girder 3.2.4.dev21__tar.gz → 3.2.4.dev30__tar.gz

girder-3.2.4.dev30/.github/workflows/codespell.yml

@@ -0,0 +1,22 @@
+# Codespell configuration is within setup.cfg
+---
+name: Codespell
+
+on:
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Annotate locations with typos
+        uses: codespell-project/codespell-problem-matcher@v1
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2

{girder-3.2.4.dev21 → girder-3.2.4.dev30}/CHANGELOG.rst

@@ -183,7 +183,7 @@ Server
   (`#2499 <https://github.com/girder/girder/pull/2499>`_)
 * When a plugin supplying an assetstore fails to load, other assetstores could not be listed.
   (`#2498 <https://github.com/girder/girder/pull/2498>`_)
-* Run pip installation of plugins using a subprocess rather than the pip module, for forward compatbility
+* Run pip installation of plugins using a subprocess rather than the pip module, for forward compatibility
   with pip. (`#2669 <https://github.com/girder/girder/pull/2669>`_)
 * Correct complex plugin dependencies parsing. (`#2496 <https://github.com/girder/girder/pull/2496>`_)
 

{girder-3.2.4.dev21 → girder-3.2.4.dev30}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: girder
-Version: 3.2.4.dev21
+Version: 3.2.4.dev30
 Summary: Web-based data management platform
 Home-page: https://girder.readthedocs.org
 Author: Kitware, Inc.

{girder-3.2.4.dev21 → girder-3.2.4.dev30}/clients/python/girder_client/__init__.py

@@ -531,7 +531,7 @@ class GirderClient:
         """
         This is a generator that will yield records using the given path and
         params until exhausted. Paging of the records is done internally, but
-        can be overriden by manually passing a ``limit`` value to select only
+        can be overridden by manually passing a ``limit`` value to select only
         a single page. Passing an ``offset`` will work in both single-page and
         exhaustive modes.
         """
@@ -772,7 +772,7 @@ class GirderClient:
 
         :param folderId: Id of the target folder.
         :param access: JSON document specifying access control.
-        :param public: Boolean specificying the public value.
+        :param public: Boolean specifying the public value.
         """
         if access is not None and not isinstance(access, str):
             access = json.dumps(access)

{girder-3.2.4.dev21 → girder-3.2.4.dev30}/devops/ansible-role-girder/library/girder.py

@@ -814,7 +814,7 @@ EXAMPLES = """
 def unjsonify(a):
     """Convert json parts to python objects.
 
-    Tries to convert a json string or a compund object consisting of partial
+    Tries to convert a json string or a compound object consisting of partial
     json strings to a full python object.  Returns either a json scalar (string,
     int, float), a list or dict of json scalars, or any combination of lists and
     dicts that eventually end at json scalars.
@@ -1767,7 +1767,7 @@ def main():
     :returns: Nothing
     :rtype: NoneType
     """
-    # Default spec for initalizing and authenticating
+    # Default spec for initializing and authenticating
     argument_spec = {
         # __init__
         'host': {},

{girder-3.2.4.dev21 → girder-3.2.4.dev30}/devops/ansible-role-girder/molecule/ansible-module/test_access.yml

@@ -220,7 +220,7 @@
       - "{{ 'alice' not in group_access }}"
       # bill should be a moderator
       - "{{ 'bill' in  group_access }}"
-      # Note that groupby gives us a dict of lists - thats why we
+      # Note that groupby gives us a dict of lists - that's why we
       # do group_access[...][0][...].
       - "{{ group_access['bill'][0]['level'] == 1 }}"
       # chris should be an admin
@@ -392,7 +392,7 @@
       - "{{ 'alice' not in group_access }}"
       # bill should be a moderator
       - "{{ 'bill' in  group_access }}"
-      # Note that groupby gives us a dict of lists - thats why we
+      # Note that groupby gives us a dict of lists - that's why we
       # do group_access[...][0][...].
       - "{{ group_access['bill'][0]['level'] == 1 }}"
       # chris should be an admin

{girder-3.2.4.dev21 → girder-3.2.4.dev30}/devops/ansible-role-girder/molecule/ansible-module/test_assetstore.yml

@@ -44,7 +44,7 @@
 
 # Removing an assetstore that doesn't exist should
 # show no change
-- name: Check that deleting an assetstore that doesnt exist doesnt trigger a failure
+- name: Check that deleting an assetstore that doesn't exist doesn't trigger a failure
   assert:
     that:
       - ret["changed"] == false  # noqa 601

{girder-3.2.4.dev21 → girder-3.2.4.dev30}/devops/ansible-role-girder/molecule/ansible-module/test_user.yml

@@ -24,7 +24,7 @@
 
 # More than one user
 # First user's login is 'admin'
-# First user has admin priviledges
+# First user has admin privileges
 - assert:
     that:
       - ret["gc_return"]|length > 0

{girder-3.2.4.dev21 → girder-3.2.4.dev30}/docs/development.rst

@@ -192,7 +192,7 @@ Girder's legacy automated tests are written with Python's
 test cases are still covered only by unitest.
 
