From 0767e2c82b1fbcc05f53ee79b0fabc847758d8f9 Mon Sep 17 00:00:00 2001 From: Dorian Portillo Date: Fri, 15 Nov 2024 17:06:37 -0800 Subject: [PATCH 01/42] refactor: :recycle: transfer validation api to codefair repo (#106) --- validator-api/.dockerignore | 23 + validator-api/.flake8 | 3 + validator-api/.flaskenv | 2 + .../.github/workflows/build-and-deploy.yml | 44 + validator-api/.gitignore | 44 + validator-api/.markdownlint.json | 10 + validator-api/.pydocstyle.ini | 14 + validator-api/.pylint.ini | 413 ++++ validator-api/.tool-versions | 2 + validator-api/.vscode/extensions.json | 3 + validator-api/Dockerfile | 40 + validator-api/LICENSE | 21 + validator-api/README.md | 102 + validator-api/apis/__init__.py | 124 ++ validator-api/apis/test.http | 7 + validator-api/app.py | 84 + validator-api/config.py | 18 + validator-api/docker-compose.yaml | 11 + validator-api/entrypoint.sh | 3 + validator-api/poetry.lock | 1758 +++++++++++++++++ validator-api/pyproject.toml | 167 ++ 21 files changed, 2893 insertions(+) create mode 100644 validator-api/.dockerignore create mode 100644 validator-api/.flake8 create mode 100644 validator-api/.flaskenv create mode 100644 validator-api/.github/workflows/build-and-deploy.yml create mode 100644 validator-api/.gitignore create mode 100644 validator-api/.markdownlint.json create mode 100644 validator-api/.pydocstyle.ini create mode 100644 validator-api/.pylint.ini create mode 100644 validator-api/.tool-versions create mode 100644 validator-api/.vscode/extensions.json create mode 100644 validator-api/Dockerfile create mode 100644 validator-api/LICENSE create mode 100644 validator-api/README.md create mode 100644 validator-api/apis/__init__.py create mode 100644 validator-api/apis/test.http create mode 100644 validator-api/app.py create mode 100644 validator-api/config.py create mode 100644 validator-api/docker-compose.yaml create mode 100644 validator-api/entrypoint.sh create mode 100644 validator-api/poetry.lock create mode 100644 validator-api/pyproject.toml diff --git a/validator-api/.dockerignore b/validator-api/.dockerignore new file mode 100644 index 0000000..2b3ef87 --- /dev/null +++ b/validator-api/.dockerignore @@ -0,0 +1,23 @@ +.DS_Store +dist +dist-ssr +coverage +*.local + + +# Editor directories and files +.vscode/* +!.vscode/extensions.json +.idea +*.suo +*.ntvs* +*.njsproj +*.sln +*.sw? + +# API Platform specific files +*.pyc +/config.ps1 + +# Environment variables +.env diff --git a/validator-api/.flake8 b/validator-api/.flake8 new file mode 100644 index 0000000..2f20d8e --- /dev/null +++ b/validator-api/.flake8 @@ -0,0 +1,3 @@ +[flake8] +max-line-length = 120 +ignore= W293,W503 \ No newline at end of file diff --git a/validator-api/.flaskenv b/validator-api/.flaskenv new file mode 100644 index 0000000..01ea7b9 --- /dev/null +++ b/validator-api/.flaskenv @@ -0,0 +1,2 @@ +FLASK_APP=app +FLASK_RUN_PORT=5000 \ No newline at end of file diff --git a/validator-api/.github/workflows/build-and-deploy.yml b/validator-api/.github/workflows/build-and-deploy.yml new file mode 100644 index 0000000..9ed1915 --- /dev/null +++ b/validator-api/.github/workflows/build-and-deploy.yml @@ -0,0 +1,44 @@ +name: Build and push validator api image to Azure Container Registry + +on: + push: + branches: + - main + pull_request: + types: [closed] + branches: + - main + workflow_dispatch: + +concurrency: + group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} + cancel-in-progress: true + +jobs: + build: + name: Build and push Docker image + if: github.event_name == 'push' || (github.event_name == 'pull_request' && github.event.pull_request.merged == true) + runs-on: ubuntu-latest + env: + AZURE_REGISTRY_LOGIN_SERVER: ${{ secrets.AZURE_REGISTRY_LOGIN_SERVER }} + AZURE_REGISTRY_USERNAME: ${{ secrets.AZURE_REGISTRY_USERNAME }} + AZURE_REGISTRY_PASSWORD: ${{ secrets.AZURE_REGISTRY_PASSWORD }} + + steps: + - name: Checkout + uses: actions/checkout@v2 + + - name: Login to Azure Container Registry + uses: azure/docker-login@v1 + with: + login-server: ${{ secrets.AZURE_REGISTRY_LOGIN_SERVER }} + username: ${{ secrets.AZURE_REGISTRY_USERNAME }} + password: ${{ secrets.AZURE_REGISTRY_PASSWORD }} + + - name: Build and push Docker image + uses: docker/build-push-action@v2 + with: + context: . + file: ./Dockerfile + push: true + tags: ${{ secrets.AZURE_REGISTRY_LOGIN_SERVER }}/cwl-validator-api:latest diff --git a/validator-api/.gitignore b/validator-api/.gitignore new file mode 100644 index 0000000..da55802 --- /dev/null +++ b/validator-api/.gitignore @@ -0,0 +1,44 @@ +# Logs +logs +*.log +npm-debug.log* +yarn-debug.log* +yarn-error.log* +pnpm-debug.log* +lerna-debug.log* + +node_modules +.DS_Store +dist +dist-ssr +coverage +*.local + +/cypress/videos/ +/cypress/screenshots/ + +# Editor directories and files +.vscode/* +!.vscode/extensions.json +.idea +*.suo +*.ntvs* +*.njsproj +*.sln +*.sw? + +# API Platform specific files +*.pyc +/config.ps1 + +# Environment variables +.env +.venv + +# Virutal Environments +.venv + +# Database +postgres-data/* +redis-data/* +storage/* diff --git a/validator-api/.markdownlint.json b/validator-api/.markdownlint.json new file mode 100644 index 0000000..bd7eaef --- /dev/null +++ b/validator-api/.markdownlint.json @@ -0,0 +1,10 @@ +{ + "default": true, + "MD013": false, + "MD024": { + "siblings_only": true + }, + "MD033": false, + "MD036": false, + "MD046": false +} diff --git a/validator-api/.pydocstyle.ini b/validator-api/.pydocstyle.ini new file mode 100644 index 0000000..cbed52d --- /dev/null +++ b/validator-api/.pydocstyle.ini @@ -0,0 +1,14 @@ +[pydocstyle] + +# D211: No blank lines allowed before class docstring +add_select = D211 + +# D100: Missing docstring in public module +# D101: Missing docstring in public class +# D102: Missing docstring in public method +# D103: Missing docstring in public function +# D104: Missing docstring in public package +# D105: Missing docstring in magic method +# D107: Missing docstring in __init__ +# D202: No blank lines allowed after function docstring +add_ignore = D100,D101,D102,D103,D104,D105,D107,D202 \ No newline at end of file diff --git a/validator-api/.pylint.ini b/validator-api/.pylint.ini new file mode 100644 index 0000000..d459611 --- /dev/null +++ b/validator-api/.pylint.ini @@ -0,0 +1,413 @@ +[MASTER] + +# A comma-separated list of package or module names from where C extensions may +# be loaded. Extensions are loading into the active Python interpreter and may +# run arbitrary code +extension-pkg-whitelist= + +# Add files or directories to the blacklist. They should be base names, not +# paths. +ignore=CVS + +# Add files or directories matching the regex patterns to the blacklist. The +# regex matches against base names, not paths. +ignore-patterns= + +# Python code to execute, usually for sys.path manipulation such as +# pygtk.require(). +#init-hook= + +# Use multiple processes to speed up Pylint. +jobs=0 + +# List of plugins (as comma separated values of python modules names) to load, +# usually to register additional checkers. +load-plugins= + +# Pickle collected data for later comparisons. +persistent=yes + +# Specify a configuration file. +#rcfile= + +# Allow loading of arbitrary C extensions. Extensions are imported into the +# active Python interpreter and may run arbitrary code. +unsafe-load-any-extension=no + + +[MESSAGES CONTROL] + +# Only show warnings with the listed confidence levels. Leave empty to show +# all. Valid levels: HIGH, INFERENCE, INFERENCE_FAILURE, UNDEFINED +confidence= + +# Disable the message, report, category or checker with the given id(s). You +# can either give multiple identifiers separated by comma (,) or put this +# option multiple times (only on the command line, not in the configuration +# file where it should appear only once).You can also use "--disable=all" to +# disable everything first and then reenable specific checks. For example, if +# you want to run only the similarities checker, you can use "--disable=all +# --enable=similarities". If you want to run only the classes checker, but have +# no Warning level messages displayed, use"--disable=all --enable=classes +# --disable=W" +disable= + fixme, + global-statement, + invalid-name, + missing-docstring, + redefined-outer-name, + too-few-public-methods, + too-many-locals, + too-many-arguments, + line-too-long, + unnecessary-pass, + broad-except, + duplicate-code, + too-many-branches, + too-many-return-statements, + too-many-public-methods, + too-many-ancestors, + too-many-instance-attributes, + too-many-statements, + attribute-defined-outside-init, + unsupported-assignment-operation, + unsupported-delete-operation, + too-many-nested-blocks, + protected-access, + +# Enable the message, report, category or checker with the given id(s). You can +# either give multiple identifier separated by comma (,) or put this option +# multiple time (only on the command line, not in the configuration file where +# it should appear only once). See also the "--disable" option for examples. +enable= + + +[REPORTS] + +# Python expression which should return a note less than 10 (10 is the highest +# note). You have access to the variables errors warning, statement which +# respectively contain the number of errors / warnings messages and the total +# number of statements analyzed. This is used by the global evaluation report +# (RP0004). +evaluation=10.0 - ((float(5 * error + warning + refactor + convention) / statement) * 10) + +# Template used to display messages. This is a python new-style format string +# used to format the message information. See doc for all details +#msg-template= + +# Set the output format. Available formats are text, parseable, colorized, json +# and msvs (visual studio).You can also give a reporter class, eg +# mypackage.mymodule.MyReporterClass. +output-format=text + +# Tells whether to display a full report or only the messages +reports=no + +# Activate the evaluation score. +score=no + + +[REFACTORING] + +# Maximum number of nested blocks for function / method body +max-nested-blocks=5 + + +[BASIC] + +# Regular expression matching correct argument names +argument-rgx=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$ + +# Regular expression matching correct attribute names +attr-rgx=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$ + +# Bad variable names which should always be refused, separated by a comma +bad-names=foo,bar,baz,toto,tutu,tata + +# Regular expression matching correct class attribute names +class-attribute-rgx=([A-Za-z_][A-Za-z0-9_]{2,30}|(__.*__))$ + +# Regular expression matching correct class names +class-rgx=[A-Z_][a-zA-Z0-9]+$ + +# Regular expression matching correct constant names +const-rgx=(([A-Z_][A-Z0-9_]*)|(__.*__))$ + +# Minimum line length for functions/classes that require docstrings, shorter +# ones are exempt. +docstring-min-length=-1 + +# Regular expression matching correct function names +function-rgx=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$ + +# Good variable names which should always be accepted, separated by a comma +good-names=i,j,k,ex,Run,_,id + +# Include a hint for the correct naming format with invalid-name +include-naming-hint=no + +# Regular expression matching correct inline iteration names +inlinevar-rgx=[A-Za-z_][A-Za-z0-9_]*$ + +# Regular expression matching correct method names +method-rgx=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$ + +# Regular expression matching correct module names +module-rgx=(([a-z_][a-z0-9_]*)|([A-Z][a-zA-Z0-9]+))$ + +# Colon-delimited sets of names that determine each other's naming style when +# the name regexes allow several styles. +name-group= + +# Regular expression which should only match function or class names that do +# not require a docstring. +no-docstring-rgx=^_ + +# List of decorators that produce properties, such as abc.abstractproperty. Add +# to this list to register other decorators that produce valid properties. +property-classes=abc.abstractproperty + +# Regular expression matching correct variable names +variable-rgx=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$ + + +[FORMAT] + +# Expected format of line ending, e.g. empty (any line ending), LF or CRLF. +expected-line-ending-format= + +# Regexp for a line that is allowed to be longer than the limit. +ignore-long-lines=^.*((https?:)|(pragma:)|(TODO:)).*$ + +# Number of spaces of indent required inside a hanging or continued line. +indent-after-paren=4 + +# String used as indentation unit. This is usually " " (4 spaces) or "\t" (1 +# tab). +indent-string=' ' + +# Maximum number of characters on a single line. +max-line-length=88 + +# Maximum number of lines in a module +max-module-lines=1000 + +# Allow the body of a class to be on the same line as the declaration if body +# contains single statement. +single-line-class-stmt=no + +# Allow the body of an if to be on the same line as the test if there is no +# else. +single-line-if-stmt=no + + +[LOGGING] + +# Logging modules to check that the string format arguments are in logging +# function parameter format +logging-modules=logging + + +[MISCELLANEOUS] + +# List of note tags to take in consideration, separated by a comma. +notes=FIXME,XXX,TODO + + +[SIMILARITIES] + +# Ignore comments when computing similarities. +ignore-comments=yes + +# Ignore docstrings when computing similarities. +ignore-docstrings=yes + +# Ignore imports when computing similarities. +ignore-imports=no + +# Minimum lines number of a similarity. +min-similarity-lines=4 + + +[SPELLING] + +# Spelling dictionary name. Available dictionaries: none. To make it working +# install python-enchant package. +spelling-dict= + +# List of comma separated words that should not be checked. +spelling-ignore-words= + +# A path to a file that contains private dictionary; one word per line. +spelling-private-dict-file= + +# Tells whether to store unknown words to indicated private dictionary in +# --spelling-private-dict-file option instead of raising a message. +spelling-store-unknown-words=no + + +[TYPECHECK] + +# List of decorators that produce context managers, such as +# contextlib.contextmanager. Add to this list to register other decorators that +# produce valid context managers. +contextmanager-decorators=contextlib.contextmanager + +# List of members which are set dynamically and missed by pylint inference +# system, and so shouldn't trigger E1101 when accessed. Python regular +# expressions are accepted. +generated-members= + +# Tells whether missing members accessed in mixin class should be ignored. A +# mixin class is detected if its name ends with "mixin" (case insensitive). +ignore-mixin-members=yes + +# This flag controls whether pylint should warn about no-member and similar +# checks whenever an opaque object is returned when inferring. The inference +# can return multiple potential results while evaluating a Python object, but +# some branches might not be evaluated, which results in partial inference. In +# that case, it might be useful to still emit no-member and other checks for +# the rest of the inferred objects. +ignore-on-opaque-inference=yes + +# List of class names for which member attributes should not be checked (useful +# for classes with dynamically set attributes). This supports the use of +# qualified names. +ignored-classes=optparse.Values,thread._local,_thread._local + +# List of module names for which member attributes should not be checked +# (useful for modules/projects where namespaces are manipulated during runtime +# and thus existing member attributes cannot be deduced by static analysis. It +# supports qualified module names, as well as Unix pattern matching. +ignored-modules= + +# Show a hint with possible names when a member name was not found. The aspect +# of finding the hint is based on edit distance. +missing-member-hint=yes + +# The minimum edit distance a name should have in order to be considered a +# similar match for a missing member name. +missing-member-hint-distance=1 + +# The total number of similar names that should be taken in consideration when +# showing a hint for a missing member. +missing-member-max-choices=1 + + +[VARIABLES] + +# List of additional names supposed to be defined in builtins. Remember that +# you should avoid to define new builtins when possible. +additional-builtins= + +# Tells whether unused global variables should be treated as a violation. +allow-global-unused-variables=yes + +# List of strings which can identify a callback function by name. A callback +# name must start or end with one of those strings. +callbacks=cb_,_cb + +# A regular expression matching the name of dummy variables (i.e. expectedly +# not used). +dummy-variables-rgx=_+$|(_[a-zA-Z0-9_]*[a-zA-Z0-9]+?$)|dummy|^ignored_|^unused_ + +# Argument names that match this expression will be ignored. Default to name +# with leading underscore +ignored-argument-names=_.