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mvdbeek
7804b18f8e
Fixes https://github.com/galaxyproject/galaxy/issues/17959: ``` NotNullViolation: null value in column "workflow_step_id" of relation "workflow_output" violates not-null constraint DETAIL: Failing row contains (3843428, null, multiqc_fastqc_html, multiqc_fastqc_html, 1d8a0c348b6f446eb4d84770365f570f). File "sqlalchemy/engine/base.py", line 1890, in _execute_context self.dialect.do_executemany( File "sqlalchemy/dialects/postgresql/psycopg2.py", line 982, in do_executemany context._psycopg2_fetched_rows = xtras.execute_values( File "psycopg2/extras.py", line 1299, in execute_values cur.execute(b''.join(parts)) IntegrityError: (psycopg2.errors.NotNullViolation) null value in column "workflow_step_id" of relation "workflow_output" violates not-null constraint DETAIL: Failing row contains (3843428, null, multiqc_fastqc_html, multiqc_fastqc_html, 1d8a0c348b6f446eb4d84770365f570f). [SQL: INSERT INTO workflow_output (workflow_step_id, output_name, label, uuid) VALUES (%(workflow_step_id)s, %(output_name)s, %(label)s, %(uuid)s) RETURNING workflow_output.id] [parameters: ({'workflow_step_id': None, 'output_name': 'multiqc_fastqc_html', 'label': 'multiqc_fastqc_html', 'uuid': '1d8a0c348b6f446eb4d84770365f570f'}, {'workflow_step_id': None, 'output_name': 'multiqc_cutadapt_html', 'label': 'multiqc_cutadapt_html', 'uuid': '11fef12f5cf24904b31dac7a277f5fda'}, {'workflow_step_id': None, 'output_name': 'multiqc_star_html', 'label': 'multiqc_star_html', 'uuid': '383da02d5a4b4af7ac2933b9cfad316f'}, {'workflow_step_id': None, 'output_name': 'STAR_BAM', 'label': 'STAR_BAM', 'uuid': '6aed76c8a4a5491bacd2f995f16df86b'}, {'workflow_step_id': None,... File "starlette/applications.py", line 123, in __call__ await self.middleware_stack(scope, receive, send) File "starlette/middleware/errors.py", line 186, in __call__ raise exc File "starlette/middleware/errors.py", line 164, in __call__ await self.app(scope, receive, _send) File "starlette_context/middleware/raw_middleware.py", line 92, in __call__ await self.app(scope, receive, send_wrapper) File "starlette/middleware/base.py", line 189, in __call__ with collapse_excgroups(): File "contextlib.py", line 155, in __exit__ self.gen.throw(typ, value, traceback) File "starlette/_utils.py", line 93, in collapse_excgroups raise exc File "starlette/middleware/base.py", line 191, in __call__ response = await self.dispatch_func(request, call_next) File "galaxy/webapps/galaxy/fast_app.py", line 108, in add_x_frame_options response = await call_next(request) File "starlette/middleware/base.py", line 165, in call_next raise app_exc File "starlette/middleware/base.py", line 151, in coro await self.app(scope, receive_or_disconnect, send_no_error) File "starlette/middleware/exceptions.py", line 62, in __call__ await wrap_app_handling_exceptions(self.app, conn)(scope, receive, send) File "starlette/_exception_handler.py", line 64, in wrapped_app raise exc File "starlette/_exception_handler.py", line 53, in wrapped_app await app(scope, receive, sender) File "starlette/routing.py", line 758, in __call__ await self.middleware_stack(scope, receive, send) File "starlette/routing.py", line 778, in app await route.handle(scope, receive, send) File "starlette/routing.py", line 299, in handle await self.app(scope, receive, send) File "starlette/routing.py", line 79, in app await wrap_app_handling_exceptions(app, request)(scope, receive, send) File "starlette/_exception_handler.py", line 64, in wrapped_app raise exc File "starlette/_exception_handler.py", line 53, in wrapped_app await app(scope, receive, sender) File "starlette/routing.py", line 74, in app response = await func(request) File "fastapi/routing.py", line 278, in app raw_response = await run_endpoint_function( File "fastapi/routing.py", line 193, in run_endpoint_function return await run_in_threadpool(dependant.call, **values) File "starlette/concurrency.py", line 42, in run_in_threadpool return await anyio.to_thread.run_sync(func, *args) File "anyio/to_thread.py", line 56, in run_sync return await get_async_backend().run_sync_in_worker_thread( File "anyio/_backends/_asyncio.py", line 2144, in run_sync_in_worker_thread return await future File "anyio/_backends/_asyncio.py", line 851, in run result = context.run(func, *args) File "galaxy/webapps/galaxy/api/workflows.py", line 987, in refactor return self.service.refactor(trans, workflow_id, payload, instance or False) File "galaxy/webapps/galaxy/services/workflows.py", line 218, in refactor return self._workflow_contents_manager.refactor(trans, stored_workflow, payload) File "galaxy/managers/workflows.py", line 1963, in refactor