Merge pull request #1728 from girder/girder-5-tox

Make CI testing compatible with large image and girder 5
girder · Dec 12, 2024 · 197b853 · 197b853
2 parents d046aa5 + 5e85390
commit 197b853
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Showing 40 changed files with 504 additions and 326 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -4,7 +4,7 @@ executors:
   toxandnode:
     working_directory: ~/project
     docker:
-      - image: girder/girder_test:py38-node16
+      - image: girder/tox-and-node
 commands:
   tox:
     description: "Run tox"
@@ -57,6 +57,7 @@ commands:
         type: string
       node:
         type: string
+        default: v20
     steps:
       - switchpython:
           version: << parameters.version >>
@@ -125,6 +126,12 @@ commands:
             nvm alias default << parameters.node >>
             NODE_DIR=$(dirname $(which node))
             echo "export PATH=$NODE_DIR:\$PATH" >> $BASH_ENV
+      - run:
+          name: Install and build large_image plugin
+          command: |
+            npm ci
+            npm run build
+          working_directory: girder/girder_large_image/web_client
       - save_cache:
           name: Save nvm cache
           key: v1-nvm-cache-<< parameters.node >>
@@ -169,7 +176,6 @@ jobs:
       - checkout
       - allservices:
           version: "3.8"
-          node: v14
       - tox:
           toxenv: test-py38
       - coverage
@@ -183,7 +189,6 @@ jobs:
       - checkout
       - allservices:
           version: "3.9"
-          node: v14
       - tox:
           toxenv: test-py39
       - coverage
@@ -197,7 +202,6 @@ jobs:
       - checkout
       - allservices:
           version: "3.10"
-          node: v14
       - tox:
           toxenv: test-py310
       - coverage
@@ -211,7 +215,6 @@ jobs:
       - checkout
       - allservices:
           version: "3.11"
-          node: v14
       - tox:
           toxenv: test-py311
       - coverage
@@ -225,7 +228,6 @@ jobs:
       - checkout
       - allservices:
           version: "3.12"
-          node: v14
       - tox:
           toxenv: test-py312
       - coverage
@@ -239,7 +241,6 @@ jobs:
       - checkout
       - allservices:
           version: "3.13"
-          node: v14
       - tox:
           toxenv: test-py313
           environ: TOX_VERBOSE=4 TOX_PREFER_BINARY=1

diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -17,3 +17,7 @@ dcda95e659a4eaa73cae85ab02f1b89059e63c32
 f517ecb2b7d8c454d1374156452be42b87ca3fd1
 # PR 1604: Handle ruff linting rule changes
 e62083dab9a190d94841b3f4089850f43e2c9932
+# PR 1728: Format client and python code
+c1ba777b9fb2c927ffc98302197766cdc3c705db
+3bff2771141b2d77821e29f96ac9de0428856e3d
+
diff --git a/docs/format_examples_datastore.py b/docs/format_examples_datastore.py
@@ -100,7 +100,8 @@
         examples=[
             dict(
                 filename='sample_image.nd2',
-                # originally from 'https://downloads.openmicroscopy.org/images/ND2/aryeh/MeOh_high_fluo_003.nd2',
+                # originally from
+                # 'https://downloads.openmicroscopy.org/images/ND2/aryeh/MeOh_high_fluo_003.nd2',
                 url='https://data.kitware.com/api/v1/file/hashsum/sha512/4e76e490c915b10f646cb516f85a4d36d52aa7eff94715b90222644180e26fef6768493887c05adf182cf0351ba0bce659204041c4698a0f6b08423586788f4d/download',
                 hash='8e23bb594cd18314f9c18e70d736088ae46f8bc696ab7dc047784be416d7a706',
             ),
@@ -127,7 +128,8 @@
         examples=[
             dict(
                 filename='US-MONO2-8-8x-execho.dcm',
-                # originally from 'https://downloads.openmicroscopy.org/images/DICOM/samples/US-MONO2-8-8x-execho.dcm',
+                # originally from
+                # 'https://downloads.openmicroscopy.org/images/DICOM/samples/US-MONO2-8-8x-execho.dcm',
                 url='https://data.kitware.com/api/v1/file/hashsum/sha512/5332044f887d82c7f3693c6ca180f07accf5f00c2b7b1a3a29ef9ae737d5f1975478b5e2d5846c391987b8051416068f57a7062e848323c700412236b35679db/download',
                 hash='7d3f54806d0315c6cfc8b7371649a242b5ef8f31e0d20221971dd8087f2ff1ea',
             ),
@@ -141,7 +143,8 @@
         examples=[
             dict(
                 filename='20191025 Test FRET 585. 423, 426.lif',
-                # originally from 'https://downloads.openmicroscopy.org/images/Leica-LIF/imagesc-30856/20191025%20Test%20FRET%20585.%20423,%20426.lif',
+                # originally from
+                # 'https://downloads.openmicroscopy.org/images/Leica-LIF/imagesc-30856/20191025%20Test%20FRET%20585.%20423,%20426.lif',
                 url='https://data.kitware.com/api/v1/file/hashsum/sha512/d25de002d8a81dfcaf6b062b9f429ca85bb81423bc09d3aa33d9d51e9392cc4ace2b8521475e373ceecaf958effd0fade163e7173c467aab66c957da14482ed7/download',
                 hash='8d4ee62868b9616b832c2eb28e7d62ec050fb032e0bc11ea0a392f5c84390c71',
             ),
@@ -155,7 +158,8 @@
         examples=[
             dict(
                 filename='Animated_PNG_example_bouncing_beach_ball.png',
-                # originally from 'https://upload.wikimedia.org/wikipedia/commons/1/14/Animated_PNG_example_bouncing_beach_ball.png',
+                # originally from
+                # 'https://upload.wikimedia.org/wikipedia/commons/1/14/Animated_PNG_example_bouncing_beach_ball.png',
                 url='https://data.kitware.com/api/v1/file/hashsum/sha512/465ebdc2e81b2576dfc96b34e82db7f968e6d4f32f0fa80ef4bb0e44ed216230e6be1a2e4b11ae301a2905cc582dd24cbd2c360d9567ff7b1dac2c871f6d1e37/download',
                 hash='3b28e2462f1b31d0d15d795e6e58baf397899c3f864be7034bf47939b5bbbc3b',
             ),