 .. note:: Unless debugging code that is already coverered by a legacy test case, it may be more
-          convenient to allow these tests to be run by Girder's CI envionment, instead of
+          convenient to allow these tests to be run by Girder's CI environment, instead of
           configuring them locally.
 
 To initialize the legacy tests, from the root ``girder`` repo, run:

{girder-3.2.4.dev21 → girder-3.2.4.dev30}/docs/mount.rst

@@ -28,7 +28,7 @@ standard system unmount commands (e.g., ``fusermount -u <mount path>`` or
 Installation
 ++++++++++++
 
-There are some additional python dependencies to use the Girder mount commnd.
+There are some additional python dependencies to use the Girder mount command.
 These can be installed via: ::
 
   $ pip install -e .[mount]

{girder-3.2.4.dev21 → girder-3.2.4.dev30}/docs/plugin-development.rst

@@ -482,7 +482,7 @@ route handler.
 *  **Exception during REST call**
 
 This event is fired if an exception is raised while the default handler is executing.
-Like the before REST call event, this event recieves the same kwargs as the default
+Like the before REST call event, this event receives the same kwargs as the default
 route handler. The caught exception is raised again after this event is handled.
 The identifier for this event is, e.g., ``rest.get.item/:id.failed``.
 
@@ -866,7 +866,7 @@ packages are installed when you plugin is "pip installed".
 
 By default, Girder does not load its installed plugins in a deterministic order.
 If your plugin depends on other Girder being loaded prior to itself, your plugin
-must explicitly load the other dependant plugins during your plugin's own loading.
+must explicitly load the other dependent plugins during your plugin's own loading.
 
 Girder will guarantee that a given plugin is actually loaded only once, so multiple
 calls to load another plugin are safe and have no effect. Finally, it is possible

{girder-3.2.4.dev21 → girder-3.2.4.dev30}/girder/api/describe.py

@@ -496,7 +496,7 @@ class Describe(Resource):
 
         wsgiRoot = cherrypy.request.app.root
 
-        # This is due to the idiosyncracy of mounting the API root at both {core_girder_route}/api
+        # This is due to the idiosyncrasy of mounting the API root at both {core_girder_route}/api
         # as well as under /api. Depending which one is being used, the API root object could be
         # either at .api.v1 or just at .v1 due to the way it's mounted in server.py.
         try:

{girder-3.2.4.dev21 → girder-3.2.4.dev30}/girder/cli/build.py

@@ -72,7 +72,7 @@ def main(dev, mode, watch, watch_plugin, npm, reinstall):
 
         for path in nodeModuleDirs:
             # Include ignore_errors=True to delete readonly files
-            # and skip over nonexistant directories
+            # and skip over nonexistent directories
             shutil.rmtree(path, ignore_errors=True)
 
         # Run npm install

{girder-3.2.4.dev21 → girder-3.2.4.dev30}/girder/cli/mount.py

@@ -170,6 +170,9 @@ class ServerFuse(fuse.Operations):
         # '/user', and 'collection' before calling this method.
         if '/' not in path.rstrip('/')[1:]:
             raise fuse.FuseOSError(errno.ENOENT)
+        flat = path.startswith('/flat')
+        if flat:
+            path = path[5:]
         try:
             # We can't filter the resource, since that removes files'
             # assetstore information and users' size information.
@@ -182,8 +185,24 @@ class ServerFuse(fuse.Operations):
         except Exception:
             logger.exception('ServerFuse server internal error')
             raise fuse.FuseOSError(errno.EROFS)
+        if flat and resource['model'] == 'item':
+            file = self._flatItemFile(resource['document'])
+            if file is not None:
+                file['name'] = resource['document']['name']
+                resource = {
+                    'model': 'file',
+                    'document': file,
+                }
         return resource   # {model, document}
 
