diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml new file mode 100644 index 0000000..5ec24b0 --- /dev/null +++ b/.github/workflows/test.yml @@ -0,0 +1,40 @@ +name: Test + +on: + push: + branches: [ main, develop, fix-*, feat-* ] + pull_request: + branches: [ main ] + +jobs: + test: + runs-on: ubuntu-latest + strategy: + fail-fast: false + matrix: + python-version: ['3.10', '3.11', '3.12'] + + steps: + - uses: actions/checkout@v4 + + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-version }} + + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install -e . + pip install pytest pytest-cov pandas + + - name: Run unit tests + run: | + python -m pytest tests/ -v --tb=short --cov=cnb_tools --cov-report=term-missing + + - name: Test CLI basics + run: | + cnb-tools + cnb-tools --help + cnb-tools submission --help + diff --git a/README.md b/README.md index 42d7c6e..c1ac2f1 100644 --- a/README.md +++ b/README.md @@ -12,7 +12,7 @@ PyPI version - Supported Python versions + Supported Python versions License @@ -33,23 +33,23 @@ but not limited to, [DREAM Challenges]. ## Requirements -- [Python 3.9+] +- [Python 3.10+] - [Synapse account] To fully utilize **cnb-tools**, you must have a Synapse account and -provide your credentials to the tool. To do so, create a `.synapseConfig` -file in your home directory and enter the following: +provide your credentials to the tool. First, generate a Synapse +[Personal Access Token (PAT)] with all token permissions enabled. -```yaml -[authentication] -authtoken= -``` +Next, run the following command, then follow the prompts to enter +your Synapse username and PAT: -Generate a new Synapse [Personal Access Token (PAT)] with all token -permissions enabled, then copy-paste it into `authtoken`. Save the file. +```console +synapse config +``` -For security, we recommend updating its permissions so that other -users on your machine do not have read access to your credentials, e.g. +This will create a `.synapseConfig` file in your home directory. For +security, we recommend updating its permissions so that other users +on your machine do not have read access to your credentials, e.g. ```console chmod 600 ~/.synapseConfig @@ -58,10 +58,9 @@ chmod 600 ~/.synapseConfig ## Installation For best practice, use a Python environment to install **cnb-tools** -rather than directly into your base env. In our docs, we will be +rather than directly into your base env. In our docs, we will be using [miniconda], but you can use [miniforge], [venv], [pyenv], etc. - ```console # Create a new env and activate it conda create -n cnb-tools python=3.12 -y @@ -114,7 +113,7 @@ docker run --rm \ [https://sage-bionetworks-challenges.github.io/cnb-tools]: https://sage-bionetworks-challenges.github.io/cnb-tools [https://github.com/Sage-Bionetworks-Challenges/cnb-tools]: https://github.com/Sage-Bionetworks-Challenges/cnb-tools [DREAM Challenges]: https://dreamchallenges.org/ -[Python 3.9+]: https://www.python.org/downloads/ +[Python 3.10+]: https://www.python.org/downloads/ [Synapse account]: https://www.synapse.org/#!LoginPlace:0 [Personal Access Token (PAT)]: https://www.synapse.org/#!PersonalAccessTokens: [miniconda]: https://docs.conda.io/projects/miniconda/en/latest/miniconda-install.html diff --git a/cnb_tools/classes/annotation.py b/cnb_tools/classes/annotation.py deleted file mode 100644 index 7e914d3..0000000 --- a/cnb_tools/classes/annotation.py +++ /dev/null @@ -1,73 +0,0 @@ -"""Class representing annotations of a challenge submission.""" - -import json - -from synapseclient import SubmissionStatus -from synapseclient.core.exceptions import SynapseHTTPError -from synapseclient.core.retry import with_retry - -from cnb_tools.classes.base import SynapseBase, UnknownSynapseID - - -class SubmissionAnnotation(SynapseBase): - def __init__(self, sub_id: int): - super().__init__(sub_id) - try: - self._curr_annotations = self.syn.getSubmissionStatus(sub_id) - except SynapseHTTPError as err: - raise UnknownSynapseID( - f"⛔ {err.response.json().get('reason')}. " - "Check the ID and try again." - ) from err - - @property - def curr_annotations(self) -> SubmissionStatus: - """Submission's current list of annotations.""" - return self._curr_annotations - - @curr_annotations.setter - def curr_annotations(self, value: SubmissionStatus): - self._curr_annotations = value - - def __str__(self) -> str: - to_print = f" Status: {self.curr_annotations.status}\n" - to_print += "Annotations:\n" - to_print += json.dumps(self.curr_annotations.submissionAnnotations, indent=2) - return to_print - - # pylint: disable=unsupported-binary-operation - def update( - self, - new_annots: dict[str, str | int | float | bool], - verbose: bool - ) -> None: - self.curr_annotations.submissionAnnotations.update(new_annots) - self.curr_annotations = self.syn.store(self.curr_annotations) - print(f"Submission ID {self.uid} annotations updated.") - - if verbose: - print("Annotations:") - print(json.dumps(self.curr_annotations.submissionAnnotations, indent=2)) - - def update_with_file(self, annots_file: str, verbose: bool) -> None: - with open(annots_file, encoding="utf-8") as f: - new_annots = json.load(f) - - # Filter annotations with null and empty-list values - new_annots = { - key: value - for key, value in new_annots.items() - if value not in [None, []] - } - with_retry( - lambda: self.update(new_annots, verbose), - wait=3, - retries=10, - retry_status_codes=[412, 429, 500, 502, 503, 504], - verbose=True, - ) - - def update_status(self, new_status: str) -> None: - self.curr_annotations.status = new_status - self.syn.store(self.curr_annotations) - print(f"Updated submission ID {self.uid} to status: {new_status}") diff --git a/cnb_tools/classes/base.py b/cnb_tools/classes/base.py deleted file mode 100644 index 0d1723a..0000000 --- a/cnb_tools/classes/base.py +++ /dev/null @@ -1,53 +0,0 @@ -"""General class representing a Synapse entity.""" - -import synapseclient -from synapseclient.core.exceptions import SynapseNoCredentialsError - - -class SynapseBase: - def __init__(self, uid=None): - self._syn = self._check_login() - self._uid = uid - - @property - def syn(self) -> str: - """Synapse object with authentication.""" - return self._syn - - @syn.setter - def syn(self, _: str) -> None: - raise SynapseInternalError("syn object is read-only") - - @property - def uid(self) -> str: - """Synapse entity's unique ID.""" - return self._uid - - @uid.setter - def uid(self, value: str) -> None: - self._uid = value - - # pylint: disable=unsupported-binary-operation - @staticmethod - def _check_login() -> synapseclient.Synapse | None: - try: - return synapseclient.login(silent=True) - except SynapseNoCredentialsError as err: - raise SynapseLoginError( - f"⛔ {err}\n\n" - "Steps on how to provide your Synapse credentials to " - "cnb-tools are available here: " - "https://sage-bionetworks-challenges.github.io/cnb-tools/#requirements" - ) from err - - -class SynapseInternalError(Exception): - pass - - -class SynapseLoginError(SystemExit): - pass - - -class UnknownSynapseID(SystemExit): - pass diff --git a/cnb_tools/classes/participant.py b/cnb_tools/classes/participant.py deleted file mode 100644 index b2ebc22..0000000 --- a/cnb_tools/classes/participant.py +++ /dev/null @@ -1,36 +0,0 @@ -"""Class representing a submission team or individual participant.""" - -import sys - -import typer -from synapseclient import Team -from synapseclient.core.exceptions import SynapseHTTPError - -from cnb_tools.classes.base import SynapseBase - - -class Participant(SynapseBase): - def __str__(self) -> str: - try: - return self.syn.getTeam(self.uid).get("name") - except SynapseHTTPError: - return self.syn.getUserProfile(self.uid).get("userName") - - # pylint: disable=unsupported-binary-operation - def create_team( - self, - name: str, - description: str | None = None, - can_public_join: bool = False - ) -> Team: - try: - team = self.syn.getTeam(name) - use_team = typer.confirm(f"Team '{name}' already exists. Use this team?") - if not use_team: - sys.exit("OK. Try again with a new challenge name.") - except ValueError: - team = Team( - name=name, description=description, canPublicJoin=can_public_join - ) - # team = self.syn.store(team) - return team diff --git a/cnb_tools/classes/queue.py b/cnb_tools/classes/queue.py deleted file mode 100644 index 70a802e..0000000 --- a/cnb_tools/classes/queue.py +++ /dev/null @@ -1,34 +0,0 @@ -"""Class representing a challenge submission evaluation queue.""" - -from synapseclient import Evaluation -from synapseclient.core.exceptions import SynapseHTTPError - -from cnb_tools.classes.base import SynapseBase, UnknownSynapseID - - -class Queue(SynapseBase): - def __init__(self, uid): - super().