ove-auto-annotate 0.0.5 → 0.0.8
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/README.md +8 -0
- package/es/index.js +74 -28
- package/lib/index.js +75 -28
- package/package.json +2 -3
- package/src/index.js +104 -43
- package/umd/ove-auto-annotate.js +34527 -797
- package/umd/ove-auto-annotate.js.map +1 -1
- package/umd/ove-auto-annotate.min.js +11 -3
- package/umd/ove-auto-annotate.min.js.map +1 -1
package/README.md
CHANGED
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@@ -1,3 +1,8 @@
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# UI:
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# Usage:
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```js
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@@ -43,6 +48,9 @@ window.createVectorEditor(yourDomNodeHere, {
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# Passing a custom list of existing annotations to choose from:
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```js
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async function getCustomAutoAnnotateList ({ annotationType, sequenceData }) { //annotationType = feature|part|oligo
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const dataToReturn = await fetch("/my/endpoint/here", { ...someParams }); //hit your endpoint here
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package/es/index.js
CHANGED
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@@ -23,6 +23,7 @@ import { formName } from "./constants";
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import { AutoAnnotateBpMatchingDialog } from "./AutoAnnotateBpMatchingDialog";
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import { parseCsvFile, validateCSVRequiredHeaders, validateCSVRow } from "./fileUtils";
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import downloadjs from "downloadjs";
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import { convertProteinSeqToDNAIupac } from "ve-sequence-utils";
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var _window$addOnGlobals = window.addOnGlobals,
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shortid = _window$addOnGlobals.shortid,
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FileUploadField = _window$addOnGlobals.FileUploadField,
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@@ -32,8 +33,8 @@ var _window$addOnGlobals = window.addOnGlobals,
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pluralize = _window$addOnGlobals.pluralize,
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reduxForm = _window$addOnGlobals.reduxForm,
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SubmissionError = _window$addOnGlobals.SubmissionError,
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-
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getFeatureToColorMap = _window$addOnGlobals.getFeatureToColorMap,
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getFeatureTypes = _window$addOnGlobals.getFeatureTypes,
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InfoHelper = _window$addOnGlobals.InfoHelper,
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showConfirmationDialog = _window$addOnGlobals.showConfirmationDialog,
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wrapDialog = _window$addOnGlobals.wrapDialog,
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@@ -79,6 +80,7 @@ export function autoAnnotatePrimers() {
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}
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export var AutoAnnotateModal = compose(wrapDialog(function (p) {
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return {
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canEscapeKeyClose: false,
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title: "Auto Annotate " + startCase(pluralize(p.annotationType))
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};
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}), withEditorProps, reduxForm({
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onChange: setSelectedImportType,
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selectedTabId: fileType
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}, /*#__PURE__*/React.createElement(Tab, {
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panel: /*#__PURE__*/React.createElement("div", null, /*#__PURE__*/React.createElement("div", null, "Select a CSV file
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style: {
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display: "flex"
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}
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}, "name,description,sequence,type,", /*#__PURE__*/React.createElement("span", {
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style: {
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display: "flex"
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}
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}, "isRegex \xA0", /*#__PURE__*/React.createElement(InfoHelper, {
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onClick: function onClick(e) {
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e.stopPropagation();
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e.preventDefault();
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showDialog({
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ModalComponent: AutoAnnotateBpMatchingDialog
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});