+    def _flatItemFile(self, item):
+        return next(File().collection.aggregate([
+            {'$match': {'itemId': item['_id']}},
+            {'$addFields': {'matchName': {'$eq': ['$name', item['name']]}}},
+            {'$sort': {'matchName': -1, '_id': 1}},
+            {'$limit': 1},
+        ]), None)
+
     def _stat(self, doc, model):
         """
         Generate stat results for a resource.
@@ -292,7 +311,8 @@ class ServerFuse(fuse.Operations):
         :returns: 0 if access is allowed.  An exception is raised if it is
             not.
         """
-        if path.rstrip('/') in ('', '/user', '/collection'):
+        if path.rstrip('/') in (
+                '', '/user', '/collection', '/flat', '/flat/user', '/flat/collection'):
             return super().access(path, mode)
         # mode is either F_OK or a bitfield of R_OK, W_OK, X_OK
         return 0
@@ -322,7 +342,8 @@ class ServerFuse(fuse.Operations):
             specified.
         :returns: an attribute dictionary.
         """
-        if path.rstrip('/') in ('', '/user', '/collection'):
+        if path.rstrip('/') in (
+                '', '/user', '/collection', '/flat', '/flat/user', '/flat/collection'):
             attr = self._defaultStat.copy()
             attr['st_mode'] = 0o500 | stat.S_IFDIR
             attr['st_size'] = 0
@@ -421,12 +442,19 @@ class ServerFuse(fuse.Operations):
         path = path.rstrip('/')
         result = ['.', '..']
         if path == '':
-            result.extend(['collection', 'user', 'stats'])
+            result.extend(['collection', 'user', 'stats', 'flat'])
+        elif path == '/flat':
+            result.extend(['collection', 'user'])
         elif path in ('/user', '/collection'):
             model = path[1:]
             docList = ModelImporter.model(model).find({}, sort=None)
             for doc in docList:
                 result.append(self._name(doc, model))
+        elif path in ('/flat/user', '/flat/collection'):
+            model = path[6:]
+            docList = ModelImporter.model(model).find({}, sort=None)
+            for doc in docList:
+                result.append(self._name(doc, model))
         else:
             resource = self._get_path(path)
             result.extend(self._list(resource['document'], resource['model']))
@@ -666,8 +694,12 @@ def mountServer(path, database=None, fuseOptions=None, quiet=False, verbose=0,
                 continue
             options[key] = value
     opClass = ServerFuse(stat=os.stat(path), options=options)
-    Setting().set(SettingKey.GIRDER_MOUNT_INFORMATION,
-                  {'path': path, 'mounttime': time.time()})
+    Setting().set(SettingKey.GIRDER_MOUNT_INFORMATION, {
+        'path': path,
+        'mounttime': time.time(),
+        'hasStats': True,
+        'hasFlat': True,
+    })
     FUSELogError(opClass, path, **options)
 
 

{girder-3.2.4.dev21 → girder-3.2.4.dev30}/girder/constants.py

@@ -33,7 +33,7 @@ def registerAccessFlag(key, name, description=None, admin=False):
     """
     Register a new access flag in the set of ACCESS_FLAGS available
     on data in the hierarchy. These are boolean switches that can be used
-    to control access to specific functionality on specific resoruces.
+    to control access to specific functionality on specific resources.
 
     :param key: The unique identifier for this access flag.
     :type key: str

{girder-3.2.4.dev21 → girder-3.2.4.dev30}/girder/models/file.py

@@ -483,19 +483,34 @@ class File(acl_mixin.AccessControlMixin, Model):
         """
         return self.getAssetstoreAdapter(file).open(file)
 
-    def getGirderMountFilePath(self, file, validate=True):
+    def getGirderMountFilePath(self, file, validate=True, preferFlat=False):
         """
-        If possible, get the path of the file on a local girder mount.
+        If possible, get the path of the file on a local girder mount.  Flat
+        paths exclude the item component, which, for some types of access of
+        relative paths can be preferred.
 
