Skip to content

Commit

Permalink
Get caprieval table from report.html
Browse files Browse the repository at this point in the history
  • Loading branch information
@sverhoeven
sverhoeven committed Feb 16, 2024
1 parent 3feb3e2 commit 3f765e3
Show file tree
Hide file tree
Showing 10 changed files with 140 additions and 434 deletions.
40 changes: 8 additions & 32 deletions app/caprieval/CaprievalReport.client.tsx
View file
Original file line number Diff line number Diff line change
Expand Up @@ -3,49 +3,25 @@ import {
StructureTable,
} from "@i-vresse/haddock3-analysis-components";
import "./CaprievalReport.client.css";
import { useMemo } from "react";

import { ScatterPlots } from "./ScatterPlots";
import { useSearchParams } from "@remix-run/react";
import { BoxPlots } from "./BoxPlots";
import type {
CaprievalStructureRow,
CaprievalClusterRow,
CaprievalPlotlyProps,
} from "./caprieval.server";
import { scores2table } from "./scores2table";
import type { CaprievalData } from "./caprieval.server";

/*
Component has to be client only due
to sorting and ngl structure viewer needing browser.
*/
* Component has to be client only due
* to sorting and ngl structure viewer needing browser.
*/

export interface Scores {
structures: CaprievalStructureRow[];
clusters: CaprievalClusterRow[];
}

interface CaprievalReportProps {
scores: Scores;
prefix: string;
plotlyPlots: CaprievalPlotlyProps;
}

export const CaprievalReport = ({
scores,
prefix,
plotlyPlots,
}: CaprievalReportProps) => {
const { scatters, boxes } = plotlyPlots;
const props = useMemo(() => scores2table(scores, prefix), [scores, prefix]);
export const CaprievalReport = ({ scatters, boxes, table }: CaprievalData) => {
const [searchParams, setSearchParams] = useSearchParams();

return (
<div className="caprieval-report flex flex-col gap-4">
{"clusters" in props ? (
<ClusterTable {...props} />
{"clusters" in table ? (
<ClusterTable {...table} />
) : (
<StructureTable {...props} />
<StructureTable {...table} />
)}
<ScatterPlots
data={scatters.data}
Expand Down
203 changes: 87 additions & 116 deletions app/caprieval/caprieval.server.ts
View file
Original file line number Diff line number Diff line change
Expand Up @@ -9,12 +9,20 @@ import {
} from "~/models/job.server";
import type { PlotlyProps } from "~/components/PlotlyPlot";
import type { DirectoryItem } from "~/bartender-client/types";
import { parseTsv } from "../models/tsv";
import { hasInteractiveVersion } from "../models/module_utils";
import {
CAPRIEVAL_SCATTERPLOT_CHOICES,
CAPRIEVAL_BOXPLOT_CHOICES,
} from "./constants";
import type {
ClusterTable,
StructureTable,
} from "@i-vresse/haddock3-analysis-components";

// Package does not expose types, so extract them from the components
export type Table =
| Parameters<typeof StructureTable>[0]
| Parameters<typeof ClusterTable>[0];

export const WeightsSchema = object({
// could use minimum/maximum from catalog,
Expand Down Expand Up @@ -66,35 +74,31 @@ export async function getCaprievalModuleInfo(
return [moduleIndex, interactivness, pad];
}

export async function getScores({
jobid,
module,
bartenderToken,
moduleIndexPadding,
export async function getReportHtml(
jobid: number,
module: number,
bartenderToken: string,
moduleIndexPadding: number,
isInteractive = false,
moduleName = "caprieval",
}: {
jobid: number;
module: number;
isInteractive?: boolean;
bartenderToken: string;
moduleIndexPadding: number;
moduleName?: string;
}) {
const prefix = buildPath({
moduleIndex: module,
moduleName,
moduleName = "caprieval"
) {
const shtml = await fetchHtml(
jobid,
module,
isInteractive,
bartenderToken,
moduleIndexPadding,
});
const structures = await getStructureScores(prefix, jobid, bartenderToken);
const clusters = await getClusterScores(prefix, jobid, bartenderToken);
return { structures, clusters };
moduleName,
`report.html`
);
const table = getTableFromHtml(shtml);
return table;
}

export interface CaprievalPlotlyProps {
export interface CaprievalData {
scatters: PlotlyProps;
boxes: PlotlyProps;
table: Table;
}

export function getPlotSelection(url: string) {
Expand All @@ -114,7 +118,7 @@ export function getPlotSelection(url: string) {
};
}