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},
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content: true ? /*#__PURE__*/React.createElement("span", null, "Any valid regexes allowed. Click for more info about regex matching") : "All valid IUPAC bases allowed as well as a couple special characters. Click for more info"
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}))), /*#__PURE__*/React.createElement("br", null), annotationType !== "feature" && /*#__PURE__*/React.createElement(React.Fragment, null, /*#__PURE__*/React.createElement("i", null, "Note: the \"type\" column is optional"), /*#__PURE__*/React.createElement("br", null)), /*#__PURE__*/React.createElement("br", null), /*#__PURE__*/React.createElement("a", {
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panel: /*#__PURE__*/React.createElement("div", null, /*#__PURE__*/React.createElement("div", null, "Select a CSV file (", /*#__PURE__*/React.createElement("a", {
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onClick: function onClick() {
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var rows = [_extends({
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name: "Example " + startCase(annotationType) + " 1",
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}, annotationType === "feature" && {
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type: "cds"
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}, {
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isRegex: false
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isRegex: false,
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matchType: "dna"
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}), _extends({
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name: "Example Protein " + startCase(annotationType),
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description: "I'm a description",
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sequence: "APGSGTGGGSGSAPG"
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}, annotationType === "feature" && {
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type: "cds"
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}, {
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isRegex: false,
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matchType: "protein"
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}), _extends({
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name: "Example " + startCase(annotationType) + " 2",
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description: "I'm another description",
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}, annotationType === "feature" && {
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type: "cds"
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}, {
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isRegex: true
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isRegex: true,
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matchType: "dna"
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})];
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var csv = unparse(rows); // const blob = new Blob([convert(sequenceData)], { type: "text/plain" });
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// const filename = `${sequenceData.name || "Untitled_Sequence"}.${fileExt}`;
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downloadjs(csv, "Example CSV Annotation Upload File.csv", "text/plain");
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}
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}, "download example")), /*#__PURE__*/React.createElement(
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}, "download example"), ") with the following columns:", /*#__PURE__*/React.createElement("br", null), /*#__PURE__*/React.createElement("br", null), /*#__PURE__*/React.createElement("div", {
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style: {
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display: "flex"
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}
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}, "name,description,sequence,type,", /*#__PURE__*/React.createElement("span", {
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style: {
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display: "flex"
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}
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}, "isRegex \xA0", /*#__PURE__*/React.createElement(InfoHelper, {
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onClick: function onClick(e) {
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e.stopPropagation();
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e.preventDefault();
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showDialog({
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ModalComponent: AutoAnnotateBpMatchingDialog
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});
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},
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content: true ? /*#__PURE__*/React.createElement("span", null, "Any valid regexes allowed. Click for more info about regex matching") : "All valid IUPAC bases allowed as well as a couple special characters. Click for more info"
