histomicsui 1.8.1.dev6__tar.gz → 1.8.1.dev145__tar.gz

{histomicsui-1.8.1.dev6 → histomicsui-1.8.1.dev145}/.circleci/config.yml

@@ -10,15 +10,59 @@ executors:
       - image: rabbitmq
     resource_class: large
 commands:
+  use_nvm:
+      description: "Use nvm"
+      parameters:
+        node:
+          type: string
+          default: v20
+      steps:
+        - run:
+            name: Use nvm
+            # see https://discuss.circleci.com/t/nvm-does-not-change-node-version-on-machine/28973/14
+            command: |
+              echo 'export NVM_DIR="/root/.nvm"' >> $BASH_ENV
+              echo '[ -s "$NVM_DIR/nvm.sh" ] && \. "$NVM_DIR/nvm.sh"' >> $BASH_ENV
+        - restore_cache:
+            name: Restore nvm cache
+            key: v1-nvm-cache-<< parameters.node >>
+        - run:
+            name: Switch node versions
+            command: |
+              nvm install << parameters.node >>
+              nvm alias default << parameters.node >>
+              NODE_DIR=$(dirname $(which node))
+              echo "export PATH=$NODE_DIR:\$PATH" >> $BASH_ENV
+        - run:
+            name: Check node versions
+            command: |
+              node --version
+              npm --version
+  build_client:
+    description: "Build HistomicsUI client"
+    steps:
+      - run:
+          name: Build client
+          command: |
+            pushd histomicsui/web_client
+            npm ci
+            npm run build
+            popd
+  install_playwright:
+    description: "Install playwright"
+    steps:
+      - run:
+          name: Install playwright with dependencies
+          command: |
+            pushd histomicsui/web_client
+            npx playwright install --with-deps
+            popd
   tox:
     description: "Run tox"
     parameters:
       env:
         type: string
     steps:
-      - run:
-          name: Preinstall phantomjs to work around an npm permission issue
-          command: npm install -g phantomjs-prebuilt --unsafe-perm
       - run:
           name: Run tests via tox
           # Piping through cat does less buffering of the output but can
@@ -42,6 +86,8 @@ jobs:
     executor: toxandnode
     steps:
       - checkout
+      - use_nvm
+      - build_client
       - tox:
           env: py310
       - coverage
@@ -49,6 +95,8 @@ jobs:
     executor: toxandnode
     steps:
       - checkout
+      - use_nvm
+      - build_client
       - tox:
           env: py311
       - coverage
@@ -56,6 +104,8 @@ jobs:
     executor: toxandnode
     steps:
       - checkout
+      - use_nvm
+      - build_client
       - tox:
           env: py312
       - coverage
@@ -63,13 +113,30 @@ jobs:
     executor: toxandnode
     steps:
       - checkout
+      - use_nvm
+      - build_client
       - tox:
           env: py313
       - coverage
+  web_client:
+    executor: toxandnode
+    environment:
+      CI: "true"
+      HEADLESS: "true"
+      GIRDER_CLIENT_TESTING_MONGO_URI: mongodb://localhost:27017
+    steps:
+      - checkout
+      - use_nvm
+      - build_client
+      - install_playwright
+      - tox:
+          env: webtest
   noanalysis:
     executor: toxandnode
     steps:
       - checkout
+      - use_nvm
+      - build_client
       - tox:
           env: noanalysis
       - coverage
@@ -84,6 +151,8 @@ jobs:
       - image: girder/tox-and-node
     steps:
       - checkout
+      - use_nvm
+      - build_client
       - deploy:
           name: Run tests via tox
           # Piping through cat does less buffering of the output but can
@@ -136,6 +205,13 @@ workflows:
             branches:
               ignore:
                 - gh-pages
+      - web_client:
+          filters:
+            tags:
+              only: /^v.*/
+            branches:
+              ignore:
+                - gh-pages
       - release:
           requires:
             - py310
@@ -147,4 +223,6 @@ workflows:
             tags:
               only: /^v.*/
             branches:
-              only: master
+              only:
+                - master
+                - girder-5

