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Glen Turner

Postcards from Semaphore


Academic publishing, now being tried by the bottom-feeders
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There are a lot of fake academic journals out there seeking to defraud authors. Not really surprising: academic publishing has such a high profit margin that even established publishers have a whiff of running a scam[1], open access has blurred the edge of what a journal is, and the sharks have moved in.

But now it seems that even scammers who once may have been Nigerian princes are now trying their hand:

From: Kate .M. (editor)
Sent: Friday, 28 August 2015 9:21 AM
Subject: Assist in Peer-Reviewing Research Papers

Dear Professor,

Thank you for your time for reading this mail. Science Publication wishes to invite you to become our Journal Review Board member.

Your professional expertise will be greatly appreciated by us as well as authors who have submitted their research manuscript for peer-review evaluation and publication.

Our journal deals on the following key studies:

Microbiology | Biochemistry | Medicine and Clinical Trials | Biotechnology | Agricultural Research and Management | Physics | Mathematics and Statistics | Pure and Applied Chemistry | Environmental Engineering Research | Electrical and Electronic Engineering | Civil Engineering and Architecture | Chemical Engineering Research | Economics | Business Management | Psychology | Sociology and Anthropology |

Please inform us of your interest to participate in our Review Board. More information will be provided to you upon your reply.

Thank you.
Assistant Editor
Science Journal Publication

NOTE: Simply Send A Blank Message With Unsubscribe As Subject to Remove Your E-mail From Our List.

For the record: not a professor.

[1] Someone else pays for research to be done. Peer review and editorial is done for free. "Page fees" are charged to authors cover the publishing costs. The journal's subscription revenue is handsome profit.


Customising a systemd unit file
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Once in a while you want to start a daemon with differing parameters from the norm.

For example, the default parameters to Fedora's packaging of ladvd give too much access to unauthenticated remote network units when it allows those units to set the port description on your interfaces[1]. So let's use that as our example.

With systemd unit files in /etc/systemd/system/ shadow those in /usr/lib/systemd/system/. So we could copy the ladvd.service unit file from /usr/lib/... to /etc/..., but we're old, experienced sysadmins and we know that this will lead to long run trouble. /usr/lib/systemd/system/ladvd.service will be updated to support some new systemd feature and we'll miss that update in the copy of the file.

What we want is an "include" command which will pull in the text of the distributor's configuration file. Then we can set about changing it. Systemd has a ".include" command. Unfortunately its parser also checks that some commands occur exactly once, so we can't modify those commands as including the file consumes that one definition.

In response, systemd allows a variable to be cleared; when the variable is set again it is counted as being set once.

Thus our modification of ladvd.service occurs by creating a new file /etc/systemd/system/ladvd.service containing:

.include /usr/lib/systemd/system/ladvd.service
[Service]
# was ExecStart=/usr/sbin/ladvd -f -a -z
# but -z allows string to be passed to kernel by unauthed external user
ExecStart=
ExecStart=/usr/sbin/ladvd -f -a

---
[1] At the very least, a security issue equal to the "rude words in SSID lists" problem. At it's worst, an overflow attack vector.

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Configuring Zotero PDF full text indexing in Debian Jessie
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Background

Zoterto is an excellent reference and citation manager. It runs within Firefox, making it very easy to record sources that you encounter on the web (and in this age of publication databases almost everything is on the web). There are plugins for LibreOffice and for Word which can then format those citations to meet your paper's requirements. Zotero's Firefox application can also output for other systems, such as Wikipedia and LaTeX. You can keep your references in the Zotero cloud, which is a huge help if you use different computers at home and work or school.

The competing product is EndNote. Frankly, EndNote belongs to a previous era of researcher methods. If you use Windows, Word and Internet Explorer and have a spare $100 then you might wish to consider it. For me there's a host of showstoppers, such as not running on Linux and not being able to bookmark a reference from my phone when it is mentioned in a seminar.

Anyway, this article isn't a Zotero versus EndNote smackdown, there's plenty of those on the web. This article is to show a how to configure Zotero's full text indexing for the RaspberryPi and other Debian machines.

