Support fetching yaml config files

CHANGELOG.md

@@ -1,5 +1,11 @@
 # Change Log
 
+## Unreleased
+
+### Improvements
+- Better handle editing polygons with holes ([857](../../pull/857))
+- Support fetching yaml config files ([860](../../pull/860))
+
 ## 1.14.4
 
 ### Improvements

girder/girder_large_image/__init__.py

@@ -39,6 +39,7 @@
 from .girder_tilesource import getGirderTileSource  # noqa
 from .loadmodelcache import invalidateLoadModelCache
 from .models.image_item import ImageItem
+from .rest import addSystemEndpoints
 from .rest.large_image_resource import LargeImageResource
 from .rest.tiles import TilesItemResource
 
@@ -322,6 +323,7 @@ def load(self, info):
         curConfig = config.getConfig().get('large_image')
         for key, value in (curConfig or {}).items():
             large_image.config.setConfig(key, value)
+        addSystemEndpoints(info['apiRoot'])
 
         girder_tilesource.loadGirderTileSources()
         TilesItemResource(info['apiRoot'])

girder/girder_large_image/rest/__init__.py

@@ -0,0 +1,122 @@
+import yaml
+
+from girder import logger
+from girder.api import access
+from girder.api.describe import Description, autoDescribeRoute
+from girder.api.rest import boundHandler
+from girder.constants import AccessType, SortDir, TokenScope
+from girder.models.file import File
+from girder.models.folder import Folder
+from girder.models.group import Group
+from girder.models.item import Item
+
+
+def addSystemEndpoints(apiRoot):
+    """
+    This adds endpoints to routes that already exist in Girder.
+
+    :param apiRoot: Girder api root class.
+    """
+    apiRoot.folder.route('GET', (':id', 'yaml_config', ':name'), getYAMLConfigFile)
+
+
+def _mergeDictionaries(a, b):
+    """
+    Merge two dictionaries recursively.  If the second dictionary (or any
+    sub-dictionary) has a special key, value of '__all__': True, the updated
+    dictionary only contains values from the second dictionary and excludes
+    the __all__ key.
+
+    :param a: the first dictionary.  Modified.
+    :param b: the second dictionary that gets added to the first.
+    :returns: the modified first dictionary.
+    """
+    if b.get('__all__') is True:
+        a.clear()
+    for key in b:
+        if isinstance(a.get(key), dict) and isinstance(b[key], dict):
+            _mergeDictionaries(a[key], b[key])
+        elif key != '__all__' or b[key] is not True:
+            a[key] = b[key]
+    return a
+
+
+def adjustConfigForUser(config, user):
+    """
+    Given the current user, adjust the config so that only relevant and
+    combined values are used.  If the root of the config dictionary contains
+    "access": {"user": <dict>, "admin": <dict>}, the base values are updated
+    based on the user's access level.  If the root of the config contains
+    "group": {<group-name>: <dict>, ...}, the base values are updated for
+    every group the user is a part of.
+
+    The order of update is groups in C-sort alphabetical order followed by
+    access/user and then access/admin as they apply.
+
+    :param config: a config dictionary.
+    """
+    if not isinstance(config, dict):
+        return config
+    if isinstance(config.get('groups'), dict):
+        groups = config.pop('groups')
+        if user:
+            for group in Group().find(
+                    {'_id': {'$in': user['groups']}}, sort=[('name', SortDir.ASCENDING)]):
+                if isinstance(groups.get(group['name']), dict):
+                    config = _mergeDictionaries(config, groups[group['name']])
+    if isinstance(config.get('access'), dict):
+        accessList = config.pop('access')
+        if user and isinstance(accessList.get('user'), dict):
+            config = _mergeDictionaries(config, accessList['user'])
+        if user and user.get('admin') and isinstance(accessList.get('admin'), dict):
+            config = _mergeDictionaries(config, accessList['admin'])
+    return config
+
+
+@access.public(scope=TokenScope.DATA_READ)
+@autoDescribeRoute(
+    Description('Get a config file.')
+    .notes(
+        'This walks up the chain of parent folders until the file is found.  '
+        'If not found, the .config folder in the parent collection or user is '
+        'checked.\n\nAny yaml file can be returned.  If the top-level is a '
+        'dictionary and contains keys "access" or "groups" where those are '
+        'dictionaries, the returned value will be modified based on the '
+        'current user.  The "groups" dictionary contains keys that are group '
+        'names and values that update the main dictionary.  All groups that '
+        'the user is a member of are merged in alphabetical order.  If a key '
+        'and value of "\\__all\\__": True exists, the replacement is total; '
+        'otherwise it is a merge.  If the "access" dictionary exists, the '
+        '"user" and "admin" subdictionaries are merged if a calling user is '
+        'present and if the user is an admin, respectively (both get merged '
+        'for admins).')
+    .modelParam('id', model=Folder, level=AccessType.READ)
+    .param('name', 'The name of the file.', paramType='path')
+    .errorResponse()
+)
+@boundHandler()
+def getYAMLConfigFile(self, folder, name):
+    user = self.getCurrentUser()
+    while folder:
+        item = Item().findOne({'folderId': folder['_id'], 'name': name},
+                              user=user, level=AccessType.READ)
+        if item:
+            for file in Item().childFiles(item):
+                if file['size'] > 10 * 1024 ** 2:
+                    logger.info('Not loading %s -- too large' % file['name'])
+                    continue
+                with File().open(file) as fptr:
+                    config = yaml.safe_load(fptr)
+                    # combine and adjust config values based on current user
+                    if isinstance(config, dict) and 'access' in config or 'group' in config:
+                        config = adjustConfigForUser(config, user)
+                    return config
+        if folder['parentCollection'] != 'folder':
+            if folder['name'] == '.config':
+                break
+            folder = Folder().findOne({
+                'parentId': folder['parentId'],
+                'parentCollection': folder['parentCollection'],
+                'name': '.config'})
+        else:
+            folder = Folder().load(folder['parentId'], user=user, level=AccessType.READ)