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})), ",matchType"), /*#__PURE__*/React.createElement("br", null), annotationType !== "feature" && /*#__PURE__*/React.createElement(React.Fragment, null, /*#__PURE__*/React.createElement("i", null, "Note: the \"type\" column is optional"), /*#__PURE__*/React.createElement("br", null))), /*#__PURE__*/React.createElement(FileUploadField, {
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validateAgainstSchema: validateAgainstSchema,
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name: "csvFile",
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fileLimit: 1,
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isRequired: true,
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disabled: fileType === "implementerDefined" && !(customAnnResponse && customAnnResponse.list && customAnnResponse.list.length),
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onClick: handleSubmit( /*#__PURE__*/function () {
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var _ref3 = _asyncToGenerator( /*#__PURE__*/_regeneratorRuntime.mark(function _callee3(_ref2) {
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var apeFile, csvFile, convertNonStandardTypes, annsToCheck, _seqsToAnnotateById, validateRow, _iterator, _step, _step$value, i, _step$value$, name, sequence, type, isRegex, csvHeaders, _yield$parseCsvFile, data, fields, _error, _iterator2, _step2, _step2$value, index, row, _error2, _yield$parseCsvFile2, _data, _iterator3, _step3, _step3$value, _i, _step3$value$, _name, _sequence, _type, annotationsToCheckById, seqId, _autoAnnotate, newAnns, _SubmissionError;
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var apeFile, csvFile, convertNonStandardTypes, annsToCheck, _seqsToAnnotateById, validateRow, _iterator, _step, _step$value, i, _step$value$, name, sequence, matchType, type, isRegex, csvHeaders, _yield$parseCsvFile, data, fields, _error, _iterator2, _step2, _step2$value, index, row, _error2, _yield$parseCsvFile2, _data, _iterator3, _step3, _step3$value, _i, _step3$value$, _name, _sequence, _type, annotationsToCheckById, seqId, _autoAnnotate, newAnns, _SubmissionError;
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return _regeneratorRuntime.wrap(function _callee3$(_context3) {
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while (1) {
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break;
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}
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cleanedType =
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cleanedType = getFeatureTypes().find(function (t) {
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return t.toLowerCase() === type.toLowerCase();
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});
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}
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_step$value = _step.value, // eslint-disable-next-line no-unused-vars
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i = _step$value[0], _step$value$ = _step$value[1], name = _step$value$.name, sequence = _step$value$.sequence, type = _step$value$.type, isRegex = _step$value$.isRegex;
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i = _step$value[0], _step$value$ = _step$value[1], name = _step$value$.name, sequence = _step$value$.sequence, matchType = _step$value$.matchType, type = _step$value$.type, isRegex = _step$value$.isRegex;
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_context3.next = 11;
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return validateRow({
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name: name,
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sequence: sequence,
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matchType: matchType,
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type: type,
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isRegex: isRegex ? "TRUE" : "FALSE"
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}, "Row " + (i + 1) + " (" + name + ")");
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case 57:
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annotationsToCheckById = {};
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annsToCheck.forEach(function (ann) {
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if (ann.matchType === "protein") {
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ann.sequence = convertProteinSeqToDNAIupac(ann.sequence);
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}
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var id = shortid();
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annotationsToCheckById[id] = _extends({}, ann, {
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sequence: ann.isRegex ? ann.sequence : convertApELikeRegexToRegex(ann.sequence),
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});
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toRet.color = toRet.color ||
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toRet.color = toRet.color || getFeatureToColorMap()[toRet.type];
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return toRet;
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}));
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} else {
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window._ove_addons.autoAnnotateParts = autoAnnotateParts;
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window._ove_addons.autoAnnotatePrimers = autoAnnotatePrimers;
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var customAnnsSchema = ["name", "sequence", typeField, "isRegex"];
