« September 2009 | Main | November 2009 »

October 28, 2009

Create Research Projects Content Type with Keyword connections

I'm going to create a simple Content Type called Research Project that will hold the Metadata information collected this summer. This will serve as a way for the UMBS community to keep tabs on what is going on.

1) Here are Modules and Sub-Modules I think I need for this:

Administer > Site Building > Modules

CCK > Content, Link, Node Reference, Number, Text, Option Widgest, User References


2) Create Research Project content type:

Administer > Content Management > Content Types > Add content type

Name: Research Project
Type: research_project
Description: Research activities at the University of Michigan Biological Station.
Title field label: Research Project Title
Default Options: Published
Default comment setting: disabled

3) Manage fields

Go to content type (Research Project) > manage fields > New Fields

Added these text fields: Researcher (Check boxes/radio buttons), Abstract

Note that it is probably appropriate to create a Taxonomy of Researchers.

4) Create Keyword taxonomy list

I want to associate keywords with the Research Project so I created a list of keywords. Working off of this list from the LTER.

Because I have a large list, I wanted to do bulk taxonomy uploads (vs 1 at a time):

I went here to get a Drupal 6 module called Taxonomy Batch Operations.

$ cd /home/data/Desktop/
$ mv taxonomy_batch_operations.tar__0.gz taxonomy_batch_operations.tar.gz
$ sudo tar xzf /home/data/Desktop/taxonomy_batch_operations.tar.gz
$ sudo cp -r taxonomy_batch_operations /var/drupal/sites/all/modules/

Then go to enable the Module.

Administer > Content management > Taxonomy > Add vocabulary

Vocabulary name: Keywords
Description: Keywords for describing research projects and datasets.
Content Types: Research Project
Settings: Tags, Multiple select, Required

5) Notice that when you go to Create content > Research Project the keywords show up there and will auto complete as you type them in.

6) I then went in a create two Research Projects and the use of a keyword taxonomy links the two . E.g. if both use keyword: groundwater then by clicking on groundwater you list all research projects assocated with that keyword.

Posted by kkwaiser at 09:27 AM | Comments (0)

October 26, 2009

Retrieve lost Admin rights in Drupal 6

I don't know what happened, but while in the process of updating the CCK and Views module, my drupal administrator lost a lot of privileges. I used the following sites to rectify the problem.


Note, I was also running into memory problems. I increased the memory from 16 mb to 64 mb:


$ sudo gedit /etc/php5/apache2/php.ini
$ /etc/init.d/apache2 reload

Posted by kkwaiser at 10:38 AM | Comments (0)

October 22, 2009

Create an SFTP site through UM LSAIT

How to create an SFTP Site for sharing data among UM and Non-UM researchers.
Drafted by K. Kwaiser

1) LSAIT can set up some filespace on LSA's Windows servers (LSA-F4\Group) - the 'Group' share is typically for collaboration. You can SFTP to the DFS servers and then access your data there.

The rest of this document documents the implementation of this option!

Cost: Free for “small” amounts of storage space

One thing to note is that on the LSA-Fileservers there is no videostream (open AVI) but it doesn't sound like you need that.

The important part of this is that All users must have UM-accounts and we can create them using the Mcommunity webapp. Hopefully reading the link will help.

Gloria Love (lsa-accounts@umich.edu) is the contact person for this option.

2) You can purchase Windows space - this if you were expecting to increase the space you needed substantially and you wanted a bit more exclusive access. I believe access would then be the same (SFTP).

Cost: ~ $2.23/GB/Year, minimum of 250 GB, includes DR backups. Accessible via CIFS, WebDAV & SFTP

See attached documents for more:

Timothy Rolston (twrolsto@umich.edu) was the contact for this information.

3) This can be done with C-Tools as well. Not sure about SFTP there but certainly could get HTTPS (SSL protected HTTP) access.

