Month: June 2016 (Page 1 of 3)

Duplicating Drupal

One of my big ongoing projects is an online Drupal database for the History of Chemistry called Situating Chemistry. The database connects the sites where chemistry has been done (pharmaceutical factories and dispensaries, bleach and dye works, fertilizer plants, university lecture halls and labs, etc.) with physical materials and the people doing the work.

John Perkins and I have built the database as a tool for researchers. We hope that they will login to the site while visiting archives, libraries, or archeological sites and will take notes in the database – both for their own use and to share the basic facts with the rest of the field.

We also built the site in the hopes that it would serve as a model for other subfields within the history of science. We were recently asked for a copy of the database that could be appropriated for the history of astronomy.

To build this new version of the database, I took backups of the Situating Chemistry database and installed them as a new database on a temporary subdomain. Doing this was not entirely straight forward or well documented, so I wanted to document the steps in case they are useful for others:

  1. Create a web space for your new Drupal install
  2. Install Drupal
  3. Overwrite the new file structure from your backup
  4. Point Drupal to the correct DB
  5. Overwrite the new DB from your backup

This workflow is fairly simple conceptually, but it requires using the either the cPanel, the command line, or in my case both. Below I’ve explained each step more fully from my own experience:

  1. Create a subdomain – From the cPanel provided by my web hosting service, I created a subdomain that I could use to host the new database temporarily until I hand it over.Screenshot of the AddOn Domain function in the cPanel for Reclaim Hosting
  2. Install Drupal – My web hosting service (and all of the web hosting services I’ve used) has a one click installation of Drupal that will get the core of Drupal up and running. I used this to install a clean version of Drupal on the new subdomain and a clean database. Situating Chemistry uses a postgreSQL database rather than the usual mySQL database in order to support mapping modules for the sites of chemistry. However the steps are the same for whatever type of DB you might use.Screenshot of the Druapl installation page in Installatron in Reclaim Hosting
  3. Replace the core Drupal file structure – Having just installed Drupal, I immediately deleted the entire file structure that the automated system had produced. I replaced this with the file structure from a copy of the backup of the Situating Chemistry database. In this way I was able to get the files for the themes and modules copied over.Screenshot of the Drupal Core files in FileManager
  4. Point this Drupal instance to the new DB – By reinstalling Drupal from the backup, I overwrote the file that tells Drupal which DB it’s using. I thus needed to change a file to reestablish the connection to the new DB and prevent any corruption of the Situating Chemistry DB. To do this, I opened the settings.php file which for Drupal is installed under the Sites/Default subdirectory. From a command line text editor, I changed the line that indicates which DB to use from the Situating Chemistry DB to the new DB.Screenshot of FileManager in Reclaim Hosting's cPanel
  5. Replace the empty new postgreSQL database with a backup – This was the hardest part of the process. From within the cPanel, you can access database manager. There you could theoretically be able to overwrite the new DB with your backup. However, I got a timeout error because of the size of my DB file. Instead I used the command line to overwrite the DB. After logging into my server, I uploaded a copy of the backed up DB to a temporary, non-public folder. I then used the chmod command to change the read-write options on the new database to give myself write privileges. Finally I used something like this to overwrite the old DB with the new: psql -W -U myUserName newDBname < backUpFileName. Once that was done running, I reversed the changes I made with chmod for security.Screenshot of Mac Terminal

By going through this process, I was able to create pretty much an exact copy of the Situating Chemistry site that I have been working on. I am going to delete out the content from this copy to create a clean version of the project for adaptation as Situating Astronomy. I will leave the taxonomies and relationships that I’ve built, but will delete out the blog posts, logos, and other project specific information from the site.

I will also use the five step workflow to build a second copy of Situating Chemistry to use as a developmental site to test out new Drupal modules and to establish workflows for importing data into the database. I have been doing way too much testing on the production site, and have occasionally caused outages when I run into a module conflict or some other form of break in the system.

Brexit and Higher Ed

Now that the vote’s in and I can no longer bury my head in disbelief, I’ve been doing a good bit of reading about the British Exit from the EU and particularly its implications for Higher Ed.