*|^ignored_|^unused_ + +# Tells whether we should check for unused import in __init__ files. +init-import=no + +# List of qualified module names which can have objects that can redefine +# builtins. +redefining-builtins-modules=six.moves,future.builtins + + +[CLASSES] + +# List of method names used to declare (i.e. assign) instance attributes. +defining-attr-methods=__init__,__new__,setUp + +# List of member names, which should be excluded from the protected access +# warning. +exclude-protected=_asdict,_fields,_replace,_source,_make + +# List of valid names for the first argument in a class method. +valid-classmethod-first-arg=cls + +# List of valid names for the first argument in a metaclass class method. +valid-metaclass-classmethod-first-arg=mcs + + +[DESIGN] + +# Maximum number of arguments for function / method +max-args=5 + +# Maximum number of attributes for a class (see R0902). +max-attributes=7 + +# Maximum number of boolean expressions in a if statement +max-bool-expr=5 + +# Maximum number of branch for function / method body +max-branches=12 + +# Maximum number of locals for function / method body +max-locals=15 + +# Maximum number of parents for a class (see R0901). +max-parents=7 + +# Maximum number of public methods for a class (see R0904). +max-public-methods=20 + +# Maximum number of return / yield for function / method body +max-returns=6 + +# Maximum number of statements in function / method body +max-statements=50 + +# Minimum number of public methods for a class (see R0903). +min-public-methods=2 + + +[IMPORTS] + +# Allow wildcard imports from modules that define __all__. +allow-wildcard-with-all=no + +# Analyse import fallback blocks. This can be used to support both Python 2 and +# 3 compatible code, which means that the block might have code that exists +# only in one or another interpreter, leading to false positives when analysed. +analyse-fallback-blocks=no + +# Deprecated modules which should not be used, separated by a comma +deprecated-modules=regsub,TERMIOS,Bastion,rexec + +# Create a graph of external dependencies in the given file (report RP0402 must +# not be disabled) +ext-import-graph= + +# Create a graph of every (i.e. internal and external) dependencies in the +# given file (report RP0402 must not be disabled) +import-graph= + +# Create a graph of internal dependencies in the given file (report RP0402 must +# not be disabled) +int-import-graph= + +# Force import order to recognize a module as part of the standard +# compatibility libraries. +known-standard-library= + +# Force import order to recognize a module as part of a third party library. +known-third-party=enchant + + +[EXCEPTIONS] + +# Exceptions that will emit a warning when being caught. Defaults to +# "Exception" +overgeneral-exceptions=builtins.BaseException, + builtins.Exception diff --git a/validator-api/.tool-versions b/validator-api/.tool-versions new file mode 100644 index 0000000..905042b --- /dev/null +++ b/validator-api/.tool-versions @@ -0,0 +1,2 @@ +python 3.11.2 +poetry 1.4.1 \ No newline at end of file diff --git a/validator-api/.vscode/extensions.json b/validator-api/.vscode/extensions.json new file mode 100644 index 0000000..4861547 --- /dev/null +++ b/validator-api/.vscode/extensions.json @@ -0,0 +1,3 @@ +{ + "recommendations": ["njpwerner.autodocstring", "aaron-bond.better-comments", "ms-python.black-formatter", "visualstudioexptteam.vscodeintellicode", "visualstudioexptteam.intellicode-api-usage-examples", "davidanson.vscode-markdownlint", "ms-python.vscode-pylance", "ms-python.pylint", "ms-python.python", "donjayamanne.python-environment-manager", "kevinrose.vsc-python-indent"] +} diff --git a/validator-api/Dockerfile b/validator-api/Dockerfile new file mode 100644 index 0000000..4df54fa --- /dev/null +++ b/validator-api/Dockerfile @@ -0,0 +1,40 @@ +FROM python:3.10-alpine +# FROM ubuntu/python:stable + +EXPOSE 5000 + +WORKDIR /app + +ENV POETRY_VERSION=1.3.2 + +# RUN apt-get update +# RUN sudo apt-get install cwltool + +RUN apk update +RUN apk add --no-cache gcc libffi-dev musl-dev +# RUN apk add --update cwltool + +RUN pip install "poetry==$POETRY_VERSION" + +# COPY poetry.lock pyproject.toml ./ +COPY pyproject.toml . + +RUN poetry config virtualenvs.create false +RUN poetry install + +RUN pip install cwltool +RUN pip install cffconvert + +COPY apis ./apis +COPY config.py . +COPY app.py . + +# COPY entrypoint.sh . + +# RUN chmod +x entrypoint.sh + +ENTRYPOINT [ "python3" ] + +CMD [ "app.py" ] + +# ENTRYPOINT ["./entrypoint.sh"] \ No newline at end of file diff --git a/validator-api/LICENSE b/validator-api/LICENSE new file mode 100644 index 0000000..1fe1fa8 --- /dev/null +++ b/validator-api/LICENSE @@ -0,0 +1,21 @@ +MIT License + +Copyright (c) 2022 AI-READI + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/validator-api/README.md b/validator-api/README.md new file mode 100644 index 0000000..8090a26 --- /dev/null +++ b/validator-api/README.md @@ -0,0 +1,102 @@ +# cwl-validator + +## Getting started + +### Prerequisites/Dependencies + +You will need the following installed on your system: + +- Python 3.8+ +- [Pip](https://pip.pypa.io/en/stable/) +- [Poetry](https://python-poetry.org/) +- [Docker](https://www.docker.com/) + +### Setup + +If you would like to update the api, please follow the instructions below. + +1. Create a local virtual environment and activate it: + + ```bash + python -m venv .venv + source .venv/bin/activate + ``` + + If you are using Anaconda, you can create a virtual environment with: + + ```bash + conda create -n cwl-validator-dev-env python=3.10 + conda activate cwl-validator-dev-env + ``` + +2. Install the dependencies for this package. We use [Poetry](https://python-poetry.org/) to manage the dependencies: + + ```bash + pip install poetry==1.3.2 + poetry install + ``` + + You can also use version 1.2.0 of Poetry, but you will need to run `poetry lock` after installing the dependencies. + +3. Add your environment variables. An example is provided at `.env.example` + + ```bash + cp .env.example .env + ``` + + Make sure to update the values in `.env` to match your local setup. + +4. Add your modifications and run the tests: + + ```bash + poetry run pytest + ``` + + If you need to add new python packages, you can use Poetry to add them: + + ```bash + poetry add + ``` + +5. Format the code: + + ```bash + poe format + ``` + +6. Check the code quality: + + ```bash + poe typecheck + poe lint + poe flake8 + ``` + + You can also use `poe precommit` to run both formatting and linting. + +7. Run the tests and check the code coverage: + + ```bash + poe test + poe test_with_capture # if you want to see console output + ``` + +## Running + +For developer mode: + +```bash +poe dev +``` + +or + +```bash +flask run --debug +``` + +For production mode: + +```bash +python3 app.py --host $HOST --port $PORT +``` diff --git a/validator-api/apis/__init__.py b/validator-api/apis/__init__.py new file mode 100644 index 0000000..82a4f88 --- /dev/null +++ b/validator-api/apis/__init__.py @@ -0,0 +1,124 @@ +"""Initialize the api system for the backend""" + +import re +import subprocess +from flask_restx import Api, Resource + + +api = Api( + title="CWL Validator API", + description="The backend api system for the CWL Validator", + doc="/docs", +) + + +@api.route("/echo", endpoint="echo") +class HelloEverynyan(Resource): + """Test if the server is active""" + + @api.response(200, "Success") + @api.response(400, "Validation Error") + def get(self): + """Returns a simple 'Server Active' message""" + + return "Server active!" + + + +@api.route("/validate-cwl", endpoint="validate-cwl") +class ValidateCWL(Resource): + """Validate a CWL file""" + @api.response(200, "Success") + @api.response(400, "Validation Error") + @api.expect(api.parser().add_argument("file_path", type=str, help="The file path or URL of the CWL file", required=True)) + def post(self): + """Validate a CWL file""" + + file_path = api.payload.get('file_path') + + # Validate and sanitize the file_path input + if not file_path: + return {"message": "Validation Error", "error": "file_path is required"}, 400 + + # Prevent path traversal attacks + if ".." in file_path or file_path.startswith("/"): + return {"message": "Validation Error", "error": "Invalid file path"}, 400 + + # Prevent command injection + if re.search(r'[;&|]', file_path): + return {"message": "Validation Error", "error": "Invalid characters in file path"}, 400 + + def clean_output(output): + # Remove ANSI escape codes + ansi_escape = re.compile(r'\x1B[@-_][0-?]*[ -/]*[@-~]') + cleaned_output = ansi_escape.sub('', output).strip() + # Remove INFO messages and unnecessary whitespace, and replace newlines with spaces + cleaned_lines = [] + for line in cleaned_output.splitlines(): + if not line.startswith("INFO"): + cleaned_lines.append(line.strip()) + return " ".join(cleaned_lines) + + try: + result = subprocess.run( + ["cwltool", "--validate", file_path], + capture_output=True, + text=True, + check=True, + ) + stdout_clean = clean_output(result.stdout) + stderr_clean = clean_output(result.stderr) + return {"message": "Validation successful", "output": stdout_clean, "error": stderr_clean}, 200 + except subprocess.CalledProcessError as e: + stdout_clean = clean_output(e.stdout) + stderr_clean = clean_output(e.stderr) + return {"message": "Validation failed", "output": stdout_clean, "error": stderr_clean}, 400 + except Exception as e: + return {"message": "An unexpected error occurred", "error": str(e)}, 500 + + +@api.route("/validate-citation", endpoint="validate-citation") +class ValidateCitation(Resource): + """Validate a CITATION.cff file""" + @api.response(200, "Success") + @api.response(400, "Validation Error") + @api.expect(api.parser().add_argument("file_path", type=str, help="The URL or path of the CITATION file", required=True)) + def post(self): + """Validate a CITATION.cff file""" + file_path = api.payload.get('file_path') + + # Validate and sanitize the file_path input + if not file_path: + return {"message": "Validation Error", "error": "file_path is required"}, 400 + + # Prevent path traversal attacks + if ".." in file_path or file_path.startswith("/"): + return {"message": "Validation Error", "error": "Invalid file path"}, 400 + + # Prevent command injection + if re.search(r'[;&|]', file_path): + return {"message": "Validation Error", "error": "Invalid characters in file path"}, 400 + + if file_path.startswith("http://") or file_path.startswith("https://"): + cmd = ["cffconvert", "--validate", "-u", file_path] + else: + cmd = ["cffconvert", "--validate", file_path] + + try: + result = subprocess.run( + cmd, + capture_output=True, + text=True, + check=True, + ) + + stdout_clean = result.stdout + stderr_clean = result.stderr + return {"message": "valid", "output": stdout_clean, "error": stderr_clean}, 200 + except subprocess.CalledProcessError as e: + stdout_clean = e.stdout + match = re.search(r'jsonschema.exceptions.ValidationError:.*', e.stderr) + stderr_clean = match.group(0) if match else "Unknown error" + return {"message": "invalid", "output": stdout_clean, "error": stderr_clean}, 400 + except Exception as e: + return {"message": "An unexpected error occurred", "error": str(e)}, 500 diff --git a/validator-api/apis/test.http b/validator-api/apis/test.http new file mode 100644 index 0000000..26a6f74 --- /dev/null +++ b/validator-api/apis/test.http @@ -0,0 +1,7 @@ +POST /validate HTTP/1.1 +Host: localhost:5000 +Content-Type: application/json + +{ + "file_path": "https://raw.githubusercontent.com/slugb0t/bash-configuration-for-windows/master/invalid.cwl", +} \ No newline at end of file diff --git a/validator-api/app.py b/validator-api/app.py new file mode 100644 index 0000000..6b7a8bd --- /dev/null +++ b/validator-api/app.py @@ -0,0 +1,84 @@ +"""Entry point for the application.""" + +import logging + +from datetime import timezone + + +from flask import Flask, g, request +from flask_cors import CORS +from waitress import serve + +from apis import api + + +def create_app(config_module=None, loglevel="INFO"): + """Initialize the core application.""" + # create and configure the app + app = Flask(__name__) + # `full` if you want to see all the details + app.config["SWAGGER_UI_DOC_EXPANSION"] = "none" + app.config["RESTX_MASK_SWAGGER"] = False + + # set up logging + logging.basicConfig(level=getattr(logging, loglevel)) + + # Initialize config + app.config.from_object(config_module or "config") + + # TODO - fix this + # csrf = CSRFProtect() + # csrf.init_app(app) + + api.init_app(app) + + cors_origins = [ + "https://staging.codefair.io", + "https://codefair.io", + "http://localhost:3001", + "http://localhost:3000" + ] + if app.debug: + cors_origins.extend(["http://localhost:3000", "http://localhost:3001"]) + + # Only allow CORS origin for localhost:3000 + # and any subdomain of azurestaticapps.net/ + CORS( + app, + resources={ + "/*": { + "origins": cors_origins, + # "origins": "*", + } + }, + allow_headers=[ + "Content-Type", + "Authorization", + "Access-Control-Allow-Origin", + "Access-Control-Allow-Credentials", + ], + supports_credentials=True, + ) + + return app + + +if __name__ == "__main__": + from argparse import ArgumentParser + + parser = ArgumentParser() + parser.add_argument( + "-P", "--port", default=5000, type=int, help="Port to listen on" + ) + parser.add_argument("-H", "--host", default="0.0.0.0", type=str, help="Host") + parser.add_argument( + "-L", "--loglevel", default="INFO", type=str, help="Logging level" + ) + args = parser.parse_args() + port = args.port + host = args.host + loglevel = args.loglevel + + flask_app = create_app(loglevel=loglevel) + + serve(flask_app, port=port, host=host) diff --git a/validator-api/config.py b/validator-api/config.py new file mode 100644 index 0000000..c05b608 --- /dev/null +++ b/validator-api/config.py @@ -0,0 +1,18 @@ +"""Configuration for the application.""" + +from os import environ +from pathlib import Path +from dotenv import dotenv_values + +# Check if `.env` file exists +env_path = Path(".") / ".env" + +LOCAL_ENV_FILE = env_path.exists() + +# Load environment variables from .env +config = dotenv_values(".env") + +def get_env(key): + """Return environment variable from .env or native environment.""" + return config.get(key) if LOCAL_ENV_FILE else environ.get(key) + diff --git a/validator-api/docker-compose.yaml b/validator-api/docker-compose.yaml new file mode 100644 index 0000000..d3fbfb4 --- /dev/null +++ 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".cache/pytest/" + +markers = [] + +[build-system] +requires = ["poetry-core>=1.3.2"] +build-backend = "poetry.core.masonry.api" From be755757312f5900b710a5537f424a47eb88e019 Mon Sep 17 00:00:00 2001 From: Sanjay Soundarajan Date: Fri, 15 Nov 2024 17:10:49 -0800 Subject: [PATCH 02/42] =?UTF-8?q?=F0=9F=9A=9A=20chore:=20rename=20`validat?= =?UTF-8?q?or-api`=20to=20`validator`?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- {validator-api => validator}/.dockerignore | 0 {validator-api => validator}/.flake8 | 0 {validator-api => validator}/.flaskenv | 0 .../.github/workflows/build-and-deploy.yml | 0 {validator-api => validator}/.gitignore | 0 {validator-api => validator}/.markdownlint.json | 0 {validator-api => validator}/.pydocstyle.ini | 0 {validator-api => validator}/.pylint.ini | 0 {validator-api => validator}/.tool-versions | 0 {validator-api => validator}/.vscode/extensions.json | 0 {validator-api => validator}/Dockerfile | 0 {validator-api => validator}/LICENSE | 0 {validator-api => validator}/README.md | 0 {validator-api => validator}/apis/__init__.py | 0 {validator-api => validator}/apis/test.http | 0 {validator-api => validator}/app.py | 0 {validator-api => validator}/config.py | 0 {validator-api => validator}/docker-compose.yaml | 0 {validator-api => validator}/entrypoint.sh | 0 {validator-api => validator}/poetry.lock | 0 {validator-api => validator}/pyproject.toml | 0 21 files changed, 0 insertions(+), 0 deletions(-) rename {validator-api => validator}/.dockerignore (100%) rename {validator-api => validator}/.flake8 (100%) rename {validator-api => validator}/.flaskenv (100%) rename {validator-api => validator}/.github/workflows/build-and-deploy.yml (100%) rename {validator-api => validator}/.gitignore (100%) rename {validator-api => validator}/.markdownlint.json (100%) rename {validator-api => validator}/.pydocstyle.ini (100%) rename {validator-api => validator}/.pylint.ini (100%) rename {validator-api => validator}/.tool-versions (100%) rename {validator-api => validator}/.vscode/extensions.json (100%) rename {validator-api => validator}/Dockerfile (100%) rename {validator-api => validator}/LICENSE (100%) rename {validator-api => validator}/README.md (100%) rename {validator-api => validator}/apis/__init__.py (100%) rename {validator-api => validator}/apis/test.http (100%) rename {validator-api => validator}/app.py (100%) rename {validator-api => validator}/config.py (100%) rename {validator-api => validator}/docker-compose.yaml (100%) rename {validator-api => validator}/entrypoint.sh (100%) rename {validator-api => validator}/poetry.lock (100%) rename {validator-api => validator}/pyproject.toml (100%) diff --git a/validator-api/.dockerignore b/validator/.dockerignore similarity index 100% rename from validator-api/.dockerignore rename to validator/.dockerignore diff --git a/validator-api/.flake8 b/validator/.flake8 similarity index 100% rename from validator-api/.flake8 rename to validator/.flake8 diff --git a/validator-api/.flaskenv b/validator/.flaskenv similarity index 100% rename from validator-api/.flaskenv rename to validator/.flaskenv diff --git a/validator-api/.github/workflows/build-and-deploy.yml b/validator/.github/workflows/build-and-deploy.yml similarity index 100% rename from validator-api/.github/workflows/build-and-deploy.yml rename to validator/.github/workflows/build-and-deploy.yml diff --git a/validator-api/.gitignore b/validator/.gitignore similarity index 100% rename from validator-api/.gitignore rename to validator/.gitignore diff --git a/validator-api/.markdownlint.json b/validator/.markdownlint.json similarity index 100% rename from validator-api/.markdownlint.json rename to validator/.markdownlint.json diff --git a/validator-api/.pydocstyle.ini b/validator/.pydocstyle.ini similarity index 100% rename from validator-api/.pydocstyle.ini rename to validator/.pydocstyle.ini diff --git a/validator-api/.pylint.ini b/validator/.pylint.ini similarity index 100% rename from validator-api/.pylint.ini rename to validator/.pylint.ini diff --git a/validator-api/.tool-versions b/validator/.tool-versions similarity index 100% rename from validator-api/.tool-versions rename to validator/.tool-versions diff --git a/validator-api/.vscode/extensions.json b/validator/.vscode/extensions.json similarity index 100% rename from validator-api/.vscode/extensions.json rename to validator/.vscode/extensions.json diff --git a/validator-api/Dockerfile b/validator/Dockerfile similarity index 100% rename from validator-api/Dockerfile rename to validator/Dockerfile diff --git a/validator-api/LICENSE b/validator/LICENSE similarity index 100% rename from validator-api/LICENSE rename to validator/LICENSE diff --git a/validator-api/README.md b/validator/README.md similarity index 100% rename from validator-api/README.md rename to validator/README.md diff --git a/validator-api/apis/__init__.py b/validator/apis/__init__.py similarity index 100% rename from validator-api/apis/__init__.py rename to validator/apis/__init__.py diff --git a/validator-api/apis/test.http b/validator/apis/test.http similarity index 100% rename from validator-api/apis/test.http rename to validator/apis/test.http diff --git a/validator-api/app.py b/validator/app.py similarity index 100% rename from validator-api/app.py rename to validator/app.py diff --git a/validator-api/config.py b/validator/config.py similarity index 100% rename from validator-api/config.py rename to validator/config.py diff --git a/validator-api/docker-compose.yaml b/validator/docker-compose.yaml similarity index 100% rename from validator-api/docker-compose.yaml rename to validator/docker-compose.yaml diff --git a/validator-api/entrypoint.sh b/validator/entrypoint.sh similarity index 100% rename from validator-api/entrypoint.sh rename to validator/entrypoint.sh diff --git a/validator-api/poetry.lock b/validator/poetry.lock similarity index 100% rename from validator-api/poetry.lock rename to validator/poetry.lock diff --git a/validator-api/pyproject.toml b/validator/pyproject.toml similarity index 100% rename from validator-api/pyproject.toml rename to validator/pyproject.toml From 8e3b3a4086c4eba912769dda4f89b8971c6745ab Mon Sep 17 00:00:00 2001 From: Sanjay Soundarajan Date: Fri, 15 Nov 2024 17:38:40 -0800 Subject: [PATCH 03/42] =?UTF-8?q?=F0=9F=91=B7=20ci:=20add=20validator=20de?= =?UTF-8?q?ploy?