How to publish an HTML5+RDFa Web site from org-mode

I’m a big fan of org-mode (see previous posts), and I’ve started maintaining (sic) my professional webpage(s) with it.

But I’ve also recently tried and publish some more Semantic/Linked Data aware documents too (again, previous posts).

Ideally, I think my preferred workflow for publishing articles or documents of some importance, would be to author them in org-mode, and then publish them as HTML5 including RDFa meta-data and annotations. Instead, I’ve more frequently been doing conversions of org-mode to LaTeX, in order to submit a printable version, and later-on decided to convert the LaTeX to HTML5+RDFa…

But one of the issues is how to properly embed the RDF meta-data inside the org-mode documents, so that the syntax is both compact and expressive enough.

I doubt there’s a universal solution, given that RDF tends to be complex, and graphs may not project easilly along a mainly linear structure of an org-mode document, but anyway, there seems to be possible middle grounds that are practically good enough.

I’ve tried and implement a solution, which reuses the principles set by John Kitchin in Extending the org-mode link syntax with attributes, i.e. implementing an HTML exporter for a particular custom link type, which will convert the plist-like syntax to some RDFa constructs.

Here’s a description of the whole solution : http://www-public.telecom-sudparis.eu/~berger_o/test-org-publishing-rdfa.html

The nice thing about org-mode, and its litterate programming babel environment, is that it allows to embed the code of the links exporter inside the org document, avoiding to dissociate the converter from the document’s source, making it auto-complete.

Next step will probably be to author a paper (or convert back a “preprint” of mines) with org-mode, in order to provide Linked Research meta-data.

Stay tuned for more details, and in the meantime, I welcome any improvement to the org/babel/elisp setup.

Edit: I’ve recorded a webcast to provide a bit more details, available on YouTube : https://youtu.be/OyI3DVqllx4

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Appel pour une “Linked Research” (recherche reliée), traduit en français

J’ai traduit en français les transparents de l’appel pour une “Linked Research” (que j’ai traduit par “recherche reliée”) de Sarven Capadisli originellement en anglais

L’objectif est d’inciter (entre autre actions) à la publication d’articles académiques sous une forme exploitable aussi bien par les humains que par les machines, et permettant ainsi d’embarquer dans le document des méta-données additionnelles.

Plus de détails dans les transparents ici : http://www-public.tem-tsp.eu/~berger_o/presentations-call-for-linked-research-fr/

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Publishing my papers as Linked Research

I intend to make the extra effort of republishing my own research papers as Linked Research, i.e. in a form readable by humans (HTML5), but also embedding meta-data (as RDF) for machine processing.

I’ve started with Authoritative Linked Data descriptions of Debian source packages using ADMS.SW (a good candidate, as it deals with Linked Data ;).

You’ll notice the menu which helps select different style sheets for preparing clean printable versions, not far from the LaTeX output usually converted to PDF.

I hope this will pave the way to more Linked Research, and less opaque publications.

The only hassle at the moment is the conversion from LaTeX to HTML5 which I’m doing manually, in Emacs + nxml-mode.

Update: Check the preprint links in my publications page, for more papers.

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New short paper : “Designing a virtual laboratory for a relational database MOOC” with Vagrant, Debian, etc.

Here’s a short preview of our latest accepted paper (to appear at CSEDU 2015), about the construction of VMs for the Relational Database MOOC using Vagrant, Debian, PostgreSQL (previous post), etc. :

Designing a virtual laboratory for a relational database MOOC

Olivier Berger, J Paul Gibson, Claire Lecocq and Christian Bac

Keywords: Remote Learning, Virtualization, Open Education Resources, MOOC, Vagrant

Abstract: Technical advances in machine and system virtualization are creating opportunities for remote learning to provide significantly better support for active education approaches. Students now, in general, have personal computers that are powerful enough to support virtualization of operating systems and networks. As a conse- quence, it is now possible to provide remote learners with a common, standard, virtual laboratory and learning environment, independent of the different types of physical machines on which they work. This greatly enhances the opportunity for producing re-usable teaching materials that are actually re-used. However, configuring and installing such virtual laboratories is technically challenging for teachers and students. We report on our experience of building a virtual machine (VM) laboratory for a MOOC on relational databases. The architecture of our virtual machine is described in detail, and we evaluate the benefits of using the Vagrant tool for building and delivering the VM.

TOC :

  • Introduction
    • A brief history of distance learning
    • Virtualization : the challenges
    • The design problem
  • The virtualization requirements
    • Scenario-based requirements
    • Related work on requirements
    • Scalability of existing approaches
  • The MOOC laboratory
    • Exercises and lab tools
    • From requirements to design
  • Making the VM as a Vagrant box
    • Portability issues
    • Delivery through Internet
    • Security
    • Availability of the box sources
  • Validation
    • Reliability Issues with VirtualBox
    • Student feedback and evaluation
  • Future work
    • Laboratory monitoring
    • More modular VMs
  • Conclusions

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Testing the RuneStone interactive Python courses server in docker

I’ve been working on setting up a Docker container environment allowing to test the RuneStone Interactive server.

