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Updating annotations #180

Merged
merged 9 commits into from
Jun 14, 2020
Merged

Updating annotations #180

merged 9 commits into from
Jun 14, 2020

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thomasyu888
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  • Fixes #xxxx (Link the github issue if applicable)
  • Did you run your tests locally (instructions here)?
  • Did you add a good description about your changes or additions?

Uses new submissionAnnotations for SubmissionStatus. This allows for submissionviews to be populated.

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pep8speaks commented Jun 11, 2020 •
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Hello @thomasyu888! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻

Comment last updated at 2020-06-13 23:53:35 UTC

vpchung
vpchung approved these changes Jun 12, 2020
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All the TODOs were a bit overwhelming, but for the most part, looks good to me!

challengeutils/annotations.py
return annos


def _convert_to_annotation_cls(
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Just wanted to double-check:
This function will be removed once synapseclient 2.1.0 is released as well? Since everything it's dependent on will be removed?

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This function will actually remain unless I add it to the synapseclient

@thomasyu888 thomasyu888 merged commit dd88d06 into develop Jun 14, 2020
@thomasyu888 thomasyu888 deleted the update-annotations branch June 14, 2020 00:04
thomasyu888 added a commit that referenced this pull request Jul 16, 2020
@thomasyu888 @vpchung
v3.0 release (#190)
e2c5331 
* Updating annotations (#180)

* Test annotations

* Add in support to update a submission's status in annotation submission

* Fix tess

* Add tests for converting dict or synapse style annotations to Annotations cls

* Test updating annotations

* Add EOL

* Add line

* Fix

* Increase version

* Increase version in conf.py

* Add to docs

* Add function

* Add to docs

* Patch convert to synapse cls

* Add in function to delete submission (#182)

* Add to docs and update cli syntax

* Upgrade synapseclient to 2.1.0 (#185)

* Update required synapseclient version to 2.1.0

* Remove redundant functions that are already in synapseclient

* No need to mock a response

* No longer need to return status code while using with_retry function

* Rename cli (#188)

* Add thread service (#184)

* Add Thread model

* Add in typing

* use kwargs when possible

* Add typing

* Fix comments

* Fix tests

* Update challengeutils/synapseservices/discussion.py

* Add reply service (#189)

* Add in reply service

* Use kwargs and use Reply obj

* use Reply obj

* Fix

* Fix test

* Fix discussion tests

* Update challengeutils/synapseservices/discussion.py

* Update challengeutils/discussion.py

* Patch project sub (#191)

* Fix

* add tests

* update conditional for private writeup with admin access

Co-authored-by: verena <9377970+vpchung@users.noreply.github.com>

* validate docker submission (#86)

* validate docker

* Add in validate docker script

* Remove

* Remove

* Add doc string

* Add doc string

* Add validate docker submission

* Lint

* Remove params

* Rework validate docker

* Rename

* Simply code

* Update

* Remove extra line

* Simply cli

* Define invalid reasons first

* Add command validate docker to docs

* Test docker tools

* Add tests

* Test validate docker

* Complete tests for validate docker

* Fix

* Import Response model

* Fix dockertools

* Create submission module

* Change project_submission to submission

* Move functions arond

* Rename

* Fix tests and shift functions around

* Remove download current leading submission and put in submission.py (#193)

* Fix tests

* Remove test and fix cli

* Fix validate docker

* Remove

* lint

* add logic for private writeup that must be shared with admin (#195)

* add logic for private writeup that must be shared with admin

* error message for admin permissions should not print if `public` is flagged

* move try-catch to each permissions check; add and edit tests

Co-authored-by: verena <vpchung@users.noreply.github.com>

* Add annotate sub (#194)

* add annotate_submission that just takes in json

* Fix tests

* Don't add in annotations if None or empty list

* Test None and [] annotation values aren't added

* Update docs (#192)

* Update docs

* update docs and version

* Fix

* No longer support synapseclient<2.1.0

* Add submission id

* Add in docker validate

* Fix

* Fix docs

Co-authored-by: Verena Chung <9377970+vpchung@users.noreply.github.com>
Co-authored-by: verena <vpchung@users.noreply.github.com>
thomasyu888 added a commit that referenced this pull request Jan 1, 2021
@thomasyu888 @vpchung
Release 3.1 (#198)
496535f 
* Use dataclass

* add uri into challenge class

* Use dataclass and dataclass json

* Add challenge service

* Fix

* Add in dataclasses req

* Add in requirement

* Use specific version

* Fix tests

* Remove last line

* Revise challenge data obj + add challengeApi

* Add tests

* Add tests for challenge service

* test rest calls

* Move synapse services to within challengeutils folder

* Fix tests

* Fix tests

* Fix functions

* Rename

* Switch to challenge instead of util

* Fix tests and finish up refactor

* Remove duplicate

* Remove unused var

* Push dev version

* Fix

* Have consistent spacing

* Setter functions don't return anything

* Update to 1.6.1

* Fix client issue

* Only the getter needs to be documented'