__init__(uid) - try: - self._queue = self.syn.getEvaluation(uid) - except SynapseHTTPError as err: - raise UnknownSynapseID( - f"⛔ {err.response.json().get('reason')}. " - "Check the ID and try again." - ) from err - - @property - def queue(self) -> Evaluation: - """Synapse evaluation queue.""" - return self._queue - - @queue.setter - def queue(self, value: Evaluation) -> None: - self._queue = value - - def __str__(self) -> str: - return self.queue.name - - def get_challenge_name(self) -> str: - parent_id = self.queue.contentSource - return self.syn.get(parent_id).name diff --git a/cnb_tools/classes/submission.py b/cnb_tools/classes/submission.py deleted file mode 100644 index 2347274..0000000 --- a/cnb_tools/classes/submission.py +++ /dev/null @@ -1,61 +0,0 @@ -"""Class representing a challenge submission.""" - -from pathlib import Path -from synapseclient.core.exceptions import SynapseHTTPError - -from cnb_tools.classes.annotation import SubmissionAnnotation -from cnb_tools.classes.base import SynapseBase, UnknownSynapseID -from cnb_tools.classes.participant import Participant -from cnb_tools.classes.queue import Queue - - -class Submission(SynapseBase): - def __init__(self, sub_id: int): - super().__init__(sub_id) - try: - self._submission = self.syn.getSubmission(sub_id, downloadFile=False) - except SynapseHTTPError as err: - raise UnknownSynapseID( - f"⛔ {err.response.json().get('reason')}. " - "Check the ID and try again." - ) from err - - @property - def submission(self): - """Synapse submission.""" - return self._submission - - @submission.setter - def submission(self, value) -> None: - self._sumission = value - - def delete(self) -> None: - self.syn.delete(self.submission) - print(f"Submission deleted: {self.uid}") - - def download(self, dest) -> None: - if "dockerDigest" in self.submission: - print( - f"Submission ID {self.uid} is a Docker image 🐳 To " - "'download', run the following:\n\n" - f"docker pull {self.submission.dockerRepositoryName}" - f"@{self.submission.dockerDigest}\n\n" - "If you receive an error, try logging in first with: " - "docker login docker.synapse.org" - ) - else: - self.syn.getSubmission(self.uid, downloadLocation=dest) - location = Path.cwd() if str(dest) == "." else dest - print(f"Submission ID {self.uid} downloaded to: {location}") - - def info(self, verbose) -> None: - challenge = Queue(self.submission.evaluationId).get_challenge_name() - submitter_id = self.submission.get("teamId") or self.submission.get("userId") - submitter = Participant(submitter_id) - print(f" ID: {self.uid}") - print(f" Challenge: {challenge}") - print(f" Date: {self.submission.createdOn[:10]}") - print(f" Submitter: {submitter}") - if verbose: - annotations = SubmissionAnnotation(self.uid) - print(annotations) diff --git a/cnb_tools/commands/submission_cli.py b/cnb_tools/commands/submission_cli.py index 79df49f..5dacd17 100644 --- a/cnb_tools/commands/submission_cli.py +++ b/cnb_tools/commands/submission_cli.py @@ -13,9 +13,8 @@ from typing_extensions import Annotated import typer -from cnb_tools.classes.base import UnknownSynapseID -from cnb_tools.classes.annotation import SubmissionAnnotation -from cnb_tools.classes.submission import Submission +from cnb_tools.modules.base import UnknownSynapseID +from cnb_tools.modules import annotation, submission class Status(str, Enum): @@ -49,8 +48,7 @@ def annotate( ] = False, ): """Annotate one or more submission(s) with a JSON file.""" - submission_annots = SubmissionAnnotation(submission_id) - submission_annots.update_with_file(json_file, verbose) + annotation.update_annotations_from_file(submission_id, str(json_file), verbose) @app.command() @@ -70,8 +68,7 @@ def change_status( """Update one or more submission statuses.""" for submission_id in submission_ids: try: - submission_annots = SubmissionAnnotation(submission_id) - submission_annots.update_status(new_status) + annotation.update_submission_status(submission_id, new_status.value) except UnknownSynapseID as err: if skip_errors: print(f"Unknown submission ID: {submission_id} - skipping...") @@ -110,8 +107,7 @@ def delete( if force: for submission_id in submission_ids: try: - submission = Submission(submission_id) - submission.delete() + submission.delete_submission(submission_id) except UnknownSynapseID as err: if skip_errors: print(f"Unknown submission ID: {submission_id} - skipping...") @@ -134,8 +130,7 @@ def download( ] = ".", ): """Get a submission (file/Docker image)""" - submission = Submission(submission_id) - submission.download(dest) + submission.download_submission(submission_id, str(dest)) @app.command() @@ -154,8 +149,7 @@ def info( ] = False, ): """Get information about a submission""" - submission = Submission(submission_id) - submission.info(verbose) + submission.print_submission_info(submission_id, verbose) @app.command() @@ -173,7 +167,5 @@ def reset( ): """Reset one or more submission to RECEIVED.""" change_status( - submission_ids=submission_ids, - new_status="RECEIVED", - skip_errors=skip_errors + submission_ids=submission_ids, new_status="RECEIVED", skip_errors=skip_errors ) diff --git a/cnb_tools/main_cli.py b/cnb_tools/main_cli.py index 06fc7ae..17bb07c 100644 --- a/cnb_tools/main_cli.py +++ b/cnb_tools/main_cli.py @@ -5,6 +5,7 @@ $ cnb-tools --help $ cnb-tools --version """ + from typing import Optional from typing_extensions import Annotated import typer diff --git a/cnb_tools/modules/annotation.py b/cnb_tools/modules/annotation.py new file mode 100644 index 0000000..53ffefd --- /dev/null +++ b/cnb_tools/modules/annotation.py @@ -0,0 +1,128 @@ +"""Module for managing the annotations of challenge submissions. + +This module provides utility functions that extend synapseclient for managing +submission annotations in Synapse challenges. +""" + +import json + +from synapseclient import SubmissionStatus +from synapseclient.core.exceptions import SynapseHTTPError +from synapseclient.core.retry import with_retry + +from cnb_tools.modules.base import get_synapse_client, UnknownSynapseID + + +def get_submission_status(submission_id: int) -> SubmissionStatus: + """Get the submission status object containing annotations. + + Args: + submission_id: ID of the submission + + Returns: + SubmissionStatus object with current annotations + + Raises: + UnknownSynapseID: If the submission ID is invalid + """ + syn = get_synapse_client() + try: + return syn.getSubmissionStatus(submission_id) + except SynapseHTTPError as err: + raise UnknownSynapseID( + f"⛔ {err.response.json().get('reason')}. " "Check the ID and try again." + ) from err + + +def format_annotations(submission_status: SubmissionStatus) -> str: + """Format submission annotations for display. + + Args: + submission_status: SubmissionStatus object + + Returns: + Formatted string representation of status and annotations + """ + output = f" Status: {submission_status.status}\n" + output += "Annotations:\n" + output += json.dumps(submission_status.submissionAnnotations, indent=2) + return output + + +def update_annotations( + submission_id: int, + new_annotations: dict[str, str | int | float | bool], + verbose: bool = False, +) -> SubmissionStatus: + """Update submission annotations. + + Args: + submission_id: ID of the submission + new_annotations: Dictionary of annotations to add/update + verbose: If True, print updated annotations + + Returns: + Updated SubmissionStatus object + """ + syn = get_synapse_client() + status = get_submission_status(submission_id) + status.submissionAnnotations.update(new_annotations) + status = syn.store(status) + + print(f"Submission ID {submission_id} annotations updated.") + + if verbose: + print("Annotations:") + print(json.dumps(status.submissionAnnotations, indent=2)) + + return status + + +def update_annotations_from_file( + submission_id: int, annots_file: str, verbose: bool = False +) -> SubmissionStatus: + """Update submission annotations from a JSON file. + + Args: + submission_id: ID of the submission + annots_file: Path to JSON file containing annotations + verbose: If True, print updated annotations + + Returns: + Updated SubmissionStatus object + """ + with open(annots_file, encoding="utf-8") as f: + new_annotations = json.load(f) + + # Filter annotations with null and empty-list values + new_annotations = { + key: value for key, value in new_annotations.items() if value not in [None, []] + } + + return with_retry( + lambda: update_annotations(submission_id, new_annotations, verbose), + wait=3, + retries=10, + retry_status_codes=[412, 429, 500, 502, 503, 504], + verbose=True, + ) + + +def update_submission_status(submission_id: int, new_status: str) -> SubmissionStatus: + """Update submission status. + + Args: + submission_id: ID of the submission + new_status: New status value (e.g., 'ACCEPTED', 'REJECTED', 'SCORED') + + Returns: + Updated SubmissionStatus object + """ + syn = get_synapse_client() + status = get_submission_status(submission_id) + status.status = new_status + status = syn.store(status) + + print(f"Updated submission ID {submission_id} to status: {new_status}") + + return status diff --git a/cnb_tools/modules/base.py b/cnb_tools/modules/base.py new file mode 100644 index 0000000..7a5ff2e --- /dev/null +++ b/cnb_tools/modules/base.py @@ -0,0 +1,28 @@ +"""Base module for cnb-tools, including Synapse client management and custom exceptions.""" + +import synapseclient +from synapseclient.core.exceptions import SynapseNoCredentialsError + + +def get_synapse_client(): + try: + return synapseclient.login(silent=True) + except