Release 3.1 (#198)

* 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>
Sage-Bionetworks · Jan 1, 2021 · 496535f · 496535f
1 parent e2c5331
commit 496535f
Show file tree

Hide file tree

Showing 12 changed files with 229 additions and 143 deletions.
diff --git a/.github/workflows/sphinx-ghpages.yaml b/.github/workflows/sphinx-ghpages.yaml
@@ -36,6 +36,6 @@ jobs:
         with:
           branch: gh-pages
           directory: gh-pages
-          github_token: ${{ secrets.ACCESS_TOKEN }}
+          github_token: ${{ secrets.GITHUB_TOKEN }}
           force: true
       # ===============================
diff --git a/challengeutils/__version__.py b/challengeutils/__version__.py
@@ -1 +1 @@
-__version__ = "3.0.0"
+__version__ = "3.1.0"
diff --git a/challengeutils/teams.py b/challengeutils/teams.py
@@ -0,0 +1,120 @@
+"""Team related functions"""
+from typing import Union
+
+from synapseclient import Synapse, Team, UserProfile
+from synapseclient.core.utils import id_of
+
+
+def _get_team_count(syn: Synapse, teamid: int) -> dict:
+    """Rest call wrapper for getting team member count
+
+    Args:
+        syn: Synapse object
+        teamid: Synapse team id
+    """
+    count = syn.restGET(f"/teamMembers/count/{teamid}")
+    return count
+
+
+def get_team_count(syn: Synapse, team: Union[int, str, Team]) -> int:
+    """Get number of team members
+
+    Args:
+        syn: Synapse object
+        team: synaspeclient.Team, its id, or name.
+    """
+    team_obj = syn.getTeam(team)
+    count = _get_team_count(syn, team_obj.id)
+    return count['count']
+
+
+def remove_team_member(syn, team, user):
+    """Removes team member
+
+    Args:
+        syn: Synapse object
+        team: synaspeclient.Team or its id
+        user: synapseclient.UserProfile or its id
+    """
+    teamid = id_of(team)
+    userid = id_of(user)
+    syn.restDELETE(f"/team/{teamid}/member/{userid}")
+
+
+class NewUserProfile(UserProfile):
+    '''
+    Create new user profile that makes Userprofiles hashable
+    SYNPY-879
+    '''
+    def __hash__(self):
+        return int(self['ownerId'])
+
+
+def _get_team_set(syn, team):
+    '''
+    Helper function to return a set of usernames
+
+    Args:
+        syn: Synapse object
+        team: Synapse team id, name or object
+
+    Returns:
+        Set of synapse user profiles in team
+    '''
+    members = syn.getTeamMembers(team)
+    members_set = set(NewUserProfile(**member['member']) for member in members)
+    return members_set
+
+
+def team_members_diff(syn, a, b):
+    '''
+    Calculates the diff between teama and teamb
+
+    Args:
+        syn: Synapse object
+        a: Synapse Team id or name
+        b: Synapse Team id or name
+
+    Returns:
+        Set of synapse user profiles in teama but not in teamb
+    '''
+    uniq_teama_members = _get_team_set(syn, a)
+    uniq_teamb_members = _get_team_set(syn, b)
+    members_not_in_teamb = uniq_teama_members.difference(uniq_teamb_members)
+    return members_not_in_teamb
+
+
+def team_members_intersection(syn, a, b):
+    '''
+    Calculates the intersection between teama and teamb
+
+    Args:
+        syn: Synapse object
+        a: Synapse Team id or name
+        b: Synapse Team id or name
+
+    Returns:
+        Set of synapse user profiles that belong in both teams
+    '''
+    uniq_teama_members = _get_team_set(syn, a)
+    uniq_teamb_members = _get_team_set(syn, b)
+    intersect_members = uniq_teama_members.intersection(uniq_teamb_members)
+    return intersect_members
+
+
+def team_members_union(syn, a, b):
+    '''
+    Calculates the union between teama and teamb
+
+    Args:
+        syn: Synapse object
+        a: Synapse Team id or name
+        b: Synapse Team id or name
+
+    Returns:
+        Set of a combination of synapse user profiles from both teams
+    '''
+    uniq_teama_members = _get_team_set(syn, a)
+    uniq_teamb_members = _get_team_set(syn, b)
+    union_members = uniq_teama_members.union(uniq_teamb_members)
+    return union_members
diff --git a/challengeutils/utils.py b/challengeutils/utils.py
@@ -11,6 +11,7 @@
 from synapseclient.annotations import (is_submission_status_annotations,
                                        to_submission_status_annotations)
 from synapseclient.core.exceptions import SynapseHTTPError
+from synapseclient.core.utils import id_of
 
 logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)
@@ -285,85 +286,6 @@ def change_all_submission_status(syn, evaluationid, submission_status='SCORED',
         syn.store(status)
 