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .github/workflows/deploy-staging.yml | 57 + .../.github/workflows/build-and-deploy.yml | 44 - validator/.kamal/hooks/docker-setup.sample | 3 + validator/.kamal/hooks/post-deploy.sample | 14 + .../.kamal/hooks/post-proxy-reboot.sample | 3 + validator/.kamal/hooks/pre-build.sample | 51 + validator/.kamal/hooks/pre-connect.sample | 47 + validator/.kamal/hooks/pre-deploy.sample | 109 + .../.kamal/hooks/pre-proxy-reboot.sample | 3 + validator/.kamal/secrets | 23 + validator/.tool-versions | 2 - validator/.vscode/extensions.json | 3 - validator/Dockerfile | 39 +- validator/LICENSE | 2 +- validator/README.md | 53 +- validator/apis/__init__.py | 2 +- validator/config/deploy.yml | 100 + validator/poetry.lock | 1758 ----------------- validator/pyproject.toml | 167 -- validator/requirements.txt | 7 + 20 files changed, 433 insertions(+), 2054 deletions(-) delete mode 100644 validator/.github/workflows/build-and-deploy.yml create mode 100644 validator/.kamal/hooks/docker-setup.sample create mode 100644 validator/.kamal/hooks/post-deploy.sample create mode 100644 validator/.kamal/hooks/post-proxy-reboot.sample create mode 100644 validator/.kamal/hooks/pre-build.sample create mode 100644 validator/.kamal/hooks/pre-connect.sample create mode 100644 validator/.kamal/hooks/pre-deploy.sample create mode 100644 validator/.kamal/hooks/pre-proxy-reboot.sample create mode 100644 validator/.kamal/secrets delete mode 100644 validator/.tool-versions delete mode 100644 validator/.vscode/extensions.json create mode 100644 validator/config/deploy.yml delete mode 100644 validator/poetry.lock delete mode 100644 validator/pyproject.toml create mode 100644 validator/requirements.txt diff --git a/.github/workflows/deploy-staging.yml b/.github/workflows/deploy-staging.yml index 28fc6ea..cff31bc 100644 --- a/.github/workflows/deploy-staging.yml +++ b/.github/workflows/deploy-staging.yml @@ -105,6 +105,63 @@ jobs: ZENODO_CLIENT_SECRET: ${{ secrets.ZENODO_CLIENT_SECRET }} ZENODO_REDIRECT_URI: ${{ secrets.ZENODO_REDIRECT_URI }} + steps: + - uses: actions/checkout@v4 + + - uses: ruby/setup-ruby@v1 + with: + ruby-version: 3.3.1 + bundler-cache: true + + - run: gem install kamal + + - uses: webfactory/ssh-agent@v0.9.0 + with: + ssh-private-key: ${{ secrets.SSH_PRIVATE_KEY }} + + - name: Login to Azure Container Registry + uses: azure/docker-login@v1 + with: + login-server: ${{ secrets.KAMAL_REGISTRY_LOGIN_SERVER }} + username: ${{ secrets.KAMAL_REGISTRY_USERNAME }} + password: ${{ secrets.KAMAL_REGISTRY_PASSWORD }} + + - name: Set up Docker Buildx for cache + uses: docker/setup-buildx-action@v3 + + - run: kamal version + + # Setup kamal for the first time + # Might need to run `sudo usermod -aG docker $USER | newgrp docker | docker ps` to add the user to the docker group if the user is not already in the docker group + # - run: kamal setup + + # Login to the registry on the server + - run: kamal registry login + # - run: kamal registry login --verbose + + # Suggestion to use lock release and redeploy after reading comments from others. Deploying two builds could cause locking issues when the first is cancelled. + - run: kamal lock release + # - run: kamal lock release --verbose + + # Deploy the app for all other times + - run: kamal redeploy + # - run: kamal redeploy --verbose + + deploy-validator: + runs-on: ubuntu-latest + environment: stg + defaults: + run: + working-directory: validator + + env: + DOCKER_BUILDKIT: 1 + KAMAL_REGISTRY_LOGIN_SERVER: ${{ secrets.KAMAL_REGISTRY_LOGIN_SERVER }} + KAMAL_REGISTRY_USERNAME: ${{ secrets.KAMAL_REGISTRY_USERNAME }} + KAMAL_REGISTRY_PASSWORD: ${{ secrets.KAMAL_REGISTRY_PASSWORD }} + KAMAL_SERVER_IP: ${{ secrets.KAMAL_SERVER_IP }} + KAMAL_VALIDATOR_DOMAIN: ${{ secrets.KAMAL_VALIDATOR_DOMAIN }} + steps: - uses: actions/checkout@v4 diff --git a/validator/.github/workflows/build-and-deploy.yml b/validator/.github/workflows/build-and-deploy.yml deleted file mode 100644 index 9ed1915..0000000 --- a/validator/.github/workflows/build-and-deploy.yml +++ /dev/null @@ -1,44 +0,0 @@ -name: Build and push validator api image to Azure Container Registry - -on: - push: - branches: - - main - pull_request: - types: [closed] - branches: - - main - workflow_dispatch: - -concurrency: - group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} - cancel-in-progress: true - -jobs: - build: - name: Build and push Docker image - if: github.event_name == 'push' || (github.event_name == 'pull_request' && github.event.pull_request.merged == true) - runs-on: ubuntu-latest - env: - AZURE_REGISTRY_LOGIN_SERVER: ${{ secrets.AZURE_REGISTRY_LOGIN_SERVER }} - AZURE_REGISTRY_USERNAME: ${{ secrets.AZURE_REGISTRY_USERNAME }} - AZURE_REGISTRY_PASSWORD: ${{ secrets.AZURE_REGISTRY_PASSWORD }} - - steps: - - name: Checkout - uses: actions/checkout@v2 - - - name: Login to Azure Container Registry - uses: azure/docker-login@v1 - with: - login-server: ${{ secrets.AZURE_REGISTRY_LOGIN_SERVER }} - username: ${{ secrets.AZURE_REGISTRY_USERNAME }} - password: ${{ secrets.AZURE_REGISTRY_PASSWORD }} - - - name: Build and push Docker image - uses: docker/build-push-action@v2 - with: - context: . - file: ./Dockerfile - push: true - tags: ${{ secrets.AZURE_REGISTRY_LOGIN_SERVER }}/cwl-validator-api:latest diff --git a/validator/.kamal/hooks/docker-setup.sample b/validator/.kamal/hooks/docker-setup.sample new file mode 100644 index 0000000..2fb07d7 --- /dev/null +++ b/validator/.kamal/hooks/docker-setup.sample @@ -0,0 +1,3 @@ +#!/bin/sh + +echo "Docker set up on $KAMAL_HOSTS..." diff --git a/validator/.kamal/hooks/post-deploy.sample b/validator/.kamal/hooks/post-deploy.sample new file mode 100644 index 0000000..75efafc --- /dev/null +++ b/validator/.kamal/hooks/post-deploy.sample @@ -0,0 +1,14 @@ +#!/bin/sh + +# A sample post-deploy hook +# +# These environment variables are available: +# KAMAL_RECORDED_AT +# KAMAL_PERFORMER +# KAMAL_VERSION +# KAMAL_HOSTS +# KAMAL_ROLE (if set) +# KAMAL_DESTINATION (if set) +# KAMAL_RUNTIME + +echo "$KAMAL_PERFORMER deployed $KAMAL_VERSION to $KAMAL_DESTINATION in $KAMAL_RUNTIME seconds" diff --git a/validator/.kamal/hooks/post-proxy-reboot.sample b/validator/.kamal/hooks/post-proxy-reboot.sample new file mode 100644 index 0000000..1435a67 --- /dev/null +++ b/validator/.kamal/hooks/post-proxy-reboot.sample @@ -0,0 +1,3 @@ +#!/bin/sh + +echo "Rebooted kamal-proxy on $KAMAL_HOSTS" diff --git a/validator/.kamal/hooks/pre-build.sample b/validator/.kamal/hooks/pre-build.sample new file mode 100644 index 0000000..f87d811 --- /dev/null +++ b/validator/.kamal/hooks/pre-build.sample @@ -0,0 +1,51 @@ +#!/bin/sh + +# A sample pre-build hook +# +# Checks: +# 1. We have a clean checkout +# 2. A remote is configured +# 3. The branch has been pushed to the remote +# 4. The version we are deploying matches the remote +# +# These environment variables are available: +# KAMAL_RECORDED_AT +# KAMAL_PERFORMER +# KAMAL_VERSION +# KAMAL_HOSTS +# KAMAL_ROLE (if set) +# KAMAL_DESTINATION (if set) + +if [ -n "$(git status --porcelain)" ]; then + echo "Git checkout is not clean, aborting..." >&2 + git status --porcelain >&2 + exit 1 +fi + +first_remote=$(git remote) + +if [ -z "$first_remote" ]; then + echo "No git remote set, aborting..." >&2 + exit 1 +fi + +current_branch=$(git branch --show-current) + +if [ -z "$current_branch" ]; then + echo "Not on a git branch, aborting..." >&2 + exit 1 +fi + +remote_head=$(git ls-remote $first_remote --tags $current_branch | cut -f1) + +if [ -z "$remote_head" ]; then + echo "Branch not pushed to remote, aborting..." >&2 + exit 1 +fi + +if [ "$KAMAL_VERSION" != "$remote_head" ]; then + echo "Version ($KAMAL_VERSION) does not match remote HEAD ($remote_head), aborting..." >&2 + exit 1 +fi + +exit 0 diff --git a/validator/.kamal/hooks/pre-connect.sample b/validator/.kamal/hooks/pre-connect.sample new file mode 100644 index 0000000..18e61d7 --- /dev/null +++ b/validator/.kamal/hooks/pre-connect.sample @@ -0,0 +1,47 @@ +#!/usr/bin/env ruby + +# A sample pre-connect check +# +# Warms DNS before connecting to hosts in parallel +# +# These environment variables are available: +# KAMAL_RECORDED_AT +# KAMAL_PERFORMER +# KAMAL_VERSION +# KAMAL_HOSTS +# KAMAL_ROLE (if set) +# KAMAL_DESTINATION (if set) +# KAMAL_RUNTIME + +hosts = ENV["KAMAL_HOSTS"].split(",") +results = nil +max = 3 + +elapsed = Benchmark.realtime do + results = hosts.map do |host| + Thread.new do + tries = 1 + + begin + Socket.getaddrinfo(host, 0, Socket::AF_UNSPEC, Socket::SOCK_STREAM, nil, Socket::AI_CANONNAME) + rescue SocketError + if tries < max + puts "Retrying DNS warmup: #{host}" + tries += 1 + sleep rand + retry + else + puts "DNS warmup failed: #{host}" + host + end + end + + tries + end + end.map(&:value) +end + +retries = results.sum - hosts.size +nopes = results.count { |r| r == max } + +puts "Prewarmed %d DNS lookups in %.2f sec: %d retries, %d failures" % [ hosts.size, elapsed, retries, nopes ] diff --git a/validator/.kamal/hooks/pre-deploy.sample b/validator/.kamal/hooks/pre-deploy.sample new file mode 100644 index 0000000..1b280c7 --- /dev/null +++ b/validator/.kamal/hooks/pre-deploy.sample @@ -0,0 +1,109 @@ +#!/usr/bin/env ruby + +# A sample pre-deploy hook +# +# Checks the Github status of the build, waiting for a pending build to complete for up to 720 seconds. +# +# Fails unless the combined status is "success" +# +# These environment variables are available: +# KAMAL_RECORDED_AT +# KAMAL_PERFORMER +# KAMAL_VERSION +# KAMAL_HOSTS +# KAMAL_COMMAND +# KAMAL_SUBCOMMAND +# KAMAL_ROLE (if set) +# KAMAL_DESTINATION (if set) + +# Only check the build status for production deployments +if ENV["KAMAL_COMMAND"] == "rollback" || ENV["KAMAL_DESTINATION"] != "production" + exit 0 +end + +require "bundler/inline" + +# true = install gems so this is fast on repeat invocations +gemfile(true, quiet: true) do + source "https://rubygems.org" + + gem "octokit" + gem "faraday-retry" +end + +MAX_ATTEMPTS = 72 +ATTEMPTS_GAP = 10 + +def exit_with_error(message) + $stderr.puts message + exit 1 +end + +class GithubStatusChecks + attr_reader :remote_url, :git_sha, :github_client, :combined_status + + def initialize + @remote_url = `git config --get remote.origin.url`.strip.delete_prefix("https://github.com/") + @git_sha = `git rev-parse HEAD`.strip + @github_client = Octokit::Client.new(access_token: ENV["GITHUB_TOKEN"]) + refresh! + end + + def refresh! + @combined_status = github_client.combined_status(remote_url, git_sha) + end + + def state + combined_status[:state] + end + + def first_status_url + first_status = combined_status[:statuses].find { |status| status[:state] == state } + first_status && first_status[:target_url] + end + + def complete_count + combined_status[:statuses].count { |status| status[:state] != "pending"} + end + + def total_count + combined_status[:statuses].count + end + + def current_status + if total_count > 0 + "Completed #{complete_count}/#{total_count} checks, see #{first_status_url} ..." + else + "Build not started..." + end + end +end + + +$stdout.sync = true + +puts "Checking build status..." +attempts = 0 +checks = GithubStatusChecks.new + +begin + loop do + case checks.state + when "success" + puts "Checks passed, see #{checks.first_status_url}" + exit 0 + when "failure" + exit_with_error "Checks failed, see #{checks.first_status_url}" + when "pending" + attempts += 1 + end + + exit_with_error "Checks are still pending, gave up after #{MAX_ATTEMPTS * ATTEMPTS_GAP} seconds" if attempts == MAX_ATTEMPTS + + puts checks.current_status + sleep(ATTEMPTS_GAP) + checks.refresh! + end +rescue Octokit::NotFound + exit_with_error "Build status could not be found" +end diff --git a/validator/.kamal/hooks/pre-proxy-reboot.sample b/validator/.kamal/hooks/pre-proxy-reboot.sample new file mode 100644 index 0000000..061f805 --- /dev/null +++ b/validator/.kamal/hooks/pre-proxy-reboot.sample @@ -0,0 +1,3 @@ +#!/bin/sh + +echo "Rebooting kamal-proxy on $KAMAL_HOSTS..." diff --git a/validator/.kamal/secrets b/validator/.kamal/secrets new file mode 100644 index 0000000..6a64f4b --- /dev/null +++ b/validator/.kamal/secrets @@ -0,0 +1,23 @@ +# Secrets defined here are available for reference under registry/password, env/secret, builder/secrets, +# and accessories/*/env/secret in config/deploy.yml. All secrets should be pulled from either +# password manager, ENV, or a file. DO NOT ENTER RAW CREDENTIALS HERE! This file needs to be safe for git. + +# Option 1: Read secrets from the environment +KAMAL_REGISTRY_PASSWORD=$KAMAL_REGISTRY_PASSWORD +KAMAL_REGISTRY_USERNAME=$KAMAL_REGISTRY_USERNAME +KAMAL_REGISTRY_LOGIN_SERVER=$KAMAL_REGISTRY_LOGIN_SERVER + +# Kamal config +KAMAL_VALIDATOR_DOMAIN=$KAMAL_VALIDATOR_DOMAIN +KAMAL_SERVER_IP=$KAMAL_SERVER_IP + +# Option 2: Read secrets via a command +# RAILS_MASTER_KEY=$(cat config/master.key) + +# Option 3: Read secrets via kamal secrets helpers +# These will handle logging in and fetching the secrets in as few calls as possible +# There are adapters for 1Password, LastPass + Bitwarden +# +# SECRETS=$(kamal secrets fetch --adapter 1password --account my-account --from MyVault/MyItem KAMAL_REGISTRY_PASSWORD RAILS_MASTER_KEY) +# KAMAL_REGISTRY_PASSWORD=$(kamal secrets extract KAMAL_REGISTRY_PASSWORD $SECRETS) +# RAILS_MASTER_KEY=$(kamal secrets extract RAILS_MASTER_KEY $SECRETS) diff --git a/validator/.tool-versions b/validator/.tool-versions deleted file mode 100644 index 905042b..0000000 --- a/validator/.tool-versions +++ /dev/null @@ -1,2 +0,0 @@ -python 3.11.2 -poetry 1.4.1 \ No newline at end of file diff --git a/validator/.vscode/extensions.json b/validator/.vscode/extensions.json deleted file mode 100644 index 4861547..0000000 --- a/validator/.vscode/extensions.json +++ /dev/null @@ -1,3 +0,0 @@ -{ - "recommendations": ["njpwerner.autodocstring", "aaron-bond.better-comments", "ms-python.black-formatter", "visualstudioexptteam.vscodeintellicode", "visualstudioexptteam.intellicode-api-usage-examples", "davidanson.vscode-markdownlint", "ms-python.vscode-pylance", "ms-python.pylint", "ms-python.python", "donjayamanne.python-environment-manager", "kevinrose.vsc-python-indent"] -} diff --git a/validator/Dockerfile b/validator/Dockerfile index 4df54fa..24899ee 100644 --- a/validator/Dockerfile +++ b/validator/Dockerfile @@ -1,40 +1,23 @@ FROM python:3.10-alpine -# FROM ubuntu/python:stable - -EXPOSE 5000 WORKDIR /app -ENV POETRY_VERSION=1.3.2 - -# RUN apt-get update -# RUN sudo apt-get install cwltool +EXPOSE 5000 -RUN apk update +# Install system dependencies RUN apk add --no-cache gcc libffi-dev musl-dev -# RUN apk add --update cwltool - -RUN pip install "poetry==$POETRY_VERSION" -# COPY poetry.lock pyproject.toml ./ -COPY pyproject.toml . - -RUN poetry config virtualenvs.create false -RUN poetry install - -RUN pip install cwltool -RUN pip install cffconvert +# Install Python dependencies directly via pip +COPY requirements.txt . +RUN pip install --no-cache-dir -r requirements.txt +# Copy application files COPY apis ./apis -COPY config.py . -COPY app.py . - -# COPY entrypoint.sh . +COPY config.py app.py entrypoint.sh ./ -# RUN chmod +x entrypoint.sh +# Optional: Ensure the entrypoint script is executable +RUN chmod +x entrypoint.sh +# Set default entrypoint and command ENTRYPOINT [ "python3" ] - -CMD [ "app.py" ] - -# ENTRYPOINT ["./entrypoint.sh"] \ No newline at end of file +CMD [ "app.py" ] \ No newline at end of file diff --git a/validator/LICENSE b/validator/LICENSE index 1fe1fa8..01d0924 100644 --- a/validator/LICENSE +++ b/validator/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) 2022 AI-READI +Copyright (c) 2024 FAIR Data Innovations Hub Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/validator/README.md b/validator/README.md index 8090a26..c59339e 100644 --- a/validator/README.md +++ b/validator/README.md @@ -8,7 +8,6 @@ You will need the following installed on your system: - Python 3.8+ - [Pip](https://pip.pypa.io/en/stable/) -- [Poetry](https://python-poetry.org/) - [Docker](https://www.docker.com/) ### Setup @@ -29,56 +28,10 @@ If you would like to update the api, please follow the instructions below. conda activate cwl-validator-dev-env ``` -2. Install the dependencies for this package. We use [Poetry](https://python-poetry.org/) to manage the dependencies: +2. Install the dependencies for this package. ```bash - pip install poetry==1.3.2 - poetry install - ``` - - You can also use version 1.2.0 of Poetry, but you will need to run `poetry lock` after installing the dependencies. - -3. Add your environment variables. An example is provided at `.env.example` - - ```bash - cp .env.example .env - ``` - - Make sure to update the values in `.env` to match your local setup. - -4. Add your modifications and run the tests: - - ```bash - poetry run pytest - ``` - - If you need to add new python packages, you can use Poetry to add them: - - ```bash - poetry add - ``` - -5. Format the code: - - ```bash - poe format - ``` - -6. Check the code quality: - - ```bash - poe typecheck - poe lint - poe flake8 - ``` - - You can also use `poe precommit` to run both formatting and linting. - -7. Run the tests and check the code coverage: - - ```bash - poe test - poe test_with_capture # if you want to see console output + pip install -r requirements.txt ``` ## Running @@ -86,7 +39,7 @@ If you would like to update the api, please follow the instructions below. For developer mode: ```bash -poe dev +python3 app.py --host $HOST --port $PORT ``` or diff --git a/validator/apis/__init__.py b/validator/apis/__init__.py index 82a4f88..0627812 100644 --- a/validator/apis/__init__.py +++ b/validator/apis/__init__.py @@ -118,7 +118,7 @@ def post(self): except subprocess.CalledProcessError as e: stdout_clean = e.stdout match = re.search(r'jsonschema.exceptions.ValidationError:.