Installing Zotero

There are two parts to install: a plugin for Firefox, and extensions for Word or LibreOffice. (OpenOffice works too, but to be frank again, LibreOffice is the mainstream project of that application these days.)

Zotero keeps its database as part of your Firefox profile. Now if you're about to embark on a multi-year research project you may one day have trouble with Firefox and someone will suggest clearing your Firefox profile, and Firefox once again works fine. But then you wonder, "where are my years of carefully-collected references?" And then you cry before carefully trying to re-sync.

So the first task in serious use of Zotero on Linux is to move that database out of Firefox. After installing Zotero on Firefox press the "Z" button, press the Gear icon, select "Preferences" from the dropbox menu. On the resulting panel select "Advanced" and "Files and folders". Press the radio button "Data directory location -- custom" and enter a directory name.

I'd suggest using a directory named "/home/vk5tu/.zotero" or "/home/vk5tu/zotero" (amended for your own userid, of course). The standalone client uses a directory named "/home/vk5tu/.zotero" but there are advantages to not keeping years of precious data in some hidden directory.

After making the change quit from Firefox. Now move the directory in the Firefox profile to whereever you told Zotero to look:

$ cd
$ mv .mozilla/firefox/*.default/zotero .zotero

Full text indexing of PDF files

Zotero can create a full-text index of PDF files. You want that. The directions for configuring the tools are simple.

Too simple. Because downloading a statically-linked binary from the internet which is then run over PDFs from a huge range of sources is not the best of ideas.

The page does have instructions for manual configuration but the page lacks a worked example. Let's do that here.

Manual configuration of PDF full indexing utilities on Debian

Install the pdftotext and pdfinfo programs:

    $ sudo apt-get install poppler-utils

Find the kernel and architecture:

$ uname --kernel-name --machine
Linux armv7l

In the Zotero data directory create a symbolic link to the installed programs. The printed kernel-name and machine is part of the link's name:

$ cd ~/.zotero
$ ln -s $(which pdftotext) pdftotext-$(uname -s)-$(uname -m)
$ ln -s $(which pdfinfo) pdfinfo-$(uname -s)-$(uname -m)

Install a small helper script to alter pdftotext paramaters:

$ cd ~/.zotero
$ wget -O redirect.sh https://raw.githubusercontent.com/zotero/zotero/4.0/resource/redirect.sh
$ chmod a+x redirect.sh

Create some files named *.version containing the version numbers of the utilities. The version number appears in the third field of the first line on stderr:

$ cd ~/.zotero
$ pdftotext -v 2>&1 | head -1 | cut -d ' ' -f3 > pdftotext-$(uname -s)-$(uname -m).version
$ pdfinfo -v 2>&1 | head -1 | cut -d ' ' -f3 > pdfinfo-$(uname -s)-$(uname -m).version

Start Firefox and Zotero's gear icon, "Preferences", "Search" should report something like:

PDF indexing
  pdftotext version 0.26.5 is installed
  pdfinfo version 0.26.5 is installed

Do not press "check for update". The usual maintenance of the operating system will keep those utilities up to date.

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Notes for upgrading RaspberryPi from Raspbian Wheezy to Raspbian Jessie
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Debian distributions for the Raspberry Pis

The Raspian distribution is Debian recompiled and tuned for the ARM instruction set used in the original Raspberry Pi Model A, Model B, and Model B+.

The Raspberry Pi2 has a more recent ARM instruction set. That gives RaspberryPi2 users two paths to Debian Jessie: use the Raspbian distribution or use the stock Debian ARM distribution with a hack for the Raspberry Pi kernel.

This article is about upgrading an existing Raspbian Wheezy distribution to Raspbian Jessie. Some Linux systems administration skill is required to do this.

Alter /etc/apt/sources.list

Edit the files /etc/apt/sources.list and /etc/apt/sources.list.d/*.list replacing every occurance of "wheezy" with "jessie".

For example is /etc/apt/sources.list says:

deb http://mirrordirector.raspbian.org/raspbian/ wheezy main contrib non-free rpi

then alter that to:

deb http://mirrordirector.raspbian.org/raspbian/ jessie main contrib non-free rpi

Similarly /etc/apt/sources.list.d/raspi.list contained:

deb http://archive.raspberrypi.org/debian/ wheezy main

and this becomes:

deb http://archive.raspberrypi.org/debian/ jessie main

The repository described by the file /etc/apt/sources.list.d/collabora.list doesn't yet have a Jessie section.

