Release 4.0.0

.github/workflows/pythonapp.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.6, 3.7, 3.8]
+        python-version: [3.6, 3.7, 3.8, 3.9]
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python ${{ matrix.python-version }}

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.6
+FROM python:3.8
 
 WORKDIR /root/challengeutils
 COPY ./ ./

challengeutils/__version__.py

@@ -1 +1 @@
-__version__ = "3.2.0"
+__version__ = "4.0.0"

challengeutils/submission.py

@@ -1,17 +1,26 @@
 """Functions that interact with submissions"""
 import os
 import re
+import sys
 import time
+from typing import Union
 
 import pandas as pd
 import synapseutils
-from synapseclient import AUTHENTICATED_USERS, entity, Project
+from synapseclient import (AUTHENTICATED_USERS, entity, Project, Synapse,
+                           SubmissionViewSchema)
 from synapseclient.annotations import to_submission_status_annotations
 from synapseclient.core.exceptions import SynapseHTTPError
+from synapseclient.core.utils import id_of
 
 from . import dockertools
 from . import permissions
 from . import utils
+from . import annotations
+
+WORKFLOW_LAST_UPDATED_KEY = "orgSagebionetworksSynapseWorkflowOrchestratorWorkflowLastUpdated"
+WORKFLOW_START_KEY = "orgSagebionetworksSynapseWorkflowOrchestratorExecutionStarted"
+TIME_REMAINING_KEY = "orgSagebionetworksSynapseWorkflowOrchestratorTimeRemaining"
 
 
 def append_writeup_to_main_submission(row, syn):
@@ -145,7 +154,7 @@ def _validate_public_permissions(syn, proj):
         syn_users_perms = syn.getPermissions(
             proj.entityId, AUTHENTICATED_USERS)
         public_perms = syn.getPermissions(proj.entityId)
-        if set(syn_users_perms) == {"READ", "DOWNLOAD"} and \
+        if ("READ" in syn_users_perms and "DOWNLOAD" in syn_users_perms) and \
                 "READ" in public_perms:
             error = ""
 
@@ -166,7 +175,7 @@ def _validate_admin_permissions(syn, proj, admin):
     try:
         # Remove error message if admin has read and download permissions.
         admin_perms = syn.getPermissions(proj.entityId, admin)
-        if set(admin_perms) == {"READ", "DOWNLOAD"}:
+        if "READ" in admin_perms and "DOWNLOAD" in admin_perms:
             error = ""
 
     except SynapseHTTPError as e:
@@ -310,3 +319,48 @@ def download_current_lead_sub(syn, submissionid, status,
                                               cutoff_annotation, verbose)
         return path
     return None
+
+
+def stop_submission_over_quota(
+        syn: Synapse,
+        submission_view: Union[str, SubmissionViewSchema],
+        quota: int = sys.maxsize
+    ):
+    """Stops any submission that has exceeded the run time quota by using
+    submission views.  A submission view must first exist.
+    Rerunning submissions will require setting TimeRemaining annotation
+    to a positive integer.
+
+    Args:
+        syn: Synapse connection
+        submission_view: Submission View or its Synapse Id.
+        quota: Quota in milliseconds. Default is sys.maxsize.
+               One hour is 3600000.
+
+    """
+    if not isinstance(quota, int):
+        raise ValueError("quota must be an integer")
+    if quota <= 0:
+        raise ValueError("quota must be larger than 0")
+
+    try:
+        view_query = syn.tableQuery(
+            f"select {WORKFLOW_LAST_UPDATED_KEY}, {WORKFLOW_START_KEY}, id, "
+            f"status from {id_of(submission_view)} where "
+            "status = 'EVALUATION_IN_PROGRESS'"
+        )
+    except SynapseHTTPError as http_error:
+        raise ValueError(
+            "Submission view must have columns: "
+            f"{WORKFLOW_LAST_UPDATED_KEY}, {WORKFLOW_START_KEY}, id"
+        ) from http_error
+
+    view_querydf = view_query.asDataFrame()
+    runtime = (view_querydf[WORKFLOW_LAST_UPDATED_KEY] -
+               view_querydf[WORKFLOW_START_KEY])
+    submissions_over_quota_idx = runtime > quota
+    over_quotadf = view_querydf[submissions_over_quota_idx]
+    for index, row in over_quotadf.iterrows():
+        add_annotations = {TIME_REMAINING_KEY: 0}
+        annotations.annotate_submission(syn, row['id'], add_annotations,
+                                        is_private=False, force=True)

docs/about/changelog.rst

@@ -8,6 +8,25 @@ For older releases, visit the `GitHub releases`_.
 
