merge: staging changes into main

.ebextensions/autoscaling.config

@@ -0,0 +1,6 @@
+Resources:
+  AWSEBAutoScalingGroup:
+    Type: "AWS::AutoScaling::AutoScalingGroup"
+    Properties:
+      HealthCheckType: ELB
+      HealthCheckGracePeriod: 300

.gitignore

@@ -160,6 +160,7 @@ dynamodb_local_latest/*
 
 # Build files
 Pipfile.lock
+uv.lock
 
 # client-side things
 curation/client/node_modules

client/src/components/Pages/Assay/Assay.tsx

@@ -6,8 +6,11 @@ import {
   Box,
   FormControl,
   FormControlLabel,
+  InputLabel,
+  MenuItem,
   Radio,
   RadioGroup,
+  Select,
   TextField,
   Typography,
 } from "@material-ui/core";
@@ -20,6 +23,25 @@ interface Props {
   index: number;
 }
 
+const ASSAY_OPTIONS = [
+  {
+    name: "fluorescence in-situ hybridization assay",
+    identifier: "obi:OBI_0003094",
+  },
+  { name: "sequencing assay", identifier: "obi:OBI_0600047" },
+  { name: "DNA sequencing assay", identifier: "obi:OBI_0000626" },
+  { name: "RNA-seq assay", identifier: "obi:OBI_0001271" },
+  {
+    name: "comparative genomic hybridization by array assay",
+    identifier: "obi:OBI_0001393",
+  },
+  {
+    name: "RT-PCR",
+    identifier: "obi:OBI_0000552",
+  },
+  { name: "custom", identifier: "" },
+];
+
 export const Assay: React.FC<Props> = () => {
   const { colorTheme } = useColorTheme();
   const useStyles = makeStyles(() => ({
@@ -69,6 +91,17 @@ export const Assay: React.FC<Props> = () => {
   const [assayName, setAssayName] = useState(
     fusion?.assay?.assayName !== undefined ? fusion?.assay?.assayName : ""
   );
+  const [selectedAssayOption, setSelectedAssayOption] = useState(() => {
+    return (
+      ASSAY_OPTIONS.find((a) => a.name === assayName) || {
+        name: "",
+        identifier: "",
+      }
+    );
+  });
+  const isCustom = selectedAssayOption
+    ? selectedAssayOption?.name === "custom"
+    : false;
 
   const [assayId, setAssayId] = useState(
     fusion?.assay?.assayId !== undefined ? fusion?.assay?.assayId : ""
@@ -89,6 +122,7 @@ export const Assay: React.FC<Props> = () => {
   };
 
   const propertySetterMap = {
+    assaySelectedOption: [setSelectedAssayOption, "assaySelectedOption"],
     assayName: [setAssayName, "assayName"],
     assayId: [setAssayId, "assayId"],
     methodUri: [setMethodUri, "methodUri"],
@@ -116,6 +150,19 @@ export const Assay: React.FC<Props> = () => {
     const setterFunction: CallableFunction = propertySetterMap[propertyName][0];
     const jsonName: string = propertySetterMap[propertyName][1];
     const assay: FusionAssay = JSON.parse(JSON.stringify(fusion.assay));
+    if (propertyName === "assaySelectedOption") {
+      value = ASSAY_OPTIONS.find((a) => a.name === value);
+      setterFunction(value);
+      const newAssayName = value.name === "custom" ? "" : value?.name;
+      const newAssayId = value.identifier;
+
+      setAssayId(newAssayId);
+      setAssayName(newAssayName);
+      assay["assayId"] = newAssayId;
+      assay["assayName"] = newAssayName;
+      setFusion({ ...fusion, assay: assay });
+      return;
+    }
     if (value !== assay[jsonName]) {
       setterFunction(value);
       assay[jsonName] = value;
@@ -168,6 +215,24 @@ export const Assay: React.FC<Props> = () => {
         <Typography variant="h5" className={classes.prompt}>
           Provide assay metadata:
         </Typography>
+        <InputLabel id="select-assay-option">Select assay</InputLabel>
+        <Select
+          label="Select assay"
+          labelId="assay-option-select-label"
+          value={selectedAssayOption?.name}
+          onChange={(event) =>
+            handleValueChange("assaySelectedOption", event.target.value)
+          }
+          style={{ width: 550 }}
+        >
+          {ASSAY_OPTIONS.map((assayOption) => (
+            <MenuItem key={assayOption.name} value={assayOption.name}>
+              {assayOption.name}{" "}
+              {assayOption.identifier ? `(${assayOption.identifier})` : null}
+            </MenuItem>
+          ))}
+        </Select>
+
         <HelpTooltip
           placement="left"
           title={
@@ -181,7 +246,8 @@ export const Assay: React.FC<Props> = () => {
           <TextField
             label="Assay name"
             margin="dense"
-            value={assayName}
+            value={assayName || ""}
+            disabled={!isCustom}
             onChange={(event) =>
               handleValueChange("assayName", event.target.value)
             }
@@ -201,6 +267,7 @@ export const Assay: React.FC<Props> = () => {
             label="Assay ID"
             margin="dense"
             value={assayId}
+            disabled={!isCustom}
             onChange={(event) =>
               handleValueChange("assayId", event.target.value)
             }

