| Name | fairscape-cli JSON |
| Version |
1.1.5
JSON |
| download |
| home_page | None |
| Summary | A utility for packaging objects and validating metadata for FAIRSCAPE |
| upload_time | 2025-07-24 18:15:06 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.8 |
| license | Copyright 2023 THE RECTOR AND VISITORS OF THE UNIVERSITY OF VIRGINIA
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. |
| keywords |
fairscape
reproducibility
fair
b2ai
cli
ro-crate
|
| VCS |
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# fairscape-cli
A utility for packaging objects and validating metadata for FAIRSCAPE.
---
## **Documentation**: [https://fairscape.github.io/fairscape-cli/](https://fairscape.github.io/fairscape-cli/)
## Features
fairscape-cli provides a Command Line Interface (CLI) that allows the client side to create, manage, and publish scientific data packages:
- **RO-Crate Management:** Create and manipulate [RO-Crate](https://www.researchobject.org/ro-crate/) packages locally.
- Initialize RO-Crates in new or existing directories.
- Add data, software, and computation metadata.
- Copy files into the crate structure alongside metadata registration.
- **Schema Handling:** Define, infer, and validate data schemas (Tabular, HDF5).
- Create schema definition files.
- Add properties with constraints.
- Infer schemas directly from data files.
- Validate data files against specified schemas.
- Register schemas within RO-Crates.
- **Data Import:** Fetch data from external sources and convert them into RO-Crates.
- Import NCBI BioProjects.
- Convert Portable Encapsulated Projects (PEPs) to RO-Crates.
- **Build Artifacts:** Generate derived outputs from RO-Crates.
- Create detailed HTML datasheets summarizing crate contents.
- Generate provenance evidence graphs (JSON and HTML).
- **Release Management:** Organize multiple related RO-Crates into a cohesive release package.
- Initialize a release structure.
- Automatically link sub-crates and propagate metadata.
- Build a top-level datasheet for the release.
- **Publishing:** Publish RO-Crate metadata to external repositories.
- Upload RO-Crate directories or zip files to Fairscape.
- Create datasets on Dataverse instances.
- Mint or update DOIs on DataCite.
## Requirements
Python 3.8+
## Installation
```console
$ pip install fairscape-cli
```
## Command Overview
The CLI is organized into several top-level commands:
rocrate: Core local RO-Crate manipulation (create, add files/metadata).
schema: Operations on data schemas (create, infer, add properties, add to crate).
validate: Validate data against schemas.
import: Fetch external data into RO-Crate format (e.g., bioproject, pep).
build: Generate outputs from RO-Crates (e.g., datasheet, evidence-graph).
release: Manage multi-part RO-Crate releases (e.g., create, build).
publish: Publish RO-Crates to repositories (e.g., fairscape, dataverse, doi).
Use --help for details on any command or subcommand:
```console
$ fairscape-cli --help
$ fairscape-cli rocrate --help
$ fairscape-cli rocrate add --help
$ fairscape-cli schema create --help
```
## Examples
### Creating an RO-Crate
Create an RO-Crate in a specified directory:
```console
$ fairscape-cli rocrate create \
--name "My Analysis Crate" \
--description "RO-Crate containing analysis scripts and results" \
--organization-name "My Org" \
--project-name "My Project" \
--keywords "analysis" \
--keywords "python" \
--author "Jane Doe" \
--version "1.1.0" \
./my_analysis_crate
```
Initialize an RO-Crate in the current working directory:
```console
# Navigate to an empty directory first if desired
# mkdir my_analysis_crate && cd my_analysis_crate
$ fairscape-cli rocrate init \
--name "My Analysis Crate" \
--description "RO-Crate containing analysis scripts and results" \
--organization-name "My Org" \
--project-name "My Project" \
--keywords "analysis" \
--keywords "python"
```
### Adding Content and Metadata to an RO-Crate
These commands support adding both the file and its metadata (add) or just the metadata (register).
