Install woes

[Paul Hoffman]

I've installed Fedora 4.3.0 on Ubuntu 14.04 using OpenJDK 8 and Jetty 8
but it doesn't appear to be running correctly, and I'm hoping that
someone who has deployed Fedora under Jetty might have some words of
wisdom as to what I should do next.

I've been following the Deploying Fedora 4 Complete Guide, though not to
the letter as it's not really written that way.

* Install OpenJDK 8, Jetty 8, Solr
* Copy fcrepo-webapp-4.3.0.war to ~jetty/webapps
* Start up Jetty (service jetty8 start)
* Create a data directory at /var/local/fedora-data
* chown -R jetty:jetty ~jetty /var/local/fedora-data

I set the following in /etc/default/jetty8:

NO_START=0
VERBOSE=yes
JAVA_OPTIONS="-Xmx256m -Djava.awt.headless=true -Dfcrepo.home=/var/local/fedora-data"
JAVA_HOME="/usr/lib/jvm/java-8-openjdk-amd64"

After starting Jetty I could see that the WAR file was not uncompressed within
~jetty/webapps, but after a little poking around I found it in
/var/cache/jetty8/data along with root and solr webapps:

# ls -l /var/cache/jetty8/data
total 12
drwxr-xr-x 3 jetty jetty 4096 Aug 27 17:03 jetty--8080-fcrepo-webapp-4.3.0-_fcrepo-webapp-4.3.0-any-
drwxr-xr-x 4 jetty jetty 4096 Aug 27 17:03 jetty--8080-root--any-
drwxr-xr-x 4 jetty jetty 4096 Aug 27 17:03 jetty--8080-solr-_solr-any-

However, I don't know what to do next. http://localhost:8080/ leads to a Jetty
welcome page, but http://localhost:8080/rest/ leads to 404 Not Found and
http://localhost:8080/fcrepo-webapp-4.3.0/rest/ leads to 503 Service
Unavailable.

In case it helps, I'll just note that Jetty's log file
(/var/log/jetty8/2015_08_27.stderrout.log) logs something that I find baffling
-- "Object of class 'org.eclipse.jetty.webapp.WebAppContext' is not of type
'org.eclipse.jetty.webapp.WebAppContext'". Huh? I suppose in Java a class is
not a type, but...?

I'm only including the beginning of the log as everything after this
appears to relate to solr:

2015-08-27 17:03:35.339:WARN:oejd.WebAppDeployer:WebAppDeployer is deprecated. Use WebAppProvider
2015-08-27 17:03:35.341:INFO:oejs.Server:jetty-8.1.3.v20120416
2015-08-27 17:03:38.091:WARN:oejw.WebAppContext:Failed startup of context o.e.j.w.WebAppContext{/fcrepo-webapp-4.3.0,file:/var/lib/jetty8/webapps/fcrepo-webapp-4.3.0/},file:/var/lib/jetty8/webapps/fcrepo-webapp-4.3.0/
java.lang.IllegalArgumentException: Object of class 'org.eclipse.jetty.webapp.WebAppContext' is not of type 'org.eclipse.jetty.webapp.WebAppContext'. Object Class and type Class are from different loaders.
at org.eclipse.jetty.xml.XmlConfiguration$JettyXmlConfiguration.configure(XmlConfiguration.java:318)
[call tree truncated]
2015-08-27 17:03:38.145:INFO:oejw.StandardDescriptorProcessor:NO JSP Support for , did not find org.apache.jasper.servlet.JspServlet
2015-08-27 17:03:38.229:INFO:oejsh.ContextHandler:started o.e.j.w.WebAppContext{,file:/var/lib/jetty8/webapps/root/},file:/var/lib/jetty8/webapps/root/
2015-08-27 17:03:38.229:INFO:oejsh.ContextHandler:started o.e.j.w.WebAppContext{,file:/var/lib/jetty8/webapps/root/},file:/var/lib/jetty8/webapps/root/
2015-08-27 17:03:39.017:WARN:oejw.JettyWebXmlConfiguration:Unable to process jetty-web.xml
java.lang.ClassNotFoundException: org.mortbay.jetty.webapp.WebAppContext
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
[call tree truncated]

Thanks in advance,

Paul.

