Merge branch 'master' into update-with-master

.pre-commit-config.yaml

@@ -2,7 +2,7 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.5.0
+  rev: v4.6.0
   hooks:
   - id: check-added-large-files
   - id: check-ast
@@ -25,6 +25,7 @@ repos:
   - id: fix-byte-order-marker
   - id: forbid-new-submodules
   - id: mixed-line-ending
+  - id: no-commit-to-branch
   - id: trailing-whitespace
 - repo: https://github.com/pre-commit/pygrep-hooks
   rev: v1.10.0
@@ -42,7 +43,7 @@ repos:
     files: README.rst
     name: rst-linter of README.rst
 - repo: https://github.com/codespell-project/codespell
-  rev: v2.2.6
+  rev: v2.3.0
   hooks:
   - id: codespell
     args:
@@ -61,13 +62,13 @@ repos:
         - './histomicsui/web_client/package.json'
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.1.3
+  rev: v0.6.0
   hooks:
     - id: ruff
       args: [--fix, --exit-non-zero-on-fix]
       types_or: [python, pyi, jupyter]
 - repo: https://github.com/asottile/pyupgrade
-  rev: v3.15.0
+  rev: v3.17.0
   hooks:
     - id: pyupgrade
       args:
@@ -78,6 +79,6 @@ repos:
   hooks:
     - id: autopep8
 - repo: https://github.com/PyCQA/flake8
-  rev: 6.1.0
+  rev: 7.1.1
   hooks:
     - id: flake8

README.rst

@@ -1,6 +1,19 @@
-=======================================
-HistomicsUI |build-status| |codecov-io|
-=======================================
+===========
+HistomicsUI
+===========
+
+|build-status| |codecov-io| |doi-badge|
+
+.. |build-status| image:: https://circleci.com/gh/DigitalSlideArchive/HistomicsUI.svg?style=svg
+    :target: https://circleci.com/gh/DigitalSlideArchive/HistomicsUI
+    :alt: Build Status
+
+.. |codecov-io| image:: https://img.shields.io/codecov/c/github/DigitalSlideArchive/HistomicsUI.svg
+    :target: https://codecov.io/github/DigitalSlideArchive/HistomicsUI?branch=master
+    :alt: codecov.io
+
+.. |doi-badge| image:: https://img.shields.io/badge/DOI-10.5281%2Fzenodo.5474914-blue.svg
+   :target: https://zenodo.org/doi/10.5281/zenodo.5474914
 
 Organize, visualize, and analyze histology images.
 
@@ -87,7 +100,7 @@ If you are making changes to the HistomicsUI frontend, you can make Girder watch
 Annotations and Metadata from Jobs
 ----------------------------------
 
-This handles ingesting annotations and metadata that are uploaded and associating them with existing large image items in the Girder database.  These annotations and metadata re commonly generated through jobs, such as HistomicTK tasks, but can also be added manually.
+This handles ingesting annotations and metadata that are uploaded and associating them with existing large image items in the Girder database.  These annotations and metadata are commonly generated through jobs, such as HistomicTK tasks, but can also be added manually.
 
 If a file is uploaded to the Girder system that includes a ``reference`` record, and that ``reference`` record contains an ``identifier`` field and at least one of a ``fileId`` and an ``itemId`` field, specific identifiers can be used to ingest the results.  If a ``userId`` is specified in the ``reference`` record, permissions for adding the annotation or metadata are associated with that user.
 
@@ -117,15 +130,6 @@ This work was funded in part by the NIH grant U24-CA194362-01_.
 .. _Girder Worker: https://girder-worker.readthedocs.io/en/latest/
 .. _large_image: https://github.com/girder/large_image
 .. _slicer_cli_web: https://github.com/girder/slicer_cli_web
-.. _slicer execution model: https://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation
 .. _celery: http://www.celeryproject.org/
 .. _HistomicsTK: https://github.com/DigitalSlideArchive/HistomicsTK
 .. _Digital Slide Archive: https://github.com/DigitalSlideArchive/digital_slide_archive
-
-.. |build-status| image:: https://circleci.com/gh/DigitalSlideArchive/HistomicsUI.svg?style=svg
-    :target: https://circleci.com/gh/DigitalSlideArchive/HistomicsUI
-    :alt: Build Status
-
-.. |codecov-io| image:: https://img.shields.io/codecov/c/github/DigitalSlideArchive/HistomicsUI.svg
-    :target: https://codecov.io/github/DigitalSlideArchive/HistomicsUI?branch=master
-    :alt: codecov.io

histomicsui/__init__.py

@@ -187,6 +187,7 @@ def validateLoginSessionExpiryMinutes(doc):
     PluginSettings.HUI_HELP_URL,
     PluginSettings.HUI_HELP_TOOLTIP,
     PluginSettings.HUI_HELP_TEXT,
+    PluginSettings.HUI_LOGIN_TEXT,
 })
 def validateHistomicsUIHelp(doc):
     pass
@@ -396,7 +397,7 @@ def lookUpToken(token, parentType, parent):
         # Auto-ingest annotations into database when a file with an identifier
         # ending in 'AnnotationFile' is uploaded (usually .anot files).
         events.bind('data.process', 'histomicsui.annotations', handlers.process_annotations)
-        # Auto-ingest metadta into parent when a file with an identifier
+        # Auto-ingest metadata into parent when a file with an identifier
         # ending in 'ItemMetadata' is uploaded (usually .meta files).
         events.bind('data.process', 'histomicsui.metadata', handlers.process_metadata)
 