 
-class NewUserProfile(synapseclient.team.UserProfile):
-    '''
-    Create new user profile that makes Userprofiles hashable
-    SYNPY-879
-    '''
-    def __hash__(self):
-        return int(self['ownerId'])
-
-
-def _get_team_set(syn, team):
-    '''
-    Helper function to return a set of usernames
-
-    Args:
-        syn: Synapse object
-        team: Synapse team id, name or object
-
-    Returns:
-        Set of synapse user profiles in team
-    '''
-    members = syn.getTeamMembers(team)
-    members_set = set(NewUserProfile(**member['member']) for member in members)
-    return members_set
-
-
-def team_members_diff(syn, a, b):
-    '''
-    Calculates the diff between teama and teamb
-
-    Args:
-        syn: Synapse object
-        a: Synapse Team id or name
-        b: Synapse Team id or name
-
-    Returns:
-        Set of synapse user profiles in teama but not in teamb
-    '''
-    uniq_teama_members = _get_team_set(syn, a)
-    uniq_teamb_members = _get_team_set(syn, b)
-    members_not_in_teamb = uniq_teama_members.difference(uniq_teamb_members)
-    return members_not_in_teamb
-
-
-def team_members_intersection(syn, a, b):
-    '''
-    Calculates the intersection between teama and teamb
-
-    Args:
-        syn: Synapse object
-        a: Synapse Team id or name
-        b: Synapse Team id or name
-
-    Returns:
-        Set of synapse user profiles that belong in both teams
-    '''
-    uniq_teama_members = _get_team_set(syn, a)
-    uniq_teamb_members = _get_team_set(syn, b)
-    intersect_members = uniq_teama_members.intersection(uniq_teamb_members)
-    return intersect_members
-
-
-def team_members_union(syn, a, b):
-    '''
-    Calculates the union between teama and teamb
-
-    Args:
-        syn: Synapse object
-        a: Synapse Team id or name
-        b: Synapse Team id or name
-
-    Returns:
-        Set of a combination of synapse user profiles from both teams
-    '''
-    uniq_teama_members = _get_team_set(syn, a)
-    uniq_teamb_members = _get_team_set(syn, b)
-    union_members = uniq_teama_members.union(uniq_teamb_members)
-    return union_members
-
-
 def _check_date_range(date_str, start_datetime, end_datetime):
     '''
     Helper function to check if the date is within range

diff --git a/requirements.txt b/requirements.txt
@@ -1,2 +1,2 @@
 pandas==1.0.1
-synapseclient==2.1.0
+synapseclient==2.2.2
diff --git a/setup.py b/setup.py
@@ -26,4 +26,4 @@
       scripts=['bin/runqueue.py'],
       entry_points={'console_scripts': ['challengeutils = challengeutils.__main__:main']},
       install_requires=['pandas>=1.0.0',
-                        'synapseclient>2'])
+                        'synapseclient>=2.2.0'])
diff --git a/tests/test_get_team_stats.py b/tests/test_get_team_stats.py
diff --git a/tests/test_processor.py b/tests/test_processor.py
@@ -23,7 +23,7 @@
                                       evaluationId=2, versionNumber=1,
                                       id="syn222", filePath="foo",
                                       userId="222")
-SUBMISSION_STATUS = synapseclient.SubmissionStatus(status="RECEIVED")
+SUBMISSION_STATUS = synapseclient.SubmissionStatus(status="RECEIVED", id="111", etag="222")
 EVALUATION = synapseclient.Evaluation(name="foo", id="222",
                                       contentSource=CHALLENGE_SYNID)
 SYN_USERPROFILE = synapseclient.UserProfile(ownerId="111", userName="foo")

diff --git a/tests/test_scorer.py b/tests/test_scorer.py
@@ -22,7 +22,7 @@
                                       evaluationId=2, versionNumber=1,
                                       id="syn222", filePath="foo",
                                       userId="222")
-SUBMISSION_STATUS = synapseclient.SubmissionStatus(status="RECEIVED")
+SUBMISSION_STATUS = synapseclient.SubmissionStatus(status="RECEIVED", id="111", etag="222")
 EVALUATION = synapseclient.Evaluation(name="foo", id="222",
                                       contentSource=CHALLENGE_SYNID)
 SYN_USERPROFILE = synapseclient.UserProfile(ownerId="111", userName="foo")