4) The LSA-RSG group could even setup a virtual server for you as I understand it from Karen Pachla - similar to the VaaS group you spoke to (ITS folks, yes?).


1)How to create a SFTP site through LSA IT
a.Contact lsa-accounts@umich.edu to request an SFTP site on the LSA-F4 Group drive
i.Include as estimate of how much file space you will need
ii.The default drive space is 10 Gb, additional space available in 10 Gb increments
b.To set up access for researchers sent lsa-accounts@umich.edu a list of UM uniqnames that will need access
i.You can specify (sub)-directory permissions types when you send in the uniqnames
2)If you need to create uniqnames, send the following information to lsa-accounts@umich.edu:

You need the following information in to create a UM uniqname:

Suggested uniqname (optional)
Full name
Valid address
Valid non-UM email address (IMPORTANT!!)
Contact telephone number
Date of Birth

a.This site lists details about uniqnames (e.g. expiration dates, changing passwords, etc.):

MCommunity Sponsor System Overview (R1458) http://www.itcs.umich.edu/itcsdocs/r1458/

3)Connecting to the SFTP site
a.See the attached documents for instructions:

- ConnectInstructionsForAccessToUMBSGroupSharedSpace.docx
- UMBS_SFTP_Manual.doc
- http://lw.lsa.umich.edu/lsait/admin/mac/ConnectingToWindows.pdf

b.If a researcher is not able to login:
i.Make sure the server name is spelled correctly
ii.Synchronize UMICH.EDU Kerberos password and Windows Active Directory password. The Kerberos password is the one you use to access mail.umich.edu or Wolverine Access:

On the LSA Windows Workstations for logon and accessing file space to work correctly the user must synchronize their Kerberos and Windows passwords. To synchronize these passwords please open the following website address https://accounts.www.umich.edu/kpasswd-bin/kpasswd.cgi

c.To access Frequently Asked Questions for getting started with using LSA Windows Services:

Note, more documentation is available for this process:

- Create_SFTP_through_LSAIT.doc
Instructions on how to create an SFTP site

These docs are referenced within the former:
- Recharge_FileService_User_Agreement.doc
- Recharge_FileService.doc
- UMBS_SFTP_Manual.doc
- ConnectInstructionsForAccessToUMBSGroupSharedSpace.docx

During the process, I became certified to create unique names. The following is an email from Gloria on how to become certified to create uniqnames.

- Become_certified_to_create_UM_Uniqnames.doc

This pdf accompanies the preceding doc:
- Mcommunity_Authorization_Form.pdf

Thanks again for your help.


Posted by kkwaiser at 11:02 AM | Comments (0)

October 20, 2009

Set up a Virtual Web Server at UM


1) Go through LSA for virtual server.
- Doesn't work. They suggested VaaS.

2) VaaS - Essentially blank server space. ~$500/year

3) UMWeb - virtual webserver. This is the step I'm going with and the rest of this post documents the process.

- Post-hoc Cost Estimate: $30/year (IFS Group Space) + $50/year (UMWeb server space) = $80/year. We have 5Gb on the IFS drive and around 10Gb (I believe!) of database space. For comparison purposes, web hosting from Godaddy.com runs from $50 - $150/year.

- Question to Mark Montague of ITCS regarding how much space we may need on the IFS group directory:

Hi Mark, I think I'm going to set up a virtual server with MySQL and PHP but I had a question about table space. I'm pretty sure I am going to need to create an IFS group directory. When setting the storage space on this directory, do I need to account for the MySQL tablespace? Or will that IFS directory only be for photos and other webcontent we want to add? Hope this makes sense. Thanks, Kyle

Mark's reply:
The database resides on a dedicated database server, not in IFS. So you only need IFS space for files (PHP, HTML, CSS, media files, and other
Mark Montague
Webmaster team

- CREATE IFS group directory (needed in order to set up a virtual server):

Talking to ITS Account Office about whether we can use a "Course Home Directory" for our IFS space or if the UMBS needs to pay for its own space... Turns out we will need to create our own IFS group space. Cost for UMBS group directory = $0.50/Gb/month

Pam and I set it up at this website and started with 5 Gb. Note that Alicia, Karie, Pam and I are administrators on this drive space. It is called "umbsweb" and should probably only be used for data hosted on the umbs.lsa.umich.edu website. Also note that the UMOD group is xbs-UMBSAnnArbor.

