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TeselaGen · Jan 3, 2024 · 04c5445 · 04c5445
2 parents 5308bba + 9df9f71
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -6,27 +6,27 @@ Generated by [`auto-changelog`](https://github.com/CookPete/auto-changelog).
 
 #### 0.2.0
 
-- Fixed condition for removing * [`#52`](https://github.com/NicolasCARPi/tg-oss/pull/52)
-- Removed * aa from dna translation at the end of sequence [`#50`](https://github.com/NicolasCARPi/tg-oss/pull/50)
--  export feat locs [`#45`](https://github.com/NicolasCARPi/tg-oss/pull/45)
-- unifying sequence filtering so filterSequenceString is always hit and… [`#31`](https://github.com/NicolasCARPi/tg-oss/pull/31)
-- fixed genbank file embedded in another genbank comment [`#36`](https://github.com/NicolasCARPi/tg-oss/pull/36)
-- fix the ORF start codons label for RNA sequence [`#27`](https://github.com/NicolasCARPi/tg-oss/pull/27)
-- adding more null pointer checks for tgSelect, making annotation start… [`#30`](https://github.com/NicolasCARPi/tg-oss/pull/30)
-- Fix ove and ui imports for vitest [`#25`](https://github.com/NicolasCARPi/tg-oss/pull/25)
-- Reorder tgSelect results [`#20`](https://github.com/NicolasCARPi/tg-oss/pull/20)
-- fixing annotation range issue and adding test  [`#23`](https://github.com/NicolasCARPi/tg-oss/pull/23)
-- add beforeReadOnlyChange handler [`#21`](https://github.com/NicolasCARPi/tg-oss/pull/21)
-- disable edit lock while loading [`#15`](https://github.com/NicolasCARPi/tg-oss/pull/15)
-- Add tests [`#11`](https://github.com/NicolasCARPi/tg-oss/pull/11)
-- editLock Tooltip & onChangeEditLock [`#9`](https://github.com/NicolasCARPi/tg-oss/pull/9)
-- use user defined annotationVisibility props at the first place [`#6`](https://github.com/NicolasCARPi/tg-oss/pull/6)
-- fix detection of reverse features [`#7`](https://github.com/NicolasCARPi/tg-oss/pull/7)
-- support RNA sequence in gb file [`#5`](https://github.com/NicolasCARPi/tg-oss/pull/5)
-- CLN-54033: support RNA sequence [`#1`](https://github.com/NicolasCARPi/tg-oss/pull/1)
-- Export validateSequenceArray [`#2`](https://github.com/NicolasCARPi/tg-oss/pull/2)
-- genbank ss-DNA should not be overwirte to DNA [`#1`](https://github.com/NicolasCARPi/tg-oss/pull/1)
-- closes #35 [`#35`](https://github.com/NicolasCARPi/tg-oss/issues/35)
-- Make CONTRIBUTING.md a real document [`2539850`](https://github.com/NicolasCARPi/tg-oss/commit/2539850faec88acff5d5109682361e7c8643e25f)
-- make links in readme all relative [`b5b775d`](https://github.com/NicolasCARPi/tg-oss/commit/b5b775d1078c6d91ed3f03828ab31c2fab59edd6)
-- try with relative link [`e04af75`](https://github.com/NicolasCARPi/tg-oss/commit/e04af75702cb8d0988e3ef147ac5a05328d938e4)
+- Fixed condition for removing * [`#52`](https://github.com/TeselaGen/tg-oss/pull/52)
+- Removed * aa from dna translation at the end of sequence [`#50`](https://github.com/TeselaGen/tg-oss/pull/50)
+-  export feat locs [`#45`](https://github.com/TeselaGen/tg-oss/pull/45)
+- unifying sequence filtering so filterSequenceString is always hit and… [`#31`](https://github.com/TeselaGen/tg-oss/pull/31)
+- fixed genbank file embedded in another genbank comment [`#36`](https://github.com/TeselaGen/tg-oss/pull/36)
+- fix the ORF start codons label for RNA sequence [`#27`](https://github.com/TeselaGen/tg-oss/pull/27)
+- adding more null pointer checks for tgSelect, making annotation start… [`#30`](https://github.com/TeselaGen/tg-oss/pull/30)
+- Fix ove and ui imports for vitest [`#25`](https://github.com/TeselaGen/tg-oss/pull/25)
+- Reorder tgSelect results [`#20`](https://github.com/TeselaGen/tg-oss/pull/20)
+- fixing annotation range issue and adding test  [`#23`](https://github.com/TeselaGen/tg-oss/pull/23)
+- add beforeReadOnlyChange handler [`#21`](https://github.com/TeselaGen/tg-oss/pull/21)
+- disable edit lock while loading [`#15`](https://github.com/TeselaGen/tg-oss/pull/15)
+- Add tests [`#11`](https://github.com/TeselaGen/tg-oss/pull/11)
+- editLock Tooltip & onChangeEditLock [`#9`](https://github.com/TeselaGen/tg-oss/pull/9)
+- use user defined annotationVisibility props at the first place [`#6`](https://github.com/TeselaGen/tg-oss/pull/6)
+- fix detection of reverse features [`#7`](https://github.com/TeselaGen/tg-oss/pull/7)
+- support RNA sequence in gb file [`#5`](https://github.com/TeselaGen/tg-oss/pull/5)
+- CLN-54033: support RNA sequence [`#1`](https://github.com/TeselaGen/tg-oss/pull/1)
+- Export validateSequenceArray [`#2`](https://github.com/TeselaGen/tg-oss/pull/2)
+- genbank ss-DNA should not be overwirte to DNA [`#1`](https://github.com/TeselaGen/tg-oss/pull/1)
+- closes #35 [`#35`](https://github.com/TeselaGen/tg-oss/issues/35)
+- updating table styling to remove table last row bottom margin, removing unused S3Download, removing axios dep, updating deps [`8a6fb1f`](https://github.com/TeselaGen/tg-oss/commit/8a6fb1f047550f617c3e56b8c3ebf145967076ef)
+- tiny [`d9a5ad3`](https://github.com/TeselaGen/tg-oss/commit/d9a5ad328d87389199ba39118985f79f6a90b6e0)
+- updating linting [`8150150`](https://github.com/TeselaGen/tg-oss/commit/815015023979b1780768e88d061525bc92d135a6)
diff --git a/docs/pull_request_template.md b/docs/pull_request_template.md
@@ -0,0 +1,3 @@
+<!-- please include this @tnrich tag so I get an email :) -->
+
+@tnrich
diff --git a/packages/ove/package.json b/packages/ove/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@teselagen/ove",
-  "version": "0.3.63",
+  "version": "0.4.1",
   "main": "./src/index.js",
   "exports": {
     ".": {

