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Posts about technology and arts.

What Are Identification Keys

In biology, an identification key is a printed or computer-aided device that aids the identification of biological entities, such as plants, animals, fossils, microorganisms, and pollen grains. Identification keys are also used in many other scientific and technical fields to identify various kinds of entities, such as diseases, soil types, minerals, or archaeological and anthropological artifacts

When you work writing software, it is common that at one point or another of the product development you will work with a SME, or subject-matter expert. This person is someone experienced in a field such as telecom billing, insurance, taxes, or even nature and environment.

Questions too specific, that land away from the knowledge area of software engineers, are normally addressed by the SME. Sometimes the knowledge from a SME can be spread in a team after they have worked together for a while.

Most of my time in New Zealand I have been working with environmental sciences. In one project, I remember hearing other developers mention ID’s, Keys, and Identification Keys. I had not worked with environmental sciences before, and only learned about its Portuguese translation (“Chave”, or “Chave de Identificação”, or “Chave Dicotêmica”) recently.

They are mechanisms, digital or physical, that help you identify plants, animals, fossils, etc. And I found out later that there are many identification key software written for the Web, desktop, and also other medias like PDF’s, and even printed version.

And also in New Zealand I found how fun identifying species can be with the iNaturalist app and community. If you are like me before, and had not heard about it before, search around more about it. It is a very simple concept, common to biologists, people who work with taxonomy, marine life, birds.

If you are in New Zealand, or just interested about it, here are some links to get you started identifying the local species.

Have fun!

Using formatter exclusions with Eclipse

Sometimes when you are formatting your code in Eclipse, you may want to prevent some parts of the code from being formatted. Especially when using Java 8 lambdas and optionals.

Here’s some code before being formatted by Eclipse’s default formatter rules.

Code adapted from: blog post Java d’eau ‐ Java 8: Streams in Hibernate and Beyond

session.createQuery("SELECT h FROM Hare h", Hare.class)
    .stream()
    .filter(h -> h.getId() == 1)
    .map(Hare::getName)
    .forEach(System.out::println);

Then after formatting.

session.createQuery("SELECT h FROM Hare h", Hare.class).stream().filter(h -> h.getId() == 1).map(Hare::getName)
                .forEach(System.out::println);

Which doesn’t look very appealing, ay? You can change this behaviour at least in two ways. The first by telling the formatter to ignore this block, through a special formatter tag in your code.

First you need to enable this feature in Eclipse, as it is disabled by default. This setting is found in the preferences JavaCode StyleFormatterEditOff/On Tags.

A screen shot of Eclipse formatter settings
Enabling formatter tags in Eclipse

Then formatting the following code won’t change a thing in the block surrounded by the formatter tags.

/* @Formatter:off */
session.createQuery("SELECT h FROM Hare h", Hare.class)
    .stream()
    .filter(h -> h.getId() == 1)
    .map(Hare::getName)
    .forEach(System.out::println);
/* @Formatter:on */

But having to type these tags can become annoying, and cause more commits and pull requests to be unnecessarily created. So an alternative approach can be to change the formatter behaviour globally.

This can be done in Eclipse in another option under the formatter options, JavaCode StyleFormatterEditLine WrappingFunction CallsQualified invocations.

You will have to choose “Wrap all elements, except first element if not necessary” under Line wrapping policy. And also check “Force split, even if line shorter than maximum line width”.

A screen shot of Eclipse formatter settings
Enabling custom formatter behaviour globally

Once it is done, your code will look like the following no matter what.

session.createQuery("SELECT h FROM Hare h", Hare.class)
    .stream()
    .filter(h -> h.getId() == 1)
    .map(Hare::getName)
    .forEach(System.out::println);

Happy coding!

♥ Open Source

Quickly Verifying jar Signatures For ASF Releases

The release process within the Apache Software Foundation includes a series of steps. Amongst these steps is the voting process. In Apache Commons, the release instructions includes a note on artefact signatures.