- Set up a domain name (umbs.lsa.umich.edu):

We also need to set up a domain name, I've emailed hostmaster@umich.edu to inquire about this. See "UMBS Domain Name" below the fold for documentation (email correspondence) on this step. The long/short is that our domain name will be umbs.lsa.umich.edu.

- Request a Virtual Host

Pam and I did so by going to this website. It took maybe 5 minutes to request (although I do not have the site yet!)

UMBS Domain Name:

The following is an email string that charts how we came to settle on umbs.lsa.umich.edu. You will want to read from the bottom up!

Hi Kyle,

There isn't any particular setup for it, We just create an entry in UMBS' DNS tables for the hostname. ITS just needs to provide us a destination address to plug into the table when they are done setting things up.


-----Original Message-----
From: Kyle Steven Brown-Kwaiser [mailto:kkwaiser@umich.edu]
Sent: Tuesday, October 20, 2009 1:08 PM
To: hostmaster@lsa.umich.edu
Subject: Re: UMBS Domain name

Hello Hostmaster,

I would like to set up a domain name (umbs.lsa.umich.edu) that will allow the University of Michigan Biological Station to use the ITS web hosting services. What steps are necessary to do this?


Kyle Kwaiser
UMBS Information Manager


On Tue, 20 Oct 2009 12:39:44 -0400,

No special approval is required for umbs.lsa.umich.edu that I'm aware of (hostmaster@lsa.umich.edu would have the authoritative word, though). But I know the LSA hostmaster has previously set up such names so LSA units can use our hosting services.

--- Tony Winkler ITS Web Production Team

Quoting Kyle Steven Brown-Kwaiser :

Hi Tony and Bob, Thanks for the speedy turn around. Would I need an OK from the LSA Dean's office to get "umbs.lsa.umich.edu"?


NOTE to Karie and Phil: The DNS policy guides the creation of new web domain names on campus. See attached for the policy.


On Tue, 20 Oct 2009 12:24:25 -0400,

We could host content for www.lsa.umich.edu/umbs on our servers only if the LSA webmaster were willing to configure a reverse proxy on their servers. Has any thought been given to "umbs.lsa.umich.edu" for this site? That name meets the DNS policy, and has the advantage of being a distinct hostname that could be pointed directly to one of our servers. It also has fewer points of failure than a reverse proxy, since it doesn't require an intermediary webserver.

--- Tony Winkler ITS Web Production Team


Quoting :

We need to ask the webmasters, so I am forwarding this note.

Bob Harold hostmaster,


Message from kkwaiser@umich.edu
Date: Tue, 20 Oct 2009 12:09:35 -0400
Subject: Re: UMBS Domain name

Hi Bob, I did not know I would need to approach the Dean's office. To be clear, if we are to use the UMWeb servers do we need to create a new domain name? For example, can we somehow use our current name: http://www.lsa.umich.edu/umbs and still use ITCS server space?

BTW, I've talked to LSA IT and it is not an option to use their server space.

Thank you, kbk

On Tue, 20 Oct 2009 11:45:11 -0400,

Looks like this falls under LS&A. In that case the dean appears to be T. McDonald. Please ask the dean to send an email containing the request (your wording is good) to hostmaster@umich.edu. After that, we run it past our management for approval also.