client/src/components/Pages/Domains/DomainForm/DomainForm.tsx

@@ -94,7 +94,7 @@ const DomainForm: React.FC = () => {
     return [<MenuItem key={-1} value="" disabled></MenuItem>].concat(
       Object.keys(domainOptions).map((geneId: string, index: number) => (
         <MenuItem key={index} value={geneId}>
-          {`${globalGenes[geneId].label}(${geneId})`}
+          {`${globalGenes[geneId].name}(${geneId})`}
         </MenuItem>
       ))
     );

client/src/components/Pages/Domains/Main/Domains.tsx

@@ -108,7 +108,7 @@ export const Domain: React.FC<Props> = () => {
         avatar={<Avatar>{domain.status === "preserved" ? "P" : "L"}</Avatar>}
         label={
           <React.Fragment>
-            {domainLabelString} <b>{`(${domain.associatedGene.label})`}</b>
+            {domainLabelString} <b>{`(${domain.associatedGene.name})`}</b>
           </React.Fragment>
         }
         onDelete={() => handleRemove(domain)}

client/src/components/Pages/Gene/StructureDiagram/StructureDiagram.tsx

@@ -43,7 +43,7 @@ export const StructureDiagram: React.FC = () => {
 
         const regEls = [];
         suggestion.regulatoryElements.forEach((el) => {
-          regEls.push(el.gene.label);
+          regEls.push(el.gene.name);
         });
 
         return (

client/src/components/Pages/Structure/Input/GeneElementInput/GeneElementInput.tsx

@@ -23,7 +23,7 @@ const GeneElementInput: React.FC<GeneElementInputProps> = ({
   icon,
 }) => {
   const [errors, setErrors] = useState<string[]>([]);
-  const [gene, setGene] = useState<string>(element.gene?.label || "");
+  const [gene, setGene] = useState<string>(element.gene?.name || "");
   const [geneText, setGeneText] = useState<string>("");
   const validated = gene !== "" && geneText == "";
   const [expanded, setExpanded] = useState<boolean>(!validated);

client/src/components/Pages/Structure/Input/RegulatoryElementInput/RegulatoryElementInput.tsx

@@ -57,47 +57,90 @@ const RegulatoryElementInput: React.FC<RegulatoryElementInputProps> = ({
   const [elementClass, setElementClass] = useState<RegulatoryClass | "default">(
     regElement?.regulatoryClass || "default"
   );
+  const [featureId, setFeatureId] = useState<string>(
+    regElement?.featureId || ""
+  );
   const [gene, setGene] = useState<string>(
-    regElement?.associatedGene?.label || ""
+    regElement?.associatedGene?.name || ""
   );
   const [geneText, setGeneText] = useState<string>("");
 
-  const validated = gene !== "" && geneText == "" && elementClass !== "default";
+  const [chromosome, setChromosome] = useState<string>(
+    regElement?.featureLocation?.name || ""
+  );
+  const [genomicStart, setGenomicStart] = useState<string>(() => {
+    const start = regElement?.featureLocation?.start;
+
+    if (typeof start === "number") {
+      return String(start + 1);
+    }
+
+    return "";
+  });
+  const [genomicEnd, setGenomicEnd] = useState<string>(() => {
+    const end = regElement?.featureLocation?.end;
+
+    if (typeof end == "number") {
+      return String(end);
+    }
+    return "";
+  });
+
+  const validated =
+    (gene !== "" && geneText == "" && elementClass !== "default") ||
+    (chromosome !== "" && genomicStart !== "" && genomicEnd !== "");
   const [expanded, setExpanded] = useState<boolean>(!validated);
 
   const [errors, setErrors] = useState<string[]>([]);
 
   useEffect(() => {
     if (validated) handleAdd();
-  }, [gene, geneText, elementClass]);
+  }, [
+    gene,
+    geneText,
+    elementClass,
+    featureId,
+    chromosome,
+    genomicStart,
+    genomicEnd,
+  ]);
 