histomicsui/constants.py

@@ -19,4 +19,5 @@ class PluginSettings:
     HUI_HELP_URL = 'histomicsui.help_url'
     HUI_HELP_TOOLTIP = 'histomicsui.help_tooltip'
     HUI_HELP_TEXT = 'histomicsui.help_text'
+    HUI_LOGIN_TEXT = 'histomicsui.login_text'
     HUI_LOGIN_SESSION_EXPIRY_MINUTES = 'histomicsui.login_session_expiry_minutes'

histomicsui/handlers.py

@@ -6,6 +6,7 @@
 
 import cherrypy
 import girder.utility
+import girder_large_image_annotation
 import orjson
 from girder.constants import AccessType
 from girder.exceptions import RestException
@@ -97,7 +98,9 @@ def read_entire_file():
     if time.time() - startTime > 10:
         logger.info('Decoded json in %5.3fs', time.time() - startTime)
 
-    if not isinstance(data, list):
+    if not isinstance(data, list) or (
+            hasattr(girder_large_image_annotation.utils, 'isGeoJSON') and
+            girder_large_image_annotation.utilsisGeoJSON(data)):
         data = [data]
 
     for annotation in data:

histomicsui/rest/hui_resource.py

@@ -50,6 +50,7 @@ def getPublicSettings(self, params):
         keys = [
             PluginSettings.HUI_BRAND_NAME,
             PluginSettings.HUI_DEFAULT_DRAW_STYLES,
+            PluginSettings.HUI_LOGIN_TEXT,
             PluginSettings.HUI_PANEL_LAYOUT,
             PluginSettings.HUI_QUARANTINE_FOLDER,
             PluginSettings.HUI_WEBROOT_PATH,

histomicsui/rest/system.py

@@ -17,6 +17,7 @@
 import datetime
 import os
 
+from girder import logger
 from girder.api import access
 from girder.api.describe import Description, autoDescribeRoute, describeRoute
 from girder.api.rest import RestException, boundHandler, filtermodel
@@ -44,6 +45,8 @@ def addSystemEndpoints(apiRoot):
     apiRoot.item.route('GET', ('query',), getItemsByQuery)
     # Added to the folder route
     apiRoot.folder.route('GET', ('query',), getFoldersByQuery)
+    # Added to the file route
+    apiRoot.file.route('GET', ('query',), getFilesByQuery)
     # Added to the system route
     apiRoot.system.route('PUT', ('restart',), restartServer)
     apiRoot.system.route('GET', ('setting', 'default'), getSettingDefault)
@@ -197,6 +200,22 @@ def getItemsByQuery(self, query, limit, offset, sort):
     return Item().findWithPermissions(query, offset=offset, limit=limit, sort=sort, user=user)
 
 
+@access.admin(scope=TokenScope.DATA_READ)
+@filtermodel(model=File)
+@autoDescribeRoute(
+    Description('List files that match a query.')
+    .responseClass('File', array=True)
+    .jsonParam('query', 'Find files that match this Mongo query.',
+               required=True, requireObject=True)
+    .pagingParams(defaultSort='_id')
+    .errorResponse(),
+)
+@boundHandler()
+def getFilesByQuery(self, query, limit, offset, sort):
+    user = self.getCurrentUser()
+    return File().findWithPermissions(query, offset=offset, limit=limit, sort=sort, user=user)
+
+
 @access.public(scope=TokenScope.DATA_READ)
 @filtermodel(model=Folder)
 @autoDescribeRoute(
@@ -461,5 +480,12 @@ def getMultipleResourcePaths(self, resources):
         model = ModelImporter.model(kind)
         for id in resources[kind]:
             doc = model.load(id=id, user=user, level=AccessType.READ)
-            results[kind][id] = path_util.getResourcePath(kind, doc, user=user)
+            if doc is None:
+                logger.info(f'Failed to load {kind} {id}')
+                continue
+            try:
+                results[kind][id] = path_util.getResourcePath(kind, doc, user=user)
+            except Exception:
+                logger.info(f'Failed to resolve path for {kind} {id} {doc}')
+                continue
     return results

histomicsui/web_client/dialogs/metadataPlot.js

@@ -1,6 +1,9 @@
 import metadataPlotDialog from '../templates/dialogs/metadataPlot.pug';
+import '../stylesheets/dialogs/metadataPlot.styl';
 
 const View = girder.views.View;
+const $ = girder.$;
+const girderModal = girder.utilities.girderModal;
 
 const MetadataPlotDialog = View.extend({
     events: {
@@ -19,6 +22,7 @@ const MetadataPlotDialog = View.extend({
                 plotOptions: this.plotOptions
             })
         ).girderModal(this);
+
         return this;
     },
 