* Create list registered challenges function + command line tool

* Add to client docs

* Split up admin/user guide

* lint

* Remove dependency for synapseclient < 2, fix setup.py, fix imports

* import mock from unittest

* Software untested for 3.9

* Fix import

* ADd in downloading of submissions

* Update challengeutils/challenge.py

* Update challengeutils/__version__.py

* Remove

* update docs theme; rearrange toc and pages (#155)

* update docs theme; rearrange toc and pages

* fixed requirements; added more pages and docs

* fixed changelog description

* fix versioning

* added v2.0 information to changelog

* add link to GitHub contributors in authors

* update badges; reformat word for consistency

* minor fixes

* added remaining commands to CLI page

* temporarily removing client overview for doc release; will re-add later

* remove emoji from v1.5.2 release notes and add actual info

Co-authored-by: verena <vpchung@users.noreply.github.com>

* Push 2.0.1

* Create CODE_OF_CONDUCT.md (#158)

* Create CONTRIBUTING.md (#159)

* Remove image

* update readme

* Edit

* Fix contributing guide path

* Add space

* Add to change log

* Remove travis dependency (#163)

* Create pythonapp.yml

* Install challengeutils

* Remove travis dependency

* Only run test on PR

* update version

* Remove functionality to invite members to team (#167)

* Create _copy_thread which just copies the threads, copy_thread now copies replies (#169)

* Fix createchallenge bug (#171)

* Make sure to not redefine 'challenge'

* Dont pass object into rest post call

* Fix tests

* Add in sage name and year

* Automate code coverage (#165)

* Add in testing of synapse service module

* Test code coverage

* Fix

* Add init

* Update

* Remove

* Add inits

* Add inits

* Remove

* Try uploading artifact

* Add in flake8

* install all dependencies

* Rename to build

* Remove duplicated test func

* Refactor mirror wiki (#143)

* Update version

* Refactor mirrowiki

* Update mirrorwiki

* Add dry run flag, fix docs

* Remove comments

* Increase update wiki pages and maps helper

* Add test mirrorwiki

* Make most functions convenience functions

* Fix indent

* add tests

* Add test

* Fix

* Add integration test

* Add integration tests

* Remove synapseclient<2 support for challenge.py

* Add -f

* Add in stdout for wiki titles that exist in destionation but not entity

* Update tests/test_mirrorwiki.py

* Add to documentation (#175)

* Add in development requirements

* Add to contributing guide on how to develop

* Update documentation

* Update version and add to changelog

* Update CONTRIBUTING.md

* Add release procedure

* Add in more contributing guide

* Edit PR template

* Update .github/PULL_REQUEST_TEMPLATE.md

Co-authored-by: Verena Chung <9377970+vpchung@users.noreply.github.com>

Co-authored-by: Verena Chung <9377970+vpchung@users.noreply.github.com>

* writeup commands (#130)

* validate project function

* added output param to command; added unittest plans

* bug fix; add archive_project function

* refactor writeups into smaller functions

* added tests

* adding validation status to return value of validate_project()

* updated validateproject doc; changed default "public" value to False

* added tests for overall command functionality

* added docstrings to tests

* Update docstring to follow Google standards

Co-Authored-By: Thomas Yu <thomas.yu@sagebase.org>

* update names; modularize permissions function further; update tests

* fixed and added remaining tests; update package paths

* use entity name as new archive name

* Update challengeutils/project_submission.py

Co-authored-by: Thomas Yu <thomas.yu@sagebase.org>

* removed import alias and unused imports; parametrized tests

Co-authored-by: verena <vpchung@users.noreply.github.com>
Co-authored-by: Thomas Yu <thomas.yu@sagebase.org>

* Updating annotations (#180)

* Test annotations

* Add in support to update a submission's status in annotation submission

* Fix tess

* Add tests for converting dict or synapse style annotations to Annotations cls

* Test updating annotations

* Add EOL

* Add line

* Fix

* Increase version

* Increase version in conf.py

* Add to docs

* Add function

* Add to docs

* Patch convert to synapse cls

* Add in function to delete submission (#182)

* Add to docs and update cli syntax

* Upgrade synapseclient to 2.1.0 (#185)

* Update required synapseclient version to 2.1.0

* Remove redundant functions that are already in synapseclient

* No need to mock a response

* No longer need to return status code while using with_retry function

* Rename cli (#188)

* Add thread service (#184)

* Add Thread model

* Add in typing

* use kwargs when possible

* Add typing

* Fix comments

* Fix tests

* Update challengeutils/synapseservices/discussion.py

* Add reply service (#189)

* Add in reply service

* Use kwargs and use Reply obj

* use Reply obj

* Fix

* Fix test

* Fix discussion tests

* Update challengeutils/synapseservices/discussion.py

* Update challengeutils/discussion.py

* Patch project sub (#191)