*', e.stderr) - stderr_clean = match.group(0) if match else "Unknown error" + stderr_clean = match[0] if match else "Unknown error" return {"message": "invalid", "output": stdout_clean, "error": stderr_clean}, 400 except Exception as e: return {"message": "An unexpected error occurred", "error": str(e)}, 500 diff --git a/validator/config/deploy.yml b/validator/config/deploy.yml new file mode 100644 index 0000000..f98d813 --- /dev/null +++ b/validator/config/deploy.yml @@ -0,0 +1,100 @@ +# Name of your application. Used to uniquely configure containers. +service: codefair-validator + +# Name of the container image. +image: codefair-validator + +# Deploy to these servers. +servers: + web: + hosts: + - <%= ENV["KAMAL_SERVER_IP"] %> + # job: + # hosts: + # - 192.168.0.1 + # cmd: bin/jobs + +# Enable SSL auto certification via Let's Encrypt and allow for multiple apps on a single web server. +# Remove this section when using multiple web servers and ensure you terminate SSL at your load balancer. +# +# Note: If using Cloudflare, set encryption mode in SSL/TLS setting to "Full" to enable CF-to-app encryption. +proxy: + ssl: true + host: <%= ENV["KAMAL_VALIDATOR_DOMAIN"] %> + # Proxy connects to your container on port 80 by default. + app_port: 5000 + +# Credentials for your image host. +registry: + # Specify the registry server, if you're not using Docker Hub + # server: registry.digitalocean.com / ghcr.io / ... + server: <%= ENV["KAMAL_REGISTRY_LOGIN_SERVER"] %> + username: <%= ENV["KAMAL_REGISTRY_USERNAME"] %> + + # Always use an access token rather than real password (pulled from .kamal/secrets). + password: + - KAMAL_REGISTRY_PASSWORD + +# Configure builder setup. +builder: + arch: amd64 + +# Inject ENV variables into containers (secrets come from .kamal/secrets). +# +# env: +# secret: +# - xx +# clear: +# xx: xx + +# Aliases are triggered with "bin/kamal ". You can overwrite arguments on invocation: +# "bin/kamal logs -r job" will tail logs from the first server in the job section. +# +# aliases: +# shell: app exec --interactive --reuse "bash" + +# Use a different ssh user than root +# +ssh: + user: fairdataihub + +# Use a persistent storage volume. +# +# volumes: +# - "app_storage:/app/storage" + +# Bridge fingerprinted assets, like JS and CSS, between versions to avoid +# hitting 404 on in-flight requests. Combines all files from new and old +# version inside the asset_path. +# +# asset_path: /app/public/assets + +# Configure rolling deploys by setting a wait time between batches of restarts. +# +# boot: +# limit: 10 # Can also specify as a percentage of total hosts, such as "25%" +# wait: 2 + +# Use accessory services (secrets come from .kamal/secrets). +# +# accessories: +# db: +# image: mysql:8.0 +# host: 192.168.0.2 +# port: 3306 +# env: +# clear: +# MYSQL_ROOT_HOST: '%' +# secret: +# - MYSQL_ROOT_PASSWORD +# files: +# - config/mysql/production.cnf:/etc/mysql/my.cnf +# - db/production.sql:/docker-entrypoint-initdb.d/setup.sql +# directories: +# - data:/var/lib/mysql +# redis: +# image: valkey/valkey:8 +# host: 192.168.0.2 +# port: 6379 +# directories: +# - data:/data diff --git a/validator/poetry.lock b/validator/poetry.lock deleted file mode 100644 index 71a3eb9..0000000 --- a/validator/poetry.lock +++ /dev/null @@ -1,1758 +0,0 @@ -# This file is automatically @generated by Poetry and should not be changed by hand. - 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-[package.extras] -doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] -test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"] - -[metadata] -lock-version = "2.0" -python-versions = "^3.10" -content-hash = "61630ea064ca7ff166749421b6205c19316c6b2e4a7c4239a1dc8901a93ce45f" diff --git a/validator/pyproject.toml b/validator/pyproject.toml deleted file mode 100644 index ef72cb2..0000000 --- a/validator/pyproject.toml +++ /dev/null @@ -1,167 +0,0 @@ -[tool.poetry] - -name = "cwl-validation-api" -version = "0.1.0" -description = "API for CWL validation" - -license = "MIT" -authors = ["FAIR Data Innovations Hub "] - -readme = "README.md" -homepage = "https://codefair.io" -documentation = "https://docs.codefair.io" -repository = "https://github.com/fairdataihub/codefair" - - -keywords = [] -classifiers = [ - "Development Status :: 1 - Planning", - "Intended Audience :: Developers", - "License :: OSI Approved", - "License :: OSI Approved :: MIT License", - "Natural Language :: English", - "Operating System :: OS Independent", - "Programming Language :: Python", - "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.10", -] - - -[tool.poetry.dependencies] -python = "^3.10" - -# Core -Flask = "^2.3.2" -Flask-Cors = "^4.0.0" -flask-restx = "^1.1.0" -waitress = "^2.1.2" - - -# API Client -requests = "^2.31.0" - -# Database - -minilog = "*" -art = "^6.0" -jsonschema = "^4.17.3" -dicttoxml = "^1.7.16" -types-requests = "^2.30.0.0" - -pyflakes = "^3.0.1" -faker = "^18.11.2" - - -[tool.poetry.group.dev.dependencies] - -# Environment -python-dotenv = "^1.0.0" - -# Formatters -black = "^23.3.0" -tomli = "^2.0.1" -isort = "^5.12.0" - -# Linters -mypy = "^1.4.1" -pydocstyle = "^6.3.0" -pylint = "^2.17.4" -flake8 = "^6.0.0" - -# Testing -pytest = "^7.1" -pytest-describe = "^2.0" -pytest-expecter = "^3.0" -pytest-random = "*" -pytest-cov = "^3.0" -freezegun = "*" - -# Reports -coveragespace = "^6.0" - -# Documentation -mkdocs = "~1.3" -pygments = "^2.11.1" - -# Scripting -poethepoet = "^0.20.0" - -# Jupyter -# jupyter = "^1.0.0" - -# Types -types-python-dateutil = "^2.8.19.14" -types-waitress = "^2.1.4.9" - -# Environment - -[tool.poe.tasks] - -dev = "flask run --debug" -dev_docker = "docker run -p 5000:5000 fairhub-flask-api:local" - -freeze_dependencies = "pip list --format=freeze > requirements.txt" - -docs = "mkdocs serve" - -flake8 = "flake8 app.py" - -format_with_isort = "isort app.py" -format_with_black = "black app.py" - -format = ["format_with_isort", "format_with_black"] - -typecheck = "mypy app.py" - -pylint = "pylint app.py --rcfile=.pylint.ini" - -lint = ["flake8", "typecheck", "pylint"] - -precommit = ["format", "flake8", "typecheck", "pylint"] - -pytest = "pytest -rx -W ignore::DeprecationWarning" -pytest_with_capture = "pytest -s -W ignore::DeprecationWarning" - -jupyter = "jupyter notebook" - -export_requirements = "poetry export -f requirements.txt --output requirements.txt --without-hashes" -build_docker_image = "docker build --tag cwl-validate:local ." - -[tool.black] - -quiet = true - -[tool.isort] - -profile = "black" - -[tool.mypy] - -ignore_missing_imports = true -no_implicit_optional = true -check_untyped_defs = true - -cache_dir = ".cache/mypy/" - -[tool.pytest.ini_options] - -addopts = """ ---strict-markers - --r sxX ---show-capture=log - ---cov-report=html ---cov-report=term-missing:skip-covered ---no-cov-on-fail -""" - -filterwarnings = ["ignore", "default:::flask_restx.*"] - -cache_dir = ".cache/pytest/" - -markers = [] - -[build-system] -requires = ["poetry-core>=1.3.2"] -build-backend = "poetry.core.masonry.api" diff --git a/validator/requirements.txt b/validator/requirements.txt new file mode 100644 index 0000000..c69611f --- /dev/null +++ b/validator/requirements.txt @@ -0,0 +1,7 @@ +Flask +flask-restx +Flask-Cors +python-dotenv +waitress +cwltool +cffconvert From aba85b38cf791108bed2e07050a5767fef13b143 Mon Sep 17 00:00:00 2001 From: Sanjay Soundarajan Date: Fri, 15 Nov 2024 17:41:39 -0800 Subject: [PATCH 04/42] =?UTF-8?q?=F0=9F=91=B7=20ci:=20add=20validator=20he?= =?UTF-8?q?althcheck?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- validator/apis/__init__.py | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/validator/apis/__init__.py b/validator/apis/__init__.py index 0627812..e3d52e7 100644 --- a/validator/apis/__init__.py +++ b/validator/apis/__init__.py @@ -23,7 +23,14 @@ def get(self): return "Server active!" +@api.route("/up", endpoint="up") +class Up(Resource): + """Health check for kamal""" + @api.response(200, "Success") + def get(self): + """Returns a simple message""" + return ":)" @api.route("/validate-cwl", endpoint="validate-cwl") class ValidateCWL(Resource): From 242bde1dd8893d0fb6aa11ac7204cc1fb41f06ae Mon Sep 17 00:00:00 2001 From: Sanjay Soundarajan Date: Fri, 15 Nov 2024 17:42:40 -0800 Subject: [PATCH 05/42] =?UTF-8?q?=F0=9F=91=B7=20ci:=20add=20validator=20de?= =?UTF-8?q?ploy=20for=20prod?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .github/workflows/deploy-main.yml | 57 +++++++++++++++++++++++++++++++ 1 file changed, 57 insertions(+) diff --git a/.github/workflows/deploy-main.yml b/.github/workflows/deploy-main.yml index 398881b..a487d2a 100644 --- a/.github/workflows/deploy-main.yml +++ b/.github/workflows/deploy-main.yml @@ -105,6 +105,63 @@ jobs: ZENODO_CLIENT_SECRET: ${{ secrets.ZENODO_CLIENT_SECRET }} ZENODO_REDIRECT_URI: ${{ secrets.ZENODO_REDIRECT_URI }} + steps: + - uses: actions/checkout@v4 + + - uses: ruby/setup-ruby@v1 + with: + ruby-version: 3.3.1 + bundler-cache: true + + - run: gem install kamal + + - uses: webfactory/ssh-agent@v0.9.0 + with: + ssh-private-key: ${{ secrets.SSH_PRIVATE_KEY }} + + - name: Login to Azure Container Registry + uses: azure/docker-login@v1 + with: + login-server: ${{ secrets.KAMAL_REGISTRY_LOGIN_SERVER }} + username: ${{ secrets.KAMAL_REGISTRY_USERNAME }} + password: ${{ secrets.KAMAL_REGISTRY_PASSWORD }} + + - name: Set up Docker Buildx for cache + uses: docker/setup-buildx-action@v3 + + - run: kamal version + + # Setup kamal for the first time + # Might need to run `sudo usermod -aG docker $USER | newgrp docker | docker ps` to add the user to the docker group if the user is not already in the docker group + # - run: kamal setup + + # Login to the registry on the server + - run: kamal registry login + # - run: kamal registry login --verbose + + # Suggestion to use lock release and redeploy after reading comments from others. Deploying two builds could cause locking issues when the first is cancelled. + - run: kamal lock release + # - run: kamal lock release --verbose + + # Deploy the app for all other times + - run: kamal redeploy + # - run: kamal redeploy --verbose + + deploy-validator: + runs-on: ubuntu-latest + environment: stg + defaults: + run: + working-directory: validator + + env: + DOCKER_BUILDKIT: 1 + KAMAL_REGISTRY_LOGIN_SERVER: ${{ secrets.KAMAL_REGISTRY_LOGIN_SERVER }} + KAMAL_REGISTRY_USERNAME: ${{ secrets.KAMAL_REGISTRY_USERNAME }} + KAMAL_REGISTRY_PASSWORD: ${{ secrets.KAMAL_REGISTRY_PASSWORD }} + KAMAL_SERVER_IP: ${{ secrets.KAMAL_SERVER_IP }} + KAMAL_VALIDATOR_DOMAIN: ${{ secrets.KAMAL_VALIDATOR_DOMAIN }} + steps: - uses: actions/checkout@v4 From 303824b526e6ae4f6c79717e6ebb128594c450a4 Mon Sep 17 00:00:00 2001 From: slugb0t Date: Thu, 21 Nov 2024 17:12:11 -0800 Subject: [PATCH 06/42] refactor: :recycle: update codefair name --- ui/server/api/[owner]/[repo]/cwl-validation/rerun.post.ts | 2 +- ui/server/api/[owner]/[repo]/license/custom_title.put.ts | 2 +- ui/server/api/[owner]/[repo]/release/zenodo/index.post.ts | 2 +- ui/server/api/[owner]/[repo]/rerun.post.ts | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/ui/server/api/[owner]/[repo]/cwl-validation/rerun.post.ts b/ui/server/api/[owner]/[repo]/cwl-validation/rerun.post.ts index 6234251..703ad6d 100644 --- a/ui/server/api/[owner]/[repo]/cwl-validation/rerun.post.ts +++ b/ui/server/api/[owner]/[repo]/cwl-validation/rerun.post.ts @@ -77,7 +77,7 @@ export default defineEventHandler(async (event) => { if ( issue.user?.login !== "codefair-test[bot]" && issue.user?.login !== "codefair-staging[bot]" && - issue.user?.login !== "codefair-app[bot]" + issue.user?.login !== "codefair-io[bot]" ) { throw createError({ statusCode: 400, diff --git a/ui/server/api/[owner]/[repo]/license/custom_title.put.ts b/ui/server/api/[owner]/[repo]/license/custom_title.put.ts index 91e2191..690e2e7 100644 --- a/ui/server/api/[owner]/[repo]/license/custom_title.put.ts +++ b/ui/server/api/[owner]/[repo]/license/custom_title.put.ts @@ -99,7 +99,7 @@ export default defineEventHandler(async (event) => { if ( issue.user?.login !== "codefair-test[bot]" && issue.user?.login !== "codefair-staging[bot]" && - issue.user?.login !== "codefair-app[bot]" + issue.user?.login !== "codefair-io[bot]" ) { throw createError({ statusCode: 400, diff --git a/ui/server/api/[owner]/[repo]/release/zenodo/index.post.ts b/ui/server/api/[owner]/[repo]/release/zenodo/index.post.ts index f86ed10..b8deac1 100644 --- a/ui/server/api/[owner]/[repo]/release/zenodo/index.post.ts +++ b/ui/server/api/[owner]/[repo]/release/zenodo/index.post.ts @@ -246,7 +246,7 @@ export default defineEventHandler(async (event) => { if ( issue.user?.login !== "codefair-test[bot]" && issue.user?.login !== "codefair-staging[bot]" && - issue.user?.login !== "codefair-app[bot]" + issue.user?.login !== "codefair-io[bot]" ) { throw createError({ statusCode: 400, diff --git a/ui/server/api/[owner]/[repo]/rerun.post.ts b/ui/server/api/[owner]/[repo]/rerun.post.ts index c5d216c..00aaa06 100644 --- a/ui/server/api/[owner]/[repo]/rerun.post.ts +++ b/ui/server/api/[owner]/[repo]/rerun.post.ts @@ -65,7 +65,7 @@ export default defineEventHandler(async (event) => { if ( issue.user?.login !== "codefair-test[bot]" && issue.user?.login !== "codefair-staging[bot]" && - issue.user?.login !== "codefair-app[bot]" + issue.user?.login !== "codefair-io[bot]" ) { throw createError({ statusCode: 400, From 96d4e82a8b5d643d2ff724afdb5fe0a00dde0b34 Mon Sep 17 00:00:00 2001 From: Dorian Portillo Date: Mon, 2 Dec 2024 12:17:27 -0800 Subject: [PATCH 07/42] =?UTF-8?q?feat:=20=E2=9C=A8=20Metadata=20+=20licens?= =?UTF-8?q?e=20validators=20+=20bug=20patches=20(#107)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * merge: :twisted_rightwards_arrows: merge main to staging * refactor: ♻️ 🐛 Codefair 3.1.0 (#89) * fix: :bug: patch removing pull_request.closed bug on metadata pr merge * fix: :bug: don't update firstPublished in the codemeta file + better logs * fix: :bug: patch error on reading db entry when it doesn't exist * chore: :loud_sound: better log on successful Zenodo publish * style: :art: margins between text and icon * feat: :sparkles: links to the list of tools used for codefair in /codefair * refactor: :sparkles: :recycle: abstract the license validation fn * doc: :bookmark: update changelog * feat: :sparkles: :recycle: abstraction to zenodo workflow * wip: :construction: abstracting zenodo workflow * feat: :sparkles: add help link in the Zenodo release page * refactor: :recycle: :sparkles: abstract out github release functions * refactor: :loud_sound: :recycle: improve error tracing in metadata file * chore: :hammer: remove todo * refactor: :sparkles: :recycle: abstracted Zenodo workflow (bot) * wip: :construction: save custom license content when no assertion is provided * ✨ feat: add support for custom licenses (#90) * ✨ feat: add support for custom licenses * 🐛 fix: reset citation license field * 🐛 fix: update zenodo workflow for custom licenses * fix: :bug: license is valid with custom license * feat: :sparkles: custom license template * ✨ feat: update codemeta, license and cwl ui paths (#91) * ✨ feat: update meta paths for consistency * 🚚 fix: updatel icense request path * ✨ feat: add support for custom license title (#92) * refactor: :recycle: :sparkles: new patches for license, cwl, metadata UI's * refactor: :sparkles: :recycle: apply migrations from UI to bot * feat: :sparkles: request custom license title from user * refactor: :recycle: hide message box when custom license title is blank * refactor: :recycle: issue dashboard requests custom title * feat: ✨ Saving custom title (#93) * feat: :sparkles: save custom title option * refactor: :recyle: reuse saveLicenseDraft for storing custom license title * refactor: :recycle: join draft and save title buttons together * refactor: :recycle: use naive-ui's properties for styling * chore: :hammer: remove typo * chore: :hammer: remove unused variables * feat: :sparkles: toasts for custom title saved button * refactor: :recycle: function rename * feat: :sparkles: create Zenodo metadata fn handles custom licenses * feat: :sparkles: custom license reference for archival workflow * refactor: :recycle: stop creating identifiers for new db entries * refactor: :recycle: :bug: revert allowing custom licenses for zenodo * refactor: ♻️ Custom License Support (#94) * refactor: :recycle: :sparkles: custom title saved updates dashboard, disable create release btn when custom license * refactor: :recycle: block progress of fair release if license is custom * feat: :sparkles: listener for when custom license title is saved through UI * feat: :sparkles: prevent fair release if not fair compliant * refactor: :recycle: improve license validation and update template text for custom licenses * refactor: :recycle: re-render issue from ui side * refactor: :recycle: update to message explaining custom licenses * db calls running in parallel * fix: :bug: prevent Zendo section from being seen when the license is custom * fix: :bug: trim license content before comparison --------- Co-authored-by: Sanjay Soundarajan * refactor: :recycle: safety checks for protected middleware * refacotr: :recycle: update protectRoute to redirect to login when no user or session * feat: :fix: redirect to login if not signed in * refactor: :recycle: remove import * chore: :loud_sound: :hammer: remove logs * docs: :memo: update changelog * fix: :bug: check license content all times * fix: :bug: update on zenodo ui page * feat: :sparkles: delete branch after pr has been closed/merged * chore: :hammer: spacing in changelog * wip: :construction: individual validation requests for license and metadata * feat: :sparkles: license validation endpoint * wip: :construction: creating updated metadata validation * wip: :construction: patches for metadata revalidation workflow * wip: :construction: validation for codemeta * doc: :bookmark: jsdoc comments on fns * fix: 🐛 template renderer will stop using old links (#99) * fix: :bug: rerender template will stop using old links * doc: :memo: update CHANGELOG * doc: :memo: update metadata * fix: :bug: preserve authors and contributors from codemeta * feat: :sparkles: re-validated codemeta from repo dashboard * fix: :bug: await metadata validation * feat: :sparkles: codemeta validation extended with microservice validator * refactor: :recycle: update timestamps to be unix format * feat: :sparkles: clean privatekey env before use * refactor: :recycle: update cwl validation endpoint * wip: :construction: send validation message to db * feat: :sparkles: create migrations for metadata validation messages * wip: :construction: creating json schema for codemeta.json validations * 👷 ci: setup deployment environments (#101) * 👷 ci: setup for staging env (#103) Co-authored-by: Sanjay Soundarajan Co-authored-by: slugb0t fix: 🐛 template renderer will stop using old links (#99) * fix: :bug: adjust env variables used after env changes * 👷 ci: cleanup dockerfile * feat: :sparkles: codemeta schema first draft * 👷 ci: cleanup dockerfile * 👷 ci: cleanup dockerfile * 👷 ci: cleanup dockerfile * 👷 ci: setup for staging env * 👷 ci: setup for staging env * 👷 ci: setup for staging env * 👷 ci: setup for staging env * 👷 ci: cleanup dockerfile * 👷 ci: fix staging deploys (#104) * wip: :construction: abstracting cwl workflow * refactor: :recycle: update codemeta schema to validate against the raw codemeta.json files * refactor: :recycle: update codemeta schema for additional fields * feat: :sparkles: validating raw content of codemeta.json file for 3.0 * refactor: :recycle: create required fields for codemeta schema * wip: :construction: testing validation responses for db * handle codemeta.json 3.0 and 2.0 versioning * fix: :bug: correct branch watch for staging deployment action * doc: :bookmark: update changelog for 3.2.0 release * feat: :sparkles: align bot prisma with ui * fix: :bug: bug patch for cwl workflow * feat: :sparkles: metadata workflow update * refactor: :recycle: preserving authors and contributors * wip: :construction: update the metadata workflow after discussions * fix: :bug: don't create cwlobject twice * refactor: :recycle: send 200 status when invalid codemeta * refactor: :recycle: update codemeta validation schema * refactor: :recycle: do not revalidate metadata files for push events unless metadata files are updated themselves * wip: :construction: seperate rerun validation with regather information * wip: :construction: remove command from issue dashboard if error occurs (allows retry) * refactor: :recycle: update the issue body after successful validation (remove the command from the issue body) * refactor: :recycle: add additional key to codemeta schema * refactor: :recycle: remove the regather options from the UI as validation is still needed when regathering * fix: :bug: pr button updated with new links * fix: :bug: patch variable declaration not in scope * refactor: :recycle: update on the dropdown icons * refactor: :recycle: update the keys of the cwl object * refactor: :recycle: update the getcwlfiles function --------- Co-authored-by: Sanjay Soundarajan --- CHANGELOG.md | 11 + bot/api/github/webhooks.js | 3 +- bot/archival/index.js | 3 +- bot/cwl/index.js | 168 ++--- bot/index.js | 558 ++++++++++------ bot/license/index.js | 4 +- bot/main.js | 3 +- bot/metadata/index.js | 596 +++++++++++++----- .../migration.sql | 3 + bot/prisma/schema.prisma | 219 +++---- ui/pages/dashboard/[owner]/[repo]/index.vue | 65 +- .../migration.sql | 3 + ui/prisma/schema.prisma | 219 +++---- .../[repo]/license/custom_title.put.ts | 1 - ui/server/api/[owner]/[repo]/rerun.post.ts | 31 +- validator/apis/__init__.py | 137 +++- validator/codemeta-schema.json | 288 +++++++++ validator/requirements.txt | 1 + 18 files changed, 1615 insertions(+), 698 deletions(-) create mode 100644 bot/prisma/migrations/20241114193552_metadata_validation_messages/migration.sql create mode 100644 ui/prisma/migrations/20241114193552_metadata_validation_messages/migration.sql create mode 100644 validator/codemeta-schema.json diff --git a/CHANGELOG.md b/CHANGELOG.md index 882c4ee..5e91e6b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,17 @@ All notable changes the Codefair App will be documented in this file. The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html). +## v3.2.0 - 11-22-2024 + +### Added + +- Introducde metadata and license validation capabilities, allows for re-validation of metadata files and licenses through the UI. +- Add support for validation codemeta.json and CITATION.cff files using a new schema and validation endpoints. + +## Fixed + +- Fixed issues related to filtering what is consider a cwl file in the repository. + ## v3.1.1 - 11-12-2024 ### Fixed diff --git a/bot/api/github/webhooks.js b/bot/api/github/webhooks.js index 0992d6c..c419a1b 100644 --- a/bot/api/github/webhooks.js +++ b/bot/api/github/webhooks.js @@ -2,11 +2,12 @@ const { createNodeMiddleware, createProbot } = require("probot"); const app = require("../../index.js"); +const privateKey = process.env.PRIVATE_KEY.replace(/\\n/g, "\n"); const probot = createProbot({ overrides: { appId: process.env.APP_ID, - privateKey: process.env.GH_APP_PRIVATE_KEY.replace(/\\n/g, "\n"), + privateKey, secret: process.env.WEBHOOK_SECRET, }, }); diff --git a/bot/archival/index.js b/bot/archival/index.js index 7204ac9..d51cc3f 100644 --- a/bot/archival/index.js +++ b/bot/archival/index.js @@ -386,7 +386,7 @@ export async function createZenodoMetadata(codemetadata, repository) { // creators: zenodoCreators, // access_right: zenodoMetadata.zenodo_metadata.accessRight, // publication_date: new_date, - // // TODO: Ask user for language + // // rights: [ // { // description: {en: existingLicense?.license_content}, @@ -467,7 +467,6 @@ export async function uploadReleaseAssetsToZenodo( repository, tagVersion, ) { - // TODO: Add try catches for each fetch const startTime = performance.now(); if (draftReleaseAssets.length > 0) { for (const asset of draftReleaseAssets) { diff --git a/bot/cwl/index.js b/bot/cwl/index.js index 8d0a73f..5c7c3a3 100644 --- a/bot/cwl/index.js +++ b/bot/cwl/index.js @@ -23,6 +23,11 @@ export function getCWLFiles(context, owner, repoName) { consola.info("Checking for CWL files in the repository..."); const cwlFiles = []; + const cwlObject = { + contains_cwl_files: false, + files: [], + removed_files: [], + } const searchDirectory = async function (path) { try { @@ -33,9 +38,8 @@ export function getCWLFiles(context, owner, repoName) { }); for (const file of repoContent.data) { - const fileSplit = file.name.split("."); - if (file.type === "file" && fileSplit.includes("cwl")) { - cwlFiles.push(file); + if (file.type === "file" && file.name.endsWith(".cwl")) { + cwlObject.files.push(file); } if (file.type === "dir") { await searchDirectory(file.path); @@ -44,7 +48,7 @@ export function getCWLFiles(context, owner, repoName) { } catch (error) { if (error.status === 404) { // Repository is empty - resolve(cwlFiles); + resolve(cwlObject); return; } consola.error( @@ -57,8 +61,23 @@ export function getCWLFiles(context, owner, repoName) { // Call the async function and handle its promise searchDirectory("") - .then(() => { - resolve(cwlFiles); + .then(async () => { + // Check if the db entry exists for the repository + const existingCWL = await dbInstance.cwlValidation.findUnique({ + where: { + repository_id: context.payload.repository.id, + } + }); + + if (existingCWL) { + if (existingCWL?.contains_cwl_files) { + cwlObject.contains_cwl_files = existingCWL.contains_cwl_files; + } + } + + cwlObject.contains_cwl_files = cwlFiles.files.length > 0; + + resolve(cwlObject); }) .catch(reject); }); @@ -71,7 +90,7 @@ export function getCWLFiles(context, owner, repoName) { */ export async function validateCWLFile(downloadUrl) { try { - const response = await fetch("https://cwl-validate.codefair.io/validate", { + const response = await fetch("https://cwl-validate.codefair.io/validate-cwl", { body: JSON.stringify({ file_path: downloadUrl, }), @@ -164,73 +183,76 @@ export async function applyCWLTemplate( } consola.start("Validating CWL files for", repository.name); - // Validate each CWL file from list - for (const file of subjects.cwl.files) { - const fileSplit = file.name.split("."); - - if (fileSplit.includes("cwl")) { - const downloadUrl = - file?.commitId && !privateRepo - ? file.download_url.replace("/main/", `/${file.commitId}/`) - : file.download_url; // Replace the branch with the commit id if commit id is available and the repo is public - - const [isValidCWL, validationMessage] = - await validateCWLFile(downloadUrl); - - if (!isValidCWL && validOverall) { - // Overall status of CWL validations is invalid - validOverall = false; - } - - if (!isValidCWL) { - failedCount += 1; - } - - const [modifiedValidationMessage, lineNumber1, lineNumber2] = - replaceRawGithubUrl(validationMessage, downloadUrl, file.html_url); - - // Add the line numbers to the URL if they exist - if (lineNumber1) { - file.html_url += `#L${lineNumber1}`; - if (lineNumber2) { - file.html_url += `-L${lineNumber2}`; + // Validate each CWL file from list\ + consola.info(`Validating ${JSON.stringify(subjects.cwl)} CWL files`); + if (subjects.cwl.files.length > 0) { + for (const file of subjects.cwl.files) { + const fileSplit = file.name.split("."); + + if (fileSplit.includes("cwl")) { + const downloadUrl = + file?.commitId && !privateRepo + ? file.download_url.replace("/main/", `/${file.commitId}/`) + : file.download_url; // Replace the branch with the commit id if commit id is available and the repo is public + + const [isValidCWL, validationMessage] = + await validateCWLFile(downloadUrl); + + if (!isValidCWL && validOverall) { + // Overall status of CWL validations is invalid + validOverall = false; } - } - - // Create a new object for the file entry to be added to the db - const newDate = new Date(); - cwlFiles.push({ - href: file.html_url, - last_modified: newDate, - last_validated: newDate, - path: file.path, - validation_message: modifiedValidationMessage, - validation_status: isValidCWL ? "valid" : "invalid", - }); - - // Apply the validation file count to the analytics collection on the db - const analyticsCollection = dbInstance.analytics; - await analyticsCollection.upsert({ - create: { - cwl_validated_file_count: 1, // Start count at 1 when creating - id: repository.id, // Create a new record if it doesn't exist - }, - update: { - cwl_validated_file_count: { - increment: 1, + + if (!isValidCWL) { + failedCount += 1; + } + + const [modifiedValidationMessage, lineNumber1, lineNumber2] = + replaceRawGithubUrl(validationMessage, downloadUrl, file.html_url); + + // Add the line numbers to the URL if they exist + if (lineNumber1) { + file.html_url += `#L${lineNumber1}`; + if (lineNumber2) { + file.html_url += `-L${lineNumber2}`; + } + } + + // Create a new object for the file entry to be added to the db + const newDate = Math.floor(Date.now() / 1000); + cwlFiles.push({ + href: file.html_url, + last_modified: newDate, + last_validated: newDate, + path: file.path, + validation_message: modifiedValidationMessage, + validation_status: isValidCWL ? "valid" : "invalid", + }); + + // Apply the validation file count to the analytics collection on the db + const analyticsCollection = dbInstance.analytics; + await analyticsCollection.upsert({ + create: { + cwl_validated_file_count: 1, // Start count at 1 when creating + id: repository.id, // Create a new record if it doesn't exist }, - }, - where: { - id: repository.id, - }, - }); - - // Add the file to the table content of the issue dashboard - tableContent += `| ${file.path} | ${isValidCWL ? "✔️" : "❌"} |\n`; - - consola.success( - `File: ${file.path} is ${isValidCWL ? "valid" : "invalid"}`, - ); + update: { + cwl_validated_file_count: { + increment: 1, + }, + }, + where: { + id: repository.id, + }, + }); + + // Add the file to the table content of the issue dashboard + tableContent += `| ${file.path} | ${isValidCWL ? "✔️" : "❌"} |\n`; + + consola.success( + `File: ${file.path} is ${isValidCWL ? "valid" : "invalid"}`, + ); + } } } @@ -238,7 +260,7 @@ export async function applyCWLTemplate( if (!existingCWL) { await dbInstance.cwlValidation.create({ data: { - contains_cwl_files: subjects.cwl.contains_cwl, + contains_cwl_files: subjects.cwl.contains_cwl_files, files: cwlFiles, identifier, overall_status: validOverall ? "valid" : "invalid", diff --git a/bot/index.js b/bot/index.js index 5d120e2..6cf3010 100644 --- a/bot/index.js +++ b/bot/index.js @@ -4,6 +4,7 @@ import * as express from "express"; import { consola } from "consola"; import { renderIssues, createIssue } from "./utils/renderer/index.js"; import dbInstance from "./db.js"; +import yaml from "js-yaml"; import { checkEnvVariable, isRepoEmpty, @@ -15,12 +16,12 @@ import { getReleaseById, downloadRepositoryZip, } from "./utils/tools/index.js"; -import { checkForLicense } from "./license/index.js"; +import { checkForLicense, validateLicense } from "./license/index.js"; import { checkForCitation } from "./citation/index.js"; import { checkForCodeMeta } from "./codemeta/index.js"; import { getCWLFiles, applyCWLTemplate } from "./cwl/index.js"; import { getZenodoDepositionInfo, createZenodoMetadata, updateZenodoMetadata, uploadReleaseAssetsToZenodo, parseZenodoInfo, getZenodoToken, publishZenodoDeposition, updateGitHubRelease } from "./archival/index.js"; -import { validateMetadata, getCitationContent, getCodemetaContent, updateMetadataIdentifier } from "./metadata/index.js"; +import { validateMetadata, getCitationContent, getCodemetaContent, updateMetadataIdentifier, convertCodemetaForDB, convertCitationForDB, gatherMetadata, convertDateToUnix, applyDbMetadata, applyCodemetaMetadata, applyCitationMetadata } from "./metadata/index.js"; checkEnvVariable("GH_APP_NAME"); checkEnvVariable("CODEFAIR_APP_DOMAIN"); @@ -128,23 +129,22 @@ export default async (app, { getRouter }) => { owner, repository.name, ); - const cwl = await getCWLFiles(context, owner, repository.name); + const cwlObject = await getCWLFiles(context, owner, repository.name); - const cwlObject = { - contains_cwl: cwl.length > 0 || false, - files: cwl, - removed_files: [], - }; + // const cwlObject = { + // contains_cwl: cwl.length > 0 || false, + // files: cwl, + // removed_files: [], + // }; - // If existing cwl validation exists, update the contains_cwl value - // If existing cwl validation exists, update the contains_cwl value - const cwlExists = await dbInstance.cwlValidation.findUnique({ - where: { repository_id: repository.id }, - }); + // // If existing cwl validation exists, update the contains_cwl value + // const cwlExists = await dbInstance.cwlValidation.findUnique({ + // where: { repository_id: repository.id }, + // }); - if (cwlExists?.contains_cwl_files) { - cwlObject.contains_cwl = cwlExists.contains_cwl_files; - } + // if (cwlExists?.contains_cwl_files) { + // cwlObject.contains_cwl = cwlExists.contains_cwl_files; + // } const subjects = { citation, @@ -343,12 +343,16 @@ export default async (app, { getRouter }) => { // Grab the commits being pushed const { commits } = context.payload; - let cwl = []; + let cwlObject = { + contains_cwl_files: false, + files: [], + removed_files: [], + } let license = await checkForLicense(context, owner, repository.name); let citation = await checkForCitation(context, owner, repository.name); let codemeta = await checkForCodeMeta(context, owner, repository.name); if (fullCodefairRun) { - cwl = await getCWLFiles(context, owner, repository.name); + cwlObject = await getCWLFiles(context, owner, repository.name); } // Check if any of the commits added a LICENSE, CITATION, or codemeta file @@ -433,15 +437,13 @@ export default async (app, { getRouter }) => { }); cwlFile.data.commitId = file.commitId; - cwl.push(cwlFile.data); + cwlObject.files.push(cwlFile.data); } } - const cwlObject = { - contains_cwl: cwl.length > 0 || false, - files: cwl.filter(file => !removedCWLFiles.includes(file.path)), - removed_files: removedCWLFiles, - }; + cwlObject.contains_cwl_files = cwlObject.files.length > 0 || false; + cwlObject.files = cwl.filter(file => !removedCWLFiles.includes(file.path)); + cwlObject.removed_files = removedCWLFiles; const cwlExists = await db.cwlValidation.findUnique({ where: { @@ -451,7 +453,7 @@ export default async (app, { getRouter }) => { // Does the repository already contain CWL files if (cwlExists) { - cwlObject.contains_cwl = cwlExists.contains_cwl_files; + cwlObject.contains_cwl_files = cwlExists.contains_cwl_files; } const subjects = { @@ -482,6 +484,7 @@ export default async (app, { getRouter }) => { const definedPRTitles = [ "feat: ✨ LICENSE file added", "feat: ✨ Add code metadata files", + "feat: ✨ Update code metadata files", ]; const emptyRepo = await isRepoEmpty(context, owner, repository.name); @@ -559,12 +562,12 @@ export default async (app, { getRouter }) => { // Append the PR badge after the "LICENSE ❌" section issueBody = issueBody.replace( - `## LICENSE ❌\n\nTo make your software reusable a license file is expected at the root level of your repository. If you would like Codefair to add a license file, click the \"Add license\" button below to go to our interface for selecting and adding a license. You can also add a license file yourself and Codefair will update the the dashboard when it detects it on the main branch.\n\n[![License](https://img.shields.io/badge/Add_License-dc2626.svg)](${CODEFAIR_DOMAIN}/add/license/${response.identifier})`, - `## LICENSE ❌\n\nTo make your software reusable a license file is expected at the root level of your repository. If you would like Codefair to add a license file, click the "Add license" button below to go to our interface for selecting and adding a license. You can also add a license file yourself and Codefair will update the the dashboard when it detects it on the main branch.\n\n[![License](https://img.shields.io/badge/Add_License-dc2626.svg)](${CODEFAIR_DOMAIN}/add/license/${response.identifier})\n\n${licensePRBadge}` + `(${CODEFAIR_DOMAIN}/dashboard/${owner}/${repository.name}/edit/license)`, + `(${CODEFAIR_DOMAIN}/dashboard/${owner}/${repository.name}/edit/license)\n\n${licensePRBadge}` ); } - if (prTitle === "feat: ✨ Add code metadata files") { + if (prTitle === "feat: ✨ Add code metadata files" || prTitle === "feat: ✨ Update code metadata files") { const response = await db.codeMetadata.update({ data: { pull_request_url: prLink, @@ -578,17 +581,19 @@ export default async (app, { getRouter }) => { consola.error("Error updating the code metadata PR URL"); return; } - // Use a regular expression to match the "Metadata ❌" section - const metadataSectionRegex = /## Metadata ❌\n\nTo make your software FAIR, a CITATION\.cff and codemeta\.json are expected at the root level of your repository\. These files are not found in the repository\. If you would like Codefair to add these files, click the "Add metadata" button below to go to our interface for providing metadata and generating these files\.\n\n\[!\[Metadata\]\(https:\/\/img\.shields\.io\/badge\/Add_Metadata-dc2626\.svg\)\]\(([^)]+)\)/; // Define the replacement string with the new metadata PR badge + consola.info("Updating the metadata PR badge"); + consola.info("Owner:", owner); + consola.info("Repository:", repository.name); const metadataPRBadge = `A pull request for the metadata files is open. You can view the pull request:\n\n[![Metadata](https://img.shields.io/badge/View_PR-6366f1.svg)](${prLink})`; // Perform the replacement while preserving the identifier issueBody = issueBody.replace( - metadataSectionRegex, - `## Metadata ❌\n\nTo make your software FAIR, a CITATION.cff and codemeta.json are expected at the root level of your repository. These files are not found in the repository. If you would like Codefair to add these files, click the "Add metadata" button below to go to our interface for providing metadata and generating these files.