histomicsui 1.4.7.dev44__tar.gz → 1.4.7.dev49__tar.gz

{histomicsui-1.4.7.dev44 → histomicsui-1.4.7.dev49}/.circleci/config.yml

@@ -84,7 +84,7 @@ jobs:
     steps:
       - checkout
       - tox:
-          env: flake8,lintclient
+          env: lint,lintclient
   release:
     docker:
       - image: girder/tox-and-node

{histomicsui-1.4.7.dev44 → histomicsui-1.4.7.dev49}/.git-blame-ignore-revs

@@ -11,3 +11,5 @@ b566911831095bb4c161e2161e2d1a33cf3f4f18
 f1c2190ab04ab867c655b4217f807e9f567772c8
 # PR 296: Use stylus-supremacy for linting and reformating stylus files
 9475b89640a6de84788b79ba68d5ed9aeb1a9ff4
+# PR 359: Apply ruff formatting and linting
+97b21f031e4769043b2c3a464ea4cf8e9a60c219

{histomicsui-1.4.7.dev44 → histomicsui-1.4.7.dev49}/.pre-commit-config.yaml

@@ -2,7 +2,7 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v4.5.0
   hooks:
   - id: check-added-large-files
   - id: check-ast
@@ -42,7 +42,7 @@ repos:
     files: README.rst
     name: rst-linter of README.rst
 - repo: https://github.com/codespell-project/codespell
-  rev: v2.2.5
+  rev: v2.2.6
   hooks:
   - id: codespell
     args:
@@ -59,8 +59,15 @@ repos:
       args:
         - '--options'
         - './histomicsui/web_client/package.json'
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.1.0
+  hooks:
+    - id: ruff
+      args: [--fix, --exit-non-zero-on-fix]
+      types_or: [python, pyi, jupyter]
 - repo: https://github.com/asottile/pyupgrade
-  rev: v3.10.1
+  rev: v3.15.0
   hooks:
     - id: pyupgrade
       args:

{histomicsui-1.4.7.dev44 → histomicsui-1.4.7.dev49}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: histomicsui
-Version: 1.4.7.dev44
+Version: 1.4.7.dev49
 Summary: Organize, visualize, and analyze histology images.
 Home-page: https://github.com/DigitalSlideArchive/histomicsui
 Author: Kitware, Inc.

{histomicsui-1.4.7.dev44 → histomicsui-1.4.7.dev49}/histomicsui/__init__.py

@@ -19,6 +19,7 @@ import os
 import re
 from functools import wraps
 
+import cherrypy
 from bson import json_util
 from girder import events, logger, plugin
 from girder.api import access
@@ -30,6 +31,7 @@ from girder.models.file import File
 from girder.models.folder import Folder
 from girder.models.item import Item
 from girder.models.setting import Setting
+from girder.models.token import Token
 from girder.settings import SettingDefault, SettingKey
 from girder.utility import config
 from girder.utility import path as path_util
@@ -56,7 +58,7 @@ except DistributionNotFound:
 
 _template = os.path.join(
     os.path.dirname(__file__),
-    'webroot.mako'
+    'webroot.mako',
 )
 
 
@@ -153,29 +155,35 @@ def validateListOrJSON(doc):
 })
 def validateHistomicsUIColor(doc):
     if not doc['value']:
-        raise ValidationException('The banner color may not be empty', 'value')
+        msg = 'The banner color may not be empty'
+        raise ValidationException(msg, 'value')
     elif not re.match(r'^#[0-9A-Fa-f]{6}$', doc['value']):
-        raise ValidationException('The banner color must be a hex color triplet', 'value')
+        msg = 'The banner color must be a hex color triplet'
+        raise ValidationException(msg, 'value')
 
 
 @setting_utilities.validator(PluginSettings.HUI_BRAND_NAME)
 def validateHistomicsUIBrandName(doc):
     if not doc['value']:
-        raise ValidationException('The brand name may not be empty', 'value')
+        msg = 'The brand name may not be empty'
+        raise ValidationException(msg, 'value')
 