* Fix

* add tests

* update conditional for private writeup with admin access

Co-authored-by: verena <9377970+vpchung@users.noreply.github.com>

* validate docker submission (#86)

* validate docker

* Add in validate docker script

* Remove

* Remove

* Add doc string

* Add doc string

* Add validate docker submission

* Lint

* Remove params

* Rework validate docker

* Rename

* Simply code

* Update

* Remove extra line

* Simply cli

* Define invalid reasons first

* Add command validate docker to docs

* Test docker tools

* Add tests

* Test validate docker

* Complete tests for validate docker

* Fix

* Import Response model

* Fix dockertools

* Create submission module

* Change project_submission to submission

* Move functions arond

* Rename

* Fix tests and shift functions around

* Remove download current leading submission and put in submission.py (#193)

* Fix tests

* Remove test and fix cli

* Fix validate docker

* Remove

* lint

* add logic for private writeup that must be shared with admin (#195)

* add logic for private writeup that must be shared with admin

* error message for admin permissions should not print if `public` is flagged

* move try-catch to each permissions check; add and edit tests

Co-authored-by: verena <vpchung@users.noreply.github.com>

* Add annotate sub (#194)

* add annotate_submission that just takes in json

* Fix tests

* Don't add in annotations if None or empty list

* Test None and [] annotation values aren't added

* Update docs (#192)

* Update docs

* update docs and version

* Fix

* No longer support synapseclient<2.1.0

* Add submission id

* Add in docker validate

* Fix

* Fix docs

* Add -dev

* Add in function to remove members from team (#197)

* Add in function to remove members from team

* Remove extra space

* Use github token instead of personal access token (#199)

* update synapse to at least v2.2.0 (#200)

* Update challengeutils/__version__.py

* Get team member count rest call (#201)

* Get team member count rest call

* Add tests

* Add tests

* Update tests/test_teams.py

* Update challengeutils/__version__.py

* Move to team module (#202)

* move team related functions to team module

* ilnt

Co-authored-by: Verena Chung <9377970+vpchung@users.noreply.github.com>
Co-authored-by: verena <vpchung@users.noreply.github.com>
thomasyu888 added a commit that referenced this pull request Feb 2, 2021
@thomasyu888 @vpchung
Release 3.2 (#209)
f002c10 
* Use dataclass

* add uri into challenge class

* Use dataclass and dataclass json

* Add challenge service

* Fix

* Add in dataclasses req

* Add in requirement

* Use specific version

* Fix tests

* Remove last line

* Revise challenge data obj + add challengeApi

* Add tests

* Add tests for challenge service

* test rest calls

* Move synapse services to within challengeutils folder

* Fix tests

* Fix tests

* Fix functions

* Rename

* Switch to challenge instead of util

* Fix tests and finish up refactor

* Remove duplicate

* Remove unused var

* Push dev version

* Fix

* Have consistent spacing

* Setter functions don't return anything

* Update to 1.6.1

* Fix client issue

* Only the getter needs to be documented'

* Create list registered challenges function + command line tool

* Add to client docs

* Split up admin/user guide

* lint

* Remove dependency for synapseclient < 2, fix setup.py, fix imports

* import mock from unittest

* Software untested for 3.9

* Fix import

* ADd in downloading of submissions

* Update challengeutils/challenge.py

* Update challengeutils/__version__.py

* Remove

* update docs theme; rearrange toc and pages (#155)

* update docs theme; rearrange toc and pages

* fixed requirements; added more pages and docs

* fixed changelog description

* fix versioning

* added v2.0 information to changelog

* add link to GitHub contributors in authors

* update badges; reformat word for consistency

* minor fixes

* added remaining commands to CLI page

* temporarily removing client overview for doc release; will re-add later

* remove emoji from v1.5.2 release notes and add actual info

Co-authored-by: verena <vpchung@users.noreply.github.com>

* Push 2.0.1

* Create CODE_OF_CONDUCT.md (#158)

* Create CONTRIBUTING.md (#159)

* Remove image

* update readme

* Edit

* Fix contributing guide path

* Add space

* Add to change log

* Remove travis dependency (#163)

* Create pythonapp.yml

* Install challengeutils

* Remove travis dependency

* Only run test on PR

* update version

* Remove functionality to invite members to team (#167)

* Create _copy_thread which just copies the threads, copy_thread now copies replies (#169)

* Fix createchallenge bug (#171)

* Make sure to not redefine 'challenge'

* Dont pass object into rest post call

* Fix tests

* Add in sage name and year

* Automate code coverage (#165)

* Add in testing of synapse service module

* Test code coverage

* Fix

* Add init

* Update

* Remove

* Add inits

* Add inits

* Remove

* Try uploading artifact

* Add in flake8

* install all dependencies

* Rename to build

* Remove duplicated test func

* Refactor mirror wiki (#143)

