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Source: naming_conventions.md

Version: 2023.02.02

The following notebook describes AgResearch naming conventions for any eResearch project
or dataset.Core needs for the naming conventions:

Requirements

  • All names MUST fulfill needs of their users, user groups, or Communities of Practice.

  • All names MUST be interoperable across Linux, Windows and Mac operating systems.

  • All names MUST be parseable by a set of regular expressions defined in this notebook.

Common Needs

  • To be able to list all projects and datasets in a chronological order, all names MUST start with four digit version of the current year eg. 2022 2023.

  • All names MUST be lower case insensitive. Do not assume case sensitivity across operating systems eg. Project, PROJECT, project are three different names on Linux, but it is the same name on Windows.

  • All names MUST only contain upper/lower case letters, digits, underscore and hyphen characters to achieve interoperability across the operating systems.

  • All names MUST have between 8 to 64 characters in total. Minimum amount of characters is derived from the current dataset names and maximum of 64 was agreed during a eRI project review on 2 February 2023.

RegExp for Common Needs

We can derive the following regular expression from the common needs:

Code Block
([0-9]{4})([a-zA-Z0-

...

9_-]

...

{4,60})

Python example:
import re
common = Here is a sample Python code to illustrate the naming convention regular expression in action for existing datasets with shortest and longest names that currently exist in AgResearch HPC:

Code Block
    import re
    common = r"([0-9]{4})([a-zA-Z0-

...

9_-]

...

{4,60})"

...


    sample_

...

names = [
        "2010_SVS"
        "2011-KCCG"
        "2012_GCAM"
        "2013_Hyperspectral_Curiosity_HSI_Lamb",
        "2014-Clostridium_butyricum_OPP0023470",
        "2015-Rumen_Microbes_Genome_SequenceData",
    ]
    for sample_name in sample_names:
        matches = re.findall(common, sample_name)

...


        print(matches)

...

  • Bioinformatics - bio

ToDo

  • limit the names to max practical length based on the operating system constraints

  • year | team | leader / species expand the regexp

...