--
Paul Hoffman <pa...@flo.org>
Systems Librarian
Fenway Libraries Online
c/o Wentworth Institute of Technology
550 Huntington Ave.
Boston, MA 02115
(617) 442-2384 (FLO main number)

[Andrew Woods]

Hello Paul,

Everything you have detailed seems correct. Is it possible that you used to have a Jetty7 on your machine, the residue of which is causing interference?

http://stackoverflow.com/questions/10492555/jettyrun-causes-class-not-found-exception-for-org-mortbay-jetty-webapp-webappco

Andrew

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[Paul Hoffman]

On Thu, Aug 27, 2015 at 07:29:31PM -0400, Andrew Woods wrote:
> Hello Paul,
> Everything you have detailed seems correct. Is it possible that you used to
> have a Jetty7 on your machine, the residue of which is causing interference?
> http://stackoverflow.com/questions/10492555/jettyrun-causes-class-not-found-exception-for-org-mortbay-jetty-webapp-webappco

Indeed -- and I still do! When I installed Jetty 8 from the OpenJDK PPA
(recall that I am on Ubuntu 14.04) I apparently pulled in Jetty 7 --
probably by installing solr-jetty or some other packages.

Then later I messed up the home dir for jetty, such that its webapps dir
contained Jetty 7 stuff -- grep -rc eclipse vs. grep -rc mortbay made that
clear.

At this point I think I'll try wiping it clean and reinstalling. I'll
remove all Java stuff, then install them using the OpenJDK PPA.

[...time passes...]

And that's done -- I think all is well now but here's what I did, just
for the record...

# apt-get remove jetty jetty8 java-common open-jre-headless [and a bunch of other stuff]

Jetty 7 and 8 couldn't be removed until I got rid of their init scripts:

# rm -f /etc/init.d/jetty*

I also ran apt-get autoremove to get rid of a lot of cruft pulled in (I
gather) by default-jre.

I saved my paltry /etc/default/jetty* files:

# mv /etc/default/jetty* /tmp/

I deleted the jetty user, its home dir, and a bunch of other Jetty dirs
(both 7 and 8):

# userdel -r jetty
# rm -Rf /usr/share/jetty* /var/lib/jetty* /etc/jetty* /var/log/jetty* /etc/cron.daily/jetty*

I then started over with OpenJDK 8:

# apt-get install openjdk-8-jre-headless

When I attempted to reinstall Jetty 8, it wasn't happy that I had
removed the jetty user, so I recreated it (and its group) using the UID
and GID it had before, which I had *not* wisely written down but which
were fortunately still in my scrollback buffer:

# groupadd -g 121 jetty
# useradd -u 112 -g 121 jetty

(It's possible that I've missed some vital secondary groups, but time
will tell.)

Then I tried again and it succeeded:

# apt-get install jetty8

I did *not* install solr-jetty, since it depends on default-jdk (and
default-jre and default-jre-headless, all of which are from Java 7).
Not sure what I'll do about that down the road, but what the heck. :-)

At this point I have only one Java install:

# update-java-alternatives -l
java-1.8.0-openjdk-amd64 1069 /usr/lib/jvm/java-1.8.0-openjdk-amd64

And I don't see any traces of Jetty 7:

# fgrep -rc eclipse ~jetty/etc/
0

So I think I'm in much better shape to get things going.

Thanks for the help!

[Andrew Woods]

Hello Paul,

Thanks for your detailed notes. It provides a helpful record for the list.

I am glad to hear you are up and running.

Andrew

[Paul Hoffman]

On Fri, Aug 28, 2015 at 12:25:32PM -0400, Andrew Woods wrote:
> Thanks for your detailed notes. It provides a helpful record for the list.
> I am glad to hear you are up and running.

Oh, I'm not up and running, I'm just unstuck. Well, I'm stuck, but it's
a totally different stuck.

My current problem is missing files -- things I deleted this morning
that I expected to reappear when I reinstalled jetty8 but -- surprise!
-- didn't reappear at all.

I restored the init script (/etc/init.d/jetty8) but when I try to run it
it fails, because /etc/jetty8/jetty.conf doesn't exist. In fact,
/etc/jetty8 is empty except for /etc/jetty8/contexts, which itself is
empty. I deleted all these things, of course, but expected them to
reappear when I reinstalled jetty8. /usr/share/jetty8 was repopulated,
which was nice, but I'm far from up and running.

*Sigh*!

I hate package managers. If I thought it wouldn't just lead to a fresh
new hell, I'd install OpenJDK 9 from source, Jetty 9 from source, etc.,
etc., etc.

Or is that perhaps worth pursuing after all? Has anyone here followed
the Deploying Fedora 4 Complete Guide in a recent(ish) Ubuntu?