refactored_workflow, action_executions = self.do_refactor(trans, stored_workflow, refactor_request) File "galaxy/managers/workflows.py", line 1948, in do_refactor refactored_workflow, errors = self.update_workflow_from_raw_description( File "galaxy/managers/workflows.py", line 728, in update_workflow_from_raw_description trans.tag_handler.set_tags_from_list( File "galaxy/model/tags.py", line 94, in set_tags_from_list self.apply_item_tags(user, item, unicodify(new_tags_str, "utf-8"), flush=flush) File "galaxy/model/tags.py", line 265, in apply_item_tags self.apply_item_tag(user, item, name, value, flush=flush) File "galaxy/model/tags.py", line 249, in apply_item_tag self.sa_session.commit() File "<string>", line 2, in commit File "sqlalchemy/orm/session.py", line 1454, in commit self._transaction.commit(_to_root=self.future) File "sqlalchemy/orm/session.py", line 832, in commit self._prepare_impl() File "sqlalchemy/orm/session.py", line 811, in _prepare_impl self.session.flush() File "sqlalchemy/orm/session.py", line 3449, in flush self._flush(objects) File "sqlalchemy/orm/session.py", line 3588, in _flush with util.safe_reraise(): File "sqlalchemy/util/langhelpers.py", line 70, in __exit__ compat.raise_( File "sqlalchemy/util/compat.py", line 211, in raise_ raise exception File "sqlalchemy/orm/session.py", line 3549, in _flush flush_context.execute() File "sqlalchemy/orm/unitofwork.py", line 456, in execute rec.execute(self) File "sqlalchemy/orm/unitofwork.py", line 630, in execute util.preloaded.orm_persistence.save_obj( File "sqlalchemy/orm/persistence.py", line 245, in save_obj _emit_insert_statements( File "sqlalchemy/orm/persistence.py", line 1156, in _emit_insert_statements c = connection._execute_20( File "sqlalchemy/engine/base.py", line 1710, in _execute_20 return meth(self, args_10style, kwargs_10style, execution_options) File "sqlalchemy/sql/elements.py", line 334, in _execute_on_connection return connection._execute_clauseelement( File "sqlalchemy/engine/base.py", line 1577, in _execute_clauseelement ret = self._execute_context( File "sqlalchemy/engine/base.py", line 1953, in _execute_context self._handle_dbapi_exception( File "sqlalchemy/engine/base.py", line 2134, in _handle_dbapi_exception util.raise_( File "sqlalchemy/util/compat.py", line 211, in raise_ raise exception File "sqlalchemy/engine/base.py", line 1890, in _execute_context self.dialect.do_executemany( File "sqlalchemy/dialects/postgresql/psycopg2.py", line 982, in do_executemany context._psycopg2_fetched_rows = xtras.execute_values( File "psycopg2/extras.py", line 1299, in execute_values cur.execute(b''.join(parts)) ``` broken in https://github.com/galaxyproject/galaxy/commit/b00a94c1f7972dcd1060069fe83fece7b8943165
.. figure:: https://galaxyproject.org/images/galaxy-logos/galaxy_project_logo.jpg
:alt: Galaxy Logo
The latest information about Galaxy can be found on the `Galaxy Community Hub <https://galaxyproject.org/>`__.
Community support is available at `Galaxy Help <https://help.galaxyproject.org/>`__.
.. image:: https://img.shields.io/badge/chat-gitter-blue.svg
:target: https://gitter.im/galaxyproject/Lobby
:alt: Chat on gitter
.. image:: https://img.shields.io/badge/chat-irc.freenode.net%23galaxyproject-blue.svg
:target: https://webchat.freenode.net/?channels=galaxyproject
:alt: Chat on irc
.. image:: https://img.shields.io/badge/release-documentation-blue.svg
:target: https://docs.galaxyproject.org/en/master/
:alt: Release Documentation
.. image:: https://travis-ci.org/galaxyproject/galaxy.svg?branch=dev
:target: https://travis-ci.org/galaxyproject/galaxy
:alt: Inspect the test results
Galaxy Quickstart
=================
Galaxy requires Python 3.7 . To check your Python version, run:
.. code:: console
$ python -V
Python 3.7.6
Start Galaxy:
.. code:: console
$ sh run.sh
Once Galaxy completes startup, you should be able to view Galaxy in your
browser at: http://localhost:8080
For more installation details please see: https://getgalaxy.org/
Documentation is available at: https://docs.galaxyproject.org/
Tutorials on how to use Galaxy, perform scientific analyses with it, develop Galaxy and its tools, and admin a Galaxy server are at: https://training.galaxyproject.org/
Tools
=====
Tools can be either installed from the Tool Shed or added manually.
For details please see the `tutorial <https://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial/>`__.
Note that not all dependencies for the tools provided in the
``tool_conf.xml.sample`` are included. To install them please visit
"Manage dependencies" in the admin interface.
Issues and Galaxy Development
=============================
Please see `CONTRIBUTING.md <CONTRIBUTING.md>`_ .