Jonasfj.dk/Blog
A blog by Jonas Finnemann Jensen


September 13, 2020
Reviving a php4/mysql4 LAMP Application with docker
Filed under: Computer,English,Linux,School by jonasfj at 2:15 pm

Back in high school (HTX 2005-2008) I operated a custom MediaWiki application for collaborative note taking, tracking home work and occasional sharing of homework 🙈. In case you don’t know MediaWiki is the software behind wikipedia.org. At the time I was using a Danish hosting provider, and couldn’t get LaTeX integration working properly, so I ended up hacking MediaWiki to use mimetex. Similarly, I added a few extensions for calendar integration, raw HTML, etc. These hacks and extensions made upgrading MediaWiki challenging, hence, I never upgraded past MediaWiki 1.5.5 released in 2006.

It should not surprise anyone that the wiki was full of spam a few years later. Even though, write access was only granted to trusted users. Some bot must have been scanning the internet for MediaWiki installations with known vulnerabilities, and automatically exploited those vulnerabilities to post spam. Naturally, I ended up taking the wiki offline, being too busy to fix it.

Then earlier this year I decided that it was the time to revive my old wiki. But how do you revive an ancient php4 / mysql4 application? It’s probably possible to tweak it such that it works on newer versions of PHP and MySQL. But my database dumps from mysql4 didn’t import on mysql5 without hacks, and some of my extensions didn’t work with php5. So I decided to go looking for a way to install and run php4 and mysql4.

Initially, I went looking for a docker image or virtual machine with a php4 and mysql4 LAMP stack pre-configured. But I had no such luck, there was a few php4 docker images, but they were running mysql5. Then I found the End-Of-Life Debian images on hub.docker.com/r/debian/eol/. Using debian/eol:sarge it is easy to install php4 and mysql4 from the package manager, as illustrated in the Dockerfile below.

FROM debian/eol:sarge

ENV DEBIAN_FRONTEND noninteractive

# Install php4, mysql4, apache2, imagemagick, build-essential and phpmyadmin (for good measure)
RUN apt-get update -y \
  && apt-get install -y \
    mysql-server \
    mysql-client \
    php4 \
    apache2 \
    libapache2-mod-php4 \
    php4-mysql \
    imagemagick \
    build-essential \
    phpmyadmin

# Enable mod_rewrite
RUN a2enmod rewrite \
  && sed -i 's/AllowOverride None/AllowOverride all/' /etc/apache2/sites-available/default

# Launch apache2 and mysql when starting the container
ENTRYPOINT /bin/bash -c 'apache2 > /dev/null && mysqld > /dev/null & exec bash --login'

The Dockerfile above will create an image with a php4/mysql4 LAMP stack serving from /var/www/. For simple LAMP applications all that remains is to configure mysql users, restore database from SQL dump, and copy php files and resources into /var/www/. This can be done with a few commands as illustrated below.

# Setup mysql with empty root password
mysqladmin -u root password ''

# Create $DATABASE_USERNAME with $DATABASE_PASSWORD
echo "GRANT ALL PRIVILEGES ON *.* TO '$DATABASE_USERNAME'@'localhost' IDENTIFIED BY '$DATABASE_PASSWORD';" | mysql;

# Create $DATABASE_NAME and load contents from SQL dump.
echo "CREATE DATABASE $DATABASE_NAME; USE $DATABASE_NAME;" | cat - /src/database-dump.sql | mysql

# Copy php files and resources to /var/www
cp -r /src /var/www

From php4 your application can connect to localhost:socket with the $DATABASE_USERNAME and $DATABASE_PASSWORD created above. Obviously, one should never expose this Docker image to the internet (ie. deploy it to a server). Debian Sarge haven’t received security updates for years. But we can crawl the site and convert it to static files using wget. Simply run the LAMP app as a Docker container locally, find the IP of the Docker container, and run wget as follows:

wget \
  --no-clobber \
  --recursive \
  --user-agent='Mozilla/5.0 (X11; Linux i686; rv:10.0) Gecko/20100101 Firefox/10.0' \
  --page-requisites \
  --adjust-extension \
  --span-hosts \
  --convert-links \
  --restrict-file-names=windows,ascii \
  --trust-server-names \
  --domains "$DOCKER_CONTAINER_IP" \
  -e robots=off \
  --tries 1 \
  "http://$DOCKER_CONTAINER_IP/"