@@ -34,6 +38,11 @@ const MetadataPlotDialog = View.extend({
                 configOptions[series] = val;
             }
         });
+        ['u'].forEach((series) => {
+            const opts = this.$('#h-plot-series-' + series + ' option');
+            const val = opts.filter((idx, o) => o.selected).map((idx, o) => $(o).val()).get();
+            configOptions[series] = val.length ? val : undefined;
+        });
         this.result = configOptions;
         this.$el.modal('hide');
     }

histomicsui/web_client/package.json

@@ -31,10 +31,12 @@
         "bootstrap-submenu": "^2.0.4",
         "copy-webpack-plugin": "^4.5.2",
         "petite-vue": "^0.4.1",
+        "plotly.js": "2.34.0",
         "sinon": "^2.1.0",
         "tinycolor2": "~1.4.1",
         "url-search-params-polyfill": "^8.1.1",
         "vue": "^2.7.16",
+        "uuid": "^8.3.2",
         "vue-color": "^2.8.1",
         "vue-loader": "~15.9.8",
         "vue-template-compiler": "~2.6.14"

histomicsui/web_client/panels/AnnotationSelector.js

@@ -329,6 +329,7 @@ var AnnotationSelector = Panel.extend({
                     this.trigger('h:deleteAnnotation', models[id]);
                 }
             });
+            this.collection.trigger('h:refreshed', this.collection);
             return null;
         });
     },

histomicsui/web_client/panels/DrawWidget.js

@@ -134,6 +134,12 @@ var DrawWidget = Panel.extend({
             this.$('button.h-draw[data-type="' + this._drawingType + '"]').addClass('active');
             this.drawElement(undefined, this._drawingType);
         }
+        this._bindHUIModeChange();
+        this._updateConstraintValueInputs();
+        return this;
+    },
+
+    _bindHUIModeChange() {
         if (this.viewer.annotationLayer && this.viewer.annotationLayer._boundHUIModeChange !== this) {
             this.viewer.annotationLayer._boundHUIModeChange = this;
             this.viewer.annotationLayer.geoOff(geo.event.annotation.mode);
@@ -154,8 +160,6 @@ var DrawWidget = Panel.extend({
                 }
             });
         }
-        this._updateConstraintValueInputs();
-        return this;
     },
 
     /**
@@ -625,6 +629,9 @@ var DrawWidget = Panel.extend({
      *      if it hasn't changed.
      */
     drawElement(evt, type, forceRefresh) {
+        if (type) {
+            this._bindHUIModeChange();
+        }
         var $el;
         if (evt) {
             $el = this.$(evt.currentTarget);
@@ -661,7 +668,12 @@ var DrawWidget = Panel.extend({
             }
 
             this.viewer.startDrawMode(type, options)
-                .then((element, annotations, opts) => this._addDrawnElements(element, annotations, opts));
+                .then((element, annotations, opts) => this._addDrawnElements(element, annotations, opts))
+                .fail(() => {
+                    if (this._drawingType && this._drawingType !== this.viewer.annotationLayer.mode() && this.viewer.annotationLayer.mode() !== 'edit') {
+                        this.drawElement(undefined, this._drawingType, !!this._drawingType);
+                    }
+                });
         }
         this.$('button.h-draw[data-type]').removeClass('active');
         if (this._drawingType) {
@@ -676,6 +688,7 @@ var DrawWidget = Panel.extend({
         this.drawElement(undefined, null);
         this.viewer.annotationLayer._boundHUIModeChange = false;
         this.viewer.annotationLayer.geoOff(geo.event.annotation.state);
+        this.viewer.annotationLayer.geoOff(geo.event.annotation.mode);
     },
 
     drawingType() {
@@ -832,6 +845,12 @@ var DrawWidget = Panel.extend({
      * @param {object} group The new group.
      */
     _setStyleGroup(group) {
+        group = Object.assign({}, group);
+        Object.keys(group).forEach((k) => {
+            if (!['fillColor', 'lineColor', 'lineWidth', 'label', 'group', 'id'].includes(k)) {
+                delete group[k];
+            }
+        });
         this._style.set(group);
         if (!group.group && this._style.id !== this.parentView._defaultGroup) {
             this._style.set('group', this._style.id);
@@ -923,13 +942,7 @@ var DrawWidget = Panel.extend({
 
         this._updateConstraintValueInputs();
 
-        if (opts.size_mode === 'fixed_aspect_ratio') {
-            this.viewer.startDrawMode(this._drawingType, {modeOptions: {constraint: opts.fixed_width / opts.fixed_height}});
-        } else if (opts.size_mode === 'fixed_size') {
-            this.viewer.startDrawMode(this._drawingType, {modeOptions: {constraint: {width: opts.fixed_width, height: opts.fixed_height}}});
-        } else {
-            this.viewer.startDrawMode(this._drawingType);
-        }
+        this.drawElement(null, this._drawingType, true);
     },
 
     /**