RuneStone Interactive allows the publication of courses containing interactive Python examples, and while most of the content is static (the Python examples are run innside a Python interpreter implemented in JavaScript, hence locally in the JS VM of the Web browser), the tool also offers an environment allowing to monitor the progress of learners in a course, which is dynamic and is queried by the browser over AJAX APIs.

That’s the part which I wanted to be able to operate for test purposes. As it is a web2py application, it’s not exactly obvious to gather all dependencies and run locally. Well, in fact it is, but I want to understand the architecture of the tool to be able to understand the deployment constraints, so making a docker image will help in this purpose.

The result is the following :

Now, it’s easier to test the writing of a new course (yet another container above the latter one), and directly test for real.

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Configuring the start of multiple docker container with Vagrant in a portable manner

I’ve mentioned earlier the work that our students did on migrating part of the elements of the Database MOOC lab VM to docker.

While docker seems quite cool, let’s face it, participants to the MOOCs aren’t all using Linux where docker can be available directly. Hence the need to use boot2docker, for instance on Windows.

Then we’re back quite close to the architecture of the Vagrang VM, which relies too on a VirtualBox VM to run a Linux machine (boot2docker does exactly that with a minimal Linux which runs docker).

If VirtualBox is to be kept around, then why not stick to Vagrant also, as it offers a docker provider. This docker provider for Vagrant helps configure basic parameters of docker containers in a Vagrantfile, and basically uses the vagrant up command instead of using docker build + docker run. If on Linux, it only triggers docker, and if not, then it’ll start boot2docker (or any other Linux box) in between.

This somehow offers a unified invocation command, which renders a bit more portable the documentation.

Now, there are some tricks when using this docker provider, in particular for debugging what’s happening inside the VM.

One nice feature is that you can debug on Linux what is to be executed on Windows, by explicitely requiring the start of the intermediary boot2docker VM even if it’s not really needed.

By using a custom secondary Vagrantfile for that VM, it is possible to tune some parameters of that VM (like its graphic memory to allow to start it with a GUI allowing to connect — another alternative is to “ssh -p 2222 docker@localhost” once you know that its password is ‘tcuser’).

I’ve committed an example of such a setup in the moocbdvm project’s Git, which duplicates the docker provisioning files that our students had already published in the dedicated GitHub repo.

Here’s an interesting reference post about Vagrant + docker and multiple containers, btw.

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Student project contributions on using docker to build headless virtualised labs for MOOC participants

After having used Vagrant to create Virtual Machines (VMs) ready made for MOOC participants, I’ve been investigating the use of docker for a similar need.

In order to move on, I’ve applied a clever trick by proposing a project to students of ours (3rd year engineering school end-of-classes project of the ASR major).

The project was addressing several needs :

  • a functional need: being able to monitor what happens inside the VMs run on the participant’s side, so that MOOC labs aren’t performed in a black box;
  • a non functional need: investigate the potential benefits of docker, compared to Vagrant.

The students (François Monniot and Alexis Mousset) have worked very well, and we have a few apps in the result, that allow us to assemble a POC in order to complete our evaluation.

In following posts, I will describe some of these components and will present some ideas and maybe results on the technology’s potential. The impatient reader may directly browse their code on GitHub, starting from the dedicated site.

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Shell script to connecting to a Shibboleth protected web app with curl

Here’s a shell script I’ve created (reusing one meant for CAS protected resources), which will allow to connect to a Web application protected by the Shibboleth SSO mechanism.
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Offline backup/mirror of a Moodle course, using httrack

I havent’ found much details online on how to perform a Moodle course mirror that could be browsed offline using httrack.

This could be useful both for backup purposes, or for distant learners with connectivity issues.

In my case, there’s a login/password dialog that grants access to the moodle platform, which can be processed by httrack by capturing the POST form results using the “catchurl” option.

The strategy I’ve used is to add filters so that everything is excluded and only explicitely mentioned filters are then allowed to be mirrored. This allows to perform the backup connected with a user that may have high privileges, while avoiding to disappear in loops or complex links following for UI rendering variants of Moodle’s interface.
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BoF “retour expérience enseignement Python” lors de la PyConFr 2014

Nous avons organisé une BoF “retour expérience enseignement Python” lors de la PyConFr 2014 à Lyon.

Cette BoF s’inscrivait dans la continuité des présentations du thème Enseignement / Recherche de la conférence.

Environ 40 participants ont pris sur leur temps de pause (merci aux organisateurs de nous avoir fourni des sandwiches de façon prioritaire) pour partager des éléments de retour d’expérience.

