diff --git a/.flake8 b/.flake8 index e203c689..0a0c58f9 100644 --- a/.flake8 +++ b/.flake8 @@ -5,3 +5,5 @@ [flake8] max-complexity = 15 max-line-length = 120 +per-file-ignores = + src/hermes/commands/marketplace.py:E231 diff --git a/.github/ISSUE_TEMPLATE/add-plugin-to-marketplace.yml b/.github/ISSUE_TEMPLATE/add-plugin-to-marketplace.yml index 11437b35..48bc5af2 100644 --- a/.github/ISSUE_TEMPLATE/add-plugin-to-marketplace.yml +++ b/.github/ISSUE_TEMPLATE/add-plugin-to-marketplace.yml @@ -13,7 +13,7 @@ body: value: | Thank you for building a plugin for Hermes and sharing it with the community! - The [Hermes plugin marketplace](https://hermes.software-metadata.pub#plugins) is a curated list of plugins on our website that allows you to share plugins that you developed, and others to find them. + The [Hermes plugin marketplace](https://hermes.software-metadata.pub/marketplace) is a curated list of plugins on our website that allows you to share plugins that you developed, and others to find them. Via this issue template, you can send us the required information to add your plugin to the marketplace. Alternatively, you may file a pull request, adding the plugin to [`plugins.json`](https://github.com/softwarepub/hermes/tree/develop/docs/source/plugins.json) yourself. diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 7e29bb9b..5d893e25 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -24,7 +24,7 @@ jobs: - name: Set up Python uses: actions/setup-python@v5 with: - python-version: "3.10" + python-version: "3.12" - name: Install pypa/build run: >- python3 -m diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index c0e02b6c..394fd5c8 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -15,7 +15,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ["3.10"] # Ignore Python < 3.10, they are unsupported + python-version: ["3.12"] # Ignore Python < 3.11, they are unsupported steps: - uses: actions/checkout@v4 @@ -26,11 +26,9 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip poetry - poetry install + poetry install --with dev - name: Lint with flake8 run: | - # stop the build if there are Python syntax errors or undefined names - poetry run flake8 ./test/ ./src/ --count --select=E9,F63,F7,F82 --show-source --statistics # Stop build on errors poetry run flake8 ./test/ ./src/ --count --statistics - name: Test with pytest diff --git a/.readthedocs.yaml b/.readthedocs.yaml index ee7315e5..675219ea 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -7,12 +7,17 @@ version: 2 build: os: ubuntu-20.04 tools: - python: "3.10" + python: "3.12" jobs: + post_create_environment: + # Install poetry + # https://python-poetry.org/docs/#installing-manually + - pip install "poetry>=2.1.3,<3.0.0" post_install: - - pip install "poetry>=1.2.0,<1.3.0" - - poetry config virtualenvs.create false - - poetry install --with docs + # Install dependencies with 'docs' dependency group + # https://python-poetry.org/docs/managing-dependencies/#dependency-groups + # VIRTUAL_ENV needs to be set manually for now, see #11150 + - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install --with docs # Build documentation in the docs/source directory with Sphinx sphinx: diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100644 index 00000000..72eae7c3 --- /dev/null +++ b/CHANGELOG.md @@ -0,0 +1,60 @@ + + +# Changelog + +All notable changes to this project will be documented in this file. + +The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/), +and this project tries to adhere to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). + +## [0.9.1] - 2026-01-12 + +### Added + +- Added ADR for `init` plugin (#324) + +### Fixed + +- Broken HERMES DOI in marketplace plugin metadata (#326) +- hermes init fails with cryptic error message in non-git directory (#308) +- Make --initial deposits work on Rodare (#348) +- Fix GitHub link in docs (#319) +- `hermes init` cancellation should remove created files (#328) +- `pyproject.toml` compliance with PEP 621 (#347) +- Improve marketplace visibility (#426) + +### Changed + +- Update poetry to more recent version. (#347) + +### Security + +- Patch raw logging of '-O' values that could have included arbitrary secrets. (https://github.com/softwarepub/hermes/security/advisories/GHSA-jm5j-jfrm-hm23) + +## [0.9.0] - 2025-02-26 + +### Added + +- Added the hermes init subcommand + +### Fixed + +- Fixes multiple bugs + +### Changed + +- Refactored plugin system further + +## [0.8.1] - 2024-08-13 + +### Added + +- Integrated pyproject.toml plugin into the publication process + +### Changed + +- Improved logging output for better error dissemination \ No newline at end of file diff --git a/CITATION.cff b/CITATION.cff index 1556b8ff..70b7b76f 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -14,7 +14,7 @@ title: hermes message: >- If you use this software, please cite it using the metadata from this file. -version: 0.9.0 +version: 0.9.1 license: "Apache-2.0" abstract: "Tool to automate software publication. Not stable yet." type: software diff --git a/GOVERNANCE.md b/GOVERNANCE.md index 3c2cdbae..b0eae368 100644 --- a/GOVERNANCE.md +++ b/GOVERNANCE.md @@ -80,5 +80,5 @@ If no successor is named, the Steering Group seeks a successor. One member of the Steering Group steps in as interim maintainer until a successor is found. -In addition, all contributors with write access to repositories and regular activities should be added as "authors" to project and build system metadata in alphabetical order. -They may also qualify for scholarly authorship, which is managed in citation metadata as necessary and may be ordered by other criteria. +Authorship is defined by the [steering group](#hermes-steering-group) and declared in +[`CITATION.cff`](https://github.com/softwarepub/hermes/blob/main/CITATION.cff). diff --git a/docs/adr/0002-use-a-common-data-model.md b/docs/adr/0002-use-a-common-data-model.md index 4ca30906..29a9de90 100644 --- a/docs/adr/0002-use-a-common-data-model.md +++ b/docs/adr/0002-use-a-common-data-model.md @@ -20,7 +20,7 @@ We need a data model that's to exchange data between modules. The chosen option determines the serialization of the data model, too. -See also [ADR 11](./0011-record-provenance-of-metadata.md) about provenance records in the data model. +See also [ADR 11](./0011-record-provenance-of-metadata) about provenance records in the data model. ## Considered Options diff --git a/docs/adr/0003-define-interfaces-for-inter-module-data-exchange.md b/docs/adr/0003-define-interfaces-for-inter-module-data-exchange.md index 00933d74..f537a686 100644 --- a/docs/adr/0003-define-interfaces-for-inter-module-data-exchange.md +++ b/docs/adr/0003-define-interfaces-for-inter-module-data-exchange.md @@ -14,7 +14,7 @@ SPDX-License-Identifier: CC-BY-SA-4.0 This depends on the data model (ADR 0002). Do we have to expose different parts of the data model structure at different points in the workflow? -Superseded: decisions in [ADR 2](./0002-use-a-common-data-model.md) (use JSON-LD) and [ADR 11](./0011-record-provenance-of-metadata.md) (create a unified data model of metadata and provenance) will result in a context [DAO](https://en.wikipedia.org/wiki/Data_access_object) from beginning till end of a run. +Superseded: decisions in [ADR 2](./0002-use-a-common-data-model) (use JSON-LD) and [ADR 11](./0011-record-provenance-of-metadata) (create a unified data model of metadata and provenance) will result in a context [DAO](https://en.wikipedia.org/wiki/Data_access_object) from beginning till end of a run. ## Decision Drivers diff --git a/docs/adr/0013-plugin-init.md b/docs/adr/0013-plugin-init.md new file mode 100644 index 00000000..9c678074 --- /dev/null +++ b/docs/adr/0013-plugin-init.md @@ -0,0 +1,45 @@ + +# Installing plugins from the marketplace using hermes init + +* Status: accepted +* Deciders: nheeb +* Date: 2025-03-04 + +## Context and Problem Statement + +For a smooth user experience common plugins (those which are on the marketplace) should be installable via `hermes init`. That however means we need to decide on a way for the plugins to ask question during that same init process. + +## Considered Options + +* **Full install**: Plugins are installed locally during `hermes init`, can hook into the init process, and ask questions themselves to adjust the `hermes.toml` or similar. +* **No install**: Plugins are only added to the CI pipeline as `pip install ...` lines. Additional questions for the init process could be added in the marketplace input mask along with a property name under which the answer is stored in the `hermes.toml`. +* **Partial install**: Plugins are only added to the CI pipeline as `pip install ...` lines. Additional questions for the init process are handled in a "detached" script that is downloaded, executed locally, and then deleted again (this script may only have dependencies of Hermes). + +## Decision Outcome + +Chosen option: "**Partial install**", because it is a good trade-off between giving plugins more controll over their init process and not being too invasive with local installs. + +## Pros and Cons of the Options + +### Full install +- (+) Plugins have a lot of control over how they design their own init process. +- (+) The plugin can be used locally on the device directly if the user intends to do so. +- (-) The plugin might be installed unnecessarily, as locally only the init part may be executed. +- (-) The plugin may introduce many dependencies that the user doesn’t necessarily need. +- (-) There could be environment complications (e.g., if Hermes was installed with `pipx`). + +### No install +- (+) Nothing is installed locally via `hermes init`. +- (+) Overall, slightly less effort for the init command and plugin developers. +- (-) The marketplace would need input masks for an arbitrary number of such questions. +- (-) Plugins have little control over how they design their own init process. +- (-) Plugins intended for local use must be installed manually. + +### Partial install +- (+) Nothing is installed locally via `hermes init`. +- (+) Plugins have relatively high control over how they design their own init process. +- (-) Plugins intended for local use must be installed manually. diff --git a/docs/adr/0014-standardized-provenance-recording.md b/docs/adr/0014-standardized-provenance-recording.md new file mode 100644 index 00000000..4eb6df4e --- /dev/null +++ b/docs/adr/0014-standardized-provenance-recording.md @@ -0,0 +1,62 @@ + +# Standardized provenance recording + +* Status: proposed +* Deciders: sdruskat, skernchen, notactuallyfinn +* Date: 2025-10-17 + +Technical story: +* https://github.com/softwarepub/hermes/pull/442 +* https://github.com/softwarepub/hermes/issues/363 + +## Context and Problem Statement + +To consolidate traceability of the metadata, and resolution based on metadata sources in case of duplicates, etc., we need to record the provenance of metadata values in a __standardized__ way. +To achieve this, we use the [PROV-O ontology](https://www.w3.org/TR/prov-o/) serialized as [JSON-LD](https://www.w3.org/TR/json-ld/). Additionally, HERMES should make it possible to record as much of the provenance as possible *centrally*, i.e., as part of the core codebase. This is to keep plugin developers from having to supply their own provenance solutions. + +To do this, we need to specify what provenance information is recorded and how it can be implemented in HERMES to make it easy to use. + +## Considered Options + +* Provide HERMES API-methods that also document themselves + +## Decision Outcome + +Chosen option: + +## Pros and Cons of the Options + +### Provide HERMES API-methods that also document themselves + +Provide API-methods for loading, writing, making web requests, etc. that document themselves.
+Those methods take also the function that should be used for the task at hand and just define a framework in which we implement the provenance-data recording.
