Code

Enable question chaining#660

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cortadocodes merged 215 commits intomainoctue/octue-sdk-python:mainfrom improve-ask-multipleoctue/octue-sdk-python:improve-ask-multipleCopy head branch name to clipboardJul 15, 2024

+2,508-1,918

Commits

Commits on May 29, 2024

• REF: Factor out number of questions in Child.ask_multiple

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• ENH: Log ultimately failed questions in Child.ask_multiple

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• ENH: Improve logging of errors in Child.ask_multiple

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• TST: Test logging errors from Child.ask_multiple

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• ENH: Allow existing subscriptions in create_push_subscription

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• ENH: Add overrides option to Runner.from_configuration

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• ENH: Make datasets recursive by default in Dataset.__init__

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Commits on May 31, 2024

• WIP: Temporarily provide updated schema locally

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• FEA: Add parent question UUID to questions and provide it in Runner

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• WIP: Temporarily add hardcoded schema version number

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• REF: Make question_uuid an explicit argument of Service._emit_event

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• ENH: Update emulators with parent question UUID

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• FIX: Move question UUID to correct place in log handler

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• FIX: Add missing parent_question_uuid parameters

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• WIP: Add originator_question_uuid to local schema

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• FEA: Add originator question UUID to question attributes

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• REF: Use keyword arguments in Service

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Commits on Jun 3, 2024

• TST: Update EventReplayer tests with new question UUID fields

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• REF: Rename originator event attribute to parent

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• FEA: Add new originator event attribute

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• ENH: Add originator argument to Child and ChildEmulator

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• ENH: Set originator question UUID and originator from question in runner

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• FIX: Fix sending exceptions in answer_pub_sub_question

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• FIX: Add missing arguments in cloud emulators

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• FIX: Serialise None value pub/sub attributes

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• OPS: Update event handler and its bigquery table

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• TST: Use new example service SRUID

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Commits on Jun 4, 2024

• ENH: Remove unnecessary sender argument from get_events

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• FEA: Update get_events to work with parent and originator questions

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• ENH: Order events retrieved by get_events by datetime not order

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• FIX: Fix typo in events query

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• FIX: Unflatten new event attributes in get_events

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• ENH: Provide SRUID to Child internal service instead of name

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• TST: Fix template app tests

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• ENH: Remove name argument from Service

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• FIX: Set analysis ID at start of Runner.run

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• REF: Make parent question UUID setting clearer in Runner

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• REF: Factor out finalising and cleaning up in Runner

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• DEP: Loosen Sphinx range required

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• DEP: Loosen other docs package ranges

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• DOC: Update docs with new get_events usage

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• DOC: Update Dataset docs

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• DOC: Clarify Child.ask_multiple docs

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• DOC: Update ChildEmulator docs

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• ENH: Update internal_service_name argument in ChildEmulator

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• REF: Move test emulator files into test data directory

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• DOC: Clarify question asking docs

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• DOC: Add missing docstring params

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• FIX: Set originator in MockService.ask

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• DOC: Adjust docstrings

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• REF: Factor out routing metadata in Service.answer

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• DOC: Update docstrings

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• REF: Simplify error logging in Child.ask_multiple

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• REF: Avoid using gen_uuid in Runner

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• REF: Simplify default args for originators

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• DOC: Improve docstrings

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Commits on Jun 5, 2024

• REF: Use more appropriate error and improve docstring in get_events

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• REF: Factor out validation in get_events

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• REF: Factor out fields in get_events

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• FIX: Query correct question UUID in get_events

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• FEA: Use version 0.11.0 of service communication schema

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• FIX: Deserialise parent_question_uuid properly in get_events

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• TST: Update deployment test SRUID

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• ENH: Give feedback on (un)successful push subscription creation in CLI

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• FEA: Add retry count event attribute

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• WIP: Temporarily include new schema locally

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• FEA: Add retry_count kwarg to Service.ask

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• FIX: Extract retry_count attribute for all events

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• FIX: Add retry_count arg to log handler

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• TST: Update tests

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• ENH: Allow retried questions to have the same UUID