SynapseNoCredentialsError as err: + raise SynapseLoginError( + f"⛔ {err}\n\n" + "Steps on how to provide your Synapse credentials to " + "cnb-tools are available here: " + "https://sage-bionetworks-challenges.github.io/cnb-tools/#requirements" + ) from err + + +class SynapseInternalError(Exception): + pass + + +class SynapseLoginError(SystemExit): + pass + + +class UnknownSynapseID(SystemExit): + pass diff --git a/cnb_tools/modules/participant.py b/cnb_tools/modules/participant.py new file mode 100644 index 0000000..df26593 --- /dev/null +++ b/cnb_tools/modules/participant.py @@ -0,0 +1,57 @@ +"""Module for managing submission teams or individual participants. + +This module provides utility functions that extend synapseclient for managing +teams and participants in Synapse challenges. +""" + +import sys + +import typer +from synapseclient import Team +from synapseclient.core.exceptions import SynapseHTTPError + +from cnb_tools.modules.base import get_synapse_client + + +def get_participant_name(participant_id: int) -> str: + """Get the name of a participant (team or user). + + Args: + participant_id: Team ID or User ID + + Returns: + Team name or username + """ + syn = get_synapse_client() + try: + return syn.getTeam(participant_id).get("name") + except SynapseHTTPError: + return syn.getUserProfile(participant_id).get("userName") + + +def create_team( + name: str, description: str | None = None, can_public_join: bool = False +) -> Team: + """Create a new team or get an existing team by name. + + Args: + name: Team name + description: Team description (optional) + can_public_join: Whether the team can be joined publicly + + Returns: + Team object (existing or new) + + Raises: + SystemExit: If user chooses not to use an existing team + """ + syn = get_synapse_client() + try: + team = syn.getTeam(name) + use_team = typer.confirm(f"Team '{name}' already exists. Use this team?") + if not use_team: + sys.exit("OK. Try again with a new challenge name.") + except ValueError: + team = Team(name=name, description=description, canPublicJoin=can_public_join) + # team = syn.store(team) + return team diff --git a/cnb_tools/modules/queue.py b/cnb_tools/modules/queue.py new file mode 100644 index 0000000..637b0e9 --- /dev/null +++ b/cnb_tools/modules/queue.py @@ -0,0 +1,59 @@ +"""Module for managing the challenge submission evaluation queues. + +This module provides utility functions that extend synapseclient for managing +evaluation queues in Synapse challenges. +""" + +from synapseclient import Evaluation +from synapseclient.core.exceptions import SynapseHTTPError + +from cnb_tools.modules.base import get_synapse_client, UnknownSynapseID + + +def get_evaluation(evaluation_id: int) -> Evaluation: + """Get an evaluation queue by ID. + + Args: + evaluation_id: Evaluation queue ID + + Returns: + Evaluation object + + Raises: + UnknownSynapseID: If the evaluation ID is invalid + """ + syn = get_synapse_client() + try: + return syn.getEvaluation(evaluation_id) + except SynapseHTTPError as err: + raise UnknownSynapseID( + f"⛔ {err.response.json().get('reason')}. " "Check the ID and try again." + ) from err + + +def get_evaluation_name(evaluation_id: int) -> str: + """Get the name of an evaluation queue. + + Args: + evaluation_id: Evaluation queue ID + + Returns: + Evaluation queue name + """ + evaluation = get_evaluation(evaluation_id) + return evaluation.name + + +def get_challenge_name_from_evaluation(evaluation_id: int) -> str: + """Get the challenge name for an evaluation queue. + + Args: + evaluation_id: Evaluation queue ID + + Returns: + Challenge name + """ + syn = get_synapse_client() + evaluation = get_evaluation(evaluation_id) + parent_id = evaluation.contentSource + return syn.get(parent_id).name diff --git a/cnb_tools/modules/submission.py b/cnb_tools/modules/submission.py new file mode 100644 index 0000000..0efed20 --- /dev/null +++ b/cnb_tools/modules/submission.py @@ -0,0 +1,131 @@ +"""Module for managing challenge submissions. + +This module provides utility functions that extend synapseclient for managing +submissions in Synapse challenges. +""" + +from pathlib import Path +from synapseclient import Submission as SynapseSubmission +from synapseclient.core.exceptions import SynapseHTTPError + +from cnb_tools.modules.base import get_synapse_client, UnknownSynapseID +from cnb_tools.modules import annotation + + +def get_submission(submission_id: int, download_file: bool = False) -> SynapseSubmission: + """Get a submission by ID. + + Args: + submission_id: ID of the submission + download_file: If True, download the submission file + + Returns: + Synapse Submission object + + Raises: + UnknownSynapseID: If the submission ID is invalid + """ + syn = get_synapse_client() + try: + return syn.getSubmission(submission_id, downloadFile=download_file) + except SynapseHTTPError as err: + raise UnknownSynapseID( + f"⛔ {err.response.json().get('reason')}. " + "Check the ID and try again." + ) from err + + +def delete_submission(submission_id: int) -> None: + """Delete a submission. + + Args: + submission_id: ID of the submission to delete + """ + syn = get_synapse_client() + submission = get_submission(submission_id) + syn.delete(submission) + print(f"Submission deleted: {submission_id}") + + +def download_submission(submission_id: int, dest: str = ".") -> None: + """Download a submission file or display Docker pull command. + + Args: + submission_id: ID of the submission + dest: Destination directory for download (default: current directory) + """ + syn = get_synapse_client() + submission = get_submission(submission_id) + + if "dockerDigest" in submission: + print( + f"Submission ID {submission_id} is a Docker image 🐳 To " + "'download', run the following:\n\n" + f"docker pull {submission.dockerRepositoryName}" + f"@{submission.dockerDigest}\n\n" + "If you receive an error, try logging in first with: " + "docker login docker.synapse.org" + ) + else: + syn.getSubmission(submission_id, downloadLocation=dest) + location = Path.cwd() if str(dest) == "." else dest + print(f"Submission ID {submission_id} downloaded to: {location}") + + +def get_submitter_name(submitter_id: int) -> str: + """Get the name of a submitter (team or user). + + Args: + submitter_id: Team ID or User ID + + Returns: + Team name or username + """ + syn = get_synapse_client() + try: + return syn.getTeam(submitter_id).get("name") + except SynapseHTTPError: + return syn.getUserProfile(submitter_id).get("userName") + + +def get_challenge_name(evaluation_id: int) -> str: + """Get the challenge name for an evaluation queue. + + Args: + evaluation_id: Evaluation queue ID + + Returns: + Challenge name + """ + syn = get_synapse_client() + try: + evaluation = syn.getEvaluation(evaluation_id) + parent_id = evaluation.contentSource + return syn.get(parent_id).name + except SynapseHTTPError as err: + raise UnknownSynapseID( + f"⛔ {err.response.json().get('reason')}. " + "Check the ID and try again." + ) from err + + +def print_submission_info(submission_id: int, verbose: bool = False) -> None: + """Print information about a submission. + + Args: + submission_id: ID of the submission + verbose: If True, also print submission annotations + """ + submission = get_submission(submission_id) + challenge = get_challenge_name(submission.evaluationId) + submitter_id = submission.get("teamId") or submission.get("userId") + submitter = get_submitter_name(submitter_id) + + print(f" ID: {submission_id}") + print(f" Challenge: {challenge}") + print(f" Date: {submission.createdOn[:10]}") + print(f" Submitter: {submitter}") + + if verbose: + status = annotation.get_submission_status(submission_id) + print(annotation.format_annotations(status)) diff --git a/cnb_tools/validation_toolkit.py b/cnb_tools/validation_toolkit.py index 207d730..0e5af66 100644 --- a/cnb_tools/validation_toolkit.py +++ b/cnb_tools/validation_toolkit.py @@ -1,5 +1,3 @@ -from typing import Union - from pandas import Series @@ -100,9 +98,7 @@ def check_nan_values(pred_col: Series) -> str: return "" -def check_binary_values( - pred_col: Series, label1: int = 0, label2: int = 1 -) -> str: +def check_binary_values(pred_col: Series, label1: int = 0, label2: int = 1) -> str: """Check that values are binary (default: 0 or 1). Tip: Example Use Case @@ -123,9 +119,7 @@ def check_binary_values( def check_values_range( - pred_col: Series, - min_val: Union[int, float] = 0, - max_val: Union[int, float] = 1 + pred_col: Series, min_val: int | float = 0, max_val: int | float = 1 ) -> str: """Check that values are between min and max values, inclusive. diff --git a/docs/changelog/release-notes.md b/docs/changelog/release-notes.md index 23fb3bb..14ba41f 100644 --- a/docs/changelog/release-notes.md +++ b/docs/changelog/release-notes.md @@ -7,7 +7,15 @@ - Add How-To tutorial on how the Validation Toolkit can be used ### Bug fixes -- Remove custom classes, as to prevent future confusion with synapseclient's classes +- Refactor all modules to remove custom classes ([#24](https://github.com/Sage-Bionetworks-Challenges/cnb-tools/issues/24)) + - Convert `annotation.py`, `submission.py`, `participant.py`, and `queue.py` to functional utilities + - All modules now act as extensions to `synapseclient` rather than wrapping it with custom classes + - Synapse authentication is now handled automatically within each function via `get_synapse_client()` + - Simplifies API usage and prevents confusion with synapseclient's native classes + +### Internal +- Drop support for Python 3.9 (reached [end of life](https://devguide.python.org/versions/)) +- Add unit tests ## 0.3.2 diff --git a/docs/index.md b/docs/index.md index 5992611..5bcd313 100644 --- a/docs/index.md +++ b/docs/index.md @@ -9,7 +9,7 @@ PyPI version - Supported Python versions + Supported Python versions License @@ -29,23 +29,23 @@ but not limited to, [DREAM Challenges]. ## Requirements -- [Python 3.9+] +- [Python 3.10+] - [Synapse account] To fully utilize **cnb-tools**, you must have a Synapse account and -provide your credentials to the tool. To do so, create a `.synapseConfig` -file in your home directory and enter the following: +provide your credentials to the tool. First, generate a Synapse +[Personal Access Token (PAT)] with all token permissions enabled. -```yaml -[authentication] -authtoken= -``` +Next, run the following command, then follow the prompts to enter +your Synapse username and PAT: -Generate a new Synapse [Personal Access Token (PAT)] with all token -permissions enabled, then copy-paste it into `authtoken`. Save the file. +```console +synapse config +``` -For security, we recommend updating its permissions so that other -users on your machine do not have read access to your credentials, e.g. +This will create a `.synapseConfig` file in your home directory. For +security, we recommend updating its permissions so that other users +on your machine do not have read access to your credentials, e.g. ```console @@ -120,7 +120,7 @@ $ docker run --rm \ [https://sage-bionetworks-challenges.github.io/cnb-tools]: https://sage-bionetworks-challenges.github.io/cnb-tools [https://github.com/Sage-Bionetworks-Challenges/cnb-tools]: https://github.com/Sage-Bionetworks-Challenges/cnb-tools [DREAM Challenges]: https://dreamchallenges.org/ -[Python 3.9+]: https://www.python.org/downloads/ +[Python 3.10+]: https://www.python.org/downloads/ [Synapse account]: https://www.synapse.org/#!LoginPlace:0 [Personal Access Token (PAT)]: https://www.synapse.org/#!PersonalAccessTokens: [miniconda]: https://docs.conda.io/projects/miniconda/en/latest/miniconda-install.html diff --git a/poetry.lock b/poetry.lock index c32cc7b..2927b42 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.2.1 and should not be changed by hand. [[package]] name = "anyio" @@ -6,6 +6,7 @@ version = "4.3.0" description = "High level compatibility layer for multiple asynchronous event loop implementations" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "anyio-4.3.0-py3-none-any.whl", hash = "sha256:048e05d0f6caeed70d731f3db756d35dcc1f35747c8c403364a8332c630441b8"}, {file = "anyio-4.3.0.tar.gz", hash = "sha256:f75253795a87df48568485fd18cdd2a3fa5c4f7c5be8e5e36637733fce06fed6"}, @@ -19,7 +20,7 @@ typing-extensions = {version = ">=4.1", markers = "python_version < \"3.11\""} [package.extras] doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"] -test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)"] +test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17) ; platform_python_implementation == \"CPython\" and platform_system != \"Windows\""] trio = ["trio (>=0.23)"] [[package]] @@ -28,6 +29,7 @@ version = "2.0.4" description = "Simple LRU cache for asyncio" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "async-lru-2.0.4.tar.gz", hash = "sha256:b8a59a5df60805ff63220b2a0c5b5393da5521b113cd5465a44eb037d81a5627"}, {file = "async_lru-2.0.4-py3-none-any.whl", hash = "sha256:ff02944ce3c288c5be660c42dbcca0742b32c3b279d6dceda655190240b99224"}, @@ -42,6 +44,7 @@ version = "1.0.1" description = "Like atexit, but for asyncio" optional = false python-versions = ">=3.6" +groups = ["main"] files = [ {file = "asyncio-atexit-1.0.1.tar.gz", hash = "sha256:1d0c71544b8ee2c484d322844ee72c0875dde6f250c0ed5b6993592ab9f7d436"}, {file = "asyncio_atexit-1.0.1-py3-none-any.whl", hash = "sha256:d93d5f7d5633a534abd521ce2896ed0fbe8de170bb1e65ec871d1c20eac9d376"}, @@ -56,6 +59,7 @@ version = "2.15.0" description = "Internationalization utilities" optional = false python-versions = ">=3.8" +groups = ["docs"] files = [ {file = "Babel-2.15.0-py3-none-any.whl", hash = "sha256:08706bdad8d0a3413266ab61bd6c34d0c28d6e1e7badf40a2cebe67644e2e1fb"}, {file = "babel-2.15.0.tar.gz", hash = "sha256:8daf0e265d05768bc6c7a314cf1321e9a123afc328cc635c18622a2f30a04413"}, @@ -64,23 +68,13 @@ files = [ [package.extras] dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"] -[[package]] -name = "backoff" -version = "2.2.1" -description = "Function decoration for backoff and retry" -optional = false -python-versions = ">=3.7,<4.0" -files = [ - {file = "backoff-2.2.1-py3-none-any.whl", hash = "sha256:63579f9a0628e06278f7e47b7d7d5b6ce20dc65c5e96a6f3ca99a6adca0396e8"}, - {file = "backoff-2.2.1.tar.gz", hash = "sha256:03f829f5bb1923180821643f8753b0502c3b682293992485b0eef2807afa5cba"}, -] - [[package]] name = "certifi" version = "2024.2.2" description = "Python package for providing Mozilla's CA Bundle." optional = false python-versions = ">=3.6" +groups = ["main", "docs"] files = [ {file = "certifi-2024.2.2-py3-none-any.whl", hash = "sha256:dc383c07b76109f368f6106eee2b593b04a011ea4d55f652c6ca24a754d1cdd1"}, {file = "certifi-2024.2.2.tar.gz", hash = "sha256:0569859f95fc761b18b45ef421b1290a0f65f147e92a1e5eb3e635f9a5e4e66f"}, @@ -92,6 +86,7 @@ version = "3.3.2" description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." optional = false python-versions = ">=3.7.0" +groups = ["main", "docs"] files = [ {file = "charset-normalizer-3.3.2.tar.gz", hash = "sha256:f30c3cb33b24454a82faecaf01b19c18562b1e89558fb6c56de4d9118a032fd5"}, {file = "charset_normalizer-3.3.2-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:25baf083bf6f6b341f4121c2f3c548875ee6f5339300e08be3f2b2ba1721cdd3"}, @@ -191,6 +186,7 @@ version = "8.1.7" description = "Composable command line interface toolkit" optional = false python-versions = ">=3.7" +groups = ["main", "docs"] files = [ {file = "click-8.1.7-py3-none-any.whl", hash = "sha256:ae74fb96c20a0277a1d615f1e4d73c8414f5a98db8b799a7931d1582f3390c28"}, {file = "click-8.1.7.tar.gz", hash = "sha256:ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de"}, @@ -199,27 +195,18 @@ files = [ [package.dependencies] colorama = {version = "*", markers = "platform_system == \"Windows\""} -[[package]] -name = "cloudpickle" -version = "3.0.0" -description = "Pickler class to extend the standard pickle.Pickler functionality" -optional = false -python-versions = ">=3.8" -files = [ - {file = "cloudpickle-3.0.0-py3-none-any.whl", hash = "sha256:246ee7d0c295602a036e86369c77fecda4ab17b506496730f2f576d9016fd9c7"}, - {file = "cloudpickle-3.0.0.tar.gz", hash = "sha256:996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882"}, -] - [[package]] name = "colorama" version = "0.4.6" description = "Cross-platform colored terminal text." optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" +groups = ["main", "docs", "test"] files = [ {file = "colorama-0.4.6-py2.py3-none-any.whl", hash = "sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6"}, {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"}, ] +markers = {test = "sys_platform == \"win32\""} [[package]] name = "deprecated" @@ -227,6 +214,7 @@ version = "1.2.14" description = "Python @deprecated decorator to deprecate old python classes, functions or methods." optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +groups = ["main"] files = [ {file = "Deprecated-1.2.14-py2.py3-none-any.whl", hash = "sha256:6fac8b097794a90302bdbb17b9b815e732d3c4720583ff1b198499d78470466c"}, {file = "Deprecated-1.2.14.tar.gz", hash = "sha256:e5323eb936458dccc2582dc6f9c322c852a775a27065ff2b0c4970b9d53d01b3"}, @@ -244,6 +232,8 @@ version = "1.2.1" description = "Backport of PEP 654 (exception groups)" optional = false python-versions = ">=3.7" +groups = ["main", "test"] +markers = "python_version == \"3.10\"" files = [ {file = "exceptiongroup-1.2.1-py3-none-any.whl", hash = "sha256:5258b9ed329c5bbdd31a309f53cbfb0b155341807f6ff7606a1e801a891b29ad"}, {file = "exceptiongroup-1.2.1.tar.gz", hash = "sha256:a4785e48b045528f5bfe627b6ad554ff32def154f42372786903b7abcfe1aa16"}, @@ -258,6 +248,7 @@ version = "2.1.0" description = "Copy your docs directly to the gh-pages branch." optional = false python-versions = "*" +groups = ["docs"] files = [ {file = "ghp-import-2.1.0.tar.gz", hash = "sha256:9c535c4c61193c2df8871222567d7fd7e5014d835f97dc7b7439069e2413d343"}, {file = "ghp_import-2.1.0-py3-none-any.whl", hash = "sha256:8337dd7b50877f163d4c0289bc1f1c7f127550241988d568c1db512c4324a619"}, @@ -271,20 +262,21 @@ dev = ["flake8", "markdown", "twine", "wheel"] [[package]] name = "googleapis-common-protos" -version = "1.63.0" +version = "1.72.0" description = "Common protobufs used in Google APIs" optional = false python-versions = ">=3.7" +groups = ["main"] files = [ - {file = "googleapis-common-protos-1.63.0.tar.gz", hash = "sha256:17ad01b11d5f1d0171c06d3ba5c04c54474e883b66b949722b4938ee2694ef4e"}, - {file = "googleapis_common_protos-1.63.0-py2.py3-none-any.whl", hash = "sha256:ae45f75702f7c08b541f750854a678bd8f534a1a6bace6afe975f1d0a82d6632"}, + {file = "googleapis_common_protos-1.72.0-py3-none-any.whl", hash = "sha256:4299c5a82d5ae1a9702ada957347726b167f9f8d1fc352477702a1e851ff4038"}, + {file = "googleapis_common_protos-1.72.0.tar.gz", hash = "sha256:e55a601c1b32b52d7a3e65f43563e2aa61bcd737998ee672ac9b951cd49319f5"}, ] [package.dependencies] -protobuf = ">=3.19.5,<3.20.0 || >3.20.0,<3.20.1 || >3.20.1,<4.21.1 || >4.21.1,<4.21.2 || >4.21.2,<4.21.3 || >4.21.3,<4.21.4 || >4.21.4,<4.21.5 || >4.21.5,<5.0.0.dev0" +protobuf = ">=3.20.2,<4.21.1 || >4.21.1,<4.21.2 || >4.21.2,<4.21.3 || >4.21.3,<4.21.4 || >4.21.4,<4.21.5 || >4.21.5,<7.0.0" [package.extras] -grpc = ["grpcio (>=1.44.0,<2.0.0.dev0)"] +grpc = ["grpcio (>=1.44.0,<2.0.0)"] [[package]] name = "griffe" @@ -292,6 +284,7 @@ version = "0.45.0" description = "Signatures for entire Python programs. Extract the structure, the frame, the skeleton of your project, to generate API documentation or find breaking changes in your API." optional = false python-versions = ">=3.8" +groups = ["docs"] files = [ {file = "griffe-0.45.0-py3-none-any.whl", hash = "sha256:90fe5c90e1b0ca7dd6fee78f9009f4e01b37dbc9ab484a9b2c1578915db1e571"}, {file = "griffe-0.45.0.tar.gz", hash = "sha256:85cb2868d026ea51c89bdd589ad3ccc94abc5bd8d5d948e3d4450778a2a05b4a"}, @@ -302,35 +295,37 @@ colorama = ">=0.4" [[package]] name = "h11" -version = "0.14.0" +version = "0.16.0" description = "A pure-Python, bring-your-own-I/O implementation of HTTP/1.1" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" +groups = ["main"] files = [ - {file = "h11-0.14.0-py3-none-any.whl", hash = "sha256:e3fe4ac4b851c468cc8363d500db52c2ead036020723024a109d37346efaa761"}, - {file = "h11-0.14.0.tar.gz", hash = "sha256:8f19fbbe99e72420ff35c00b27a34cb9937e902a8b810e2c88300c6f0a3b699d"}, + {file = "h11-0.16.0-py3-none-any.whl", hash = "sha256:63cf8bbe7522de3bf65932fda1d9c2772064ffb3dae62d55932da54b31cb6c86"}, + {file = "h11-0.16.0.tar.gz", hash = "sha256:4e35b956cf45792e4caa5885e69fba00bdbc6ffafbfa020300e549b208ee5ff1"}, ] [[package]] name = "httpcore" -version = "1.0.5" +version = "1.0.9" description = "A minimal low-level HTTP client." optional = false python-versions = ">=3.8" +groups = ["main"] files = [ - {file = "httpcore-1.0.5-py3-none-any.whl", hash = "sha256:421f18bac248b25d310f3cacd198d55b8e6125c107797b609ff9b7a6ba7991b5"}, - {file = "httpcore-1.0.5.tar.gz", hash = "sha256:34a38e2f9291467ee3b44e89dd52615370e152954ba21721378a87b2960f7a61"}, + {file = "httpcore-1.0.9-py3-none-any.whl", hash = "sha256:2d400746a40668fc9dec9810239072b40b4484b640a8c38fd654a024c7a1bf55"}, + {file = "httpcore-1.0.9.tar.gz", hash = "sha256:6e34463af53fd2ab5d807f399a9b45ea31c3dfa2276f15a2c3f00afff6e176e8"}, ] [package.dependencies] certifi = "*" -h11 = ">=0.13,<0.15" +h11 = ">=0.16" [package.extras] asyncio = ["anyio (>=4.0,<5.0)"] http2 = ["h2 (>=3,<5)"] socks = ["socksio (==1.*)"] -trio = ["trio (>=0.22.0,<0.26.0)"] +trio = ["trio (>=0.22.0,<1.0)"] [[package]] name = "httpx" @@ -338,6 +333,7 @@ version = "0.27.0" description = "The next generation HTTP client." optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "httpx-0.27.0-py3-none-any.whl", hash = "sha256:71d5465162c13681bff01ad59b2cc68dd838ea1f10e51574bac27103f00c91a5"}, {file = "httpx-0.27.0.tar.gz", hash = "sha256:a0cb88a46f32dc874e04ee956e4c2764aba2aa228f650b06788ba6bda2962ab5"}, @@ -351,7 +347,7 @@ idna = "*" sniffio = "*" [package.extras] -brotli = ["brotli", "brotlicffi"] +brotli = ["brotli ; platform_python_implementation == \"CPython\"", "brotlicffi ; platform_python_implementation != \"CPython\""] cli = ["click (==8.*)", "pygments (==2.*)", "rich (>=10,<14)"] http2 = ["h2 (>=3,<5)"] socks = ["socksio (==1.*)"] @@ -362,6 +358,7 @@ version = "3.7" description = "Internationalized Domain Names in Applications (IDNA)" optional = false python-versions = ">=3.5" +groups = ["main", "docs"] files = [ {file = "idna-3.7-py3-none-any.whl", hash = "sha256:82fee1fc78add43492d3a1898bfa6d8a904cc97d8427f683ed8e798d07761aa0"}, {file = "idna-3.7.tar.gz", hash = "sha256:028ff3aadf0609c1fd278d8ea3089299412a7a8b9bd005dd08b9f8285bcb5cfc"}, @@ -373,6 +370,7 @@ version = "6.11.0" description = "Read metadata from Python packages" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "importlib_metadata-6.11.0-py3-none-any.whl", hash = "sha256:f0afba6205ad8f8947c7d338b5342d5db2afbfd82f9cbef7879a9539cc12eb9b"}, {file = "importlib_metadata-6.11.0.tar.gz", hash = "sha256:1231cf92d825c9e03cfc4da076a16de6422c863558229ea0b22b675657463443"}, @@ -384,7 +382,7 @@ zipp = ">=0.5" [package.extras] docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"] perf = ["ipython"] -testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)", "pytest-ruff"] +testing = ["flufl.flake8", "importlib-resources (>=1.3) ; 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Easy to code. Based on Python type hints." optional = false python-versions = ">=3.6" +groups = ["main"] files = [ {file = "typer-0.9.4-py3-none-any.whl", hash = "sha256:aa6c4a4e2329d868b80ecbaf16f807f2b54e192209d7ac9dd42691d63f7a54eb"}, {file = "typer-0.9.4.tar.gz", hash = "sha256:f714c2d90afae3a7929fcd72a3abb08df305e1ff61719381384211c4070af57f"}, @@ -1338,25 +1735,39 @@ version = "4.11.0" description = "Backported and Experimental Type Hints for Python 3.8+" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "typing_extensions-4.11.0-py3-none-any.whl", hash = "sha256:c1f94d72897edaf4ce775bb7558d5b79d8126906a14ea5ed1635921406c0387a"}, {file = "typing_extensions-4.11.0.tar.gz", hash = "sha256:83f085bd5ca59c80295fc2a82ab5dac679cbe02b9f33f7d83af68e241bea51b0"}, ] +[[package]] +name = "tzdata" +version = "2025.2" +description = "Provider of IANA time zone data" +optional = false +python-versions = ">=2" +groups = ["main"] +files = [ + {file = "tzdata-2025.2-py2.py3-none-any.whl", hash = "sha256:1a403fada01ff9221ca8044d701868fa132215d84beb92242d9acd2147f667a8"}, + {file = "tzdata-2025.2.tar.gz", hash = "sha256:b60a638fcc0daffadf82fe0f57e53d06bdec2f36c4df66280ae79bce6bd6f2b9"}, +] + [[package]] name = "urllib3" version = "1.26.18" description = "HTTP library with thread-safe connection pooling, file post, and more." optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" +groups = ["main", "docs"] files = [ {file = "urllib3-1.26.18-py2.py3-none-any.whl", hash = "sha256:34b97092d7e0a3a8cf7cd10e386f401b3737364026c45e622aa02903dffe0f07"}, {file = "urllib3-1.26.18.tar.gz", hash = "sha256:f8ecc1bba5667413457c529ab955bf8c67b45db799d159066261719e328580a0"}, ] [package.extras] -brotli = ["brotli (==1.0.9)", "brotli (>=1.0.9)", "brotlicffi (>=0.8.0)", "brotlipy (>=0.6.0)"] -secure = ["certifi", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "ipaddress", "pyOpenSSL (>=0.14)", "urllib3-secure-extra"] +brotli = ["brotli (==1.0.9) ; os_name != \"nt\" and python_version < \"3\" and platform_python_implementation == \"CPython\"", "brotli (>=1.0.9) ; python_version >= \"3\" and platform_python_implementation == \"CPython\"", "brotlicffi (>=0.8.0) ; (os_name != \"nt\" or python_version >= \"3\") and platform_python_implementation != \"CPython\"", "brotlipy (>=0.6.0) ; os_name == \"nt\" and python_version < \"3\""] +secure = ["certifi", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "ipaddress ; python_version == \"2.7\"", "pyOpenSSL (>=0.14)", "urllib3-secure-extra"] socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] [[package]] @@ -1365,6 +1776,7 @@ version = "4.0.0" description = "Filesystem events monitoring" optional = false python-versions = ">=3.8" +groups = ["docs"] files = [ {file = "watchdog-4.0.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:39cb34b1f1afbf23e9562501673e7146777efe95da24fab5707b88f7fb11649b"}, {file = "watchdog-4.0.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:c522392acc5e962bcac3b22b9592493ffd06d1fc5d755954e6be9f4990de932b"}, @@ -1406,6 +1818,7 @@ version = "1.16.0" description = "Module for decorators, wrappers and monkey patching." optional = false python-versions = ">=3.6" +groups = ["main"] files = [ {file = "wrapt-1.16.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:ffa565331890b90056c01db69c0fe634a776f8019c143a5ae265f9c6bc4bd6d4"}, {file = "wrapt-1.16.