         :param file: The file document.
         :param validate: if True, check if the path exists and raise an
             exception if it does not.
+        :param preferFlat: if True and the mount supports it, return the flat
+            path that doesn't include item information.
         :returns: a girder mount path to the file or None if no such path is
             available.
         """
         mount = Setting().get(SettingKey.GIRDER_MOUNT_INFORMATION)
         if mount:
-            path = mount['path'].rstrip('/') + path_util.getResourcePath('file', file, force=True)
+            resPath = path_util.getResourcePath('file', file, force=True)
+            path = os.path.join(mount['path'], resPath.lstrip('/'))
+            if preferFlat and mount.get('hasFlat'):
+                flatpath = os.path.join(mount['path'], 'flat', os.path.dirname(resPath).lstrip('/'))
+                # An item can have multiple files, while flatten returns the
+                # "first" file, which might not be the file that was requested.
+                # Perform a simple size check to verify it is the file
+                # requested.  This happens even if validation is False.
+                if (
+                        os.path.exists(path) and os.path.exists(flatpath)
+                        and os.path.getsize(path) == os.path.getsize(flatpath)):
+                    return flatpath
             if not validate or os.path.exists(path):
                 return path
         if validate:

{girder-3.2.4.dev21 → girder-3.2.4.dev30}/girder/plugin.py

@@ -103,7 +103,7 @@ class GirderPlugin(metaclass=_PluginMeta):
 
         By default, this dictionary will be assembled from the CLIENT_SOURCE_PATH property by
         inspecting the package.json file in the indicated directory.  Plugins can override this
-        method customize the behaivor for advanced usage.
+        method customize the behavior for advanced usage.
         """
         if self.CLIENT_SOURCE_PATH is None:
             return {}

{girder-3.2.4.dev21 → girder-3.2.4.dev30}/girder/utility/path.py

@@ -41,7 +41,7 @@ def split(path):
     :rtype: `list`
     """
     # It would be better to split by the regex `(?<!\\)(?>\\\\)*/`,
-    # but python does't support atomic grouping. :(
+    # but python doesn't support atomic grouping. :(
     chunks = path.split('/')
     processed = [chunks[0]]
 

{girder-3.2.4.dev21 → girder-3.2.4.dev30}/girder/utility/progress.py

@@ -102,7 +102,7 @@ def setResponseTimeLimit(duration=600, onlyExtend=True):
     :param onlyExtend: if True, only ever increase the timeout.  If False, the
                        new duration always replaces the old one.
     """
-    # CherryPy 12.0 no longer has a timeout propery on a response.  Since we
+    # CherryPy 12.0 no longer has a timeout property on a response.  Since we
     # had only been using this to extend the time, if the timeout property is
     # not present, do nothing.
     if (cherrypy.response and getattr(cherrypy.response, 'time', None)

{girder-3.2.4.dev21 → girder-3.2.4.dev30}/girder/utility/server.py

@@ -197,7 +197,7 @@ def staticFile(path, contentType=None):
     :param path: The path of the static file to serve from this route.
     :type path: str
     :param contentType: The MIME type of the static file. If set to None, the
-                        content type wll be guessed by the file extension of
+                        content type will be guessed by the file extension of
                         the 'path' argument.
     """
     return _StaticFileRoute(path, contentType)