 
 @setting_utilities.validator(PluginSettings.HUI_WEBROOT_PATH)
 def validateHistomicsUIWebrootPath(doc):
     if not doc['value']:
-        raise ValidationException('The webroot path may not be empty', 'value')
+        msg = 'The webroot path may not be empty'
+        raise ValidationException(msg, 'value')
     if re.match(r'^girder$', doc['value']):
-        raise ValidationException('The webroot path may not be "girder"', 'value')
+        msg = 'The webroot path may not be "girder"'
+        raise ValidationException(msg, 'value')
 
 
 @setting_utilities.validator(PluginSettings.HUI_ALTERNATE_WEBROOT_PATH)
 def validateHistomicsUIAlternateWebrootPath(doc):
     if re.match(r'(^,|)girder(,|$)', doc['value']):
-        raise ValidationException('The alternate webroot path may not contain "girder"', 'value')
+        msg = 'The alternate webroot path may not contain "girder"'
+        raise ValidationException(msg, 'value')
 
 
 @setting_utilities.validator(PluginSettings.HUI_QUARANTINE_FOLDER)
@@ -195,14 +203,14 @@ SettingDefault.defaults.update({
     PluginSettings.HUI_HELP_URL:
         'https://github.com/DigitalSlideArchive/HistomicsUI/blob/master/docs/controls.rst',
     PluginSettings.HUI_HELP_TOOLTIP: 'Mouse and keyboard controls',
-    PluginSettings.HUI_HELP_TEXT: 'Help'
+    PluginSettings.HUI_HELP_TEXT: 'Help',
 })
 
 
 @setting_utilities.validator({
     PluginSettings.HUI_HELP_URL,
     PluginSettings.HUI_HELP_TOOLTIP,
-    PluginSettings.HUI_HELP_TEXT
+    PluginSettings.HUI_HELP_TEXT,
 })
 def validateHistomicsUIHelp(doc):
     pass
@@ -255,10 +263,27 @@ class WebrootHistomicsUI(Webroot):
             'huiBannerColor': Setting().get(PluginSettings.HUI_BANNER_COLOR),
             'huiHelpURL': Setting().get(PluginSettings.HUI_HELP_URL),
             'huiHelpTooltip': Setting().get(PluginSettings.HUI_HELP_TOOLTIP),
-            'huiHelpText': Setting().get(PluginSettings.HUI_HELP_TEXT)
+            'huiHelpText': Setting().get(PluginSettings.HUI_HELP_TEXT),
         })
         return super()._renderHTML()
 
+    def GET(self, **params):
+        print(params)
+        if params.get('token'):
+            try:
+                token = Token().load(params['token'], force=True, objectId=False)
+                if token:
+                    cookie = cherrypy.response.cookie
+                    cookie['girderToken'] = str(token['_id'])
+                    cookie['girderToken']['path'] = '/'
+                    days = float(Setting().get(SettingKey.COOKIE_LIFETIME))
+                    cookie['girderToken']['expires'] = int(days * 3600 * 24)
+                    cookie['girderToken']['sameSite'] = 'None'
+                    cookie['girderToken']['secure'] = True
+            except Exception:
+                pass
+        return self._renderHTML()
+
 
 def restrict_downloads(info):
     """
@@ -308,8 +333,9 @@ def restrict_downloads(info):
             def wrapped(*args, **kwargs):
                 if (not getCurrentToken() and len(args) >= 1 and
                         args[0] and args[0].get('size', 0) >= limit):
+                    msg = 'You must be logged in or have a valid auth token.'
                     raise AccessException(
-                        'You must be logged in or have a valid auth token.')
+                        msg)
                 return fun(*args, **kwargs)
             return wrapped
         File().download = limitLengthDownload(