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var customAnnsSchemaNoType = ["name", "sequence", typeField, "isRegex"];
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var customAnnsSchemaNoType = ["name", "sequence", typeField, "isRegex"];
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var validateAgainstSchema = {
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fields: [{
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path: "name",
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type: "string",
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isRequired: true
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}, {
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path: "description",
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type: "string"
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}, {
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path: "sequence",
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isRequired: true
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}, {
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path: "type",
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type: "dropdown",
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values: getFeatureTypes(),
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defaultValue: "misc_feature"
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}, {
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path: "isRegex",
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type: "boolean"
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}, {
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path: "matchType",
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type: "dropdown",
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defaultValue: "dna",
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values: ["dna", "protein"]
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}]
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};
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package/lib/index.js
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var _veSequenceUtils = require("ve-sequence-utils");
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function _createForOfIteratorHelperLoose(o, allowArrayLike) { var it = typeof Symbol !== "undefined" && o[Symbol.iterator] || o["@@iterator"]; if (it) return (it = it.call(o)).next.bind(it); if (Array.isArray(o) || (it = _unsupportedIterableToArray(o)) || allowArrayLike && o && typeof o.length === "number") { if (it) o = it; var i = 0; return function () { if (i >= o.length) return { done: true }; return { done: false, value: o[i++] }; }; } throw new TypeError("Invalid attempt to iterate non-iterable instance.\nIn order to be iterable, non-array objects must have a [Symbol.iterator]() method."); }
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pluralize = _window$addOnGlobals.pluralize,
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reduxForm = _window$addOnGlobals.reduxForm,
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SubmissionError = _window$addOnGlobals.SubmissionError,
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getFeatureToColorMap = _window$addOnGlobals.getFeatureToColorMap,
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getFeatureTypes = _window$addOnGlobals.getFeatureTypes,
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InfoHelper = _window$addOnGlobals.InfoHelper,
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showConfirmationDialog = _window$addOnGlobals.showConfirmationDialog,
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wrapDialog = _window$addOnGlobals.wrapDialog,
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canEscapeKeyClose: false,
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title: "Auto Annotate " + startCase(pluralize(p.annotationType))
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onChange: setSelectedImportType,
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selectedTabId: fileType
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}, /*#__PURE__*/React.createElement(Tab, {
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panel: /*#__PURE__*/React.createElement("div", null, /*#__PURE__*/React.createElement("div", null, "Select a CSV file
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style: {
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display: "flex"
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}
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}, "name,description,sequence,type,", /*#__PURE__*/React.createElement("span", {
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style: {
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display: "flex"
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}
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}, "isRegex \xA0", /*#__PURE__*/React.createElement(InfoHelper, {
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onClick: function onClick(e) {
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e.stopPropagation();
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showDialog({
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ModalComponent: _AutoAnnotateBpMatchingDialog.AutoAnnotateBpMatchingDialog
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});
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},
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}, "download example")), /*#__PURE__*/React.createElement(