Add a dataset file and its metadata:
```console
$ fairscape-cli rocrate add dataset \
--name "Raw Measurements" \
--author "John Smith" \
--version "1.0" \
--date-published "2023-10-27" \
--description "Raw sensor measurements from Experiment A." \
--keywords "raw-data" \
--keywords "sensors" \
--data-format "csv" \
--source-filepath "./source_data/measurements.csv" \
--destination-filepath "data/measurements.csv" \
./my_analysis_crate
```
Add a software script file and its metadata:
```console
$ fairscape-cli rocrate add software \
--name "Analysis Script" \
--author "Jane Doe" \
--version "1.1.0" \
--description "Python script for processing raw measurements." \
--keywords "analysis" \
--keywords "python" \
--file-format "py" \
--source-filepath "./scripts/process_data.py" \
--destination-filepath "scripts/process_data.py" \
./my_analysis_crate
```
Register computation metadata (metadata only):
```console
# Assuming the script and dataset were added previously and have GUIDs:
# Dataset GUID: ark:59852/dataset-raw-measurements-xxxx
# Software GUID: ark:59852/software-analysis-script-yyyy
$ fairscape-cli rocrate register computation \
--name "Data Processing Run" \
--run-by "Jane Doe" \
--date-created "2023-10-27T14:30:00Z" \
--description "Execution of the analysis script on the raw measurements." \
--keywords "processing" \
--used-dataset "ark:59852/dataset-raw-measurements-xxxx" \
--used-software "ark:59852/software-analysis-script-yyyy" \
--generated "ark:59852/dataset-processed-results-zzzz" \
./my_analysis_crate
# Note: You would typically register the generated dataset ('processed-results') separately.
```
Register dataset metadata (metadata only, file assumed present or external):
```console
$ fairscape-cli rocrate register dataset \
--name "Processed Results" \
--guid "ark:59852/dataset-processed-results-zzzz" \
--author "Jane Doe" \
--version "1.0" \
--description "Processed results from the analysis script." \
--keywords "results" \
--data-format "csv" \
--filepath "results/processed.csv" \
--generated-by "ark:59852/computation-data-processing-run-wwww" \
./my_analysis_crate
```
### Schema Management
Create a tabular schema definition file:
```console
$ fairscape-cli schema create \
--name 'Measurement Schema' \
--description 'Schema for raw sensor measurements' \
--schema-type tabular \
--separator ',' \
--header true \
./measurement_schema.json
```
Add properties to the tabular schema file:
```console
# Add a string property (column 0)
$ fairscape-cli schema add-property string \
--name 'Timestamp' \
--index 0 \
--description 'Measurement time (ISO8601)' \
./measurement_schema.json
# Add a number property (column 1)
$ fairscape-cli schema add-property number \
--name 'Value' \
--index 1 \
--description 'Sensor reading' \
--minimum 0 \
./measurement_schema.json
```
Infer a schema from an existing data file:
```console
$ fairscape-cli schema infer \
--name "Inferred Results Schema" \
--description "Schema inferred from processed results" \
./my_analysis_crate/results/processed.csv \
./processed_schema.json
```
Add an existing schema file to an RO-Crate:
```console
$ fairscape-cli schema add-to-crate \
./measurement_schema.json \
./my_analysis_crate
```
### Validation
Validate a data file against a schema file:
```console
# Successful validation
$ fairscape-cli validate schema \