   const handleAdd = () => {
     if (elementClass === "default") return;
-    getRegulatoryElement(elementClass, gene).then((reResponse) => {
+    getRegulatoryElement(
+      elementClass,
+      gene,
+      featureId,
+      chromosome,
+      genomicStart,
+      genomicEnd
+    ).then((reResponse) => {
       if (reResponse.warnings && reResponse.warnings.length > 0) {
         setErrors(reResponse.warnings);
         return;
       }
-      getRegElementNomenclature(reResponse.regulatoryElement).then(
-        (nomenclatureResponse) => {
-          if (
-            nomenclatureResponse.warnings &&
-            nomenclatureResponse.warnings.length > 0
-          ) {
-            setErrors(nomenclatureResponse.warnings);
-            return;
+      if (reResponse.regulatoryElement) {
+        getRegElementNomenclature(reResponse.regulatoryElement).then(
+          (nomenclatureResponse) => {
+            if (
+              nomenclatureResponse.warnings &&
+              nomenclatureResponse.warnings.length > 0
+            ) {
+              setErrors(nomenclatureResponse.warnings);
+              return;
+            }
+            setErrors([]);
+            const newRegElement: ClientRegulatoryElement = {
+              ...reResponse.regulatoryElement,
+              elementId: element.elementId,
+              displayClass: regulatoryClassItems[elementClass][1],
+              nomenclature: nomenclatureResponse.nomenclature || "",
+            };
+            setRegElement(newRegElement);
+            setFusion({ ...fusion, ...{ regulatoryElement: newRegElement } });
           }
-          setErrors([]);
-          const newRegElement: ClientRegulatoryElement = {
-            ...reResponse.regulatoryElement,
-            elementId: element.elementId,
-            displayClass: regulatoryClassItems[elementClass][1],
-            nomenclature: nomenclatureResponse.nomenclature || "",
-          };
-          setRegElement(newRegElement);
-          setFusion({ ...fusion, ...{ regulatoryElement: newRegElement } });
-        }
-      );
+        );
+      }
     });
   };
 
@@ -107,8 +150,12 @@ const RegulatoryElementInput: React.FC<RegulatoryElementInputProps> = ({
     setRegElement(undefined);
     setFusion(cloneFusion);
     setElementClass("default");
+    setFeatureId("");
     setGene("");
     setGeneText("");
+    setChromosome("");
+    setGenomicStart("");
+    setGenomicEnd("");
     setErrors([]);
   };
 
@@ -118,10 +165,18 @@ const RegulatoryElementInput: React.FC<RegulatoryElementInputProps> = ({
         regulatoryClassItems={regulatoryClassItems}
         elementClass={elementClass}
         setElementClass={setElementClass}
+        featureId={featureId}
+        setFeatureId={setFeatureId}
         gene={gene}
         setGene={setGene}
         geneText={geneText}
         setGeneText={setGeneText}
+        chromosome={chromosome}
+        setChromosome={setChromosome}
+        genomicStart={genomicStart}
+        setGenomicStart={setGenomicStart}
+        genomicEnd={genomicEnd}
+        setGenomicEnd={setGenomicEnd}
       />
     </>
   );

client/src/components/Pages/Structure/Input/TemplatedSequenceElementInput/TemplatedSequenceElementInput.tsx

@@ -1,14 +1,14 @@
 import React, { useState, useEffect, KeyboardEvent } from "react";
-import { TextField, Box, Typography } from "@material-ui/core";
+import { TextField, Typography } from "@material-ui/core";
 import { StructuralElementInputProps } from "../StructuralElementInputProps";
 import {
   getTemplatedSequenceElement,
   getTemplatedSequenceNomenclature,
 } from "../../../../../services/main";
 import { ClientTemplatedSequenceElement } from "../../../../../services/ResponseModels";
 import StructuralElementInputAccordion from "../StructuralElementInputAccordion";
-import StrandSwitch from "../../../../main/shared/StrandSwitch/StrandSwitch";
 import HelpTooltip from "../../../../main/shared/HelpTooltip/HelpTooltip";
+import ChromosomeField from "../../../../main/shared/ChromosomeField/ChromosomeField";
 
 interface TemplatedSequenceElementInputProps
   extends StructuralElementInputProps {
@@ -106,38 +106,19 @@ const TemplatedSequenceElementInput: React.FC<
   const inputElements = (
     <>
       <div className="top-inputs">
-        <HelpTooltip
-          placement="bottom"
-          title={
-            <>
-              <Typography>The chromosome on which the segment lies.</Typography>
-              <Typography>
-                RefSeq identifiers (e.g.{" "}
-                <Typography variant="overline">NC_000001.11</Typography>) are
-                preferred.
-              </Typography>
-            </>
+        <ChromosomeField
+          fieldValue={chromosome}
+          onChange={(event, _child) =>
+            setChromosome(event.target.value as string)
           }
-        >
-          <TextField
-            margin="dense"
-            style={{ height: 38, width: 125 }}
-            label="Chromosome"
-            value={chromosome}
-            onChange={(event) => setChromosome(event.target.value)}
-            onKeyDown={handleEnterKey}
-          />
-        </HelpTooltip>
-        <Box mt="18px">
-          <StrandSwitch setStrand={setStrand} selectedStrand={strand} />
-        </Box>
+        />
       </div>
       <div className="bottom-inputs">
         <HelpTooltip
           placement="bottom"
           title={
             <Typography>
-              The starting genomic position of the segment. Inter-residue.
+              The starting genomic position (residue) of the segment.
             </Typography>
           }
         >
@@ -154,7 +135,7 @@ const TemplatedSequenceElementInput: React.FC<
           placement="bottom"
           title={
             <Typography>
-              The ending genomic position of the segment. Inter-residue.
+              The ending genomic position (residue) of the segment.
             </Typography>
           }
         >