If your old LAMP application contains absolute links, one can temporarily tweak /etc/hosts to make the domain point to docker container. Also checkout the wget manual for more options, depending on our URL patterns --restrict-file-names=nocontrol might look better. To successfully render my old MediaWiki setup into static files I tweaked the theme to remove unnecessary links. But wget also has options to exclude certain directories for patterns. In my case the final result is visible at jopsen.dk/wiki, these are my high school notes (in Danish).

I had actually dreaded this project a bit, fearing that I would have to follow a lengthy install guide to setup a server on a slow virtual machine. But thanks to the amazing Debian EOL images for docker reviving and old php4 / mysql4 LAMP app was almost a breeze — who knew restarting apache could make you feel all nostalgic ūüėÄ



September 22, 2013
Model Checking Weighted Kripke Structures in the Browser
Filed under: Computer,English,School by jonasfj at 7:01 pm

I recently graduated from Aalborg University with Master degree in Computer Science. Since then, Lars K√¶rlund √ėstergaard and I, along with our professors Jiri Srba and Kim Guldstrand Larsen published a paper on our work at SPIN 2013. Lars and I attended the conference at Stony Brook University, New York, where I presented the paper. I’ve long planned to write a series of blog posts about these things, but since I started at Mozilla I’ve been way too busy doing other interesting things. I do, however, despise the fact that my paper is hidden behind a pay-wall at Springer. So I feel compelled to use my co-author rights and release the paper here along with a few other documents, that contains proofs and results in greater detail.

Anyways, as the headline suggests this post is mainly about model checking of Weighted Computation Tree Logic (WCTL) on Weighted Kripke Structures (WKS) in a web browser. To test out the techniques we developed for local model checking, we implemented, WKTool, a browser based model checking tool, complete with graphical user-interface, syntax highlighting, inline error messages, graphical state-space exploration, and of course on-the-fly model checking using Web Workers.

If Kripke structures and branching time logics are foreign concepts to you, this post is probably of limited interest. However, if you’re familiar with the¬†Calculus of Communicating Systems¬†(CCS) as used in various versions of the Concurrency Workbench, this post will give an informal introduction to the syntax of the Weighted Calculus of Communicating Systems (WCCS) and WCTL as using in WKTool.

Weighted Calculus of Communicating Systems

The following table outlines the syntax for WCCS expressions. The concepts are similar to those from Concurrency Workbench, parallel composition allows input and output actions to synchronize, and restriction forces synchronization. However, it maybe observed that actions prefixes also carry a weight. This is the weight of the transition with the action is executed, on synchronization the maximum weight is used (though this is not a technical restriction).

Expression Syntax
Process Definition M := P;
Action Prefix <c,8>.P  or <c!,8>.P or <c>.P
Atomic Label a:P
Parallel Composition P | Q
Choice P + Q
Restriction P \ {c} or P \ {c1, c2, c3}
Renaming P [a1 => a2, a3 => a4] or P [c1 -> c2, c3 -> c4]
Empty Process 0

As WCCS defines Kripke structures and not Labelled Transistion Systems (LTS) we shall also specify atomic propositions. These are also prefixed with colon, in parallel and choice composition the atomic propositions from both sub-processes are considered. In fact, the action prefix is the only construction from which atomic propositions of the sub-process isn’t considered.