\n\n[![Metadata](https://img.shields.io/badge/Add_Metadata-dc2626.svg)](${CODEFAIR_DOMAIN}/add/code-metadata/${response.identifier})\n\n${metadataPRBadge}` + `(${CODEFAIR_DOMAIN}/dashboard/${owner}/${repository.name}/edit/code-metadata)`, + `(${CODEFAIR_DOMAIN}/dashboard/${owner}/${repository.name}/edit/code-metadata)\n\n${metadataPRBadge}` ); + consola.info(issueBody); } // Update the issue with the new body @@ -663,7 +668,7 @@ export default async (app, { getRouter }) => { ); const cwlObject = { - contains_cwl: cwl.length > 0 || false, + contains_cwl_files: cwl.length > 0 || false, files: cwl, removed_files: [], }; @@ -675,7 +680,7 @@ export default async (app, { getRouter }) => { }); if (cwlExists) { - cwlObject.contains_cwl = cwlExists.contains_cwl_files; + cwlObject.contains_cwl_files = cwlExists.contains_cwl_files; if (cwlExists.files.length > 0) { // Remove the files that are not in cwlObject @@ -714,53 +719,209 @@ export default async (app, { getRouter }) => { issueBody.includes("") ) { consola.start("Rerunning full repository validation..."); + try { + const license = await checkForLicense(context, owner, repository.name); + const citation = await checkForCitation(context, owner, repository.name); + const codemeta = await checkForCodeMeta(context, owner, repository.name); + const cwlObject = await getCWLFiles(context, owner, repository.name); + + // If existing cwl validation exists, update the contains_cwl value + const cwlExists = await db.cwlValidation.findUnique({ + where: { + repository_id: repository.id, + }, + }); + + if (cwlExists?.contains_cwl_files) { + cwlObject.contains_cwl_files = cwlExists.contains_cwl_files; + + if (cwlExists.files.length > 0) { + // Remove the files that are not in cwlObject + const cwlFilePaths = cwlObject.files.map((file) => file.path); + cwlObject.removed_files = cwlExists.files.filter((file) => { + return !cwlFilePaths.includes(file.path); + }); + } + } + + const subjects = { + citation, + codemeta, + cwl: cwlObject, + license, + }; + + const issueBody = await renderIssues( + context, + owner, + repository, + false, + subjects, + ); + + await createIssue(context, owner, repository, ISSUE_TITLE, issueBody); + } catch (error) { + // Remove the command from the issue body + const issueBodyRemovedCommand = issueBody.substring(0, issueBody.indexOf(`Last updated`)); + const lastModified = await applyLastModifiedTemplate(issueBodyRemovedCommand); + await createIssue(context, owner, repository, ISSUE_TITLE, lastModified); + throw new Error("Error rerunning license validation", error); + } + } - const license = await checkForLicense(context, owner, repository.name); - const citation = await checkForCitation(context, owner, repository.name); - const codemeta = await checkForCodeMeta(context, owner, repository.name); - const cwl = await getCWLFiles(context, owner, repository.name); - - const cwlObject = { - contains_cwl: cwl.length > 0 || false, - files: cwl, - removed_files: [], - }; - - // If existing cwl validation exists, update the contains_cwl value - const cwlExists = await db.cwlValidation.findUnique({ - where: { - repository_id: repository.id, - }, - }); - - if (cwlExists?.contains_cwl_files) { - cwlObject.contains_cwl = cwlExists.contains_cwl_files; - - if (cwlExists.files.length > 0) { - // Remove the files that are not in cwlObject - const cwlFilePaths = cwlObject.files.map((file) => file.path); - cwlObject.removed_files = cwlExists.files.filter((file) => { - return !cwlFilePaths.includes(file.path); + if (issueBody.includes("")) { + // Run the license validation again + consola.start("Rerunning License Validation..."); + try { + const licenseRequest = await context.octokit.rest.licenses.getForRepo({ + owner, + repo: repository.name, + }); + + const existingLicense = await db.licenseRequest.findUnique({ + where: { + repository_id: repository.id, + } + }); + + const license = licenseRequest.data.license ? true : false; + + if (!license) { + throw new Error("License not found in the repository"); + } + + const { licenseId, licenseContent, licenseContentEmpty } = validateLicense(licenseRequest, existingLicense); + + consola.info("License validation complete:", licenseId, licenseContent, licenseContentEmpty); + + // Update the database with the license information + if (existingLicense) { + await db.licenseRequest.update({ + data: { + license_id: licenseId, + license_content: licenseContent, + license_status: licenseContentEmpty ? "valid" : "invalid", + }, + where: { + repository_id: repository.id, + } + }); + } else { + await db.licenseRequest.create({ + data: { + license_id: licenseId, + license_content: licenseContent, + license_status: licenseContentEmpty ? "valid" : "invalid", + }, + where: { + repository_id: repository.id, + } }); } - } - const subjects = { - citation, - codemeta, - cwl: cwlObject, - license, - }; + // Update the issue body + const issueBodyRemovedCommand = issueBody.substring(0, issueBody.indexOf(`Last updated`)); + const lastModified = await applyLastModifiedTemplate(issueBodyRemovedCommand); + await createIssue(context, owner, repository, ISSUE_TITLE, lastModified); + } catch (error) { + // Remove the command from the issue body + const issueBodyRemovedCommand = issueBody.substring(0, issueBody.indexOf(`Last updated`)); + const lastModified = await applyLastModifiedTemplate(issueBodyRemovedCommand); + await createIssue(context, owner, repository, ISSUE_TITLE, lastModified); + throw new Error("Error rerunning license validation", error); + } + } - const issueBody = await renderIssues( - context, - owner, - repository, - false, - subjects, - ); + if (issueBody.includes("")) { + consola.start("Validating metadata files..."); + try { + let metadata = await gatherMetadata(context, owner, repository); + let containsCitation = false, + containsCodemeta = false, + validCitation = false, + validCodemeta = false; + + const existingMetadataEntry = await db.codeMetadata.findUnique({ + where: { + repository_id: repository.id, + } + }); + + if (existingMetadataEntry?.metadata) { + // Update the metadata variable + consola.info("Existing metadata in db found"); + containsCitation = existingMetadataEntry.contains_citation; + containsCodemeta = existingMetadataEntry.contains_codemeta; + metadata = applyDbMetadata(existingMetadataEntry, metadata); + } + + const citation = await getCitationContent(context, owner, repository); + const codemeta = await getCodemetaContent(context, owner, repository); + + if (codemeta) { + containsCodemeta = true; + validCodemeta = await validateMetadata(codemeta, "codemeta", repository); + metadata = await applyCodemetaMetadata(codemeta, metadata, repository); + } + + if (citation) { + containsCitation = true; + validCitation = await validateMetadata(citation, "citation", repository); + metadata = await applyCitationMetadata(citation, metadata, repository); + // consola.info("Metadata so far after citation update", JSON.stringify(metadata, null, 2)); + } + + // Ensure all dates have been converted to ISO strings split by the T + if (metadata.creationDate) { + metadata.creationDate = convertDateToUnix(metadata.creationDate); + } + if (metadata.firstReleaseDate) { + metadata.firstReleaseDate = convertDateToUnix(metadata.firstReleaseDate); + } + if (metadata.currentVersionReleaseDate) { + metadata.currentVersionReleaseDate = convertDateToUnix(metadata.currentVersionReleaseDate); + } + + consola.warn("Metadata:", JSON.stringify(metadata, null, 2)); + // update the database with the metadata information + if (existingMetadataEntry) { + await db.codeMetadata.update({ + data: { + codemeta_status: validCodemeta ? "valid" : "invalid", + citation_status: validCitation ? "valid" : "invalid", + contains_citation: containsCitation, + contains_codemeta: containsCodemeta, + metadata: metadata, + }, + where: { + repository_id: repository.id, + } + }) + } else { + await db.codeMetadata.create({ + data: { + codemeta_status: validCodemeta ? "valid" : "invalid", + citation_status: validCitation ? "valid" : "invalid", + contains_citation: containsCitation, + contains_codemeta: containsCodemeta, + metadata: metadata, + }, + where: { + repository_id: repository.id, + } + }) + } - await createIssue(context, owner, repository, ISSUE_TITLE, issueBody); + const issueBodyRemovedCommand = issueBody.substring(0, issueBody.indexOf(`Last updated`)); + const lastModified = await applyLastModifiedTemplate(issueBodyRemovedCommand); + await createIssue(context, owner, repository, ISSUE_TITLE, lastModified); + } catch (error) { + // Remove the command from the issue body + const issueBodyRemovedCommand = issueBody.substring(0, issueBody.indexOf(`Last updated`)); + const lastModified = await applyLastModifiedTemplate(issueBodyRemovedCommand); + await createIssue(context, owner, repository, ISSUE_TITLE, lastModified); + throw new Error("Error rerunning metadata validation", error); + } } if (issueBody.includes("")) { // Run database queries in parallel using Promise.all - const [licenseResponse, metadataResponse, cwlResponse] = await Promise.all([ - db.licenseRequest.findUnique({ - where: { - repository_id: repository.id, - } - }), - db.codeMetadata.findUnique({ - where: { - repository_id: repository.id, - } - }), - db.cwlValidation.findUnique({ - where: { - repository_id: repository.id, - } - }) - ]); - - const license = !!licenseResponse?.license_id; - const citation = !!metadataResponse?.contains_citation; - const codemeta = !!metadataResponse?.contains_codemeta; - const cwl = !!cwlResponse?.contains_cwl_files; - - const cwlObject = { - contains_cwl: cwl, - files: cwlResponse?.files || [], - removed_files: [], - }; - - const subjects = { - citation, - codemeta, - cwl: cwlObject, - license, - }; - - const issueBody = await renderIssues( - context, - owner, - repository, - false, - subjects, - ); - - await createIssue(context, owner, repository, ISSUE_TITLE, issueBody); + consola.start("Re-rendering issue dashboard..."); + try { + const [licenseResponse, metadataResponse, cwlResponse] = await Promise.all([ + db.licenseRequest.findUnique({ + where: { + repository_id: repository.id, + } + }), + db.codeMetadata.findUnique({ + where: { + repository_id: repository.id, + } + }), + db.cwlValidation.findUnique({ + where: { + repository_id: repository.id, + } + }) + ]); + + const license = !!licenseResponse?.license_id; + const citation = !!metadataResponse?.contains_citation; + const codemeta = !!metadataResponse?.contains_codemeta; + const cwl = !!cwlResponse?.contains_cwl_files; + + const cwlObject = { + contains_cwl_files: cwl, + files: cwlResponse?.files || [], + removed_files: [], + }; + + const subjects = { + citation, + codemeta, + cwl: cwlObject, + license, + }; + + const issueBody = await renderIssues( + context, + owner, + repository, + false, + subjects, + ); + + await createIssue(context, owner, repository, ISSUE_TITLE, issueBody); + } catch (error) { + // Remove the command from the issue body + const issueBodyRemovedCommand = issueBody.substring(0, issueBody.indexOf(`Last updated`)); + const lastModified = await applyLastModifiedTemplate(issueBodyRemovedCommand); + await createIssue(context, owner, repository, ISSUE_TITLE, lastModified); + throw new Error("Error rerunning re-rendering dashboard", error) + } } }); @@ -1016,7 +1186,7 @@ export default async (app, { getRouter }) => { const cwl = await getCWLFiles(context, owner, repository.name); // This variable is an array of cwl files const cwlObject = { - contains_cwl: cwl.length > 0 || false, + contains_cwl_files: cwl.length > 0 || false, files: cwl, removed_files: [], }; @@ -1028,7 +1198,7 @@ export default async (app, { getRouter }) => { }); if (cwlExists) { - cwlObject.contains_cwl = cwlExists.contains_cwl_files; + cwlObject.contains_cwl_files = cwlExists.contains_cwl_files; } const subjects = { @@ -1052,76 +1222,86 @@ export default async (app, { getRouter }) => { }); app.on("pull_request.closed", async (context) => { - // Remove the PR url from the database - const prLink = context.payload.pull_request.html_url; - const owner = context.payload.repository.owner.login; - const { repository } = context.payload; - - // Seach for the issue with the title FAIR Compliance Dashboard and authored with the github bot - const issues = await context.octokit.issues.listForRepo({ - creator: `${GH_APP_NAME}[bot]`, - owner, - repo: repository.name, - state: "open", - }); - - // Find the issue with the exact title "FAIR Compliance Dashboard" - const dashboardIssue = issues.data.find(issue => issue.title === "FAIR Compliance Dashboard"); - - if (!dashboardIssue) { - consola.error("FAIR Compliance Dashboard issue not found"); - return; - } - - // Get the current body of the issue - let issueBody = dashboardIssue.body; - - if (context.payload.pull_request.title === "feat: ✨ Add code metadata files") { - const response = await db.codeMetadata.update({ - data: { - pull_request_url: "", - }, - where: { - repository_id: context.payload.repository.id, - }, + if (context.payload.pull_request.user.login === `${GH_APP_NAME}[bot]`) { + // Remove the PR url from the database + const prLink = context.payload.pull_request.html_url; + const owner = context.payload.repository.owner.login; + const { repository } = context.payload; + + // Seach for the issue with the title FAIR Compliance Dashboard and authored with the github bot + const issues = await context.octokit.issues.listForRepo({ + creator: `${GH_APP_NAME}[bot]`, + owner, + repo: repository.name, + state: "open", }); - - if (!response) { - consola.error("Error updating the license request PR URL"); + + // Find the issue with the exact title "FAIR Compliance Dashboard" + const dashboardIssue = issues.data.find(issue => issue.title === "FAIR Compliance Dashboard"); + + if (!dashboardIssue) { + consola.error("FAIR Compliance Dashboard issue not found"); return; } - - const metadataPRBadge = `A pull request for the metadata files is open. You can view the pull request:\n\n[![Metadata](https://img.shields.io/badge/View_PR-6366f1.svg)](${prLink})`; - - // Append the Metadata PR badge after the "Metadata" section - issueBody = issueBody.replace( - `## Metadata\n\nTo make your software FAIR a CITATION.cff and codemeta.json metadata files are expected at the root level of your repository. Codefair will check for these files after a license file is detected.\n\n[![Metadata](https://img.shields.io/badge/Add_Metadata-dc2626.svg)](${CODEFAIR_DOMAIN}/add/code-metadata/${response.identifier})\n\n${metadataPRBadge}`, - `## Metadata\n\nTo make your software FAIR a CITATION.cff and codemeta.json metadata files are expected at the root level of your repository. Codefair will check for these files after a license file is detected.\n\n[![Metadata](https://img.shields.io/badge/Add_Metadata-dc2626.svg)](${CODEFAIR_DOMAIN}/add/code-metadata/${response.identifier})` - ); - } - - if (context.payload.pull_request.title === "feat: ✨ LICENSE file added") { - const response = await db.licenseRequest.update({ - data: { - pull_request_url: "", - }, - where: { - repository_id: context.payload.repository.id, - }, + + // Get the current body of the issue + let issueBody = dashboardIssue.body; + + if (context.payload.pull_request.title === "feat: ✨ Add code metadata files" || context.payload.pull_request.title === "feat: ✨ Update code metadata files") { + const response = await db.codeMetadata.update({ + data: { + pull_request_url: "", + }, + where: { + repository_id: context.payload.repository.id, + }, + }); + + if (!response) { + consola.error("Error updating the license request PR URL"); + return; + } + + const metadataPRBadge = `A pull request for the metadata files is open. You can view the pull request:\n\n[![Metadata](https://img.shields.io/badge/View_PR-6366f1.svg)](${prLink})`; + + // Append the Metadata PR badge after the "Metadata" section + issueBody = issueBody.replace( + `(${CODEFAIR_DOMAIN}/dashboard/${owner}/${repository.name}/edit/code-metadata)\n\n${metadataPRBadge}`, + `(${CODEFAIR_DOMAIN}/dashboard/${owner}/${repository.name}/edit/code-metadata)` + ); + } + + if (context.payload.pull_request.title === "feat: ✨ LICENSE file added") { + const response = await db.licenseRequest.update({ + data: { + pull_request_url: "", + }, + where: { + repository_id: context.payload.repository.id, + }, + }); + + // Define the PR badge markdown for the LICENSE section + const licensePRBadge = `A pull request for the LICENSE file is open. You can view the pull request:\n\n[![License](https://img.shields.io/badge/View_PR-6366f1.svg)](${prLink})`; + + // Append the PR badge after the "LICENSE ❌" section + issueBody = issueBody.replace( + `\n\n[![License](https://img.shields.io/badge/Add_License-dc2626.svg)](${CODEFAIR_DOMAIN}/dashboard/${owner}/${repository.name}/edit/license)\n\n${licensePRBadge}`, + `\n\n[![License](https://img.shields.io/badge/Add_License-dc2626.svg)](${CODEFAIR_DOMAIN}/dashboard/${owner}/${repository.name}/edit/license)`, + ); + } + + // Update the issue with the new body + await createIssue(context, owner, repository, ISSUE_TITLE, issueBody); + + // Delete the branch name from GitHub + const branchName = context.payload.pull_request.head.ref; + await context.octokit.git.deleteRef({ + owner, + ref: `heads/${branchName}`, + repo: repository.name, }); - - // Define the PR badge markdown for the LICENSE section - const licensePRBadge = `A pull request for the LICENSE file is open. You can view the pull request:\n\n[![License](https://img.shields.io/badge/View_PR-6366f1.svg)](${prLink})`; - - // Append the PR badge after the "LICENSE ❌" section - issueBody = issueBody.replace( - `## LICENSE ❌\n\nTo make your software reusable a license file is expected at the root level of your repository. If you would like Codefair to add a license file, click the "Add license" button below to go to our interface for selecting and adding a license. You can also add a license file yourself and Codefair will update the the dashboard when it detects it on the main branch.\n\n[![License](https://img.shields.io/badge/Add_License-dc2626.svg)](${CODEFAIR_DOMAIN}/add/license/${response.identifier})\n\n${licensePRBadge}`, - `## LICENSE ❌\n\nTo make your software reusable a license file is expected at the root level of your repository. If you would like Codefair to add a license file, click the \"Add license\" button below to go to our interface for selecting and adding a license. You can also add a license file yourself and Codefair will update the the dashboard when it detects it on the main branch.