Difference between revisions of "Installing EPrints on RHEL/Fedora/CentOS"

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==Requirements==
 
==Requirements==
 +
* RedHat Enterprise (RHEL) / CentOS 7 or 8 (or Fedora 25+).
 +
* Pre-install MySQL server and client and make sure the former is enabled and running.
 +
** RHEL / Fedora:
 +
yum install mysql-server mysql
 +
systemctl enable mysql
 +
systemctl start mysql
 +
** CentOS:
 +
yum install mariadb-server mariadb
 +
systemctl enable mariadb
 +
systemctl start mariadb
  
* RedHat Enterprise (RHEL) / CentOS 7 or Fedora 25+. These instructions will more than likely work for RHEL / CentOS 6 but have not been as thoroughly tested.
+
== Installing from EPrints RPM ==
   
+
 
== Installing from EPrints 3.3.x RPM ==
+
=== Installing from rpm.eprints.org ===
 +
'''Please note that rpm.eprints.org is no longer fully supported and packages are no longer signed.  It is planned to start signing packages again in the future but there have been some issues with the signing keys.'''
 +
 
 +
* As root, using yum (or dnf in RHEL/CentOS 8+ and more recent Fedora versions) install ''epel-release'' package so ''eprints'' RPM dependencies can be met from the EPEL repository where necessary:
 +
yum install epel-release
 +
dnf install epel-release
 +
 
 +
* As root, edit /etc/yum.repos.d/eprints.repo and add the following (If you want to install EPrints 3.3 rather than EPrints 3.4 change the baseurl to ''http://rpm.eprints.org/eprints3''):
 +
  [eprints_3_4]
 +
name=EPrints Repository Software - $basearch
 +
baseurl=http://rpm.eprints.org/eprints3.4
 +
enabled=1
 +
gpgcheck=0
 +
 
 +
* As root, now run one of the following commands to download the cache for this new package repositories.  You may be prompted to accept the GPG key for the EPEL repository:
 +
yum makecache
 +
dnf makecache
 +
 
 +
* Finally, install EPrints using yum (or dnf):
 +
yum install eprints
 +
dnf install eprints
  
Add the rpm.eprints.org repository key:
+
=== Installing RPM locally ===
 +
* Download latest RPM for EPrints 3.3 or 3.4 from http://files.eprints.org/
  
  rpm -ivh http://rpm.eprints.org/rpm-eprints-org-key-1-1.noarch.rpm
+
* Then install EPrints using yum (or dnf in RHEL/CentOS 8+ and more recent Fedora versions) substituting for the filename of the file you downloaded from https://files.eprints.org
 +
yum install eprints-3.3.16-1.el7.rpm
 +
dnf install eprints-3.4.3-1.el7.pm
  
... the rpm.eprints.org EPrints repository:
+
=== Installing publications flavour ===
 +
EPrints 3.4 RPMs only come with the in-built 'zero' flavour and not the typical publications flavour. Before trying to set up you archive you will need to (as the eprints user) download the latest publications flavour tarball from https://files.eprints.org/ and unpack it into /usr/share/eprints/:
 +
wget https://files.eprints.org/2551/8/eprints-3.4.3-flavours.tar.gz
 +
tar -xzvf eprints-3.4.3-flavours.tar.gz -C /usr/share/eprints/
 +
mv /usr/share/eprints/eprints-3.4.3/flavours /usr/share/eprints/
 +
rmdir /usr/share/eprints/eprints-3.4.3/
 +
Before trying to create a publications flavour archive, you will need to install (as the root user) the ''TeX::Encode'' module or you will see error messages regarding a missing dependency for the BibTeX import and export plugins. (You may need to first install ''cpan'' with YUM).
 +
yum install cpan
 +
cpan TeX::Encode
  
  rpm -ivh http://rpm.eprints.org/eprints/noarch/rpm-eprints-org-1-1.noarch.rpm
+
== Installing EPrints 3.4.x from Source ==
 +
'''N.B. Installing from source is generally discouraged particularly for production repositories. However, if want to develop the EPrints code or a plugin or Bazaar package it may be useful to install from source, ideally from [https://github.com/eprints/eprints3.4 EPrints Core Git repository].'''
  