girder/test_girder/girder_utilities.py

@@ -1,3 +1,4 @@
+import io
 import os
 from test.datastore import datastore
 from test.utilities import BigTIFFHeader, JFIFHeader, JPEGHeader, PNGHeader, TIFFHeader  # noqa
@@ -38,6 +39,13 @@ def uploadTestFile(fileName, user, assetstore, folderName='Public', name=None):
     return uploadFile(imagePath, user=user, assetstore=assetstore, folderName=folderName, name=None)
 
 
+def uploadText(text, user, assetstore, folder, name):
+    file = Upload().uploadFromFile(
+        io.BytesIO(text.encode()), len(text), name,
+        parentType='folder', parent=folder, user=user, assetstore=assetstore)
+    return file
+
+
 def respStatus(resp):
     return int(resp.output_status.split()[0])
 

girder/test_girder/test_large_image.py

@@ -18,7 +18,10 @@
 
     from girder import events
     from girder.exceptions import ValidationException
+    from girder.models.collection import Collection
     from girder.models.file import File
+    from girder.models.folder import Folder
+    from girder.models.group import Group
     from girder.models.item import Item
     from girder.models.setting import Setting
 except ImportError:
@@ -400,3 +403,75 @@ def testHistogramCaching(server, admin, user, fsAssetstore):
     resp = server.request(path='/large_image/histograms', user=admin)
     assert utilities.respStatus(resp) == 200
     assert resp.json == 0
+
+
+@pytest.mark.usefixtures('unbindLargeImage')
+@pytest.mark.plugin('large_image')
+def testYAMLConfigFile(server, admin, user, fsAssetstore):
+    # Create some resources to use in the tests
+    collection = Collection().createCollection(
+        'collection A', admin)
+    colFolderA = Folder().createFolder(
+        collection, 'folder A', parentType='collection',
+        creator=admin)
+    colFolderB = Folder().createFolder(
+        colFolderA, 'folder C', creator=admin)
+    groupA = Group().createGroup('Group A', admin)
+
+    resp = server.request(
+        path='/folder/%s/yaml_config/sample.json' % str(colFolderB['_id']),
+        method='GET')
+    assert utilities.respStatus(resp) == 200
+    assert resp.json is None
+
+    colFolderConfig = Folder().createFolder(
+        collection, '.config', parentType='collection',
+        creator=admin)
+    utilities.uploadText(
+        json.dumps({'keyA': 'value1'}),
+        admin, fsAssetstore, colFolderConfig, 'sample.json')
+    resp = server.request(
+        path='/folder/%s/yaml_config/sample.json' % str(colFolderB['_id']))
+    assert utilities.respStatus(resp) == 200
+    assert resp.json['keyA'] == 'value1'
+
+    utilities.uploadText(
+        json.dumps({'keyA': 'value2'}),
+        admin, fsAssetstore, colFolderA, 'sample.json')
+    resp = server.request(
+        path='/folder/%s/yaml_config/sample.json' % str(colFolderB['_id']))
+    assert utilities.respStatus(resp) == 200
+    assert resp.json['keyA'] == 'value2'
+
+    utilities.uploadText(
+        json.dumps({
+            'keyA': 'value3',
+            'groups': {
+                'Group A': {'access': {'user': {'keyA': 'value4'}}}},
+            'access': {'user': {'keyA': 'value5'}, 'admin': {'keyA': 'value6'}}}),
+        admin, fsAssetstore, colFolderB, 'sample.json')
+    resp = server.request(
+        path='/folder/%s/yaml_config/sample.json' % str(colFolderB['_id']))
+    assert utilities.respStatus(resp) == 200
+    assert resp.json['keyA'] == 'value3'
+
+    resp = server.request(
+        path='/folder/%s/yaml_config/sample.json' % str(colFolderB['_id']), user=user)
+    assert utilities.respStatus(resp) == 200
+    assert resp.json['keyA'] == 'value5'
+
+    resp = server.request(
+        path='/folder/%s/yaml_config/sample.json' % str(colFolderB['_id']), user=admin)
+    assert utilities.respStatus(resp) == 200
+    assert resp.json['keyA'] == 'value6'
+
+    Group().addUser(groupA, user)
+    resp = server.request(
+        path='/folder/%s/yaml_config/sample.json' % str(colFolderB['_id']), user=user)
+    assert utilities.respStatus(resp) == 200
+    assert resp.json['keyA'] == 'value4'
+
+    resp = server.request(
+        path='/folder/%s/yaml_config/sample.json' % str(colFolderB['_id']), user=admin)
+    assert utilities.respStatus(resp) == 200
+    assert resp.json['keyA'] == 'value6'