Compendium Navigator

Project description

Python program that parses the standardized File System Structure (sFSS; Project Compendium) directories and files and, subsequently, writes a html file to easily navigate the FSS and inspect the files.

This Python script is part of ENCORE (Enhancing Computational Research) to navigate the File System Structure (sFSS)

Date: 9 May 2023
Last update: 30 July 2024
Developed by: Prof. dr. Antoine van Kampen, Dr. Aldo Jongejan, Utkarsh Mahamune (www.bioinformaticslaboratory.eu)
Operating System(s) / version(s) used during development: Windows 11
Tested: on Unix, MacOS and Windows 10 and 11 (does not run on Windows 7)
Specific hardware requirements: None.
Software environment: Python 3 / Anaconda

DOI: https://doi.org/10.5281/zenodo.7985655

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VERSIONS

• Version 1.0 (9 May 2023) - Compatible with ENCORE Template Version 3.x

• Version 1.5 (23 May 2023) - Compatible with ENCORE Template Version 3.x and 4.x

• Version 1.5.1 (30 July 2024) - Compatible with ENCORE Template Version 3.x and 4.x

Note: updates of the sFSS navigator can be obtained from the https://github.com/EDS-Bioinformatics-Laboratory/FSS-Navigator/releases

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DIRECTORIES

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• 0_SoftwareEnvironment. 'requirements' files and guide to setup Python environment necessary to execute Navigate.py

• CompendiumNavigator. Code, documentation, and required configuration files for the Compendium Navigator.

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**COMPENDIUM NAVIGATOR FILES AND DIRECTORIES **

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These files/directories are found in the directory \CompendiumNavigator

• Navigate.py. Main program

• Test_Navigate_model.py. Python program to test if Navigate.py can be imported and executed as a module. Note: this works from command line but for unknown reason not from within DataSpell.

• Input

  • 0_PROJECT.md. General description of project. This file is one of the pre-defined files of CORE and should be present in the root of the FSS.

  • • 0_GETTINGSTARTED.txt. Template document (plain text format). Copy this file to your favourite word processor to add content.

      • Examples:

        • 0_GETTINGSTARTED.docx. Template document (Microsoft Word format to show how to include links). The docx file can be saved as html (make sure you use utf-8 encoding).

        • 0_GETTINGSTARTED.tex. Template document (LaTex format to show how to include links). The LaTex file can be converted with Pandoc to html.

        • 0_GETTINGSTARTED.html. Example of exported html file used by the FSS navigator.

  • Navigation.conf. Configuration file that determines the content of Navigation.html. This file should be in the root of the FSS.

  • _navigate-template.html_. (template that will be copied to Navigation.html). This file should be present in the directory .navigate

• Output

  • Navigation.html. This file is generated by Navigate.py and will be written in the root of the FSS. Open this file in your web-browser to navigate the project.

• Other

  • github.txt: file with the name of the Compendium Navigator GitHub repository. This file is used by the Navigator.

• Directories

  • .navigate. This directory contains temporary files (generated by Navigate.py) that are used by Navigation.html. In addition, it should contain navigate-template.html. This directory should be located in the root of the sFSS.
  • bin. Compiled versions of the Compendium Navigator
  • Results. Some random figures and files to test the Compendium Navigator

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Code documentation

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The Python code is documented using docstrings. The directory \CodeDocumentation contains documentation generated by Sphinx (https://www.sphinx-doc.org/en/master/). See Lab Journal in \ProjectDocumentation for more information.

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TESTING THE COMPENDIUM NAVIGATOR

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1. Download the Compendium Navigator project from Zenodo (https://doi.org/10.5281/zenodo.7985655).
2. The root of the project contains the Navigate.py script and the compiled versions. Execute the Python program or one of the executables (Windows, MacOS, Unix shell script). This will generate Navigate.html, which you can open in your browser.
3. You can change the configuration in Navigation.conf and/or change the 0_GETTINGSTARTED.docx (which then needs to be save to 0_GETTINGSTARTED.html; utf-8 format)
4. If you wish to modify/extend the Navigator then, preferably, you make the changes in \Processing\CompendiumNavigator\Code and, subsequently, copy the modified code (and compiled versions) back to the root directory.

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INSTALLATION AND EXECUTION IN EXISTING sFSS

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Typically, if you have setup an ENCORE-based project, then the Compendium Navigator is already part of your project since it is distributed as part of the ENCORE template). Thus, there is no need for any installation.

In case you want to use a newer version of the Compendium Navigator for an ENCORE-based project that you previously setup, then first check compatibility [here]. Subsequently, you have several options:

• Download a Compendium Navigator release [here]. All releases include the compiled versions. Copy the files from \Processing.....\Code to the root of your ENCORE-based project.
• Download the Compendium Navigator project from Zenodo [here]. In principle the various Zenodo versions correspond to the GitHub releases. These included the compiled versions. Copy the files from \Processing.....\Code to the root of your ENCORE-based project.
• Copy or clone the latest files from the Compendium Navigator repository [here]. Copy the files from \Processing.....\Code to the root of your ENCORE-based project. These will not include the compiled versions. Below you will find instructions for compilation if necessary.

Running Navigate.py

Make sure that you have all required Python packages installed in your Python environment. See \Processing\0_SoftwareEnvironment for instructions.

1. Enter the title of the projection Navigation.conf and change any of the other settings if necessary.
2. Run the Python program from the command line. For example:
   • python.exe Navigate.py
   • python.exe Navigate.py -h
   • python.exe Navigate.py -C myconf.txt
3. Open Navigation.html in web-browser

Notes:

• If the content of the sFSS is changed then you need to rerun the Python program. Navigation.html is not automatically (magically) updated.

