Ecosyste.ms: Issues

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GitHub / fractal-analytics-platform/fractal-server issues and pull requests

#742 - Drop `WorkflowTask.arguments` property (close #741)

Pull Request - State: closed - Opened by tcompa over 1 year ago - 1 comment

#741 - Drop obsolete `WorkflowTask.arguments` property

Issue - State: closed - Opened by tcompa over 1 year ago
Labels: High Priority

#740 - Expose `pinned_package_versions` for task collection

Issue - State: closed - Opened by tcompa over 1 year ago - 3 comments
Labels: High Priority

#738 - Allow users to delete their own tasks

Issue - State: closed - Opened by tcompa over 1 year ago
Labels: High Priority

#737 - Expose `args_schema` and `args_schema_version` in task POST/PATCH endpoints

Issue - State: closed - Opened by tcompa over 1 year ago
Labels: High Priority

#736 - Review normalization of package and extra names

Issue - State: closed - Opened by tcompa over 1 year ago - 6 comments
Labels: maintenance, task collection

#735 - Review task collection after task-package refactor

Issue - State: closed - Opened by tcompa over 1 year ago - 1 comment
Labels: High Priority

#732 - SQLite and ALTER

Issue - State: closed - Opened by tcompa over 1 year ago - 6 comments
Labels: bug, sqlite

#729 - How to handle import/export of workflows with custom tasks

Issue - State: closed - Opened by tcompa over 1 year ago - 3 comments

#726 - Refresh database definition, due to "No support for ALTER of constraints in SQLite dialect"

Issue - State: closed - Opened by tcompa over 1 year ago
Labels: High Priority, sqlite

#724 - Check broken relationships in CI

Issue - State: closed - Opened by tcompa over 1 year ago - 2 comments
Labels: maintenance

#717 - Add `task.owner` optional-string column

Issue - State: closed - Opened by tcompa over 1 year ago

#716 - Add `task.version` optional-string column

Issue - State: closed - Opened by tcompa over 1 year ago

#715 - Update task-add endpoint, to set `task.owner`

Issue - State: closed - Opened by tcompa over 1 year ago

#714 - Add `UserOAuth.username` column

Issue - State: closed - Opened by tcompa over 1 year ago

#713 - Require pydantic>=1.10.8 (ref #706)

Pull Request - State: closed - Opened by tcompa over 1 year ago - 1 comment

#712 - Add test to check that DB schemas are up-to-date

Issue - State: open - Opened by tcompa over 1 year ago
Labels: maintenance

#711 - remove typing-extensions, update pydantic, install

Pull Request - State: closed - Opened by ychiucco over 1 year ago - 1 comment

#710 - Inherit from both `pydantic.BaseModel` and `sqlmodel.SQLModel`

Pull Request - State: open - Opened by ychiucco over 1 year ago - 3 comments

#709 - Inherit from both `pydantic.BaseModel` and `sqlmodel.SQLModel`

Issue - State: open - Opened by ychiucco over 1 year ago
Labels: maintenance

#708 - Deprecate `task.default_args`

Issue - State: closed - Opened by tcompa over 1 year ago

#707 - Work towards task.args_schema

Pull Request - State: closed - Opened by tcompa over 1 year ago - 1 comment

#706 - Remove pin `typing-extensions = "4.5.0"`

Issue - State: closed - Opened by ychiucco over 1 year ago - 1 comment
Labels: maintenance

#705 - update common

Pull Request - State: closed - Opened by ychiucco over 1 year ago - 3 comments

#704 - Task review

Pull Request - State: closed - Opened by tcompa over 1 year ago - 1 comment

#703 - Prevent removal with linked Jobs

Pull Request - State: closed - Opened by ychiucco over 1 year ago - 2 comments

#702 - Task-review overview

Issue - State: open - Opened by tcompa over 1 year ago - 3 comments
Labels: High Priority, Overview

#700 - Prevent removal of datasets/workflows in relation with jobs

Issue - State: closed - Opened by tcompa over 1 year ago

#699 - Add possible disk-out-of-space reason to error message (close #492)

Pull Request - State: closed - Opened by tcompa over 1 year ago - 1 comment

#698 - In submit_workflow, decorate failures in preliminary checks

Issue - State: closed - Opened by tcompa over 1 year ago - 2 comments
Labels: maintenance

#697 - Task refactor

Issue - State: open - Opened by tcompa over 1 year ago
Labels: task collection

#696 - Fix bug in stop-job endpoint (close #695)