Paul.

[Alan Witkowski]

I think the more recent versions of fedora require jetty9, or at least that's the impression that i got when i tried and failed to install it. You may have luck with fedora v4.0 or 4.1, but i just ended up going with tomcat instead of jetty in the end.

Anyway, here are the instructions i made for ubuntu 15.04 and tomcat8. 14.04 only has tomcat7 and java7, so you'll at least need to get java8 from a PPA (which looks like you've done). Not sure if it works with tomcat7 but you can try it.

-- Install tomcat 8 --

sudo apt-get purge default-jre default-jre-headless

sudo apt-get install tomcat8 openjdk-8-jre-headless

-- Set up fedora storage --

sudo service tomcat8 stop 

sudo mkdir -p /var/lib/fedora

sudo chown tomcat8:tomcat8 /var/lib/fedora

sudo vi /etc/default/tomcat8

Change JAVA_OPTS to:

JAVA_OPTS="-Djava.awt.headless=true -Xmx2048m -XX:+UseConcMarkSweepGC -Dfcrepo.home=/var/lib/fedora"

-- Download fedora 4.3.0 -- 

wget "https://github.com/fcrepo4/fcrepo4/releases/download/fcrepo-4.3.0/fcrepo-webapp-4.3.0.war"

sudo mv /var/lib/tomcat8/ROOT /var/lib/tomcat8/_ROOT

sudo mv fcrepo-webapp-4.3.0.war /var/lib/tomcat8/webapps/ROOT.war

sudo chown tomcat8:tomcat8 /var/lib/tomcat8/webapps/ROOT.war

sudo service tomcat8 start

Browse to:

http://localhost:8080/rest

[Paul Hoffman]

On Wed, Sep 02, 2015 at 03:38:31PM -0700, Alan Witkowski wrote:
> I think the more recent versions of fedora require jetty9, or at least
> that's the impression that i got when i tried and failed to install it. You
> may have luck with fedora v4.0 or 4.1, but i just ended up going with
> tomcat instead of jetty in the end.
>
> Anyway, here are the instructions i made for ubuntu 15.04 and tomcat8.

> [...]

Thanks, this looks very helpful -- specific commands, yay! I should
probably abandon my preference for Jetty over Tomcat -- a dubious
preference, not grounded in hard experience.

[Paul Hoffman]

On Wed, Sep 02, 2015 at 03:38:31PM -0700, Alan Witkowski wrote:

> I think the more recent versions of fedora require jetty9, or at least
> that's the impression that i got when i tried and failed to install it. You
> may have luck with fedora v4.0 or 4.1, but i just ended up going with
> tomcat instead of jetty in the end.
>
> Anyway, here are the instructions i made for ubuntu 15.04 and tomcat8.
> 14.04 only has tomcat7 and java7, so you'll at least need to get java8 from
> a PPA (which looks like you've done). Not sure if it works with tomcat7 but
> you can try it.

Thanks again for the info. Everything seems fine now except I'm not
seeing the feature tour -- do I need a GUI browser to have any hope of
seeing it?

Anyhow, just FTR I'll flesh out your unstructions with some details on
what I did. I'll omit the sudo's since I did it all as root -- lately
sudo has been annoying me.

> -- Install tomcat 8 --
> sudo apt-get purge default-jre default-jre-headless

I started by purging tomcat7:

apt-get purge tomcat7

This resulted in an attempt to stop the tomcat7 service, which failed,
and the failure triggered an attempt to *start* the tomcat7 service,
which failed, causing the purge to fail. Which is so silly...

Somehow I thought to delete the tomcat7 user and try apt-get purge
again, and this did the trick -- no service stop/start nonsense and
tomcat7 is gone.

> sudo apt-get install tomcat8 openjdk-8-jre-headless

I couldn't find a PPA for tomcat8 -- I don't know why I assumed I would
-- so I created the tomcat8 user and group manually, then downloaded the
core binary package from tomcat.apache.org and untarred it in ~tomcat8
(i.e., /var/lib/tomcat8). Naturally this didn't not give me an init
script. If I had kept the init script for tomcat7 I could have tweaked
that for tomcat8, but noooooo...

> -- Set up fedora storage --
> sudo service tomcat8 stop

I skipped this, since it wasn't running.

