diff --git a/.github/workflows/build_cli.yml b/.github/workflows/build_cli.yml new file mode 100644 index 0000000..d7d3ece --- /dev/null +++ b/.github/workflows/build_cli.yml @@ -0,0 +1,30 @@ +name: Integration Tests + +on: [push] + +jobs: + build: + runs-on: ${{ matrix.os }} + strategy: + fail-fast: false + max-parallel: 1 + matrix: + os: ['windows-latest', 'ubuntu-latest', 'macos-latest'] + + steps: + - uses: actions/checkout@v2 + - uses: actions/setup-python@v2 + with: + python-version: "3.10" + - run: pip install . + - run: pip install pyinstaller + - run: pyinstaller -F ./dvuploader/cli.py -n dvuploader-${{ matrix.os }} --distpath ./bin + - name: Push + run: | + git config --global user.name "Build Bot" + git config --global user.email "build.bot@bot.com" + + git pull + git add ./bin/\* + git commit -a -m "šŸ¤– Built DVUploader for ${{ matrix.os }}" + git push diff --git a/README.md b/README.md index 1b37c41..9ba5fa8 100644 --- a/README.md +++ b/README.md @@ -36,6 +36,8 @@ python3 -m pip install . ## Quickstart +### Programmatic usage + In order to perform a direct upload, you need to have a Dataverse instance running and a cloud storage provider. The following example shows how to upload files to a Dataverse instance. Simply provide the files of interest and utilize the `upload` method of a `DVUploader` instance. ```python @@ -59,3 +61,55 @@ dvuploader.upload( ) ``` +### Command Line Interface + +DVUploader ships with a CLI ready to use outside scripts. In order to upload files to a Dataverse instance, simply provide the files of interest, persistent identifier and credentials. + +#### Using arguments + +```bash +dvuploader my_file.txt my_other_file.txt \ + --pid doi:10.70122/XXX/XXXXX \ + --api-token XXXXXX-XXXX-XXXX-XXXX-XXXXXXXXXXXX \ + --dataverse-url https://demo.dataverse.org/ \ +``` + +#### Using a config file + +Alternatively, you can also supply a `config` file that contains all necessary informations for the uploader. The `config` file is a JSON/YAML file that contains the following keys: + +* `persistent_id`: Persistent identifier of the dataset to upload to. +* `dataverse_url`: URL of the Dataverse instance. +* `api_token`: API token of the Dataverse instance. +* `files`: List of files to upload. Each file is a dictionary with the following keys: + * `filepath`: Path to the file to upload. + * `directoryLabel`: Optional directory label to upload the file to. + * `description`: Optional description of the file. + * `mimetype`: Mimetype of the file. + * `categories`: Optional list of categories to assign to the file. + * `restrict`: Boolean to indicate that this is a restricted file. Defaults to False. + +In the following example, we upload three files to a Dataverse instance. The first file is uploaded to the root directory of the dataset, while the other two files are uploaded to the directory `some/dir`. + +```yaml +# config.yml +persistent_id: doi:10.70122/XXX/XXXXX +dataverse_url: https://demo.dataverse.org/ +api_token: XXXXXX-XXXX-XXXX-XXXX-XXXXXXXXXXXX +files: + - filepath: ./small.txt + - filepath: ./medium.txt + directoryLabel: some/dir + - filepath: ./big.txt + directoryLabel: some/dir +``` + +The `config` file can then be used as follows: + +```bash +dvuploader --config-path config.yml +``` + +#### CLI Binaries + +DVUploader ships with binaries for Linux, MacOS and Windows. You can download the binaries from the `bin` [directory](./bin) and use them in a similar fashion as described above. diff --git a/bin/dvuploader-macos-latest b/bin/dvuploader-macos-latest new file mode 100755 index 0000000..7044a0a Binary files /dev/null and b/bin/dvuploader-macos-latest