During the course of the VOTE, make sure that one or more of the reviewers have verified the signatures and hash files included with the release artifacts. If no one specifically mentions having done that during the VOTE, ask on the dev list and make sure someone does this before you proceed with the release.

Tired of always having to manually check several artefacts, or having to come up with the correct shell commands to iterate through a list of files, the other day I wrote a simple script to download the KEYS file, import it, download all the artefacts, then iterate through them and verify the signature.

Here’s the script. Licensed under the GPL licence.

#!/usr/bin/env bash

url=""

# From: https://blog.mafr.de/2007/08/05/cmdline-options-in-shell-scripts/
USAGE="Usage: `basename $0` [-hv] https://repository.apache.org/.../commons/commons-configuration/2.2/"

# Parse command line options.
while getopts hv: OPT; do
    case "$OPT" in
        h)
            echo $USAGE
            exit 0
            ;;
        v)
            echo "`basename $0` version 0.0.1"
            exit 0
            ;;
        \?)
            # getopts issues an error message
            echo $USAGE >&2
            exit 1
            ;;
    esac
done

# Remove the switches we parsed above.
shift `expr $OPTIND - 1`

# We want at least one non-option argument. 
# Remove this block if you don't need it.
if [ $# -eq 0 ]; then
    echo $USAGE >&2
    exit 1
fi

# Access additional arguments as usual through 
# variables $@, $*, $1, $2, etc. or using this loop:
URL=$1

echo "url: ${URL}"

# Use a local temporary directory
BUILD_DIR=$(mktemp -d)
pushd "$BUILD_DIR"

echo "build dir: ${BUILD_DIR}"

# Download KEYS file
KEYS_URL=https://www.apache.org/dist/commons/KEYS

echo "importing KEYS from: ${KEYS_URL}"

wget "$KEYS_URL"
gpg --import KEYS

# Download JARs and signature files
echo "downloading all jars and signature files..."

wget -r -nd -np -e robots=off --wait 1 -R "index.html*" "${URL}"

# Check the files
for x in *.jar; do gpg --verify "${x}".asc; done

# EOF

The script can be found at GitHub too: https://github.com/kinow/dork-scripts/tree/3c519a74f28c08310ce2e65f8e860d61fd0c5c07/gpg/asf-sigs

Removing Javadoc SVN Id Tags with Shell Script

Subversion supports Keyword Substitution, which performs substitution of some keywords such as Author, Date, and Id. The Id is the date, time, and user that last modified the file.

It used to be common to all Apache Commons components to have a line as follows in the header of each Java class.

/**
 * SomeClass class.
 *
 * @version $Id$
 */
public class SomeClass {
    
}

Then the generated Javadoc would contain the date of when the class was altered. Although useful, with proper versioning, it becomes obsolete. It is much more important to know what is the version of the software, not the last time it was modified or by whom. In case you have a problem with that specific file, you can always check the history of the file using git log, or git bisect, or …

Apache Commons components that are migrated to git need to have these lines removed. git does not support these Subversion Keywords so it is never properly rendered. And as every time I have to remove these lines I come up with some shell script snippet, I decided to document the last one I wrote, so that it can save me some time ‐ and perhaps for somebody else too?

find . -name "*.java" -exec sed -i '/^.*\*\s*@version\s*\$Id\$.*$/d' {} \;

And then push a commit with the change :-) In case you know some regex, you can change it and use the same command syntax to remove comments, specific configuration lines, etc.

That’s all. Happy scripting!

♥ Open Source

Enabling Markdown Extension Tables For Piecrust

PieCrust is a Python static site generator. It allows users to write content in Markdown. But if you try adding a table, the content by default will be generated as plain text.

You have to enable Markdown extension tables. PieCrust will load it when creating the Markdown instance.

# config.yml
markdown:
  extensions:
    - tables

Et, voilà! Happy blogging!

♥ Open Source

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