* Update version

* Refactor mirrowiki

* Update mirrorwiki

* Add dry run flag, fix docs

* Remove comments

* Increase update wiki pages and maps helper

* Add test mirrorwiki

* Make most functions convenience functions

* Fix indent

* add tests

* Add test

* Fix

* Add integration test

* Add integration tests

* Remove synapseclient<2 support for challenge.py

* Add -f

* Add in stdout for wiki titles that exist in destionation but not entity

* Update tests/test_mirrorwiki.py

* Add to documentation (#175)

* Add in development requirements

* Add to contributing guide on how to develop

* Update documentation

* Update version and add to changelog

* Update CONTRIBUTING.md

* Add release procedure

* Add in more contributing guide

* Edit PR template

* Update .github/PULL_REQUEST_TEMPLATE.md

Co-authored-by: Verena Chung <9377970+vpchung@users.noreply.github.com>

Co-authored-by: Verena Chung <9377970+vpchung@users.noreply.github.com>

* writeup commands (#130)

* validate project function

* added output param to command; added unittest plans

* bug fix; add archive_project function

* refactor writeups into smaller functions

* added tests

* adding validation status to return value of validate_project()

* updated validateproject doc; changed default "public" value to False

* added tests for overall command functionality

* added docstrings to tests

* Update docstring to follow Google standards

Co-Authored-By: Thomas Yu <thomas.yu@sagebase.org>

* update names; modularize permissions function further; update tests

* fixed and added remaining tests; update package paths

* use entity name as new archive name

* Update challengeutils/project_submission.py

Co-authored-by: Thomas Yu <thomas.yu@sagebase.org>

* removed import alias and unused imports; parametrized tests

Co-authored-by: verena <vpchung@users.noreply.github.com>
Co-authored-by: Thomas Yu <thomas.yu@sagebase.org>

* Updating annotations (#180)

* Test annotations

* Add in support to update a submission's status in annotation submission

* Fix tess

* Add tests for converting dict or synapse style annotations to Annotations cls

* Test updating annotations

* Add EOL

* Add line

* Fix

* Increase version

* Increase version in conf.py

* Add to docs

* Add function

* Add to docs

* Patch convert to synapse cls

* Add in function to delete submission (#182)

* Add to docs and update cli syntax

* Upgrade synapseclient to 2.1.0 (#185)

* Update required synapseclient version to 2.1.0

* Remove redundant functions that are already in synapseclient

* No need to mock a response

* No longer need to return status code while using with_retry function

* Rename cli (#188)

* Add thread service (#184)

* Add Thread model

* Add in typing

* use kwargs when possible

* Add typing

* Fix comments

* Fix tests

* Update challengeutils/synapseservices/discussion.py

* Add reply service (#189)

* Add in reply service

* Use kwargs and use Reply obj

* use Reply obj

* Fix

* Fix test

* Fix discussion tests

* Update challengeutils/synapseservices/discussion.py

* Update challengeutils/discussion.py

* Patch project sub (#191)

* Fix

* add tests

* update conditional for private writeup with admin access

Co-authored-by: verena <9377970+vpchung@users.noreply.github.com>

* validate docker submission (#86)

* validate docker

* Add in validate docker script

* Remove

* Remove

* Add doc string

* Add doc string

* Add validate docker submission

* Lint

* Remove params

* Rework validate docker

* Rename

* Simply code

* Update

* Remove extra line

* Simply cli

* Define invalid reasons first

* Add command validate docker to docs

* Test docker tools

* Add tests

* Test validate docker

* Complete tests for validate docker

* Fix

* Import Response model

* Fix dockertools

* Create submission module

* Change project_submission to submission

* Move functions arond

* Rename

* Fix tests and shift functions around

* Remove download current leading submission and put in submission.py (#193)

* Fix tests

* Remove test and fix cli

* Fix validate docker

* Remove

* lint

* add logic for private writeup that must be shared with admin (#195)

* add logic for private writeup that must be shared with admin

* error message for admin permissions should not print if `public` is flagged

* move try-catch to each permissions check; add and edit tests

Co-authored-by: verena <vpchung@users.noreply.github.com>

* Add annotate sub (#194)

* add annotate_submission that just takes in json

* Fix tests

* Don't add in annotations if None or empty list

* Test None and [] annotation values aren't added

* Update docs (#192)

* Update docs

* update docs and version

* Fix

* No longer support synapseclient<2.1.0

* Add submission id

* Add in docker validate

* Fix

* Fix docs

* Add -dev

* Add in function to remove members from team (#197)

* Add in function to remove members from team

* Remove extra space

* Use github token instead of personal access token (#199)

* update synapse to at least v2.2.0 (#200)

* Update challengeutils/__version__.py

* Get team member count rest call (#201)