Upgrade your XML libraries:
+
First, install the EPEL YUM package repository and run yum repolist to ensure the GPG key is installed:
  
  yum upgrade libxml2 libxslt perl-XML-LibXML perl-XML-LibXSLT
+
  yum install epel-release
 +
yum repolist
  
Install EPrints 3:
+
Now, install all the dependencies that would be installed through the eprints RPM.
  
  yum install eprints
+
  yum install libxml2 libxslt httpd mod_perl perl-DBI perl-DBD-MySQL perl-IO-Socket-SSL perl-Time-HiRes \
 +
    perl-CGI perl-Digest-MD5 perl-Digest-SHA perl-JSON perl-XML-LibXML perl-XML-LibXSLT perl-XML-SAX \
 +
    perl-MIME-Lite perl-Text-Unidecode perl-JSON perl-Unicode-Collate perl-Pod-LaTeX perl-LWP-Protocol-https \
 +
    perl-IO-String tetex-latex wget gzip tar ImageMagick elinks poppler-utils chkconfig unzip cpan
  
===Other sources for dependencies===
+
Next, create the eprints user
  
The following RPM repositories may be useful for finding other non-critical dependencies required by EPrints that are not part of the core RHEL system.
+
adduser eprints
  
http://fedoraproject.org/wiki/EPEL - Fedora Extras for RHEL.
+
Next, clone the Git repository from GitHub to /opt/ and set the eprints user as the owner. It is probably best to checkout the latest release rather than using HEAD, which may have known issues:
  
http://pkgs.repoforge.org/rpmforge-release/ - RPMforge, which covers a very large range of Perl modules plus others.
+
yum install git
 +
git clone https://github.com/eprints/eprints3.4.git /opt/eprints3
 +
cd /opt/eprints3/
 +
git checkout tags/v3.4.3
 +
chown -R eprints:eprints .  
  
[http://www.imagemagick.org/script/binary-releases.php ImageMagick] provide an RPM for RHEL/CentOS 5. At time of writing the RPM requires fftw3, fltk, jasper and openexr which are available from ''RPMForge''. libwebp is available from [http://rpm.eprints.org/RHEL/5/ rpm.eprints.org].
+
Next, as the eprints user copy /opt/eprints3/perl_lib/EPrints/SystemSettings.pm.tmpl to /opt/eprints3/perl_lib/Eprints/SystemSettings.pm
  
you may also need to tell SELinux to allow apache to talk on the network (maybe only if your database is on a separate server
+
EPrints is now fully installed at /opt/eprints3. However, you will not yet have a running archive. Follow the [[Getting Started with EPrints 3]] instructions to set this up.
  
setsebool -P httpd_can_network_connect=1
+
Now update Apache configuration to set it up to use the eprints user and group, by ensuring the following lines are set thus in /etc/httpd/conf/httpd.conf:
  
 +
User  eprints
 +
Group eprints
  
== Installing EPrints 3.3.x from Source ==
+
Now add the file /etc/httpd/conf.d/eprints.conf with the following line:
'''N.B. Installing from source is generally discouraged particularly for production repositories.  However, if want to develop the EPrints code or a plugin or Bazaar package it may be useful to install from source, ideally from [https://github.com/eprints/eprints EPrints Core Git repository].'''
 
  
...
+
Include /opt/eprints3/cfg/apache.conf
  
 +
There is a good chance your operating system will have SELinux enabled.  If so, follow the instructions under Troubleshooting for how to let EPrints do what it needs to do through SELinux.
  