Voici quelques éléments qui m’ont semblé intéressants, qui pourront peut-être vous intéresser, qui ont été abordés durant la BoF, ou que j’ai collectés dans les présentations de la matinée (j’ai un peu délaissé l’amphi de l’après-midi, pour aller discuter avec quelques connaissances aussi présentes à la conf) :

  • enseignement :
    • deux environnements assez populaires : IPython notebooks, et Sage. Le deuxième éventuellement intégré avec le premier (SageCell). Les deux permettent d’avoir une interface Web qui semble offrir un certain avantage pour une population d’apprenants “génération FaceBook” qui trouve facile de rentrer du texte dans des zones de saisie d’une page Web (contrairement à des environnements type ligne de commande ou éditeurs plutôt effrayants). Avantage de disposer de LaTeX ou de texte (et plus) et de code dans un même document.
    • Même si Matlab reste assez utilisé dans certains labos (poids du legacy), l’enseignement semble pas mal passer à IPython, même si certains inconvénients existent parfois (plantages des kernels avec MatPlotLib, par ex.).
    • Livre : Calcul mathématique avec Sage
    • Les notebooks permettent de rendre la programmation vivante : le prof tape le code : montre les erreurs, les typos, etc. Rend le
      processus plus accessible.
    • Côté notation des devoirs, corrections deux solutions en environnements MOOC avec de nombreux apprenants :
  • Recherche :
    • le LaTeX embarqué dans des Notebooks IPython amène certains à s’y intéresser alors qu’ils n’y viendraient pas naturellement (“elle
      est belle ta formule, t’as fait ça comment ?” : double clic, et hop ;)
    • On commence à croiser des Notebooks IPython en matériel supplémentaire pour des publications académiques
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Le MOOC Bases de données relationnelles est lancé

Nous venons de lancer la première édition du MOOC sur les bases de données relationnelles de Télécom SudParis. Au programme, de la théorie (algèbre relationnelle), de la pratique (dans SQLite dans les navigateurs basés sur WebKit, et plus tard dans PostgreSQL dans une box Vagrant basée sur Debian (voir post précédent)), des contenus et logiciels libres (autant que possible) et pas mal de rush pour finaliser tout ça dans le Moodle.

On débute avec plus de 800 inscrits à la fin du premier jour (y compris les 180 étudiants ingénieurs de 2ème année de Télécom SudParis, qui suivront le cours présentiel en parallèle du MOOC, et collaboreront avec les apprenants externes pour les travaux personnels).

Il est toujours possible de s’inscrire : le gros du travail commence en semaine 2 (qui commence lundi 15/09 à 00h00 heure de Paris).

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Building a lab VM based on Debian for a MOOC, using Vagrant + VirtualBox

We’ve been busy setting up a Virtual Machine (VM) image to be used by participants of a MOOC that’s opening in early september on Relational Databases at Telecom SudParis.

We’ve chosen to use Vagrant and VirtualBox which are used to build, distribute and run the box, providing scriptability (reproducibility) and making it portable on most operating systems.

The VM itself contains a Debian (jessie) minimal system which runs (in the background) PostgreSQL, Apache + mod_php, phpPgAdmin, and a few applications of our own to play with example databases already populated in PostgreSQL.
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Using RDFAlchemy together with RDFLib’s SPARQLStore to query DBPedia and process resources in OO way

I’ve been searching for interesting ways to manipulate RDF graphs in Python, to create an application that would handle Linked Data Resources in an OO-way, i.e. using Python classes and not tables/sets/lists of triples. The data will be persisted in graphs in a triple store, accessed through a SPARQL enpoint.

In this post, I’ll illustrate how I managed to tie RDFLib’s SPARQLStore plugin and RDFAlchemy to reach a rather nice looking result.

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Debian docker containers using a modified baseimage-docker

I have been testing Docker for a few weeks now, and investigated the use of baseimage-docker, which provides support for supervising services with runit, and includes OpenSSH, among other things, based on an Ubuntu base system. Of couse, I’m interested in a Debian counterpart.

I had initially followed instructions provided by Steve Kemp which also prepared a Debian image including OpenSSH and runit, but it appears that baseimage-docker provides more tiny bits that avoid reinventing the wheel.

I’ve then forked the baseimage-docker to do a quick and dirty adaptation for Debian. There’s a sid variant (my ‘debian’ branch) and a wheezy one (my ‘wheezy’ branch, unsurprisingly). I haven’t used all features of baseimage-docker, so things might break for sure.

For the records, I’m playing with it as a base image to construct a docker-based container running the FusionForge test suite.

Did I warn you it’s quick and dirty and without any warranty ? Hoping that this is useful anyway.

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Tagged a first version of the TWiki to FusionForge’s MediaWiki converter

As announced previously, I’ve been hacking on a migration tool allowing to import into the MediaWiki of a FusionForge project, a conversion of the contents of a TWiki wiki.

I’ve succesfully imported a first project (from PicoForge to FusionForge) using the tool, so I’ve decided to tag a first release and make the Git repo accessible.

More details at : https://fusionforge.int-evry.fr/projects/pytwiki2mediawi/

Feel free to ask here in the comments or by email, in case of need.

And, yes, my Python is most likely awful, but at least, this works, and much more featureful than existing tools I could test.

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