Glycan icon - Githubissues

HadleyKing commented 1 year ago

The CFDE site uses Material Design Icons to represent datatypes. I have chose the following for Glycan icons for the time being: https://pictogrammers.com/library/mdi/icon/square-wave/

You can submit new icons to the site via their contribution link. Maybe we submit one?

u8sand commented 1 year ago

Note that they just have a lot which is why it's being used but it's not a requirement. There are also a few blueprints icons and another directory with scripts to convert some images into the icons.

The ultimate requirement of these icons is a single svg path spec, you can throw a png into icons/services/src and use npm run codegen:icons (may require some dependencies) which will attempt to extract such a path from a raster.

HadleyKing commented 1 year ago

@u8sand Thanks for the breadcrumbs! I was thinking of that first, since all of GlyGen's various contributors and sources have their own icons for favicons and whatnot, but I thought using the package would be more appropriate since I saw everyone else doing it. ;-) @jeet-vora and I can pick some of the favicons and convert them.

HadleyKing commented 1 year ago

@u8sand: This is not a priority but....

I added an icon next to the other two like you suggested.

I installed a venv and the requirements.txt and ran the npm run codegen:icons and then got to following error:

hadley_king:02/08/23 10:55:04:playbook-partnership:npm run codegen:icons

> playbook-partnership@1.0.0 codegen:icons
> python cli/convert-icons.py icons/services/src icons/services/index.ts

['cli/convert-icons.py', 'icons/services/src', 'icons/services/index.ts']
converting GlyGen
Traceback (most recent call last):
  File "/Users/hadley_king/GitHub/nih-cfde/playbook-partnership/cli/convert-icons.py", line 82, in <module>
    main(*sys.argv[1:])
  File "/Users/hadley_king/GitHub/nih-cfde/playbook-partnership/cli/convert-icons.py", line 70, in main
    print(
  File "/Users/hadley_king/GitHub/nih-cfde/playbook-partnership/cli/convert-icons.py", line 73, in <genexpr>
    f"export var {slugify(icon_file.stem)}_icon = {repr(convert_path(icon_file.parent/icon_file.stem, icon_file.suffix))};"
  File "/Users/hadley_king/GitHub/nih-cfde/playbook-partnership/cli/convert-icons.py", line 51, in convert_path
    convert('-flatten', f"{base}{ext}", f"{base}.tmp.pbm")
  File "/Users/hadley_king/GitHub/nih-cfde/playbook-partnership/cli/convert-icons.py", line 14, in convert
    def convert(*args): shell('convert', *args)
  File "/Users/hadley_king/GitHub/nih-cfde/playbook-partnership/cli/convert-icons.py", line 13, in shell
    def shell(*args): assert Popen(args, stdin=sys.stdin, stdout=sys.stdout, stderr=sys.stderr).wait() == 0
  File "/Users/hadley_king/.pyenv/versions/3.10.6/lib/python3.10/subprocess.py", line 969, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/Users/hadley_king/.pyenv/versions/3.10.6/lib/python3.10/subprocess.py", line 1845, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'convert'

I tried debugging with the convert-icons.py script a bit an adding a convert directory but had no success. Any suggestions?

u8sand commented 1 year ago

There is a tool called convert part of imagemagick. It can likely be installed with homebrew on Mac , some package manager on Linux, and maybe Choco or something on windows.

Alternatively the docker image should have it installed but it may be a bit tricky to use that I don't have any instructions yet. I will add those instructions when I get a chance.

HadleyKing commented 1 year ago

@u8sand That worked a little... ran brew install imagemagick and then brew install potrace. Now getting the following:

hadley_king:02/23/23 :playbook-partnership:npm run codegen:icons

> playbook-partnership@1.0.0 codegen:icons
> python cli/convert-icons.py icons/services/src icons/services/index.ts

['cli/convert-icons.py', 'icons/services/src', 'icons/services/index.ts']
converting Enrichr
extracting Enrichr
Traceback (most recent call last):
  File "/Users/hadley_king/GitHub/nih-cfde/playbook-partnership/cli/convert-icons.py", line 82, in <module>
    main(*sys.argv[1:])
  File "/Users/hadley_king/GitHub/nih-cfde/playbook-partnership/cli/convert-icons.py", line 70, in main
    print(
  File "/Users/hadley_king/GitHub/nih-cfde/playbook-partnership/cli/convert-icons.py", line 73, in <genexpr>
    f"export var {slugify(icon_file.stem)}_icon = {repr(convert_path(icon_file.parent/icon_file.stem, icon_file.suffix))};"
  File "/Users/hadley_king/GitHub/nih-cfde/playbook-partnership/cli/convert-icons.py", line 60, in convert_path
    result = extract_path(base)
  File "/Users/hadley_king/GitHub/nih-cfde/playbook-partnership/cli/convert-icons.py", line 41, in extract_path
    for path in g.iterfind(f"{ns}path")
AttributeError: 'NoneType' object has no attribute 'iterfind'

I have done some trouble shooting and come up with nothing so far. Again, not a real priority.

u8sand commented 1 year ago

Hi @HadleyKing , actually I ran into this issue as well trying to get it working on Ubuntu. I think I'm somehow utilizing some very new version of one of these tools, in any case I was able to make my dev environment reproducible with docker. Assuming you have docker and docker-compose installed, you should be able to run:

docker-compose run dev npm run codegen:icons

Versions in that image, fyi

$ python --version
Python 3.10.9
$ convert -version
Version: ImageMagick 7.1.0-61 Q16-HDRI x86_64 20866 https://imagemagick.org
$ potrace -version
potrace 1.16. Copyright (C) 2001-2019 Peter Selinger.