diff --git a/girder/girder_large_image/__init__.py b/girder/girder_large_image/__init__.py
@@ -18,14 +18,14 @@
 import hashlib
 import json
 import logging
-from pathlib import Path
 import os
 import re
 import threading
 import time
 import warnings
 from importlib.metadata import PackageNotFoundError
 from importlib.metadata import version as _importlib_version
+from pathlib import Path
 
 import yaml
 from girder_jobs.constants import JobStatus
@@ -243,7 +243,7 @@ def checkForLargeImageFiles(event):  # noqa
             except Exception:
                 pass
     # We couldn't automatically set this as a large image
-    girder.logger.info(
+    logger.info(
         'Saved file %s cannot be automatically used as a largeImage' % str(file['_id']))
 
 

diff --git a/girder/girder_large_image/web_client/eventStream.js b/girder/girder_large_image/web_client/eventStream.js
@@ -1,11 +1,11 @@
 /* This implements a polling fallback if event streams are disabled on the
  * server. */
 
-const eventStream = girder.utilities.eventStream;
-const { restRequest } = girder.rest;
-
 import largeImageConfig from './views/configView';
 
+const eventStream = girder.utilities.eventStream;
+const {restRequest} = girder.rest;
+
 eventStream.on('g:eventStream.disable', () => {
     largeImageConfig.getSettings(() => {
         if (largeImageConfig.settings['large_image.notification_stream_fallback'] === false) {

diff --git a/girder/girder_large_image/web_client/index.js b/girder/girder_large_image/web_client/index.js
@@ -5,5 +5,5 @@ import * as vue from './vue';
 export {
     utils,
     views,
-    vue,
+    vue
 };
diff --git a/girder/girder_large_image/web_client/main.js b/girder/girder_large_image/web_client/main.js
@@ -10,7 +10,7 @@ import './views/imageViewerSelectWidget';
 // expose symbols under girder.plugins
 import * as largeImage from './index';
 
-const { registerPluginNamespace } = girder.pluginUtils;
+const {registerPluginNamespace} = girder.pluginUtils;
 const SearchFieldWidget = girder.views.widgets.SearchFieldWidget;
 
 registerPluginNamespace('large_image', largeImage);

diff --git a/girder/girder_large_image/web_client/package.json b/girder/girder_large_image/web_client/package.json
@@ -62,7 +62,11 @@
             "vue/require-prop-types": "off",
             "vue/multiline-html-element-content-newline": "off"
         },
-        "root": true
+        "ignorePatterns": ["dist/**"],
+        "root": true,
+        "globals": {
+            "girder": "readonly"
+        }
     },
     "eslintIgnore": [
         "**/node_modules/"

diff --git a/girder/girder_large_image/web_client/routes.js b/girder/girder_large_image/web_client/routes.js
@@ -1,11 +1,11 @@
+import ConfigView from './views/configView';
+
 const $ = girder.$;
 const Backbone = girder.Backbone;
 const events = girder.events;
 const router = girder.router;
-const { exposePluginConfig } = girder.utilities.PluginUtils;
-const { parseQueryString, splitRoute } = girder.misc;
-
-import ConfigView from './views/configView';
+const {exposePluginConfig} = girder.utilities.PluginUtils;
+const {parseQueryString, splitRoute} = girder.misc;
 
 exposePluginConfig('large_image', 'plugins/large_image/config');
 

diff --git a/girder/girder_large_image/web_client/utils.js b/girder/girder_large_image/web_client/utils.js
@@ -157,4 +157,4 @@ function setFrameQuad(tileinfo, layer, options) {
     layer.setFrameQuad.status = status;
 }
 