\n\n[![License](https://img.shields.io/badge/Add_License-dc2626.svg)](${CODEFAIR_DOMAIN}/add/license/${response.identifier})`, - ); } - - // Update the issue with the new body - await createIssue(context, owner, repository, ISSUE_TITLE, issueBody); } ); }; diff --git a/bot/license/index.js b/bot/license/index.js index 0118689..7d95b0f 100644 --- a/bot/license/index.js +++ b/bot/license/index.js @@ -155,7 +155,7 @@ export async function createLicense(context, owner, repo, license) { } } -function validateLicense(licenseRequest, existingLicense) { +export function validateLicense(licenseRequest, existingLicense) { let licenseId = licenseRequest.data?.license?.spdx_id || null; let licenseContent = ""; let licenseContentEmpty = true; @@ -175,7 +175,7 @@ function validateLicense(licenseRequest, existingLicense) { licenseContent = ""; } - console.log("Existing License:", existingLicense?.license_id); + // console.log("Existing License:", existingLicense?.license_id); // consola.warn(existingLicense?.license_content.trim()); // consola.info("dfl;aksjdfl;ksajl;dfkjas;ldfjk") // consola.warn(licenseContent.trim()); diff --git a/bot/main.js b/bot/main.js index e540929..f7d7ff8 100644 --- a/bot/main.js +++ b/bot/main.js @@ -1,13 +1,14 @@ import { Server, Probot } from "probot"; import app from "./index.js"; // import "dotenv/config"; +const privateKey = process.env.PRIVATE_KEY.replace(/\\n/g, "\n"); async function startServer() { const server = new Server({ port: process.env.PORT || 3000, Probot: Probot.defaults({ appId: process.env.GH_APP_ID, - privateKey: process.env.GH_APP_PRIVATE_KEY.replace(/\\n/g, "\n"), + privateKey, secret: process.env.WEBHOOK_SECRET, }), }); diff --git a/bot/metadata/index.js b/bot/metadata/index.js index 607e3dc..217a6ce 100644 --- a/bot/metadata/index.js +++ b/bot/metadata/index.js @@ -9,6 +9,7 @@ import { import dbInstance from "../db.js"; const CODEFAIR_DOMAIN = process.env.CODEFAIR_APP_DOMAIN; +const { GH_APP_NAME } = process.env; /** * * Converts the date to a Unix timestamp @@ -30,7 +31,7 @@ export function convertDateToUnix(date) { * @param {JSON} codemetaContent - The codemeta.json file content * @returns {JSON} - The metadata object for the database */ -export async function convertMetadataForDB(codemetaContent, repository) { +export async function convertCodemetaForDB(codemetaContent, repository) { // eslint-disable-next-line prefer-const const sortedAuthors = []; // eslint-disable-next-line prefer-const @@ -71,8 +72,6 @@ export async function convertMetadataForDB(codemetaContent, repository) { } if (codemetaContent?.contributor) { - // const sortedContributors = []; - // Loop through all contributors codemetaContent?.contributor.forEach((contributor) => { // If the contributor is a Person or Organization, we need to add them @@ -108,10 +107,6 @@ export async function convertMetadataForDB(codemetaContent, repository) { }); } - - // Now search through sortedAuthors and sortedContributors and check if uri begins with '_:' and if so, delete the key - // consola.info("Sorted authors:", JSON.stringify(sortedAuthors, null, 2)); - // consola.info("Sorted contributors:", sortedContributors); for (let i = 0; i < sortedAuthors.length; i++) { if (sortedAuthors[i].uri.startsWith("_:")) { delete sortedAuthors[i].uri; @@ -190,6 +185,38 @@ export async function convertMetadataForDB(codemetaContent, repository) { }; } +/** + * * Converts the CITATION.cff file content to a metadata object for the database + * @param {YAML} citationContent - The CITATION.cff file content loaded as a YAML object + * @param {Object} repository - The repository information + * @returns {Object} - The metadata object for the database + */ +export async function convertCitationForDB(citationContent, repository) { + const authors = []; + + if (citationContent?.authors) { + citationContent.authors.forEach((author) => { + authors.push({ + affiliation: author.affiliation || "", + email: author.email || "", + familyName: author["family-names"] || "", + givenName: author["given-names"] || "", + }) + }); + } + + return { + authors, + uniqueIdentifier: citationContent?.doi || null, + license: citationContent?.license || null, + codeRepository: citationContent["repository-code"] || null, + description: citationContent.abstract || null, + currentVersionReleaseDate: citationContent["date-released"] || null, + currentVersion: citationContent.version || null, + keywords: citationContent.keywords || null, + } +} + /** * * Gathers metadata to create a citation.cff and codemeta.json file * @@ -200,7 +227,7 @@ export async function convertMetadataForDB(codemetaContent, repository) { * @returns {object} - An object containing the metadata for the repository */ export async function gatherMetadata(context, owner, repo) { - consola.start("Gathering metadata..."); + consola.start("Gathering initial metadata from GitHub API..."); // Get the metadata of the repo const repoData = await context.octokit.repos.get({ @@ -270,6 +297,13 @@ export async function gatherMetadata(context, owner, repo) { return codeMeta; } +/** + * * Gets the metadata for the repository and returns it as a string + * @param {Object} context - The GitHub context object + * @param {String} owner - The owner of the repository + * @param {Object} repository - Object containing the repository information + * @returns - The content of the codemeta.json file as a string object + */ export async function getCodemetaContent(context, owner, repository) { try { const codemetaFile = await context.octokit.repos.getContent({ @@ -281,6 +315,7 @@ export async function getCodemetaContent(context, owner, repository) { return { content: Buffer.from(codemetaFile.data.content, "base64").toString(), sha: codemetaFile.data.sha, + file_path: codemetaFile.data.download_url, } // return JSON.parse(Buffer.from(codemetaFile.data.content, "base64").toString()); @@ -289,6 +324,13 @@ export async function getCodemetaContent(context, owner, repository) { } } +/** + * * Get the content of the CITATION.cff file + * @param {Object} context - The GitHub context object + * @param {String} owner - The owner of the repository + * @param {Object} repository - The repository information + * @returns {String} - The content of the CITATION.cff file as a string object (need to yaml load it) + */ export async function getCitationContent(context, owner, repository) { try { const citationFile = await context.octokit.repos.getContent({ @@ -300,21 +342,64 @@ export async function getCitationContent(context, owner, repository) { return { content: Buffer.from(citationFile.data.content, "base64").toString(), sha: citationFile.data.sha, + file_path: citationFile.data.download_url, } } catch (error) { throw new Error("Error getting CITATION.cff file", error); } } -export async function validateMetadata(content, fileType) { +/** + * * Ensures the metadata is valid based on certain fields + * @param {String} content - The content of the metadata file + * @param {String} fileType - The type of metadata file (codemeta or citation) + * @param {String} file_path - Raw GitHub file path + * @returns + */ +export async function validateMetadata(metadataInfo, fileType, repository) { if (fileType === "codemeta") { try { - JSON.parse(content); + const cleanContent = metadataInfo.content.trim(); + const normalizedContent = cleanContent.replace(/^\uFEFF/, ''); // Remove BOM if present + const loaded_file = JSON.parse(normalizedContent); // Verify the required fields are present - if (!content.name || !content.authors || !content.description) { + if (!loaded_file.name || !loaded_file.author || !loaded_file.description) { + return false; + } + + consola.start("Sending content to metadata validator"); + try { + const response = await fetch("http://127.0.0.1:5000/validate-codemeta", { + method: "POST", + headers: { + "Content-Type": "application/json", + }, + body: JSON.stringify({ + file_content: loaded_file, + }) + }); + + if (!response.ok) { + throw new Error("Error validating the codemeta.json file", response.json()); + } + const data = await response.json(); + consola.info("Codemeta validation response", data); + + await dbInstance.codeMetadata.update({ + where: { + repository_id: repository.id, + }, + data: { + codemeta_validation_message: data.message === "valid" ? data.output : data.error, + } + }); + + return data.message === "valid"; + + } catch (error) { + consola.error("Error validating the codemeta.json file", error); return false; } - return true; } catch (error) { return false; } @@ -322,12 +407,44 @@ export async function validateMetadata(content, fileType) { if (fileType === "citation") { try { - yaml.load(content); + const loaded_file = yaml.load(metadataInfo.content); // Verify the required fields are present - if (!content.title || !content.authors) { + if (!loaded_file.title || !loaded_file.authors) { + return false; + } + + try { + // TODO: CHANGE THIS BEFORE DEPLOYING TO MAIN + const response = await fetch("http://127.0.0.1:5000/validate-citation", { + method: "POST", + headers: { + "Content-Type": "application/json", + }, + body: JSON.stringify({ + file_path: metadataInfo.file_path, + }) + }); + + if (!response.ok) { + throw new Error("Error validating the CITATION.cff file", response); + } + + const data = await response.json(); + + await dbInstance.codeMetadata.update({ + where: { + repository_id: repository.id, + }, + data: { + citation_validation_message: data.message === "valid" ? data.output : data.error, + } + }); + + return data.message === "valid"; + } catch (error) { + consola.error("Error validating the CITATION.cff file", error); return false; } - return true; } catch (error) { return false; } @@ -335,6 +452,15 @@ export async function validateMetadata(content, fileType) { } +/** + * * Updates the metadata files with the Zenodo identifier + * @param {Object} context - The GitHub context object + * @param {String} owner - The owner of the repository + * @param {Object} repository - The repository information + * @param {String} identifier - The Zenodo identifier + * @param {String} version - The version of the software + * @returns {Object} - The updated codemeta.json file + */ export async function updateMetadataIdentifier(context, owner, repository, identifier, version) { try { // Get the citation file @@ -435,6 +561,235 @@ export async function updateMetadataIdentifier(context, owner, repository, ident } +export function applyDbMetadata(existingMetadataEntry, metadata) { + const existingMetadata = existingMetadataEntry.metadata; + + metadata.name = existingMetadata.name || metadata.name || ""; + metadata.authors = existingMetadata.authors || metadata.authors || []; + metadata.contributors = existingMetadata.contributors || metadata.contributors || []; + metadata.applicationCategory = existingMetadata.applicationCategory || metadata.applicationCategory || null; + metadata.codeRepository = existingMetadata.codeRepository || metadata.codeRepository || ""; + metadata.continuousIntegration = existingMetadata.continuousIntegration || metadata.continuousIntegration || ""; + metadata.creationDate = existingMetadata.creationDate || metadata.creationDate || null; + metadata.currentVersion = existingMetadata.currentVersion || metadata.currentVersion || ""; + metadata.currentVersionDownloadURL = existingMetadata.currentVersionDownloadURL || metadata.currentVersionDownloadURL || ""; + metadata.currentVersionReleaseDate = existingMetadata.currentVersionReleaseDate || metadata.currentVersionReleaseDate || null; + metadata.currentVersionReleaseNotes = existingMetadata.currentVersionReleaseNotes || metadata.currentVersionReleaseNotes || ""; + metadata.description = existingMetadata.description || metadata.description || ""; + metadata.developmentStatus = existingMetadata.developmentStatus || metadata.developmentStatus || null; + metadata.firstReleaseDate = existingMetadata.firstReleaseDate || metadata.firstReleaseDate || null; + metadata.fundingCode = existingMetadata.fundingCode || metadata.fundingCode || ""; + metadata.fundingOrganization = existingMetadata.fundingOrganization || metadata.fundingOrganization || ""; + metadata.isPartOf = existingMetadata.isPartOf || metadata.isPartOf || ""; + metadata.isSourceCodeOf = existingMetadata.isSourceCodeOf || metadata.isSourceCodeOf || ""; + metadata.issueTracker = existingMetadata.issueTracker || metadata.issueTracker || ""; + metadata.keywords = existingMetadata.keywords || metadata.keywords || []; + metadata.license = existingMetadata.license || metadata.license || null; + metadata.operatingSystem = existingMetadata.operatingSystem || metadata.operatingSystem || []; + metadata.otherSoftwareRequirements = existingMetadata.otherSoftwareRequirements || metadata.otherSoftwareRequirements || []; + metadata.programmingLanguages = existingMetadata.programmingLanguages || metadata.programmingLanguages || []; + metadata.referencePublication = existingMetadata.referencePublication || metadata.referencePublication || ""; + metadata.relatedLinks = existingMetadata.relatedLinks || metadata.relatedLinks || []; + metadata.reviewAspect = existingMetadata.reviewAspect || metadata.reviewAspect || ""; + metadata.reviewBody = existingMetadata.reviewBody || metadata.reviewBody || ""; + metadata.runtimePlatform = existingMetadata.runtimePlatform || metadata.runtimePlatform || []; + metadata.uniqueIdentifier = existingMetadata.uniqueIdentifier || metadata.uniqueIdentifier || ""; + + return metadata; +} + +export async function applyCodemetaMetadata(codemeta, metadata, repository) { + consola.info("Codemeta found"); + const codemetaContent = JSON.parse(codemeta.content); + const convertedCodemeta = await convertCodemetaForDB(codemetaContent, repository); + + metadata.name = convertedCodemeta.name || metadata.name || ""; + metadata.applicationCategory = convertedCodemeta.applicationCategory || metadata.applicationCategory || null; + metadata.codeRepository = convertedCodemeta.codeRepository || metadata.codeRepository || ""; + metadata.continuousIntegration = convertedCodemeta.continuousIntegration || metadata.continuousIntegration || ""; + metadata.creationDate = convertedCodemeta.creationDate || metadata.creationDate || null; + metadata.currentVersion = convertedCodemeta.currentVersion || metadata.currentVersion || ""; + metadata.currentVersionDownloadURL = convertedCodemeta.currentVersionDownloadURL || metadata.currentVersionDownloadURL || ""; + metadata.currentVersionReleaseDate = convertedCodemeta.currentVersionReleaseDate || metadata.currentVersionReleaseDate || null; + metadata.currentVersionReleaseNotes = convertedCodemeta.currentVersionReleaseNotes || metadata.currentVersionReleaseNotes || ""; + metadata.description = convertedCodemeta.description || metadata.description || ""; + metadata.developmentStatus = convertedCodemeta.developmentStatus || metadata.developmentStatus || null; + metadata.firstReleaseDate = convertedCodemeta.firstReleaseDate || metadata.firstReleaseDate || null; + metadata.fundingCode = convertedCodemeta.fundingCode || metadata.fundingCode || ""; + metadata.fundingOrganization = convertedCodemeta.fundingOrganization || metadata.fundingOrganization || ""; + metadata.isPartOf = convertedCodemeta.isPartOf || metadata.isPartOf || ""; + metadata.reviewAspect = convertedCodemeta.reviewAspect || metadata.reviewAspect || ""; + metadata.reviewBody = convertedCodemeta.reviewBody || metadata.reviewBody || ""; + metadata.runtimePlatform = convertedCodemeta.runtimePlatform || metadata.runtimePlatform || []; + metadata.uniqueIdentifier = convertedCodemeta.uniqueIdentifier || metadata.uniqueIdentifier || ""; + + if (metadata.authors) { + if (convertedCodemeta.authors.length > 0) { + const updatedAuthors = convertedCodemeta.authors.map((author) => { + // Find a matching author in metadata + const foundAuthor = metadata.authors.find( + (existingAuthor) => + existingAuthor?.familyName === author?.familyName && + existingAuthor?.givenName === author?.givenName + ); + + if (foundAuthor) { + // Merge roles, avoiding duplicates based on `role` and `startDate` + const mergedRoles = [ + ...foundAuthor.roles, + ...author.roles.filter( + (newRole) => + !foundAuthor.roles.some( + (existingRole) => + existingRole.role === newRole.role && + existingRole.startDate === newRole.startDate + ) + ) + ]; + + // Merge and prioritize data from `author` + return { + ...foundAuthor, + ...author, + affiliation: author.affiliation || foundAuthor.affiliation || "", + email: author.email || foundAuthor.email || "", + uri: author.uri || foundAuthor.uri || "", + roles: mergedRoles + }; + } + + // If no match, return the current author from convertedCodemeta + return author; + }); + + // Merge updated authors with any authors in metadata not present in convertedCodemeta + const nonUpdatedAuthors = metadata.authors.filter( + (existingAuthor) => + !convertedCodemeta.authors.some( + (author) => + author.familyName === existingAuthor.familyName && + author.givenName === existingAuthor.givenName + ) + ); + + metadata.authors = [...nonUpdatedAuthors, ...updatedAuthors]; + } + } + + if (metadata.contributors) { + if (convertedCodemeta.contributors.length > 0) { + const updatedContributors = convertedCodemeta.contributors.map((contributor) => { + // Find a matching contributor in metadata + const foundContributor = metadata.contributors.find( + (existingContributor) => + existingContributor?.familyName === contributor?.familyName && + existingContributor?.givenName === contributor?.givenName + ); + + if (foundContributor) { + // Merge roles, avoiding duplicates based on `role` and `startDate` + const mergedRoles = [ + ...foundContributor.roles, + ...contributor.roles.filter( + (newRole) => + !foundContributor.roles.some( + (existingRole) => + existingRole.role === newRole.role && + existingRole.startDate === newRole.startDate + ) + ) + ]; + + // Merge and prioritize data from `contributor` + return { + ...foundContributor, + ...contributor, + affiliation: contributor.affiliation || foundContributor.affiliation || "", + email: contributor.email || foundContributor.email || "", + uri: contributor.uri || foundContributor.uri || "", + roles: mergedRoles + }; + } + + // If no match, return the current contributor from convertedCodemeta + return contributor; + }); + + // Merge updated contributors with any contributors in metadata not present in convertedCodemeta + const nonUpdatedContributors = metadata.contributors.filter( + (existingContributor) => + !convertedCodemeta.contributors.some( + (contributor) => + contributor.familyName === existingContributor.familyName && + contributor.givenName === existingContributor.givenName + ) + ); + + metadata.contributors = [...nonUpdatedContributors, ...updatedContributors]; + } + } else if (convertedCodemeta.contributors.length > 0) { + // If metadata.contributors is empty, directly assign convertedCodemeta.contributors + metadata.contributors = [...convertedCodemeta.contributors]; + } + + return metadata; +} + +export async function applyCitationMetadata(citation, metadata, repository) { + consola.info("Citation found"); + const citationContent = yaml.load(citation.content); + const convertedCitation = await convertCitationForDB(citationContent, repository); + + metadata.license = convertedCitation.license || metadata.license || null; + metadata.codeRepository = convertedCitation.codeRepository || metadata.codeRepository || ""; + metadata.currentVersion = convertedCitation.currentVersion || metadata.currentVersion || ""; + metadata.currentVersionReleaseDate = convertedCitation.currentVersionReleaseDate || metadata.currentVersionReleaseDate || null; + metadata.keywords = convertedCitation.keywords || metadata.keywords || []; + metadata.uniqueIdentifier = convertedCitation.uniqueIdentifier || metadata.uniqueIdentifier || ""; + + consola.info("metadata.authors", metadata.authors); + consola.info("convertedCitation.authors", convertedCitation.authors); + + if (convertedCitation.authors) { + // Check if the authors are already in the metadata, if so update the details of the author + if (metadata.authors.length > 0) { + const updatedAuthors = convertedCitation.authors.map((author) => { + // Find an existing author in metadata.authors with the same familyName and givenName + const foundAuthor = metadata.authors.find( + (existingAuthor) => + existingAuthor.familyName === author.familyName && + existingAuthor.givenName === author.givenName + ); + + consola.info("foundAuthor in citation", foundAuthor); + consola.info("author", author); + + if (foundAuthor) { + // Update author details, preserving information from convertedCitation + return { + ...foundAuthor, // Existing details from metadata.authors + ...author, // Overwrite with any additional information from convertedCitation + affiliation: author.affiliation || foundAuthor.affiliation || "", + email: author.email || foundAuthor.email || "" + }; + } + + // If no matching author is found, return the current author from convertedCitation + return author; + }); + + // Update metadata.authors with the consolidated list + metadata.authors = updatedAuthors; + } else { + // If metadata.authors is empty, simply assign convertedCitation.authors + metadata.authors = [...convertedCitation.authors]; + } + } + + return metadata; +} + + // TODO: Prevent the user from creating/updating metadata if custom license file exists and has no license title /** * * Applies the metadata template to the base template (CITATION.cff and codemeta.json) @@ -454,155 +809,102 @@ export async function applyMetadataTemplate( owner, context, ) { - let url = `${CODEFAIR_DOMAIN}/dashboard/${owner}/${repository.name}/edit/code-metadata`; - if ((!subjects.codemeta || !subjects.citation) && subjects.license) { - // License was found but no codemeta.json or CITATION.cff exists - const identifier = createId(); - let validCitation = false; - let validCodemeta = false; - - const existingMetadata = await dbInstance.codeMetadata.findUnique({ - where: { - repository_id: repository.id, - }, - }); + const githubAction = context.payload?.pusher?.name; + const identifier = createId(); + + // TODO: Move the workflow around to get the metadata from github api last + const url = `${CODEFAIR_DOMAIN}/dashboard/${owner}/${repository.name}/edit/code-metadata`; + let revalidate = true; + let containsCitation = subjects.citation, + containsCodemeta = subjects.codemeta, + validCitation = false, + validCodemeta = false; + const existingMetadata = await dbInstance.codeMetadata.findUnique({ + where: { + repository_id: repository.id, + }, + }); + const dataObject = { + contains_citation: containsCitation, + contains_codemeta: containsCodemeta, + contains_metadata: containsCitation && containsCodemeta, + } - if (subjects.codemeta) { - try { - const codemetaFile = await context.octokit.repos.getContent({ - owner, - path: "codemeta.json", - repo: repository.name, - }); + if (githubAction && githubAction !