{histomicsui-1.4.7.dev44 → histomicsui-1.4.7.dev49}/histomicsui/handlers.py

@@ -129,7 +129,7 @@ def process_annotations(event):  # noqa
 
     file = File().load(
         event.info.get('file', {}).get('_id'),
-        level=AccessType.READ, user=user
+        level=AccessType.READ, user=user,
     )
     startTime = time.time()
 
@@ -139,7 +139,8 @@ def process_annotations(event):  # noqa
     try:
         if file['size'] > int(large_image.config.getConfig(
                 'max_annotation_input_file_length', 1024 ** 3)):
-            raise Exception('File is larger than will be read into memory.')
+            msg = 'File is larger than will be read into memory.'
+            raise Exception(msg)
         data = []
         with File().open(file) as fptr:
             while True:
@@ -189,12 +190,15 @@ def quarantine_item(item, user, makePlaceholder=True):
     """
     folder = Setting().get(PluginSettings.HUI_QUARANTINE_FOLDER)
     if not folder:
-        raise RestException('The quarantine folder is not configured.')
+        msg = 'The quarantine folder is not configured.'
+        raise RestException(msg)
     folder = Folder().load(folder, force=True, exc=True)
     if not folder:
-        raise RestException('The quarantine folder does not exist.')
+        msg = 'The quarantine folder does not exist.'
+        raise RestException(msg)
     if str(folder['_id']) == str(item['folderId']):
-        raise RestException('The item is already in the quarantine folder.')
+        msg = 'The item is already in the quarantine folder.'
+        raise RestException(msg)
     originalFolder = Folder().load(item['folderId'], force=True)
     quarantineInfo = {
         'originalFolderId': item['folderId'],
@@ -202,7 +206,7 @@ def quarantine_item(item, user, makePlaceholder=True):
         'originalBaseParentId': item['baseParentId'],
         'originalUpdated': item['updated'],
         'quarantineUserId': user['_id'],
-        'quarantineTime': datetime.datetime.now(datetime.timezone.utc)
+        'quarantineTime': datetime.datetime.now(datetime.timezone.utc),
     }
     item = Item().move(item, folder)
     if makePlaceholder:
@@ -216,7 +220,7 @@ def quarantine_item(item, user, makePlaceholder=True):
     if makePlaceholder:
         placeholderInfo = {
             'quarantined': True,
-            'quarantineTime': quarantineInfo['quarantineTime']
+            'quarantineTime': quarantineInfo['quarantineTime'],
         }
         placeholder.setdefault('meta', {})['quarantine'] = placeholderInfo
         placeholder = Item().updateItem(placeholder)
@@ -232,10 +236,12 @@ def restore_quarantine_item(item, user):
     :returns: the modified item.
     """
     if not item.get('meta', {}).get('quarantine'):
-        raise RestException('The item has no quarantine record.')
+        msg = 'The item has no quarantine record.'
+        raise RestException(msg)
     folder = Folder().load(item['meta']['quarantine']['originalFolderId'], force=True)
     if not folder:
-        raise RestException('The original folder is not accessible.')
+        msg = 'The original folder is not accessible.'
+        raise RestException(msg)
     if 'placeholderItemId' in item['meta']['quarantine']:
         placeholder = Item().load(item['meta']['quarantine']['placeholderItemId'], force=True)
     else:
@@ -256,7 +262,7 @@ def process_metadata(event):
         return
     file = File().load(
         event.info.get('file', {}).get('_id'),
-        level=AccessType.READ, user=results['user']
+        level=AccessType.READ, user=results['user'],
     )
 
     if not file:

{histomicsui-1.4.7.dev44 → histomicsui-1.4.7.dev49}/histomicsui/models/aperio.py

@@ -15,7 +15,7 @@ class Aperio(Item):
     aperio_re = re.compile(
         r'^(?P<barcode>(?P<case>' +
         TCGAModel.case_re.pattern + r')[0-9a-z-]*)\.xml',
-        flags=re.I
+        flags=re.I,
     )
 
     def initialize(self, **kwargs):
@@ -32,14 +32,16 @@ class Aperio(Item):
         try:
             Item().load(imageId, force=True)
         except Exception:
+            msg = 'The item is not associated with a valid image.'
             raise ValidationException(
-                'The item is not associated with a valid image.'
+                msg,
             )
 
         files = Item().childFiles(doc)
         if files.count() != 1:
+            msg = 'The annotation item must have exactly one file.'
             raise ValidationException(
-                'The annotation item must have exactly one file.'
+                msg,
             )
 
         meta.setdefault('tag', None)
@@ -72,7 +74,7 @@ class Aperio(Item):
             name = doc['name']
             d = self.aperio_re.match(name).groupdict()
             image = TCGAImage().findOne({
-                'tcga.barcode': d['barcode'].upper()
+                'tcga.barcode': d['barcode'].upper(),
             })
             self.importDocument(doc, image, **kwargs)
 
@@ -84,7 +86,8 @@ class Aperio(Item):
                 except ValidationException:
                     pass
         else:
-            raise ValidationException('Invalid model type')
+            msg = 'Invalid model type'
+            raise ValidationException(msg)
 
     def findAperio(self, image, tag=None, **kwargs):
         """Find Aperio annotations associated with the given image."""

{histomicsui-1.4.7.dev44 → histomicsui-1.4.7.dev49}/histomicsui/models/case.py

@@ -9,24 +9,27 @@ class Case(TCGAModel, Folder):
 
     TCGAType = 'case'
     TCGAIndices = [
-        'tcga.label'
+        'tcga.label',
     ]
 
     def validate(self, doc, **kwargs):
         if doc.get('parentCollection') != 'folder':
+            msg = 'A Case model must be a child of a folder'
             raise ValidationException(
-                'A Case model must be a child of a folder'
+                msg,
             )
         super().validate(doc, **kwargs)
         cohort = Cohort().load(
             doc['parentId'], force=True)
         if not cohort or self.getTCGAType(cohort) != 'cohort':
+            msg = 'A Case model must be a child of a cohort'
             raise ValidationException(
-                'A Case model must be a child of a cohort'
+                msg,
             )
         if not self.case_re.match(self.getTCGA(doc).get('label', '')):
+            msg = 'Invalid label in TCGA metadata'
             raise ValidationException(
-                'Invalid label in TCGA metadata'
+                msg,
             )
         return doc
 
@@ -35,11 +38,12 @@ class Case(TCGAModel, Folder):
 
         recurse = kwargs.get('recurse', False)
         parent = Cohort().load(
-            doc.get('parentId'), force=True
+            doc.get('parentId'), force=True,
         )
         if not parent:
+            msg = 'Invalid folder document'
             raise ValidationException(
-                'Invalid folder document'
+                msg,
             )
         tcga = self.getTCGA(parent)
         tcga['label'] = doc['name']
@@ -51,7 +55,7 @@ class Case(TCGAModel, Folder):
 
         childModel = Slide()
         children = Folder().childFolders(
-            doc, 'folder', user=kwargs.get('user')
+            doc, 'folder', user=kwargs.get('user'),
         )
         for child in children:
             try:

{histomicsui-1.4.7.dev44 → histomicsui-1.4.7.dev49}/histomicsui/models/cohort.py

@@ -11,8 +11,9 @@ class Cohort(TCGAModel, Folder):
     def validate(self, doc, **kwargs):
         super().validate(doc, **kwargs)
         if doc['parentCollection'] != 'collection':
+            msg = 'A Cohort model must be a child of a collection'
             raise ValidationException(
-                'A Cohort model must be a child of a collection'
+                msg,
             )
         return doc
 