British academia seems to have been overwhelmingly in favor of staying a part of the EU. A poll conducted by Times Higher Ed found, “Nearly 90 percent of those working in British higher education will vote to remain in the European Union in the June 23 referendum.” On Monday, the vice-chancellors of 103 British universities published an open letter expressing their concerns over the (then possible) exit from the EU. The closing of the letter expressed expressed the joint sentiment succinctly, “For us it is crystal clear that our outstanding universities – and our students – are stronger in Europe.”

Students and younger people in general also voted to stay in the EU.


Many in the leave camp have relied on economic arguments. Boris Johnson has said repeatedly that England sends £350m to the EU each week, usually failing to note that much of that is returned in rebates and private spending. The Guardian estimated the total to be closer to £136m a week or £7.1bn annually. This is still a considerable amount of money, but is equivalent to only a quarter of 1% of the British GDP.

However many within the Higher Education system have pointed to the economic benefits that they receive from the European Union. Cambridge Professor Ross Anderson estimated that that university would lose £100m a year. The first £60m of that estimate was from EU grants and contracts while another £10m comes from teaching English as a second language. A study by Universities UK estimated that British universities as a whole received £836m in grants and contracts from the EU.

Citing the decreased matriculation of Scottish students sense their reclassification as ‘overseas students,’ Anderson suggested that the £100m was a conservative estimate and could be much worse if EU and foreign matriculation decreased. In the open letter from the vice-chancellors, they noted that EU students contributed £3.7bn annually to the British economy. Britain has the single largest share of grant-funded students from programs like Horizon 2020 of any EU member state. If Britain restricts the free-movement of EU citizens (surely part of the point of Brexit), it would likely lose even the possibility of external membership to such programs.

Faculty and Staff

In their coverage of Brexit, Nature reports that 15% of UK university staff come from the EU. The Times Higher Ed poll mentioned above found that an astounding 40% of respondents would consider leaving Britain in the case of Brexit passing. In an article published today by Times Higher Ed on a possible “Brain Drain,” David Price, vice-provost (research) at UCL, said that the vote was “likely to be a disaster for the long-term future for UK research and HE sector”.

The only positives that I’ve seen for higher education in relation to the Brexit are speculations that maybe some of the money that had been going to the EU will now be spent on Higher Education. While this is of course possible, there’s no actual evidence that it will happen or even policy proposals to encourage hope that anyone in parliament is thinking about it.

Persistent Student Writing

I have written before about my dislike for disposable writing assignments in college courses. Like math homework, they serve a purpose in having students practice various concepts, but both are seen by students as busy work. Research papers can be made more palatable by giving students enough choice in the topic to establish personal relevance. However, as long as the paper ends up filed away in either the instructor’s or the student’s filing cabinet, it remains merely an ineffective exercise with a single reader.

One common alternative is the course blog. In my class on science and literature, one of my student’s wrote a blog post on the representation of vivisection in the Island of Doctor Moreau, which has been read 319 times so far this year. The thing is that the paper was written in 2014. All told, since he posted it, the paper has been viewed 1,239 times. Lately, the post has been getting about 55 views a week, primarily from Google searches about the book. This student writing a junior level paper that could have been filed away in my cabinet contributed to public knowledge about H.G. Wells and vivisection in the 19th and early 20th centuries.

While I worry about the proliferation of abandoned course blogs, that course site from the summer of 2014 still gets about 600 views a month, about twice as many as this personal blog. Here’s a breakdown of the top posts for May:

Table of views in May for my After Newton blog

I think it’s easier to motivate students to put in work on their research and writing when they know it will be publicly available and possibly widely read. There is also value in showing students that they can contribute to the knowledge community and challenging them to do so.

A second possibility for public writing, and one that frankly dwarfs the course blog in terms of readership, is writing for Wikipedia. My mentor, Peter Barker, taught a survey course on the history of science since 1700 last fall. In that course, Peter asked his students to make edits to improve the Wikipedia articles on the various subjects that they were studying.

Screen Shot of the Wiki Education Dashboard

Notice that the 84 articles edited by the students have been viewed 3.67 million times since those edits were made. That’s so incredible I assumed it must be a glitch, but you can access the views by article on the site. Obviously, most of the articles weren’t created by the students. But as we ask students to join intellectual discussions in our courses and contribute to the broader knowledge community, why would we ever choose to assign a single reader paper over writing for a public audience.

Page 1 of 3

Powered by WordPress & Theme by Anders Norén