-export { setFrameQuad };
+export {setFrameQuad};
diff --git a/girder/girder_large_image/web_client/views/configView.js b/girder/girder_large_image/web_client/views/configView.js
@@ -7,7 +7,7 @@ const events = girder.events;
 const restRequest = girder.rest.restRequest;
 const BrowserWidget = girder.views.widgets.BrowserWidget;
 const PluginConfigBreadcrumbWidget = girder.views.widgets.PluginConfigBreadcrumbWidget;
-const { AccessType } = girder.constants;
+const {AccessType} = girder.constants;
 
 /**
  * Show the default quota settings for users and collections.

diff --git a/girder/girder_large_image/web_client/views/fileList.js b/girder/girder_large_image/web_client/views/fileList.js
@@ -3,11 +3,11 @@ import '../stylesheets/fileList.styl';
 
 const $ = girder.$;
 const _ = girder._;
-const { restRequest } = girder.rest;
+const {restRequest} = girder.rest;
 const events = girder.events;
 const FileListWidget = girder.views.widgets.FileListWidget;
-const { wrap } = girder.utilities.PluginUtils;
-const { AccessType } = girder.constants;
+const {wrap} = girder.utilities.PluginUtils;
+const {AccessType} = girder.constants;
 
 wrap(FileListWidget, 'render', function (render) {
     render.call(this);

diff --git a/girder/girder_large_image/web_client/views/imageViewerSelectWidget.js b/girder/girder_large_image/web_client/views/imageViewerSelectWidget.js
@@ -7,7 +7,7 @@ import FrameSelector from '../vue/components/FrameSelector.vue';
 
 const $ = girder.$;
 const _ = girder._;
-const { wrap } = girder.utilities.PluginUtils;
+const {wrap} = girder.utilities.PluginUtils;
 const eventStream = girder.utilities.EventStream;
 const ItemView = girder.views.body.ItemView;
 const View = girder.views.View;

diff --git a/girder/girder_large_image/web_client/views/imageViewerWidget/base.js b/girder/girder_large_image/web_client/views/imageViewerWidget/base.js
@@ -1,6 +1,6 @@
 const $ = girder.$;
 const View = girder.views.View;
-const { getApiRoot, restRequest } = girder.rest;
+const {getApiRoot, restRequest} = girder.rest;
 
 var ImageViewerWidget = View.extend({
     initialize: function (settings) {

diff --git a/girder/girder_large_image/web_client/views/imageViewerWidget/geojs.js b/girder/girder_large_image/web_client/views/imageViewerWidget/geojs.js
@@ -3,11 +3,11 @@ import Hammer from '@egjs/hammerjs';
 import * as d3 from 'd3';
 
 import ImageViewerWidget from './base';
-import { setFrameQuad } from '../../utils.js';
+import {setFrameQuad} from '../../utils.js';
 
 const $ = girder.$;
 const _ = girder._;
-const { restRequest } = girder.rest;
+const {restRequest} = girder.rest;
 
 window.hammerjs = Hammer;
 window.Hammer = Hammer;
@@ -37,8 +37,8 @@ var GeojsImageViewerWidget = ImageViewerWidget.extend({
             return this;
         }).then(() => {
             this.trigger('g:beforeFirstRender', this);
-            this.render();
-        })
+            return this.render();
+        });
     },
 
     render: function () {

diff --git a/girder/girder_large_image/web_client/views/imageViewerWidget/index.js b/girder/girder_large_image/web_client/views/imageViewerWidget/index.js
@@ -9,5 +9,5 @@ export {
     leaflet,
     openlayers,
     openseadragon,
-    slideatlas,
+    slideatlas
 };
diff --git a/girder/girder_large_image/web_client/views/imageViewerWidget/openlayers.js b/girder/girder_large_image/web_client/views/imageViewerWidget/openlayers.js
@@ -1,7 +1,7 @@
 import ImageViewerWidget from './base';
 
 const $ = girder.$;
-const { restRequest } = girder.rest;
+const {restRequest} = girder.rest;
 
 var OpenlayersImageViewerWidget = ImageViewerWidget.extend({
     initialize: function (settings) {

diff --git a/girder/girder_large_image/web_client/views/imageViewerWidget/slideatlas.js b/girder/girder_large_image/web_client/views/imageViewerWidget/slideatlas.js
@@ -2,7 +2,7 @@ import ImageViewerWidget from './base';
 
 const $ = girder.$;
 const Backbone = girder.Backbone;
-const { parseQueryString, splitRoute } = girder.misc;
+const {parseQueryString, splitRoute} = girder.misc;
 
 // var baseSAUrl = 'https://unpkg.com/slideatlas-viewer@4.4.1/dist/';
 var baseSAUrl = 'https://cdn.jsdelivr.net/npm/slideatlas-viewer@4/dist/';
-Original file line number
+Diff line change
@@ Expand Up / @@ -5,5 +5,5 @@ import * as vue from './vue'; @@
     export {
         utils,
         views,
-        vue,
+        vue
     };