histomicsui-1.8.1.dev145/.circleci/get_version.py

@@ -0,0 +1,19 @@
+import re
+
+import setuptools_scm
+
+
+def main():
+    version = setuptools_scm.get_version()
+    expected_version_regex = r'(\d+\.\d+\.\d+)a(\d+).+$'
+    match = re.match(expected_version_regex, version)
+    if not match:
+        error_message = f'Version {version} does not match the expected format'
+        raise ValueError(error_message)
+    base_version = match.group(1)
+    alpha_version = match.group(2)
+    print(f'{base_version}a{alpha_version}')
+
+
+if __name__ == '__main__':
+    main()

histomicsui-1.8.1.dev145/.circleci/publish_pypi.sh

@@ -0,0 +1,16 @@
+#!/bin/bash
+
+set -e
+
+export SETUPTOOLS_SCM_PRETEND_VERSION=`python -m setuptools_scm | sed "s/.* //"`
+if [ "${CIRCLE_BRANCH-:}" = "master" ]; then
+    export SETUPTOOLS_SCM_PRETEND_VERSION=`echo $SETUPTOOLS_SCM_PRETEND_VERSION | sed "s/\+.*$//"`
+elif [ "${CIRCLE_BRANCH-:}" = "girder-5" ]; then
+    SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+    pip install setuptools-scm
+    export SETUPTOOLS_SCM_PRETEND_VERSION=$(python "$SCRIPT_DIR/get_version.py")
+fi
+
+python -m build
+twine check dist/*
+twine upload --skip-existing dist/*

{histomicsui-1.8.1.dev6 → histomicsui-1.8.1.dev145}/.git-blame-ignore-revs

@@ -13,3 +13,7 @@ f1c2190ab04ab867c655b4217f807e9f567772c8
 9475b89640a6de84788b79ba68d5ed9aeb1a9ff4
 # PR 359: Apply ruff formatting and linting
 97b21f031e4769043b2c3a464ea4cf8e9a60c219
+# PR 443: Format Girder 5
+d184bf1c2d5c12e643f8e5536c7707744c72e7ba
+0e0e6009391bcbf9bde7be6ebbb121cf84ae1f32
+cbc3c3952acef976b7b0be732e9ebb7686e98c8e

{histomicsui-1.8.1.dev6 → histomicsui-1.8.1.dev145}/.gitignore

@@ -12,6 +12,7 @@ env/
 build/
 develop-eggs/
 dist/
+dist-app/
 downloads/
 eggs/
 .eggs/

{histomicsui-1.8.1.dev6 → histomicsui-1.8.1.dev145}/.pre-commit-config.yaml

@@ -48,7 +48,8 @@ repos:
   - id: codespell
     args:
       - --ignore-words-list
-      - "hist,indext,pixelx,thex,subtile"
+      - "hist,indext,pixelx,thex,subtile,afterAll"
+      - --exclude-file=histomicsui/web_client/package-lock.json
 - repo: https://github.com/syntaqx/git-hooks
   rev: v0.0.18
   hooks:

{histomicsui-1.8.1.dev6 → histomicsui-1.8.1.dev145}/MANIFEST.in

@@ -6,3 +6,6 @@ graft histomicsui
 graft docs
 prune test
 global-exclude *.py[co] *.cmake __pycache__ node_modules
+
+prune histomicsui/web_client
+recursive-include histomicsui/web_client/dist/*