diff --git a/packages/ove/src/LinearView/index.js b/packages/ove/src/LinearView/index.js
@@ -307,7 +307,9 @@ class _LinearView extends React.Component {
                   updateLabelsForInViewFeatures();
                 },
                 rowContainerStyle: {
-                  height: isNaN(height - 36) ? "auto" : height - 36,
+                  height: isNaN(height - 36)
+                    ? "auto"
+                    : height - 36 - (hideName ? 0 : 20),
                   width: innerWidth + 26,
                   paddingRight: marginWidth / 2,
                   ...(isLinViewZoomed &&

diff --git a/packages/ove/src/LinearView/style.css b/packages/ove/src/LinearView/style.css
@@ -1,10 +1,13 @@
 .veLinearView .veRowItemWrapper {
   display: flex;
   justify-content: center;
-}
-.veLinearView.isLinViewZoomed .veRowItemWrapper {
   overflow: auto;
 }
+
+/* tnw: we had added overflow: auto; only when isLinViewZoomed to prevent the scrollbar from showing up in cases where we didn't want it. We'll need to figure how to prevent the scrollbar from appearing in a different way since we DO need to the scrollbar in certain cases even when isLinViewZoomed=false */
+/* .veLinearView.isLinViewZoomed .veRowItemWrapper {
+  overflow: auto;
+} */
 .sequenceNameText {
   text-align: center;
   padding-top: 20px;