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}, "download example"), ") with the following columns:", /*#__PURE__*/React.createElement("br", null), /*#__PURE__*/React.createElement("br", null), /*#__PURE__*/React.createElement("div", {
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})), ",matchType"), /*#__PURE__*/React.createElement("br", null), annotationType !== "feature" && /*#__PURE__*/React.createElement(React.Fragment, null, /*#__PURE__*/React.createElement("i", null, "Note: the \"type\" column is optional"), /*#__PURE__*/React.createElement("br", null))), /*#__PURE__*/React.createElement(FileUploadField, {
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var apeFile, csvFile, convertNonStandardTypes, annsToCheck, _seqsToAnnotateById, validateRow, _iterator, _step, _step$value, i, _step$value$, name, sequence, type, isRegex, csvHeaders, _yield$parseCsvFile, data, fields, _error, _iterator2, _step2, _step2$value, index, row, _error2, _yield$parseCsvFile2, _data, _iterator3, _step3, _step3$value, _i, _step3$value$, _name, _sequence, _type, annotationsToCheckById, seqId, _autoAnnotate, newAnns, _SubmissionError;
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var apeFile, csvFile, convertNonStandardTypes, annsToCheck, _seqsToAnnotateById, validateRow, _iterator, _step, _step$value, i, _step$value$, name, sequence, matchType, type, isRegex, csvHeaders, _yield$parseCsvFile, data, fields, _error, _iterator2, _step2, _step2$value, index, row, _error2, _yield$parseCsvFile2, _data, _iterator3, _step3, _step3$value, _i, _step3$value$, _name, _sequence, _type, annotationsToCheckById, seqId, _autoAnnotate, newAnns, _SubmissionError;
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cleanedType =
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cleanedType = getFeatureTypes().find(function (t) {
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}
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i = _step$value[0], _step$value$ = _step$value[1], name = _step$value$.name, sequence = _step$value$.sequence, type = _step$value$.type, isRegex = _step$value$.isRegex;
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i = _step$value[0], _step$value$ = _step$value[1], name = _step$value$.name, sequence = _step$value$.sequence, matchType = _step$value$.matchType, type = _step$value$.type, isRegex = _step$value$.isRegex;
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return validateRow({
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name: name,
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sequence: sequence,
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matchType: matchType,
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type: type,
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421
|
isRegex: isRegex ? "TRUE" : "FALSE"
|
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422
|
}, "Row " + (i + 1) + " (" + name + ")");
|
|
@@ -530,6 +546,10 @@ var AutoAnnotateModal = compose(wrapDialog(function (p) {
|
|
|
530
546
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case 57:
|
|
531
547
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annotationsToCheckById = {};
|
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|
annsToCheck.forEach(function (ann) {
|
|
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|
+
if (ann.matchType === "protein") {
|
|
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|
+
ann.sequence = (0, _veSequenceUtils.convertProteinSeqToDNAIupac)(ann.sequence);
|
|
551
|
+
}
|
|
552
|
+
|
|
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553
|
var id = shortid();
|
|
534
554
|
annotationsToCheckById[id] = _extends({}, ann, {
|
|
535
555
|
sequence: ann.isRegex ? ann.sequence : convertApELikeRegexToRegex(ann.sequence),
|
|
@@ -551,7 +571,7 @@ var AutoAnnotateModal = compose(wrapDialog(function (p) {
|
|
|
551
571
|
id: shortid()
|
|
552
572
|
});
|
|
553
573
|
|
|
554
|
-
toRet.color = toRet.color ||
|
|
574
|
+
toRet.color = toRet.color || getFeatureToColorMap()[toRet.type];
|
|
555
575
|
return toRet;
|
|
556
576
|
}));
|
|
557
577
|
} else {
|
|
@@ -597,4 +617,31 @@ window._ove_addons.autoAnnotateFeatures = autoAnnotateFeatures;
|
|
|
597
617
|
window._ove_addons.autoAnnotateParts = autoAnnotateParts;
|
|
598
618
|
window._ove_addons.autoAnnotatePrimers = autoAnnotatePrimers;
|
|
599
619
|
var customAnnsSchema = ["name", "sequence", typeField, "isRegex"];
|
|
600
|
-
var customAnnsSchemaNoType = ["name", "sequence", typeField, "isRegex"];
|
|
620
|
+
var customAnnsSchemaNoType = ["name", "sequence", typeField, "isRegex"];
|
|
621
|
+
var validateAgainstSchema = {
|
|
622
|
+
fields: [{
|
|
623
|
+
path: "name",
|
|
624
|
+
type: "string",
|
|
625
|
+
isRequired: true
|
|
626
|
+
}, {
|
|
627
|
+
path: "description",
|
|
628
|
+
type: "string"
|
|
629
|
+
}, {
|
|
630
|
+
path: "sequence",
|
|
631
|
+
type: "string",
|
|
632
|
+
isRequired: true
|
|
633
|
+
}, {
|
|
634
|
+
path: "type",
|
|
635
|
+
type: "dropdown",
|
|
636
|
+
values: getFeatureTypes(),
|
|
637
|
+
defaultValue: "misc_feature"
|
|
638
|
+
}, {
|
|
639
|
+
path: "isRegex",
|
|
640
|
+
type: "boolean"
|
|
641
|
+
}, {
|
|
642
|
+
path: "matchType",
|
|
643
|
+
type: "dropdown",
|
|
644
|
+
defaultValue: "dna",
|
|
645
|
+
values: ["dna", "protein"]
|
|
646
|
+
}]
|
|
647
|
+
};
|
package/package.json
CHANGED
|
@@ -1,12 +1,11 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "ove-auto-annotate",
|
|
3
|
-
"version": "0.0.