+Like so: +```python +class HermesPlugin(): + def load(func, path: str, *args, **kwargs): + # TODO: handle and record byte formats properly + with open(path) as fi: + data = func(fi, *args, **kwargs) + prov.record("load", path, func.__name__, data) # also module of func + return data + + def write(func, path: str, data, *args, **kwargs): + # TODO: handle and record byte formats properly + with open(path) as fi: + func(fi, data, *args, **kwargs) + prov.record("write", path, func.__name__, data) # also module of func +``` + +* Good, because allows for recording of provenance information of the plugins +* Good, because it isn't making plugin development harder +* Bad, because API methods may not cover all I/O functionality python provides +* Bad, because it doesn't cover merging, mapping, etc. + +All provenance information should be recorded in the following format where addtional properties of agents, activites and entities are values of suitable vocabularies (from Schema.org, CodeMeta and potentially other schemas): + +![](./hermes-prov-diagram/hermes-prov.svg)
+source: [hermes-prov.drawio](./hermes-prov-diagram/hermes-prov.drawio) diff --git a/docs/adr/hermes-prov-diagram/hermes-prov.drawio b/docs/adr/hermes-prov-diagram/hermes-prov.drawio new file mode 100644 index 00000000..4173db36 --- /dev/null +++ b/docs/adr/hermes-prov-diagram/hermes-prov.drawio @@ -0,0 +1,2138 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/docs/adr/hermes-prov-diagram/hermes-prov.drawio.license b/docs/adr/hermes-prov-diagram/hermes-prov.drawio.license new file mode 100644 index 00000000..2e24f7a4 --- /dev/null +++ b/docs/adr/hermes-prov-diagram/hermes-prov.drawio.license @@ -0,0 +1,3 @@ +SPDX-FileCopyrightText: 2025 German Aerospace Center (DLR) + +SPDX-License-Identifier: CC-BY-SA-4.0 diff --git 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 \ No newline at end of file diff --git a/docs/adr/hermes-prov-diagram/hermes-prov.svg.license b/docs/adr/hermes-prov-diagram/hermes-prov.svg.license new file mode 100644 index 00000000..2e24f7a4 --- /dev/null +++ b/docs/adr/hermes-prov-diagram/hermes-prov.svg.license @@ -0,0 +1,3 @@ +SPDX-FileCopyrightText: 2025 German Aerospace Center (DLR) + +SPDX-License-Identifier: CC-BY-SA-4.0 diff --git a/docs/source/conf.py b/docs/source/conf.py index 9ee616da..6c03b2bf 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -128,9 +128,10 @@ def read_version_from_pyproject(): # Sphinx API docs configuration, see https://sphinx-autoapi.readthedocs.io/en/latest/reference/config.html autoapi_type = "python" -autoapi_dirs = ["../../src"] +autoapi_file_patterns = ["*.py"] autoapi_root = "api" -autoapi_ignore = ["*__main__*"] +autoapi_dirs = ["../../src"] +autoapi_ignore = ["*/__main__.py"] # -- Options for HTML output ------------------------------------------------- diff --git a/docs/source/dev/start.md b/docs/source/dev/start.md index 17607101..b24f1b85 100644 --- a/docs/source/dev/start.md +++ b/docs/source/dev/start.md @@ -30,7 +30,7 @@ You can either download it as a zipped package or clone the whole Git repository You can clone the repository and enter the project directory as follows: ```shell -git clone https://gitlab.com/hermes-hmc/hermes.git +git clone https://github.com/softwarepub/hermes.git cd hermes ``` diff --git a/docs/source/index.md b/docs/source/index.md index 648c4cf3..609a508e 100644 --- a/docs/source/index.md +++ b/docs/source/index.md @@ -9,6 +9,7 @@ SPDX-FileContributor: Oliver Bertuch SPDX-FileContributor: Stephan Druskat SPDX-FileContributor: Michael Meinel SPDX-FileContributor: David Pape +SPDX-FileContributor: Michael Fritzsche --> ![](_static/img/header.png) @@ -45,15 +46,9 @@ automatic submission to publication repositories. ## Plugins -```{plugin-markup} plugins.json plugins-schema.json -``` - Hermes is built to be extensible for your needs. -This is a list of available plugins for the different steps in the Hermes workflow: - -```{datatemplate:json} plugins.json -:template: plugins.md -``` +The list of available plugins for the different steps in the Hermes workflow can be found +[here](./plugins/marketplace.md). ## Documentation @@ -70,6 +65,12 @@ This is a list of available plugins for the different steps in the Hermes workfl tutorials/* ``` +```{toctree} +:maxdepth: 1 +:caption: Plugins Marketplace +plugins/marketplace +``` + ```{toctree} :maxdepth: 1 :caption: Developers diff --git a/docs/source/plugins/marketplace.md b/docs/source/plugins/marketplace.md new file mode 100644 index 00000000..eee36cc5 --- /dev/null +++ b/docs/source/plugins/marketplace.md @@ -0,0 +1,30 @@ + + + + +# Plugin Marketplace + +The HERMES Marketplace offers you a list of available plugins for all steps of the HERMES workflow.
+Furthermore you can publish your own to make it available for everyone. + +## Available Plugins + +This is the list of available plugins grouped by the steps of the HERMES workflow. + +```{plugin-markup} plugins.json plugins-schema.json +``` +```{datatemplate:json} plugins.json +:template: plugins.md +``` + +## Publish your Plugin + +If you have written your own plugin for HERMES you can publish it here for others to use.
+To do that please fill out +[this form](https://github.com/softwarepub/hermes/issues/new?template=add-plugin-to-marketplace.yml). diff --git a/docs/source/plugins-schema.json b/docs/source/plugins/plugins-schema.json similarity index 100% rename from docs/source/plugins-schema.json rename to docs/source/plugins/plugins-schema.json diff --git a/docs/source/plugins-schema.json.license b/docs/source/plugins/plugins-schema.json.license similarity index 100% rename from docs/source/plugins-schema.json.license rename to docs/source/plugins/plugins-schema.json.license diff --git a/docs/source/plugins.json b/docs/source/plugins/plugins.json similarity index 85% rename from docs/source/plugins.json rename to docs/source/plugins/plugins.json index 16cec4ad..04d69099 100644 --- a/docs/source/plugins.json +++ b/docs/source/plugins/plugins.json @@ -15,6 +15,17 @@ "harvested_files": ["codemeta.json"], "builtin": true }, + { + "name": "'file_exists' Harvester", + "description": "Harvest plugin that figures out whether certain frequently used files (README, LICENSE, ...) exist. Custom search patterns for other types of files can be configured.", + "author": "Hermes team", + "steps": ["harvest"], + "harvested_files": [ + "readme", + "license" + ], + "builtin": true + }, { "name": "hermes-plugin-git", "description": "Harvest plugin for Git repository metadata.", diff --git a/docs/source/plugins.json.license b/docs/source/plugins/plugins.json.license similarity index 100% rename from docs/source/plugins.json.license rename to docs/source/plugins/plugins.json.license diff --git a/docs/source/tutorials/writing-a-plugin-for-hermes.md b/docs/source/tutorials/writing-a-plugin-for-hermes.md index 424596c1..647a2e80 100644 --- a/docs/source/tutorials/writing-a-plugin-for-hermes.md +++ b/docs/source/tutorials/writing-a-plugin-for-hermes.md @@ -164,4 +164,8 @@ You can now write plugins for HERMES. To fill the plugin with code, you can check our [hermes-plugin-git](https://github.com/softwarepub/hermes-plugin-git) repository. There is the code to check the local git history and extract contributors of the given branch. +Now that you have created your own plugin consider publishing it to the +[HERMES Marketplace](../plugins/marketplace.md) so that others can use it as +well and the HERMES project gets more versatile. + If you have any questions, wishes or requests, feel free to contact us. diff --git a/hermes.toml b/hermes.toml index 3aa44a8f..ed60a0fd 100644 --- a/hermes.toml +++ b/hermes.toml @@ -3,7 +3,10 @@ # SPDX-License-Identifier: CC0-1.0 [harvest] -sources = [ "cff", "toml" ] # ordered priority (first one is most important) +sources = [ "cff", "toml", "file_exists" ] # ordered priority (first one is most important) + +[harvest.file_exists.search_patterns] +community = ["contributing.md", "governance.md"] [deposit] target = "invenio_rdm" @@ -18,4 +21,3 @@ record_id = 13221384 depositions = "api/deposit/depositions" licenses = "api/vocabularies/licenses" communities = "api/communities" - diff --git a/poetry.lock b/poetry.lock index df93853e..36e3277f 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.2.1 and should not be changed by hand. [[package]] name = "accessible-pygments" @@ -6,6 +6,7 @@ version = "0.0.5" description = "A collection of accessible pygments styles" optional = false python-versions = ">=3.9" +groups = ["docs"] files = [ {file = "accessible_pygments-0.0.5-py3-none-any.whl", hash = "sha256:88ae3211e68a1d0b011504b2ffc1691feafce124b845bd072ab6f9f66f34d4b7"}, {file = "accessible_pygments-0.0.5.tar.gz", hash = "sha256:40918d3e6a2b619ad424cb91e556bd3bd8865443d9f22f1dcdf79e33c8046872"}, @@ -20,13 +21,14 @@ tests = ["hypothesis", "pytest"] [[package]] name = "alabaster" -version = "0.7.16" +version = "1.0.0" description = "A light, configurable Sphinx theme" optional = false -python-versions = ">=3.9" +python-versions = ">=3.10" +groups = ["docs"] files = [ - {file = "alabaster-0.7.16-py3-none-any.whl", hash = "sha256:b46733c07dce03ae4e150330b975c75737fa60f0a7c591b6c8bf4928a28e2c92"}, - {file = "alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65"}, + 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Helmholtz-Zentrum Dresden-Rossendorf # # SPDX-License-Identifier: CC0-1.0 -# SPDX-FileContributor: Stephan Druskat +# SPDX-FileContributor: Stephan Druskat # SPDX-FileContributor: Michael Meinel # SPDX-FileContributor: David Pape -[tool.poetry] -# Reference at https://python-poetry.org/docs/pyproject/ +[project] name = "hermes" -version = "0.9.0" +version = "0.9.1" description = "Workflow to publish research software with rich metadata" -homepage = "https://software-metadata.pub" -license = "Apache-2.0" -# All natural persons doing regular contributions and equipped with write access to the repo. -# Alphabetical order of last name. See also GOVERNANCE.md. +license = "Apache-2.0 AND LicenseRef-BSD-Caltech" authors = [ - "Oliver Bertuch ", - "Stephan Druskat ", - "Nitai Heeb ", - "Sophie Kernchen ", - "Michael Meinel ", - "David Pape " + { name = "Michael Meinel", email = "michael.meinel@dlr.de" }, + { name = "Stephan Druskat", email = "stephan.druskat@dlr.de" }, + { name = "Oliver Bertuch", email = "o.bertuch@fz-juelich.de" }, + { name = "Oliver Knodel", email = "o.knodel@hzdr.de" }, + { name = "David Pape", email = "d.pape@hzdr.de" }, + { name = "Sophie Kernchen", email = "sohpie.kernchen@dlr.de" }, + { name = "Nitai Heeb", email = "n.heeb@fz-juelich.de" }, +] +maintainers = [ + { name = "Stephan Druskat", email = "stephan.druskat@dlr.de" }, ] - readme = "README.md" repository = "https://github.com/softwarepub/hermes" +keywords = ["software", "publication", "metadata", "automation"] + +dependencies = [ + "ruamel.yaml>=0.17.21, <0.18.0", + "jsonschema>=3.0.0, <4.0.0", + "pyld>=2.0.3, <3.0.0", + "cffconvert>=2.0.0, <3.0.0", + "toml>=0.10.2, <1.0.0", + "pyparsing>=3.0.9, <4.0.0", + "requests>=2.28.1, <3.0.0", + "pydantic>=2.5.1, <3.0.0", + "pydantic-settings>=2.1.0, <3.0.0", + "requests-oauthlib>=2.0.0, <3.0.0", + "pynacl>=1.6.2, <2.0.0", +] +requires-python = ">=3.11, <4.0.0" + +[project.urls] +homepage = "https://hermes.software-metadata.pub" documentation = "https://hermes.software-metadata.pub" -keywords = ["publishing", "metadata", "automation"] +repository = "https://github.com/softwarepub/hermes.git" +issues = "https://github.com/softwarepub/hermes/issues" -include = [ - "hermes/schema/*.json", -] -# Stating our package explicitely here to enable -# a) including contrib packages in the future and -# b) rename the package for development snapshot releases to TestPyPI -packages = [ - { include = "hermes", from = "src" } -] +[project.scripts] +hermes = "hermes.commands.cli:main" +hermes-marketplace = "hermes.commands.marketplace:main" + + +[project.entry-points."hermes.harvest"] +cff = "hermes.commands.harvest.cff:CffHarvestPlugin" +codemeta = "hermes.commands.harvest.codemeta:CodeMetaHarvestPlugin" +file_exists = "hermes.commands.harvest.file_exists:FileExistsHarvestPlugin" + +[project.entry-points."hermes.deposit"] +file = "hermes.commands.deposit.file:FileDepositPlugin" +invenio = "hermes.commands.deposit.invenio:InvenioDepositPlugin" +invenio_rdm = "hermes.commands.deposit.invenio_rdm:IvenioRDMDepositPlugin" +rodare = "hermes.commands.deposit.rodare:RodareDepositPlugin" + +[project.entry-points."hermes.postprocess"] +config_invenio_record_id = "hermes.commands.postprocess.invenio:config_record_id" +config_invenio_rdm_record_id = "hermes.commands.postprocess.invenio_rdm:config_record_id" +cff_doi = "hermes.commands.postprocess.invenio:cff_doi" [tool.poetry.dependencies] -python = "^3.10" -"ruamel.yaml" = "^0.17.21" -jsonschema = "^3.0.0" -pyld = "^2.0.3" -cffconvert = "^2.0.0" -toml = "^0.10.2" -pyparsing = "^3.0.9" -requests = "^2.28.1" -pydantic = "^2.5.1" -pydantic-settings = "^2.1.0" -requests-oauthlib = "^2.0.0" -pynacl = "^1.5.0" +python = ">=3.11,<4.0.0" [tool.poetry.group.dev.dependencies] pytest = "^7.1.1" @@ -66,41 +85,24 @@ requests-mock = "^1.10.0" optional = true [tool.poetry.group.docs.dependencies] -Sphinx = "^6.2.1" +Sphinx = "~=8.2" # Sphinx - Additional modules -myst-parser = "^2.0.0" -sphinx-book-theme = "^1.0.1" -sphinx-favicon = "^0.2" -sphinxcontrib-contentui = "^0.2.5" -sphinxcontrib-images = "^0.9.4" -sphinx-icon = "^0.1.2" -sphinx-autobuild = "^2021.3.14" -sphinx-autoapi = "^3.0.0" -sphinxemoji = "^0.2.0" -sphinxext-opengraph = "^0.6.3" -sphinxcontrib-mermaid="^0.8.1" -sphinx-togglebutton="^0.3.2" +myst-parser = "~=4.0" +sphinx-book-theme = "~=1.1" +sphinx-favicon = "~=0.2" +sphinxcontrib-contentui = "~=0.2" +sphinxcontrib-images = "~=1.0" +sphinx-icon = "~=0.1" +sphinx-autobuild = "2021.3.14" +sphinx-autoapi = "~=3.6" +sphinxemoji = "~=0.2" +sphinxext-opengraph = "~=0.6" +sphinxcontrib-mermaid="~=0.8" +sphinx-togglebutton="~=0.3.2" reuse = "^1.1.2" -sphinxcontrib-datatemplates = "^0.11.0" - -[tool.poetry.plugins.console_scripts] -hermes = "hermes.commands.cli:main" -hermes-marketplace = "hermes.commands.marketplace:main" +sphinxcontrib-datatemplates = "~=0.11" -[tool.poetry.plugins."hermes.harvest"] -cff = "hermes.commands.harvest.cff:CffHarvestPlugin" -codemeta = "hermes.commands.harvest.codemeta:CodeMetaHarvestPlugin" - -[tool.poetry.plugins."hermes.deposit"] -file = "hermes.commands.deposit.file:FileDepositPlugin" -invenio = "hermes.commands.deposit.invenio:InvenioDepositPlugin" -invenio_rdm = "hermes.commands.deposit.invenio_rdm:IvenioRDMDepositPlugin" -rodare = "hermes.commands.deposit.rodare:RodareDepositPlugin" -[tool.poetry.plugins."hermes.postprocess"] -config_invenio_record_id = "hermes.commands.postprocess.invenio:config_record_id" -config_invenio_rdm_record_id = "hermes.commands.postprocess.invenio_rdm:config_record_id" -cff_doi = "hermes.commands.postprocess.invenio:cff_doi" [tool.taskipy.tasks] docs-build = "poetry run sphinx-build -M html docs/source docs/build -W" @@ -108,6 +110,7 @@ docs-clean = "poetry run sphinx-build -M clean docs/source docs/build" docs-live = "poetry run sphinx-autobuild docs/source docs/build" flake8 = "poetry run flake8 ./test/ ./src/ --count --select=E9,F63,F7,F82 --statistics" + [tool.pytest.ini_options] norecursedirs = "docs/*" testpaths = [ @@ -115,6 +118,9 @@ testpaths = [ ] addopts = "--cov=hermes --cov-report term" + [build-system] -requires = ["poetry-core>=1.2.0"] +requires = [ + "poetry-core>=2.1.3, <3.0.0" +] build-backend = "poetry.core.masonry.api" diff --git a/src/hermes/commands/cli.py b/src/hermes/commands/cli.py index 06a18ca7..09a8e650 100644 --- a/src/hermes/commands/cli.py +++ b/src/hermes/commands/cli.py @@ -16,6 +16,7 @@ HermesHarvestCommand, HermesProcessCommand, HermesCurateCommand, HermesDepositCommand, HermesPostprocessCommand, HermesInitCommand) from hermes.commands.base import HermesCommand +from hermes.utils import mask_options_values def main() -> None: @@ -63,7 +64,7 @@ def main() -> None: logger.init_logging() log = logger.getLogger("hermes.cli") - log.debug("Running hermes with the following command line arguments: %s", args) + log.debug("Running hermes with the following command line arguments: %s", mask_options_values(args)) try: log.debug("Loading settings...") diff --git a/src/hermes/commands/deposit/invenio.py b/src/hermes/commands/deposit/invenio.py index e88066c6..703e9a5b 100644 --- a/src/hermes/commands/deposit/invenio.py +++ b/src/hermes/commands/deposit/invenio.py @@ -152,7 +152,7 @@ def resolve_doi(self, doi) -> str: :return: The record ID on the respective instance. """ - res = self.client.get(f'https://doi.org/{doi}') + res = self.client.get(f'https://doi.org/{doi}') # noqa E231 # This is a mean hack due to DataCite answering a 404 with a 200 status if res.url == 'https://datacite.org/404.html': diff --git a/src/hermes/commands/deposit/rodare.py b/src/hermes/commands/deposit/rodare.py index c164e342..0106cd7f 100644 --- a/src/hermes/commands/deposit/rodare.py +++ b/src/hermes/commands/deposit/rodare.py @@ -49,39 +49,28 @@ class RodareDepositPlugin(InvenioDepositPlugin): robis_publication_url = "https://www.hzdr.de/publications/Publ-{pub_id}" def prepare(self) -> None: - """Update the context with the Robis identifier from the config.""" + """Update the context with the Robis identifier from the config. + + All HZDR publications must be registered in Robis (https://www.hzdr.de/robis). + The first release of a software may only be performed when the registration in + Robis is finalized and approved, and a publication form was added. + """ super().prepare() if not self.config.robis_pub_id: raise MisconfigurationError( f"deposit.{self.platform_name}.robis_pub_id is not configured. " - "You can get a robis_pub_id by publishing the software via Robis. " - f"HERMES may be used for subsequent releases. {self.robis_url}" + "You can get a robis_pub_id by registering the planned publication in " + 'Robis and adding a "Software Publication" as publication form. ' + "After approval of the publication, you may add the Robis Publ-Id to " + "the HERMES config file and proceed with the publication. " + f"{self.robis_url}" ) self.ctx.update( self.invenio_context_path["robis_pub_id"], self.config.robis_pub_id ) - def create_initial_version(self) -> None: - """Disallow creation of initial versions using HERMES. - - HZDR publications must all be registered in Robis (https://www.hzdr.de/robis). - There is a workflow in place that guides users from Robis to Rodare and - automatically transfers metadata for them. Starting the publication workflow in - Rodare is discouraged. - - Subsequent releases of the software may be published on Rodare directly as the - connection to Robis is in place by then. - - This code should never be reached. So, raising a ``RuntimeError`` is just a - precaution. - """ - raise RuntimeError( - "Please initiate the publication process in Robis. " - f"HERMES may be used for subsequent releases. {self.robis_url}" - ) - def related_identifiers(self): """Update the related identifiers with link to Robis. diff --git a/src/hermes/commands/harvest/cff.py b/src/hermes/commands/harvest/cff.py index e333b27c..1f621b17 100644 --- a/src/hermes/commands/harvest/cff.py +++ b/src/hermes/commands/harvest/cff.py @@ -80,7 +80,7 @@ def _convert_cff_to_codemeta(self, cff_data: str) -> t.Any: def _validate(self, cff_file: pathlib.Path, cff_dict: t.Dict) -> bool: audit_log = logging.getLogger('audit.cff') - cff_schema_url = f'https://citation-file-format.github.io/{_CFF_VERSION}/schema.json' + cff_schema_url = f'https://citation-file-format.github.io/{_CFF_VERSION}/schema.json' # noqa E231 # TODO: we should ship the schema we reference to by default to avoid unnecessary network traffic. # If the requested version is not already downloaded, go ahead and download it. @@ -101,7 +101,7 @@ def _validate(self, cff_file: pathlib.Path, cff_dict: t.Dict) -> bool: audit_log.info('') audit_log.info('See the Citation File Format schema guide for further details:') audit_log.info( - f'.') + f'.') # noqa E231 return False elif len(errors) == 0: diff --git a/src/hermes/commands/harvest/file_exists.py b/src/hermes/commands/harvest/file_exists.py new file mode 100644 index 00000000..ee6b4e8a --- /dev/null +++ b/src/hermes/commands/harvest/file_exists.py @@ -0,0 +1,286 @@ +# SPDX-FileCopyrightText: 2025 Helmholtz-Zentrum Dresden-Rossendorf +# SPDX-License-Identifier: Apache-2.0 +# SPDX-FileContributor: David Pape + +"""Module for the ``FileExistsHarvestPlugin`` and it's associated models and helpers.""" + +from collections import defaultdict +from dataclasses import dataclass +from functools import cache +from pathlib import Path +from typing import Dict, Iterable, List, Optional, Set +from typing_extensions import Self +import subprocess + +from pydantic import BaseModel + +from hermes.commands.harvest.base import HermesHarvestCommand, HermesHarvestPlugin +from hermes.utils import guess_file_type + + +@dataclass(kw_only=True) +class URL: + """Basic model of a ``schema:URL``. + + See also: https://schema.org/URL + """ + + url: str + + @classmethod + def from_path(cls, path: Path) -> Self: + return cls(url=path.as_uri()) + + def as_codemeta(self) -> dict: + return { + "@type": "schema:URL", + "@value": self.url, + } + + +# TODO: Support common subtypes of ``MediaObject`` such as ``TextObject`` and +# ``ImageObject``? This would require either mapping mime types to text/image/binary/... +# which probably has many special cases (e.g. ``application/toml`` → text, +# ``image/svg+xml`` → text, ...), or figuring this out using the file itself, e.g. +# using libmagic. +@dataclass(kw_only=True) +class MediaObject: + """Basic model of a ``schema:MediaObject``. + + See also: https://schema.org/MediaObject + """ + + content_size: Optional[str] + encoding_format: Optional[str] + url: URL + + @classmethod + def from_path(cls, path: Path) -> Self: + size = None + try: + size = str(path.stat().st_size) # string! + except FileNotFoundError: + pass + type_, _encoding = guess_file_type(path) + url = URL.from_path(path) + return cls(content_size=size, encoding_format=type_, url=url) + + def as_codemeta(self) -> dict: + return { + "@type": "schema:MediaObject", + "schema:contentSize": self.content_size, + "schema:encodingFormat": self.encoding_format, + "schema:url": self.url.as_codemeta(), + } + + +@dataclass(kw_only=True) +class CreativeWork: + """Basic model of a ``schema:CreativeWork``. + + See also: https://schema.org/CreativeWork + """ + + name: str + associated_media: MediaObject + keywords: Set[str] + + @classmethod + def from_path(cls, path: Path, keywords: Iterable[str]) -> Self: + text_object = MediaObject.from_path(path) + return cls(name=path.stem, associated_media=text_object, keywords=set(keywords)) + + def as_codemeta(self) -> dict: + return { + "@type": "schema:CreativeWork", + "schema:name": self.name, + "schema:associatedMedia": self.associated_media.as_codemeta(), + "schema:keywords": list(self.keywords), + } + + +class FileExistsHarvestSettings(BaseModel): + """Settings for ``file_exists`` harvester.""" + + enable_git_ls_files: bool = True + keep_untagged_files: bool = False + search_patterns: Dict[str, List[str]] = {} + + +class FileExistsHarvestPlugin(HermesHarvestPlugin): + """Harvest plugin that finds and tags files based on patterns. + + Files are searched using ``git ls-files`` or a recursive traversal of the working + directory. If available, ``git ls-files`` is used. This can be disabled via the + options. + + The found files are then tagged based on patterns such as ``readme.md`` + or ``licenses/*.txt``. Matching of the file paths is implemented using the ``match`` + function of Python's ``Path`` objects. This means, matching is performed from the + end of the path. Search patterns are case-insensitive and use ``/`` as the path + separator. + + Files are tagged using the name of the file name pattern's "group" as the keyword. + If a file matches multiple patterns, all appropriate keywords are added. Depending + on configuration of ``keep_untagged_files``, files without any tags are then removed + from the file list (this is the default). + + Files that were tagged with ``readme`` are added to the data model as a + ``schema:URL`` using the ``codemeta:readme`` property. Files that were tagged + ``license`` are added to the data model as a ``schema:URL`` using the + ``schema:license`` property. All files are added to the data model as a + ``schema:CreativeWork`` using the ``schema:hasPart`` property. All