December 23, 2009
One of the options for working with images in Drupal involves using the Gallery module which acts as a bridge to the Gallery2 opensource software package. Because the LTER content types used Gallery2, I'm installing it to evaluate whether or not to keep it in. Here's what I've done:
- Installed the Gallery module from Drupal
- Installed Gallery2 following this website.
$ sudo apt-get install gallery2
$ whereis gallery2
$ cd /var/drupal/
$ sudo ln -s /usr/share/gallery2/
$ dpkg -L gallery2
- Navigated to http://localhost/drupal/gallery2/install
- Following install wizard
- create login.txt and place in /usr/share/gallery2
- Standard installation...
- storage directory: /var/lib/gallery2/g2data
- set up a DB user through phpMyAdmin
- Set admin id
- installed all modules
* The ImageMagick module was installed, but needs configuration to be activated
* The Multiroot module was installed, but needs configuration to be activated
* The Nokia Image Upload module was installed, but needs configuration to be activated
* The URL Rewrite module was installed, but needs configuration to be activated
- Go to http://localhost/drupal/admin/settings/gallery and specify the URL as http://localhost/drupal/gallery2
- Skipped clean URLs of this step
- Did user synchronization
That's it for now. Merry Christmas.
December 22, 2009
Manage Images and Photos in Drupal
Photo and image management is not straightforward in Drupal. As an example, here is a list websites that appear helpful:
- A solid overview of many of the modules listed here.
- A tutorial on how to build an AJAX photo gallery using LightBox
- A list of websites that demo various Drupal photo/image modules.
- A tutorial on Image Picker.
- Possibly more related modules here.
And here is a list of modules that are potentially useful:
- Image Picker
- Lightbox 2
- Gallery integrates with Gallery2
- Acidfree Albums
- Image Assist
- Embedded Media Field
- CCK Imagefield
- Imagefield Extended
- Imagefield Crop
- Image FUpload a bulk uploading module
- Image Cache
- Image Publishing
December 14, 2009
Pro's and con's of using a controlled (keyword) vocabulary
One of the many information resources that we need to standardize at the Biological Station is the list of index terms (i.e. keywords). In contemplating the creation of a controlled vocabulary for documenting data sets, bibliographic entries, study sites and research projects many decision points have arisen. Here is a summary.
Pro's of building a controlled vocabulary for indexing:
- Consistency within terminology can improve search ability. E.g., use of "forests" instead of "forest", "forests" instead of "trees", "carbon dioxide" instead of CO2
- Consistency across information resources. The same terminology will be used to describe data sets, bibliographic entries, study sites and research projects
- Incorporating external controlled vocabulary (LTER keywords) will facilitate integration of UMBS data resources with network-scale databases.
- Use of keyword auto-complete when creating metadata may yield use of more descriptive terms as compared to "top-of-the-head" categorization
- UMBS can make a contribution to the creation of a controlled vocabulary for use by other field stations and for ecology in general
- Building a controlled vocabulary can be time consuming
- Potential that keyword lists will not adequately represent new research directions
- No guarantee that anonymous users will use correct terms
Plan to create a UMBS controlled (keyword) vocabulary
Here is an outline of what will need to happen for the UMBS to have an established list of keywords.
1. Extract keywords from the UMBS bibliography, this will be the starting point.
- This list is not comma-delimited, meaning multi-term keywords will need to be manually identified and computer scripts will need to be used to reformat the terms and add commas
2. Parse the raw keyword list into 3 parts:
- a) keywords redundant with the LTER list (including synonyms and lexical variants)
- b) taxonomic descriptors (latin names and species-specific common names?)
- c) candidate-keywords for a UMBS keyword list.
3. Build UMBS keyword list using the candidate-keyword list:
- Identify how to treat hyphens, spaces and plurals
- Declare as equivalent lexical variants (e.g. analyze vs analyse)
- Identify synonyms
- Remove candidate-keywords that require context to make sense (e.g. "change", "description")
Savoy, J. (2005). Bibliographic database access using free-text and controlled vocabulary: An evaluation. Information Processing & Management, 41(4), 873-890.