== Troubleshooting ==
+
Finally, restart Apache:
  
=== Failed to parse XML file ===
+
  service httpd restart
  
When installing EPrints on RHEL6 (may apply to other versions), If you get the error:
+
You should now be able to access your vanilla repository at the hostname you specified when running '''epadmin create''' from the [[Getting Started with EPrints 3]] instructions. You should then login as the admin user you created during this process and turn on the indexer. This can be done by clicking on the '''Admin''' link under the Logged in menu, then clicking on the '''System Tools''' tab and finally the '''Start Indexer''' button.
  Failed to parse XML file:
 
  /usr/share/eprints/lib/lang/en/phrases/system.xml: Entity: line 396: parser error : Entity 'nbsp' not defined age or title page. If there are more...
 
  
Run
+
== Non-critical Dependencies ==
  sed -i 's/'''&'''nbsp;/ /g' /usr/share/eprints/lib/lang/en/phrases/system.xml
+
Some of EPrints non-core functionality may not work out of the box as these dependencies are not included as part of the RPM.  Here is a list of known additional packages (and the YUM repositories in which they can be found) or CPAN modules than can be installed. The latter should be installed using the ''cpan'' command as the root user.
 +
 +
* '''perl-Geo-IP (epel)''' - Allows IRstats2 to determine the location of views/downloads for publications.]
 +
* '''perl-Spreadsheet-WriteExcel (epel)''' - To allow Multiline Excel export.
 +
* '''CPAN module Text::Refer''' - Required for EndNote import.
 +
* '''CPAN module TeX::Encode''' - Required for BibTex export needed for publications flavour.
 +
* '''perl-Image-ExifTool (epel)''' - Sometimes needed to support generation of thumbnails for uploaded documents/images.
 +
* '''perl-LWP-Protocol-https (base)''' - Needed by DataCite plugin to register repository DOIs.
  
then navigate to the root of your EPrints install (/opt/eprints or /usr/share/eprints) and run
+
== Next steps ==
bin/generate_views *repository_id*
 
bin/epadmin reload *repository_id*
 
  
=== Upgrade from previous 3.3 ===
+
Configure eprints per [[Getting_Started_with_EPrints_3]].
After a upgrading from previous 3.3, your existing repository's database may need updating.
 
bin/epadmin update [archive_id]
 
  
=== Using SELinux ===
+
== Operating System Version Specific Requirements ==
  
If you're using SELinux on your server you will need to give Apache read/write access to the documents directory for all repositories you create and the eprints var folder (indexer log, ticker files):
+
=== RHEL / CentOS 7 ===
 +
No significant issues.
  
chcon -R -h -t httpd_sys_script_rw_t /usr/share/eprints/archives/[repoid]/documents/
+
=== RHEL / CentOS / Rocky 8 ===
chcon -R -h -t httpd_sys_script_rw_t /usr/share/eprints/var/
+
{{:Issues with installing EPrints on RHEL / CentOS / Rocky 8}}
 +
 
 +
== Troubleshooting ==
 +
* [[EPrints and SELinux|Advice for enabling SELinux with EPrints]]

Latest revision as of 00:24, 30 June 2021


Requirements

  • RedHat Enterprise (RHEL) / CentOS 7 or 8 (or Fedora 25+).
  • Pre-install MySQL server and client and make sure the former is enabled and running.
    • RHEL / Fedora:
yum install mysql-server mysql
systemctl enable mysql
systemctl start mysql
    • CentOS:
yum install mariadb-server mariadb
systemctl enable mariadb
systemctl start mariadb

Installing from EPrints RPM

Installing from rpm.eprints.org

Please note that rpm.eprints.org is no longer fully supported and packages are no longer signed. It is planned to start signing packages again in the future but there have been some issues with the signing keys.