|
|
3
|
+
"version": "0.0.8",
|
|
4
4
|
"scripts": {
|
|
5
5
|
"build": "nwb build-react-component --copy-files --no-demo",
|
|
6
|
-
"
|
|
6
|
+
"prepublishOnly": "npm run build"
|
|
7
7
|
},
|
|
8
8
|
"dependencies": {
|
|
9
|
-
"downloadjs": "^1.4.7",
|
|
10
9
|
"papaparse": "^5.3.1"
|
|
11
10
|
},
|
|
12
11
|
"devDependencies": {
|
package/src/index.js
CHANGED
|
@@ -11,6 +11,7 @@ import {
|
|
|
11
11
|
validateCSVRow
|
|
12
12
|
} from "./fileUtils";
|
|
13
13
|
import downloadjs from "downloadjs";
|
|
14
|
+
import { convertProteinSeqToDNAIupac } from "ve-sequence-utils";
|
|
14
15
|
|
|
15
16
|
const {
|
|
16
17
|
shortid,
|
|
@@ -21,8 +22,8 @@ const {
|
|
|
21
22
|
pluralize,
|
|
22
23
|
reduxForm,
|
|
23
24
|
SubmissionError,
|
|
24
|
-
|
|
25
|
-
|
|
25
|
+
getFeatureToColorMap,
|
|
26
|
+
getFeatureTypes,
|
|
26
27
|
InfoHelper,
|
|
27
28
|
showConfirmationDialog,
|
|
28
29
|
wrapDialog,
|
|
@@ -68,6 +69,7 @@ export function autoAnnotatePrimers() {
|
|
|
68
69
|
|
|
69
70
|
export const AutoAnnotateModal = compose(
|
|
70
71
|
wrapDialog((p) => ({
|
|
72
|
+
canEscapeKeyClose: false,
|
|
71
73
|
title: `Auto Annotate ${startCase(pluralize(p.annotationType))}`
|
|
72
74
|
})),
|
|
73
75
|
withEditorProps,
|
|
@@ -120,41 +122,7 @@ export const AutoAnnotateModal = compose(
|
|
|
120
122
|
panel={
|
|
121
123
|
<div>
|
|
122
124
|
<div>
|
|
123
|
-
Select a CSV file
|
|
124
|
-
<br></br>
|
|
125
|
-
<div style={{ display: "flex" }}>
|
|
126
|
-
name,description,sequence,type,
|
|
127
|
-
<span style={{ display: "flex" }}>
|
|
128
|
-
isRegex
|
|
129
|
-
<InfoHelper
|
|
130
|
-
onClick={(e) => {
|
|
131
|
-
e.stopPropagation();
|
|
132
|
-
e.preventDefault();
|
|
133
|
-
showDialog({
|
|
134
|
-
ModalComponent: AutoAnnotateBpMatchingDialog
|
|
135
|
-
});
|
|
136
|
-
}}
|
|
137
|
-
content={
|
|
138
|
-
true ? (
|
|
139
|
-
<span>
|
|
140
|
-
Any valid regexes allowed. Click for more info about
|
|
141
|
-
regex matching
|
|
142
|
-
</span>
|
|
143
|
-
) : (
|
|
144
|
-
`All valid IUPAC bases allowed as well as a couple special characters. Click for more info`
|
|
145
|
-
)
|
|
146
|
-
}
|
|
147
|
-
></InfoHelper>
|
|
148
|
-
</span>
|
|
149
|
-
</div>
|
|
150
|
-
<br></br>
|
|
151
|
-
{annotationType !== "feature" && (
|
|
152
|
-
<React.Fragment>
|
|
153
|
-
<i>Note: the "type" column is optional</i>
|
|
154
|
-
<br></br>
|
|
155
|
-
</React.Fragment>
|
|
156
|
-
)}
|
|
157
|
-
<br></br>
|
|
125
|
+
Select a CSV file (
|
|
158
126
|
<a
|
|
159
127
|
onClick={() => {
|
|
160
128
|
const rows = [
|
|
@@ -165,7 +133,18 @@ export const AutoAnnotateModal = compose(
|
|
|
165
133
|