• A compiled version of this program will become available in the future to prevent that Python should be installed on your computer.

• Navigate.py can also be imported as a module:

  import Navigate
  
  Navigate.create_navigate()
  

​ Note: for unknown reason, using this import does not work if executed from DataSpell/PyCharm. It does work if the script is executed from the command line.

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CONFIGURING NAVIGATION

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The output of the Python program can be configured by changing the settings in Navigation.conf.

In this configuration file you can specify

• Title of the project
• Files and subdirectories to include/exclude in the directory tree

Notes:

• The project title is also in 0_PROJECT.md. However, since there is no standardized way of formatting this title or to have it one the first or second line of the file it is difficult to extract and re-format. Consequently, it should now also be specified in the configuration file. The code to parse it from 0_PROJECT.md is still in the Python program.

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COMPILATION

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WINDOWS

A Windows executable is also available: Navigate.exe. This executable was created using pyinstaller (https://pyinstaller.org/en/stable/):

Requires installation of pyinstaller and pywin32:

To compile:

> pyinstaller --onefile Navigate.py

or

> pyinstaller --onefile --add-binary "c:\path\to\python39.dll;." Navigate.py

Notes:

• If Navigate.py is in a Dropbox folder then first stop syncing before compilation. Otherwise the program will not compile.
• The compilation process will make a 'build' and 'dist' directory in the root of the sFSS. The 'dist' directory contains the executable program (Navigate.exe) that should be copied to the root of the sFSS. The 'build' and 'dist' directories can be removed. In addition, you can remove the *.spec file.
• Note that the executable might be blocked by Windows defender or other anti-virus software. Not sure how to solve this. See also, for example, https://stackoverflow.com/questions/43777106/program-made-with-pyinstaller-now-seen-as-a-trojan-horse-by-avg
• The executable runs on Windows 10 and 11. The executable doesn't run on Windows 7 (see for example, https://groups.google.com/g/pyinstaller/c/XcTSSsPP5ac). It should run on Windows 8 but this was not tested. To have an executable for Windows 7, the executable should be build with Windows 7.

Unix/Linux

If Python 3 is installed on your Unix/Linux computer, then the easiest way (without compilation) is to

• Add #!/usr/bin/env python3 at the start of your script. This might be different on your Unix system (e.g., #!/usr/bin/python).
• Change the name from Navigate.py to Navigate
• Make the script executable from the command line: chmod +x ./Navigate

Now you can execute the script

MacOS

Compile:

>pyinstaller --onefile Navigate.py

or for MacIntel

>pyinstaller --onefile --windowed Navigate.py

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TESTING

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The code is located in \20230508_ParseDirectory\Processing\20230508_ParseDirectory\Code\Navigate.py

To test the program, copy Navigate.py to the root of the FSS \20230508_ParseDirectory and run the Python program.

This Python program parses a complete File System Structure (sFSS) starting from its root.

The final navigation file Navigation.html that is produced by this program is written to the root of the sFSS. This navigation file is a copy of the navigation-template.html in the \20230508\.navigate directory. This template defines four iframes that hold content of the FSS.

The files required to navigate the sFSS are also written to the .navigate directory. E.g.,

• 0_gettingstarted.html (copied from 0_GETTINGSTARTED.html in the root of the FSS)

• 0_project.html (copied from 0_PROJECT.md in the root of the FSS)

• fss.html the directory structure of the FSS and relevant files

In addition, the .navigate directory will hold html copies of all markdown files (*.md) in the sFSS. Markdown files do not render correctly in a html iframe. Therefore, if during parsing a markdown file is encountered it will be converted to html. The html file is copied to .navigate. To prevent that files are overwritten, the filename of the html file contains a randomly generated string. In the browser (Navigation.html) you will still see the filename of the markdown file, but the href link points to the corresponding html file in .navigate.

All files in the .navigate directory are deleted (except navigate-template) if the Python program is executed.

There should be a 0_GETTINGSTARTED.html. This file can be made in any editor (Microsoft Word, LaTex, etc) and then converted to an html file. Make sure that you convert to an utf-8 encoded html file.

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KNOWN ISSUES

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• If the structure of the sFSS changes in the future then it may be necessary to update the paths in the Python program.
• The Python program assumes a strict naming of the pre-defined files in the sFSS according as outlined in the usage rules of the sFSS.
• The 0_GETTINGSTARTED.html should be a utf-8 (unicode) encoded file.
• Directories starting with a dot (e.g., .git) are not recognized as a directory. Not really a problem but needs to be solved.
• The construct 'item in' searches for substrings. Therefore, if you have a file test.abc and in the configuration file you specify filesInclude = xtest.abc, then test.abc is also included in the tree.
• Currently, it is not possible to specify a different location for .navigate using the command line options. This directory should be in the root of the sFSS. If .navigate is at a different location, then the links in the html files (parsed from markdown) will no longer work. Can probably be quite easily fixed by making a change to the parse functions.
• Figures are shown in a separate browser tab since these are not automatically scaled to the size of the iframe in navigate-template.html
• Note that the Windows executable might be blocked by Windows defender or other anti-virus software. Not sure how to solve this. See also, for example, https://stackoverflow.com/questions/43777106/program-made-with-pyinstaller-now-seen-as-a-trojan-horse-by-avg.
• See also: https://github.com/EDS-Bioinformatics-Laboratory/FSS-Navigator/issues