  • As root, using yum (or dnf in RHEL/CentOS 8+ and more recent Fedora versions) install epel-release package so eprints RPM dependencies can be met from the EPEL repository where necessary:
yum install epel-release
dnf install epel-release
  • As root, edit /etc/yum.repos.d/eprints.repo and add the following (If you want to install EPrints 3.3 rather than EPrints 3.4 change the baseurl to http://rpm.eprints.org/eprints3):
[eprints_3_4]
name=EPrints Repository Software - $basearch
baseurl=http://rpm.eprints.org/eprints3.4
enabled=1
gpgcheck=0
  • As root, now run one of the following commands to download the cache for this new package repositories. You may be prompted to accept the GPG key for the EPEL repository:
yum makecache
dnf makecache
  • Finally, install EPrints using yum (or dnf):
yum install eprints
dnf install eprints

Installing RPM locally

  • Then install EPrints using yum (or dnf in RHEL/CentOS 8+ and more recent Fedora versions) substituting for the filename of the file you downloaded from https://files.eprints.org
yum install eprints-3.3.16-1.el7.rpm
dnf install eprints-3.4.3-1.el7.pm

Installing publications flavour

EPrints 3.4 RPMs only come with the in-built 'zero' flavour and not the typical publications flavour. Before trying to set up you archive you will need to (as the eprints user) download the latest publications flavour tarball from https://files.eprints.org/ and unpack it into /usr/share/eprints/:

wget https://files.eprints.org/2551/8/eprints-3.4.3-flavours.tar.gz
tar -xzvf eprints-3.4.3-flavours.tar.gz -C /usr/share/eprints/
mv /usr/share/eprints/eprints-3.4.3/flavours /usr/share/eprints/
rmdir /usr/share/eprints/eprints-3.4.3/

Before trying to create a publications flavour archive, you will need to install (as the root user) the TeX::Encode module or you will see error messages regarding a missing dependency for the BibTeX import and export plugins. (You may need to first install cpan with YUM).

yum install cpan
cpan TeX::Encode

Installing EPrints 3.4.x from Source

N.B. Installing from source is generally discouraged particularly for production repositories. However, if want to develop the EPrints code or a plugin or Bazaar package it may be useful to install from source, ideally from EPrints Core Git repository.

First, install the EPEL YUM package repository and run yum repolist to ensure the GPG key is installed:

yum install epel-release
yum repolist

Now, install all the dependencies that would be installed through the eprints RPM.

yum install libxml2 libxslt httpd mod_perl perl-DBI perl-DBD-MySQL perl-IO-Socket-SSL perl-Time-HiRes \
    perl-CGI perl-Digest-MD5 perl-Digest-SHA perl-JSON perl-XML-LibXML perl-XML-LibXSLT perl-XML-SAX \
    perl-MIME-Lite perl-Text-Unidecode perl-JSON perl-Unicode-Collate perl-Pod-LaTeX perl-LWP-Protocol-https \
    perl-IO-String tetex-latex wget gzip tar ImageMagick elinks poppler-utils chkconfig unzip cpan

Next, create the eprints user

adduser eprints

Next, clone the Git repository from GitHub to /opt/ and set the eprints user as the owner. It is probably best to checkout the latest release rather than using HEAD, which may have known issues:

yum install git
git clone https://github.com/eprints/eprints3.4.git /opt/eprints3
cd /opt/eprints3/
git checkout tags/v3.4.3
chown -R eprints:eprints . 

Next, as the eprints user copy /opt/eprints3/perl_lib/EPrints/SystemSettings.pm.tmpl to /opt/eprints3/perl_lib/Eprints/SystemSettings.pm

EPrints is now fully installed at /opt/eprints3. However, you will not yet have a running archive. Follow the Getting Started with EPrints 3 instructions to set this up.

Now update Apache configuration to set it up to use the eprints user and group, by ensuring the following lines are set thus in /etc/httpd/conf/httpd.conf:

User  eprints
Group eprints

Now add the file /etc/httpd/conf.d/eprints.conf with the following line:

Include /opt/eprints3/cfg/apache.conf

There is a good chance your operating system will have SELinux enabled. If so, follow the instructions under Troubleshooting for how to let EPrints do what it needs to do through SELinux.

Finally, restart Apache:

 service httpd restart

You should now be able to access your vanilla repository at the hostname you specified when running epadmin create from the Getting Started with EPrints 3 instructions. You should then login as the admin user you created during this process and turn on the indexer. This can be done by clicking on the Admin link under the Logged in menu, then clicking on the System Tools tab and finally the Start Indexer button.