Pull Request - State: closed - Opened by tcompa over 1 year ago - 1 comment

#695 - Fix bug in stop-job endpoint

Issue - State: closed - Opened by tcompa over 1 year ago

#694 - Remove references to overwrite input in tests

Pull Request - State: closed - Opened by tcompa over 1 year ago - 1 comment

#693 - Remove references to `overwrite_input` in tests

Issue - State: closed - Opened by tcompa over 1 year ago
Labels: maintenance

#692 - Docs & changelog

Pull Request - State: closed - Opened by tcompa over 1 year ago - 1 comment

#691 - Make SLURM-executor _completion method more robust

Pull Request - State: closed - Opened by tcompa over 1 year ago - 2 comments

#690 - SLURM-executor shutdown still "randomly" fails in the CI

Issue - State: closed - Opened by tcompa over 1 year ago - 2 comments
Labels: Priority, slurm

#689 - Fix (or drop?) inconsistent project name uniqueness constraint

Pull Request - State: closed - Opened by ychiucco over 1 year ago - 1 comment

#688 - More flexible allow origins

Pull Request - State: closed - Opened by ychiucco over 1 year ago - 1 comment

#687 - Add `end_timestamp` to `applyworkflow` (server)

Pull Request - State: closed - Opened by ychiucco over 1 year ago - 1 comment
Labels: maintenance

#686 - Install tasks via SLURM

Issue - State: open - Opened by tcompa over 1 year ago - 2 comments
Labels: slurm, task collection

#685 - Review behavior of task collection when folder already exists

Issue - State: closed - Opened by tcompa over 1 year ago - 3 comments
Labels: maintenance

#684 - Update common and DB schema

Pull Request - State: closed - Opened by tcompa over 1 year ago - 1 comment
Labels: maintenance

#683 - Update common and DB schema (notably to remove ApplyWorkflow.overwrite_input)

Issue - State: closed - Opened by tcompa over 1 year ago
Labels: maintenance

#682 - Review use of output_dataset in apply-workflow endpoint

Pull Request - State: closed - Opened by tcompa over 1 year ago - 1 comment
Labels: maintenance

#681 - Make output_dataset_id a required argument of apply-workflow endpoint

Pull Request - State: closed - Opened by tcompa over 1 year ago - 1 comment
Labels: maintenance

#680 - Update ongoing-mainteinance CHANGELOG

Issue - State: closed - Opened by tcompa over 1 year ago
Labels: maintenance

#679 - In FractalSlurmExecutor make working-dir attributes required

Pull Request - State: closed - Opened by tcompa over 1 year ago - 1 comment
Labels: maintenance

#678 - Improve coverage

Pull Request - State: closed - Opened by ychiucco over 1 year ago - 1 comment
Labels: maintenance

#677 - Improve coverage after new endpoints

Issue - State: closed - Opened by tcompa over 1 year ago
Labels: maintenance

#676 - Update ci.yml with coverage concurrency options

Pull Request - State: closed - Opened by tcompa over 1 year ago - 1 comment
Labels: maintenance

#675 - Add concurrency option to coverage

Issue - State: closed - Opened by tcompa over 1 year ago - 2 comments
Labels: maintenance

#674 - Remove automatic creation of default dataset when creating a project

Issue - State: closed - Opened by tcompa over 1 year ago - 5 comments
Labels: maintenance

#673 - Fix task collection with sqlite

Pull Request - State: closed - Opened by tcompa over 1 year ago - 2 comments
Labels: maintenance

#672 - Check existence of local task package

Issue - State: closed - Opened by tcompa over 1 year ago

#671 - Include extras for local-package collection (close #670)

Pull Request - State: closed - Opened by tcompa over 1 year ago - 2 comments
Labels: maintenance

#670 - Task collection: package-extras not installed

Issue - State: closed - Opened by jluethi over 1 year ago - 3 comments
Labels: bug

#669 - Remove foreign keys from payloads (server)

Pull Request - State: closed - Opened by ychiucco over 1 year ago - 2 comments
Labels: maintenance

#668 - When creating a Job, the associated workflow and datasets must be part of the same project

Issue - State: closed - Opened by tcompa over 1 year ago - 1 comment
Labels: bug, maintenance

#667 - Review job table to allow deleting datasets or workflows

Issue - State: closed - Opened by tcompa over 1 year ago - 12 comments

#666 - Delete a project with associated jobs

Pull Request - State: closed - Opened by tcompa over 1 year ago - 1 comment

#665 - workflow-apply error handling

Pull Request - State: closed - Opened by ychiucco over 1 year ago - 2 comments

#664 - Use StaticPool, for sqlite engine (ref #661)

Pull Request - State: closed - Opened by tcompa over 1 year ago - 2 comments
Labels: maintenance

#663 - Project deletion currently not working when there is an associated workflow job

Issue - State: closed - Opened by jluethi over 1 year ago - 3 comments

#662 - Provisionally fix sqlite issue (#661)

Pull Request - State: closed - Opened by tcompa over 1 year ago - 2 comments

#661 - Task collection broken with sqlite?