Bob Harold hostmaster,


Message from kkwaiser@umich.edu
Date: Tue, 20 Oct 2009 11:24:02 -0400
Subject: UMBS Domain name
To: hostmaster@umich.edu

Hi there, I am in the process of requesting virtual server space through UMWeb and I would like to secure a domain name for the University of Michigan Biological Station. Preferably, the domain name would be www.umbs.umich.edu. To do so, should I have our Director write a letter (phrased as above) with the request? What other information should be included?

Thanks in advance for you help,
Kyle Kwaiser
UMBS Information Manager

----- End message from kkwaiser@umich.edu -----

Posted by kkwaiser at 10:51 AM | Comments (0)

October 19, 2009

GLEON recap

Summary of GLEON 9 conference
Kyle Kwaiser, UMBS Information Manager
Camp Manito-Wish in Boulder Junction, Wisconsin.
October 12-16th, 2009

My overall impression is that the strength of GLEON (Global Lakes Ecological Observatory Network) is the collaborative energy brought by individual researchers. There were about 90 attendees at this conference with ~40% being first-time attendees. Given the relative inaccessibility of northern Wisconsin there were a good number of international scientists and information managers.

I observed a great deal of interest in our buoy deployment and believe it will benefit the UMBS to encourage our researchers/students to attend other GLEON conferences and lakes. A reoccurring theme from the LTER All Scientist Meeting was that I spent a lot of time introducing the UMBS (who, what, where). I enjoy talking up the UMBS but I think we need to work on getting our name out there more. I should not have to clarify that KBS is an MSU affiliate and that they work in an agricultural landscape. One possible solution to this is to request that UMBS researchers prominently display their connections to UMBS in papers and presentations. This point warrants further consideration.

GLEON is a young organization and I am interested to see how it copes with turnover in key staff (e.g., web and database developers) and whether or not the bottom-up structure leads to leadership gaps in important areas. That said, I believe there are avenues for UMBS folks (staff, researchers and students) to take leadership roles in this organization. This point also warrants further consideration.

UMBS GLEON membership:
After discussing the matter with Karie and Phil, I am going to begin the process to make UMBS a member of GLEON. There is a perfunctory process to becoming a GLEON member. Here is the application website to give you an idea of how simple it is.

Here is a map of current site members (notice Flathead and Archbold are currently members, RMBL does not appear to be). Individual membership is also a possibility and is something I believe we should encourage our researchers to do.

Potential membership benefits:
GLEON has funding for student travel within GLEON sites and separate funding for student-exchange program. This would be a good way to get our aquatics faculty/students interested.

Of course, our researchers would also be put into a good position to collaborate with groups that are collecting data similar to ours (assuming they take it upon themselves to attend GLEON conferences.)

GLEON offers technical assistance in data management and sensor deployment. Right now, MHL has the ability to cover these needs for us but additional support never hurts.

Data Turbine:
Data Turbine is essentially server software specifically designed for processing (e.g. QA/QC, plotting) and routing sensor data streams to websites and databases. It was originally developed by NASA for aeronautics sensors and a group at the San Diego Supercomputing Sensor has tailored it to environmental field sensors and tested it in Wisconsin lakes.

The Data Turbine group is currently looking for collaborators as the software has recently exited the testing phase and is entering the deployment phase. I am going to pass this information onto the Marine Hydrodynamics Lab who may find it useful with the U-GLOS system.

Sameer Tilak (stilak@ucsd.edu) is a developer on the project and would be a good contact if we chose to use Data Turbine for anything.

Information Technology working group:
I sat in on 3 of 4 meetings among this group. We discussed Technical Documentation needed for individual sites to stream buoy data to the GLEON website. I pressed fairly hard on this point but did not obtain much documentation. Apparently, said documents exist in rough draft form but I cannot verify it (I even volunteered to contribute to the documentation when we begin streaming data to GLEON!) I will continue to request the documentation and plan to get it before our buoy goes online.

Other conversations included the need to establish QA/QC protocols for incoming data. Currently, most of the data stored is raw. There is also a need for getting the most recent datasets from the individual sites into the GLEON database.