diff --git a/packages/ove/src/Menlo.ttf b/packages/ove/src/Menlo.ttf
diff --git a/packages/ove/src/Monaco.ttf b/packages/ove/src/Monaco.ttf
diff --git a/packages/ove/src/RowItem/Axis.js b/packages/ove/src/RowItem/Axis.js
@@ -111,8 +111,11 @@ const Axis = function (props) {
           i === 0 //if first label in row, or last label in row, we add checks to make sure the axis number labels don't go outside of the width of the row
             ? Math.max(positionLength, xCenter)
             : i === tickMarkPositions.length - 1
-            ? Math.min(bpsPerRow * charWidth - positionLength, xCenter)
-            : xCenter;
+              ? Math.min(bpsPerRow * charWidth - positionLength, xCenter)
+              : xCenter;
+      }
+      if (i === tickMarkPositions.length - 1) {
+        x = Math.min(x, xEnd - positionLength / 2);
       }
       tickMarkSVG.push(
         <text

diff --git a/packages/ove/src/RowItem/StackedAnnotations/PointedAnnotation.js b/packages/ove/src/RowItem/StackedAnnotations/PointedAnnotation.js
@@ -302,7 +302,7 @@ function PointedAnnotation(props) {
             annotation.labelClassName
           )}
           style={{
-            fontSize: ".9em",
+            // fontSize: ".8em",
             fill: _textColor
           }}
           transform={`translate(${textOffset},${height - 2})`}

diff --git a/packages/ove/src/style.css b/packages/ove/src/style.css
@@ -1,19 +1,35 @@
+@font-face {
+  font-family: "Menlo";
+  src: url("./Menlo.ttf");
+  font-weight: normal;
+  font-style: normal;
+  font-display: block;
+}
+@font-face {
+  font-family: "Monaco";
+  src: url("./Monaco.ttf");
+  font-weight: normal;
+  font-style: normal;
+  font-display: block;
+}
 .ve-monospace-font {
-  font-family: Monaco, monospace;
-  font-size: 11px;
+  font-family: Menlo, Monaco, monospace;
+  font-size: 10px;
 }
 .rowViewTextContainer text {
   user-select: none;
 }
-.translationLayer text {
+.translationLayer text,
+.tg-prime-direction,
+.sequenceNameText,
+.veAxis text {
   user-select: none;
 }
 .ve-sequence-reverse {
   fill: #b0b0b0;
 }
 
 .veCircularView .ve-monospace-font {
-  font-family: "Lucida Console", Monaco, monospace;
   font-size: 14px;
 }
 

diff --git a/packages/sequence-utils/package.json b/packages/sequence-utils/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@teselagen/sequence-utils",
-  "version": "0.3.15",
+  "version": "0.3.17",
   "type": "commonjs",
   "dependencies": {
     "bson-objectid": "^2.0.4",

diff --git a/packages/sequence-utils/src/filterSequenceString.js b/packages/sequence-utils/src/filterSequenceString.js
@@ -1,9 +1,27 @@
+import { debounce, uniq } from "lodash";
 import {
   ambiguous_dna_letters,
   ambiguous_rna_letters,
   extended_protein_letters
 } from "./bioData";
 
