@teselagen/ove 0.5.31-beta.1 → 0.5.31-beta.3

package/src/helperComponents/AddOrEditAnnotationDialog/index.js

@@ -429,7 +429,7 @@ class AddOrEditAnnotationDialog extends React.Component {
           <RenderBases
             {...{
               // ...this.props,
-              // bases,
+              bases,
               defaultLinkedOligoMessage,
               getLinkedOligoLink,
               readOnly: this.props.readOnly,

package/src/helperComponents/AddOrEditPrimerDialog/index.js

@@ -25,7 +25,6 @@ import { Menu, MenuItem } from "@blueprintjs/core";
 import MeltingTemp from "../../StatusBar/MeltingTemp";
 import { getStructuredBases } from "../../RowItem/StackedAnnotations/getStructuredBases";
 
-// TODO: Default value here is not working
 const CustomContentEditable = generateField(function CustomContentEditable({
   input,
   disabled,
@@ -34,9 +33,9 @@ const CustomContentEditable = generateField(function CustomContentEditable({
   start,
   end,
   primerBindsOn,
-  bases,
   forward
 }) {
+  const bases = input.value;
   const [hasTempError, setTempError] = useState(false);
   const inputRef = useRef(null);
   const [caretPosition, setCaretPosition] = useState({ start: 0, end: 0 });
@@ -171,7 +170,6 @@ const RenderBases = props => {
       normalizedSelection,
       sequenceData.sequence
     );
-    console.log("bps", bps);
     if (!forward) {
       bps = getReverseComplementSequenceString(bps);
     }

package/src/helperComponents/EnzymesDialog/index.js

@@ -372,7 +372,6 @@ class EnzymesDialog extends React.Component {
                     <h5>Edit group name</h5>
                     <div style={{ display: "flex" }}>
                       <InputGroup
-                        // TODO: Table is failing here so no way to test it
                         defaultValue={selectedEnzymeGroup}
                         autoFocus
                         className="veEditEnzymeGroupName"

package/src/helperComponents/PropertiesDialog/GenericAnnotationProperties.js

@@ -44,15 +44,58 @@ const genericAnnotationProperties = ({
     constructor(props) {
       super(props);
       this.commands = commands(this);
+    }
+    onRowSelect = ([record]) => {
+      if (!record) return;
+      const { dispatch, editorName } = this.props;
+      dispatch({
+        type: "SELECTION_LAYER_UPDATE",
+        payload: record,
+        meta: {
+          editorName
+        }
+      });
+    };
+    render() {
+      const {
+        readOnly,
+        annotations = {},
+        annotationVisibility,
+        sequenceLength,
+        selectionLayer,
+        sequence,
+        isProtein,
+        allPartTags,
+        annotationPropertiesSelectedEntities:
+          _annotationPropertiesSelectedEntities,
+        selectedAnnotationId
+      } = this.props;
+      const annotationPropertiesSelectedEntities =
+        _annotationPropertiesSelectedEntities.filter(a => annotations[a.id]);
+
+      const deleteAnnotation = this.props[`delete${annotationTypeUpper}`];
+
+      const annotationsToUse = map(annotations, annotation => {
+        return {
+          ...annotation,
+          ...(annotation.strand === undefined && {
+            strand: annotation.forward ? 1 : -1
+          }),
+          size: getRangeLength(annotation, sequenceLength)
+        };
+      });
+
+      const keyedPartTags = getKeyedTagsAndTagOptions(allPartTags) ?? {};
+
       this.schema = {
         fields: [
           {
             path: "name",
             type: "string",
 
-            render: (name, ann, row, props) => {
+            render: (name, ann) => {
               const checked =
-                !props.annotationVisibility[
+                !this.props.annotationVisibility[
                   `${annotationType}IndividualToHide`
                 ][ann.id];
 
@@ -64,9 +107,9 @@ const genericAnnotationProperties = ({
                       e.stopPropagation();
                       const upperType = startCase(annotationType);
                       if (checked) {
-                        props[`hide${upperType}Individual`]([ann.id]);
+                        this.props[`hide${upperType}Individual`]([ann.id]);
                       } else {
-                        props[`show${upperType}Individual`]([ann.id]);
+                        this.props[`show${upperType}Individual`]([ann.id]);
                       }
                     }}
                     style={{
@@ -89,10 +132,10 @@ const genericAnnotationProperties = ({
                 {
                   path: "bases",
                   type: "string",
-                  render: (bases, primer, row, props) => {
+                  render: (bases, primer) => {
                     let bps = bases;
                     if (!bases) {
-                      bps = getSequenceWithinRange(primer, props.sequence);
+                      bps = getSequenceWithinRange(primer, this.props.sequence);
                       if (!primer.forward) {
                         bps = getReverseComplementSequenceString(bps);
                       }
@@ -121,13 +164,13 @@ const genericAnnotationProperties = ({
                   }
                 }
               ]),
-          sizeSchema,
+          sizeSchema(this.props.isProtein),
           ...(withTags && this.props.allPartTags
             ? [
                 {
                   path: "tags",
                   type: "string",
-                  getValueToFilterOn: (o, { keyedPartTags }) => {
+                  getValueToFilterOn: o => {
                     const toRet = (o.tags || [])
                       .map(tagId => {
                         const tag = keyedPartTags[tagId];
@@ -137,7 +180,7 @@ const genericAnnotationProperties = ({
                       .join(" ");
                     return toRet;
                   },
-                  render: (tags, b, c, { keyedPartTags = {} }) => {
+                  render: tags => {
                     return (
                       <div style={{ display: "flex" }}>
                         {(tags || []).map((tagId, i) => {
@@ -154,46 +197,6 @@ const genericAnnotationProperties = ({
           { path: "strand", type: "number" }
         ]
       };
-    }
-    onRowSelect = ([record]) => {
-      if (!record) return;
-      const { dispatch, editorName } = this.props;
-      dispatch({
-        type: "SELECTION_LAYER_UPDATE",
-        payload: record,
-        meta: {
-          editorName
-        }
-      });
-    };
-    render() {
-      const {
-        readOnly,
-        annotations = {},
-        annotationVisibility,
-        sequenceLength,
-        selectionLayer,
-        sequence,
-        isProtein,
-        allPartTags,
-        annotationPropertiesSelectedEntities:
-          _annotationPropertiesSelectedEntities,
-        selectedAnnotationId
-      } = this.props;
-      const annotationPropertiesSelectedEntities =
-        _annotationPropertiesSelectedEntities.filter(a => annotations[a.id]);
-
-      const deleteAnnotation = this.props[`delete${annotationTypeUpper}`];
-
-      const annotationsToUse = map(annotations, annotation => {
-        return {
-          ...annotation,
-          ...(annotation.strand === undefined && {
-            strand: annotation.forward ? 1 : -1
-          }),
-          size: getRangeLength(annotation, sequenceLength)
-        };
-      });
 