Two groups of researchers have published pan-GLEON studies. Neither of these studies used data from the GLEON database (they solicited data from individual sites) which highlights the need to improve this resource. Right now, GLEON has developed critical tools for data sharing but they are not mature enough and are not highly used by researchers. This is something to consider before as we begin streaming data to GLEON (i.e., how useful will it be to our researchers?).

The GLEON IT group has developed a controlled vocabulary list for use with lake data collection. The current vocab list is on the GLEON website. GLEON has also recently passed a data access policy. I have requested a copy to compare to our policy.

I met John Lenters from the University of Nebraska will pass his contact information to Guy Meadows. John has deployed buoys year-round in the arctic and is involved in a buoy deployment on Granite Island on Lake Superior (north of Marquette.)

Craig Williamson at Miami of Ohio and his collaborators at Kent State recently received IGERT funding. They will be deploying lake buoys in the coming year(s) and are looking for additional collaborators. I am open to suggestions as to how best to evaluate if UMBS researchers could benefit from this.

That's it for now!

Posted by kkwaiser at 10:11 AM | Comments (0)

October 06, 2009

Enable clean URLs in Drupal 6

Here is how I enabled clean URLs on Drupal6/Ubuntu 9.04:

This site held the key.

Edited settings.php:
$ sudo gedit /etc/drupal/6/sites/default/settings.php &
Added the following:
$base_url = 'http://localhost/drupal6';

Change .htaccess:
$ sudo gedit /usr/share/drupal6/.htaccess &
Added this line:
RewriteBase /drupal6

Change 000-default following this site:
$ sudo gedit /etc/apache2/sites-enabled/000-default &

< Directory /var/www/>
Options Indexes FollowSymLinks MultiViews
#AllowOverride None
AllowOverride All
Order allow,deny
allow from all
< /Directory>

Note: I added a space between "< Directory" because, as html, the Directory lines disappear.

Then do this:

$ sudo a2enmod rewrite
$ sudo /etc/init.d/apache2 force-reload
$ sudo /etc/init.d/apache2 restart

See below the fold for miscellaneous notes I accrued during this process.

Here are some potentially useful sites:

This one addresses Clean URLs on Ubuntu but an error that arises (see following) gets in the way.

For this error:
httpd: Could not reliably determine the server's fully qualified domain name, using for ServerName
(13)Permission denied: make_sock: could not bind to address
no listening sockets available, shutting down
Unable to open logs


To see what ports are being listened on:
$ sudo netstat -anp | grep '^tcp.*LISTEN'

To see apach version information and file locations:
$ apache2 -v
$ apache2 -V

I added "ServerName localhost" to:
$ sudo gedit /etc/apache2/httpd.conf &
$ sudo /etc/init.d/apache2 restart

and the error "Could not reliably determine..." disappears. Note I was using this site.

Changes /etc/apache2/conf.d to include this:

Alias /sev /etc/drupal/6/sites/sev

Options Indexes +FollowSymLinks
AllowOverride All
order allow,deny
allow from all

and the Options permission directive goes away but I still don't have a website.

Posted by kkwaiser at 04:45 PM | Comments (0)

Adding image css to style.css in Drupal 6

Open the style.css sheet for your active theme:

$ sudo gedit /etc/drupal/6/sites/default/files/color/garland-11f64863/style.css

Add the following to the bottom of the style sheet:

.align-right { float:right; margin: 0 0 15px 15px; }
.align-left { float:left; margin: 0 15px 15px 0; }
.frame { padding: 5px; border: 1px solid #aaa; }

Code taken from here.

And this is what the Education page looks like now:

leaf graphic

Posted by kkwaiser at 11:31 AM | Comments (0)

Create link hierarchies in Drupal 6

Start here:

Ok, Framework 2.3, which is set to release in about a week, will fully support Dynamic Persistent Menu. Then will allow secondary links to be shown upon hovering over the primary link.