Weighted Computation Tree Logic

The full syntax of WCTL is given in the help section of WKTool, conceptually there are few surprises here. WCTL features boolean operators, atomic proposition and boolean constants as expected. However, for existential and universal until modalities, WCTL adds an optional upper-bound. For example the property E a U[<=8] b holds if there exists a path such that the atomic property a holds until the atomic property b holds, and the accumulated weight at this point does not exceed 8. Similar upper-bound is available for universal until and derived modalities.

For the existential and universal weak-until modalities WCTL offers a lower-bound constraint. For example the property E a W[>=8] b holds if there exists a path such that the atomic property a always holds, or there is a path such that the atomic property a holds until the atomic property b holds and the accumulated weight at this point isn’t less than 8. Observe that the bound has no effect if there is a path where the atomic property¬†a¬†always¬†holds, thus, a zero-cycle might satisfy this property.

In the examples above the nested properties are atomic, however, WKTool does in fact support nested fixed-points when the min-max encoding us used.

Weighted On-The-Fly Model Checking with WKTool

WKTool is hosted at¬†wktool.jonasfj.dk, you can save your models to local storage (in your browser) or export them in a JSON format that can be shared or loaded later. I’m sure most of the features are easy to locate, but do notice that under “Load” > “Load Example” the 4 last examples are the scalable¬†models used for benchmarks in our paper. Try them out, the default scaling parameters are sane and they come with properties that can be verified, some of them even have comments to help you understand what they do.

wktool-screenshot

WKTool available GNU GPLv3¬†and the sources are hosted at¬†github.com/jonasfj/WKTool, it’s all in CoffeeScript using PEG.js for parsers, CodeMirror¬†with custom lexers¬†for highlighting, Buckets.js for data structures, Arbor.js for visualization and twitter-bootstrap for awesome styling.

 

 



July 20, 2011
Petri Nets With Discrete Variables, – A Bachelor Project
Filed under: Computer,English,School by jonasfj at 1:50 pm

A few days ago a diploma dropped in the door, meaning that after 3 years at Aalborg University I’ve got a “Bachelor of Science (BSc) in Computer Science”, as it says on the paper… I’m¬†of course¬†continuing as a master student next – no reason to get out “there” in the real world, where you have to work, assuming you don’t what to starve ūüôā

Anyways, it¬†occurred¬†to me that I haven’t blogged about my Bachelor project. So I better get it done now, as I’m off for vacation in California later tonight… This semester we worked in groups of 3, and was supposed to write a 12-20 pages article, as opposed to a 100-200 pages report. Which turned out to be quite challenging, but also somewhat nice, because we got to polish every sentence.

As the title of the post indicates we did a project about Petri nets, a very simple but powerful modeling language. To achieve a “feeling” of novelty we introduced global discrete variables, that you can condition on and modify in transitions, and called our new model for Petri nets With Discrete Variables (PNDV). Whilst, to my knowledge, this have not been done before, we didn’t focus on showing that PNDVs where particularly useful for any specific purpose. So that part of the project feels a little shoehorned, at least to me, and maybe only me, because we all got an A for the project.

Nevertheless, assuming that the PNDV model (we invented) is interesting, then the graphical Petri net editor and verification tool we wrote during this project might also be interesting. In a desperate search for a name we came up with PeTe, yes is spelled pretty weird, but also quite cute ūüôā

Given a PNDV or Petri net PeTe can determine if a state satisfying a given formula is possible. This problem is very hard (EXPSPACE-hard), but we had a lot of fun writing different search strategies for exploring the state space of a PNDV. Most notably we found that even quite simple heuristics can provide a huge performance improvement by guiding a search in state space. We also had great success with over-approximation, by using state equation and trap testing to disprove the satisfyability of a formula.

