Merge branch 'develop' of github.com:PecanProject/pecan into dataone-…

…download-util

CHANGELOG.md

@@ -7,6 +7,9 @@ For more information about this file see also [Keep a Changelog](http://keepacha
 
 ## [Unreleased]
 
+### Fixes
+- Fixed remote code execution #1545
+
 ## [1.5.10] - Prerelease
 ### Added
 - Added PEcAn.utils::download.file() to allow for use of alternative FTP programs

book_source/_bookdown.yml

@@ -77,7 +77,7 @@ rmd_files: [
   "installation/Installing-PEcAn-Ubuntu.Rmd",
   "installation/Installing-PEcAn-models.Rmd",
   "installation/PEcAn-in-the-Cloud.Rmd",
-  "installation/centos.shiny.Rmd",
+  "installation/shiny.Rmd",
   "installation/thredds.Rmd",
   "misc/faq.Rmd"
 ]

book_source/installation/centos.shiny.Rmd → book_source/installation/shiny.Rmd

@@ -2,31 +2,14 @@
 authors - Alexey Shiklomanov
         - Rob Kooper
 
-**NOTE: Instructions are only tested for CentOS 6.5.**
+**NOTE: Instructions are only tested for CentOS 6.5 and Ubuntu 16.04**
 **NOTE: Pretty much every step here requires root access.**
 
 ## Install the Shiny R package and Shiny server
 
-The `shiny` R package can be installed directly in R via `install.packages("shiny")`.
+Follow the instructions on the [Shiny download page][shiny-download] for the operating system you are using.
 
-Download and install the Shiny server binary ([link](https://www.rstudio.com/products/shiny/download-server)).
-
-## CentOS
-
-```
-wget https://download3.rstudio.org/centos5.9/x86_64/shiny-server-1.4.2.786-rh5-x86_64.rpm
-sudo yum install --nogpgcheck shiny-server-1.4.2.786-rh5-x86_64.rpm
-```
-
-## Ubuntu 
-
-NOTE: The additional `gdebi` dependence may be optional and `dpkg` may work just fine, but I haven't tested this out.
-
-```
-$ sudo apt-get install gdebi-core
-$ wget https://download3.rstudio.org/ubuntu-12.04/x86_64/shiny-server-1.4.2.786-amd64.deb
-$ sudo gdebi shiny-server-1.4.2.786-amd64.deb
-```
+[shiny-download]: https://www.rstudio.com/products/shiny/download-server/
 
 ## Modify the shiny configuration file
 
@@ -77,35 +60,90 @@ server {
 }
 ```
 
-## Set the httpd proxy
+If you change the configuration, for example to add a new location, you will need to restart Shiny server.
+*If you are setting up a new instance of Shiny*, skip this step and continue with the guide, since there are a few more steps to get Shiny working.
+*If there is an instance of Shiny already running*, you can restart it with:
 
-Create a file `/etc/httpd/conf.d/shiny.conf` containing the following proxy settings:
+```
+## On CentOS
+sudo service shiny-server stop
+sudo service shiny-server start
+
+## On Ubuntu
+sudo systemctl stop shiny-server.service
+sudo systemctl start shiny-server.service
+```
+
+## Set the Apache proxy
+
+Create a file with the following name, based on the version of the operating system you are using:
+
+* Ubuntu 16.04 (pecan1, pecan2, test-pecan) -- `/etc/apache2/conf-available/shiny.conf`
+* CentOS 6.5 (psql-pecan) -- `/etc/httpd/conf.d/shiny.conf`
+
+Into this file, add the following:
 
 ```
 ProxyPass           /shiny/ http://localhost:3838/
 ProxyPassReverse    /shiny/ http://localhost:3838/
 RedirectMatch permanent ^/shiny$ /shiny/
 ```
 
-## Create a symbolic link to the shiny server service
+### **Ubuntu only:** Enable the new shiny configuration
 
 ```
-sudo ln -s /opt/shiny-server/config/init.d/redhat/shiny-server /etc/init.d
+sudo a2enconf shiny
 ```
 
-## Start the shiny server and restart httpd
+This will create a symbolic link to the newly created `shiny.conf` file inside the `/etc/apache2/conf-enabled` directory.
+You can do `ls -l /etc/apache2/conf-enabled` to confirm that this worked.
+
+## Enable and start the shiny server, and restart apache
+
+### On CentOS
 
 ```
+sudo ln -s /opt/shiny-server/config/init.d/redhat/shiny-server /etc/init.d
 sudo service shiny-server stop
 sudo service shiny-server start
 sudo service httpd restart
 ```
 
 You can check that Shiny is running with `service shiny-server status`.
 
+### On Ubuntu
+
+Enable the Shiny server service.
+This will make sure Shiny runs automatically on startup.
+
+```
+sudo systemctl enable shiny-server.service
+```
+
+Restart Apache.
+
+```
+sudo apachectl restart
+```
+
+Start the Shiny server.
+
+```
+sudo systemctl start shiny-server.service
+```
+
+If there are problems, you can stop the `shiny-server.service` with...
+
+```
+sudo systemctl stop shiny-server.service
+```
+
+...and then use `start` again to restart it.
+
+
 ## Troubleshooting
 
-Refer to the log files for shiny (`/var/log/shiny-server.log`) and httpd (`/var/log/httpd/error-log`).
+Refer to the log files for shiny (`/var/log/shiny-server.log`) and httpd (on CentOS, `/var/log/httpd/error-log`; on Ubuntu, `/var/log/apache2/error-log`).