+let allWarnings = [];
+
+let makeToast = () => {
+  if (typeof window !== "undefined" && window.toastr && allWarnings.length) {
+    window.toastr.warning(allWarnings.join("\n"));
+  }
+  allWarnings = [];
+};
+
+makeToast = debounce(makeToast, 200);
+
+function showWarnings(warnings) {
+  allWarnings = allWarnings.concat(warnings);
+  makeToast.cancel();
+  makeToast();
+}
+
 export default function filterSequenceString(
   sequenceString = "",
   {
@@ -62,16 +80,12 @@ export default function filterSequenceString(
     warnings.push(
       `${
         name ? `Sequence ${name}: ` : ""
-      }Invalid character(s) detected and removed: ${invalidChars
+      }Invalid character(s) detected and removed: ${uniq(invalidChars)
         .slice(0, 100)
         .join(", ")} `
     );
   }
-  if (typeof window !== "undefined" && window.toastr && warnings.length) {
-    warnings.forEach(warning => {
-      window.toastr.warning(warning);
-    });
-  }
+  showWarnings(warnings);
 
   return [sanitizedVal, warnings];
 }
@@ -85,13 +99,15 @@ export function getAcceptedChars({
   return isProtein
     ? `${extended_protein_letters.toLowerCase()}}`
     : isOligo
-    ? ambiguous_rna_letters.toLowerCase() + "t"
-    : isRna
-    ? ambiguous_rna_letters.toLowerCase() + "t"
-    : isMixedRnaAndDna
-    ? ambiguous_rna_letters.toLowerCase() + ambiguous_dna_letters.toLowerCase()
-    : //just plain old dna
-      ambiguous_rna_letters.toLowerCase() + ambiguous_dna_letters.toLowerCase();
+      ? ambiguous_rna_letters.toLowerCase() + "t"
+      : isRna
+        ? ambiguous_rna_letters.toLowerCase() + "t"
+        : isMixedRnaAndDna
+          ? ambiguous_rna_letters.toLowerCase() +
+            ambiguous_dna_letters.toLowerCase()
+          : //just plain old dna
+            ambiguous_rna_letters.toLowerCase() +
+            ambiguous_dna_letters.toLowerCase();
 }
 export function getReplaceChars({
   isOligo,
@@ -102,14 +118,14 @@ export function getReplaceChars({
   return isProtein
     ? {}
     : // {".": "*"}
-    isOligo
-    ? {}
-    : isRna
-    ? { t: "u" }
-    : isMixedRnaAndDna
-    ? {}
-    : //just plain old dna
-      {};
+      isOligo
+      ? {}
+      : isRna
+        ? { t: "u" }
+        : isMixedRnaAndDna
+          ? {}
+          : //just plain old dna
+            {};
 }
 
 export const filterRnaString = (s, o) =>

diff --git a/packages/sequence-utils/src/filterSequenceString.test.js b/packages/sequence-utils/src/filterSequenceString.test.js
@@ -8,23 +8,17 @@ describe("filterSequenceString", () => {
     });
     expect(str).toBe("tatuuaga");
     // expect(warnings[0]).toBe('Replaced "t" with "u" 2 times');
-    expect(warnings[0]).toBe(
-      "Invalid character(s) detected and removed: -, - "
-    );
+    expect(warnings[0]).toBe("Invalid character(s) detected and removed: - ");
   });
   it("should not convert u's to t's for isDna (default isDna=true) seqs", () => {
     const [str, warnings] = filterSequenceString("tatuuag--a", {});
     // expect(warnings[0]).toBe('Replaced "u" with "t" 2 times');
-    expect(warnings[0]).toBe(
-      "Invalid character(s) detected and removed: -, - "
-    );
+    expect(warnings[0]).toBe("Invalid character(s) detected and removed: - ");
     expect(str).toBe("tatuuaga");
   });
   it("should filter out unwanted chars", () => {
     const [str, warnings] = filterSequenceString("tatag--a");
-    expect(warnings[0]).toBe(
-      "Invalid character(s) detected and removed: -, - "
-    );
+    expect(warnings[0]).toBe("Invalid character(s) detected and removed: - ");
     expect(str).toBe("tataga");
   });
   it("should handle additional chars option", () => {
@@ -51,7 +45,7 @@ describe("filterSequenceString", () => {
     );
     // expect(warnings[0]).toBe(`Replaced "." with "*" 2 times`);
     expect(warnings[0]).toBe(
-      'Invalid character(s) detected and removed: 3, 4, 2, ", ", ", ,, ,, ., ., / '
+      'Invalid character(s) detected and removed: 3, 4, 2, ", ,, ., / '
     );
     expect(str).toBe("bbbxtgalmfwkqespvicyhrnd");
   });