export async function getCaprievalPlots({
export async function getCaprievalData({
jobid,
module,
bartenderToken,
Expand All @@ -123,6 +127,7 @@ export async function getCaprievalPlots({
boxSelection,
isInteractive = false,
moduleName = "caprieval",
structurePrefix = "files/output/module",
}: {
jobid: number;
module: number;
Expand All @@ -132,7 +137,8 @@ export async function getCaprievalPlots({
scatterSelection: string;
boxSelection: string;
moduleName?: string;
}): Promise<CaprievalPlotlyProps> {
structurePrefix?: string;
}): Promise<CaprievalData> {
const shtml = await fetchHtml(
jobid,
module,
Expand Down Expand Up @@ -161,7 +167,26 @@ export async function getCaprievalPlots({
// plot id is always 1 for non-report plot as html file contains just one plot
const bplotId = boxSelection === "report" ? 2 : 1;
const boxes = getPlotFromHtml(bhtml, bplotId);
return { scatters, boxes };

let thtml: string;
if (scatterSelection === "report") {
thtml = shtml;
} else if (boxSelection === "report") {
thtml = bhtml;
} else {
thtml = await fetchHtml(
jobid,
module,
isInteractive,
bartenderToken,
moduleIndexPadding,
moduleName,
`report.html`
);
}
const table = prefixTable(getTableFromHtml(thtml), structurePrefix);

return { scatters, boxes, table };
}

async function fetchHtml(
Expand Down Expand Up @@ -191,102 +216,26 @@ async function fetchHtml(
}

export function getPlotFromHtml(html: string, plotId = 1) {
return getDataFromHtml<PlotlyProps>(html, `data${plotId}`);
}

export function getTableFromHtml(html: string, tableId = 2) {
return getDataFromHtml<Table>(html, `datatable${tableId}`);
}

export function getDataFromHtml<T>(html: string, id: string) {
// this is very fragile, but much faster then using a HTML parser
// as order of attributes is not guaranteed
// see commit meessage of this line for benchmark
const re = new RegExp(
`<script id="data${plotId}" type="application\\/json">([\\s\\S]*?)<\\/script>`
`<script id="${id}" type="application\\/json">([\\s\\S]*?)<\\/script>`
);
const a = html.match(re);
const dataAsString = a![1].trim();
return JSON.parse(dataAsString) as PlotlyProps;
}

export interface CaprievalStructureRow {
model: string;
md5: number | "-";
caprieval_rank: number;
score: number;
irmsd: number;
fnat: number;
lrmsd: number;
ilrmsd: number;
dockq: number;
"cluster-id": number | "-";
"cluster-ranking": number | "-";
"model-cluster-ranking": number | "-";
air: number;
angles: number;
bonds: number;
bsa: number;
cdih: number;
coup: number;
dani: number;
desolv: number;
dihe: number;
elec: number;
improper: number;
rdcs: number;
rg: number;
sym: number;
total: number;
vdw: number;
vean: number;
xpcs: number;
}

async function getStructureScores(
prefix: string,
jobid: number,
bartenderToken: string
) {
const path = `${prefix}capri_ss.tsv`;
const response = await getJobfile(jobid, path, bartenderToken);
const body = await response.text();
return parseTsv<CaprievalStructureRow>(body);
}

export interface CaprievalClusterRow {
cluster_rank: number | "-";
cluster_id: number | "-";
n: number;
under_eval: number | "-";
score: number;
score_std: number;
irmsd: number;
irmsd_std: number;
fnat: number;
fnat_std: number;
lrmsd: number;
lrmsd_std: number;
ilrmsd?: number;
ilrmsd_std?: number;
dockq: number;
dockq_std: number;
air: number;
air_std: number;
bsa: number;
bsa_std: number;
desolv: number;
desolv_std: number;
elec: number;
elec_std: number;
total: number;
total_std: number;
vdw: number;
vdw_std: number;
caprieval_rank: number;
}

async function getClusterScores(
prefix: string,
jobid: number,
bartenderToken: string
) {
const path = `${prefix}capri_clt.tsv`;
const response = await getJobfile(jobid, path, bartenderToken);
const body = await response.text();
return parseTsv<CaprievalClusterRow>(body, true);
if (!a) {
throw new Error(`could not find script with id ${id}`);
}
const dataAsString = a[1].trim();
return JSON.parse(dataAsString) as T;
}

export function getLastCaprievalModule(files: DirectoryItem): [number, number] {
Expand Down Expand Up @@ -320,3 +269,25 @@ export function buildBestRankedPath(
suffix: "summary.tgz",
});
}

function prefixTable(table: Table, structurePrefix: string) {
if ("clusters" in table) {
type Cluster = Parameters<typeof ClusterTable>[0]["clusters"][0];
table.clusters = table.clusters.map((row) => {
return Object.fromEntries(
Object.entries(row).map(([key, value]) => {
if (key.startsWith("best")) {
return [key, `${structurePrefix}${value}`];
}
return [key, value];
})
) as Cluster;
});
} else {
table.structures = table.structures.map((row) => ({
...row,
model: `${structurePrefix}${row.model}`,
}));
}
return table;
}
Loading

0 comments on commit 3f765e3

Please sign in to comment.