* Get team member count rest call

* Add tests

* Add tests

* Update tests/test_teams.py

* Update challengeutils/__version__.py

* Move to team module (#202)

* move team related functions to team module

* ilnt

* Pull and push synapse wikis in markdown + wiki config (#133)

* Create functions to - download and upload synapse wikis in markdown + wiki config

* Add doc strings

* Add cli

* add more details in print

* Change to pull and push wiki, remove config_path and use workdir

* Add docs

* Add docs

* Add docs

* Edit

* Edit docs

* Use workdir parameter for all wiki commands

* Add docs

* add doc

* Add tests

* Add tests

* Lint

* Make improvements

* Add fine grain validationg

* Lint

* Test for strings and ints

* Fix tests

* Remove

* Edit

* Comment out valiate-wiki-config function

* Fix

* Make sure to use isfile instead of os.path.exists

* Edit

* Add wikiId in front of markdown path

* Add comment

* Update wiki

* Update docs/client/source.rst

* Bump version

* Update challengeutils/__main__.py

Co-authored-by: Verena Chung <9377970+vpchung@users.noreply.github.com>
Co-authored-by: verena <vpchung@users.noreply.github.com>
thomasyu888 added a commit that referenced this pull request Mar 6, 2021
@thomasyu888 @vpchung
Release 4.0.0 (#215)
663a389 
* Use dataclass

* add uri into challenge class

* Use dataclass and dataclass json

* Add challenge service

* Fix

* Add in dataclasses req

* Add in requirement

* Use specific version

* Fix tests

* Remove last line

* Revise challenge data obj + add challengeApi

* Add tests

* Add tests for challenge service

* test rest calls

* Move synapse services to within challengeutils folder

* Fix tests

* Fix tests

* Fix functions

* Rename

* Switch to challenge instead of util

* Fix tests and finish up refactor

* Remove duplicate

* Remove unused var

* Push dev version

* Fix

* Have consistent spacing

* Setter functions don't return anything

* Update to 1.6.1

* Fix client issue

* Only the getter needs to be documented'

* Create list registered challenges function + command line tool

* Add to client docs

* Split up admin/user guide

* lint

* Remove dependency for synapseclient < 2, fix setup.py, fix imports

* import mock from unittest

* Software untested for 3.9

* Fix import

* ADd in downloading of submissions

* Update challengeutils/challenge.py

* Update challengeutils/__version__.py

* Remove

* update docs theme; rearrange toc and pages (#155)

* update docs theme; rearrange toc and pages

* fixed requirements; added more pages and docs

* fixed changelog description

* fix versioning

* added v2.0 information to changelog

* add link to GitHub contributors in authors

* update badges; reformat word for consistency

* minor fixes

* added remaining commands to CLI page

* temporarily removing client overview for doc release; will re-add later

* remove emoji from v1.5.2 release notes and add actual info

Co-authored-by: verena <vpchung@users.noreply.github.com>

* Push 2.0.1

* Create CODE_OF_CONDUCT.md (#158)

* Create CONTRIBUTING.md (#159)

* Remove image

* update readme

* Edit

* Fix contributing guide path

* Add space

* Add to change log

* Remove travis dependency (#163)

* Create pythonapp.yml

* Install challengeutils

* Remove travis dependency

* Only run test on PR

* update version

* Remove functionality to invite members to team (#167)

* Create _copy_thread which just copies the threads, copy_thread now copies replies (#169)

* Fix createchallenge bug (#171)

* Make sure to not redefine 'challenge'

* Dont pass object into rest post call

* Fix tests

* Add in sage name and year

* Automate code coverage (#165)

* Add in testing of synapse service module

* Test code coverage

* Fix

* Add init

* Update

* Remove

* Add inits

* Add inits

* Remove

* Try uploading artifact

* Add in flake8

* install all dependencies

* Rename to build

* Remove duplicated test func

* Refactor mirror wiki (#143)

* Update version

* Refactor mirrowiki

* Update mirrorwiki

* Add dry run flag, fix docs

* Remove comments

* Increase update wiki pages and maps helper

* Add test mirrorwiki

* Make most functions convenience functions

* Fix indent

* add tests

* Add test

* Fix

* Add integration test

* Add integration tests

* Remove synapseclient<2 support for challenge.py

* Add -f

* Add in stdout for wiki titles that exist in destionation but not entity

* Update tests/test_mirrorwiki.py

* Add to documentation (#175)

* Add in development requirements

* Add to contributing guide on how to develop

* Update documentation

* Update version and add to changelog

* Update CONTRIBUTING.md

* Add release procedure

* Add in more contributing guide

* Edit PR template

* Update .github/PULL_REQUEST_TEMPLATE.md

Co-authored-by: Verena Chung <9377970+vpchung@users.noreply.github.com>

Co-authored-by: Verena Chung <9377970+vpchung@users.noreply.github.com>

* writeup commands (#130)