diff --git a/packages/ui/package.json b/packages/ui/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@teselagen/ui",
-  "version": "0.3.55",
+  "version": "0.3.62",
   "main": "./src/index.js",
   "exports": {
     ".": {

diff --git a/packages/ui/src/DataTable/index.js b/packages/ui/src/DataTable/index.js
@@ -99,6 +99,8 @@ class DataTable extends React.Component {
   constructor(props) {
     super(props);
     if (this.props.helperProp) {
+      this.props.helperProp.updateValidationHelper =
+        this.updateValidationHelper;
       this.props.helperProp.addEditableTableEntities =
         this.addEditableTableEntities;
       this.props.helperProp.getEditableTableInfoAndThrowFormError =
@@ -797,18 +799,21 @@ class DataTable extends React.Component {
       });
     }
   };
+  updateValidationHelper = () => {
+    const { entities, reduxFormCellValidation } = computePresets(this.props);
+    this.updateValidation(entities, reduxFormCellValidation);
+  };
 
   updateValidation = (entities, newCellValidate) => {
     const { change, schema } = computePresets(this.props);
-    change(
-      "reduxFormCellValidation",
-      validateTableWideErrors({
-        entities,
-        schema,
-        newCellValidate,
-        props: this.props
-      })
-    );
+    const tableWideErr = validateTableWideErrors({
+      entities,
+      schema,
+      newCellValidate,
+      props: this.props
+    });
+    change("reduxFormCellValidation", tableWideErr);
+    this.forceUpdate();
   };
   handleDeleteCell = () => {
     const {
@@ -943,7 +948,9 @@ class DataTable extends React.Component {
         // keep this so that pasting into spreadsheets works.
         format: "text/plain"
       });
-    window.toastr.success(message);
+    if (message) {
+      window.toastr.success(message);
+    }
   };
 
   handleCopyTable = e => {
@@ -1244,8 +1251,8 @@ class DataTable extends React.Component {
     compactClassName += extraCompact
       ? " tg-extra-compact-table"
       : compact
-      ? " tg-compact-table"
-      : "";
+        ? " tg-compact-table"
+        : "";
 
     const hasFilters =
       filters.length ||
@@ -1534,10 +1541,10 @@ class DataTable extends React.Component {
                   const nextCellId = up
                     ? cellIdAbove
                     : down
-                    ? cellIdBelow
-                    : left
-                    ? cellIdToLeft
-                    : cellIdToRight;
+                      ? cellIdBelow
+                      : left
+                        ? cellIdToLeft
+                        : cellIdToRight;
 
                   e.stopPropagation();
                   e.preventDefault();
@@ -1745,8 +1752,8 @@ class DataTable extends React.Component {
                 extraCompact
                   ? itemSizeEstimators.compact
                   : compact
-                  ? itemSizeEstimators.normal
-                  : itemSizeEstimators.comfortable
+                    ? itemSizeEstimators.normal
+                    : itemSizeEstimators.comfortable
               }
               TfootComponent={() => {
                 return <button>hasdfasdf</button>;
@@ -2027,7 +2034,8 @@ class DataTable extends React.Component {
         this.startCellEdit(cellId);
       },
       ...(err && {
-        "data-tip": err?.message || err
+        "data-tip": err?.message || err,
+        "data-no-child-data-tip": true
       }),
       onContextMenu: e => {
         if (!isPrimarySelected) {
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,3 @@
		<!-- please include this @tnrich tag so I get an email :) -->

		@tnrich