       return (
         <DataTable
@@ -337,7 +340,6 @@ const genericAnnotationProperties = ({
           formName="annotationProperties"
           noRouter
           isProtein={isProtein}
-          keyedPartTags={getKeyedTagsAndTagOptions(allPartTags)}
           compact
           isInfinite
           schema={this.schema}

package/src/helperComponents/PropertiesDialog/OrfProperties.js

@@ -80,7 +80,7 @@ class OrfProperties extends React.Component {
                 displayName: "Size (aa)",
                 type: "number"
               },
-              sizeSchema,
+              sizeSchema(this.props.isProtein),
               { path: "frame", type: "number" },
               { path: "strand", type: "number" }
             ]

package/src/helperComponents/PropertiesDialog/utils.js

@@ -2,11 +2,11 @@ import React from "react";
 import { convertDnaCaretPositionOrRangeToAA } from "@teselagen/sequence-utils";
 import { convertRangeTo1Based } from "@teselagen/range-utils";
 
-export const sizeSchema = {
+export const sizeSchema = isProtein => ({
   path: "size",
   type: "number",
-  render: (val, _record, i, props) => {
-    const record = props.isProtein
+  render: (val, _record) => {
+    const record = isProtein
       ? convertDnaCaretPositionOrRangeToAA(_record)
       : _record;
     const base1Range = convertRangeTo1Based(record);
@@ -14,7 +14,7 @@ export const sizeSchema = {
 
     return (
       <span>
-        {props.isProtein ? Math.floor(val / 3) : val}{" "}
+        {isProtein ? Math.floor(val / 3) : val}{" "}
         <span style={{ fontSize: 10 }}>
           {hasJoinedLocations ? (
             record.locations.map((loc, i) => {
@@ -34,4 +34,4 @@ export const sizeSchema = {
       </span>
     );
   }
-};
+});

package/src/helperComponents/RemoveDuplicates/index.js

@@ -17,30 +17,6 @@ import { forEach, camelCase, startCase } from "lodash-es";
 import { sizeSchema } from "../PropertiesDialog/utils";
 import { getRangeLength } from "@teselagen/range-utils";
 
-const schema = {
-  fields: [
-    // ...(noColor
-    //   ? []
-    //   : [
-    //       {
-    //         path: "color",
-    //         type: "string",
-    //         render: color => {
-    //           return (
-    //             <ColorPickerPopover>
-    //               <div style={{ height: 20, width: 20, background: color }} />
-    //             </ColorPickerPopover>
-    //           );
-    //         }
-    //       }
-    //     ]),
-    { path: "name", type: "string" },
-    // ...(noType ? [] : [{ path: "type", type: "string" }]),
-    sizeSchema,
-    { path: "strand", type: "string" }
-  ]
-};
-
 class RemoveDuplicatesDialog extends React.Component {
   state = {
     dups: []
@@ -89,6 +65,30 @@ class RemoveDuplicatesDialog extends React.Component {
     const { duplicatesToRemoveSelectedEntities, hideModal, type } = this.props;
 
     const selectedIds = this.state.dups.map(d => d.id);
+
+    const schema = {
+      fields: [
+        // ...(noColor
+        //   ? []
+        //   : [
+        //       {
+        //         path: "color",
+        //         type: "string",
+        //         render: color => {
+        //           return (
+        //             <ColorPickerPopover>
+        //               <div style={{ height: 20, width: 20, background: color }} />
+        //             </ColorPickerPopover>
+        //           );
+        //         }
+        //       }
+        //     ]),
+        { path: "name", type: "string" },
+        // ...(noType ? [] : [{ path: "type", type: "string" }]),
+        sizeSchema(this.props.isProtein),
+        { path: "strand", type: "string" }
+      ]
+    };
     // const sequenceLength = sequenceData.sequence.length;
     // const isCirc = (this.state || {}).circular;
     return (