@@ -28,7 +29,7 @@ class Cohort(TCGAModel, Folder):
 
         childModel = Case()
         children = Folder().childFolders(
-            doc, 'folder', user=kwargs.get('user')
+            doc, 'folder', user=kwargs.get('user'),
         )
         for child in children:
             try:

{histomicsui-1.4.7.dev44 → histomicsui-1.4.7.dev49}/histomicsui/models/image.py

@@ -14,27 +14,32 @@ class Image(TCGAModel, Item):
     def validate(self, doc, **kwargs):
         super().validate(doc, **kwargs)
         if 'largeImage' not in doc:
+            msg = 'An image item must be a "large_image"'
             raise ValidationException(
-                'An image item must be a "large_image"'
+                msg,
             )
         slide = Slide().load(
             doc['folderId'], force=True)
         if not slide or self.getTCGAType(slide) != 'slide':
+            msg = 'An image must be a child of a slide'
             raise ValidationException(
-                'An image must be a child of a slide'
+                msg,
             )
         tcga = self.getTCGA(doc)
         if not self.case_re.match(tcga.get('case', '')):
+            msg = 'Invalid case name in TCGA metadata'
             raise ValidationException(
-                'Invalid case name in TCGA metadata'
+                msg,
             )
         if not self.barcode_re.match(tcga.get('barcode', '')):
+            msg = 'Invalid barcode in TCGA metadata'
             raise ValidationException(
-                'Invalid barcode in TCGA metadata'
+                msg,
             )
         if not self.uuid_re.match(tcga.get('uuid', '')):
+            msg = 'Invalid uuid in TCGA metadata'
             raise ValidationException(
-                'Invalid uuid in TCGA metadata'
+                msg,
             )
 
         return doc
@@ -46,11 +51,12 @@ class Image(TCGAModel, Item):
         try:
             return ImageItem.createImageItem(
                 doc, file,
-                user=user, token=token, createJob=False
+                user=user, token=token, createJob=False,
             )
         except Exception:
+            msg = 'Could not generate a large_image item'
             raise ValidationException(
-                'Could not generate a large_image item'
+                msg,
             )
 
     def _findImageFile(self, doc):
@@ -64,18 +70,20 @@ class Image(TCGAModel, Item):
         token = kwargs.get('token')
         fileId = self._findImageFile(doc)
         if fileId is None:
+            msg = 'Could not find a TCGA slide in item'
             raise ValidationException(
-                'Could not find a TCGA slide in item'
+                msg,
             )
         self._setLargeImage(doc, fileId, user, token)
 
         name = doc['name']
         parent = Slide().load(
-            doc.get('folderId'), force=True
+            doc.get('folderId'), force=True,
         )
         if not parent:
+            msg = 'Invalid item document'
             raise ValidationException(
-                'Invalid item document'
+                msg,
             )
         tcga = self.getTCGA(parent)
         tcga.update(self.parseImage(name))

{histomicsui-1.4.7.dev44 → histomicsui-1.4.7.dev49}/histomicsui/models/meta.py

@@ -58,13 +58,13 @@ class TCGAModel:
     #: Matches valid uuid's
     uuid_re = re.compile(
         r'[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}',
-        flags=re.I
+        flags=re.I,
     )
 
     #: Matches valid tcga barcodes
     barcode_re = re.compile(
         case_re.pattern + r'[0-9a-z-]*',
-        flags=re.I
+        flags=re.I,
     )
 
     #: Parses tcga slide image file names
@@ -72,7 +72,7 @@ class TCGAModel:
         r'^(?P<barcode>(?P<case>' +
         case_re.pattern + r')[0-9a-z-]*)\.' +
         r'(?P<uuid>' + uuid_re.pattern + r')\.svs$',
-        flags=re.I
+        flags=re.I,
     )
 