Upgrade

The number of packages to upgrade will depend on how many packages you installed in addition to those which originally arrived with Raspbian Wheezy. In general, the mark is somewhere around 1GB of data.

Upgrades are best done from the old-fashioned text console. Press Crtl-Alt-F1 and login as root.

Enter:

# apt-get update
# apt-get dist-upgrade
# apt-get autoremove

Do not reboot when that command completes. We'll fix a few of the more common issues with the upgrade at this most convenient moment.

Correct errors

udev rules

There are two files containing syntax errors in /lib/udev/rules.d/ which cause udev to fail to start: 60-python-pifacecommon.rules and 60-python3-pifacecommon.rules. These files are not owned by any packages, which is a little annoying and naive of their authors. Rename them to stop udev attempting to read them and failing.

# cd /etc/udev/rules.d
# mv 60-python-pifacecommon.rules 60-python-pifacecommon.rules.failed
# mv 60-python3-pifacecommon.rules 60-python3-pifacecommon.rules.failed

ifplugd replaced by wicd

Networking of plugin interfaces is done using ifplugd in Wheezy. This is done using wicd in Jessie.

# apt-get purge ifplugd

systemd is the cgroups controller

The init system is done using System V-style scripts in Wheezy. This is done using systemd in Jessie.

Systemd uses control groups so that unexpected process stop is reported to systemd. In Linux a control group can only have one controlling process, which has to be systemd in Jessie. This isn't a poor outcome, as systemd makes a fine controller.

However if another process attempts to be the control groups controller then systemd can fail when starting processes. So remove any existing controllers:

# apt-get purge cgmanager cgroup-bin cgroup-tools libcgroup1

systemd is the init system

A package called systemd-shim allow other init systems to use logind and other programs, as systemd-shim provides just enough of systemd's function. Jessie uses systemd, so we don't need systemd-shim. Unfortunately the dist-upgrade seems to pull this in:

# apt-get purge systemd-shim

[Thanks to ktb on the RaspberryPi.org forums for correcting a typo here.]

Allow logging to the journal

systemd doubles the number of system loggers, by adding a new logger called journald. It can provide logs to the usual syslogd. However when debugging startup issues it can be useful to have journald write the files itself. To do this create the directory /var/log/journal/

journald keeps its logs in binary. Use journalctl -xb to see the logs. The -1 parameter is hand to view the log of the previous boot.

Consider booting in single user mode

You might choose to give yourself a way to debug startup issues by having the kernel start in single user mode. Edit /boot/cmdline.txt, appending the text single

The workflow here is:

  • Boot RPi.

  • Press Ctrl-D when asked for a password to enter single user mode. The boot will continue into multi-user mode.

  • If this hangs then press Ctrl+Alt+Del to shut down.

  • Restart RPi. This time provide the root password at the single user mode password prompt. Use journalctl to view the log of the previous boot and examine what went wrong.

  • Correct the error, and use shutdown -r now to try again from the top.

Once you have sorted issues during system init then remove the single phrase from /boot/cmdline.txt so that the system boots into multiuser mode.

Reboot

Reboot and work through issues resulting from the upgrade.

Clean up

# apt-get clean

Journald is a enterprise-level logging solution, so it is keen on flushing data to disk. This radically increases the number of flash blocks written and this reduction in flash card lifetime isn't appreciated on the RPi. So it's probably best to remove /var/log/journal/* and allow journald to log to RAM and syslog instead.


Fedora 21: automatic software updates
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The way Fedora does automatic software updates has changed with the replacement of yum(8) with dnf(8).