However, to do this, you must first go to Admin>Site Building>Menus then go to the settings tab at the top. The source for secondary links must be set to 'Primary Links' also. This essentially bypasses the real secondary links menu, and instead uses the hierarchy set within Primary Links. You must set your new 'Secondary Links' under the 'Primary Links' menu by going to 'Edit' on each item and changing the parent element to the primary link you wish for it to be under. In Drupal 6, you can simply drag your desired 'Secondary Links' to the right a bit to nest it under a 'Primary Link'

This basic functionality should also work without the Dynamic Persistent Menu module and on all current versions of framework.

If you want to show the lower-level links on hover then you need something like this, the Nice Menus module.

More work remains on this one...

Posted by kkwaiser at 10:56 AM | Comments (0)

Make content available in Drupal 6

This "How to..." covers adding a link to the homepage and making content available to anonymous (the public) users. I have created a Bibliography content type and will make that available to the public in this example.

Currently, in order to view and search the bibliography a user has to be logged in with Administrator rights. When I logout and try to navigate to my bibliography, I get an Access Denied error.

leaf graphic

To Fix:

1) Log in
2) Create a link at the top of the homepage for the Bibliography

- Administer > Menus > Primary Links > Add item
Path: biblio
Menu link title: Bibliography
Description: Research publications of the UMBS
Save > Save Configuration

- A link should appear in the header now

3) Make content available

- Administer > Permissions
- Under Anonymous User, check the appropriate content
- e.g., access biblio content, search content, use advanced search
- Save

4) Now logout and use the link to navigate to the bibliography:

leaf graphic

Posted by kkwaiser at 09:52 AM | Comments (0)

October 01, 2009

Install new theme in Drupal 6

Going to install a new theme for shticks and giggles. I will be following these instructions.

After browsing themes, I decided to go with the Acquia Slate for its post-millenial, modern accents.

Create a new directory for downloaded themes:

$ sudo mkdir /etc/drupal/6/sites/all/themes
$ cd /etc/drupal/6/sites/all/themes/

Untar the downloaded theme into the specified directory:
$ sudo tar xzf /home/data/Desktop/acquia_slate-6.x-1.4.tar.gz

After going to Administer > Themes, Drupal presents Acquia Slate as an option. Here's the home page now:

leaf graphic

Fairly obvious that it needs formatting but I like the layout. This drives home the point of deciding on styling and layout ahead of time?

Posted by kkwaiser at 05:00 PM | Comments (0)

Change Site Name and Slogan in Drupal 6

Here is how you change the Site Name (at least one way) and a second approach to changing the Slogan. Both result in text of your choice being placed in the header area.

It appears there are multiple ways to change the site name area but I'm following this forum.

This is how things look like with the default settings:

leaf graphic

(right-click > View Image for full size)

To change "localhost" to something else I open settings.php.

$ sudo gedit /usr/share/drupal6/sites/default/settings.php &

and go to the bottom:

#$conf = array(
# 'site_name' => 'Your Site Name',
# 'theme_default' => 'minnelli',
# 'anonymous' => 'Visitor',

And change it to the following:

$conf = array(
'site_name' => 'The University of Michigan Biological Station',
# 'theme_default' => 'minnelli',
# 'anonymous' => 'Visitor',

leaf graphic

So, I just found an easier way to do pretty much the same thing. The impetus for this portion comes from this site. It also involves only the web administer interface (instead of the settings.php file) so may be superior in more than one way.

Go to Administer > Site configuration > Site information and set the Slogan to "The University of Michigan Biological Station". The Slogan appears to the right of the Site Name, meaning you can turn off the Site Name and turn on the Slogan and you should get the same outcome as described above.

Also note that their are Global and Theme-specific settings under Administer > Site Building > Themes. The Theme configuration appears to trump the Global.

Posted by kkwaiser at 04:15 PM | Comments (0)