Merge pull request #3082 from kbase/develop

Merge to main for 5.1.2 release.

.dockerignore

@@ -4,7 +4,6 @@ Dockerfile
 .vscode
 js-coverage/
 python-coverage/
-narrbase-image/
 node_modules/
 **/__pycache__
 karma-result.json

Dockerfile

@@ -11,7 +11,7 @@
 # Made available under the KBase Open Source License
 #
 
-FROM kbase/narrbase:6.2
+FROM ghcr.io/kbase/narrative-base-image:7.0.0
 
 # These ARGs values are passed in via the docker build command
 ARG BUILD_DATE
@@ -22,16 +22,6 @@ ARG SKIP_MINIFY
 
 EXPOSE 8888
 
-# install NodeJS 16.x (latest LTS until ~October 2022, https://nodejs.org/en/about/releases/)
-# N.b. this version of node is not available in the conda `base` environment as kbase/narrbase:6.2
-# installs ancient versions of node (6.x) and npm (3.x).
-RUN \
-    curl -fsSL https://deb.nodesource.com/setup_16.x | bash - && \
-    apt-get install -y nodejs && \
-    source activate base && \
-    conda update -n base -c defaults conda && \
-    python -m pip install --upgrade pip setuptools wheel
-
 # Copy in the narrative repo
 ADD ./ /kb/dev_container/narrative
 ADD ./kbase-logdb.conf /tmp/kbase-logdb.conf

Makefile

@@ -70,9 +70,6 @@ build-docs:
 	-mkdir docs
 	cp -R src/biokbase-doc/_build/html/* docs/
 
-docker-base:
-	docker build -t kbase/narrbase:3.0 base/
-
 docker-narrative:
 	docker build -t kbase/narrative:1.0.3 .
 

RELEASE_NOTES.md

@@ -4,6 +4,12 @@ The Narrative Interface allows users to craft KBase Narratives using a combinati
 
 This is built on the Jupyter Notebook v6.0.2 (more notes will follow).
 
+### Version 5.1.2
+- PTV-1823 - fixed problem where text input fields for apps were displaying incorrect data on reload
+- DATAUP-778 - fixed bug where xsvGenerator would not run if the paramDisplay value was not present
+- updated data icon coloring scheme
+- refactored narrative Docker image management (see new [narrative-base-image](https://github.com/kbase/narrative-base-image) repo)
+
 ### Version 5.1.1
 - PTV-1798 - fixed issue where invalid component ID was causing data list not to load properly
 - DATAUP-762 - fixed bug where previously run cells were showing errors in the View Configure tab

deployment/services/kbase-ui/narrative_version

@@ -1 +1 @@
-{"version":"4.2.0","git_hash":"bf62933"}
+{"version":"5.1.1","git_hash":"27fda32ec"}

kbase-extension/static/kbase/config/icons.json

@@ -66,40 +66,82 @@
              "#316A4E"
   ],
   "color_mapping": {
-      "AssemblyInput": "#F44336",
-      "Assembly": "#920D58",
-      "ChromatographyMatrix": "#E91E63",
-      "Collection": "#E91E63",
-      "ContigSet": "#3F51B5",
-      "DomainAlignment": "#000000",
-      "EstimateKResult": "#000000",
-      "ExpressionMatrix": "#2196F3",
-      "ExpressionSample": "#2196F3",
-      "ExpressionSeries": "#2196F3",
-      "FBA": "#673AB7",
-      "FBAModel": "#673AB7",
-      "FeatureClusters": "#AEEA00",
-      "FeatureSet": "#AEEA00",
-      "FunctionalMatrix": "#000000",
-      "Genome": "#3F51B5",
-      "GenomeAnnotation": "#920D58",
-      "GenomeComparison": "#3F51B5",
-      "GenomeSet": "#3F51B5",
-      "Heatmap": "#795548",
-      "Media": "#795548",
-      "Metagenome": "#795548",
-      "AnnotatedMetagenomeAssembly": "#1D7EEA",
+      "AmpliconMatrix": "#C1CD23",
+      "AnnotatedMetagenomeAssembly": "#006630",
+      "Assembly": "#66B1DB",
+      "AssemblyFile": "#66B1DB",
+      "AssemblyInput": "##66B1DB",
+      "AssemblyReport": "#795548",
+      "AssemblySet": "#66B1DB",
+      "Associations": "#FFDB33",
+      "AttributeMapping": "#C1CD23",
+      "BinnedContigs": "#66B1DB",
+      "Biom": "#006630",
+      "Bowtie2Indexes": "#B8D4EC",
+      "ChemicalAbundanceMatrix": "#AAE0E4",
+      "ClusterSet": "#66489D",
+      "Collection": "#D2232A",
+      "CompoundSet": "#AAE0E4",
+      "ContigSet": "#66B1DB",
+      "DifferentialExpressionMatrix": "#FFDB33",
+      "DifferentialExpressionMatrixSet": "#FFDB33",
+      "DomainAnnotation": "#66489D",
+      "DomainLibrary": "#66489D",
+      "DomainModelSet": "#66489D",
+      "EscherMap": "#AAE0E4",
+      "EstimateKResult": "#FFDB33",
+      "ExpressionMatrix": "#FFDB33",
+      "ExpressionSample": "#FFDB33",
+      "ExpressionSeries": "#FFDB33",
+      "ExpressionSet": "#FFDB33",
+      "FBA": "#AAE0E4",
+      "FBAModel": "#AAE0E4",
+      "FBAModelAttribureMapping": "#AAE0E4",
+      "FBAModelSet": "#AAE0E4",
+      "FBAPathwayAnalysis": "#AAE0E4",
+      "FeatureClusters": "#D2232A",
+      "FeatureSet": "#D2232A",
+      "FeatureSetSet": "#D2232A",
+      "FigureProperties": "#AAE0E4",
+      "FloatTable": "#F58423",
+      "FunctionalMatrix": "#C1CD23",
+      "FunctionalProfile": "#C1CD23",
+      "Genome": "#D2232A",
+      "GenomeComparison": "#66489D",
+      "GenomeSet": "#D2232A",
+      "GFFAnnotation": "#D2232A",
+      "Heatmap": "#AAE0E4",
+      "Media": "#AAE0E4",
+      "MetaboliteMatrix": "#AAE0E4",
+      "Metagenome": "#006630",
+      "ModelComparison": "#AAE0E4",
+      "MSA": "#B8D4EC",
       "Network": "#795548",
-      "PairedEndLibrary": "#795548",
-      "Pangenome": "#795548",
-      "PhenotypeSet": "#795548",
-      "PhenotypeSimulationSet": "#795548",
-      "ProteomeComparison": "#795548",
-      "ReferenceAssembly": "#795548",
-      "SingleEndLibrary": "#795548",
-      "Taxon": "#920D58",
-      "TaxonomicMatrix": "#795548",
-      "Tree": "#795548",
-      "SampleSet": "#316A4E"
+      "NewModelTemplate": "#AAE0E4",
+      "PairedEndLibrary": "#EDA7AA",
+      "Pangenome": "#66489D",
+      "PCAMatrix": "#C1CD23",
+      "PhenotypeSet": "#AAE0E4",
+      "PhenotypeSimulationSet": "#AAE0E4",
+      "ProteomeComparison": "#66489D",
+      "RNASeqAlignment": "#B8D4EC",
+      "RNASeqAlignmentSet": "#B8D4EC",
+      "RNASeqExpression": "#FFDB33",
+      "RNASeqSampleSet": "#FFDB33",
+      "ReactionMatrix": "#AAE0E4",
+      "ReadsAlignmentSet": "#B8D4EC",
+      "ReadsSet": "#EDA7AA",
+      "ReferenceAssembly": "#D2232A",
+      "ReferenceAnnotation": "#D2232A",
+      "Report": "#795548",
+      "SampleSet": "#C1CD23",
+      "SequenceSet": "#B8D4EC",
+      "SingleEndLibrary": "#EDA7AA",
+      "StringDataTable": "#F58423",
+      "Taxon": "#795548",
+      "TaxonomicMatrix": "#66489D",
+      "TraitMatrix": "#66489D",
+      "Tree": "#66489D",
+      "Variations": "#B8D4EC"
   }
 }