The heuristics and methods implemented in PeTe is presented in the article we wrote, available for download below. This article also present some, in my¬†opinion, rather shoehorned results, like translation from Discrete Timed Arc Petri Net to PNDV. I also can’t help but feel that the direction and goal in the article could have been more clear. But done is done, and I’m off to vacation when I’ve added some links ūüôā



December 15, 2010
A Project on Optimal Triangulation of Bayesian Networks
Filed under: Computer,English,School by jonasfj at 11:28 am

This semester we did a project in machine intelligence, however, as I find probability calculus and Bayesian networks utterly boring I convinced my group to do a project about triangulation of Bayesian networks. A triangulation of an undirected graph G, is a set of edges called fill-ins, such that G with these fill-ins added is a chordal graph (a graph that doesn’t have a chord-less cycle of more than 3 node). Triangulation is of graphs is used for many purposes, and with difference optimality criteria, such as minimum fill-ins, minimum clique size (tree width) and minimum maximal clique sum (optimal table size), as is relevant for Bayesian networks.

The problem of finding an optimal triangulation is NP-Hard (with respect to mentioned optimality criteria). And since there’s many fairly good simple greedy heuristics, it can be argued that algorithms for optimal triangulation of Bayesian networks are uninteresting. However, to check of a greedy heuristic is good, optimal triangulations are needed. It’s also possible that optimal triangulation might be worthwhile if ¬†computed offline, especially if the application needs to process a lot of data or work on an embedded platform. Or whatever, optimality is always slightly interesting, if not for anything useful, than for the fun of finding them…

In this project we implemented some simple greedy triangulation heuristics, compared their result to the optimal solutions. But most interesting is probably our work on search algorithms for optimal triangulations of Bayesian networks. We based our work on two articles by Thorsten J. Ottosen and Finn V. Jensen, who does a best or depth first search in the space of all elimination orders. As far as we’re aware these articles are the only ones that proposes algorithms for optimal triangulation of ¬†Bayesian networks.

In this project we’ve created good improvements to the optimal triangulation algorithms. We reduce the search space by excluding elimination orders resulting in the same triangulation.¬†Our improvements provides around 5x speedup on sparse graphs, and can be applied to regardless of the optimality criterion. I think this project was really cool, because I got to play with something that was new and fairly untouched. And the fact that I managed to propose a a few interesting improvements didn’t make it any less cool ūüôā

Report and source code:



June 25, 2010
groo, a GRim Object Oriented programming language
Filed under: Computer,English,School by jonasfj at 1:46 am

Hmm… Not the official title of my fourth semester project at Aalborg University. For which I just got an A… and have been thinking about publishing since I handed it in.

This semester my group have designed and implemented a small statically typed object oriented language slightly inspired by Python. We wrote our own lexer and parser generator in Python, and implemented the compiler in C++. And just for the record we implemented the DFA of the lexer and PDA of the parser using goto’s, inspired by re2c, this was quite fun and the result very fast.

The language is called groo (that was the best name we could come up with), it compiles into gril (groo intermediate language) which in turn run on VROOM (groo virtual machine) where memory is managed by MOM (Mark-sweep Object Manager). Whilst this isn’t the best project yet, and all the acronyms doesn’t make much sens, I really like to say that when we need to release memory we call MOM to clean up ūüôā
(I appoligies for my crazy sens of humor).

I don’t think the project is of much use to anybody else… But if you want to play with simple, well documented compiler in C++, this might be it… Also the parser generator is AFAIK pretty unique, haven’t see anybody else implement a parser using goto’s… Anyway the project report and groo compiler source code is all in English and available here:



December 20, 2009
Foodolini, A food management system
Filed under: English,School by jonasfj at 11:51 am

Now I’m done with my third semester at Aalborg University. The focus on this semester was software engineering with the Object-Oriented Analysis (OOA&D). Personally I found this subject rather boring, I guess making pretty diagrams trying explain technical stuff in a manner “mortals” can understand maybe utterly uninteresting ūüôā

Anyway, for this project we analyzed, designed and implemented system for managing recipes and food in a common household. The system was suppose to compute nutritional intake and manage diets and exercises as well, however, these features were never fully designed and implemented. Nevertheless, it uses the USDA National Nutrient Database for Standard Reference, to find the nutritional content of various groceries.