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:e4fdb9275308292e880dcbeb12546df7f3e0f96c6b41197e0cf37d2826359020"}, @@ -1485,6 +1898,7 @@ version = "3.18.2" description = "Backport of pathlib-compatible object wrapper for zip files" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "zipp-3.18.2-py3-none-any.whl", hash = "sha256:dce197b859eb796242b0622af1b8beb0a722d52aa2f57133ead08edd5bf5374e"}, {file = "zipp-3.18.2.tar.gz", hash = "sha256:6278d9ddbcfb1f1089a88fde84481528b07b0e10474e09dcfe53dad4069fa059"}, @@ -1495,6 +1909,6 @@ docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.link testing = ["big-O", "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 = "^3.9" -content-hash = "173cc8bb0b09db652af4c46e683c3bafdf365328c34eccc6b0089909d92b0e7f" +lock-version = "2.1" +python-versions = ">=3.10,<3.14" +content-hash = "dffc126d383906d864314633e479606d4dc927bfc97db6c58f115e950b54a102" diff --git a/pyproject.toml b/pyproject.toml index 4b86505..68aeec6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "cnb-tools" -version = "0.3.2" +version = "0.3.3" description = "Convenience tools/functions for challenges and benchmarking on Synapse.org" license = "Apache-2.0" authors = ["Sage CNB Team "] @@ -11,14 +11,13 @@ readme = "README.md" repository = "https://github.com/Sage-Bionetworks-Challenges/cnb-tools" documentation = "https://sage-bionetworks-challenges.github.io/cnb-tools" classifiers = [ - "Development Status :: 3 - Alpha", + "Development Status :: 4 - Beta", "Intended Audience :: Developers", "Intended Audience :: Science/Research", "License :: OSI Approved :: Apache Software License", "Natural Language :: English", "Programming Language :: Python", "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3.12", @@ -28,9 +27,11 @@ classifiers = [ ] [tool.poetry.dependencies] -python = "^3.9" +python = ">=3.10,<3.14" typer = {extras = ["all"], version = "^0.9.0"} -synapseclient = "^4.2.0" +synapseclient = "^4.7.0" +click = ">=8.0.0,<8.2.0" +pandas = ">=2.0.3" [tool.poetry.scripts] cnb-tools = "cnb_tools.main_cli:app" @@ -39,14 +40,14 @@ cnb-tools = "cnb_tools.main_cli:app" "Bug Tracker" = "https://github.com/Sage-Bionetworks-Challenges/cnb-tools/issues" [tool.poetry.group.test.dependencies] -pytest = "^7.4.3" +pytest = ">=7.4.3" [tool.poetry.group.docs.dependencies] -mkdocs = "^1.5.3" -mkdocs-material = "^9.4.14" -mkdocstrings = "^0.24.0" -mkdocstrings-python = "^1.7.5" -termynal = "^0.11.1" +mkdocs = ">=1.5.3" +mkdocs-material = ">=9.4.14" +mkdocstrings = ">=0.24.0" +mkdocstrings-python = ">=1.7.5" +termynal = ">=0.11.1" [build-system] requires = ["poetry-core"] diff --git a/tests/__init__.py b/tests/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/tests/conftest.py b/tests/conftest.py new file mode 100644 index 0000000..480bfd8 --- /dev/null +++ b/tests/conftest.py @@ -0,0 +1,107 @@ +"""Shared pytest fixtures for cnb-tools tests.""" + +import os +import sys +from unittest.mock import MagicMock + +import pandas as pd +import pytest +from synapseclient import Evaluation, SubmissionStatus + + +def pytest_configure(config): + """Allow test scripts to import scripts from parent folder.""" + src_path = os.path.abspath(os.path.join(os.path.dirname(__file__), "..")) + sys.path.insert(0, src_path) + + +@pytest.fixture +def mock_syn(): + """Fixture for mocked Synapse client.""" + return MagicMock() + + +@pytest.fixture +def mock_submission_status(): + """Fixture for mocked SubmissionStatus.""" + status = MagicMock(spec=SubmissionStatus) + status.status = "SCORED" + status.submissionAnnotations = MagicMock() + status.submissionAnnotations.__getitem__ = lambda self, key: { + "score": 0.95, + "passed": True, + }.get(key) + return status + + +@pytest.fixture +def mock_submission_file(): + """Fixture for mocked file submission.""" + sub = MagicMock() + sub.id = "12345" + sub.evaluationId = "98765" + sub.createdOn = "2025-11-26T10:30:00.000Z" + sub.get.side_effect = lambda key: {"teamId": 111, "userId": 222}.get(key) + return sub + + +@pytest.fixture +def mock_submission_docker(): + """Fixture for mocked Docker submission.""" + sub = MagicMock() + sub.id = "12345" + sub.evaluationId = "98765" + sub.dockerRepositoryName = "docker.synapse.org/syn12345/model" + sub.dockerDigest = "sha256:abc123" + sub.__contains__ = lambda self, key: key == "dockerDigest" + return sub + + +@pytest.fixture +def mock_evaluation(): + """Fixture for mocked Evaluation.""" + eval_obj = MagicMock(spec=Evaluation) + eval_obj.id = "98765" + eval_obj.name = "Test Queue" + eval_obj.contentSource = "syn12345" + return eval_obj + + +@pytest.fixture +def truth_ids(): + """Fixture for truth IDs.""" + return pd.Series(["id1", "id2", "id3"], name="ids") + + +@pytest.fixture +def pred_ids_valid(): + """Fixture for valid prediction IDs.""" + return pd.Series(["id1", "id2", "id3"], name="ids") + + +@pytest.fixture +def pred_ids_invalid(): + """Fixture for invalid prediction IDs.""" + return pd.Series(["id1", "id1", "id4"], name="ids") + + +@pytest.fixture +def pred_values_valid(): + """Fixture for valid prediction values.""" + return pd.DataFrame( + { + "predictions": [0, 1, 1], + "probabilities": [0.25, 0.6, 0.83], + } + ) + + +@pytest.fixture +def pred_values_invalid(): + """Fixture for invalid prediction values.""" + return pd.DataFrame( + { + "predictions": [0, 1, None], + "probabilities": [-0.5, 1.0, 1.5], + } + ) diff --git a/tests/test_annotation.py b/tests/test_annotation.py new file mode 100644 index 0000000..769241a --- /dev/null +++ b/tests/test_annotation.py @@ -0,0 +1,137 @@ +"""Unit tests for cnb_tools.modules.annotation""" + +from unittest.mock import MagicMock, Mock, mock_open, patch + +import pytest +from synapseclient.core.exceptions import SynapseHTTPError + +from cnb_tools.modules import annotation +from cnb_tools.modules.base import UnknownSynapseID + + +class TestGetSubmissionStatus: + """Tests for get_submission_status function""" + + @patch("cnb_tools.modules.annotation.get_synapse_client") + def test_get_submission_status_success( + self, mock_get_client, mock_syn, mock_submission_status + ): + """Test successfully getting submission status""" + mock_get_client.return_value = mock_syn + mock_syn.getSubmissionStatus.return_value = mock_submission_status + + result = annotation.get_submission_status(12345) + + mock_syn.getSubmissionStatus.assert_called_once_with(12345) + assert result == mock_submission_status + + @patch("cnb_tools.modules.annotation.get_synapse_client") + def test_get_submission_status_invalid_id(self, mock_get_client, mock_syn): + """Test error handling for invalid submission ID""" + mock_get_client.return_value = mock_syn + mock_response = Mock() + mock_response.json.return_value = {"reason": "Submission not found"} + mock_syn.getSubmissionStatus.side_effect = SynapseHTTPError( + response=mock_response + ) + + with pytest.raises(UnknownSynapseID) as exc_info: + annotation.get_submission_status(99999) + assert "Submission not found" in str(exc_info.value) + + +class TestUpdateAnnotations: + """Tests for update_annotations function""" + + @patch("cnb_tools.modules.annotation.get_synapse_client") + @patch("cnb_tools.modules.annotation.get_submission_status") + def test_update_annotations_success( + self, mock_get_status, mock_get_client, mock_syn, mock_submission_status, capsys + ): + """Test successfully updating annotations""" + mock_get_client.return_value = mock_syn + mock_get_status.return_value = mock_submission_status + mock_syn.store.return_value = mock_submission_status + + # Mock the submissionAnnotations attribute as a dictionary + mock_submission_status.submissionAnnotations = MagicMock() + + new_annots = {"new_field": "value"} + result = annotation.update_annotations(12345, new_annots, verbose=False) + + mock_submission_status.submissionAnnotations.update.assert_called_once_with( + new_annots + ) + mock_syn.store.assert_called_once_with(mock_submission_status) + + captured = capsys.readouterr() + assert "Submission ID 12345 annotations updated" in captured.out + assert result == mock_submission_status + + @patch("cnb_tools.modules.annotation.get_synapse_client") + @patch("cnb_tools.modules.annotation.get_submission_status") + def test_update_annotations_verbose( + self, mock_get_status, mock_get_client, mock_syn, mock_submission_status, capsys + ): + """Test updating annotations with verbose output""" + mock_get_client.return_value = mock_syn + mock_get_status.return_value = mock_submission_status + mock_syn.store.return_value = mock_submission_status + + # Mock submissionAnnotations as a dict for JSON serialization + mock_submission_status.submissionAnnotations = {"score": 0.95, "passed": True} + + annotation.update_annotations(12345, {"test": "value"}, verbose=True) + + captured = capsys.readouterr() + assert "Annotations:" in captured.out + assert "score" in captured.out + + +class TestUpdateAnnotationsFromFile: + """Tests for update_annotations_from_file function""" + + @patch("cnb_tools.modules.annotation.with_retry") + @patch( + "builtins.open", + new_callable=mock_open, + read_data='{"score": 0.85, "status": "pass", "null_field": null, "empty_list": []}', + ) + def test_update_annotations_from_file(self, mock_file, mock_retry): + """Test updating annotations from JSON file""" + mock_retry.return_value = MagicMock() + + annotation.update_annotations_from_file(12345, "test.json", verbose=False) + + mock_file.assert_called_once_with("test.json", encoding="utf-8") + + # Verify with_retry was called + assert mock_retry.called + + # Verify null and empty list values were filtered + call_args = mock_retry.call_args + assert call_args[1]["wait"] == 3 + assert call_args[1]["retries"] == 10 + + +class TestUpdateSubmissionStatus: + """Tests for update_submission_status