kbase-extension/static/kbase/js/widgets/appWidgets2/input/textInput.js

@@ -4,34 +4,31 @@ define([
     'widgets/appWidgets2/validation',
     'common/events',
     'common/ui',
-    'common/props',
     'common/runtime',
     '../inputUtils',
     'widgets/appWidgets2/validators/constants',
     'bootstrap',
-], (Promise, html, Validation, Events, UI, Props, Runtime, inputUtils, Constants) => {
+], (Promise, html, Validation, Events, UI, Runtime, inputUtils, Constants) => {
     'use strict';
 
     const t = html.tag,
         div = t('div'),
-        input = t('input'),
-        model = Props.make({
-            data: {
-                value: null,
-            },
-            onUpdate: function () {
-                //syncModelToControl();
-                //autoValidate();
-            },
-        });
+        input = t('input');
 
     function factory(config) {
         const spec = config.parameterSpec,
             runtime = Runtime.make(),
             busConnection = runtime.bus().connect(),
-            channel = busConnection.channel(config.channelName);
+            channel = busConnection.channel(config.channelName),
+            model = {
+                value: null,
+            };
         let parent, container, ui;
 
+        // INIT
+
+        setModelValue(config.initialValue);
+
         // CONTROL
 
         function getControlValue() {
@@ -48,19 +45,17 @@ define([
             if (value === undefined) {
                 return;
             }
-            if (model.getItem('value') === value) {
-                return;
-            }
-            model.setItem('value', value);
+            model.value = value;
         }
 
         function resetModelValue() {
             setModelValue(spec.data.defaultValue);
         }
 
-        // sync the dom to the model.
+        // sync the dom to the model and validate
         function syncModelToControl() {
-            setControlValue(model.getItem('value', null));
+            setControlValue(model.value);
+            autoValidate();
         }
 
         // VALIDATION
@@ -78,7 +73,7 @@ define([
         }
 
         function autoValidate() {
-            return validate(model.getItem('value')).then((result) => {
+            return validate(model.value).then((result) => {
                 channel.emit('validation', result);
             });
         }
@@ -118,7 +113,7 @@ define([
                     cancelTouched();
                     importControlValue()
                         .then((value) => {
-                            model.setItem('value', value);
+                            setModelValue(value);
                             channel.emit('changed', {
                                 newValue: value,
                             });
@@ -199,22 +194,18 @@ define([
                 const events = Events.make();
                 container.innerHTML = render(events);
                 events.attachEvents(container);
-                // model.setItem('value', config.initialValue);
                 syncModelToControl();
-                autoValidate();
 
                 channel.on('reset-to-defaults', () => {
                     resetModelValue();
                 });
                 channel.on('update', (message) => {
                     setModelValue(message.value);
                     syncModelToControl();
-                    autoValidate();
                 });
                 channel.on('focus', () => {
                     doFocus();
                 });
-                // channel.emit('sync');
             });
         }
 
@@ -227,10 +218,6 @@ define([
             });
         }
 
-        // INIT
-
-        setModelValue(config.initialValue);
-
         return {
             start,
             stop,