== `${GH_APP_NAME}[bot]`) { + // Push event was made, only update the metadata if the pusher updated the codemeta.json or citation.cff + const updatedFiles = context.payload.head_commit.modified; + const addedFiles = context.payload.head_commit.added; + revalidate = false; - JSON.parse(Buffer.from(codemetaFile.data.content, "base64").toString()); + if (updatedFiles.includes("codemeta.json") || updatedFiles.includes("CITATION.cff")) { + revalidate = true; + } - validCodemeta = true; - } catch (error) { - consola.error("Error getting codemeta.json file", error); - } + if (addedFiles.includes("codemeta.json") || addedFiles.includes("CITATION.cff")) { + revalidate = true; } + } + if (revalidate) { + // Revalidation steps + let metadata = gatherMetadata(context, owner, repository); + if (existingMetadata?.metadata) { + containsCitation = existingMetadata.contains_citation; + containsCodemeta = existingMetadata.contains_metadata; + metadata = applyDbMetadata(existingMetadata, metadata); + } + + if (subjects.codemeta) { + const codemeta = await getCodemetaContent(context, owner, repository); + containsCodemeta = true; + validCodemeta = await validateMetadata(codemeta, "codemeta", repository); + metadata = await applyCodemetaMetadata(codemeta, metadata, repository); + consola.info(metadata); + } + if (subjects.citation) { - try { - const citationFile = await context.octokit.repos.getContent({ - owner, - path: "CITATION.cff", - repo: repository.name, - }); - - yaml.load(Buffer.from(citationFile.data.content, "base64").toString()); - validCitation = true; - } catch (error) { - consola.error("Error getting CITATION.cff file", error); - } + const citation = await getCitationContent(context, owner, repository); + containsCitation = true; + validCitation = await validateMetadata(citation, "citation", repository); + metadata = await applyCitationMetadata(citation, metadata, repository); + consola.info(metadata); } - if (!existingMetadata) { - // Entry does not exist in db, create a new one - const gatheredMetadata = await gatherMetadata(context, owner, repository); - await dbInstance.codeMetadata.create({ - data: { - citation_status: validCitation ? "valid" : "invalid", - codemeta_status: validCodemeta ? "valid" : "invalid", - contains_citation: subjects.citation, - identifier, - contains_codemeta: subjects.codemeta, - contains_metadata: subjects.codemeta && subjects.citation, - metadata: gatheredMetadata, - repository: { - connect: { - id: repository.id, - }, - }, - }, - }); - } else { - // Get the identifier of the existing metadata request - await dbInstance.codeMetadata.update({ - data: { - citation_status: validCitation ? "valid" : "invalid", - codemeta_status: validCodemeta ? "valid" : "invalid", - contains_citation: subjects.citation, - contains_codemeta: subjects.codemeta, - contains_metadata: subjects.codemeta && subjects.citation, - }, - where: { repository_id: repository.id }, - }); - } + // Add metadata to database object + dataObject.metadata = metadata; + dataObject.citation_status = validCitation ? "valid" : "invalid"; + dataObject.codemeta_status = validCodemeta ? "valid" : "invalid"; + } + + if ((!subjects.codemeta || !subjects.citation) && subjects.license) { + // License was found but no codemeta.json or CITATION.cff exists const metadataBadge = `[![Metadata](https://img.shields.io/badge/Add_Metadata-dc2626.svg)](${url})`; baseTemplate += `\n\n## Metadata ❌\n\nTo make your software FAIR, a CITATION.cff and codemeta.json are expected at the root level of your repository. These files are not found in the repository. If you would like Codefair to add these files, click the "Add metadata" button below to go to our interface for providing metadata and generating these files.\n\n${metadataBadge}`; } if (subjects.codemeta && subjects.citation && subjects.license) { - const codemetaContent = await getCodemetaContent(context, owner, repository); - // const citationContent = await getCitationContent(context, owner, repository); - - const validCodemeta = true; - const validCitation = true; + const metadataBadge = `[![Metadata](https://img.shields.io/badge/Edit_Metadata-0ea5e9.svg)](${url}?)`; + baseTemplate += `\n\n## Metadata ✔️\n\nA CITATION.cff and a codemeta.json file are found in the repository. They may need to be updated over time as new people are contributing to the software, etc.\n\n${metadataBadge}`; + } - // Convert the content to the structure we use for code metadata - const metadata = await convertMetadataForDB(JSON.parse(codemetaContent.content), repository); + if (!existingMetadata) { + // Entry does not exist in db, create a new one + dataObject.identifier = identifier; + dataObject.repository = { + connect: { + id: repository.id, + } + }; - // Fetch license details from database - const license = await dbInstance.licenseRequest.findUnique({ - where: { - repository_id: repository.id, - }, + await dbInstance.codeMetadata.create({ + data: dataObject, }); - - if (license?.license_id) { - metadata.license = `https://spdx.org/licenses/${license.license_id}`; - } - - // License, codemeta.json and CITATION.cff files were found - const identifier = createId(); - - const existingMetadata = await dbInstance.codeMetadata.findUnique({ - where: { - repository_id: repository.id, - }, + } else { + // Get the identifier of the existing metadata request + await dbInstance.codeMetadata.update({ + data: dataObject, + where: { repository_id: repository.id }, }); - - if (!existingMetadata) { - // Entry does not exist in db, create a new one - const newDate = new Date(); - // const gatheredMetadata = await gatherMetadata(context, owner, repository); - await dbInstance.codeMetadata.create({ - data: { - citation_status: validCitation ? "valid" : "invalid", - codemeta_status: validCodemeta ? "valid" : "invalid", - contains_citation: subjects.citation, - contains_codemeta: subjects.codemeta, - contains_metadata: subjects.codemeta && subjects.citation, - created_at: newDate, - identifier, - metadata, - repository: { - connect: { - id: repository.id, - }, - }, - updated_at: newDate, - }, - }); - } else { - // Get the identifier of the existing metadata request - await dbInstance.codeMetadata.update({ - data: { - citation_status: validCitation ? "valid" : "invalid", - codemeta_status: validCodemeta ? "valid" : "invalid", - contains_citation: subjects.citation, - contains_codemeta: subjects.codemeta, - contains_metadata: subjects.codemeta && subjects.citation, - metadata, - updated_at: new Date(), - }, - where: { repository_id: repository.id }, - }); - } - const metadataBadge = `[![Metadata](https://img.shields.io/badge/Edit_Metadata-0ea5e9.svg)](${url}?)`; - baseTemplate += `\n\n## Metadata ✔️\n\nA CITATION.cff and a codemeta.json file are found in the repository. They may need to be updated over time as new people are contributing to the software, etc.\n\n${metadataBadge}`; } if (!subjects.license) { diff --git a/bot/prisma/migrations/20241114193552_metadata_validation_messages/migration.sql b/bot/prisma/migrations/20241114193552_metadata_validation_messages/migration.sql new file mode 100644 index 0000000..4c82b4f --- /dev/null +++ b/bot/prisma/migrations/20241114193552_metadata_validation_messages/migration.sql @@ -0,0 +1,3 @@ +-- AlterTable +ALTER TABLE "CodeMetadata" ADD COLUMN "citation_validation_message" TEXT NOT NULL DEFAULT '', +ADD COLUMN "codemeta_validation_message" TEXT NOT NULL DEFAULT ''; diff --git a/bot/prisma/schema.prisma b/bot/prisma/schema.prisma index 4f9d23d..0bfc4b0 100644 --- a/bot/prisma/schema.prisma +++ b/bot/prisma/schema.prisma @@ -8,74 +8,58 @@ datasource db { } model User { - id String @id - github_id Int @unique - username String - access_token String @default("") - - created_at DateTime @default(now()) - last_login DateTime - + id String @id + username String + access_token String @default("") + github_id Int @unique + created_at DateTime @default(now()) + last_login DateTime sessions Session[] - ZenodoToken ZenodoToken[] ZenodoDeposition ZenodoDeposition[] + ZenodoToken ZenodoToken? } model Session { id String @id + userId String expiresAt DateTime - - userId String - user User @relation(fields: [userId], references: [id], onDelete: Cascade) + user User @relation(fields: [userId], references: [id], onDelete: Cascade) } model Installation { - id Int @id - owner String - repo String - - installation_id Int - - latest_commit_date String @default("") - latest_commit_message String @default("") - latest_commit_sha String @default("") - latest_commit_url String @default("") - - disabled Boolean @default(false) - action_count Int @default(0) - - issue_number Int @default(0) - - owner_is_organization Boolean @default(false) - - created_at DateTime @default(now()) - updated_at DateTime @updatedAt - - CodeMetadata CodeMetadata? - CwlValidation CwlValidation? - LicenseRequest LicenseRequest? - ZenodoDeposition ZenodoDeposition? + id Int @id + owner String + repo String + installation_id Int + latest_commit_date String @default("") + latest_commit_message String @default("") + latest_commit_sha String @default("") + latest_commit_url String @default("") + disabled Boolean @default(false) + issue_number Int @default(0) + owner_is_organization Boolean @default(false) + action_count Int @default(0) + created_at DateTime @default(now()) + updated_at DateTime @updatedAt + CodeMetadata CodeMetadata? + CwlValidation CwlValidation? + LicenseRequest LicenseRequest? + ZenodoDeposition ZenodoDeposition? } model LicenseRequest { - id String @id @default(cuid()) - identifier String @unique - - contains_license Boolean @default(false) - license_status String @default("") - - license_id String? - license_content String @default("") - - custom_license_title String @default("") - - pull_request_url String @default("") - - created_at DateTime @default(now()) - updated_at DateTime @updatedAt - - repository_id Int @unique - repository Installation @relation(fields: [repository_id], references: [id], onDelete: Cascade) + id String @id @default(cuid()) + identifier String @unique + repository_id Int @unique + contains_license Boolean @default(false) + license_status String @default("") + license_id String? + license_content String @default("") + pull_request_url String @default("") + created_at DateTime @default(now()) + updated_at DateTime @updatedAt + custom_license_title String @default("") + repository Installation @relation(fields: [repository_id], references: [id], onDelete: Cascade) } model Ping { @@ -84,91 +68,68 @@ model Ping { } model CodeMetadata { - id String @id @default(cuid()) - identifier String @unique - - contains_codemeta Boolean @default(false) - contains_citation Boolean @default(false) - contains_metadata Boolean @default(false) - - codemeta_status String @default("") - citation_status String @default("") - - pull_request_url String @default("") - - metadata Json @default("{}") - - created_at DateTime @default(now()) - updated_at DateTime @updatedAt - - repository_id Int @unique - repository Installation @relation(fields: [repository_id], references: [id], onDelete: Cascade) + id String @id @default(cuid()) + identifier String @unique + repository_id Int @unique + codemeta_validation_message String @default("") + citation_validation_message String @default("") + codemeta_status String @default("") + contains_codemeta Boolean @default(false) + citation_status String @default("") + contains_citation Boolean @default(false) + contains_metadata Boolean @default(false) + pull_request_url String @default("") + metadata Json @default("{}") + created_at DateTime @default(now()) + updated_at DateTime @updatedAt + repository Installation @relation(fields: [repository_id], references: [id], onDelete: Cascade) } model CwlValidation { - id String @id @default(cuid()) - identifier String @unique - - contains_cwl_files Boolean @default(false) - overall_status String @default("") - - files Json @default("[]") - - created_at DateTime @default(now()) - updated_at DateTime @updatedAt - - repository_id Int @unique - repository Installation @relation(fields: [repository_id], references: [id], onDelete: Cascade) + id String @id @default(cuid()) + identifier String @unique + repository_id Int @unique + contains_cwl_files Boolean @default(false) + overall_status String @default("") + files Json @default("[]") + created_at DateTime @default(now()) + updated_at DateTime @updatedAt + repository Installation @relation(fields: [repository_id], references: [id], onDelete: Cascade) } model ZenodoToken { - id String @id @default(cuid()) - - token String - expires_at DateTime - + id String @id @default(cuid()) + token String + expires_at DateTime refresh_token String - - user_id String @unique - user User @relation(fields: [user_id], references: [id], onDelete: Cascade) + user_id String @unique + user User @relation(fields: [user_id], references: [id], onDelete: Cascade) } model ZenodoDeposition { - id String @id @default(cuid()) - - repository_id Int @unique - repository Installation @relation(fields: [repository_id], references: [id], onDelete: Cascade) - - existing_zenodo_deposition_id Boolean? //null, false, true - - zenodo_id Int? - zenodo_metadata Json @default("{}") - - last_published_zenodo_doi String? - - github_release_id Int? - github_tag_name String? - - status String @default("unpublished") // inProgress, published, error, draft - - user_id String - user User @relation(fields: [user_id], references: [id], onDelete: Cascade) + id String @id @default(cuid()) + repository_id Int @unique + existing_zenodo_deposition_id Boolean? + zenodo_id Int? + zenodo_metadata Json @default("{}") + last_published_zenodo_doi String? + github_release_id Int? + github_tag_name String? + status String @default("unpublished") + user_id String + repository Installation @relation(fields: [repository_id], references: [id], onDelete: Cascade) + user User @relation(fields: [user_id], references: [id], onDelete: Cascade) } model Analytics { - id Int @id - - cwl_validated_file_count Int @default(0) - cwl_rerun_validation Int @default(0) - - license_created Int @default(0) - - update_codemeta Int @default(0) - update_citation Int @default(0) - - create_release Int @default(0) - zenodo_release Int @default(0) - - created_at DateTime @default(now()) - updated_at DateTime @updatedAt + id Int @id + cwl_validated_file_count Int @default(0) + cwl_rerun_validation Int @default(0) + license_created Int @default(0) + update_codemeta Int @default(0) + update_citation Int @default(0) + created_at DateTime @default(now()) + updated_at DateTime @updatedAt + create_release Int @default(0) + zenodo_release Int @default(0) } diff --git a/ui/pages/dashboard/[owner]/[repo]/index.vue b/ui/pages/dashboard/[owner]/[repo]/index.vue index 7a2b352..cd22fab 100644 --- a/ui/pages/dashboard/[owner]/[repo]/index.vue +++ b/ui/pages/dashboard/[owner]/[repo]/index.vue @@ -44,6 +44,22 @@ const settingsOptions = [ }, ]; +const licenseSettingsOptions = [ + { + icon: renderIcon("mdi:github"), + key: "re-validate-license", + label: "Re-validate license", + } +]; + +const metadataSettingsOptions = [ + { + icon: renderIcon("mdi:github"), + key: "re-validate-metadata", + label: "Re-validate metadata files", + } +]; + const { data, error } = await useFetch(`/api/${owner}/${repo}/dashboard`, { headers: useRequestHeaders(["cookie"]), }); @@ -97,7 +113,7 @@ const rerunCwlValidation = async () => { }); }; -const rerunCodefairChecks = async () => { +const rerunCodefairChecks = async (rerunType: string) => { push.info({ title: "Submitting request", message: @@ -106,6 +122,9 @@ const rerunCodefairChecks = async () => { await $fetch(`/api/${owner}/${repo}/rerun`, { headers: useRequestHeaders(["cookie"]), + body: { + rerunType, + }, method: "POST", }) .then(() => { @@ -140,7 +159,7 @@ const handleSettingsSelect = (key: any) => { }, }); } else if (key === "rerun-codefair-on-repo") { - rerunCodefairChecks(); + rerunCodefairChecks("full-repo"); } else if (key === "view-codefair-settings") { if (data.value?.isOrganization) { navigateTo( @@ -161,6 +180,10 @@ const handleSettingsSelect = (key: any) => { }, ); } + } else if (key === "re-validate-license") { + rerunCodefairChecks("license"); + } else if (key === "re-validate-metadata") { + rerunCodefairChecks("metadata"); } }; @@ -211,7 +234,7 @@ const handleSettingsSelect = (key: any) => { This repository uses a custom license. + + + + + + + + @@ -282,6 +320,7 @@ const handleSettingsSelect = (key: any) => { data?.licenseRequest?.containsLicense && data?.codeMetadataRequest?.containsMetadata " + class="align-middle items-center" > { codemeta.json + + + + + + @@ -517,7 +571,10 @@ const handleSettingsSelect = (key: any) => {