function""" + + @patch("cnb_tools.modules.annotation.get_synapse_client") + @patch("cnb_tools.modules.annotation.get_submission_status") + def test_update_submission_status( + self, mock_get_status, mock_get_client, mock_syn, mock_submission_status, capsys + ): + """Test updating submission status""" + mock_get_client.return_value = mock_syn + mock_get_status.return_value = mock_submission_status + mock_syn.store.return_value = mock_submission_status + + result = annotation.update_submission_status(12345, "ACCEPTED") + + assert mock_submission_status.status == "ACCEPTED" + mock_syn.store.assert_called_once_with(mock_submission_status) + + captured = capsys.readouterr() + assert "Updated submission ID 12345 to status: ACCEPTED" in captured.out + assert result == mock_submission_status diff --git a/tests/test_participant.py b/tests/test_participant.py new file mode 100644 index 0000000..181ee39 --- /dev/null +++ b/tests/test_participant.py @@ -0,0 +1,91 @@ +"""Unit tests for cnb_tools.modules.participant""" + +from unittest.mock import MagicMock, patch + +import pytest +from synapseclient import Team +from synapseclient.core.exceptions import SynapseHTTPError + +from cnb_tools.modules import participant + + +class TestGetParticipantName: + """Tests for get_participant_name function""" + + @patch("cnb_tools.modules.participant.get_synapse_client") + def test_get_participant_name_team(self, mock_get_client, mock_syn): + """Test getting team name""" + mock_get_client.return_value = mock_syn + mock_syn.getTeam.return_value = {"name": "Dream Team"} + + result = participant.get_participant_name(12345) + + assert result == "Dream Team" + mock_syn.getTeam.assert_called_once_with(12345) + + @patch("cnb_tools.modules.participant.get_synapse_client") + def test_get_participant_name_user(self, mock_get_client, mock_syn): + """Test getting username when team lookup fails""" + mock_get_client.return_value = mock_syn + mock_syn.getTeam.side_effect = SynapseHTTPError(response=MagicMock()) + mock_syn.getUserProfile.return_value = {"userName": "john_doe"} + + result = participant.get_participant_name(67890) + + assert result == "john_doe" + mock_syn.getUserProfile.assert_called_once_with(67890) + + +class TestCreateTeam: + """Tests for create_team function""" + + @patch("cnb_tools.modules.participant.typer.confirm") + @patch("cnb_tools.modules.participant.get_synapse_client") + def test_create_team_new(self, mock_get_client, mock_confirm, mock_syn): + """Test creating a new team""" + mock_get_client.return_value = mock_syn + mock_syn.getTeam.side_effect = ValueError("Team not found") + + result = participant.create_team( + name="New Team", description="Test description", can_public_join=True + ) + + assert isinstance(result, Team) + assert result.name == "New Team" + assert result.description == "Test description" + assert result.canPublicJoin is True + + @patch("cnb_tools.modules.participant.typer.confirm") + @patch("cnb_tools.modules.participant.get_synapse_client") + def test_create_team_existing_confirmed( + self, mock_get_client, mock_confirm, mock_syn + ): + """Test using an existing team when user confirms""" + mock_get_client.return_value = mock_syn + existing_team = MagicMock(spec=Team) + existing_team.name = "Dream Team" + mock_syn.getTeam.return_value = existing_team + mock_confirm.return_value = True + + result = participant.create_team(name="Dream Team") + + assert result == existing_team + mock_confirm.assert_called_once_with( + "Team 'Dream Team' already exists. Use this team?" + ) + + @patch("cnb_tools.modules.participant.typer.confirm") + @patch("cnb_tools.modules.participant.get_synapse_client") + def test_create_team_existing_declined( + self, mock_get_client, mock_confirm, mock_syn + ): + """Test declining to use existing team exits""" + mock_get_client.return_value = mock_syn + existing_team = MagicMock(spec=Team) + mock_syn.getTeam.return_value = existing_team + mock_confirm.return_value = False + + with pytest.raises(SystemExit) as exc_info: + participant.create_team(name="Existing Team") + + assert "Try again with a new challenge name" in str(exc_info.value) diff --git a/tests/test_queue.py b/tests/test_queue.py new file mode 100644 index 0000000..6a58d1b --- /dev/null +++ b/tests/test_queue.py @@ -0,0 +1,73 @@ +"""Unit tests for cnb_tools.modules.queue""" + +from unittest.mock import MagicMock, Mock, patch + +import pytest +from synapseclient.core.exceptions import SynapseHTTPError + +from cnb_tools.modules import queue +from cnb_tools.modules.base import UnknownSynapseID + + +class TestGetEvaluation: + """Tests for get_evaluation function""" + + @patch("cnb_tools.modules.queue.get_synapse_client") + def test_get_evaluation_success(self, mock_get_client, mock_syn, mock_evaluation): + """Test successfully getting an evaluation""" + mock_get_client.return_value = mock_syn + mock_syn.getEvaluation.return_value = mock_evaluation + + result = queue.get_evaluation(98765) + + mock_syn.getEvaluation.assert_called_once_with(98765) + assert result == mock_evaluation + + @patch("cnb_tools.modules.queue.get_synapse_client") + def test_get_evaluation_invalid_id(self, mock_get_client, mock_syn): + """Test error handling for invalid evaluation ID""" + mock_get_client.return_value = mock_syn + mock_response = Mock() + mock_response.json.return_value = {"reason": "Evaluation not found"} + mock_syn.getEvaluation.side_effect = SynapseHTTPError(response=mock_response) + + with pytest.raises(UnknownSynapseID) as exc_info: + queue.get_evaluation(99999) + + assert "Evaluation not found" in str(exc_info.value) + + +class TestGetEvaluationName: + """Tests for get_evaluation_name function""" + + @patch("cnb_tools.modules.queue.get_evaluation") + def test_get_evaluation_name(self, mock_get_eval, mock_evaluation): + """Test getting evaluation name""" + mock_get_eval.return_value = mock_evaluation + + result = queue.get_evaluation_name(98765) + + assert result == "Test Queue" + mock_get_eval.assert_called_once_with(98765) + + +class TestGetChallengeNameFromEvaluation: + """Tests for get_challenge_name_from_evaluation function""" + + @patch("cnb_tools.modules.queue.get_synapse_client") + @patch("cnb_tools.modules.queue.get_evaluation") + def test_get_challenge_name_from_evaluation( + self, mock_get_eval, mock_get_client, mock_syn, mock_evaluation + ): + """Test getting challenge name from evaluation""" + mock_get_eval.return_value = mock_evaluation + mock_get_client.return_value = mock_syn + + mock_challenge = MagicMock() + mock_challenge.name = "Amazing Challenge" + mock_syn.get.return_value = mock_challenge + + result = queue.get_challenge_name_from_evaluation(98765) + + assert result == "Amazing Challenge" + mock_syn.get.assert_called_once_with("syn12345") diff --git a/tests/test_submission.py b/tests/test_submission.py new file mode 100644 index 0000000..76f778c --- /dev/null +++ b/tests/test_submission.py @@ -0,0 +1,196 @@ +"""Unit tests for cnb_tools.modules.submission""" + +from unittest.mock import MagicMock, Mock, patch + +import pytest +from synapseclient.core.exceptions import SynapseHTTPError + +from cnb_tools.modules import submission +from cnb_tools.modules.base import UnknownSynapseID + + +class TestGetSubmission: + """Tests for get_submission function""" + + @patch("cnb_tools.modules.submission.get_synapse_client") + def test_get_submission_success( + self, mock_get_client, mock_syn, mock_submission_file + ): + """Test successfully getting a submission""" + mock_get_client.return_value = mock_syn + mock_syn.getSubmission.return_value = mock_submission_file + + result = submission.get_submission(12345, download_file=False) + + mock_syn.getSubmission.assert_called_once_with(12345, downloadFile=False) + assert result == mock_submission_file + + @patch("cnb_tools.modules.submission.get_synapse_client") + def test_get_submission_invalid_id(self, mock_get_client, mock_syn): + """Test error handling for invalid submission ID""" + mock_get_client.return_value = mock_syn + mock_response = Mock() + mock_response.json.return_value = {"reason": "Submission not found"} + mock_syn.getSubmission.side_effect = SynapseHTTPError(response=mock_response) + + with pytest.raises(UnknownSynapseID) as exc_info: + submission.get_submission(99999) + + assert "Submission not found" in str(exc_info.value) + + +class TestDeleteSubmission: + """Tests for delete_submission function""" + + @patch("cnb_tools.modules.submission.get_synapse_client") + @patch("cnb_tools.modules.submission.get_submission") + def test_delete_submission( + self, mock_get_sub, mock_get_client, mock_syn, mock_submission_file, capsys + ): + """Test deleting a submission""" + mock_get_client.return_value = mock_syn + mock_get_sub.return_value = mock_submission_file + + submission.delete_submission(12345) + + mock_get_sub.assert_called_once_with(12345) + mock_syn.delete.assert_called_once_with(mock_submission_file) + + captured = capsys.readouterr() + assert "Submission deleted: 12345" in captured.out + + +class TestDownloadSubmission: + """Tests for download_submission