Issue - State: closed - Opened by tcompa over 1 year ago - 9 comments
Labels: bug, Priority, sqlite

#660 - Refactor User model

Pull Request - State: closed - Opened by tcompa over 1 year ago - 1 comment
Labels: maintenance

#658 - Use FRACTAL_SLURM_WORKER_PYTHON for venv/pip operations on tasks

Pull Request - State: closed - Opened by tcompa over 1 year ago - 1 comment

#657 - Use sqlalchemy URL objects (ref #650)

Pull Request - State: closed - Opened by tcompa over 1 year ago - 1 comment

#656 - Review use of threadsafety in sqlite

Issue - State: closed - Opened by tcompa over 1 year ago - 1 comment

#655 - Add `finally` block to close db session, at the end of `get_db` of `get_sync_db`

Issue - State: closed - Opened by tcompa over 1 year ago - 2 comments

#654 - In `submit_workflow`, take a `WorkflowRead` `workflow` argument, rather than `Workflow`

Issue - State: closed - Opened by tcompa over 1 year ago - 1 comment
Labels: maintenance

#653 - Review use of DB-session as context manager, or check whether more try/except/rollback should be used

Issue - State: closed - Opened by tcompa over 1 year ago - 1 comment
Labels: maintenance

#652 - In workflow-apply endpoint, only use async DB sessions

Issue - State: closed - Opened by tcompa over 1 year ago - 1 comment
Labels: maintenance

#651 - Review DB connections

Pull Request - State: closed - Opened by tcompa over 1 year ago - 1 comment

#650 - Support connecting to postgres via UNIX socket

Issue - State: closed - Opened by tcompa over 1 year ago - 7 comments
Labels: High Priority

#649 - Review db connections in API and background tasks

Issue - State: closed - Opened by tcompa over 1 year ago - 5 comments
Labels: High Priority

#648 - Improve error message for missing (or invalid?) manifest file

Issue - State: closed - Opened by tcompa over 1 year ago - 1 comment
Labels: maintenance

#647 - Database locked after unknown issue

Issue - State: closed - Opened by jluethi over 1 year ago - 14 comments

#646 - Cryptography ImportError: /lib64/libc.so.6: version `GLIBC_2.28'

Issue - State: closed - Opened by jluethi over 1 year ago - 1 comment

#645 - More flexible `allow_origins`

Issue - State: closed - Opened by tcompa over 1 year ago - 1 comment

#644 - TaskExecutionError: pickle file is not deserialized when invalid executable given for task

Issue - State: closed - Opened by jluethi over 1 year ago - 1 comment
Labels: maintenance, july2023

#643 - [docs] Make it clear that `SlurmConfig` (and its `mem_per_task_MB` attribute) are internals

Issue - State: closed - Opened by tcompa over 1 year ago
Labels: maintenance, july2023

#642 - Bugfix for user_local_export

Pull Request - State: closed - Opened by tcompa over 1 year ago - 1 comment

#641 - `user_local_exports` is not set correctly

Issue - State: closed - Opened by tcompa over 1 year ago

#639 - Populate `WorkflowTask.args` based on defaults in `WorkflowTask.task.args_schema`

Issue - State: closed - Opened by tcompa over 1 year ago - 2 comments
Labels: High Priority

#638 - Fill `Task.args_schema` column during task collection

Issue - State: open - Opened by tcompa over 1 year ago - 3 comments
Labels: Priority

#637 - Add port 4173 to allowed CORS origins (close #634)

Pull Request - State: closed - Opened by tcompa over 1 year ago - 1 comment

#636 - Update dependencies in poetry.lock

Pull Request - State: closed - Opened by tcompa over 1 year ago - 1 comment

#635 - Include logs for successful workflow executions (close #618)

Pull Request - State: closed - Opened by tcompa over 1 year ago - 1 comment

#634 - Also expose 4173 port for CORS

Issue - State: closed - Opened by tcompa over 1 year ago - 1 comment
Labels: High Priority

#633 - Document the `bind` option for both uvicorn/gunicorn

Issue - State: closed - Opened by tcompa over 1 year ago - 1 comment

#632 - Catch IntegrityError upon admin-user creation (close #628)

Pull Request - State: closed - Opened by tcompa over 1 year ago - 3 comments

#631 - Implement `FractalSlurmExecutor.shutdown`

Pull Request - State: closed - Opened by tcompa over 1 year ago - 1 comment

#630 - Implement endpoint to stop workflow execution

Issue - State: closed - Opened by tcompa over 1 year ago - 1 comment
Labels: High Priority