file URLs are + given using the ``file:`` protocol and the absolute path of the file at the time of + harvesting. + """ + + settings_class = FileExistsHarvestSettings + + # key: group name (used as keywords when tagging), value: list of patterns + base_search_patterns = { + "readme": [ + "readme", + "readme.md", + "readme.markdown", + "readme.rst", + "readme.txt", + ], + "license": [ + "license", + "license.txt", + "license.md", + "licenses/*.txt", + ], + } + + def __init__(self): + self.working_directory: Path = Path.cwd() + self.settings: FileExistsHarvestSettings = FileExistsHarvestSettings() + + # mapping from tag name to list of file name patterns + self.search_patterns: Dict[str, List[str]] = self.base_search_patterns + # mapping from file name pattern to set of tags + self.search_pattern_keywords: Dict[str, Set[str]] = defaultdict(set) + # flat list of file name patterns + self.search_pattern_list: List[str] = [] + + def __call__(self, command: HermesHarvestCommand): + self.working_directory = command.args.path.resolve() + self.settings = command.settings.file_exists + + # update search patterns from config + self.search_patterns.update(self.settings.search_patterns) + + # create inverse lookup table + for key, patterns in self.search_patterns.items(): + for pattern in patterns: + self.search_pattern_keywords[pattern].add(key) + + # create flat list for easy iteration + self.search_pattern_list = sum(self.search_patterns.values(), start=[]) + + files_tags = self._filter_files(self._tag_files(self._find_files())) + creative_works = [ + CreativeWork.from_path(file, list(tags)) + for file, tags in files_tags.items() + ] + + data = { + "schema:hasPart": [work.as_codemeta() for work in creative_works], + "schema:license": [ + work.associated_media.url.as_codemeta() + for work in creative_works + if work.keywords and "license" in work.keywords + ], + "codemeta:readme": [ + work.associated_media.url.as_codemeta() + for work in creative_works + if work.keywords and "readme" in work.keywords + ], + } + + return data, {"workingDirectory": str(self.working_directory)} + + def _find_files(self) -> List[Path]: + """Find files. + + If the setting ``enable_git_ls_files`` is ``True``, ``git ls-files`` is used to + find matching files. If it is set to ``False`` or getting the list from git + fails, the working directory is searched recursively. + """ + files = None + if self.settings.enable_git_ls_files: + files = _git_ls_files(self.working_directory) + if files is None: + files = _ls_files(self.working_directory) + return files + + def _tag_files(self, paths: Iterable[Path]) -> Dict[Path, Set[str]]: + """Tag file paths based on patterns. + + The files are tagged using the "group" names of the search pattern as the + keywords. + """ + paths_tags = {} + for path in paths: + paths_tags[path] = set() + for pattern in self.search_pattern_list: + if _path_matches_pattern(path, pattern): + tags = self.search_pattern_keywords[pattern] + paths_tags[path].update(tags) + return paths_tags + + def _filter_files(self, files_tags: Dict[Path, Set[str]]) -> Dict[Path, Set[str]]: + """Filter out untagged files if required. + + If the setting ``keep_untagged_files`` is set to ``True``, the filter is not + applied. + """ + if self.settings.keep_untagged_files: + return files_tags + return {path: tags for path, tags in files_tags.items() if tags} + + +def _path_matches_pattern(path: Path, pattern: str) -> bool: + """Case-insensitive path matching. + + Python 3.12 introduces the ``case_sensitive`` kwarg to the ``match`` function. For + older Python versions, we have to implement this behaviour ourselves. + """ + return Path(str(path).casefold()).match(pattern.casefold()) + + +def _ls_files(working_directory: Path) -> List[Path]: + """Get a list of all files by recursively searching the ``working_directory``. + + Only regular files (i.e. files which are not directories, pipes, etc.) are returned. + """ + return [file for file in working_directory.rglob("*") if file.is_file()] + + +@cache +def _git_ls_files(working_directory: Path) -> Optional[List[Path]]: + """Get a list of all files by calling ``git ls-file`` in ``working_directory``. + + ``git ls-file`` is called with the ``--cached`` flag which lists all files tracked + by git. The returned file paths are converted to a list of ``Path`` objects. Files + that are tracked by git but don't exist on disk are not returned. If the git command + fails or git is not found, ``None`` is returned. + + The result of this function is cached. Git is only executed once per given + ``working_directory``. + """ + try: + result = subprocess.run( + ["git", "ls-files", "--cached"], + capture_output=True, + cwd=working_directory, + text=True, + ) + except FileNotFoundError: + return None + if result.returncode != 0: + return None + filenames = result.stdout.splitlines() + files = [Path(filename).resolve() for filename in filenames] + return [file for file in files if file.exists()] diff --git a/src/hermes/commands/init/base.py b/src/hermes/commands/init/base.py index 8effcf69..b61edbaf 100644 --- a/src/hermes/commands/init/base.py +++ b/src/hermes/commands/init/base.py @@ -6,8 +6,9 @@ import logging import os import re -import subprocess +import shutil import sys +import traceback from dataclasses import dataclass from enum import Enum, auto from importlib import metadata @@ -20,9 +21,10 @@ from requests import HTTPError import hermes.commands.init.util.slim_click as sc +from hermes.commands import marketplace from hermes.commands.base import HermesCommand, HermesPlugin from hermes.commands.init.util import (connect_github, connect_gitlab, - connect_zenodo) + connect_zenodo, git_info) TUTORIAL_URL = "https://hermes.software-metadata.pub/en/latest/tutorials/automated-publication-with-ci.html" @@ -53,75 +55,32 @@ class DepositPlatform(Enum): @dataclass class HermesInitFolderInfo: + """ + Contains information about the current state of the target project directory. + """ def __init__(self): self.absolute_path: str = "" self.has_git_folder: bool = False - self.git_remote_url: str = "" - self.git_base_url: str = "" - self.used_git_hoster: GitHoster = GitHoster.Empty self.has_hermes_toml: bool = False self.has_gitignore: bool = False self.has_citation_cff: bool = False self.has_readme: bool = False - self.current_branch: str = "" self.current_dir: str = "" self.dir_list: list[str] = [] self.dir_folders: list[str] = [] -def is_git_installed(): - try: - result = subprocess.run(['git', '--version'], capture_output=True, text=True) - return result.returncode == 0 - except FileNotFoundError: - return False - - def scout_current_folder() -> HermesInitFolderInfo: """ This method looks at the current directory and collects all init relevant data. - + This method is not meant to contain any user interactions. @return: HermesInitFolderInfo object containing the gathered knowledge """ info = HermesInitFolderInfo() current_dir = os.getcwd() info.current_dir = current_dir info.absolute_path = str(current_dir) - info.has_git_folder = os.path.isdir(os.path.join(current_dir, ".git")) - # git-enabled project - if info.has_git_folder: - # Get remote name for next command - # TODO: missing case of multiple configured remotes (should we make the user choose?) - git_remote = str(subprocess.run(['git', 'remote'], capture_output=True, text=True).stdout).strip() - sc.debug_info(f"git remote = {git_remote}") - - # Get remote url via Git CLI and convert it to an HTTP link in case it's an SSH remote. - # TODO: unchecked usage of empty remote name - info.git_remote_url = convert_remote_url( - str(subprocess.run(['git', 'remote', 'get-url', git_remote], capture_output=True, text=True).stdout) - ) - # TODO: missing an "else" part! - # TODO: can't these three pieces be stitched together to only execute when there is a remote? - # TODO: is the url parsing necessary of it's hosted on github? - if info.git_remote_url: - parsed_url = urlparse(info.git_remote_url) - info.git_base_url = f"{parsed_url.scheme}://{parsed_url.netloc}/" - sc.debug_info(f"git base url = {info.git_base_url}") - if "github.com" in info.git_remote_url: - info.used_git_hoster = GitHoster.GitHub - elif connect_gitlab.is_url_gitlab(info.git_base_url): - info.used_git_hoster = GitHoster.GitLab - - # Extract current branch name information by parsing Git output - # TODO: no exception or handling in case branch is empty (e.g. detached HEAD) - # TODO: why not use git rev-parse --abbrev-ref HEAD ? - branch_info = str(subprocess.run(['git', 'branch'], capture_output=True, text=True).stdout) - for line in branch_info.splitlines(): - if line.startswith("*"): - info.current_branch = line.split()[1].strip() - break - info.has_hermes_toml = os.path.isfile(os.path.join(current_dir, "hermes.toml")) info.has_gitignore = os.path.isfile(os.path.join(current_dir, ".gitignore")) info.has_citation_cff = os.path.isfile(os.path.join(current_dir, "CITATION.cff")) @@ -132,11 +91,23 @@ def scout_current_folder() -> HermesInitFolderInfo: if os.path.isdir(os.path.join(current_dir, f)) and not f.startswith(".") ] - return info -def download_file_from_url(url, filepath, append: bool = False): +def get_git_hoster_from_url(url: str) -> GitHoster: + """ + Returns the matching GitHoster value to the given url. Returns GitHoster.Empty if none is found. + """ + parsed_url = urlparse(url) + git_base_url = f"{parsed_url.scheme}://{parsed_url.netloc}/" # noqa E231 + if "github.com" in url: + return GitHoster.GitHub + elif connect_gitlab.is_url_gitlab(git_base_url): + return GitHoster.GitLab + return GitHoster.Empty + + +def download_file_from_url(url, filepath, append: bool = False) -> None: try: with requests.get(url, stream=True) as r: r.raise_for_status() @@ -152,20 +123,11 @@ def string_in_file(file_path, search_string: str) -> bool: return any(search_string in line for line in file) -def convert_remote_url(url: str) -> str: +def get_builtin_plugins(plugin_commands: list[str]) -> dict[str: HermesPlugin]: """ - Takes any url produced by 'git remote get-url origin' and returns a unified version with https & without .git + Returns a list of installed HermesPlugins based on a list of related command names. + This is currently not used (we use the marketplace code instead) but maybe later. """ - url = url.strip() - # Remove .git from the end of the url - url = url.removesuffix(".git") - # Convert ssh url into http url - if re.findall(r"^.+@.+\..+:.+\/.+$", url): - url = re.sub(r"^.+@(.+\..+):(.+\/.+)$", r"https://\1/\2", url) - return url - - -def get_builtin_plugins(plugin_commands: list[str]) -> dict[str: HermesPlugin]: plugins = {} for plugin_command_name in plugin_commands: entry_point_group = f"hermes.{plugin_command_name}" @@ -177,7 +139,7 @@ def get_builtin_plugins(plugin_commands: list[str]) -> dict[str: HermesPlugin]: return plugins -def get_handler_by_name(name: str) -> logging.Handler: +def get_handler_by_name(name: str) -> logging.Handler | None: """Own implementation of logging.getHandlerByName so that we don't require Python 3.12""" for logger_name in logging.root.manager.loggerDict: logger = logging.getLogger(logger_name) @@ -200,9 +162,14 @@ class HermesInitCommand(HermesCommand): def __init__(self, parser: argparse.ArgumentParser): super().