Svenonius, E. (1986). Unanswered questions in the design of controlled vocabularies. Journal of the American Society for Information Science, 37(5), 331-430.
Svenonius, E. (2003). Design of controlled vocabularies Taylor & Francis.
December 11, 2009
Funding Opportunities for Field Stations
Took a look as some of the funding opportunities the Biological Station might qualify for. This is will be an ongoing list:
|Improvements in Facilities, Communications, and Equipment at Biological Field Stations and Marine Laboratories (FSML)||NSF, Harvard Forest just got one.|
|Improvements to Biological Research Collections (BRC)||We can digitize and integrate our collections with others.|
|Major Research Instrumentation Program (MRI-R²)|
|Carbon and Water in the Earth System|
Summary of initial keyword situation
An interesting question has arisen while formatting the Biological Station bibliography. What to do with all of those keywords? A quick and dirty analysis shows the keyword list from the bibliography has the following attributes:
3158 - number of keywords in the UMBS bibliography
2562 - number of keywords in the UMBS bibliography used 5 times or less
639 - number of keywords in the LTER Keyword list (v.0.9)
283 - number of overlapping keywords between UMBS and LTER lists
(Right-click > view image for the fullsize image)
Here is a list of the 100 most used keywords in the UMBS Bibliography:
December 08, 2009
Get Tabs working with CCK
When creating custom content types, you can group similar fields to make things a bit easier one the eyes. Going one step further you can break up the content type into separate tabs which will reduce scrolling time.
It's fairly easy to set up but there is a bug so I thought I should post this. Basically, the bug leaves the Help text out of the newly created tabs.
The modules I installed to get tabs working:
- Tabs 6.x-1.2 tabs-6.x-1.2.tar.gz (http://drupal.org/project/tabs)
- CCK Fieldgroup Tabs 6.x-1.0 (http://drupal.org/project/cck_fieldgroup_tabs)
To fix use the patch given here: http://drupal.org/node/559850
This is the file that is modified:
December 06, 2009
sftp in Ubuntu 9.10
For whatever reason, I have not been able to sftp to the LSA servers using FileZilla, the Nautilus browser (it crashes) or the terminal command:
So I installed putty and putty-tools
$ sudo apt-get install putty
And have been able to get it working from the command line:
$ psftp servername.umich.edu
commands of note:
ls, cd, lcd, pwd, lpwd, put, get, mv
psftp> put -r LTER_ContentTypes
psftp > ls /Dept/umbs/dept/
I've since gotten sftp via the terminal to work:
$ sftp email@example.com
to specify a port:
$ sftp -oPort=[portnumber] firstname.lastname@example.org
December 02, 2009
Work the Firewall in Ubuntu
Quick notes on how to firewall apache and open ports if needed:
This Ubuntu documentation is helpful.
This How To is the best.
$ sudo ufw enable
$ sudo ufw allow 22
$ sudo ufw deny 22
$ sudo ufw disable
$ sudo ufw status verbose
$ sudo /usr/sbin/apache2ctl restart
Allow an IP address through the firewall
$ sudo ufw allow from
IP address shows up und inet addr:
File of concern:
Some delete statements:
$ sudo ufw delete deny from
$ sudo ufw delete allow from
$ sudo ufw delete deny 80
December 01, 2009
Re-install Open Office on Ubuntu
For whatever reason, I could not open a dbf file with the Open Office Calc program. This is how I fixed it (not that I understand why this worked):
1. Started following this tutorial.
2. I was then getting a document recovery error so I install Java Runtime Environment following this tutorial. I also tried comment 1 out.
3. I still had a document recovery error so I tried this.
4. That still didn't do it so I tried this command:
$ sudo aptitude remove --purge openoffice.org
And for whatever reason, my new version of OpenOffice works and will open a dbf file. Unfortunately, that took up a lot of time.