--schema-path ./measurement_schema.json \
--data-path ./my_analysis_crate/data/measurements.csv
# Example failure
$ fairscape-cli validate schema \
--schema-path ./measurement_schema.json \
--data-path ./source_data/measurements_invalid.csv
```
### Importing Data
Import an NCBI BioProject into a new RO-Crate:
```console
$ fairscape-cli import bioproject \
--accession PRJNA123456 \
--author "Importer Name" \
--output-dir ./bioproject_prjna123456_crate \
--crate-name "Imported BioProject PRJNA123456"
```
Convert a PEP project to an RO-Crate:
```console
$ fairscape-cli import pep \
./path/to/my_pep_project \
--output-path ./my_pep_rocrate \
--crate-name "My PEP Project Crate"
```
### Building Outputs
Generate an HTML datasheet for an RO-Crate:
```console
$ fairscape-cli build datasheet ./my_analysis_crate
# Output will be ./my_analysis_crate/ro-crate-datasheet.html by default
```
Generate a provenance graph for a specific item within the crate:
```console
# Assuming 'ark:59852/dataset-processed-results-zzzz' is the item of interest
$ fairscape-cli build evidence-graph \
./my_analysis_crate \
ark:59852/dataset-processed-results-zzzz \
--output-json ./my_analysis_crate/prov/results_prov.json \
--output-html ./my_analysis_crate/prov/results_prov.html
```
### Release Management
Create the structure for a multi-part release:
```console
$ fairscape-cli release create \
--name "My Big Release Q4 2023" \
--description "Combined release of Experiment A and Experiment B crates" \
--organization-name "My Org" \
--project-name "Overall Project" \
--keywords "release" \
--keywords "experiment-a" \
--keywords "experiment-b" \
--version "2.0" \
--author "Release Manager" \
--publisher "My Org Publishing" \
./my_big_release
# Manually copy or move your individual RO-Crate directories (e.g., experiment_a_crate, experiment_b_crate)
# into the ./my_big_release directory now.
```
Build the release (link sub-crates, update metadata, generate datasheet):
```console
$ fairscape-cli release build ./my_big_release
```
### Publishing
Upload an RO-Crate to Fairscape:
```console
# Ensure FAIRSCAPE_USERNAME and FAIRSCAPE_PASSWORD are set as environment variables or use options
$ fairscape-cli publish fairscape \
--rocrate ./my_analysis_crate \
--username <your_username> \
--password <your_password>
# Works with either directories or zip files
$ fairscape-cli publish fairscape \
--rocrate ./my_analysis_crate.zip \
--username <your_username> \
--password <your_password> \
--api-url https://fairscape.example.edu/api
```
Publish RO-Crate metadata to Dataverse:
```console
# Ensure DATAVERSE_API_TOKEN is set as an environment variable or use --token
$ fairscape-cli publish dataverse \
--rocrate ./my_analysis_crate/ro-crate-metadata.json \
--url https://my.dataverse.instance.edu \
--collection my_collection_alias \
--token <your_api_token>
```
Mint a DOI using DataCite:
```console
# Ensure DATACITE_USERNAME and DATACITE_PASSWORD are set or use options
$ fairscape-cli publish doi \
--rocrate ./my_analysis_crate/ro-crate-metadata.json \
--prefix 10.1234 \
--username MYORG.MYREPO \
--password <your_api_password> \
--event publish # or 'register' for draft
```
## Contribution
If you'd like to request a feature or report a bug, please create a GitHub Issue using one of the templates provided.
## License
This project is licensed under the terms of the MIT license.
