georgetown:
https://github.com/Georgetown-University-Libraries/batch-tools

Terry

On Thu, Oct 5, 2017 at 10:16 AM, Ed Warga  wrote:

> Hello,
>
> I'm beginning to think about using the API for certain management
> activities in my repo. Wondering if anyone has created any scripts to
> leverage the API in DSpace. I'm looking for =some examples to work from as
> I get started. What have you done!? Can you share any scripts or ideas?
>
> Thanks,
> Ed Warga
> Scholarly Communication Librarian
> Texas A University-Corpus Christi
>
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-- 
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Applications Programmer Analyst
Georgetown University Library Information Technology
https://github.com/terrywbrady/info
425-298-5498 (Seattle, WA)

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[dspace-tech] Re: Tomcat Cert Process for Dspace

2017-10-06 Thread Mark H. Wood 
Oh, drat, I forgot that the InCommon certificate wasn't in the OS' cert. 
bundle and I had to go get it from InCommon.  The email which told you 
where to download your certificate should also tell you where to get theirs.

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[dspace-tech] Re: Tomcat Cert Process for Dspace

2017-10-06 Thread Mark H. Wood 
On Friday, October 6, 2017 at 2:39:34 AM UTC-4, Dayne Ellanna wrote:
>
> I am having the worst time getting tomcat to do https for dspace.  I 
> followed the instructions on the dspace site but cannot make heads or tails 
> of the instructions as I am definitely not a certificate expert.  The 
> instructions use generic names and don't explain where root ca's come from 
> or generating certificate requests and from what do I generate these.  Can 
> someone give me very specific instructions about how to set up the https on 
> tomcat to run dspace.  So far I have gotten dspace to run successfully as 
> http://myserver.domain:8080/xmlui.  As per instructions on the dspace 
> site I have tried to create the RSA key, and we use incommon for our certs 
> which I can obtain, but have not been able to figure out the beginning to 
> end process for this.  I tried using curl to test but no success.  I really 
> need a succinct explanation of all the pieces, where to get them or how to 
> generate them in order to run the ssl.  HELP!
>


We also proxy through Apache HTTPD, via AJP, in part because setting up 
certificates for Tomcat is such a pain.

We are also an InCommon member so I can speak to that.  You'll need the 
"InCommon RSA Server CA" intermediate certificate.  On this Gentoo Linux 
system it's in '/etc/ssl/certs/InCommon-RSA-Server-CA.pem' and should be 
similarly named on yours.  It is signed by "USERTrust RSA Certification 
Authority", in USERTrust_RSA_Certification_Authority.crt or something 
similar, which is the root certificate.  You can see the gory details of 
certificates, including the CN (e.g. "InCommon RSA Server CA") with 
'openssl x509 -noout -text -in /path/to/some/certificate.pem'.  (Sorry, I 
only use 'keytool' when I can't avoid it, and don't know by heart the 
options for this operation.)

It's impossible to write specific letter-for-letter instructions for this 
topic that cover all supported platforms, because they disagree as to where 
things like CATALINA_BASE and JAVA_HOME are.  If you'd tell us what OS, 
distribution and version you're using, that would help.  If you did *not* 
use your OS' package manager to install Tomcat, or Java, then it would help 
to tell us where you installed them.  In the meantime, you probably can 
forget about '$JAVA_HOME/bin' and assume that 'keytool' is available just 
like any other command.  If you search your system for 'server.xml' that 
should help you locate '$CATALINA_BASE/conf'.

I recommend inventing some keystore password other than "changeit", because 
everybody knows that's the default password and thus it is no security at 
all.

Whenever you have a question about Tomcat, it would be helpful to state the 
specific version that you are using.  When you have a question about DSpace 
(or its documentation), it would be helpful to state the specific version 
that you are using.

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Re: [dspace-tech] Tomcat Cert Process for Dspace

2017-10-06 Thread Dayne Ellanna 
Tony,

For the proxy, you are routing to 8877, in my case that would be 8443
correct?

