histomicsui 1.7.2.dev2__tar.gz → 2.0.0a2__tar.gz

{histomicsui-1.7.2.dev2 → histomicsui-2.0.0a2}/.circleci/config.yml

@@ -9,15 +9,59 @@ executors:
         command: bash -c "mkdir /dev/shm/mongo && mongod --nojournal --dbpath=/dev/shm/mongo --noauth --bind_ip_all"
       - image: rabbitmq
 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
@@ -41,6 +85,8 @@ jobs:
     executor: toxandnode
     steps:
       - checkout
+      - use_nvm
+      - build_client
       - tox:
           env: py38
       - coverage
@@ -48,6 +94,8 @@ jobs:
     executor: toxandnode
     steps:
       - checkout
+      - use_nvm
+      - build_client
       - tox:
           env: py39
       - coverage
@@ -55,6 +103,8 @@ jobs:
     executor: toxandnode
     steps:
       - checkout
+      - use_nvm
+      - build_client
       - tox:
           env: py310
       - coverage
@@ -62,6 +112,8 @@ jobs:
     executor: toxandnode
     steps:
       - checkout
+      - use_nvm
+      - build_client
       - tox:
           env: py311
       - coverage
@@ -69,6 +121,8 @@ jobs:
     executor: toxandnode
     steps:
       - checkout
+      - use_nvm
+      - build_client
       - tox:
           env: py312
       - coverage
@@ -76,13 +130,30 @@ 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
@@ -97,6 +168,8 @@ 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
@@ -163,6 +236,13 @@ workflows:
             branches:
               ignore:
                 - gh-pages
+      - web_client:
+          filters:
+            tags:
+              only: /^v.*/
+            branches:
+              ignore:
+                - gh-pages
       - release:
           requires:
             - py38
@@ -176,4 +256,6 @@ workflows:
             tags:
               only: /^v.*/
             branches:
-              only: master
+              only:
+                - master
+                - girder-5

histomicsui-2.0.0a2/.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-2.0.0a2/.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-1.7.2.dev2 → histomicsui-2.0.0a2}/.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-1.7.2.dev2 → histomicsui-2.0.0a2}/.gitignore

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

{histomicsui-1.7.2.dev2 → histomicsui-2.0.0a2}/.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-1.7.2.dev2 → histomicsui-2.0.0a2}/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-1.7.2.dev2 → histomicsui-2.0.0a2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: histomicsui
-Version: 1.7.2.dev2
+Version: 2.0.0a2
 Summary: Organize, visualize, and analyze histology images.
 Home-page: https://github.com/DigitalSlideArchive/histomicsui
 Author: Kitware, Inc.
@@ -21,8 +21,11 @@ Requires-Python: >=3.8
 Description-Content-Type: text/x-rst
 License-File: LICENSE
 License-File: NOTICE
-Requires-Dist: girder-large-image-annotation>=1.31.0
-Requires-Dist: girder-slicer-cli-web[girder]>=1.4.0
+Requires-Dist: girder>=5.0.0a2
+Requires-Dist: girder-large-image==1.32.2a115
+Requires-Dist: girder-large-image-annotation==1.32.2a115
+Requires-Dist: large-image-tasks==1.32.2a115
+Requires-Dist: large-image-converter==1.32.2a115
 Requires-Dist: cachetools
 Requires-Dist: orjson
 Provides-Extra: analysis
@@ -110,6 +113,12 @@ 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-1.7.2.dev2 → histomicsui-2.0.0a2}/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-1.7.2.dev2 → histomicsui-2.0.0a2}/docs/config_options.rst

@@ -50,7 +50,6 @@ _________________
           fillColor: rgba(255, 0, 0, 0.25)
           lineColor: rgb(255, 0, 0)
           lineWidth: 2
-          hotkey: r
         -
           id: Green
           fillColor: rgba(0, 128, 0, 0.25)
@@ -62,19 +61,6 @@ _________________
           lineColor: rgb(0, 0, 255)
           lineWidth: 2
 
-If a hotkey is specified for a group, it will only be active if the group was loaded from the config file.  That is, moving to another folder where the config file does not apply will disable the hotkey.  If you want hotkeys to have modifiers (e.g., require that alt, ctrl, or meta be pressed or explicitly NOT pressed), you can add a hotkey section:
-
-::
-
-    ---
-    hotkeys:
-      -
-        key: r
-        ctrl: true
-        alt: false
-        action: group
-        param: Red
-
 UI Settings
 ___________
 

{histomicsui-1.7.2.dev2 → histomicsui-2.0.0a2}/histomicsui/__init__.py

@@ -19,10 +19,10 @@ 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
@@ -32,13 +32,11 @@ 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 pkg_resources import DistributionNotFound, get_distribution
 
 from . import handlers, rest
@@ -56,16 +54,7 @@ except DistributionNotFound:
     # 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 +88,6 @@ 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 +229,6 @@ 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.
@@ -397,7 +319,6 @@ def cleanupFSAssetstores():
 
 class GirderPlugin(plugin.GirderPlugin):
     DISPLAY_NAME = 'HistomicsUI'
-    CLIENT_SOURCE_PATH = 'web_client'
 
     def load(self, info):  # noqa
         plugin.getPlugin('jobs').load(info)
@@ -422,8 +343,8 @@ 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 +364,39 @@ class GirderPlugin(plugin.GirderPlugin):
 
         path_util.lookUpToken = lookUpToken
 
-        girderRoot = info['serverRoot']
-        huiRoot = WebrootHistomicsUI(_template)
-        huiRoot.updateHtmlVars(girderRoot.vars)
-
-        betterInvalidateJSandCSSCaches(girderRoot)
-        betterInvalidateJSandCSSCaches(huiRoot)
+        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)
+        info['serverRoot'].mount(None, f'/{Setting().get(PluginSettings.HUI_WEBROOT_PATH)}', {
+            '/': {
+                'tools.staticdir.on': True,
+                'tools.staticdir.dir': Path(__file__).parent / 'web_client' / 'dist-app',
+                'tools.staticdir.index': 'index.html',
+            },
+        })
 
         # 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
+        # TODO is something using the "hui" path?
+        # info['serverRoot'].hui = huiRoot
+        # TODO these settings are not honored at this point
+        # 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
 
         # Auto-ingest annotations into database when a file with an identifier
         # ending in 'AnnotationFile' is uploaded (usually .anot files).
@@ -473,16 +409,5 @@ 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-2.0.0a2/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']