...(annotationType === "feature" && {
|
|
166
134
|
type: `cds`
|
|
167
135
|
}),
|
|
168
|
-
isRegex: false
|
|
136
|
+
isRegex: false,
|
|
137
|
+
matchType: "dna"
|
|
138
|
+
},
|
|
139
|
+
{
|
|
140
|
+
name: `Example Protein ${startCase(annotationType)}`,
|
|
141
|
+
description: "I'm a description",
|
|
142
|
+
sequence: `APGSGTGGGSGSAPG`,
|
|
143
|
+
...(annotationType === "feature" && {
|
|
144
|
+
type: `cds`
|
|
145
|
+
}),
|
|
146
|
+
isRegex: false,
|
|
147
|
+
matchType: "protein"
|
|
169
148
|
},
|
|
170
149
|
{
|
|
171
150
|
name: `Example ${startCase(annotationType)} 2`,
|
|
@@ -174,7 +153,8 @@ export const AutoAnnotateModal = compose(
|
|
|
174
153
|
...(annotationType === "feature" && {
|
|
175
154
|
type: `cds`
|
|
176
155
|
}),
|
|
177
|
-
isRegex: true
|
|
156
|
+
isRegex: true,
|
|
157
|
+
matchType: "dna"
|
|
178
158
|
}
|
|
179
159
|
];
|
|
180
160
|
const csv = unparse(rows);
|
|
@@ -190,8 +170,44 @@ export const AutoAnnotateModal = compose(
|
|
|
190
170
|
>
|
|
191
171
|
download example
|
|
192
172
|
</a>
|
|
173
|
+
) with the following columns:<br></br>
|
|
174
|
+
<br></br>
|
|
175
|
+
<div style={{ display: "flex" }}>
|
|
176
|
+
name,description,sequence,type,
|
|
177
|
+
<span style={{ display: "flex" }}>
|
|
178
|
+
isRegex
|
|
179
|
+
<InfoHelper
|
|
180
|
+
onClick={(e) => {
|
|
181
|
+
e.stopPropagation();
|
|
182
|
+
e.preventDefault();
|
|
183
|
+
showDialog({
|
|
184
|
+
ModalComponent: AutoAnnotateBpMatchingDialog
|
|
185
|
+
});
|
|
186
|
+
}}
|
|
187
|
+
content={
|
|
188
|
+
true ? (
|
|
189
|
+
<span>
|
|
190
|
+
Any valid regexes allowed. Click for more info about
|
|
191
|
+
regex matching
|
|
192
|
+
</span>
|
|
193
|
+
) : (
|
|
194
|
+
`All valid IUPAC bases allowed as well as a couple special characters. Click for more info`
|
|
195
|
+
)
|
|
196
|
+
}
|
|
197
|
+
></InfoHelper>
|
|
198
|
+
</span>
|
|
199
|
+
,matchType
|
|
200
|
+
</div>
|
|
201
|
+
<br></br>
|
|
202
|
+
{annotationType !== "feature" && (
|
|
203
|
+
<React.Fragment>
|
|
204
|
+
<i>Note: the "type" column is optional</i>
|
|
205
|
+
<br></br>
|
|
206
|
+
</React.Fragment>
|
|
207
|
+
)}
|
|
193
208
|
</div>
|
|
194
209
|
<FileUploadField
|
|
210
|
+
validateAgainstSchema={validateAgainstSchema}
|
|
195
211
|
name="csvFile"
|
|
196
212
|
fileLimit={1}
|
|
197
213
|
isRequired
|
|
@@ -285,7 +301,7 @@ FRT GAAGTTCCTATTCTCTAGAAAGTATAGGAACTTC misc_recomb orchid pink 0 0`,
|
|
|
285
301
|
let regexConvertedSeq;
|
|
286
302
|
|
|
287
303
|
if (annotationType === "feature") {
|
|
288
|
-
const cleanedType =
|
|
304
|
+
const cleanedType = getFeatureTypes().find(
|
|
289
305
|
(t) => t.toLowerCase() === type.toLowerCase()