__init__(parser) self.folder_info: HermesInitFolderInfo = HermesInitFolderInfo() + self.hermes_was_already_installed: bool = False + self.new_created_paths: list[Path] = [] self.tokens: dict = {} self.setup_method: str = "" self.deposit_platform: DepositPlatform = DepositPlatform.Empty + self.git_remote: str = "" + self.git_remote_url = "" + self.git_hoster: GitHoster = GitHoster.Empty self.template_base_url: str = "https://raw.githubusercontent.com" self.template_branch: str = "feature/init-custom-ci" self.template_repo: str = "softwarepub/ci-templates" @@ -214,8 +181,21 @@ def __init__(self, parser: argparse.ArgumentParser): "deposit_extra_files": "", "push_branch": "main" } + self.hermes_toml_data = { + "harvest": { + "sources": ["cff"] + }, + "deposit": { + "target": "invenio_rdm", + "invenio_rdm": { + "site_url": "", + "access_right": "open" + } + } + } self.plugin_relevant_commands = ["harvest", "deposit"] self.builtin_plugins: dict[str: HermesPlugin] = get_builtin_plugins(self.plugin_relevant_commands) + self.selected_plugins: list[marketplace.PluginInfo] = [] def init_command_parser(self, command_parser: argparse.ArgumentParser) -> None: command_parser.add_argument('--template-branch', nargs=1, default="", @@ -224,12 +204,13 @@ def init_command_parser(self, command_parser: argparse.ArgumentParser) -> None: def load_settings(self, args: argparse.Namespace): pass - def refresh_folder_info(self): + def refresh_folder_info(self) -> None: + """Checks the contents of the current directory and saves relevant info in self.folder_info""" sc.debug_info("Scanning folder...") self.folder_info = scout_current_folder() sc.debug_info("Scan complete.") - def setup_file_logging(self): + def setup_file_logging(self) -> None: # Silence old StreamHandler handler = get_handler_by_name("terminal") if handler: @@ -248,42 +229,67 @@ def __call__(self, args: argparse.Namespace) -> None: if args.template_branch != "": self.template_branch = args.template_branch - # Test if init is valid in current folder - self.test_initialization() + try: + # Test if init is valid in current folder + self.test_initialization() + + sc.echo(f"Starting to initialize HERMES in {self.folder_info.absolute_path}\n") + sc.max_steps = 8 + + sc.next_step("Configure HERMES plugins") + self.choose_plugins() + self.integrate_plugins() + + sc.next_step("Configure deposition platform and setup method") + self.choose_deposit_platform() + self.integrate_deposit_platform() + self.choose_setup_method() - sc.echo(f"Starting to initialize HERMES in {self.folder_info.absolute_path} ...") - sc.max_steps = 7 + sc.next_step("Configure HERMES behaviour") + self.choose_push_branch() + self.choose_deposit_files() - sc.next_step("Configure deposition platform and setup method") - self.choose_deposit_platform() - self.choose_setup_method() + sc.next_step("Create hermes.toml file") + self.create_hermes_toml() - sc.next_step("Configure HERMES behaviour") - self.choose_push_branch() - self.choose_deposit_files() + sc.next_step("Create CITATION.cff file") + self.create_citation_cff() - sc.next_step("Create hermes.toml file") - self.create_hermes_toml() + sc.next_step("Create git CI files") + self.update_gitignore() + self.create_ci_template() - sc.next_step("Create CITATION.cff file") - self.create_citation_cff() + sc.next_step("Connect with deposition platform") + self.connect_deposit_platform() - sc.next_step("Create git CI files") - self.update_gitignore() - self.create_ci_template() + sc.next_step("Connect with git hoster") + self.configure_git_project() - sc.next_step("Connect with deposition platform") - self.connect_deposit_platform() + self.clean_up_files(False) + sc.echo("\nHERMES is now initialized and ready to be used.\n", + formatting=sc.Formats.OKGREEN+sc.Formats.BOLD) - sc.next_step("Connect with git project") - self.configure_git_project() + # Nice message on Ctrl+C + except KeyboardInterrupt: + sc.echo("") + sc.echo("HERMES init was aborted.", sc.Formats.WARNING) + self.clean_up_files(True) + sys.exit() - sc.echo("\nHERMES is now initialized and ready to be used.\n", formatting=sc.Formats.OKGREEN+sc.Formats.BOLD) + # Useful message on error + except Exception as e: + sc.echo(f"An error occurred during execution of HERMES init: {e}", + formatting=sc.Formats.FAIL+sc.Formats.BOLD) + sc.debug_info(traceback.format_exc()) + self.clean_up_files(True) + sys.exit(2) - def test_initialization(self): + def test_initialization(self) -> None: """Test if init is possible and wanted. If not: sys.exit()""" + sc.echo("Preparing HERMES initialization\n") + # Abort if git is not installed - if not is_git_installed(): + if not git_info.is_git_installed(): sc.echo("Git is currently not installed. It is recommended to use HERMES with git.", formatting=sc.Formats.WARNING) self.no_git_setup() @@ -291,6 +297,7 @@ def test_initialization(self): # Look at the current folder self.refresh_folder_info() + self.hermes_was_already_installed = self.folder_info.has_hermes_toml # Abort if there is no git if not self.folder_info.has_git_folder: @@ -300,15 +307,41 @@ def test_initialization(self): self.no_git_setup() sys.exit() + # Look at git remotes + remotes = git_info.get_remotes() + if remotes: + self.git_remote = remotes[0] + + # Let the user choose if there are multiple remotes + if len(remotes) > 1: + remote_index = sc.choose( + "Your git project has multiple remotes. For which remote do you want to setup HERMES?", + [f"{remote} ({git_info.get_remote_url(remote)})" for remote in remotes] + ) + self.git_remote = remotes[remote_index] + + # Get url & hoster from remote + if self.git_remote: + self.git_remote_url = git_info.get_remote_url(self.git_remote) + self.git_hoster = get_git_hoster_from_url(self.git_remote_url) + + # Abort with no remote + else: + sc.echo("Your git project does not have a remote. It is recommended for HERMES to " + "use either GitHub or GitLab as hosting service.", formatting=sc.Formats.WARNING) + self.no_git_setup() + sys.exit() + # Abort if neither GitHub nor gitlab is used - if self.folder_info.used_git_hoster == GitHoster.Empty: - sc.echo("Your git project ({}) is not connected to GitHub or GitLab. It is recommended for HERMES to " - "use one of those hosting services.".format(self.folder_info.git_remote_url), + if self.git_hoster == GitHoster.Empty: + project_url = " (" + self.git_remote_url + ")" if self.git_remote_url else "" + sc.echo("Your git project{} is not connected to GitHub or GitLab. It is recommended for HERMES to " + "use one of these hosting services.".format(project_url), formatting=sc.Formats.WARNING) self.no_git_setup() sys.exit() else: - sc.echo(f"Git project using {self.folder_info.used_git_hoster.name} detected.\n") + sc.echo(f"Git project using {self.git_hoster.name} detected.\n") # Abort if there is already a hermes.toml if self.folder_info.has_hermes_toml: @@ -318,30 +351,18 @@ def test_initialization(self): "(Hermes config files and related project variables will be overwritten.) "): sys.exit() - def create_hermes_toml(self): - """Creates the hermes.toml file based on a dictionary""" - deposit_url = DepositPlatformUrls.get(self.deposit_platform) - default_values = { - "harvest": { - "sources": ["cff"] - }, - "deposit": { - "target": "invenio_rdm", - "invenio_rdm": { - "site_url": deposit_url, - "access_right": "open" - } - } - } - + def create_hermes_toml(self) -> None: + """Creates the hermes.toml file based on a self.hermes_toml_data""" + hermes_toml_path = Path("hermes.toml") + self.mark_as_new_path(hermes_toml_path) if (not self.folder_info.has_hermes_toml) \ or sc.confirm("Do you want to replace your `hermes.toml` with a new one?", default=True): - with open('hermes.toml', 'w') as toml_file: + with open(hermes_toml_path, 'w') as toml_file: # noinspection PyTypeChecker - toml.dump(default_values, toml_file) + toml.dump(self.hermes_toml_data, toml_file) sc.echo("`hermes.toml` was created.", formatting=sc.Formats.OKGREEN) - def create_citation_cff(self): + def create_citation_cff(self) -> None: """If there is no CITATION.cff, the user gets the opportunity to create one online.""" if not self.folder_info.has_citation_cff: citation_cff_url = "https://citation-file-format.github.io/cff-initializer-javascript/#/" @@ -365,38 +386,45 @@ def create_citation_cff(self): else: sc.echo("Your project already contains a `CITATION.cff` file. Nice!", formatting=sc.Formats.OKGREEN) - def update_gitignore(self): + def update_gitignore(self) -> None: """Creates .gitignore if there is none and adds '.hermes' to it""" + gitignore_path = Path(".gitignore") + self.mark_as_new_path(gitignore_path) if not self.folder_info.has_gitignore: - open(".gitignore", 'w') + open(gitignore_path, 'w') sc.echo("A new `.gitignore` file was created.", formatting=sc.Formats.OKGREEN) self.refresh_folder_info() if self.folder_info.has_gitignore: - with open(".gitignore", "r") as file: + with open(gitignore_path, "r") as file: gitignore_lines = file.readlines() if any([line.startswith(".hermes") for line in gitignore_lines]): sc.echo("The `.gitignore` file already contains `.hermes/`") else: - with open(".gitignore", "a") as file: + with open(gitignore_path, "a") as file: file.write("# Ignoring all HERMES cache files\n") file.write(".hermes/\n") file.write("hermes.log\n") sc.echo("Added `.hermes/` to the `.gitignore` file.", formatting=sc.Formats.OKGREEN) def get_template_url(self, filename: str) -> str: + """Returns the full template url with a given filename.""" return (f"{self.template_base_url}/{self.template_repo}/refs/heads/" f"{self.template_branch}/{self.template_folder}/{filename}") - def create_ci_template(self): - """Downloads and configures the ci workflow files using templates from the chosen template branch""" - match self.folder_info.used_git_hoster: + def create_ci_template(self) -> None: + """Downloads and configures the ci workflow files using templates from the chosen template branch.""" + match self.git_hoster: case GitHoster.GitHub: - # TODO Replace this later with the link to the real templates (not the feature branch) template_url = self.get_template_url("TEMPLATE_hermes_github_to_zenodo.yml") - ci_file_folder = ".github/workflows" + ci_file_folder = Path(".github/workflows") ci_file_name = "hermes_github.yml" - Path(ci_file_folder).mkdir(parents=True, exist_ok=True) - ci_file_path = Path(ci_file_folder) / ci_file_name + ci_file_path = ci_file_folder / ci_file_name + # Adding paths to our list + self.mark_as_new_path(Path(".github")) + self.mark_as_new_path(ci_file_folder) + self.mark_as_new_path(ci_file_path) + # Creating folder & ci file + ci_file_folder.mkdir(parents=True, exist_ok=True) download_file_from_url(template_url, ci_file_path) self.configure_ci_template(ci_file_path) sc.echo(f"GitHub CI: File was created at {ci_file_path}", formatting=sc.Formats.OKGREEN) @@ -404,8 +432,15 @@ def create_ci_template(self): gitlab_ci_template_url = self.get_template_url("TEMPLATE_hermes_gitlab_to_zenodo.yml") hermes_ci_template_url = self.get_template_url("hermes-ci.yml") gitlab_ci_path = Path(".gitlab-ci.yml") - Path("gitlab").mkdir(parents=True, exist_ok=True) - hermes_ci_path = Path("gitlab") / "hermes-ci.yml" + gitlab_folder_path = Path("gitlab") + hermes_ci_path = gitlab_folder_path / "hermes-ci.yml" + # Adding paths to our list + self.mark_as_new_path(gitlab_ci_path) + self.mark_as_new_path(gitlab_folder_path) + self.mark_as_new_path(hermes_ci_path) + # Creating the gitlab folder + gitlab_folder_path.mkdir(parents=True, exist_ok=True) + # Creating / updating gitlab-ci if gitlab_ci_path.exists(): if string_in_file(gitlab_ci_path, "hermes-ci.yml"): sc.echo(f"It seems like your {gitlab_ci_path} file is already configured for hermes.") @@ -416,11 +451,12 @@ def create_ci_template(self): download_file_from_url(gitlab_ci_template_url, gitlab_ci_path) sc.echo(f"GitLab CI: {gitlab_ci_path} was created.", formatting=sc.Formats.OKGREEN) self.configure_ci_template(gitlab_ci_path) + # Creating hermes-ci download_file_from_url(hermes_ci_template_url, hermes_ci_path) self.configure_ci_template(hermes_ci_path) # When using gitlab.com we need to use gitlab-org-docker as tag - if "gitlab.com" in self.folder_info.git_remote_url: + if "gitlab.com" in self.git_remote_url: with open(hermes_ci_path, 'r') as file: content = file.read() new_content = re.sub(r'(tags:\n\s+- )docker', r'\1gitlab-org-docker', content) @@ -429,21 +465,23 @@ def create_ci_template(self): sc.echo(f"GitLab CI: {hermes_ci_path} was created.", formatting=sc.Formats.OKGREEN) - def configure_ci_template(self, ci_file_path): + def configure_ci_template(self, ci_file_path) -> None: """Replaces all {%parameter%} in a ci file with values from ci_parameters dict""" with open(ci_file_path, 'r') as file: content = file.read() parameters = list(set(re.findall(r'{%(.*?)