The system is called Foodolini and was implemented in C# on Mono using Gtk#, but also runs on .Net and Gtk# for .Net. Foodolini uses Sqlite as database, and we wrote a simple and neat ORM tool, inspired by SubSonic‘s SimpleRepository. However, the most interesting feature in my opinion is the bar code scanner used when registering groceries in the system. It’s implemented using a ZBar which captures and scans images from a webcam. I’ll be release C# bindings for ZBar and a Gtk# widget in an upcoming blog post, when I’ve cleaned it up a bit…

  • Foodolini 1.0.0 (sources, binaries and documentation)
  • Report (documenting the analysis, design and implementation of Foodolini)


May 24, 2009
TheMatrixDistributed, distributed realtime ray tracing
Filed under: Computer,English,School by jonasfj at 4:07 am

Now I’m finally done with my second semester project at Aalborg University, and as usually I publish my things here. This project is about distributed realtime ray tracing. Which have been fun, because ray tracing is CPU bound and it have been a joy to play with all sorts of hacks and optimizations.

The report discusses what the demand for ray tracing is, what ray tracing is and how a ray tracer can be implemented, covering the basics of ray tracing and bounding volume hierarchies. It also discusses how distribution could be done, which is the only slightly new thing in it… It’s not a perfect report there’s still some areas where the English is kind of bad and some sections that could use a rewrite or two ūüôā
Nevertheless, considering the circumstances I’m satified the result. And the group have worked fine…

Now the interesting part, TheMatrixDistributed, as a part of this project we implemented a distributed realtime ray tracer, with bounding volume hierarchies, spheres, planes and triangles that supports textures. We also did a small obj parser to import models exported from Blender. TheMatrixDistributed is implemented in C++ and it’s turned out to be quite fast, considering that the rest of my group have little to no programming experirence. When distribution to 6 dualcore laptops and a quadcore desktop we got around 8 FPS at best with 1024×768 screen and about 100,000 triangles in the scene, not filling the entire screen.

TheMatrixDistributed

The frontpage image (original 1024×768) seen above has about 1,000,000 triangles it was render on 6 dualcore laptops and a quadcore desktop at about 0.6 FPS with 4x antialias.

Though the report and TheMatrixDistributed probably isn’t of much value to anybody it’s published here if anybody should be interested. The report is released under Creative Commons Attribution-Noncommercial-Share Alike 2.5 and TheMatrixDistributed is released under GNU GPL.



December 15, 2008
RaptorMail, an encrypting GMail client
Filed under: Computer,Linux,School by jonasfj at 2:30 am

Tomorrow, I’m finally turning in my P1 project, that’s the first semester project, at Aalborg University. The project is about RSA, and usability of encrypting email clients, and as a part of the project we’ve implemented an encrypting email client for GMail. In Python, with PyGTK and SQLite as backend, e.g. access mail while not online.

Anyway, I thought I’d publish the report here for anyone to stumble upon. Honestly it’s not that great, it’s written in English and is subject to some serious gramma issues, as we’ve been pretty busy actually getting it ready… For those who does not know what a P1 project at AAU is, it is a project conducted by a group of 4-7 students. Most of the education at AAU, happens through these kind of projects, which is kind of nice and gives a lot of freedom. But just for the record, I have not written the entire report myself, so do not blame me all the horror that may be found within it… ūüôā

Enough about the report, during the project we also wrote an encrypting GMail client, called RaptorMail – don’t ask why. A GMail client is actually quite interesting, if I managed to find the time, it would be real nice to nail the last few bugs and integrate it with GPG… An application to access GMail through a non-webinterface while still maintaining the same feature set would be nice to have. And cacheing all mail for offline usage is an absolute killer-feature.

But I’m afraid I have a lot of other small projects on my mind too, so actually getting it out there is probably not going to happen. But if anybody is looking for a way to synchronize and interface GMail with a local database from Python the “gmail_cache” module I’ve written for this project is fairly comprehensive and well documented.



