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Carlos Rueda edited this page Jan 22, 2015 · 4 revisions

Log

2015-01-21

  • Noted that catalina.out was 2.1Gb -- rotate logs not working? Then ran: $ sudo /usr/sbin/logrotate /etc/logrotate.conf

  • Toward redoing the svn-2-git migration, but this time for the whole "mmisw" project at google code, I installed git 2.2.2 (from sources as there was no a direct yum installation of a recent version):

$ sudo yum install curl-devel expat-devel gettext-devel openssl-devel zlib-devel
$ wget https://www.kernel.org/pub/software/scm/git/git-2.2.2.tar.gz
$ tar zxf git-2.2.2.tar.gz
$ cd git-2.2.2/
$ make configure      # make prefix=/usr/local didn't work as expected
# ./configure --prefix=/usr/local   
$ make
$ sudo make install
$ /usr/local/bin/git --version
git version 2.2.2
$ sudo yum install subversion-perl  # because of a "Can't locate SVN/Core.pm" when trying a git clone ...

2015-01-14

  • Installed and enabled Java8 (jdk-8u25-linux-x64.rpm downloaded from oracle) (see also this ref for the alternatives command) ... but had to revert (see below).
$ sudo rpm -Uvh jdk-8u25-linux-x64.rpm
$ sudo alternatives --config java
There are 5 programs which provide 'java'.
...
 + 5           /usr/java/jdk1.7.0_21/jre/bin/java

$ sudo alternatives --install /usr/bin/java java /usr/java/jdk1.8.0_25/bin/java 6
$ sudo alternatives --config java
...
Enter to keep the current selection[+], or type selection number: 6

$ java -version
java version "1.8.0_25"
Java(TM) SE Runtime Environment (build 1.8.0_25-b17)
Java HotSpot(TM) 64-Bit Server VM (build 25.25-b02, mixed mode)
  • Similar "alternatives" enabling for javac.
  • Restarted tomcat
  • Unfortunately, according to catalina.out, bioportal is failing to start because of this bug in the old spring used. So, reverting to the previous java 7 because trying to update that dependency on the old "1005" bioportal is simply not feasible at this time.

2014-07-11

  • installed nodejs, npm, bower (for some experimentation with new prototypes, eg., orrv)

2014-06-17

2014-03-05

  • Adjusted ROOT/index.html to link to local logo ROOT/mmior.png (instead of http://mmisw.org/ont/-/img/mmior.png) so that page is more self-contained (not depending on any of the Orr services).

2013-11-10

  • sudo setsebool -P httpd_enable_homedirs on

2013-11-08

2013-09-30

  • Transferred some other stuff from previous host to new host under ~/mmisw_prev_host_other_stuff/. This includes various configs (httpd, tomcat), and some files from my home dir, including the dropbox stuff (dropbox still to be enabled on new host).
  • Enabled cron jobs to create hourly and daily db dumps (under /opt/MMI-ORR/workspace/db-backups/).

2013-09-12

# setsebool -P httpd_can_network_connect 1

See http://wiki.apache.org/httpd/13PermissionDenied

2013-09-06

  • Final transfer of DB and ontology files (~11:30am pacific)
  • Repopulated triple store
  • cutover in progress

2013-09-02

  • adjustments on tamu's instance toward upcoming cutover (basically, use mmisw.org in Ont's and OrrPortal's build.properties files). General tests ok (including password reset).
  • update of database and ontology files as of Sep/2/13 @ ~ 4pm pacific.
  • tamu's instance is ready for the cut-over with only a database/file update to be done on Friday Sept/6 onve the cutover is started.

2013-07-10

  • ports open: 80, 443, 10035
  • workaround for mysql connection problem
  • configure AG anonymous user (via graphical interface on port 10035)
  • various tests; most functionality in place now (all with mmisw.tamucc.edu for now)
  • note: permissions fixed: .../workspace/agraph should be given agraph as owner

2013-07-04

  • AllegroGraph init set up
  • Db dumps and ontology files transferred and imported

2013-05-20

  • Installed GCC, Java, Apache HTTP server, Tomcat, Ant, w3m, AllegroGraph, GWT, MySQL, BioPortal, MMISW Ont
  • Configured Apache and Tomcat
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