IGVF-1955 Update sequence-file UI for newly embedded sequencing_platf…

…orm (#622)

* Display the embedded platform on sequence files.
* Update the sequencing file tables to get the sequencing platform newly embedded in the objects themselves.
* Correct the sorting on the sequencing file table sequencing platform column.

components/file-set-files-tables.js

@@ -13,7 +13,6 @@ export default function FileSetFilesTables({
  files = [],
  fileSet,
  seqspecFiles,
- sequencingPlatforms,
  children,
 }) {
  // Extract sequencing files from `files` and group them by characteristics to determine which
@@ -55,7 +54,6 @@ export default function FileSetFilesTables({
  isIlluminaReadType
  itemPath={fileSet["@id"]}
  seqspecFiles={seqspecFiles}
- sequencingPlatforms={sequencingPlatforms}
  hasReadType
  />
  )}
@@ -66,7 +64,6 @@ export default function FileSetFilesTables({
  isIlluminaReadType={false}
  itemPath={fileSet["@id"]}
  seqspecFiles={seqspecFiles}
- sequencingPlatforms={sequencingPlatforms}
  />
  )}
  {children}
@@ -84,6 +81,4 @@ FileSetFilesTables.propTypes = {
  fileSet: PropTypes.object.isRequired,
  // seqspec files associated with the files
  seqspecFiles: PropTypes.arrayOf(PropTypes.object).isRequired,
- // Sequencing platform objects associated with `files`
- sequencingPlatforms: PropTypes.arrayOf(PropTypes.object).isRequired,
 };

components/sequencing-file-table.js

@@ -1,6 +1,7 @@
 // node_modules
 import { TableCellsIcon } from "@heroicons/react/20/solid";
 import _ from "lodash";
+import Link from "next/link";
 import PropTypes from "prop-types";
 // components
 import { DataAreaTitle, DataAreaTitleLink } from "./data-area";
@@ -72,18 +73,14 @@ const filesColumns = [
  {
  id: "sequencing_platform",
  title: "Sequencing Platform",
- display: ({ source, meta }) => {
- const matchingPlatform = meta.sequencingPlatforms.find(
- (platform) => platform["@id"] === source.sequencing_platform
- );
- return matchingPlatform?.term_name || null;
- },
- sorter: (item, meta) => {
- const matchingPlatform = meta.sequencingPlatforms.find(
- (platform) => platform["@id"] === item.sequencing_platform
+ display: ({ source }) => {
+ return (
+ <Link href={source.sequencing_platform["@id"]}>
+ {source.sequencing_platform.term_name}
+ </Link>
  );
- return matchingPlatform?.term_name || "";
  },
+ sorter: (item) => item.sequencing_platform.term_name.toLowerCase(),
  },
  {
  id: "flowcell_id",
@@ -125,7 +122,6 @@ export default function SequencingFileTable({
  itemPath = "",
  itemPathProp = "file_set.@id",
  isIlluminaReadType = undefined,
- sequencingPlatforms,
  seqspecFiles = [],
  hasReadType = false,
  isSeqspecHidden = false,
@@ -164,7 +160,6 @@ export default function SequencingFileTable({
  pager={{}}
  meta={{
  seqspecFiles,
- sequencingPlatforms,
  hasReadType,
  isSeqspecHidden,
  }}
@@ -185,8 +180,6 @@ SequencingFileTable.propTypes = {
  itemPathProp: PropTypes.string,
  // True to show only files with illumina_read_type, false to show only files without
  isIlluminaReadType: PropTypes.bool,
- // Sequencing platform objects associated with `files`
- sequencingPlatforms: PropTypes.arrayOf(PropTypes.object).isRequired,
  // seqspec files associated with `files`
  seqspecFiles: PropTypes.arrayOf(PropTypes.object),
  // True if files have illumina_read_type

pages/auxiliary-sets/[id].js

@@ -23,7 +23,6 @@ import {
  requestDocuments,
  requestFiles,
  requestFileSets,
- requestOntologyTerms,
  requestPublications,
  requestSeqspecFiles,
 } from "../../lib/common-requests";
@@ -38,7 +37,6 @@ export default function AuxiliarySet({
  files,
  relatedDatasets,
  seqspecFiles,
- sequencingPlatforms,
  inputFileSetFor,
  controlFor,
  attribution = null,
@@ -72,7 +70,6 @@ export default function AuxiliarySet({
  files={groupedFiles.other}
  fileSet={auxiliarySet}
  seqspecFiles={seqspecFiles}
- sequencingPlatforms={sequencingPlatforms}
  >
  {groupedFiles.tabular?.length > 0 && (
  <FileTable
@@ -134,8 +131,6 @@ AuxiliarySet.propTypes = {
  relatedDatasets: PropTypes.arrayOf(PropTypes.object).isRequired,
  // seqspec files associated with `files`
  seqspecFiles: PropTypes.arrayOf(PropTypes.object).isRequired,
- // Sequencing platform objects associated with `files`
- sequencingPlatforms: PropTypes.arrayOf(PropTypes.object).isRequired,
  // File sets that this file set is input for
  inputFileSetFor: PropTypes.arrayOf(PropTypes.object).isRequired,
  // File sets controlled by this file set
@@ -174,15 +169,6 @@ export async function getServerSideProps({ params, req, query }) {
  relatedDatasets = await requestFileSets(datasetPaths, request);
  }
 
- const sequencingPlatformPaths = files
- .map((file) => file.sequencing_platform)
- .filter((sequencingPlatform) => sequencingPlatform);
- const uniqueSequencingPlatformPaths = [...new Set(sequencingPlatformPaths)];
- const sequencingPlatforms =
- uniqueSequencingPlatformPaths.length > 0
- ? await requestOntologyTerms(uniqueSequencingPlatformPaths, request)
- : [];
-
  const seqspecFiles =
  files.length > 0 ? await requestSeqspecFiles(files, request) : [];
 
@@ -219,7 +205,6 @@ export async function getServerSideProps({ params, req, query }) {
  files,
  relatedDatasets,
  seqspecFiles,
- sequencingPlatforms,
  inputFileSetFor,
  controlFor,
  pageContext: { title: auxiliarySet.accession },

pages/configuration-files/[...id].js

@@ -21,7 +21,6 @@ import {
  requestDocuments,
  requestFileSets,
  requestFiles,
- requestOntologyTerms,
 } from "../../lib/common-requests";
 import { errorObjectToProps } from "../../lib/errors";
 import FetchRequest from "../../lib/fetch-request";
@@ -35,7 +34,6 @@ export default function ConfigurationFile({
  attribution,
  configurationFile,
  seqspecOf,
- sequencingPlatforms,
  documents,
  derivedFrom,
  derivedFromFileSets,
@@ -65,7 +63,6 @@ export default function ConfigurationFile({
  <SequencingFileTable
  files={seqspecOf}
  title="seqspec File Of"
- sequencingPlatforms={sequencingPlatforms}
  itemPath={configurationFile["@id"]}
  itemPathProp="seqspecs"
  isSeqspecHidden
@@ -107,8 +104,6 @@ ConfigurationFile.propTypes = {
  configurationFile: PropTypes.object.isRequired,
  // The file is a seqspec of
  seqspecOf: PropTypes.array.isRequired,
- // Sequencing platform objects associated with the files it is a seqspec of
- sequencingPlatforms: PropTypes.arrayOf(PropTypes.object).isRequired,
  // Documents set associate with this file
  documents: PropTypes.array.isRequired,
  // The file is derived from
@@ -171,14 +166,6 @@ export async function getServerSideProps({ params, req, query, resolvedUrl }) {
  request
  )
  : [];
- const sequencingPlatformPaths = seqspecOf
- .map((file) => file.sequencing_platform)
- .filter((sequencingPlatform) => sequencingPlatform);
- const uniqueSequencingPlatformPaths = [...new Set(sequencingPlatformPaths)];
- const sequencingPlatforms =
- uniqueSequencingPlatformPaths.length > 0
- ? await requestOntologyTerms(uniqueSequencingPlatformPaths, request)
- : [];
 
  const attribution = await buildAttribution(
  configurationFile,
@@ -188,7 +175,6 @@ export async function getServerSideProps({ params, req, query, resolvedUrl }) {
  props: {
  configurationFile,
  seqspecOf,
- sequencingPlatforms,
  documents,
  derivedFrom,
  derivedFromFileSets,

pages/construct-library-sets/[id].js

@@ -29,7 +29,6 @@ import buildAttribution from "../../lib/attribution";
 import {
  requestDocuments,
  requestFiles,
- requestOntologyTerms,
  requestFileSets,
  requestPublications,
  requestSeqspecFiles,
@@ -255,7 +254,6 @@ export default function ConstructLibrarySet({
  files,
  seqspecFiles,
  integratedContentFiles,
- sequencingPlatforms,
  attribution = null,
  isJson,
 }) {
@@ -312,7 +310,6 @@ export default function ConstructLibrarySet({
  files={files}
  fileSet={constructLibrarySet}
  seqspecFiles={seqspecFiles}
- sequencingPlatforms={sequencingPlatforms}
  />
  {integratedContentFiles.length > 0 && (
  <FileTable
@@ -371,8 +368,6 @@ ConstructLibrarySet.propTypes = {
  documents: PropTypes.arrayOf(PropTypes.object).isRequired,
  // Publications associated with this construct library
  publications: PropTypes.arrayOf(PropTypes.object).isRequired,
- // File sequencing platform objects
- sequencingPlatforms: PropTypes.arrayOf(PropTypes.object).isRequired,
  // Attribution for this analysis set
  attribution: PropTypes.object,
  // Is the format JSON?
@@ -407,14 +402,6 @@ export async function getServerSideProps({ params, req, query }) {
  const filePaths = constructLibrarySet.files.map((file) => file["@id"]);
  const files =
  filePaths.length > 0 ? await requestFiles(filePaths, request) : [];
- const sequencingPlatformPaths = files
- .map((file) => file.sequencing_platform)
- .filter((sequencingPlatform) => sequencingPlatform);
- const uniqueSequencingPlatformPaths = [...new Set(sequencingPlatformPaths)];
- const sequencingPlatforms =
- uniqueSequencingPlatformPaths.length > 0
- ? await requestOntologyTerms(uniqueSequencingPlatformPaths, request)
- : [];
 
  let integratedContentFiles = [];
  if (constructLibrarySet.integrated_content_files?.length > 0) {
@@ -448,7 +435,6 @@ export async function getServerSideProps({ params, req, query }) {
  files,
  seqspecFiles,
  integratedContentFiles,
- sequencingPlatforms,
  publications,
  pageContext: { title: constructLibrarySet.accession },
  attribution,

pages/measurement-sets/[id].js

@@ -34,7 +34,6 @@ import {
  requestDocuments,
  requestFiles,
  requestFileSets,
- requestOntologyTerms,
  requestPublications,
  requestSamples,
  requestSeqspecFiles,
@@ -113,7 +112,6 @@ export default function MeasurementSet({
  controlFor,
  samples,
  seqspecFiles,
- sequencingPlatforms,
  attribution = null,
  isJson,
 }) {
@@ -265,7 +263,6 @@ export default function MeasurementSet({
  files={groupedFiles.other}
  fileSet={measurementSet}
  seqspecFiles={seqspecFiles}
- sequencingPlatforms={sequencingPlatforms}
  >
  {groupedFiles.image?.length > 0 && (
  <FileTable
@@ -363,8 +360,6 @@ MeasurementSet.propTypes = {
  samples: PropTypes.arrayOf(PropTypes.object).isRequired,
  // seqspec files associated with `files`
  seqspecFiles: PropTypes.arrayOf(PropTypes.object).isRequired,
- // Sequencing platform objects associated with `files`
- sequencingPlatforms: PropTypes.arrayOf(PropTypes.object).isRequired,
  // Documents associated with this measurement set
  documents: PropTypes.arrayOf(PropTypes.object).isRequired,
  // Publications associated with this measurement set
@@ -452,16 +447,6 @@ export async function getServerSideProps({ params, req, query }) {
  const seqspecFiles =
  files.length > 0 ? await requestSeqspecFiles(files, request) : [];
 
- // Use the files to retrieve all the sequencing platform objects they link to.
- const sequencingPlatformPaths = files
- .map((file) => file.sequencing_platform)
- .filter((sequencingPlatform) => sequencingPlatform);
- const uniqueSequencingPlatformPaths = [...new Set(sequencingPlatformPaths)];
- const sequencingPlatforms =
- uniqueSequencingPlatformPaths.length > 0
- ? await requestOntologyTerms(uniqueSequencingPlatformPaths, request)
- : [];
-
  let publications = [];
  if (measurementSet.publications?.length > 0) {
  const publicationPaths = measurementSet.publications.map(
@@ -488,7 +473,6 @@ export async function getServerSideProps({ params, req, query }) {
  controlFor,
  samples,
  seqspecFiles,
- sequencingPlatforms,
  pageContext: { title: measurementSet.accession },
  attribution,
  isJson,

pages/sequence-files/[...id].js

@@ -48,7 +48,6 @@ export default function SequenceFile({
  attribution = null,
  isJson,
  seqspecs,
- sequencingPlatform = null,
 }) {
  return (
  <>
@@ -71,12 +70,12 @@ export default function SequenceFile({
  <DataAreaTitle>Sequencing Details</DataAreaTitle>
  <DataPanel>
  <DataArea>
- {sequencingPlatform && (
+ {sequenceFile.sequencing_platform && (
  <>
  <DataItemLabel>Sequencing Platform</DataItemLabel>
  <DataItemValue>
- <Link href={sequencingPlatform["@id"]}>
- {sequencingPlatform.term_name}
+ <Link href={sequenceFile.sequencing_platform["@id"]}>
+ {sequenceFile.sequencing_platform.term_name}
  </Link>
  </DataItemValue>
  </>
@@ -194,8 +193,6 @@ SequenceFile.propTypes = {
  isJson: PropTypes.bool.isRequired,
  // Linked seqspec configuration files
  seqspecs: PropTypes.arrayOf(PropTypes.object).isRequired,
- // Sequencing platform ontology term object
- sequencingPlatform: PropTypes.object,
 };
 
 export async function getServerSideProps({ params, req, query, resolvedUrl }) {
@@ -240,9 +237,6 @@ export async function getServerSideProps({ params, req, query, resolvedUrl }) {
  sequenceFile.seqspecs?.length > 0
  ? await requestSeqspecFiles([sequenceFile], request)
  : [];
- const sequencingPlatform = sequenceFile.sequencing_platform
- ? (await request.getObject(sequenceFile.sequencing_platform)).optional()
- : null;
  const attribution = await buildAttribution(
  sequenceFile,
  req.headers.cookie
@@ -259,7 +253,6 @@ export async function getServerSideProps({ params, req, query, resolvedUrl }) {
  attribution,
  isJson,
  seqspecs,
- sequencingPlatform,
  },
  };
  }