{girder-3.2.4.dev21 → girder-3.2.4.dev30}/girder/web_client/fontello/README.md

@@ -28,7 +28,7 @@ import '@girder/fontello/dist/css/animation.css';
 To add new icons to this build, visit
 [Fontello's website](https://fontello.com) and upload the
 `fontello.config.json` file within this package. Select new icons
-(but don't remove any), then download the new confguration via the site
+(but don't remove any), then download the new configuration via the site
 and overwrite `fontello.config.json` here. Then, just run:
 ```bash
 npm install && npm run build

{girder-3.2.4.dev21 → girder-3.2.4.dev30}/girder/web_client/src/collections/Collection.js

@@ -133,7 +133,7 @@ var Collection = Backbone.Collection.extend({
     },
 
     /**
-     * Sets a specific pagenumber for loading by caluclating the offset
+     * Sets a specific pagenumber for loading by calculating the offset
      * @param {Number} pageNumber The 0 indexed page that should be loaded based on the pageLimit size
      * @param {Object} params Additional parameters to pass to the fetch call
      * @returns {Promise} a fetch promise to retrieve more data
@@ -235,7 +235,7 @@ var Collection = Backbone.Collection.extend({
                     if (numUsed > newNumUsed) {
                         /*
                          * ...therefore, entries are being left out at the end,
-                         * so they necessesarily remain to be fetched.
+                         * so they necessarily remain to be fetched.
                          */
                         this._hasMorePages = true;
                         numUsed = newNumUsed;

{girder-3.2.4.dev21 → girder-3.2.4.dev30}/girder/web_client/src/views/widgets/EditAssetstoreWidget.js

@@ -34,7 +34,7 @@ var EditAssetstoreWidget = View.extend({
 
     /**
      * This maps each type of assetstore to a function to getter and setter
-     * functions. The set functions are reponsible for populating the dialog
+     * functions. The set functions are responsible for populating the dialog
      * fields with the appropriate current model values, and the get functions
      * are responsible for reading the user input values from the dialog and
      * returning a set of fields (excluding the name field) to set on the model.

{girder-3.2.4.dev21 → girder-3.2.4.dev30}/girder/web_client/src/views/widgets/ItemListWidget.js

@@ -325,7 +325,7 @@ var ItemListWidget = View.extend({
                 }
             };
 
-            // Add in scroll event to monitor the scrollPos to prevent uncessary updates and also kill observer when user scrolls
+            // Add in scroll event to monitor the scrollPos to prevent unnecessary updates and also kill observer when user scrolls
             widgetcontainer.bind('scroll.observerscroll', (evt) => {
                 if (this.tempScrollPos !== undefined && this.tempScrollPos !== widgetcontainer[0].scrollTop) {
                     this.tempScrollPos = widgetcontainer[0].scrollTop;

{girder-3.2.4.dev21 → girder-3.2.4.dev30}/girder/web_client/src/views/widgets/SearchFieldWidget.js

@@ -39,7 +39,7 @@ var SearchFieldWidget = View.extend({
         'keydown .g-search-field': function (e) {
             var code = e.keyCode || e.which;
             var list, pos;
-            if (code === 13 && this.noResourceSelected) { /* enter without resource seleted */
+            if (code === 13 && this.noResourceSelected) { /* enter without resource selected */
                 e.preventDefault();
                 if (this.$('.g-search-field').val() !== '' && !this.noResultsPage) {
                     this._goToResultPage(this.$('.g-search-field').val(), this.currentMode);

{girder-3.2.4.dev21 → girder-3.2.4.dev30}/girder/web_client/src/views/widgets/SortCollectionWidget.js

@@ -9,7 +9,7 @@ import 'bootstrap/js/dropdown';
 
 /**
  * This widget is used to provide a consistent widget for sorting
- * pages of a Collection by a choosen field.
+ * pages of a Collection by a chosen field.
  */
 var SortCollectionWidget = View.extend({
     events: {

{girder-3.2.4.dev21 → girder-3.2.4.dev30}/girder/web_client/src/views/widgets/TimelineWidget.js

@@ -42,7 +42,7 @@ var TimelineWidget = View.extend({
      * @param [settings.segments=[]] A list of segments. Each element of the list
      *    should be an object with the following keys:
      *      - start: A number or timestamp representing
-     *      - end: A numer of timestamp representing the end of this segment.
+     *      - end: A number of timestamp representing the end of this segment.
      *      - [class]: A CSS class name to apply to the segment. Uses the
      *                 widget's defaultSegmentClass if this key is not set.
      *      - [tooltip]: A tooltip value for this segment. Tooltips containing the

{girder-3.2.4.dev21 → girder-3.2.4.dev30}/girder.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: girder
-Version: 3.2.4.dev21
+Version: 3.2.4.dev30
 Summary: Web-based data management platform
 Home-page: https://girder.readthedocs.org
 Author: Kitware, Inc.

{girder-3.2.4.dev21 → girder-3.2.4.dev30}/girder.egg-info/SOURCES.txt

@@ -24,6 +24,7 @@ tox.ini
 .circleci/generatePyEnvChecksum.sh
 .circleci/publish_npm.sh
 .circleci/publish_pypi.sh
+.github/workflows/codespell.yml
 clients/python/README.rst
 clients/python/setup.py
 clients/python/girder_client/__init__.py

{girder-3.2.4.dev21 → girder-3.2.4.dev30}/scripts/test_names.sh

@@ -9,7 +9,7 @@ if [ "$DIFF" != "" ]; then
 **********************************************************
 
 Public symbols have been introduced (or removed) and those
-changes have not been commited to the scripts/publicNames.txt
+changes have not been committed to the scripts/publicNames.txt
 file. Please run the following command:
 
   python scripts/publicNames.py > scripts/publicNames.txt

{girder-3.2.4.dev21 → girder-3.2.4.dev30}/setup.cfg

@@ -23,6 +23,11 @@ title = Girder Coverage Report
 [coverage:xml]
 output = build/test/coverage/py_coverage.xml
 
+[codespell]
+skip = .git*,package-lock.json,*.css,jasmine.js,fontello.config.json
+check-hidden = true
+ignore-words-list = defin
+
 [egg_info]
 tag_build = 
 tag_date = 0