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"description": "# fairscape-cli\n\nA utility for packaging objects and validating metadata for FAIRSCAPE.\n\n---\n\n## **Documentation**: [https://fairscape.github.io/fairscape-cli/](https://fairscape.github.io/fairscape-cli/)\n\n## Features\n\nfairscape-cli provides a Command Line Interface (CLI) that allows the client side to create, manage, and publish scientific data packages:\n\n- **RO-Crate Management:** Create and manipulate [RO-Crate](https://www.researchobject.org/ro-crate/) packages locally.\n - Initialize RO-Crates in new or existing directories.\n - Add data, software, and computation metadata.\n - Copy files into the crate structure alongside metadata registration.\n- **Schema Handling:** Define, infer, and validate data schemas (Tabular, HDF5).\n - Create schema definition files.\n - Add properties with constraints.\n - Infer schemas directly from data files.\n - Validate data files against specified schemas.\n - Register schemas within RO-Crates.\n- **Data Import:** Fetch data from external sources and convert them into RO-Crates.\n - Import NCBI BioProjects.\n - Convert Portable Encapsulated Projects (PEPs) to RO-Crates.\n- **Build Artifacts:** Generate derived outputs from RO-Crates.\n - Create detailed HTML datasheets summarizing crate contents.\n - Generate provenance evidence graphs (JSON and HTML).\n- **Release Management:** Organize multiple related RO-Crates into a cohesive release package.\n - Initialize a release structure.\n - Automatically link sub-crates and propagate metadata.\n - Build a top-level datasheet for the release.\n- **Publishing:** Publish RO-Crate metadata to external repositories.\n - Upload RO-Crate directories or zip files to Fairscape.\n - Create datasets on Dataverse instances.\n - Mint or update DOIs on DataCite.\n\n## Requirements\n\nPython 3.8+\n\n## Installation\n\n```console\n$ pip install fairscape-cli\n```\n\n## Command Overview\n\nThe CLI is organized into several top-level commands:\n\n rocrate: Core local RO-Crate manipulation (create, add files/metadata).\n\n schema: Operations on data schemas (create, infer, add properties, add to crate).\n\n validate: Validate data against schemas.\n\n import: Fetch external data into RO-Crate format (e.g., bioproject, pep).\n\n build: Generate outputs from RO-Crates (e.g., datasheet, evidence-graph).\n\n release: Manage multi-part RO-Crate releases (e.g., create, build).\n\n publish: Publish RO-Crates to repositories (e.g., fairscape, dataverse, doi).\n\nUse --help for details on any command or subcommand:\n\n```console\n$ fairscape-cli --help\n$ fairscape-cli rocrate --help\n$ fairscape-cli rocrate add --help\n$ fairscape-cli schema create --help\n```\n\n## Examples\n\n### Creating an RO-Crate\n\nCreate an RO-Crate in a specified directory:\n\n```console\n$ fairscape-cli rocrate create \\\n --name \"My Analysis Crate\" \\\n --description \"RO-Crate containing analysis scripts and results\" \\\n --organization-name \"My Org\" \\\n --project-name \"My Project\" \\\n --keywords \"analysis\" \\\n --keywords \"python\" \\\n --author \"Jane Doe\" \\\n --version \"1.1.0\" \\\n ./my_analysis_crate\n```\n\nInitialize an RO-Crate in the current working directory:\n\n```console\n# Navigate to an empty directory first if desired\n# mkdir my_analysis_crate && cd my_analysis_crate\n\n$ fairscape-cli rocrate init \\\n --name \"My Analysis Crate\" \\\n --description \"RO-Crate containing analysis scripts and results\" \\\n --organization-name \"My Org\" \\\n --project-name \"My Project\" \\\n --keywords \"analysis\" \\\n --keywords \"python\"\n```\n\n### Adding Content and Metadata to an RO-Crate\n\nThese commands support adding both the file and its metadata (add) or just the metadata (register).\n\nAdd a dataset file and its metadata:\n\n```console\n$ fairscape-cli rocrate add dataset \\\n --name \"Raw Measurements\" \\\n --author \"John Smith\" \\\n --version \"1.0\" \\\n --date-published \"2023-10-27\" \\\n --description \"Raw sensor measurements from Experiment A.\" \\\n --keywords \"raw-data\" \\\n --keywords \"sensors\" \\\n --data-format \"csv\" \\\n --source-filepath \"./source_data/measurements.csv\" \\\n --destination-filepath \"data/measurements.csv\" \\\n ./my_analysis_crate\n```\n\nAdd a software script file and its metadata:\n\n```console\n$ fairscape-cli rocrate add software \\\n --name \"Analysis Script\" \\\n --author \"Jane Doe\" \\\n --version \"1.1.0\" \\\n --description \"Python script for processing raw measurements.\" \\\n --keywords \"analysis\" \\\n --keywords \"python\" \\\n --file-format \"py\" \\\n --source-filepath \"./scripts/process_data.py\" \\\n --destination-filepath \"scripts/process_data.py\" \\\n ./my_analysis_crate\n```\n\nRegister computation metadata (metadata only):\n\n```console\n# Assuming the script and dataset were added previously and have GUIDs:\n# Dataset GUID: ark:59852/dataset-raw-measurements-xxxx\n# Software GUID: ark:59852/software-analysis-script-yyyy\n\n$ fairscape-cli rocrate register computation \\\n --name \"Data Processing Run\" \\\n --run-by \"Jane Doe\" \\\n --date-created \"2023-10-27T14:30:00Z\" \\\n --description \"Execution of the analysis script on the raw measurements.\" \\\n --keywords \"processing\" \\\n --used-dataset \"ark:59852/dataset-raw-measurements-xxxx\" \\\n --used-software \"ark:59852/software-analysis-script-yyyy\" \\\n --generated \"ark:59852/dataset-processed-results-zzzz\" \\\n ./my_analysis_crate\n\n# Note: You would typically register the generated dataset ('processed-results') separately.\n```\n\nRegister dataset metadata (metadata only, file assumed present or external):\n\n```console\n$ fairscape-cli rocrate register dataset \\\n --name \"Processed Results\" \\\n --guid \"ark:59852/dataset-processed-results-zzzz\" \\\n --author \"Jane Doe\" \\\n --version \"1.0\" \\\n --description \"Processed results from the analysis script.\" \\\n --keywords \"results\" \\\n --data-format \"csv\" \\\n --filepath \"results/processed.csv\" \\\n --generated-by \"ark:59852/computation-data-processing-run-wwww\" \\\n ./my_analysis_crate\n```\n\n### Schema Management\n\nCreate a tabular schema definition file:\n\n```console\n$ fairscape-cli schema create \\\n --name 'Measurement Schema' \\\n --description 'Schema for raw sensor measurements' \\\n --schema-type tabular \\\n --separator ',' \\\n --header true \\\n ./measurement_schema.json\n```\n\nAdd properties to the tabular schema file:\n\n```console\n# Add a string property (column 0)\n$ fairscape-cli schema add-property string \\\n --name 'Timestamp' \\\n --index 0 \\\n --description 'Measurement time (ISO8601)' \\\n ./measurement_schema.json\n\n# Add a number property (column 1)\n$ fairscape-cli schema add-property number \\\n --name 'Value' \\\n --index 1 \\\n --description 'Sensor reading' \\\n --minimum 0 \\\n ./measurement_schema.json\n```\n\nInfer a schema from an existing data file:\n\n```console\n$ fairscape-cli schema infer \\\n --name \"Inferred Results Schema\" \\\n --description \"Schema inferred from processed results\" \\\n ./my_analysis_crate/results/processed.csv \\\n ./processed_schema.json\n```\n\nAdd an existing schema file to an RO-Crate:\n\n```console\n$ fairscape-cli schema add-to-crate \\\n ./measurement_schema.json \\\n ./my_analysis_crate\n```\n\n### Validation\n\nValidate a data file against a schema file:\n\n```console\n# Successful validation\n$ fairscape-cli validate schema \\\n --schema-path ./measurement_schema.json \\\n --data-path ./my_analysis_crate/data/measurements.csv\n\n# Example failure\n$ fairscape-cli validate schema \\\n --schema-path ./measurement_schema.json \\\n --data-path ./source_data/measurements_invalid.csv\n```\n\n### Importing Data\n\nImport an NCBI BioProject into a new RO-Crate:\n\n```console\n$ fairscape-cli import bioproject \\\n --accession PRJNA123456 \\\n --author \"Importer Name\" \\\n --output-dir ./bioproject_prjna123456_crate \\\n --crate-name \"Imported BioProject PRJNA123456\"\n```\n\nConvert a PEP project to an RO-Crate:\n\n```console\n$ fairscape-cli import pep \\\n ./path/to/my_pep_project \\\n --output-path ./my_pep_rocrate \\\n --crate-name \"My PEP Project Crate\"\n```\n\n### Building Outputs\n\nGenerate an HTML datasheet for an RO-Crate:\n\n```console\n$ fairscape-cli build datasheet ./my_analysis_crate\n# Output will be ./my_analysis_crate/ro-crate-datasheet.html by default\n```\n\nGenerate a provenance graph for a specific item within the crate:\n\n```console\n# Assuming 'ark:59852/dataset-processed-results-zzzz' is the item of interest\n$ fairscape-cli build evidence-graph \\\n ./my_analysis_crate \\\n ark:59852/dataset-processed-results-zzzz \\\n --output-json ./my_analysis_crate/prov/results_prov.json \\\n --output-html ./my_analysis_crate/prov/results_prov.html\n```\n\n### Release Management\n\nCreate the structure for a multi-part release:\n\n```console\n$ fairscape-cli release create \\\n --name \"My Big Release Q4 2023\" \\\n --description \"Combined release of Experiment A and Experiment B crates\" \\\n --organization-name \"My Org\" \\\n --project-name \"Overall Project\" \\\n --keywords \"release\" \\\n --keywords \"experiment-a\" \\\n --keywords \"experiment-b\" \\\n --version \"2.0\" \\\n --author \"Release Manager\" \\\n --publisher \"My Org Publishing\" \\\n ./my_big_release\n\n# Manually copy or move your individual RO-Crate directories (e.g., experiment_a_crate, experiment_b_crate)\n# into the ./my_big_release directory now.\n```\n\nBuild the release (link sub-crates, update metadata, generate datasheet):\n\n```console\n$ fairscape-cli release build ./my_big_release\n```\n\n### Publishing\n\nUpload an RO-Crate to Fairscape:\n\n```console\n# Ensure FAIRSCAPE_USERNAME and FAIRSCAPE_PASSWORD are set as environment variables or use options\n$ fairscape-cli publish fairscape \\\n --rocrate ./my_analysis_crate \\\n --username <your_username> \\\n --password <your_password>\n\n# Works with either directories or zip files\n$ fairscape-cli publish fairscape \\\n --rocrate ./my_analysis_crate.zip \\\n --username <your_username> \\\n --password <your_password> \\\n --api-url https://fairscape.example.edu/api\n```\n\nPublish RO-Crate metadata to Dataverse:\n\n```console\n# Ensure DATAVERSE_API_TOKEN is set as an environment variable or use --token\n$ fairscape-cli publish dataverse \\\n --rocrate ./my_analysis_crate/ro-crate-metadata.json \\\n --url https://my.dataverse.instance.edu \\\n --collection my_collection_alias \\\n --token <your_api_token>\n```\n\nMint a DOI using DataCite:\n\n```console\n# Ensure DATACITE_USERNAME and DATACITE_PASSWORD are set or use options\n$ fairscape-cli publish doi \\\n --rocrate ./my_analysis_crate/ro-crate-metadata.json \\\n --prefix 10.1234 \\\n --username MYORG.MYREPO \\\n --password <your_api_password> \\\n --event publish # or 'register' for draft\n```\n\n## Contribution\n\nIf you'd like to request a feature or report a bug, please create a GitHub Issue using one of the templates provided.\n\n## License\n\nThis project is licensed under the terms of the MIT license.\n",
"bugtrack_url": null,
"license": "Copyright 2023 THE RECTOR AND VISITORS OF THE UNIVERSITY OF VIRGINIA\n \n Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the \u201cSoftware\u201d), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:\n \n The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.\n \n THE SOFTWARE IS PROVIDED \u201cAS IS\u201d, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.",
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