function""" + + @patch("cnb_tools.modules.submission.get_synapse_client") + @patch("cnb_tools.modules.submission.get_submission") + def test_download_submission_file( + self, mock_get_sub, mock_get_client, mock_syn, mock_submission_file, capsys + ): + """Test downloading a file submission""" + mock_get_client.return_value = mock_syn + mock_get_sub.return_value = mock_submission_file + + submission.download_submission(12345, dest="/tmp") + + mock_syn.getSubmission.assert_called_once_with(12345, downloadLocation="/tmp") + + captured = capsys.readouterr() + assert "Submission ID 12345 downloaded to:" in captured.out + + @patch("cnb_tools.modules.submission.get_synapse_client") + @patch("cnb_tools.modules.submission.get_submission") + def test_download_submission_docker( + self, mock_get_sub, mock_get_client, mock_syn, mock_submission_docker, capsys + ): + """Test 'downloading' a Docker submission (displays pull command)""" + mock_get_client.return_value = mock_syn + mock_get_sub.return_value = mock_submission_docker + + submission.download_submission(12345) + + captured = capsys.readouterr() + assert "Docker image" in captured.out + assert "docker pull" in captured.out + assert "docker.synapse.org/syn12345/model@sha256:abc123" in captured.out + + +class TestGetSubmitterName: + """Tests for get_submitter_name function""" + + @patch("cnb_tools.modules.submission.get_synapse_client") + def test_get_submitter_name_team(self, mock_get_client, mock_syn): + """Test getting team name""" + mock_get_client.return_value = mock_syn + mock_syn.getTeam.return_value = {"name": "Test Team"} + + result = submission.get_submitter_name(111) + + assert result == "Test Team" + + @patch("cnb_tools.modules.submission.get_synapse_client") + def test_get_submitter_name_user(self, mock_get_client, mock_syn): + """Test getting username when team lookup fails""" + mock_get_client.return_value = mock_syn + mock_syn.getTeam.side_effect = SynapseHTTPError(response=Mock()) + mock_syn.getUserProfile.return_value = {"userName": "testuser"} + + result = submission.get_submitter_name(222) + + assert result == "testuser" + + +class TestGetChallengeName: + """Tests for get_challenge_name function""" + + @patch("cnb_tools.modules.submission.get_synapse_client") + def test_get_challenge_name(self, mock_get_client, mock_syn): + """Test getting challenge name from evaluation""" + mock_get_client.return_value = mock_syn + mock_eval = MagicMock() + mock_eval.contentSource = "syn98765" + mock_syn.getEvaluation.return_value = mock_eval + + mock_challenge = MagicMock() + mock_challenge.name = "Test Challenge" + mock_syn.get.return_value = mock_challenge + + result = submission.get_challenge_name(12345) + + assert result == "Test Challenge" + mock_syn.get.assert_called_once_with("syn98765") + + +class TestPrintSubmissionInfo: + """Tests for print_submission_info function""" + + @patch("cnb_tools.modules.submission.get_submission") + @patch("cnb_tools.modules.submission.get_challenge_name") + @patch("cnb_tools.modules.submission.get_submitter_name") + def test_print_submission_info_basic( + self, + mock_get_submitter, + mock_get_challenge, + mock_get_sub, + mock_submission_file, + capsys, + ): + """Test printing basic submission info""" + mock_get_sub.return_value = mock_submission_file + mock_get_challenge.return_value = "Test Challenge" + mock_get_submitter.return_value = "Test Team" + + submission.print_submission_info(12345, verbose=False) + + captured = capsys.readouterr() + assert "ID: 12345" in captured.out + assert "Challenge: Test Challenge" in captured.out + assert "Date: 2025-11-26" in captured.out + assert "Submitter: Test Team" in captured.out + + @patch("cnb_tools.modules.submission.annotation") + @patch("cnb_tools.modules.submission.get_submission") + @patch("cnb_tools.modules.submission.get_challenge_name") + @patch("cnb_tools.modules.submission.get_submitter_name") + def test_print_submission_info_verbose( + self, + mock_get_submitter, + mock_get_challenge, + mock_get_sub, + mock_annotation, + mock_submission_file, + ): + """Test printing submission info with annotations""" + mock_get_sub.return_value = mock_submission_file + mock_get_challenge.return_value = "Test Challenge" + mock_get_submitter.return_value = "Test Team" + + mock_status = MagicMock() + mock_annotation.get_submission_status.return_value = mock_status + mock_annotation.format_annotations.return_value = "Formatted annotations" + + submission.print_submission_info(12345, verbose=True) + + mock_annotation.get_submission_status.assert_called_once_with(12345) + mock_annotation.format_annotations.assert_called_once_with(mock_status) diff --git a/tests/test_validation_toolkit.py b/tests/test_validation_toolkit.py new file mode 100644 index 0000000..35ce01d --- /dev/null +++ b/tests/test_validation_toolkit.py @@ -0,0 +1,125 @@ +"""Unit tests for cnb_tools.validation_toolkit""" + +from cnb_tools import validation_toolkit + + +class TestCheckMissingKeys: + """Tests for check_missing_keys function""" + + def test_no_missing_keys(self, truth_ids, pred_ids_valid): + """Test when all keys are present""" + result = validation_toolkit.check_missing_keys(truth_ids, pred_ids_valid) + assert result == "" + + def test_missing_keys(self, truth_ids, pred_ids_invalid): + """Test when keys are missing""" + result = validation_toolkit.check_missing_keys(truth_ids, pred_ids_invalid) + assert "Found 2 missing ID(s)" in result + + def test_missing_keys_verbose(self, truth_ids, pred_ids_invalid): + """Test missing keys with verbose output""" + result = validation_toolkit.check_missing_keys( + truth_ids, pred_ids_invalid, verbose=True + ) + assert "Found 2 missing ID(s)" in result + assert "id2" in result + assert "id3" in result + + +class TestCheckUnknownKeys: + """Tests for check_unknown_keys function""" + + def test_no_unknown_keys(self, truth_ids, pred_ids_valid): + """Test when no unknown keys are present""" + result = validation_toolkit.check_unknown_keys(truth_ids, pred_ids_valid) + assert result == "" + + def test_unknown_keys(self, truth_ids, pred_ids_invalid): + """Test when unknown keys are present""" + result = validation_toolkit.check_unknown_keys(truth_ids, pred_ids_invalid) + assert "Found 1 unknown ID(s)" in result + + def test_unknown_keys_verbose(self, truth_ids, pred_ids_invalid): + """Test unknown keys with verbose output""" + result = validation_toolkit.check_unknown_keys( + truth_ids, pred_ids_invalid, verbose=True + ) + assert "Found 1 unknown ID(s)" in result + assert "id4" in result + + +class TestCheckDuplicateKeys: + """Tests for check_duplicate_keys function""" + + def test_no_duplicates(self, pred_ids_valid): + """Test when no duplicate keys are present""" + result = validation_toolkit.check_duplicate_keys(pred_ids_valid) + assert result == "" + + def test_duplicates(self, pred_ids_invalid): + """Test when duplicate keys are present""" + result = validation_toolkit.check_duplicate_keys(pred_ids_invalid) + assert "Found 1 duplicate ID(s)" in result + + def test_duplicates_verbose(self, pred_ids_invalid): + """Test duplicate keys with verbose output""" + result = validation_toolkit.check_duplicate_keys(pred_ids_invalid, verbose=True) + assert "Found 1 duplicate ID(s)" in result + assert "id1" in result + + +class TestCheckNanValues: + """Tests for check_nan_values function""" + + def test_no_nan_values(self, pred_values_valid): + """Test when no NaN values are present""" + result = validation_toolkit.check_nan_values(pred_values_valid["predictions"]) + assert result == "" + + def test_with_nan_values(self, pred_values_invalid): + """Test when NaN values are present""" + result = validation_toolkit.check_nan_values(pred_values_invalid["predictions"]) + assert "'predictions' column contains 1 NaN value(s)" in result + + +class TestCheckBinaryValues: + """Tests for check_binary_values function""" + + def test_valid_binary_values_default(self, pred_values_valid): + """Test valid binary values with default labels (0, 1)""" + result = validation_toolkit.check_binary_values( + pred_values_valid["predictions"] + ) + assert result == "" + + def test_invalid_binary_values(self, pred_values_invalid): + """Test invalid binary values""" + result = validation_toolkit.check_binary_values( + pred_values_invalid["predictions"] + ) + assert "'predictions' values should only be 0 or 1" in result + + +class TestCheckValuesRange: + """Tests for check_values_range function""" + + def test_valid_range_default(self, pred_values_valid): + """Test values within default range [0, 1]""" + result = validation_toolkit.check_values_range( + pred_values_valid["probabilities"] + ) + assert result == "" + + def test_invalid_range_below_min(self, pred_values_invalid): + """Test values below minimum""" + result = validation_toolkit.check_values_range( + pred_values_invalid["probabilities"] + ) + assert "'probabilities' values should be between [0, 1]" in result + + def test_invalid_range_above_max(self, pred_values_invalid): + """Test values above maximum""" + result = validation_toolkit.check_values_range( + pred_values_invalid["probabilities"] + ) + assert "'probabilities' values should be between [0, 1]" in result