{histomicsui-1.8.1.dev6 → histomicsui-1.8.1.dev145}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: histomicsui
-Version: 1.8.1.dev6
+Version: 1.8.1.dev145
 Summary: Organize, visualize, and analyze histology images.
 Home-page: https://github.com/DigitalSlideArchive/histomicsui
 Author: Kitware, Inc.
@@ -20,11 +20,12 @@ Requires-Python: >=3.10
 Description-Content-Type: text/x-rst
 License-File: LICENSE
 License-File: NOTICE
-Requires-Dist: girder<5
-Requires-Dist: girder-large-image-annotation>=1.33.5
-Requires-Dist: girder-slicer-cli-web[girder]>=1.4.0
-Requires-Dist: cachetools
-Requires-Dist: orjson
+Requires-Dist: girder>=5.0.0a13
+Requires-Dist: girder-jobs>=5.0.0a13
+Requires-Dist: girder-large-image==1.33.6a155
+Requires-Dist: girder-large-image-annotation==1.33.6a155
+Requires-Dist: large-image-tasks==1.33.6a155
+Requires-Dist: large-image-converter==1.33.6a155
 Provides-Extra: analysis
 Dynamic: author
 Dynamic: author-email
@@ -110,6 +111,12 @@ Now install the histomicsui package, have Girder build its UI, and start the Gir
   girder build
   girder serve
 
+Note that ``girder serve`` should only be used in development. In production, use a WSGI server such as gunicorn, e.g.::
+
+.. code-block:: bash
+
+  gunicorn girder.wsgi:app --bind=localhost:8080 --workers=4 --preload
+
 To use Girder Worker:
 
 .. code-block:: bash

{histomicsui-1.8.1.dev6 → histomicsui-1.8.1.dev145}/README.rst

@@ -68,6 +68,12 @@ Now install the histomicsui package, have Girder build its UI, and start the Gir
   girder build
   girder serve
 
+Note that ``girder serve`` should only be used in development. In production, use a WSGI server such as gunicorn, e.g.::
+
+.. code-block:: bash
+
+  gunicorn girder.wsgi:app --bind=localhost:8080 --workers=4 --preload
+
 To use Girder Worker:
 
 .. code-block:: bash

{histomicsui-1.8.1.dev6 → histomicsui-1.8.1.dev145}/histomicsui/__init__.py

@@ -1,29 +1,14 @@
-#############################################################################
-#  Copyright Kitware Inc.
-#
-#  Licensed under the Apache License, Version 2.0 ( the "License" );
-#  you may not use this file except in compliance with the License.
-#  You may obtain a copy of the License at
-#
-#    http://www.apache.org/licenses/LICENSE-2.0
-#
-#  Unless required by applicable law or agreed to in writing, software
-#  distributed under the License is distributed on an "AS IS" BASIS,
-#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-#  See the License for the specific language governing permissions and
-#  limitations under the License.
-#############################################################################
-
 import importlib.metadata
 import json
 import logging
 import os
 import re
 from functools import wraps
+from pathlib import Path
 
 import cherrypy
 from bson import json_util
-from girder import events, logger, plugin
+from girder import events, plugin
 from girder.api import access
 from girder.api.rest import getCurrentToken
 from girder.constants import AssetstoreType
@@ -33,13 +18,11 @@ 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.settings import SettingDefault
 from girder.utility import config
 from girder.utility import path as path_util
 from girder.utility import setting_utilities
 from girder.utility.model_importer import ModelImporter
-from girder.utility.webroot import Webroot
 
 from . import handlers, rest
 from .constants import PluginSettings
@@ -56,16 +39,7 @@ except importlib.metadata.PackageNotFoundError:
     # package is not installed
     pass
 
-# There are other packages that add to the root log handler; this makes the
-# system very noisy.  Stop that.
-while logging.root.hasHandlers():
-    logging.root.removeHandler(logging.root.handlers[0])
-logging.root.addHandler(logging.NullHandler())
-
-_template = os.path.join(
-    os.path.dirname(__file__),
-    'webroot.mako',
-)
+logger = logging.getLogger(__name__)
 
 
 def patchCookieParsing():
@@ -99,42 +73,6 @@ def patchCookieParsing():
         pass
 