Thanks,
Dayne

On Thu, Oct 5, 2017 at 10:39 PM, Dayne Ellanna  wrote:

> I am having the worst time getting tomcat to do https for dspace.  I
> followed the instructions on the dspace site but cannot make heads or tails
> of the instructions as I am definitely not a certificate expert.  The
> instructions use generic names and don't explain where root ca's come from
> or generating certificate requests and from what do I generate these.  Can
> someone give me very specific instructions about how to set up the https on
> tomcat to run dspace.  So far I have gotten dspace to run successfully as
> http://myserver.domain:8080/xmlui.  As per instructions on the dspace
> site I have tried to create the RSA key, and we use incommon for our certs
> which I can obtain, but have not been able to figure out the beginning to
> end process for this.  I tried using curl to test but no success.  I really
> need a succinct explanation of all the pieces, where to get them or how to
> generate them in order to run the ssl.  HELP!
>
> Thanks,
> Dayne
>
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[dspace-tech] Re: DSpace API

2017-10-06 Thread Mark H. Wood 
On Thursday, October 5, 2017 at 1:16:55 PM UTC-4, Ed Warga wrote:
>
> I'm beginning to think about using the API for certain management 
> activities in my repo. Wondering if anyone has created any scripts to 
> leverage the API in DSpace. I'm looking for =some examples to work from as 
> I get started. What have you done!? Can you share any scripts or ideas?
>
>

There are some bin/dspace commands which are designed to be 
scripting-friendly.  For example the 'user' command (which could use some 
expansion, and a companion 'group' command).  In addition, bin/dspace 
itself can execute scripts composed of multiple commands from its 
repertoire.

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Re: [dspace-tech] Tomcat Cert Process for Dspace

2017-10-06 Thread Tony Brian Albers 
On 10/06/2017 08:39 AM, Dayne Ellanna wrote:
> I am having the worst time getting tomcat to do https for dspace.  I 
> followed the instructions on the dspace site but cannot make heads or 
> tails of the instructions as I am definitely not a certificate expert.  
> The instructions use generic names and don't explain where root ca's 
> come from or generating certificate requests and from what do I generate 
> these.  Can someone give me very specific instructions about how to set 
> up the https on tomcat to run dspace.  So far I have gotten dspace to 
> run successfully as http://myserver.domain:8080/xmlui.  As per 
> instructions on the dspace site I have tried to create the RSA key, and 
> we use incommon for our certs which I can obtain, but have not been able 
> to figure out the beginning to end process for this.  I tried using curl 
> to test but no success.  I really need a succinct explanation of all the 
> pieces, where to get them or how to generate them in order to run the 
> ssl.  HELP!
> 
> Thanks,
> Dayne
> 

Dayne,

We proxy tomcat behind apache httpd to solve this exact issue. Our 
tomcat listens on port 8877.
If you want to try that, in short what you will need is to install httpd 
and set it up to run ssl. Then you can define a ssl-enabled virtualhost 
in apache that proxies your tomcat. Here is our httpd conf file for the 
virtualhost, I've added my comments in ### (with sensitive bits changed, 
but still in the right places):



# Default host when using NameVirtualHost

### ^ this creates a httpd server listening on port 80.
ServerAdmin helpd...@mydomain.edu
DocumentRoot /var/www/html
ServerName dspace-devel.mydomain.edu
ServerAlias dspace-devel

ErrorLog logs/dspace-devel.mydomain.edu-http-error_log
CustomLog logs/dspace-devel.mydomain.edu-http-access_log combined

ProxyPass / http://127.0.0.1:8877/  retry=10 connectiontimeout=5
### ^ this tells httpd to redirect it's / to localhost port 8877
timeout=300
ProxyPassReverse /  http://127.0.0.1:8877/  retry=10
### ^ this tells httpd that tomcat's url's should be rewritten to look 
###   like they're coming from httpd.
ProxyPreserveHost On
### ^ this tells httpd to keep the Host: information from the client and 
### pass it on to tomcat.




### ^ this creates a httpd server that listens on port 443.
ServerAdmin helpd...@mydomain.edu
DocumentRoot /var/www/html
ServerName dspace-devel.mydomain.edu
ServerAlias dspace-devel

ErrorLog logs/dspace-devel.mydomain.edu-https-error_log
CustomLog logs/dspace-devel.mydomain.edu-https-access_log combinedssl

Include conf.d/ssl.include
Include conf.d/ssl.include.star
### ^ these point to a file which specifies where the ssl certificates 
###   live on the host.

ProxyPass / http://127.0.0.1:8877/  retry=10 connectiontimeout=5
### ^ this tells httpd to redirect it's / to localhost port 8877
timeout=300
ProxyPassReverse /  http://127.0.0.1:8877/  retry=10
### ^ this tells httpd that tomcat's url's should be rewritten to look 
###   like they're coming from httpd.
ProxyPreserveHost On
### ^ this tells httpd to keep the Host: information from the client and 
### pass it on to tomcat.