%}', content))) for parameter in parameters: if parameter in self.ci_parameters: - content = content.replace(f'{{%{parameter}%}}', self.ci_parameters[parameter]) + value = str(self.ci_parameters[parameter]) + content = content.replace(f'{{%{parameter}%}}', value) else: - sc.echo(f"Warning: CI File Parameter {{%{parameter}%}} was not set.", - formatting=sc.Formats.WARNING) + sc.debug_info(f"CI File Parameter {{%{parameter}%}} was not set.", formatting=sc.Formats.WARNING) + content = content.replace(f'{{%{parameter}%}}', '') with open(ci_file_path, 'w') as file: file.write(content) - def get_zenodo_token(self): + def create_zenodo_token(self) -> None: + """Makes the user create a zenodo token and saves it in self.tokens.""" self.tokens[self.deposit_platform] = "" # Deactivated Zenodo OAuth as long as the refresh token bug is not fixed. if self.setup_method == "a": @@ -471,25 +509,25 @@ def get_zenodo_token(self): "(If this error persists, you should try switching to the manual setup mode.)", formatting=sc.Formats.WARNING) - def configure_git_project(self): - """Adding the token to the git secrets & changing action workflow settings""" - match self.folder_info.used_git_hoster: + def configure_git_project(self) -> None: + """Adds the token to the git secrets & changes action workflow settings.""" + match self.git_hoster: case GitHoster.GitHub: self.configure_github() case GitHoster.GitLab: self.configure_gitlab() - def configure_github(self): + def configure_github(self) -> None: oauth_success = False if self.setup_method == "a": self.tokens[GitHoster.GitHub] = connect_github.get_access_token() if self.tokens[GitHoster.GitHub]: sc.echo("OAuth at GitHub was successful.", formatting=sc.Formats.OKGREEN) sc.debug_info(github_token=self.tokens[GitHoster.GitHub]) - connect_github.create_secret(self.folder_info.git_remote_url, "ZENODO_SANDBOX", + connect_github.create_secret(self.git_remote_url, "ZENODO_SANDBOX", secret_value=self.tokens[self.deposit_platform], token=self.tokens[GitHoster.GitHub]) - connect_github.allow_actions(self.folder_info.git_remote_url, + connect_github.allow_actions(self.git_remote_url, token=self.tokens[GitHoster.GitHub]) oauth_success = True else: @@ -500,31 +538,31 @@ def configure_github(self): self.deposit_platform.name, f" ({self.tokens[self.deposit_platform]})" if self.tokens[self.deposit_platform] else "", sc.create_console_hyperlink( - self.folder_info.git_remote_url + "/settings/secrets/actions", + self.git_remote_url + "/settings/secrets/actions", "project's GitHub secrets" ) )) sc.press_enter_to_continue() sc.echo("Next open your {} and check the checkbox which reads:".format( sc.create_console_hyperlink( - self.folder_info.git_remote_url + "/settings/actions", "project settings" + self.git_remote_url + "/settings/actions", "project settings" ) )) sc.echo("Allow GitHub Actions to create and approve pull requests") sc.press_enter_to_continue() - def configure_gitlab(self): + def configure_gitlab(self) -> None: # Doing it with API / OAuth oauth_success = False if self.setup_method == "a": - gl = connect_gitlab.GitLabConnection(self.folder_info.git_remote_url) + gl = connect_gitlab.GitLabConnection(self.git_remote_url) token = "" if not gl.has_client(): sc.echo("Unfortunately HERMES does not support automatic authorization with your GitLab " "installment.") sc.echo("Go to your {} and create a new token.".format( sc.create_console_hyperlink( - self.folder_info.git_remote_url + "/-/settings/access_tokens", + self.git_remote_url + "/-/settings/access_tokens", "project's access tokens") )) sc.echo("It needs to have the 'developer' role and 'api' + 'write_repository' scope.") @@ -552,13 +590,13 @@ def configure_gitlab(self): if not oauth_success: sc.echo("Go to your {} and create a new token.".format( sc.create_console_hyperlink( - self.folder_info.git_remote_url + "/-/settings/access_tokens", "project's access tokens") + self.git_remote_url + "/-/settings/access_tokens", "project's access tokens") )) sc.echo("It needs to have the 'developer' role and 'write_repository' scope.") sc.press_enter_to_continue() sc.echo("Open your {} and go to 'Variables'".format( sc.create_console_hyperlink( - self.folder_info.git_remote_url + "/-/settings/ci_cd", "project's ci settings") + self.git_remote_url + "/-/settings/ci_cd", "project's ci settings") )) sc.echo("Then, add that token as variable with key HERMES_PUSH_TOKEN.") sc.echo("(For your safety, you should set the visibility to 'Masked'.)") @@ -570,18 +608,24 @@ def configure_gitlab(self): sc.echo("(For your safety, you should set the visibility to 'Masked'.)") sc.press_enter_to_continue() - def choose_deposit_platform(self): - """User chooses his desired deposit platform""" + def choose_deposit_platform(self) -> None: + """User chooses his desired deposit platform.""" deposit_platform_list = list(DepositPlatformNames.keys()) deposit_platform_index = sc.choose( "Where do you want to publish the software?", [DepositPlatformNames[dp] for dp in deposit_platform_list] ) self.deposit_platform = deposit_platform_list[deposit_platform_index] - def choose_setup_method(self): + def integrate_deposit_platform(self) -> None: + """Makes changes to the toml data or something else based on the chosen deposit platform.""" + deposit_url = DepositPlatformUrls.get(self.deposit_platform) + self.hermes_toml_data["deposit"]["invenio_rdm"]["site_url"] = deposit_url + + def choose_setup_method(self) -> None: + """User chooses his desired setup method: Either preferring automatic (if available) or manual.""" setup_method_index = sc.choose( f"How do you want to connect {DepositPlatformNames[self.deposit_platform]} " - f"with your {self.folder_info.used_git_hoster.name} CI?", + f"with your {self.git_hoster.name} CI?", options=[ "Automatically (using OAuth / Device Flow)", "Manually (with instructions)", @@ -589,21 +633,78 @@ def choose_setup_method(self): ) self.setup_method = ["a", "m"][setup_method_index] - def connect_deposit_platform(self): - """Acquires the access token of the chosen deposit platform""" + def connect_deposit_platform(self) -> None: + """Acquires the access token of the chosen deposit platform.""" assert self.deposit_platform != DepositPlatform.Empty match self.deposit_platform: case DepositPlatform.Zenodo: connect_zenodo.setup(using_sandbox=False) - self.get_zenodo_token() + self.create_zenodo_token() case DepositPlatform.ZenodoSandbox: connect_zenodo.setup(using_sandbox=True) - self.get_zenodo_token() - - def no_git_setup(self, start_question: str = ""): + self.create_zenodo_token() + + def choose_plugins(self) -> None: + """User chooses the plugins he wants to use.""" + plugin_infos: list[marketplace.PluginInfo] = marketplace.get_plugin_infos() + plugins_builtin: list[marketplace.PluginInfo] = list(filter(lambda p: p.builtin, plugin_infos)) + plugins_available: list[marketplace.PluginInfo] = list(filter(lambda p: not p.builtin, plugin_infos)) + plugins_selected: list[marketplace.PluginInfo] = [] + sc.echo("The following plugins are already builtin:") + for info in plugins_builtin: + sc.echo(str(info), formatting=sc.Formats.OKGREEN) + sc.echo("") + while True: + if plugins_selected: + sc.echo("The following plugins are going to be installed:") + for info in plugins_selected: + sc.echo(str(info), formatting=sc.Formats.OKCYAN) + sc.echo("") + if plugins_available: + sc.echo("The following plugins are available for installation:") + for info in plugins_available: + sc.echo(str(info), formatting=sc.Formats.WARNING, no_log=True) + if info.abstract: + sc.echo("-> " + info.abstract, formatting=sc.Formats.ITALIC+sc.Formats.WARNING, no_log=True) + sc.echo("") + else: + self.selected_plugins = plugins_selected + break + no_text = "No further plugins needed" + choice = sc.choose("Do you want to add a plugin?", + [no_text] + [f"Add {p.name}" for p in plugins_available]) + if choice == 0: + self.selected_plugins = plugins_selected + break + else: + chosen_plugin = plugins_available.pop(choice - 1) + plugins_selected.append(chosen_plugin) + + def integrate_plugins(self) -> None: + """ + Plugin installation is added to the ci-parameters. + Also for now we use this method to do custom plugin installation steps. + """ + for plugin_info in self.selected_plugins: + if not plugin_info.is_valid(): + sc.echo(f"Could not install plugin: {plugin_info.name}", formatting=sc.Formats.FAIL) + continue + pip_install = plugin_info.get_pip_install_command() + self.ci_parameters["pip_install_plugins_github"] = \ + self.ci_parameters.get("pip_install_plugins_github", "") + " - run: " + pip_install + "\n" + self.ci_parameters["pip_install_plugins_gitlab"] = \ + self.ci_parameters.get("pip_install_plugins_gitlab", "") + " - " + pip_install + "\n" + match plugin_info.name: + case "hermes-plugin-python": + self.hermes_toml_data["harvest"]["sources"].append("toml") + case "hermes-plugin-git": + self.hermes_toml_data["harvest"]["sources"].append("git") + + def no_git_setup(self, start_question: str = "") -> None: """Makes the init for a gitless project (basically just creating hermes.toml)""" if start_question == "": - start_question = "Do you want to initialize HERMES anyways? (No CI/CD files will be created)" + start_question = ("Do you want to initialize HERMES anyways? (CI/CD files for automated publishing will " + "NOT be created)") if sc.confirm(start_question): sc.max_steps = 2 @@ -613,29 +714,31 @@ def no_git_setup(self, start_question: str = ""): sc.next_step("Create CITATION.cff file") self.create_citation_cff() - sc.echo("\nHERMES is now initialized (without git integration).\n", + self.clean_up_files(False) + sc.echo("\nHERMES is now initialized (without git integration or CI/CD files).\n", formatting=sc.Formats.OKGREEN) - def choose_push_branch(self): - """User chooses the branch that should be used to activate the whole hermes process""" - # TODO make it possible to choose tags as well + def choose_push_branch(self) -> None: + """User chooses the branch that should be used to activate the whole hermes process.""" push_choice = sc.choose( "When should the automated HERMES process start?", [ - f"When I push the current branch {self.folder_info.current_branch}", - "When I push another branch", - "When a push a specific tag (not implemented)", + "When I push a branch", + "When I push a specific tag (not implemented)", ] ) if push_choice == 0: - self.ci_parameters["push_branch"] = self.folder_info.current_branch + branch = sc.answer("Enter target branch: ") + self.ci_parameters["push_branch"] = branch + sc.echo(f"The HERMES pipeline will be activated when you push on {sc.Formats.BOLD.wrap_around(branch)}", + formatting=sc.Formats.OKGREEN) + sc.echo() elif push_choice == 1: - self.ci_parameters["push_branch"] = sc.answer("Enter the other branch: ") - elif push_choice == 2: - sc.echo("Not implemented", formatting=sc.Formats.WARNING) + sc.echo("Setting up triggering by tags is currently not implemented.", formatting=sc.Formats.WARNING) + sc.echo(f"You can visit {TUTORIAL_URL} to set it up manually later-on.", formatting=sc.Formats.WARNING) - def choose_deposit_files(self): - """User chooses the files that should be included in the deposition""" + def choose_deposit_files(self) -> None: + """User chooses the files that should be included in the deposition.""" dp_name = DepositPlatformNames[self.deposit_platform] add_readme = False if self.folder_info.has_readme: @@ -685,3 +788,31 @@ def choose_deposit_files(self): else: for file in self.folder_info.dir_list: sc.echo(f"\t\t{file}", formatting=sc.Formats.OKCYAN) + + def mark_as_new_path(self, path: Path, avoid_existing: bool = True) -> None: + """ + This method should be called directly BEFORE creating a new file in the given Path. + This way we can look if something already exists there to decide later-on if we want to delete it on abort. + """ + if (not avoid_existing) or (not path.exists()): + self.new_created_paths.append(path) + + def clean_up_files(self, aborted: bool) -> None: + """ + This gets called when init is finished (successfully or aborted). + It cleans up unwanted files (like .hermes folder) and everything new when aborted. + """ + sc.echo("Cleaning unused files...") + hidden_hermes_path = Path(".hermes") + if hidden_hermes_path.exists() and hidden_hermes_path.is_dir(): + shutil.rmtree(hidden_hermes_path) + if aborted: + if not self.hermes_was_already_installed: + for path in reversed(self.new_created_paths): + try: + if path.is_dir(): + path.rmdir() + else: + os.remove(path) + except Exception as e: + sc.echo(f"Cleaning Warning: Could not remove {path}. ({e})") diff --git a/src/hermes/commands/init/util/connect_github.py b/src/hermes/commands/init/util/connect_github.py index fdb2961e..e2865dd2 100644 --- a/src/hermes/commands/init/util/connect_github.py +++ b/src/hermes/commands/init/util/connect_github.py @@ -49,7 +49,7 @@ def allow_actions(project_url: str, token): repo_name = url_split[-1] # GitHub API URLs - repo_url = f"https://api.github.com/repos/{repo_owner}/{repo_name}" + repo_url = f"https://api.github.com/repos/{repo_owner}/{repo_name}" # noqa E231 action_permissions_url = f"{repo_url}/actions/permissions/workflow" # Headers for GitHub API requests @@ -89,7 +89,7 @@ def create_secret(project_url: str, secret_name: str, secret_value, token): repo_name = url_split[-1] # GitHub API URLs - repo_url = f"https://api.github.com/repos/{repo_owner}/{repo_name}" + repo_url = f"https://api.github.com/repos/{repo_owner}/{repo_name}" # noqa E231 public_key_url = f"{repo_url}/actions/secrets/public-key" secrets_url = f"{repo_url}/actions/secrets/{secret_name}" diff --git a/src/hermes/commands/init/util/connect_gitlab.py b/src/hermes/commands/init/util/connect_gitlab.py index 32b115a8..37c5e217 100644 --- a/src/hermes/commands/init/util/connect_gitlab.py +++ b/src/hermes/commands/init/util/connect_gitlab.py @@ -16,7 +16,7 @@ site_specific_oauth_clients = [ { - "url": "https://gitlab.com/", + "url": "https://gitlab.com/", # noqa E231 "client_id": "1133e9cee188c31bd68c9d0e8531774a4aae9d2458e13d83e67991213f868007", "name_addition": "gitlab.com" }, { @@ -33,14 +33,14 @@ def is_url_gitlab(url: str) -> bool: parsed_url = urlparse(url) - return requests.get(f"{parsed_url.scheme}://{parsed_url.netloc}/api/v4/version").status_code == 401 + return requests.get(f"{parsed_url.scheme}://{parsed_url.netloc}/api/v4/version").status_code == 401 # noqa E231 class GitLabConnection: def __init__(self, project_url: str): self.project_url: str = project_url parsed_url = urlparse(project_url) - self.base_url: str = f"{parsed_url.scheme}://{parsed_url.netloc}/" + self.base_url: str = f"{parsed_url.scheme}://{parsed_url.netloc}/" # noqa E231 self.api_url: str = urljoin(self.base_url, "api/v4/") self.project_namespace_name: str = parsed_url.path.removeprefix("/") self.gitlab_instance_name: str = f"GitLab ({parsed_url.netloc})" diff --git a/src/hermes/commands/init/util/git_info.py b/src/hermes/commands/init/util/git_info.py new file mode 100644 index 00000000..e26dcf92 --- /dev/null +++ b/src/hermes/commands/init/util/git_info.py @@ -0,0 +1,106 @@ +# SPDX-FileCopyrightText: 2024 Forschungszentrum Jülich GmbH +# SPDX-License-Identifier: Apache-2.0 +# SPDX-FileContributor: Nitai Heeb + +import re +import os +import subprocess +from pathlib import Path + + +default_cwd = "" + + +def get_valid_cwd(cwd="") -> str: + """ + Returns the given cwd if valid or the default_cwd / os.getcwd() when not cwd is given. + """ + # Get default when cwd is empty + if cwd == "": + if default_cwd: + cwd = default_cwd + else: + cwd = os.getcwd() + # Test if valid + path = Path(cwd) + if not path.exists(): + raise Exception(f"Path {path} does not exist.") + elif not path.is_dir(): + raise Exception(f"Path {path} is not a directory.") + # Return + return str(path) + + +def run_git_command(command: str, cwd="") -> str: + """ + Runs any git command using subprocess. Raises Exception when returncode != 0. + :param command: The command as string with or without the 'git' main command. + :param cwd: Path to target directory ( if it differs from os.getcwd() ). + :return: The command's output. + """ + # Validate or get default cwd + cwd = get_valid_cwd(cwd) + # Get command list from string + command_list = [s for s in command.split(" ") if s != ""] + if command_list[0] != "git": + command_list.insert(0, "git") + # Run subprocess + result = subprocess.run(command_list, cwd=cwd, capture_output=True, text=True) + # Return output or error + if result.returncode != 0: + raise Exception(result.stderr) + return str(result.stdout) + + +def get_remotes() -> list[str]: + """ + Returns a list of all remotes. + """ + git_remote_output: str = run_git_command("remote").strip() + cleaned_remote_list = [s.strip() for s in git_remote_output.split("\n")] + return cleaned_remote_list + + +def convert_remote_url(url: str) -> str: + """ + Takes any url produced by 'git remote get-url ...' and returns a consistent version with https & without '.git'. + """ + url = url.strip() + # Remove .git from the end of the url + url = url.removesuffix(".git") + # Convert ssh-url into http-url using beautiful, human-readable regex + if re.findall(r"^.+@.+\..+:.+\/.+$", url): + url = re.sub(r"^.+@(.+\..+):(.+\/.+)$", r"https://\1/\2", url) + return url + + +def get_remote_url(remote: str) -> str: + """ + Returns the url of the given remote. + """ + if remote not in get_remotes(): + raise Exception(f"Remote {remote} not found.") + url_output = run_git_command(f"remote get-url {remote}") + return convert_remote_url(url_output) + + +def get_current_branch() -> str: + """ + Returns the name of the current branch. + """ + branch_info = run_git_command("branch") + for line in branch_info.splitlines(): + if line.startswith("*"): + return line.split()[1].strip() + raise Exception("Current branch not found.") + + +def is_git_installed() -> bool: + """ + Uses the --version command to check whether git is installed. + """ + try: + result = subprocess.run(['git', '--version'], capture_output=True) + return result.returncode == 0 + except Exception: + return False diff --git a/src/hermes/commands/init/util/oauth_process.py b/src/hermes/commands/init/util/oauth_process.py index ba2d88fe..6ef210a6 100644 --- a/src/hermes/commands/init/util/oauth_process.py +++ b/src/hermes/commands/init/util/oauth_process.py @@ -92,7 +92,7 @@ def open_browser(self, port: int = None) -> bool: if DEACTIVATE_BROWSER_OPENING: return False port = port or self.local_port - return webbrowser.open(f'http://localhost:{port}') + return webbrowser.open(f'http://localhost:{port}') # noqa E231 def get_tokens_from_refresh_token(self, refresh_token: str) -> dict[str: str]: """Returns access and refresh token as dict using a refresh token""" diff --git a/src/hermes/commands/init/util/slim_click.py b/src/hermes/commands/init/util/slim_click.py index 2075bcd8..a74cb15e 100644 --- a/src/hermes/commands/init/util/slim_click.py +++ b/src/hermes/commands/init/util/slim_click.py @@ -61,22 +61,28 @@ def get_log_type(self, default: int = logging.INFO) -> int: return logging.INFO return default + def wrap_around(self, text: str) -> str: + return self.get_ansi() + text + Formats.ENDC.get_ansi() -def echo(text: str, formatting: Formats = Formats.EMPTY, log_as: int = logging.NOTSET): + +def echo(text: str = "", formatting: Formats = Formats.EMPTY, log_as: int = logging.NOTSET, no_log: bool = False): """ Prints the text with the given formatting. If log_as is set or AUTO_LOG_ON_ECHO is true it gets logged as well. :param text: The printed text. :param formatting: You can use the Formats Enum to give the text a special color or formatting. :param log_as: Creates a log entry with the given text if this is set. + :param no_log: Never creates a log entry if True. """ # Get logging type from formatting if AUTO_LOG_ON_ECHO if AUTO_LOG_ON_ECHO and log_as == logging.NOTSET and text != "": log_as = formatting.get_log_type(logging.INFO) # Add text to log if there is a logger - if log_as != logging.NOTSET and default_file_logger: + if log_as != logging.NOTSET and default_file_logger and not no_log: default_file_logger.log(log_as, text) # Format the text for the console if formatting != Formats.EMPTY: + if Formats.ENDC.get_ansi() in text: + text = text.replace(Formats.ENDC.get_ansi(), Formats.ENDC.get_ansi() + formatting.get_ansi()) text = f"{formatting.get_ansi()}{text}{Formats.ENDC.get_ansi()}" # Print it if (log_as != logging.DEBUG) or PRINT_DEBUG: @@ -101,7 +107,7 @@ def confirm(text: str, default: bool = True) -> bool: print("") return False elif _answer == "": - print("Y\n" if default else "N\n") + echo("Y\n" if default else "N\n", formatting=Formats.OKCYAN) return default else: echo("Error: invalid input", formatting=Formats.FAIL) @@ -131,9 +137,9 @@ def choose(text: str, options: list[str], default: int = 0) -> int: assert 0 <= default < len(options), "Default index should match the options list." echo(text) for i, option in enumerate(options): - index = f"{i:>2d}" + index = f"{i:>2d}" # noqa E231 if i == default: - index = f"*{i:>1d}" + index = f"*{i:>1d}" # noqa E231 print(f"[{index}] {option}") while True: chosen_index = -1 @@ -164,7 +170,9 @@ def next_step(description: str): def create_console_hyperlink(url: str, word: str) -> str: """Use this to have a consistent display of hyperlinks.""" - return f"\033]8;;{url}\033\\{word}\033]8;;\033\\" if USE_FANCY_HYPERLINKS else f"{word} ({url})" + if USE_FANCY_HYPERLINKS: + return f"\033]8;;{url}\033\\{word}\033]8;;\033\\" # noqa E231,E702 + return f"{word} ({url})" class ColorLogHandler(logging.Handler): diff --git a/src/hermes/commands/marketplace.py b/src/hermes/commands/marketplace.py index 842955dc..cd672545 100644 --- a/src/hermes/commands/marketplace.py +++ b/src/hermes/commands/marketplace.py @@ -4,6 +4,8 @@ # SPDX-FileContributor: Stephan Druskat """Basic CLI to list plugins from the Hermes marketplace.""" + +from functools import cache from html.parser import HTMLParser from typing import List, Optional @@ -11,8 +13,11 @@ from pydantic import BaseModel, ConfigDict, Field from pydantic.alias_generators import to_camel -from hermes.utils import hermes_doi, hermes_user_agent +from hermes.commands.init.util import slim_click +from hermes.utils import hermes_doi, hermes_concept_doi, hermes_user_agent +# This URL must not be changed (to not break the command for older hermes versions)! +# If the marketplace site changes. The redirect on Read The Docs has to be changed instead. MARKETPLACE_URL = "https://hermes.software-metadata.pub/marketplace" @@ -63,7 +68,14 @@ class SchemaOrgSoftwareApplication(SchemaOrgModel): keywords: List["str"] = None -schema_org_hermes = SchemaOrgSoftwareApplication(id_=hermes_doi, name="hermes") +schema_org_hermes = SchemaOrgSoftwareApplication( + id_=( + hermes_doi + if hermes_doi.startswith("https://doi.org/") + else f"https://doi.org/{hermes_doi}" + ), + name="hermes", +) class PluginMarketPlaceParser(HTMLParser): @@ -86,6 +98,54 @@ def handle_data(self, data): plugin = SchemaOrgSoftwareApplication.model_validate_json(data) self.plugins.append(plugin) + def parse_plugins_from_url(self, url: str = MARKETPLACE_URL, user_agent: str = hermes_user_agent): + response = requests.get(url, headers={"User-Agent": user_agent}) + response.raise_for_status() + self.feed(response.text) + + +@cache +def _doi_is_version_of_concept_doi(doi: str, concept_doi: str) -> bool: + """Check whether ``doi`` is a version of ``concept_doi``. + + The check is performed by requesting ``doi`` from the DataCite API and checking + whether its related identifier of type ``IsVersionOf`` points to ``concept_doi``. + This is the case if ``conecpt_doi`` is the concept DOI of ``doi``. + """ + + doi = doi.removeprefix("https://doi.org/") + concept_doi = concept_doi.removeprefix("https://doi.org/") + + response = requests.get( + f"https://api.datacite.org/dois/{doi}", + headers={"User-Agent": hermes_user_agent}, + ) + response.raise_for_status() + + for identifier in response.json()["data"]["attributes"]["relatedIdentifiers"]: + if ( + identifier["relationType"] == "IsVersionOf" + and identifier["relatedIdentifier"] == concept_doi + ): + return True + + return False + + +def _is_hermes_reference(reference: Optional[SchemaOrgModel]): + """Figure out whether ``reference`` refers to HERMES.""" + if reference is None: + return False + + if reference.id_ in [ + schema_org_hermes.id_, + hermes_concept_doi, + f"https://doi.org/{hermes_concept_doi}", + ]: + return True + + return _doi_is_version_of_concept_doi(reference.id_, hermes_concept_doi) + def _sort_plugins_by_step(plugins: list[SchemaOrgSoftwareApplication]) -> dict[str, list[SchemaOrgSoftwareApplication]]: sorted_plugins = {k: [] for k in ["harvest", "process", "curate", "deposit", "postprocess"]} @@ -96,21 +156,23 @@ def _sort_plugins_by_step(plugins: list[SchemaOrgSoftwareApplication]) -> dict[s return sorted_plugins -def main(): - response = requests.get(MARKETPLACE_URL, headers={"User-Agent": hermes_user_agent}) - response.raise_for_status() +def _plugin_loc(_plugin: SchemaOrgSoftwareApplication) -> str: + return ( + "builtin" + if _is_hermes_reference(_plugin.is_part_of) + else (_plugin.url or "") + ) + +def main(): parser = PluginMarketPlaceParser() - parser.feed(response.text) + parser.parse_plugins_from_url(MARKETPLACE_URL, hermes_user_agent) print( "A detailed list of available plugins can be found on the HERMES website at", MARKETPLACE_URL + "." ) - def _plugin_loc(_plugin: SchemaOrgSoftwareApplication) -> str: - return "builtin" if _plugin.is_part_of == schema_org_hermes else (_plugin.url or "") - if parser.plugins: print() max_name_len = max(map(lambda plugin: len(plugin.name), parser.plugins)) @@ -128,3 +190,63 @@ def _plugin_loc(_plugin: SchemaOrgSoftwareApplication) -> str: if __name__ == "__main__": main() + + +class PluginInfo: + """ + This class contains all the information about a plugin which are needed for the init-Command. + """ + def __init__(self): + self.name: str = "" + self.location: str = "" + self.step: str = "" + self.builtin: bool = True + self.install_url: str = "" + self.abstract: str = "" + + def __str__(self): + step_text = f"[{self.step}]" + return f"{step_text} {slim_click.Formats.BOLD.wrap_around(self.name)} ({self.location})" + + def get_pip_install_command(self) -> str: + """ + Returns the pip install command which can be used to install the plugin. + Tries to extract the project name from the install_url (PyPI-URL) if possible. + Otherwise, it tries to use the location (Git-Project-URL) for the pip install command. + """ + if self.install_url and self.install_url.startswith("https://pypi.org/project/"): + project_name = self.install_url.rstrip("/").removeprefix("https://pypi.org/project/") + return f"pip install {project_name}" + if self.location and self.location.startswith(("https://", "git@", "ssh://")): + git_url = self.location.rstrip("/") + return f"pip install git+{git_url}" + return "" + + def is_valid(self) -> bool: + """ + Returns True if the plugin can be installed. Maybe we'll check the actual repository here later + to make sure that other things are valid too. + """ + return self.get_pip_install_command() != "" + + +def get_plugin_infos() -> list[PluginInfo]: + """ + Returns a List of PluginInfos which are meant to be used by the init-command. + """ + parser = PluginMarketPlaceParser() + parser.parse_plugins_from_url(MARKETPLACE_URL, hermes_user_agent) + infos: list[PluginInfo] = [] + if parser.plugins: + plugins_sorted = _sort_plugins_by_step(parser.plugins) + for step in plugins_sorted.keys(): + for plugin in plugins_sorted[step]: + info = PluginInfo() + info.name = plugin.name + info.step = step + info.location = _plugin_loc(plugin) + info.builtin = info.location == "builtin" + info.install_url = plugin.install_url + info.abstract = plugin.abstract + infos.append(info) + return infos diff --git a/src/hermes/commands/postprocess/invenio.py b/src/hermes/commands/postprocess/invenio.py index a7ba6b53..b536f323 100644 --- a/src/hermes/commands/postprocess/invenio.py +++ b/src/hermes/commands/postprocess/invenio.py @@ -34,8 +34,9 @@ def cff_doi(ctx): try: cff = yaml.load(open('CITATION.cff', 'r'), yaml.Loader) new_identifier = { - 'description': f"DOI for the published version {deposition['metadata']['version']} " - f"[generated by hermes]", + 'description': "DOI for the published version " + f"{deposition['metadata']['version']} " + "[generated by hermes]", 'type': 'doi', 'value': deposition['doi'] } diff --git a/src/hermes/utils.py b/src/hermes/utils.py index 20ab5f58..56c4590c 100644 --- a/src/hermes/utils.py +++ b/src/hermes/utils.py @@ -1,19 +1,106 @@ -# SPDX-FileCopyrightText: 2023 Helmholtz-Zentrum Dresden-Rossendorf (HZDR) +# SPDX-FileCopyrightText: 2023 Helmholtz-Zentrum Dresden-Rossendorf (HZDR), German Aerospace Center (DLR) # # SPDX-License-Identifier: Apache-2.0 # SPDX-FileContributor: David Pape +# SPDX-FileContributor: Stephan Druskat from importlib.metadata import metadata +from mimetypes import guess_type +from pathlib import Path +import argparse + + +def retrieve_project_urls(metadata_urls: list[str]) -> dict[str, str]: + """ + Extracts the keys and values from the project.urls section in distribution package metadata + and converts them into a dictionary. + + :param metadata_urls: The list of urls to extract from (from distribution metadata) + :return: A dictionary mapping URL names to URLs + """ + return { + url_lst[0].lower(): url_lst[1] + for url_lst in [ + metadata_url_item.split(", ", maxsplit=1) + for metadata_url_item in metadata_urls + ] + } hermes_metadata = metadata("hermes") +# Basic metadata hermes_name = hermes_metadata["name"] hermes_version = hermes_metadata["version"] -hermes_homepage = hermes_metadata["home-page"] +# Project URLs +hermes_urls = retrieve_project_urls(hermes_metadata.get_all("project-url", [])) +hermes_homepage = hermes_urls["homepage"] + +# Publication metadata # TODO: Fetch this from somewhere hermes_doi = "10.5281/zenodo.13311079" # hermes v0.8.1 +hermes_concept_doi = "10.5281/zenodo.13221383" +"""Fix "concept" DOI that always refers to the newest version.""" +# User agent hermes_user_agent = f"{hermes_name}/{hermes_version} ({hermes_homepage})" + + +def guess_file_type(path: Path): + """File type detection for non-standardised formats. + + Custom detection for file types not yet supported by Python's ``guess_type`` + function. + """ + # YAML was only added to ``guess_type`` in Python 3.14 due to the MIME type only + # having been decided in 2024. + # See: https://www.rfc-editor.org/rfc/rfc9512.html + if path.suffix in [".yml", ".yaml"]: + return ("application/yaml", None) + + # TOML is not yet part of ``guess_type`` due to the MIME type only having been + # accepted in October of 2024. + # See: https://www.iana.org/assignments/media-types/application/toml + if path.suffix == ".toml": + return ("application/toml", None) + + # cff is yaml. + # See: https://github.com/citation-file-format/citation-file-format/issues/391 + if path.name == "CITATION.cff": + return ("application/yaml", None) + + # .license files are likely license annotations according to REUSE specification. + # See: https://reuse.software/spec/ + if path.suffix == ".license": + return ("text/plain", None) + + if path.name == "poetry.lock": + return ("text/plain", None) + + # use non-strict mode to cover more file types + return guess_type(path, strict=False) + + +def mask_options_values(args: argparse.Namespace) -> argparse.Namespace: + """Masks potentially sensitive values in the 'options' argument + in the passed argparse.Namespace. + + The main use case for this is preventing potentially sensitive + data/secrets being included in raw args logging. + + :param args: The argparse.Namespace to mask. + :return: A copy of the namespace with masked sensitive values. + """ + import copy + + masked_args = copy.copy(args) + + # Mask the values for 'options' if they exist + if hasattr(masked_args, "options") and masked_args.options: + masked_args.options = [ + (key, "***REDACTED***") for key, value in masked_args.options + ] + + return masked_args diff --git a/test/hermes_test/commands/init/test_init.py b/test/hermes_test/commands/init/test_init.py index 19489c1f..c32138f3 100644 --- a/test/hermes_test/commands/init/test_init.py +++ b/test/hermes_test/commands/init/test_init.py @@ -4,9 +4,10 @@ import json import pytest -from hermes.commands.init.base import convert_remote_url, is_git_installed, string_in_file, download_file_from_url +from hermes.commands.init.base import string_in_file, download_file_from_url from unittest.mock import patch, MagicMock import hermes.commands.init.util.oauth_process as oauth_process +from hermes.commands.init.util.git_info import is_git_installed, convert_remote_url @pytest.mark.parametrize( diff --git a/test/hermes_test/test_marketplace.py b/test/hermes_test/test_marketplace.py new file mode 100644 index 00000000..9fe31045 --- /dev/null +++ b/test/hermes_test/test_marketplace.py @@ -0,0 +1,104 @@ +# SPDX-FileCopyrightText: 2025 Helmholtz-Zentrum Dresden-Rossendorf +# SPDX-License-Identifier: Apache-2.0 +# SPDX-FileContributor: David Pape + +import requests_mock + +from hermes.commands.marketplace import ( + schema_org_hermes, + SchemaOrgModel, + _is_hermes_reference, +) + + +def test_schema_org_hermes_doi_is_absolute(): + """The HERMES DOI rendered to the plugins list must always be a full URL.""" + assert isinstance(schema_org_hermes, SchemaOrgModel) + assert schema_org_hermes.id_ is not None + assert schema_org_hermes.id_.startswith("https://doi.org/") + + +def test_concept_doi_is_hermes_reference(): + """The HERMES concept DOI is a reference to HERMES. + + We must be able to figure this out without asking DataCite. + """ + with requests_mock.Mocker() as m: + assert _is_hermes_reference( + SchemaOrgModel( + type_="SoftwareSourceCode", + id_="https://doi.org/10.5281/zenodo.13221383", + ) + ) + # DataCite API was not called + assert m.call_count == 0 + + +def test_is_hermes_reference_if_datacite_api_returns_concept_doi_as_rel_id(): + with requests_mock.Mocker() as m: + m.get( + "https://api.datacite.org/dois/10.9999/fake.1000", + text=""" +{ + "data": { + "id": "10.9999/fake.1000", + "type": "dois", + "attributes": { + "doi": "10.9999/fake.1000", + "prefix": "10.9999", + "suffix": "fake.1000", + "relatedIdentifiers": [ + { + "relationType": "IsVersionOf", + "relatedIdentifier": "10.5281/zenodo.13221383", + "relatedIdentifierType": "DOI" + } + ] + } + } +} +""".strip(), + ) + # 10.5281/zenodo.13221383 retured from DataCite is HERMES concept DOI + assert _is_hermes_reference( + SchemaOrgModel( + type_="SoftwareSourceCode", id_="https://doi.org/10.9999/fake.1000" + ) + ) + # DataCite API was called once + assert m.call_count == 1 + + +def test_not_is_hermes_reference_if_datacite_api_returns_wrong_rel_id(): + with requests_mock.Mocker() as m: + m.get( + "https://api.datacite.org/dois/10.9999/fake.2000", + text=""" +{ + "data": { + "id": "10.9999/fake.2000", + "type": "dois", + "attributes": { + "doi": "10.9999/fake.2000", + "prefix": "10.9999", + "suffix": "fake.2000", + "relatedIdentifiers": [ + { + "relationType": "IsVersionOf", + "relatedIdentifier": "10.9999/fake.1999", + "relatedIdentifierType": "DOI" + } + ] + } + } +} +""".strip(), + ) + # 10.9999/fake.1999 returned from DataCite is not HERMES concept DOI + assert not _is_hermes_reference( + SchemaOrgModel( + type_="SoftwareSourceCode", id_="https://doi.org/10.9999/fake.2000" + ) + ) + # DataCite API was called once + assert m.call_count == 1 diff --git a/test/hermes_test/test_utils.py b/test/hermes_test/test_utils.py new file mode 100644 index 00000000..179e5bc9 --- /dev/null +++ b/test/hermes_test/test_utils.py @@ -0,0 +1,34 @@ +# SPDX-FileCopyrightText: 2025 German Aerospace Center (DLR) +# SPDX-FileContributor: Stephan Druskat +# +# SPDX-License-Identifier: Apache-2.0 + +import toml +from pathlib import Path +from argparse import Namespace + +pyproject = toml.load(Path(__file__).parent.parent.parent / "pyproject.toml") +expected_name = pyproject["project"]["name"] +expected_version = pyproject["project"]["version"] +expected_homepage = pyproject["project"]["urls"]["homepage"] + + +def test_hermes_user_agent(): + """ + This assumes that no other version of `hermes` than the current one is installed + in the workspace from which the tests are run. + """ + from hermes.utils import hermes_user_agent + + assert ( + hermes_user_agent == f"{expected_name}/{expected_version} ({expected_homepage})" + ) + + +def test_mask_values_options(): + from hermes.utils import mask_options_values + ns = Namespace(foo="bar", options=[("foo", "bar"), ("bar", "foo")]) + assert mask_options_values(ns) == Namespace( + foo="bar", + options=[("foo", "***REDACTED***"), ("bar", "***REDACTED***")] + )