|
|
290
306
|
);
|
|
291
307
|
if (!cleanedType) {
|
|
@@ -329,10 +345,16 @@ FRT GAAGTTCCTATTCTCTAGAAAGTATAGGAACTTC misc_recomb orchid pink 0 0`,
|
|
|
329
345
|
// eslint-disable-next-line no-unused-vars
|
|
330
346
|
i,
|
|
331
347
|
// eslint-disable-next-line no-unused-vars
|
|
332
|
-
{ name, sequence, type, isRegex }
|
|
348
|
+
{ name, sequence, matchType, type, isRegex }
|
|
333
349
|
] of customAnnResponse.list.entries()) {
|
|
334
350
|
await validateRow(
|
|
335
|
-
{
|
|
351
|
+
{
|
|
352
|
+
name,
|
|
353
|
+
sequence,
|
|
354
|
+
matchType,
|
|
355
|
+
type,
|
|
356
|
+
isRegex: isRegex ? "TRUE" : "FALSE"
|
|
357
|
+
},
|
|
336
358
|
`Row ${i + 1} (${name})`
|
|
337
359
|
);
|
|
338
360
|
}
|
|
@@ -386,6 +408,9 @@ FRT GAAGTTCCTATTCTCTAGAAAGTATAGGAACTTC misc_recomb orchid pink 0 0`,
|
|
|
386
408
|
}
|
|
387
409
|
const annotationsToCheckById = {};
|
|
388
410
|
annsToCheck.forEach((ann) => {
|
|
411
|
+
if (ann.matchType === "protein") {
|
|
412
|
+
ann.sequence = convertProteinSeqToDNAIupac(ann.sequence);
|
|
413
|
+
}
|
|
389
414
|
const id = shortid();
|
|
390
415
|
annotationsToCheckById[id] = {
|
|
391
416
|
...ann,
|
|
@@ -413,7 +438,8 @@ FRT GAAGTTCCTATTCTCTAGAAAGTATAGGAACTTC misc_recomb orchid pink 0 0`,
|
|
|
413
438
|
forward: a.strand !== -1,
|
|
414
439
|
id: shortid()
|
|
415
440
|
};
|
|
416
|
-
toRet.color =
|
|
441
|
+
toRet.color =
|
|
442
|
+
toRet.color || getFeatureToColorMap()[toRet.type];
|
|
417
443
|
return toRet;
|
|
418
444
|
})
|
|
419
445
|
);
|
|
@@ -446,3 +472,38 @@ window._ove_addons.autoAnnotatePrimers = autoAnnotatePrimers;
|
|
|
446
472
|
|
|
447
473
|
const customAnnsSchema = ["name", "sequence", typeField, "isRegex"];
|
|
448
474
|
const customAnnsSchemaNoType = ["name", "sequence", typeField, "isRegex"];
|
|
475
|
+
|
|
476
|
+
const validateAgainstSchema = {
|
|
477
|
+
fields: [
|
|
478
|
+
{
|
|
479
|
+
path: "name",
|
|
480
|
+
type: "string",
|
|
481
|
+
isRequired: true
|
|
482
|
+
},
|
|
483
|
+
{
|
|
484
|
+
path: "description",
|
|
485
|
+
type: "string"
|
|
486
|
+
},
|
|
487
|
+
{
|
|
488
|
+
path: "sequence",
|
|
489
|
+
type: "string",
|
|
490
|
+
isRequired: true
|
|
491
|
+
},
|
|
492
|
+
{
|
|
493
|
+
path: "type",
|
|
494
|
+
type: "dropdown",
|
|
495
|
+
values: getFeatureTypes(),
|
|
496
|
+
defaultValue: "misc_feature"
|
|
497
|
+
},
|
|
498
|
+
{
|
|
499
|
+
path: "isRegex",
|
|
500
|
+
type: "boolean"
|
|
501
|
+
},
|
|
502
|
+
{
|
|
503
|
+
path: "matchType",
|
|
504
|
+
type: "dropdown",
|
|
505
|
+
defaultValue: "dna",
|
|
506
|
+
values: ["dna", "protein"]
|
|
507
|
+
}
|
|
508
|
+
]
|
|
509
|
+
};
|