Crate init

[simleo]

Adds an "init" mode that allows to initialize an RO-Crate from an existing directory tree, i.e., build an RO-Crate object that references all files and directories in the tree.

Also adds an "rocrate" command with a nested interface, with init as its first implemented subcommand. rocrate init top_dir initializes the directory tree rooted at top_dir, adding an ro-crate-metadata.json that references files and directories.

$ docker run --rm -it --name ro-crate-py ro-crate-py bash
root@ea40838f1c80:/ro-crate-py# cd /tmp/
root@ea40838f1c80:/tmp# rocrate 
Usage: rocrate [OPTIONS] COMMAND [ARGS]...

Options:
  --help  Show this message and exit.

Commands:
  add
  init
root@ea40838f1c80:/tmp# rocrate init --help
Usage: rocrate init [OPTIONS] TOP_DIR

Options:
  --help  Show this message and exit.
root@ea40838f1c80:/tmp# cp -rf /ro-crate-py/test/test-data/ro-crate-galaxy-sortchangecase crate_dir
root@ea40838f1c80:/tmp# rm -fv crate_dir/ro-crate-metadata.json 
removed 'crate_dir/ro-crate-metadata.json'
root@ea40838f1c80:/tmp# cp -a crate_dir{,.bak}
root@ea40838f1c80:/tmp# rocrate init crate_dir
root@ea40838f1c80:/tmp# diff -r --brief crate_dir.bak crate_dir
Only in crate_dir: ro-crate-metadata.json
root@ea40838f1c80:/tmp# cat crate_dir/ro-crate-metadata.json 
{
    "@context": "https://w3id.org/ro/crate/1.1/context",
    "@graph": [
        {
            "@id": "./",
            "@type": "Dataset",
            "datePublished": "2021-02-12T12:11:20.426930",
            "hasPart": [
                {
                    "@id": "test/"
                },
                {
                    "@id": "LICENSE"
                },
                {
                    "@id": "sort-and-change-case.ga"
                },
                {
                    "@id": "README.md"
                },
                {
                    "@id": "test/test1/"
                },
                {
                    "@id": "test/test1/sort-and-change-case-test.yml"
                },
                {
                    "@id": "test/test1/input.bed"
                },
                {
                    "@id": "test/test1/output_exp.bed"
                }
            ]
        },
        {
            "@id": "ro-crate-metadata.json",
            "@type": "CreativeWork",
            "about": {
                "@id": "./"
            },
            "conformsTo": {
                "@id": "https://w3id.org/ro/crate/1.1"
            }
        },
        {
            "@id": "test/",
            "@type": "Dataset"
        },
        {
            "@id": "LICENSE",
            "@type": "File"
        },
        {
            "@id": "sort-and-change-case.ga",
            "@type": "File"
        },
        {
            "@id": "README.md",
            "@type": "File"
        },
        {
            "@id": "test/test1/",
            "@type": "Dataset"
        },
        {
            "@id": "test/test1/sort-and-change-case-test.yml",
            "@type": "File"
        },
        {
            "@id": "test/test1/input.bed",
            "@type": "File"
        },
        {
            "@id": "test/test1/output_exp.bed",
            "@type": "File"
        }
    ]
}

Note that the add command is not implemented yet.

[stain]

This is very nice! Thank you!

[stain]

I merged it, but there is a build issue on Windows:

https://github.com/ResearchObject/ro-crate-py/runs/1887751730?check_suite_focus=true

test/test_read.py::test_init[True] FAILED                                [ 38%]
...
         for p in fpaths:
>           assert isinstance(crate.dereference(p), File)
E           AssertionError: assert False
E            +  where False = isinstance(None, File)
E            +    where None = <bound method ROCrate.dereference of <rocrate.rocrate.ROCrate object at 0x00000199E82CCF08>>('test/test1/input.bed')
E            +      where <bound method ROCrate.dereference of <rocrate.rocrate.ROCrate object at 0x00000199E82CCF08>> = <rocrate.rocrate.ROCrate object at 0x00000199E82CCF08>.dereference

test\test_read.py:191: AssertionError
=========================== short test summary info ===========================
FAILED test/test_read.py::test_init[False] - AssertionError: assert False
FAILED test/test_read.py::test_init[True] - AssertionError: assert False

[stain]

Perhaps breaks because

crate_dir = test_data_dir / "ro-crate-galaxy-sortchangecase"

is repeated in two tests?

[simleo]

Perhaps breaks because

crate_dir = test_data_dir / "ro-crate-galaxy-sortchangecase"

is repeated in two tests?

No, every test has its own directory tree. The problems seems to be that file IDs are being added to the crate with backslashes. I'm working on a fix.

[simleo]

Windows build fixed in #47.