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• FIX: Increment retry count when retrying in Child.ask_multiple

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• ENH: Log the retry number for retried questions

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• REF: Factor out dropping redelivered questions in flask app

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• ENH: Allow explicit question retries in flask app

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• REF: Change _acknowledge_and_drop_redelivered_questions signature

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• REF: Move service accounts into separate terraform file

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• FIX: Format log messages correctly in flask app

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• FIX: Add missing argument

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• FIX: Fix getting retry_count attribute

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• ENH: Avoid errors being logged multiple times in Child.ask_multiple

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Commits on Jun 6, 2024

• ENH: Log a warning if a dataset is empty at instantiation

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• FEA: Add RegisteredTemporaryDirectory class

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• ENH: Delete registered temporary directories at Runner.run finish

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• ENH: Use RegisteredTemporaryDirectory when downloading datasets

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• ENH: Delete temporary directories before deleting temporary files

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• ENH: Log which retry Child.ask_multiple is carrying out

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• ENH: Log warning when PYTHONUNBUFFERED envvar is unset

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• ENH: Use RegisteredTemporaryDirectory in template app

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Commits on Jun 7, 2024

• ENH: Remove "analysis-" from start of question UUIDs in log context

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• ENH: Set question UUIDs in advance in Child.ask_multiple

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Commits on Jun 9, 2024

• FIX: Return question UUID alongside error from Child.ask_multiple

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• ENH: Allow exceptions to pass into convert_exception_to_primitives

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• FIX: Fix manifest deserialisation in get_events

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• TST: Update deployment test

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• TST: Update tests

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• TST: Fix test

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• TST: Test event validity in deployment test

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Commits on Jun 11, 2024

• FIX: Use service communication schema 0.13.0 to allow non-boolean forward_logs and retry_count

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• FIX: Use the schema ref for service communication

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• FIX: Hack deserialisation of event attributes from bigquery to correct types

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Commits on Jun 12, 2024

• ENH: Make limited get_events function tail by default

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• FIX: Remove erroneous count output

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Commits on Jun 24, 2024

• FIX: Fix row deserialisation in get_events

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• FIX: Remove manifest deserialisation from get_events

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• FIX: Convert numpy arrays to lists in get_events

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• TST: Update deployment test

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• ENH: Make non-tail ordering in get_events explicit

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• REF: Factor out base query in get_events

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• DOC: Document default tail behaviour in get_events

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• FIX: Remove incorrect unpacking of string

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• ENH: Add comment explaining multiple ordering in tail sql

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• TST: Update get_events tests with tail query

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• TST: Fix convert_exception_to_primitives test

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• TST: Test using get_events with tail=False

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• FIX: Order queries before applying limit

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• TST: Use event replayer in async question deployment test

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• FIX: Fix forward_logs type conversion in get_events

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Commits on Jun 25, 2024

• REF: Avoid using pandas dataframe when getting events from event store

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• DEP: Remove unneeded db-dtypes package

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• REF: Simplify event retrieval in get_events

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• ENH: Allow setting of event store table ID in service configuration

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• FEA: Stop redelivered questions by checking event store

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• TST: Make flask app tests clearer

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• TST: Test warning logged if event store not specified

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• REF: Factor out DEFAULT_SERVICE_CONFIGURATION_PATH

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• DEP: Make google-cloud-bigquery a mandatory dependency

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• FIX: Add question kind to valid event kinds

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• FIX: Get retry count correctly in flask app

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• FIX: Catch no-events error from get_events

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• FIX: Use (meta-)generation agnostic retry strategy with cloud storage

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• ENH: Add child SRUID and question UUID to no heartbeat error info

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• FIX: Enable EventReplayer to handle question events

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Commits on Jun 26, 2024

• REF: Use events' actual attributes instead of first event's

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• TST: Update tests to use new stored events format

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• REF: Remove redundant recipient argument from event handlers

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• ENH: Update validation functions to expect SRUID instead of Service

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• FIX: Allow questions to continue if event store can't be found

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• DEP: Upgrade google-cloud-secret-manager

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• FIX: Always return 2-tuple from _skip_to_earliest_waiting_event

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Commits on Jun 27, 2024

• FIX: Return correct question UUIDs with failed questions

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• ENH: Improve failed question logging in Child.ask_multiple

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• DOC: Update docstring of _skip_to_earliest_waiting_event

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Commits on Jun 28, 2024

• REF: Rename dockerfile to reflect its python version

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• ENH: Return empty list from get_events if no events for question

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• ENH: Log when a new question has been received

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• FIX: Use correct formatting in log message

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• FIX: Use correct formatting in log message

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• ENH: Improve error logging in Child.ask_multiple

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• TST: Rename variable for consistency

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• FIX: Avoid race condition between event handler and cloud run service

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• TST: Use string retry_count in tests to mirror production

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• REF: Rename variable for clarity

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• REF: Factor out question acknowledgement response in flask app

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• FIX: Avoid logging exception twice per failure in Child.ask_multiple

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Commits on Jul 1, 2024

• ENH: Use envvar to specify service configuration location by default

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• REF: Remove ordering from event handlers

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• TST: Replace "message" with "event"

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• TST: Increase wait time in asynchronous question test

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• FIX: Fix skipping invalid events in pub/sub event handler

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• ENH: Order events by datetime in EventReplayer

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• ENH: Promote log message from debug to warning level

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• REV: Revert "ENH: Order events by datetime in EventReplayer"

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Commits on Jul 2, 2024

• FIX: Return empty list if no events pulled from subscription

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• ENH: Improve docstring and warning message

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• REF: Refactor question redelivery check in flask app

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• DOC: Add param string for retry_count

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• REF: Remove redundant datetime from delivery ack and heartbeat events

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• FEA: Add ability to not include service metadata in logs in replayer

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• FIX: Update delivery ack event handler

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• TST: Update service tests

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• ENH: Use version 0.14.0 of service communication schema

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• TST: Finish event replayer test

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• ENH: Order pub/sub messages using question UUID ordering key

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• FIX: Enable message ordering in pub/sub publisher

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Commits on Jul 4, 2024

• FIX: Avoid logging that app failed when it didn't

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• ENH: Emit correct logs when no diagnostics with octue get-diagnostics

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• WIP: Attempt to solve POSIX-noncompliant filesystem interaction

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• WIP: Stop using os.getcwd

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Commits on Jul 8, 2024

• REF: Remove workaround for abspath non-posix failures

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• FIX: Cache metadata against datafile/dataset instead of path

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• ENH: Use temporary directory for Dataset path by default

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Commits on Jul 9, 2024

• FIX: Allow setting of max_workers when CPU count is indeterminate

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Commits on Jul 10, 2024

• ENH: Log max threads used by Child.ask_multiple

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• WIP: Log registered temporary directories

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• WIP: Temporarily disable local file deletion in runner

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• REV: Revert "WIP: Log registered temporary directories"

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• REV: Revert "WIP: Temporarily disable local file deletion in runner"

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• FIX: Disable delete_local_files by default and provide in config

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• TST: Update test

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Commits on Jul 11, 2024

• REF: Remove misleading log message

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• DOC: Add missing param in docstring

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• REF: Remove order event attribute

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• REF: Simplify answer_question

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• REF: Simplify attributes dict construction in Service._emit_event

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• DOC: Update docstring

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• REF: Make argument name clearer

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• DOC: Add docstring to Metadata.metadata_path

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• REV: Revert "ENH: Use temporary directory for Dataset path by default"

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• REF: Rename temporary_directories

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• REF: Simplify Child.ask_multiple

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• ENH: Ensure app failure log message is emitted

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• REF: Simplify get_events

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• FIX: Add missing space in log message

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• TST: Improve flask app tests

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• TST: Fix typo

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Commits on Jul 15, 2024

• OPS: Use new event handler function

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• OPS: Remove order column from event store

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• FIX: Remove order from get_events

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• CHO: Add version compatibility data

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• TST: Update deployment test

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• DEP: Require Sphinx>=5

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• DOC: Improve Manifest.download documentation

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• DOC: Improve Child.ask_multiple documentation

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• DOC: Improve docstring

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