So much for the virtualhost/proxy setup.

To get httpd to use ssl, you will need to have mod_ssl installed, a 
ssl.conf file telling httpd how to use ssl and include files(mentioned 
above) with information about your certificates.



Here's our ssl.conf file:

Listen 443 https
SSLPassPhraseDialog exec:/usr/libexec/httpd-ssl-pass-dialog
SSLSessionCache shmcb:/run/httpd/sslcache(512000)
SSLSessionCacheTimeout  300
SSLRandomSeed startup file:/dev/urandom  256
SSLRandomSeed connect builtin
SSLCryptoDevice builtin
SSLStaplingCacheshmcb:/run/httpd/ocsp(128000)
# The default 'combined' format extended with SSL protocol and cipher 
logging
LogFormat "%h %l %u %t \"%r\" %>s %b \"%{Referer}i\" \"%{User-Agent}i\" 
\"%{SSL_PROTOCOL}x\" \"%{SSL_CIPHER}x\"" combinedssl



This is our ssl.include file:

SSLEngine on
# modern configuration, tweak to your needs
SSLProtocol all -SSLv3 -TLSv1 -TLSv1.1
SSLCipherSuite 
ECDHE-ECDSA-AES256-GCM-SHA384:ECDHE-RSA-AES256-GCM-SHA384:ECDHE-ECDSA-CHACHA20-POLY1305:ECDHE-RSA-CHACHA20-POLY1305:ECDHE-ECDSA-AES128-GCM-SHA256:ECDHE-RSA-AES128-GCM-SHA256:ECDHE-ECDSA-AES256-SHA384:ECDHE-RSA-AES256-SHA384:ECDHE-ECDSA-AES128-SHA256:ECDHE-RSA-AES128-SHA256
SSLHonorCipherOrder on
SSLCompression  off
# OCSP Stapling, only in httpd 2.3.3 and later
SSLUseStapling  on
SSLStaplingResponderTimeout 5
SSLStaplingReturnResponderErrors off



And this is our ssl.include.star file:

SSLCertificateFile /etc/pki/tls/certs/star.mydomain.edu.crt
SSLCertificateChainFile /etc/pki/tls/certs/star.mydomain.edu.chain.crt
SSLCertificateKeyFile /etc/pki/tls/private/star.mydomain.edu.key






I hope this helps a bit. We're running CentOS so YMMV.

/tony


-- 
Tony Albers
Systems administrator, IT-development
Royal Danish Library, Victor Albecks Vej 1, 8000 Aarhus C,

Re: [dspace-tech] DSpace API

2017-10-06 Thread Claudia Jürgen 

Hello Ed,

depending on what you want to achieve, the curation task system might be
the right start.
https://wiki.duraspace.org/display/DSDOC6x/Curation+System
DSpace includes several out-of-the-box tasks which might be a template
for you.

Hope this helps

Claudia Jürgen


Am 05.10.2017 um 19:16 schrieb Ed Warga:

Hello,

I'm beginning to think about using the API for certain management
activities in my repo. Wondering if anyone has created any scripts to
leverage the API in DSpace. I'm looking for =some examples to work from as
I get started. What have you done!? Can you share any scripts or ideas?

Thanks,
Ed Warga
Scholarly Communication Librarian
Texas A University-Corpus Christi



--
Claudia Juergen
Eldorado

Technische Universität Dortmund
Universitätsbibliothek
Vogelpothsweg 76
44227 Dortmund

Tel.: +49 231-755 40 43
Fax: +49 231-755 40 32
claudia.juer...@tu-dortmund.de
www.ub.tu-dortmund.de

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[dspace-tech] Tomcat Cert Process for Dspace

2017-10-06 Thread Dayne Ellanna 
I am having the worst time getting tomcat to do https for dspace.  I 
followed the instructions on the dspace site but cannot make heads or tails 
of the instructions as I am definitely not a certificate expert.  The 
instructions use generic names and don't explain where root ca's come from 
or generating certificate requests and from what do I generate these.  Can 
someone give me very specific instructions about how to set up the https on 
tomcat to run dspace.  So far I have gotten dspace to run successfully as 
http://myserver.domain:8080/xmlui.  As per instructions on the dspace site 
I have tried to create the RSA key, and we use incommon for our certs which 
I can obtain, but have not been able to figure out the beginning to end 
process for this.  I tried using curl to test but no success.  I really 
need a succinct explanation of all the pieces, where to get them or how to 
generate them in order to run the ssl.  HELP!

Thanks,
Dayne

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