 
-def betterInvalidateJSandCSSCaches(root):
-    from girder import constants
-
-    origRenderHTML = root._renderHTML
-
-    def _renderHTML(self):
-        topBuiltDir = os.path.join(constants.STATIC_ROOT_DIR, 'built')
-        result = origRenderHTML()
-        lastUpdate = 0
-        for filename in {
-                'girder_lib.min.js', 'girder_app.min.js', 'girder_lib.min.css',
-                'Girder_Favicon.png'}:
-            filepath = os.path.join(topBuiltDir, filename)
-            if os.path.exists(filepath):
-                lastUpdate = max(lastUpdate, os.path.getmtime(filepath))
-        builtDir = os.path.join(constants.STATIC_ROOT_DIR, 'built', 'plugins')
-        for pluginName in self.vars['plugins']:
-            for filepath in [
-                os.path.join(builtDir, pluginName, 'plugin.min.css'),
-                os.path.join(builtDir, pluginName, 'plugin.min.js'),
-            ]:
-                if os.path.exists(filepath):
-                    lastUpdate = max(lastUpdate, os.path.getmtime(filepath))
-        luParam = '?_=%d' % int(lastUpdate * 1000)
-        while True:
-            match = re.search(
-                r'<(link rel="(icon|stylesheet)" [^>]*href="[^>?"]*\.(css|png)|'
-                r'script src="[^>?"]*.js)">', result)
-            if not match:
-                break
-            result = result[:match.span()[1] - 2] + luParam + result[match.span()[1] - 2:]
-        return result
-
-    root._renderHTML = _renderHTML.__get__(root)
-
-
 @setting_utilities.validator({
     PluginSettings.HUI_DEFAULT_DRAW_STYLES,
     PluginSettings.HUI_PANEL_LAYOUT,
@@ -276,37 +214,6 @@ def _saveJob(event):
         pass
 
 
-class WebrootHistomicsUI(Webroot):
-    def _renderHTML(self):
-        self.updateHtmlVars({
-            'title': Setting().get(PluginSettings.HUI_BRAND_NAME),
-            'huiBrandName': Setting().get(PluginSettings.HUI_BRAND_NAME),
-            'huiBrandColor': Setting().get(PluginSettings.HUI_BRAND_COLOR),
-            '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),
-        })
-        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):
     """
     If restrict_downloads is configured, modify endpoints to do that.
@@ -395,9 +302,18 @@ def cleanupFSAssetstores():
                     assetstore['name'], count, fullcount, total)
 
 
+class RootHandler:
+    @cherrypy.expose
+    def index(*args, **kwargs):
+        path = Path(__file__).parent / 'web_client' / 'dist-app' / 'index.html'
+        with open(path) as f:
+            content = f.read()
+        modified_content = content.replace('root=""', f'root="{os.getenv("GIRDER_URL_ROOT")}"')
+        return modified_content
+
+
 class GirderPlugin(plugin.GirderPlugin):
     DISPLAY_NAME = 'HistomicsUI'
-    CLIENT_SOURCE_PATH = 'web_client'
 
     def load(self, info):  # noqa
         plugin.getPlugin('jobs').load(info)
@@ -422,8 +338,8 @@ class GirderPlugin(plugin.GirderPlugin):
         ModelImporter.registerModel('slide', Slide, 'histomicsui')
 
         rest.addEndpoints(info['apiRoot'])
-        info['serverRoot'].updateHtmlVars({
-            'brandName': Setting().get(SettingKey.BRAND_NAME)})
+        # info['serverRoot'].updateHtmlVars({
+        #    'brandName': Setting().get(SettingKey.BRAND_NAME)})
         # Better virtual folder support
         if not getattr(Folder, '_childItemsBeforeHUI', None):
             Folder._childItemsBeforeHUI = Folder.childItems
@@ -443,24 +359,39 @@ class GirderPlugin(plugin.GirderPlugin):
 