 .. _Github releases: https://github.com/Sage-Bionetworks/challengeutils/releases
 
+v4.0.0
+------
+.. Important::
+    **Support for synapseclient<2.3.0 is no longer available**; upgrade to the
+    latest version with:
+
+    .. code:: console
+
+        $ pip install synapseclient --upgrade
+
+.. Important::
+    **Support for Python 3.6 is will be dropped in the later
+    half of this year.
+
+- Support `Python` 3.9
+- Deprecate `helpers.py` and create `stop_submissions_over_quota` function
+- Fix conditionals when validating permissions for project submissions
+
+
 v3.2.0
 ------
 

docs/conf.py

@@ -25,7 +25,7 @@
 author = 'Thomas Yu'
 
 # The short X.Y version
-version = '3.2'
+version = '4.0'
 # The full version, including alpha/beta/rc tags
 release = version
 

docs/requirements.txt

@@ -1,4 +1,4 @@
-pandas==1.0.1
-synapseclient==2.1.0
+pandas==1.1.5
+synapseclient==2.3.0
 challengeutils
 sphinx_rtd_theme

requirements.txt

@@ -1,2 +1,2 @@
-pandas==1.0.1
-synapseclient==2.2.2
+pandas
+synapseclient==2.3.0

setup.py

@@ -11,19 +11,45 @@
 with open("README.md", "r") as fh:
     long_description = fh.read()
 
-setup(name='challengeutils',
-      version=about["__version__"],
-      description='Challenge utility functions',
-      url='https://github.com/Sage-Bionetworks/challengeutils',
-      author='Thomas Yu',
-      author_email='thomasyu888@gmail.com',
-      long_description=long_description,
-      long_description_content_type="text/markdown",
-      license='Apache',
-      packages=find_packages(),
-      zip_safe=False,
-      python_requires='>=3.6, <3.9',
-      scripts=['bin/runqueue.py'],
-      entry_points={'console_scripts': ['challengeutils = challengeutils.__main__:main']},
-      install_requires=['pandas>=1.0.0',
-                        'synapseclient>=2.2.0'])
+setup(
+    name='challengeutils',
+    version=about["__version__"],
+    description='Challenge utility functions',
+    url='https://github.com/Sage-Bionetworks/challengeutils',
+    author='Thomas Yu',
+    author_email='thomasyu888@gmail.com',
+    long_description=long_description,
+    long_description_content_type="text/markdown",
+    license='Apache',
+    packages=find_packages(),
+    zip_safe=False,
+    python_requires='>=3.6, <3.10',
+    scripts=['bin/runqueue.py'],
+    entry_points={
+        'console_scripts': ['challengeutils = challengeutils.__main__:main']
+    },
+    install_requires=['pandas>=1.1.5',
+                      'synapseclient>=2.3.0'],
+    project_urls={
+        "Documentation": "https://sage-bionetworks.github.io/challengeutils/",
+        "Source Code": "https://github.com/Sage-Bionetworks/challengeutils",
+        "Bug Tracker": "https://github.com/Sage-Bionetworks/challengeutils/issues",
+    },
+    classifiers=[
+        'Development Status :: 5 - Production/Stable',
+        'Programming Language :: Python',
+        'Programming Language :: Python :: 3.6',
+        'Programming Language :: Python :: 3.7',
+        'Programming Language :: Python :: 3.8',
+        'Programming Language :: Python :: 3.9',
+        'Operating System :: MacOS',
+        'Operating System :: Microsoft :: Windows',
+        'Operating System :: Unix',
+        'Operating System :: POSIX :: Linux',
+        'Intended Audience :: Developers',
+        'Intended Audience :: Science/Research',
+        'License :: OSI Approved :: Apache Software License',
+        'Topic :: Software Development :: Libraries',
+        'Topic :: Scientific/Engineering',
+        'Topic :: Scientific/Engineering :: Bio-Informatics'],
+)