Start by disabling yum's automatic updates, if installed:

# dnf remove yum-cron yum-cron-daily

Then install the dnf automatic update software:

# dnf install dnf-automatic

Alter /etc/dnf/automatic.conf to change the "apply_updates" line:

apply_updates = yes

Instruct systemd to run the updates periodically:

# systemctl enable dnf-automatic.timer
# systemctl start dnf-automatic.timer
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Fedora: easy recovery from corrupt root partition
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When you boot Fedora with a corruption which is not automatically repaired when systemd runs fsck -a then you are asked on the console if to enter single user mode, or if to continue. If you choose to enter single user mode then you'll find that you can't run fsck /dev/md0 as the root filesystem is mounted.

Dracut has a debugging mode with named breakpoints: it will boot up to the break-point, and then dracut will drop the console into a shell.

This is useful for solving a corrupted root filesystem, we can boot up to just before the disk is mounted, breakpoint into the Dracut shell, and then run fsck on the yet-to-be-mounted root filesystem. To do this temporarily add the Dracut breakpoint parameter

dracut.break=pre-mount

to the Linux kernel.

In Fedora you do can temporarily modify the Linux kernel parameters by pressing e at the Grub bootloader prompt, arrow-ing down to the "linux" command, adding the parameter to the end of that line, and pressing F10 to run the Grub command list you see on the screen.

Dracut will load the logical volumes, assemble any RAID, and then present a shell on the console. Say fsck /dev/md0 (or whereever /etc/fstab says your / filesytem lives) and then reboot. This is a world easier than booting from a CD or USB and working out which partitions are on what logical volumes, and which logical volumes are in which RAID devices.

Breakpoints are a very fine feature of Dracut and, as this blog posting shows, very useful for solving problems which appear during the early stages of booting the machine.

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Hansard, ACT Parliament, 1992-09-16
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Mr Stuart Gill

MR STEVENSON (4.29): Madam Speaker, last year I made a number of statements in this Assembly concerning links between organised crime and the pornography industry in Australia. I had received information on these matters from Stuart Gill, who told me that he had been a senior investigator with the Costigan royal commission. He had also said that he was working with the Victoria Police as a consultant and had worked in that capacity for some time. That was later confirmed in a letter of 24 May 1991 by Inspector Cosgriff of the Victoria Police Internal Security Unit.

I hired Gill on staff to assist me in matters relating to pornography and organised crime. During that time Gill told me that a man named Gerald Gold had been named as a leading eastern States crime figure in a confidential segment of the final report of the Costigan royal commission. As a result of that information, I made statements in this Assembly concerning Mr Gold that I now believe were wrong. I later came to understand that Stuart Gill was not a police consultant but was, in fact, an informer for the Victoria Police. Gill left my employ in October last year.

Yesterday the Victorian media reported on allegations about widespread police and political corruption resulting from an investigation named Operation Iceberg. The Victoria Police Commissioner, Mr Kel Glare, stated yesterday that the allegations were not only unsubstantiated but utterly false. The commissioner said that the Operation Iceberg document was not a police report but had been prepared by a police informer. That police informer has been named as Stuart Gill. I am aware that Stuart Gill was born under the name of Paul Dummett and has also used the name Andrew McAuley.

I wish to take the opportunity to apologise to Mr Gerald Gold for any difficulties he may have been caused by statements I made in this house. Gill also stole documents from my office and spread misleading stories about me to the media. I have formed the opinion that Gill is a pathological liar. I have spoken to other people in Victoria - I made a trip to Victoria - and they have told me of certain fraud and other offences which they have said have not been prosecuted. Perhaps this situation in Victoria will give the police an opportunity to put this matter to justice.

MR HUMPHRIES (4.31): Madam Speaker, first of all, I commend Mr Stevenson for that statement. I have had many representations from Mr Gold. I think it took some courage for Mr Stevenson to come into the house and say that he was wrong in things he had said about Mr Gold based on information supplied to him. That is good news for Mr Gold and a tribute to Mr Stevenson.

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USB product IDs for documentation - success
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Motivation

In a previous posting I reported a lack of success when enquiring of the USB Implementors' Forum if a Vendor ID had been reserved for documentation.

To recap my motivation, a Vendor ID -- or at least a range of Product IDs -- is desirable to:

  • Avoid defamation, such as using a real VID:PID to illustrate a "workaround", which carries the implication that the product is less-than-perfect. Furthermore, failing to check if a VID:PID has actually been used is "reckless defamation".