> sudo mkdir -p /var/lib/fedora
> sudo chown tomcat8:tomcat8 /var/lib/fedora
> sudo vi /etc/default/tomcat8
>
> Change JAVA_OPTS to:
> JAVA_OPTS="-Djava.awt.headless=true -Xmx2048m -XX:+UseConcMarkSweepGC
> -Dfcrepo.home=/var/lib/fedora"

I did it this way:

JAVA_HOME="/usr/lib/jvm/java-8-openjdk-amd64"
JAVA_OPTS="-Djava.awt.headless=true"
CATALINA_HOME="/var/lib/tomcat8"
CATALINA_BASE="$CATALINA_HOME"
CATALINA_PID="$CATALINA_BASE/tomcat.pid"
CATALINA_OPTS="-Xmx2048m -XX:+UseConcMarkSweepGC -Dfcrepo.home=/var/lib/fedora"

Though I suspect I'll need multiple CATALINA_BASEs down the road.

> -- Download fedora 4.3.0 --
> wget
> "https://github.com/fcrepo4/fcrepo4/releases/download/fcrepo-4.3.0/fcrepo-webapp-4.3.0.war"
> sudo mv /var/lib/tomcat8/ROOT /var/lib/tomcat8/_ROOT

I think you meant this, which is what I did:

/var/lib/tomcat8/webapps/ROOT /var/lib/tomcat8/webapps/_ROOT

> sudo mv fcrepo-webapp-4.3.0.war /var/lib/tomcat8/webapps/ROOT.war
> sudo chown tomcat8:tomcat8 /var/lib/tomcat8/webapps/ROOT.war

OK, all good so far.

> sudo service tomcat8 start

Happily, my simple init script works.

> Browse to:
> http://localhost:8080/rest

Yay, it's there -- it's a big text/turtle blob, but it's there:

HTTP/1.1 200 OK
Server: Apache-Coyote/1.1
Link: <http://www.w3.org/ns/ldp#Resource>;rel="type"
Link: <http://www.w3.org/ns/ldp#Container>;rel="type"
Link: <http://www.w3.org/ns/ldp#BasicContainer>;rel="type"
Accept-Patch: application/sparql-update
Accept-Post: text/turtle,text/rdf+n3,text/n3,application/rdf+xml,application/n-triples,multipart/form-data,application/sparql-update
Allow: MOVE,COPY,DELETE,POST,HEAD,GET,PUT,PATCH,OPTIONS
Preference-Applied: return=representation
Vary: Prefer
Vary: Accept, Range, Accept-Encoding, Accept-Language
Content-Type: text/turtle
Content-Length: 6776
Date: Mon, 14 Sep 2015 16:10:31 GMT

@prefix premis: <http://www.loc.gov/premis/rdf/v1#> .
[etc.]

When I try http://localhost:8080/rest in w3m it gives my a big JSON
blob. At least it's giving me something, but where's the feature tour?
I suspect I have to use a GUI browser (*sigh!*).

[Alan Witkowski]

Thanks for catching those typos. Looks like you got it working. If you
want html in the response add "Accept: text/html" to your request
header, otherwise it returns text/turtle.

curl http://localhost/rest -H 'Accept: text/html'

Also i learned that if you ever want authentication set up you need to
use this war file instead:
https://github.com/fcrepo4-exts/fcrepo-webapp-plus/releases/download/fcrepo-webapp-plus-4.3.0/fcrepo-webapp-plus-rbacl-audit-4.3.0.war.
The other war doesn't have the BasicRolesAuthorizationDelegate class.

Here are some other basic commands you can test on your new setup.

-- Create new container "test" --
curl -i -X PUT "http://localhost:8080/rest/test"

-- Insert dc terms with file body.rdf --
curl -X PATCH -H "Content-Type: application/sparql-update" --data-binary
"@body.rdf" "http://localhost:8080/rest/test"

body.rdf:
PREFIX dc: <http://purl.org/dc/elements/1.1/>

DELETE { }
INSERT {
<> dc:title "This is the title." ;
dc:subject "Subject goes here."
}
WHERE { }

-- Remove dc term --
curl -X PATCH -H "Content-Type: application/sparql-update" --data-binary
"@delete.rdf" "http://localhost:8080/rest/test"

delete.rdf:
PREFIX dc: <http://purl.org/dc/elements/1.1/>

DELETE WHERE { ?s dc:subject ?o }

-- Delete item --
curl -X DELETE "http://localhost:8080/rest/test"

-- Delete tombstone to reuse url --
curl -X DELETE "http://localhost:8080/rest/test/fcr:tombstone"