Datafilehandling

Open the Datafile Handling from the Adminpage:


You will get an overview of the existing datafiles that are assigned to any of the samples in the system grouped by the type on a timescale

Select the tree view and you can see each Technology with each of the filetypes assigned to that technology (technology filetype).

The content is available in table form. First all the filetypes of a technology.


From there all files that are in the category of this filetype.
And from there to the "per sample" showing all datafiles for this sample.

At the bottom of this view you also get different options to download the data for this sample / class / experiment for each of the different filetypes or all filetypes.

How to add / maintain SOPs on SetupX

1. Navigate to the Menu to view / modify the SOPs:
2. Make sure a category exists that you want to assign your SOP to. Select the list of SOPs:
3. If that is not the case create a new Category by defining it at the bottom of the Catgories list
4. Navigate to the "new SOP" window and select the Category that you wish the SOP to assign to.
5. Fill out the rest of the information that is asked for and then add the file that contains the actual SOP as an attachment.
6. When ready upload it.
7. But the time you uploaded the new / updated SOP it will not be "active" yet.
8. Active it by pressing activate now next to the time when the SOP is valid. The top bar will turn green and the SOP will be "active". If the SOP replaces an older SOP the older one will be outdated.
9. All SOPs that are declared public - AND that are in a category that is public can be seen right on the main website in the upper left corner which is then linked to a list of all public SOPs. This makes it easier to share SOPs.

Adding datafiles

When adding old data to the respository or in case samples where not correctly recognized (loss of the gctof-log-file) the system allows to assign these later on.

Simple get two lists:
- a list containing all the samples IDs
- and a list containing the coressponding filenames (whithout any extension)

To get the list of sample IDs:
Simply open the minimalistic view of the experiment.
In the list of your experiments:


Use the icon left of XML:
You will get the minimalistic view from which you can easily extract the sample IDs.

(Best is to create an Excel sheet out of it)


Now navigate to the admin page and use the 3rd option of the file handling:

This will get you two big input fileds in which you can copy and paste the filenames and the samples IDs:


Insert the ids and filenames (without extension but with run number).
Then submit the form. Now the system will check on every possible combination and filetype and assign the samples to each sample.
(This process can take up to 10 minutes for very large datasets.)

After that you will get a status of what the system found and what files were assigned to each of the samples.

In case you forgot to process a number of samples or placed them in the incorrect location you can redo the entire process again. Only new data files will be assigned to the system.

revision 590.

The Revision 590 contains a new Formobject type: StringInputfieldAjax

Reminder - in this case it is required to create new hibernate mapping files:

Run: ant generate compile deploy

This version supports ajax for instant queries.

MailAPI conflict with google API

Not directly SetupX related but useful:
A conflict within the APIs from Google and Sun are causing the following error:

org.apache.commons.mail.EmailException: Sending the email to the following server failed : XXX.XXXX.com:25
at org.apache.commons.mail.Email.sendMimeMessage(Email.java:873)
at org.apache.commons.mail.Email.send(Email.java:898)
Caused by: javax.mail.NoSuchProviderException: smtp
at javax.mail.Session.getService(Session.java:611)
at javax.mail.Session.getTransport(Session.java:541)

So finally after searching for quite a while I found the solution:
http://forums.sun.com/thread.jspa?messageID=9884528#9884528

How to move SetupX behind an SSL

You can use apache mod_ssl and mod rewrite to secure setupx jboss

Here is the rewrite without SSL.

ServerAdmin XXXX
ServerName XXXX.bioinformatics.ucdavis.edu

ErrorLog /var/log/httpd/setupx_error_

log
CustomLog /var/log/httpd/setupx_access_log combined
LogLevel warn

RewriteEngine On
ProxyPreserveHost On
RewriteRule ^/(.*)$ \
http://localhost:8180/xx1/$1 [P]



You need to enable/install mod_ssl to enable SSL and you can add the following rewrite code to protect setupx in the SSL configuration section.

RewriteEngine On
ProxyPreserveHost On
RewriteRule ^/(.*)$ \
http://localhost:8180/xx1/$1 [P]

SSL can only protect a virtual host per IP address on port 443, however,
you can have multiple virtual hosts for port 80.

thanks to Zhi-Wei Lu.

note:j boss needs memory

if your JBoss is hungry for more memory:

give JBoss more memory on startup:

modify /usr/share/jboss/bin/run.conf

#Specify options to pass to the Java VM. #

JAVA_OPTS="-server -Xms128m -Xmx800m -Xdebug"