* validate project function

* added output param to command; added unittest plans

* bug fix; add archive_project function

* refactor writeups into smaller functions

* added tests

* adding validation status to return value of validate_project()

* updated validateproject doc; changed default "public" value to False

* added tests for overall command functionality

* added docstrings to tests

* Update docstring to follow Google standards

Co-Authored-By: Thomas Yu <thomas.yu@sagebase.org>

* update names; modularize permissions function further; update tests

* fixed and added remaining tests; update package paths

* use entity name as new archive name

* Update challengeutils/project_submission.py

Co-authored-by: Thomas Yu <thomas.yu@sagebase.org>

* removed import alias and unused imports; parametrized tests

Co-authored-by: verena <vpchung@users.noreply.github.com>
Co-authored-by: Thomas Yu <thomas.yu@sagebase.org>

* Updating annotations (#180)

* Test annotations

* Add in support to update a submission's status in annotation submission

* Fix tess

* Add tests for converting dict or synapse style annotations to Annotations cls

* Test updating annotations

* Add EOL

* Add line

* Fix

* Increase version

* Increase version in conf.py

* Add to docs

* Add function

* Add to docs

* Patch convert to synapse cls

* Add in function to delete submission (#182)

* Add to docs and update cli syntax

* Upgrade synapseclient to 2.1.0 (#185)

* Update required synapseclient version to 2.1.0

* Remove redundant functions that are already in synapseclient

* No need to mock a response

* No longer need to return status code while using with_retry function

* Rename cli (#188)

* Add thread service (#184)

* Add Thread model

* Add in typing

* use kwargs when possible

* Add typing

* Fix comments

* Fix tests

* Update challengeutils/synapseservices/discussion.py

* Add reply service (#189)

* Add in reply service

* Use kwargs and use Reply obj

* use Reply obj

* Fix

* Fix test

* Fix discussion tests

* Update challengeutils/synapseservices/discussion.py

* Update challengeutils/discussion.py

* Patch project sub (#191)

* Fix

* add tests

* update conditional for private writeup with admin access

Co-authored-by: verena <9377970+vpchung@users.noreply.github.com>

* validate docker submission (#86)

* validate docker

* Add in validate docker script

* Remove

* Remove

* Add doc string

* Add doc string

* Add validate docker submission

* Lint

* Remove params

* Rework validate docker

* Rename

* Simply code

* Update

* Remove extra line

* Simply cli

* Define invalid reasons first

* Add command validate docker to docs

* Test docker tools

* Add tests

* Test validate docker

* Complete tests for validate docker

* Fix

* Import Response model

* Fix dockertools

* Create submission module

* Change project_submission to submission

* Move functions arond

* Rename

* Fix tests and shift functions around

* Remove download current leading submission and put in submission.py (#193)

* Fix tests

* Remove test and fix cli

* Fix validate docker

* Remove

* lint

* add logic for private writeup that must be shared with admin (#195)

* add logic for private writeup that must be shared with admin

* error message for admin permissions should not print if `public` is flagged

* move try-catch to each permissions check; add and edit tests

Co-authored-by: verena <vpchung@users.noreply.github.com>

* Add annotate sub (#194)

* add annotate_submission that just takes in json

* Fix tests

* Don't add in annotations if None or empty list

* Test None and [] annotation values aren't added

* Update docs (#192)

* Update docs

* update docs and version

* Fix

* No longer support synapseclient<2.1.0

* Add submission id

* Add in docker validate

* Fix

* Fix docs

* Add -dev

* Add in function to remove members from team (#197)

* Add in function to remove members from team

* Remove extra space

* Use github token instead of personal access token (#199)

* update synapse to at least v2.2.0 (#200)

* Update challengeutils/__version__.py

* Get team member count rest call (#201)

* Get team member count rest call

* Add tests

* Add tests

* Update tests/test_teams.py

* Update challengeutils/__version__.py

* Move to team module (#202)

* move team related functions to team module

* ilnt

* Pull and push synapse wikis in markdown + wiki config (#133)

* Create functions to - download and upload synapse wikis in markdown + wiki config

* Add doc strings

* Add cli

* add more details in print

* Change to pull and push wiki, remove config_path and use workdir

* Add docs

* Add docs

* Add docs

* Edit

* Edit docs

* Use workdir parameter for all wiki commands

* Add docs

* add doc

* Add tests

* Add tests

* Lint

* Make improvements

* Add fine grain validationg

* Lint

* Test for strings and ints

* Fix tests

* Remove

* Edit

* Comment out valiate-wiki-config function

* Fix

* Make sure to use isfile instead of os.path.exists

* Edit

* Add wikiId in front of markdown path

* Add comment

* Update wiki

* Update docs/client/source.rst

* Bump version

* Update challengeutils/__main__.py

* fix conditionals for permissions

* Add release

* Update setup.py

* Update syn client (#214)