     #: Parses tcga pathology report file names
@@ -80,7 +80,7 @@ class TCGAModel:
         r'^(?P<case>' + case_re.pattern +
         r')\.(?P<uuid>' + uuid_re.pattern +
         r')\.pdf$',
-        flags=re.I
+        flags=re.I,
     )
 
     def initialize(self, **kwargs):
@@ -149,14 +149,15 @@ class TCGAModel:
     def getTCGACollection(self):
         """Get the unique TCGA collection from the settings collection."""
         tcga = Setting().get(
-            TCGACollectionSettingKey
+            TCGACollectionSettingKey,
         )
         if tcga is None:
+            msg = 'TCGA collection id not initialized in settings'
             raise Exception(
-                'TCGA collection id not initialized in settings'
+                msg,
             )
         return Collection().load(
-            tcga, force=True
+            tcga, force=True,
         )
 
     def __upper(self, obj, key):
@@ -170,7 +171,8 @@ class TCGAModel:
     def _parse(self, name, regex):
         m = regex.match(name)
         if m is None:
-            raise ValidationException('Invalid name')
+            msg = 'Invalid name'
+            raise ValidationException(msg)
         d = m.groupdict()
         self.__lower(d, 'uuid')
         self.__upper(d, 'barcode')
@@ -190,7 +192,7 @@ class TCGAModel:
         """Set the mime type of a file document."""
         oldType = doc.get('mimeType')
         newType = mimetypes.guess_type(
-            doc.get('name', '')
+            doc.get('name', ''),
         )[0]
         doc['mimeType'] = newType
         return newType != oldType
@@ -218,8 +220,9 @@ class TCGAModel:
                     return doc
             except ValidationException:
                 pass
+        msg = 'Invalid document id provided'
         raise ValidationException(
-            'Invalid document id provided'
+            msg,
         )
 
     def iterateItems(self, doc, **kwargs):
@@ -248,7 +251,7 @@ class TCGAModel:
         parentType = parentType.lower()
         q = {
             'parentId': parent['_id'],
-            'parentCollection': parentType
+            'parentCollection': parentType,
         }
         q.update(filters or {})
         return self.find(q, sort=sort, limit=limit, offset=offset)

{histomicsui-1.4.7.dev44 → histomicsui-1.4.7.dev49}/histomicsui/models/pathology.py

@@ -25,4 +25,5 @@ class Pathology(TCGAModel, Item):
                 except ValidationException:
                     pass
         else:
-            raise ValidationException('Invalid model type')
+            msg = 'Invalid model type'
+            raise ValidationException(msg)

{histomicsui-1.4.7.dev44 → histomicsui-1.4.7.dev49}/histomicsui/models/slide.py

@@ -11,15 +11,17 @@ class Slide(TCGAModel, Folder):
 
     def validate(self, doc, **kwargs):
         if not doc.get('parentCollection') == 'folder':
+            msg = 'A Slide model must be a child of a folder'
             raise ValidationException(
-                'A Slide model must be a child of a folder'
+                msg,
             )
         super().validate(doc, **kwargs)
         case = Case().load(
             doc['parentId'], force=True)
         if not case or self.getTCGAType(case) != 'case':
+            msg = 'A Slide model must be a child of a case'
             raise ValidationException(
-                'A Slide model must be a child of a case'
+                msg,
             )
         return doc
 
@@ -28,11 +30,12 @@ class Slide(TCGAModel, Folder):
 
         recurse = kwargs.get('recurse', False)
         parent = Case().load(
-            doc.get('parentId'), force=True
+            doc.get('parentId'), force=True,
         )
         if not parent:
+            msg = 'Invalid folder document'
             raise ValidationException(
-                'Invalid folder document'
+                msg,
             )
         tcga = self.getTCGA(parent)
         tcga.pop('meta', None)
@@ -43,7 +46,7 @@ class Slide(TCGAModel, Folder):
 
         childModel = Image()
         children = Folder().childItems(
-            doc, user=kwargs.get('user')
+            doc, user=kwargs.get('user'),
         )
         for child in children:
             try: