removing modules, adding fusion query

This largish restructuring gets rid of the `modules` part & just defines the pages. And: "mateName" etc. fusion support!

package.json

@@ -23,7 +23,7 @@
     "classnames": "^2.2.6",
     "env-cmd": "^10.1.0",
     "file-saver": "^2.0.5",
-    "fs": "0.0.1-security",
+    "fs": "^0.0.1-security",
     "json2csv": "^5.0.6",
     "leaflet": "^1.7.1",
     "lodash": "^4.17.21",

src/modules/service-pages/ontomapsComponents.js → src/components/OntomapsComponents.js

@@ -1,4 +1,4 @@
-import { ontologymapsUrl, useProgenetixApi } from "../../hooks/api"
+import { ontologymapsUrl, useProgenetixApi } from "../hooks/api"
 import Link from "next/link"
 
 export function CodeGroups({ codeGroups, ontomapsUrl }) {

src/components/SearchPage.js

@@ -0,0 +1,20 @@
+import React from "react"
+import { Layout } from "./Layout"
+import BiosamplesSearchPanel from "./searchForm/BiosamplesSearchPanel"
+import parametersConfig from "../config/beaconSearchParameters.yaml"
+import beaconQueryTypes from  "../config/beaconQueryTypes.yaml"
+import requestTypeExamples from "../config/beaconSearchExamples.yaml"
+
+export default function Page({ cytoBands }) {
+  return (
+    <Layout title="Search Samples" headline="">
+      <BiosamplesSearchPanel
+        cytoBands={cytoBands}
+        parametersConfig={parametersConfig}
+        beaconQueryTypes={beaconQueryTypes}
+        requestTypeExamples={requestTypeExamples}
+        collapsed={false}
+      />
+    </Layout>
+  )
+}

src/components/searchForm/BiosamplesSearchForm.js

@@ -223,6 +223,13 @@ export function BeaconSearchForm({
             />
           )}
           <div className="columns my-0">
+            <InputField
+              className={cn(
+                !parameters.geneId.isHidden && "column",
+                "py-0 mb-3"
+              )}
+              {...parameters.geneId} {...fieldProps}
+            />
             <InputField
               className={cn(
                 !parameters.genomicAlleleShortForm.isHidden && "column",
@@ -239,19 +246,20 @@ export function BeaconSearchForm({
             />
           </div>
           <div className="columns my-0">
-            <InputField
+            <SelectField
               className={cn(
-                !parameters.geneId && "column",
+                !parameters.analysisOperation.isHidden && "column",
                 "py-0 mb-3"
               )}
-              {...parameters.geneId} {...fieldProps}
+              {...parameters.analysisOperation}
+              {...selectProps}
             />
             <SelectField
               className={cn(
-                !parameters.analysisOperation.isHidden && "column",
+                !parameters.variantType.isHidden && "column",
                 "py-0 mb-3"
               )}
-              {...parameters.analysisOperation}
+              {...parameters.variantType}
               {...selectProps}
             />
           </div>
@@ -264,31 +272,50 @@ export function BeaconSearchForm({
               {...parameters.referenceName}
               {...selectProps}
             />
-            <SelectField
+            <InputField
               className={cn(
-                !parameters.variantType.isHidden && "column",
+                !parameters.start.isHidden && "column",
                 "py-0 mb-3"
               )}
-              {...parameters.variantType}
-              {...selectProps}
+              {...fieldProps}
+              {...parameters.start}
+              rules={{
+                validate: checkIntegerRange
+              }}
+            />
+            <InputField
+              className={cn(!parameters.end.isHidden && "column", "py-0 mb-3")}
+              {...fieldProps}
+              {...parameters.end}
+              rules={{
+                validate: checkIntegerRange
+              }}
             />
           </div>
           <div className="columns my-0">
+            <SelectField
+              className={cn(
+                !parameters.mateName.isHidden && "column",
+                "py-0 mb-3"
+              )}
+              {...parameters.mateName}
+              {...selectProps}
+            />
             <InputField
               className={cn(
-                !parameters.start.isHidden && "column",
+                !parameters.mateStart.isHidden && "column",
                 "py-0 mb-3"
               )}
               {...fieldProps}
-              {...parameters.start}
+              {...parameters.mateStart}
               rules={{
                 validate: checkIntegerRange
               }}
             />
             <InputField
-              className={cn(!parameters.end.isHidden && "column", "py-0 mb-3")}
+              className={cn(!parameters.mateEnd.isHidden && "column", "py-0 mb-3")}
               {...fieldProps}
-              {...parameters.end}
+              {...parameters.mateEnd}
               rules={{
                 validate: checkIntegerRange
               }}
@@ -666,10 +693,13 @@ function validateForm(formValues) {
   const {
     variantType,
     referenceName,
+    mateName,
     referenceBases,
     alternateBases,
     start,
     end,
+    mateStart,
+    mateEnd,
     cytoBands,
     variantQueryDigests,
     geneId,
@@ -693,6 +723,9 @@ function validateForm(formValues) {
     !alternateBases && setMissing("alternateBases")
     !start && setMissing("start")
     !end && setMissing("end")
+    !mateName && setMissing("mateName")
+    !mateStart && setMissing("mateStart")
+    !mateEnd && setMissing("mateEnd")
     !cytoBands && setMissing("cytoBands")
     !variantQueryDigests && setMissing("variantQueryDigests")
     !variantType && setMissing("variantType")

src/components/searchForm/ChromosomePreview.js

@@ -7,10 +7,16 @@ export default function ChromosomePreview({ watch, cytoBands }) {
   const { width } = useContainerDimensions(componentRef)
   const startRange = watch("start")
   const endRange = watch("end")
+  const mateStartRange = watch("mateStart")
+  const mateEndRange = watch("mateEnd")
   const referenceName = watch("referenceName")
+  const mateName = watch("mateName")
   const chro = referenceName ? refseq2chro(referenceName) : ""
+  const mateChro = mateName ? refseq2chro(mateName) : ""
   const bands = cytoBands["chr" + chro]
+  const mateBands = cytoBands["chr" + mateChro]
   const shouldDisplay = (startRange || endRange) && bands
+  const shouldDisplayMate = (mateStartRange || mateEndRange) && mateBands
 
   return (
     <div ref={componentRef}>
@@ -23,6 +29,15 @@ export default function ChromosomePreview({ watch, cytoBands }) {
           width={width}
         />
       )}
+      {shouldDisplayMate && (
+        <Chromosome
+          bands={mateBands}
+          refseqId={mateName}
+          startRange={mateStartRange}
+          endRange={mateEndRange}
+          width={width}
+        />
+      )}
     </div>
   )
 }

src/components/searchResults/BiosamplesResults.js

@@ -84,6 +84,24 @@ function QuerySummary({ query }) {
           {query.end}
         </li>
       )}
+      {query.mateName && (
+        <li>
+          <small>Adjacent Chro: </small>
+          {query.mateName}
+        </li>
+      )}
+      {query.mateStart && (
+        <li>
+          <small>Adj. Start: </small>
+          {query.mateStart}
+        </li>
+      )}
+      {query.mateEnd && (
+        <li>
+          <small>Adj. End: </small>
+          {query.mateEnd}
+        </li>
+      )}
       {query.variantType && (
         <li>
           <small>Type: </small>

src/components/searchResults/DatasetResultBox.js

@@ -2,6 +2,7 @@ import React, { useRef, useState } from "react"
 import {
   // MAX_HISTO_SAMPLES,
   // SITE_DEFAULTS,
+  getVisualizationLink,
   replaceWithProxy,
   useProgenetixApi,
   useExtendedSWR
@@ -17,7 +18,6 @@ import BiosamplesStatsDataTable from "./BiosamplesStatsDataTable"
 import { WithData } from "../Loader"
 import { openJsonInNewTab } from "../../utils/files"
 // import dynamic from "next/dynamic"
-import { getVisualizationLink } from "../../modules/service-pages/dataVisualizationPage"
 
 const HANDOVER_IDS = {
   histoplot: "histoplot",