* Update client

* Remove support for 3.6

* Limit

* Remove version for pandas

* Fix

* Don't drop support for python 3.6 yet

* Don't set pandas version

* Deprecate helpers (#213)

* Remove helpers, but refactor stopping submissions that are over a specific quota

* Remove tests for helpers

* Add in tests

* Add submission tests

* query fail

* Apply suggestions from code review

* Update docs/about/changelog.rst

* Update docs

Co-authored-by: Verena Chung <9377970+vpchung@users.noreply.github.com>
Co-authored-by: verena <vpchung@users.noreply.github.com>
thomasyu888 added a commit that referenced this pull request Aug 7, 2021
@thomasyu888 @vpchung
Release/4.1.0 (#222)
90328fa 
* Use dataclass

* add uri into challenge class

* Use dataclass and dataclass json

* Add challenge service

* Fix

* Add in dataclasses req

* Add in requirement

* Use specific version

* Fix tests

* Remove last line

* Revise challenge data obj + add challengeApi

* Add tests

* Add tests for challenge service

* test rest calls

* Move synapse services to within challengeutils folder

* Fix tests

* Fix tests

* Fix functions

* Rename

* Switch to challenge instead of util

* Fix tests and finish up refactor

* Remove duplicate

* Remove unused var

* Push dev version

* Fix

* Have consistent spacing

* Setter functions don't return anything

* Update to 1.6.1

* Fix client issue

* Only the getter needs to be documented'

* Create list registered challenges function + command line tool

* Add to client docs

* Split up admin/user guide

* lint

* Remove dependency for synapseclient < 2, fix setup.py, fix imports

* import mock from unittest

* Software untested for 3.9

* Fix import

* ADd in downloading of submissions

* Update challengeutils/challenge.py

* Update challengeutils/__version__.py

* Remove

* update docs theme; rearrange toc and pages (#155)

* update docs theme; rearrange toc and pages

* fixed requirements; added more pages and docs

* fixed changelog description

* fix versioning

* added v2.0 information to changelog

* add link to GitHub contributors in authors

* update badges; reformat word for consistency

* minor fixes

* added remaining commands to CLI page

* temporarily removing client overview for doc release; will re-add later

* remove emoji from v1.5.2 release notes and add actual info

Co-authored-by: verena <vpchung@users.noreply.github.com>

* Push 2.0.1

* Create CODE_OF_CONDUCT.md (#158)

* Create CONTRIBUTING.md (#159)

* Remove image

* update readme

* Edit

* Fix contributing guide path

* Add space

* Add to change log

* Remove travis dependency (#163)

* Create pythonapp.yml

* Install challengeutils

* Remove travis dependency

* Only run test on PR

* update version

* Remove functionality to invite members to team (#167)

* Create _copy_thread which just copies the threads, copy_thread now copies replies (#169)

* Fix createchallenge bug (#171)

* Make sure to not redefine 'challenge'

* Dont pass object into rest post call

* Fix tests

* Add in sage name and year

* Automate code coverage (#165)

* Add in testing of synapse service module

* Test code coverage

* Fix

* Add init

* Update

* Remove

* Add inits

* Add inits

* Remove

* Try uploading artifact

* Add in flake8

* install all dependencies

* Rename to build

* Remove duplicated test func

* Refactor mirror wiki (#143)

* Update version

* Refactor mirrowiki

* Update mirrorwiki

* Add dry run flag, fix docs

* Remove comments

* Increase update wiki pages and maps helper

* Add test mirrorwiki

* Make most functions convenience functions

* Fix indent

* add tests

* Add test

* Fix

* Add integration test

* Add integration tests

* Remove synapseclient<2 support for challenge.py

* Add -f

* Add in stdout for wiki titles that exist in destionation but not entity

* Update tests/test_mirrorwiki.py

* Add to documentation (#175)

* Add in development requirements

* Add to contributing guide on how to develop

* Update documentation

* Update version and add to changelog

* Update CONTRIBUTING.md

* Add release procedure

* Add in more contributing guide

* Edit PR template

* Update .github/PULL_REQUEST_TEMPLATE.md

Co-authored-by: Verena Chung <9377970+vpchung@users.noreply.github.com>

Co-authored-by: Verena Chung <9377970+vpchung@users.noreply.github.com>

* writeup commands (#130)

* validate project function

* added output param to command; added unittest plans

* bug fix; add archive_project function

* refactor writeups into smaller functions

* added tests

* adding validation status to return value of validate_project()

* updated validateproject doc; changed default "public" value to False

* added tests for overall command functionality

* added docstrings to tests

* Update docstring to follow Google standards

Co-Authored-By: Thomas Yu <thomas.yu@sagebase.org>

* update names; modularize permissions function further; update tests

* fixed and added remaining tests; update package paths

* use entity name as new archive name

* Update challengeutils/project_submission.py

Co-authored-by: Thomas Yu <thomas.yu@sagebase.org>

* removed import alias and unused imports; parametrized tests

Co-authored-by: verena <vpchung@users.noreply.github.com>
Co-authored-by: Thomas Yu <thomas.yu@sagebase.org>