differ diff --git a/bin/dvuploader-ubuntu-latest b/bin/dvuploader-ubuntu-latest new file mode 100755 index 0000000..99888c0 Binary files /dev/null and b/bin/dvuploader-ubuntu-latest differ diff --git a/bin/dvuploader-windows-latest.exe b/bin/dvuploader-windows-latest.exe new file mode 100644 index 0000000..45c41f0 Binary files /dev/null and b/bin/dvuploader-windows-latest.exe differ diff --git a/dvuploader/cli.py b/dvuploader/cli.py new file mode 100644 index 0000000..5429cea --- /dev/null +++ b/dvuploader/cli.py @@ -0,0 +1,121 @@ +import yaml +import typer + +from pydantic import BaseModel +from typing import List, Tuple +from dvuploader import DVUploader, File + + +class CliInput(BaseModel): + api_token: str + dataverse_url: str + persistent_id: str + files: List[File] + + +app = typer.Typer() + + +def _parse_yaml_config(path: str) -> Tuple[List[File], str, str, str]: + """ + Parses a configuration file and returns a Class instance + containing a list of File objects, a persistent ID, a Dataverse URL, + and an API token. + + Args: + path (str): Path to a JSON/YAML file containing specifications for the files to upload. + + Returns: + CliInput: Class instance containing a list of File objects, a persistent ID, + a Dataverse URL, and an API token. + + Raises: + ValueError: If the configuration file is invalid. + """ + return CliInput(**yaml.safe_load(open(path))) + + +def _validate_inputs( + filepaths: List[str], + pid: str, + dataverse_url: str, + api_token: str, + config_path: str, +) -> None: + if config_path and len(filepaths) > 0: + raise typer.BadParameter( + "Cannot specify both a JSON/YAML file and a list of filepaths." + ) + + _has_meta_params = all(arg is not None for arg in [pid, dataverse_url, api_token]) + _has_config_file = config_path is not None + + if _has_meta_params and _has_config_file: + print( + "\nāš ļø Warning\n" + "ā”œā”€ā”€ You have specified both a configuration file and metadata parameters via the command line.\n" + "ā•°ā”€ā”€ Will use metadata parameters specified in the config file." + ) + elif not _has_meta_params and not _has_config_file: + raise typer.BadParameter( + "You must specify either a JSON/YAML file or metadata parameters (dv_url, api_token, pid, files) via the command line." + ) + + +@app.command() +def main( + filepaths: List[str] = typer.Argument( + default=None, + help="A list of filepaths to upload.", + ), + pid: str = typer.Option( + default=None, + help="The persistent identifier of the Dataverse dataset.", + ), + api_token: str = typer.Option( + default=None, + help="The API token for the Dataverse repository.", + ), + dataverse_url: str = typer.Option( + default=None, + help="The URL of the Dataverse repository.", + ), + config_path: str = typer.Option( + default=None, + help="Path to a JSON/YAML file containing specifications for the files to upload. Defaults to None.", + ), + n_jobs: int = typer.Option( + default=-1, + help="The number of parallel jobs to run. Defaults to -1.", + ), +): + _validate_inputs( + filepaths=filepaths, + pid=pid, + dataverse_url=dataverse_url, + api_token=api_token, + config_path=config_path, + ) + + if config_path: + # PyYAML is a superset of JSON, so we can use the same function to parse both + cli_input = _parse_yaml_config(config_path) + else: + cli_input = CliInput( + api_token=api_token, + dataverse_url=dataverse_url, + persistent_id=pid, + files=[File(filepath=filepath) for filepath in filepaths], + ) + + uploader = DVUploader(files=cli_input.files) + uploader.upload( + persistent_id=cli_input.persistent_id, + dataverse_url=cli_input.dataverse_url, + api_token=cli_input.api_token, + n_jobs=n_jobs, + ) + + +if __name__ == "__main__": + typer.run(main) diff --git a/dvuploader/dvuploader.py b/dvuploader/dvuploader.py index 26ad55d..158866c 100644 --- a/dvuploader/dvuploader.py +++ b/dvuploader/dvuploader.py @@ -5,7 +5,7 @@ from typing import Dict, List from urllib.parse import urljoin -from pydantic import BaseModel +from pydantic import BaseModel, validator from joblib import Parallel, delayed from dotted_dict import DottedDict @@ -43,7 +43,7 @@ def upload( dataverse_url (str): The URL of the Dataverse repository. api_token (str): The API token for the Dataverse repository. n_jobs (int): The number of parallel jobs to run. Defaults to -1. - + Returns: None """ @@ -61,7 +61,7 @@ def upload( ) if not self.files: - print("\nāŒ No files to upload") + print("\nāŒ No files to upload\n") return # Upload files in parallel @@ -78,7 +78,7 @@ def upload( for position, file in enumerate(files) ) - print("šŸŽ‰ Done!") + print("šŸŽ‰ Done!\n") def _check_duplicates( self, @@ -104,9 +104,9 @@ def _check_duplicates( ) print("\nšŸ”Ž Checking dataset files") - + to_remove = [] - + for file in self.files: if any(map(lambda dsFile: self._check_hashes(file, dsFile), ds_files)): print( @@ -115,12 +115,12 @@ def _check_duplicates( to_remove.append(file) else: print(f"ā”œā”€ā”€ File '{file.fileName}' is new - Uploading.") - + for file in to_remove: self.files.remove(file) print("šŸŽ‰ Done") - + @staticmethod def _check_hashes(file: File, dsFile: Dict): """ @@ -133,7 +133,7 @@ def _check_hashes(file: File, dsFile: Dict): Returns: bool: True if the files have the same checksum, False otherwise. """ - + hash_algo, hash_value = tuple(dsFile.dataFile.checksum.values()) return file.checksum.value == hash_value and file.checksum.type == hash_algo diff --git a/dvuploader/file.py b/dvuploader/file.py index 95de7c2..e4263fd 100644 --- a/dvuploader/file.py +++ b/dvuploader/file.py @@ -1,7 +1,7 @@ import os from typing import List, Optional -from pydantic import BaseModel, Field, validator +from pydantic import BaseModel, Field, validator, ValidationError from dvuploader.checksum import Checksum, ChecksumTypes @@ -21,12 +21,25 @@ class File(BaseModel): fileName: Optional[str] = None checksum: Optional[Checksum] = None + @staticmethod + def _validate_filepath(path): + if not os.path.exists(path): + raise FileNotFoundError(f"Filepath {path} does not exist.") + elif not os.path.isfile(path): + raise TypeError(f"Filepath {path} is not a file.") + elif not os.access(path, os.R_OK): + raise TypeError(f"Filepath {path} is not readable.") + elif os.path.getsize(path) == 0: + raise ValueError(f"Filepath {path} is empty.") + return path + @validator("fileName", always=True) def _extract_filename(cls, v, values): return os.path.basename(values["filepath"]) @validator("checksum", always=True) def _calculate_hash(cls, v, values): + cls._validate_filepath(values["filepath"]) fpath = values["filepath"] hash_algo, hash_fun = values["checksum_type"].value diff --git a/poetry.lock b/poetry.lock index 2580e25..1f44b61 100644 --- a/poetry.lock +++ b/poetry.lock @@ -171,6 +171,21 @@ files = [ {file = "charset_normalizer-3.2.0-py3-none-any.whl", hash = "sha256:8e098148dd37b4ce3baca71fb394c81dc5d9c7728c95df695d2dca218edf40e6"}, ] +[[package]] +name = "click" +version = "8.1.7" +description = "Composable command line interface toolkit" +optional = false +python-versions = ">=3.7" +files = [ + {file = "click-8.1.7-py3-none-any.whl", hash = "sha256:ae74fb96c20a0277a1d615f1e4d73c8414f5a98db8b799a7931d1582f3390c28"}, + {file = "click-8.1.7.tar.gz", hash = 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