         path_util.lookUpToken = lookUpToken
 
-        girderRoot = info['serverRoot']
-        huiRoot = WebrootHistomicsUI(_template)
-        huiRoot.updateHtmlVars(girderRoot.vars)
-
-        betterInvalidateJSandCSSCaches(girderRoot)
-        betterInvalidateJSandCSSCaches(huiRoot)
-
-        # The interface is always available under hui and also available
-        # under the specified path.
-        info['serverRoot'].hui = huiRoot
-        webrootPath = Setting().get(PluginSettings.HUI_WEBROOT_PATH)
-        alternateWebrootPath = Setting().get(PluginSettings.HUI_ALTERNATE_WEBROOT_PATH)
-        setattr(info['serverRoot'], webrootPath, huiRoot)
-        if alternateWebrootPath:
-            for alt_webroot_path in alternateWebrootPath.split(','):
-                if alt_webroot_path:
-                    setattr(info['serverRoot'], alt_webroot_path, huiRoot)
-        info['serverRoot'].girder = girderRoot
+        plugin.registerPluginStaticContent(
+            'histomicsui',
+            css=['/style.css'],
+            js=[
+                '/girder-plugin-histomics-ui.umd.cjs',
+                '/extra/plotly.js',
+            ],
+            staticDir=Path(__file__).parent / 'web_client' / 'dist',
+            tree=info['serverRoot'],
+        )
+
+        webroot = os.getenv('HUI_WEBROOT_PATH', False)
+        if webroot:
+            Setting().set(PluginSettings.HUI_WEBROOT_PATH, webroot)
+        else:
+            webroot = Setting().get(PluginSettings.HUI_WEBROOT_PATH)
+        custom_api_root = os.getenv('GIRDER_URL_ROOT')
+        custom_api_root = None if not custom_api_root or custom_api_root == '/' else custom_api_root
+        static_opts = {
+            'tools.staticdir.on': True,
+            'tools.staticdir.dir': Path(__file__).parent / 'web_client' / 'dist-app',
+        }
+        if not custom_api_root:
+            static_opts['tools.staticdir.index'] = 'index.html'
+
+        info['serverRoot'].mount(RootHandler if custom_api_root else None, f'/{webroot}', {
+            '/': static_opts,
+        })
+        altroot = Setting().get(PluginSettings.HUI_ALTERNATE_WEBROOT_PATH)
+        if altroot and altroot != webroot:
+            info['serverRoot'].mount(RootHandler if custom_api_root else None, f'/{altroot}', {
+                '/': static_opts,
+            })
 
         # Auto-ingest annotations into database when a file with an identifier
         # ending in 'AnnotationFile' is uploaded (usually .anot files).
@@ -473,16 +404,5 @@ class GirderPlugin(plugin.GirderPlugin):
 
         handlers.json_nans_as_nulls()
 
-        def updateWebroot(event):
-            """
-            If the webroot path setting is changed, bind the new path to the
-            hui webroot resource.  Note that a change to the alternate webroot
-            requires a restart.
-            """
-            if event.info.get('key') == PluginSettings.HUI_WEBROOT_PATH:
-                setattr(info['serverRoot'], event.info['value'], huiRoot)
-
-        events.bind('model.setting.save.after', 'histomicsui', updateWebroot)
-
         restrict_downloads(info)
         cleanupFSAssetstores()

histomicsui-1.8.1.dev145/histomicsui/girder_worker_plugin.py

@@ -0,0 +1,14 @@
+import os
+
+from girder_worker import GirderWorkerPluginABC
+
+
+class HistomicsUIWorkerPlugin(GirderWorkerPluginABC):
+    def __init__(self, app, *args, **kwargs):
+        if os.getenv('CELERY_TASK_ALWAYS_EAGER', False):
+            app.conf.task_always_eager = True
+            app.conf.task_eager_propagates = True
+        self.app = app
+
+    def task_imports(self):
+        return ['histomicsui.handlers']