* Updating annotations (#180)

* Test annotations

* Add in support to update a submission's status in annotation submission

* Fix tess

* Add tests for converting dict or synapse style annotations to Annotations cls

* Test updating annotations

* Add EOL

* Add line

* Fix

* Increase version

* Increase version in conf.py

* Add to docs

* Add function

* Add to docs

* Patch convert to synapse cls

* Add in function to delete submission (#182)

* Add to docs and update cli syntax

* Upgrade synapseclient to 2.1.0 (#185)

* Update required synapseclient version to 2.1.0

* Remove redundant functions that are already in synapseclient

* No need to mock a response

* No longer need to return status code while using with_retry function

* Rename cli (#188)

* Add thread service (#184)

* Add Thread model

* Add in typing

* use kwargs when possible

* Add typing

* Fix comments

* Fix tests

* Update challengeutils/synapseservices/discussion.py

* Add reply service (#189)

* Add in reply service

* Use kwargs and use Reply obj

* use Reply obj

* Fix

* Fix test

* Fix discussion tests

* Update challengeutils/synapseservices/discussion.py

* Update challengeutils/discussion.py

* Patch project sub (#191)

* Fix

* add tests

* update conditional for private writeup with admin access

Co-authored-by: verena <9377970+vpchung@users.noreply.github.com>

* validate docker submission (#86)

* validate docker

* Add in validate docker script

* Remove

* Remove

* Add doc string

* Add doc string

* Add validate docker submission

* Lint

* Remove params

* Rework validate docker

* Rename

* Simply code

* Update

* Remove extra line

* Simply cli

* Define invalid reasons first

* Add command validate docker to docs

* Test docker tools

* Add tests

* Test validate docker

* Complete tests for validate docker

* Fix

* Import Response model

* Fix dockertools

* Create submission module

* Change project_submission to submission

* Move functions arond

* Rename

* Fix tests and shift functions around

* Remove download current leading submission and put in submission.py (#193)

* Fix tests

* Remove test and fix cli

* Fix validate docker

* Remove

* lint

* add logic for private writeup that must be shared with admin (#195)

* add logic for private writeup that must be shared with admin

* error message for admin permissions should not print if `public` is flagged

* move try-catch to each permissions check; add and edit tests

Co-authored-by: verena <vpchung@users.noreply.github.com>

* Add annotate sub (#194)

* add annotate_submission that just takes in json

* Fix tests

* Don't add in annotations if None or empty list

* Test None and [] annotation values aren't added

* Update docs (#192)

* Update docs

* update docs and version

* Fix

* No longer support synapseclient<2.1.0

* Add submission id

* Add in docker validate

* Fix

* Fix docs

* Add -dev

* Add in function to remove members from team (#197)

* Add in function to remove members from team

* Remove extra space

* Use github token instead of personal access token (#199)

* update synapse to at least v2.2.0 (#200)

* Update challengeutils/__version__.py

* Get team member count rest call (#201)

* Get team member count rest call

* Add tests

* Add tests

* Update tests/test_teams.py

* Update challengeutils/__version__.py

* Move to team module (#202)

* move team related functions to team module

* ilnt

* Pull and push synapse wikis in markdown + wiki config (#133)

* Create functions to - download and upload synapse wikis in markdown + wiki config

* Add doc strings

* Add cli

* add more details in print

* Change to pull and push wiki, remove config_path and use workdir

* Add docs

* Add docs

* Add docs

* Edit

* Edit docs

* Use workdir parameter for all wiki commands

* Add docs

* add doc

* Add tests

* Add tests

* Lint

* Make improvements

* Add fine grain validationg

* Lint

* Test for strings and ints

* Fix tests

* Remove

* Edit

* Comment out valiate-wiki-config function

* Fix

* Make sure to use isfile instead of os.path.exists

* Edit

* Add wikiId in front of markdown path

* Add comment

* Update wiki

* Update docs/client/source.rst

* Bump version

* Update challengeutils/__main__.py

* fix conditionals for permissions

* Update syn client (#214)

* Update client

* Remove support for 3.6

* Limit

* Remove version for pandas

* Fix

* Don't drop support for python 3.6 yet

* Don't set pandas version

* Deprecate helpers (#213)

* Remove helpers, but refactor stopping submissions that are over a specific quota

* Remove tests for helpers

* Add in tests

* Add submission tests

* query fail

* Fix (#220)

* Update syn login (#221)

* Update synapse login to utilize new auth token env

* Remove line

* Remove line

* Update version

Co-authored-by: Verena Chung <9377970+vpchung@users.noreply.github.com>
Co-authored-by: verena <vpchung@users.noreply.github.com>
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@thomasyu888 @pep8speaks @vpchung