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Merge pull request #32 from databio/pipeline_update
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Pipeline update
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@xuebingjie1990
xuebingjie1990 authored Jun 29, 2022
2 parents bda2478 + d7e8f7f commit 3f3282a
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Showing 16 changed files with 549 additions and 71 deletions.
2 changes: 1 addition & 1 deletion package.json
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@
"axios": "^0.21.1",
"bootstrap": "^4.6.0",
"copy-to-clipboard": "^3.3.1",
"graphql": "^15.6.1",
"graphql": "^15.7.2",
"jQuery-QueryBuilder": "^2.6.2",
"lodash": "^4.17.21",
"material-table": "1.69.1",
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8 changes: 4 additions & 4 deletions src/about.jsx
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Expand Up @@ -155,10 +155,10 @@ export default class Info extends React.Component {
fontWeight: "bold",
}}
>
Mean absolute distance from TSS
Median TSS distance
</td>
<td style={{ padding: "3px 15px", fontSize: "10pt" }}>
The average absolute distance to the Transcription
The median absolute distance to the Transcription
Start Sites (TSS)
</td>
</tr>
Expand Down Expand Up @@ -310,10 +310,10 @@ export default class Info extends React.Component {
fontWeight: "bold",
}}
>
Mean absolute distance from TSS
Median TSS distance
</td>
<td style={{ padding: "3px 15px", fontSize: "10pt" }}>
The average absolute distance to the Transcription
The average median absolute distance to the Transcription
Start Sites (TSS) of the BED set.
</td>
</tr>
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95 changes: 91 additions & 4 deletions src/bedCountsSpan.jsx
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Expand Up @@ -25,26 +25,26 @@ export default class BedCountsSpan extends React.Component {

async componentDidMount() {
let bfcount = await api
.get("/api/bed/all/data/count")
.get("/api/bed/count")
.catch(function (error) {
alert(error + "; is bedhost running at " + bedhost_api_url + "?");
});
// console.log("BED file count retrieved from the server: ", bfcount.data);
this.setState({ bed: bfcount.data });

let bscount = await api
.get("/api/bedset/all/data/count")
.get("/api/bedset/count")
.catch(function (error) {
alert(error + "; is bedhost running at " + bedhost_api_url + "?");
});
// console.log("BED set count retrieved from the server: ", bscount.data);
this.setState({ bedSet: bscount.data });

let bed = await api.get("/api/bed/all/data?ids=md5sum&limit=1").then(({ data }) => data);
let bed = await api.get("/api/bed/all/metadata?ids=md5sum&limit=1").then(({ data }) => data);
let bedurl = '/bedsplash/' + bed.data[0][0]
this.setState({ sampleBed: bedurl });

let bedset = await api.get("/api/bedset/all/data?ids=md5sum&limt=1").then(({ data }) => data)
let bedset = await api.get("/api/bedset/all/metadata?ids=md5sum&limt=1").then(({ data }) => data)
let bedseturl = '/bedsetsplash/' + bedset.data[0][0]
this.setState({ sampleBedSet: bedseturl });
this.getAPIcount()
Expand Down Expand Up @@ -85,6 +85,92 @@ export default class BedCountsSpan extends React.Component {
bedstat and bedbuncher pipeline.{" "}
</span>
<div>
<Label
style={{
marginTop: "15px",
marginBottom: "5px",
marginLeft: "15px",
fontSize: "15px",
padding: "6px 20px 6px 30px",
}}
as="a"
color="teal"
ribbon
>
Available Servers
</Label>
{
<table style={{ marginLeft: "15px" }}>
<tbody>
<tr>
<th style={{ padding: "3px 15px", fontSize: "10pt" }}>
Server Name
</th>
<th style={{ padding: "3px 15px", fontSize: "10pt" }}>
URL
</th>
<th style={{ padding: "3px 15px", fontSize: "10pt" }}>
Maintainer
</th>
<th style={{ padding: "3px 15px", fontSize: "10pt" }}>
Description
</th>
</tr>
<tr style={{ verticalAlign: "top" }}>
<td
style={{
padding: "3px 15px",
fontSize: "10pt",
fontWeight: "bold",
}}
>
Primary server
</td>
<td style={{ padding: "3px 15px", fontSize: "10pt" }}>
<a
href={"http://bedbase.org"}
className="home-link"
style={{ fontSize: "10pt" }}
>
http://bedbase.org
</a>
</td>
<td style={{ padding: "3px 15px", fontSize: "10pt" }}>
Sheffield lab
</td>
<td style={{ padding: "3px 15px", fontSize: "10pt" }}>
Main demonstration server
</td>
</tr>
<tr style={{ verticalAlign: "top" }}>
<td
style={{
padding: "3px 15px",
fontSize: "10pt",
fontWeight: "bold",
}}
>
Dev server
</td>
<td style={{ padding: "3px 15px", fontSize: "10pt" }}>
<a
href={"http://dev1.bedbase.org"}
className="home-link"
style={{ fontSize: "10pt" }}
>
http://dev1.bedbase.org
</a>
</td>
<td style={{ padding: "3px 15px", fontSize: "10pt" }}>
Sheffield lab
</td>
<td style={{ padding: "3px 15px", fontSize: "10pt" }}>
Developmental server
</td>
</tr>
</tbody>
</table>
}
<Label
style={{
marginTop: "15px",
Expand Down Expand Up @@ -203,6 +289,7 @@ export default class BedCountsSpan extends React.Component {
<span style={{ color: "lightgray" }}>Loading data </span>
</>
)}

</div>
</div>
)
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4 changes: 2 additions & 2 deletions src/bedInfo.jsx
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Expand Up @@ -129,8 +129,8 @@ export default function BedInfo(props) {
}}
>
{value.label ===
"Mean absolute distance from transcription start sites" ? (
<>Mean absolute distance from TSS</>
"Median absolute distance from transcription start sites" ? (
<>Median TSS distance</>
) : (
<>{value.label}</>
)}
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30 changes: 17 additions & 13 deletions src/bedSetSplash.jsx
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Expand Up @@ -40,10 +40,10 @@ export default class BedSetSplash extends React.Component {
async componentDidMount() {
// get table schema via fastAPI
const bed_schema = await api
.get("/api/bed/all/schema")
.get("/api/bed/schema")
.then(({ data }) => data);
const bedset_schema = await api
.get("/api/bedset/all/schema")
.get("/api/bedset/schema")
.then(({ data }) => data);

// get bedsetsplash data via Graphql
Expand All @@ -59,8 +59,10 @@ export default class BedSetSplash extends React.Component {

let bedSetFile = []
Object.entries(res).forEach(([key, value], index) => {
console.log(key)
if (bedset_schema[key.replace(/[A-Z]/g, (letter) => `_${letter.toLowerCase()}`)] &&
bedset_schema[key.replace(/[A-Z]/g, (letter) => `_${letter.toLowerCase()}`)].type === "file") {
bedset_schema[key.replace(/[A-Z]/g, (letter) => `_${letter.toLowerCase()}`)].type === "file" &&
key !== "bedsetIgdDatabasePath") {
bedSetFile.push({
id: key,
label: bedset_schema[key.replace(/[A-Z]/g, (letter) => `_${letter.toLowerCase()}`)].label.replaceAll("_", " "),
Expand Down Expand Up @@ -131,19 +133,21 @@ export default class BedSetSplash extends React.Component {
hubFilePath:
"http://genome.ucsc.edu/cgi-bin/hgTracks?db=" +
JSON.parse(res.genome).alias +
"&hubUrl=http://data.bedbase.org/outputs/bedbuncher_output/" +
"&hubUrl=" +
bedhost_api_url +
"/api/bedset/" +
this.props.match.params.bedset_md5sum +
"/bedsetHub/hub.txt",
"/track_hub",
bedSetStat: [
{
label: bed_schema["gc_content"].description,
data: [avg.gc_content.toFixed(3), sd.gc_content.toFixed(3)],
},
{
label: bed_schema["mean_absolute_tss_dist"].description,
label: bed_schema["median_tss_dist"].description,
data: [
avg.mean_absolute_tss_dist.toFixed(3),
sd.mean_absolute_tss_dist.toFixed(3),
avg.median_tss_dist.toFixed(3),
sd.median_tss_dist.toFixed(3),
],
},
{
Expand Down Expand Up @@ -332,8 +336,8 @@ export default class BedSetSplash extends React.Component {
}}
>
{value.label ===
"Mean absolute distance from transcription start sites" ? (
<>Mean absolute distance from TSS</>
"Median absolute distance from transcription start sites" ? (
<>Median TSS distance</>
) : (
<>{value.label}</>
)}
Expand Down Expand Up @@ -403,7 +407,7 @@ export default class BedSetSplash extends React.Component {
bedhost_api_url +
"/api/bedset/" +
this.props.match.params.bedset_md5sum +
"/data"
"/metadata"
}
className="home-link"
style={{
Expand Down Expand Up @@ -439,7 +443,7 @@ export default class BedSetSplash extends React.Component {
bedhost_api_url +
"/api/bedset/" +
this.props.match.params.bedset_md5sum +
"/data?ids=bedset_means&ids=bedset_standard_deviation"
"/metadata?ids=bedset_means&ids=bedset_standard_deviation"
}
className="home-link"
style={{
Expand All @@ -457,7 +461,7 @@ export default class BedSetSplash extends React.Component {
bedhost_api_url +
"/api/bedset/" +
this.props.match.params.bedset_md5sum +
"/data?ids=region_commonality"
"/metadata?ids=region_commonality"
}
className="home-link"
style={{
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2 changes: 1 addition & 1 deletion src/bedSetTable.jsx
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Expand Up @@ -115,7 +115,7 @@ export default class BedSetTable extends React.Component {
});
} else if (i !== 0) {
if (
cols[i] === "meanAbsoluteTssDist" ||
cols[i] === "medianTssDist" ||
cols[i] === "meanRegionWidth"
) {
tableColumns.push({
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2 changes: 1 addition & 1 deletion src/bedSplash.jsx
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Expand Up @@ -34,7 +34,7 @@ export default class BedSplash extends React.Component {
}

async componentDidMount() {
let schema = await api.get("/api/bed/all/schema").then(({ data }) => data);
let schema = await api.get("/api/bed/schema").then(({ data }) => data);
this.setState({ bedSchema: schema });

await api
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