  • Avoid consumer law, such as using a real VID:PID to illustrate a a configuration for a video camera, when in fact the product is a mouse.

  • Avoid improper operation, as may occur if a user cuts-and-pastes an illustrative example and that effects a real device.

  • Avoid trademark infringment.

For these reasons other registries of numbers often reserve entries for documentation: DNS names, IPv4 addresses, IPv6 addresses.

Allocation of 256 Product IDs, thanks to OpenMoko

OpenMoko has been generous enough to reserve a range of Product IDs for use by documentation:

0x1d50:0x5200 through to 0x1d50:0x52ff

Note carefully that other Product IDs within Vendor ID 0x1d50 are allocated to actual physical USB devices. Only the Product IDs 0x1d50:0x5200 through to 0x1d50:0x52ff are reserved for use by documentation.

My deep thanks to OpenMoko and Harald Welte.

Application form

The application form submitted to OpenMoko read:

  • a name and short description of your usb device project

    Documentation concerning the configuration of USB buses and devices.

    For example, documentation showing configuration techniques for Linux's udev rules.

    The meaning of "documentation" shall not extend to actual configuration of a actual device. It is constrained to showing methods for configuration. If an VID:PID for an actual device is required then these can be obtained from elsewhere.

    OpenMoko will not assign these "Documentation PIDs" to any actual device, now or forever.

    Operating systems may refuse to accept devices with these "documentation VID:PIDs". Operating systems may refuse to accept configuration which uses these "documentation VID:PIDs".

  • the license under which you are releasing the hardware and/or software/firmware of the device

    The documentation may use any license. Restricting use to only free documentation is problematic: the definition of "free" for documents is controversial; and it would be better if the PID:VIDs were well known and widely used by all authors of technical documentation.

  • a link to the project website and/or source code repository, if any

    Nil, one can be created if this is felt to be necessary (eg, to publicise the allocation).

  • if you need multiple Product IDs, please indicate + explain this at the first message, rather than applying for a second ID later

    Approximately 10.

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TFTP server, Fedora 20
vk5tu

The major system management tools have altered in recent Fedora versions, so the long-remembered phrases no longer work. Here is how to install and make available to the world a TFTP server.

$ sudo yum install tftp tftp-server
$ sudo cat <EOF >> /etc/hosts.allow
in.tftpd: ALL
EOF
$ sudo firewall-cmd --add-service tftp
$ sudo firewall-cmd --permanent --add-service tftp
$ sudo systemctl enable tftp.socket
$ sudo systemctl daemon-reload

Test with:

$ sudo cp example.bin /var/lib/tftpboot/
remote$ tftp server.example.com
tftp> get example.bin
tftp> quit

Use cp rather than mv so that SELinux sets the correct attribute on the file.

Consider that between Fedora 14 (2010) and Fedora 22 (2015) the package installation command, firewall configuration and init system configuration of this common systems administration task all change. I wonder if that invalidation of years of practice accounts for some of the opposition to those changes.

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USB Vendor ID for documentation
vk5tu

If you are writing documentation then you don't want to use an assigned magic number, like a real IP address or a real DNS name. That can readily lead to: misunderstandings; operational difficulties for the vendor's equipment if the number escapes from documentation into production; and difficulties for the author because of the risk of defamation and trademark infringement.

For these reasons standards associations commonly issue a range of their magic numbers for documentation purposes. For example, the IETF issued magic numbers for documentation in RFC2606 for DNS names, in RFC5737 for IPv4 addresses and in RFC3849 for IPv6 addresses.

I was writing some documentation for using udev, and rather than defame some vendor by suggesting that their product may need a workaround, I asked the USB Implementors' Forum if there is a USB Vendor ID for documentation purposes.

Sadly, there is not:

From: USB-IF Administration <redacted>
Subject: RE: Vendor-ID for use in documentation
Date: 11 November 2014 2:34:21 PM ACDT
To: Glen Turner <redacted>

Dear Glen,

Thank you for your message. Vendor IDs (VIDs) are owned by the vendor company and are assigned and maintained by the USB-IF only. We do not have a generic VID for documentation.

Regards, redacted

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