Non-critical Dependencies

Some of EPrints non-core functionality may not work out of the box as these dependencies are not included as part of the RPM. Here is a list of known additional packages (and the YUM repositories in which they can be found) or CPAN modules than can be installed. The latter should be installed using the cpan command as the root user.

  • perl-Geo-IP (epel) - Allows IRstats2 to determine the location of views/downloads for publications.]
  • perl-Spreadsheet-WriteExcel (epel) - To allow Multiline Excel export.
  • CPAN module Text::Refer - Required for EndNote import.
  • CPAN module TeX::Encode - Required for BibTex export needed for publications flavour.
  • perl-Image-ExifTool (epel) - Sometimes needed to support generation of thumbnails for uploaded documents/images.
  • perl-LWP-Protocol-https (base) - Needed by DataCite plugin to register repository DOIs.

Next steps

Configure eprints per Getting_Started_with_EPrints_3.

Operating System Version Specific Requirements

RHEL / CentOS 7

No significant issues.

RHEL / CentOS / Rocky 8

elinks package is no longer available

The RPM package elinks is no longer available in RHEL / CentOS / Rocky 8 even with EPEL package repository. elinks is no longer needed so if installing from source use the following YUM command line:

dnf install libxml2 libxslt httpd mod_perl perl-DBI perl-DBD-MySQL perl-IO-Socket-SSL perl-Time-HiRes \
   perl-CGI perl-Digest-MD5 perl-Digest-SHA perl-JSON perl-XML-LibXML perl-XML-LibXSLT perl-XML-SAX \
   perl-MIME-Lite perl-Text-Unidecode perl-JSON perl-Unicode-Collate perl-Pod-LaTeX tetex-latex wget \
   gzip tar ImageMagick poppler-utils chkconfig unzip cpan

Alternatively, for RHEL 8 you can enable the codeready-builder repository, which still has elinks available:

subscription-manager repos --enable "codeready-builder-for-rhel-8-$(arch)-rpms"

If you are running CentOS 8 (or Rocky 8) you can similarly enable the powertools repository:

dnf config-manager --set-enabled powertools

perl-IO-String package is no longer available

The RPM package perl-IO-String is no longer available in RHEL / CentOS / Rocky 8 even with EPEL package repository. You can enable the codeready-builder repository, which still has perl-IO-String available:

subscription-manager repos --enable "codeready-builder-for-rhel-8-$(arch)-rpms"

If you are running CentOS 8 (or Rocky 8) you can similarly enable the powertools repository:

dnf config-manager --set-enabled powertools

Sub-dependency packages perl-MIME-Types and perl-Digest-SHA1 are no longer available

perl-MIME-Lite package requires perl-MIME-Types package and perl-Apache-DBI requires perl-Digest-SHA1 package neither of which available on RHEL / CentOS / Rocky 8, even with EPEL repository enabled. You can enable the codeready-builder repository, which still has these packahes available:

subscription-manager repos --enable "codeready-builder-for-rhel-8-$(arch)-rpms"

If you are running CentOS 8 (or Rocky 8) you can similarly enable the powertools repository:

dnf config-manager --set-enabled powertools

Compatibility issues with XML::LibXSLT

Sometimes the Perl module XML::LibXSLT packaged in the perl-XML-LibXSLT package causes segmentation faults with the Apache httpd webserver. Therefore, it may be better to install this Perl module using CPAN (as the root user):

yum erase perl-XML-LibXSLT
cpan XML::LibXSLT

If you have installed the eprints RPM either locally or though DNF (i.e. new YUM). You will not be able to remove perl-XML-LibXSLT RPM without it forcing EPrints to be uninstalled. Therefore, you should manually remove /usr/lib64/perl5/vendor_perl/auto/XML/LibXSLT/ rather than uninstalling the package before installing it using CPAN.

Troubleshooting