June 28, 2008
Så blev man student, med hue på hovedet
Filed under: Dansk,Personal,School by jonasfj at 2:17 pm

I den forgangne uge er jeg blevet student, og har hermed afsluttet HTX. Med et snit på 9,6 kan jeg også godt være meget godt tilfreds med mine karakterer. Herunder ses mine eksamenskarakter:

Studie område 2 7
Matematik Skriftlig 12
Dansk Skriftlig 10
Fysik Skriftlig 12
Engelsk Mundtlig 12
Teknik 12
Dansk Mundtlig 7

Jeg synes ogs√• selv at alle mine eksamener er g√•et meget godt. Der var lige teknik, hvor tiden gik lidt for hurtigt og jeg ikke fik sagt noget fornuftigt, men s√• var projektet heldigvis s√• godt at de ikke kunne give mig mindre end 12. Til dem der ikke har h√łrt om mit afsluttende teknik projekt, s√• var det et intelligent hjem under navnet iHome. Systemet var bygget op omkring en webserver, der bestod af et atmega644, et SD-kort, en enc28j60 ethernet controller og lidt andet godt. P√• webserveren k√łrt uip (Tcp/Ip stack), Tiny FatFs (FAT implementating), diverse drivere, en simpel HTTP server til b√•de statistiske sider og Web API, diverse hardware drivere og en mDNS-responder name resolution implementering. Sidst n√¶vnte er jeg selv lidt stolt af at have skrevet, mange af de andre komponenter er tyv stj√•let andre steder fra. Webserveren var tilsluttet LCD, keypad, tribleastabilmultivibrator (alarm), d√łrl√•s, vindue √•bner samt diverse sensorer. Jeg har valgt ikke at frigive projektet da kildekoden er en smule mixed og meget hacked. Men dele af systemet er tilg√¶ngeligt i SVN hos avr-uip.



May 16, 2008
Sidste skoledag…
Filed under: Dansk,Personal,School by jonasfj at 7:22 pm

S√• er min skole tid p√• HTX forbi, nu mangler jeg blot eksamenerne og s√• er jeg student. I g√•r var det min sidste skoledag p√• HTX, og da skolen var f√¶rdig, var vi til galla p√• HTX. Hvilket var v√¶ldig hyggeligt, og danset fik vi i sagens natur heldigvis ikke ūüôā

Kl 24.00 fik vi udleveret √•rskarakter og eksamens udtr√¶kninger, og jeg fik trukket Dansk, Engelsk mundtlig samt Dansk, Fysik og Matematik skriftlig. Derudover skal jeg selvf√łlgelig op i Teknik A og desv√¶rre ogs√• studie omr√•de 2 (“desv√¶rre”, fordi ikke engang bekendtg√łrelsen definere tydeligt hvad det g√•r ud p√•). I √•rskarakter har jeg f√•et som f√łlger:

Astronomi C mdt. 10
Dansk A mdt. 10
Dansk A skr. 7
Engelsk A mdt. 7
Engelsk A skr. 7
Fysik A mdt. 12
Fysik A skr. 10
Kemi B skr. 7
Kemi B mdt. 7
Matematik A mdt. 4
Matematik A skr. 10
Programmering C mdt. 12
Teknik A samlet vurdering 10
Teknologi B samlet vurdering 10
Teknologi Historie C mdt. 7

Der er selvf√łlge intet overst√•ende jeg kan v√¶re utilfreds med, udover Dansk A mdt. selvf√łlgelig, der ville jeg nok gerne n√łjes med 7 ūüôā Men jeg f√łler ikke der grundlag for en klage. Derudover er jeg personligt lidt skuffet over min Engelsk A, hvor jeg plejer at kunne g√łre det lidt bedre, men jeg er nok faldet lidt af p√• den her til sidst… Min matematik mdt. er heller ikke overraskende, men aktivitet i matematik timerne taget i betragtning, ikke at jeg har nogle faglige problemer der. Men alt i alt er jeg godt tilfreds… Nu skal jeg bare over mine 7 eksamener.



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