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Pipeline update #32

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merged 14 commits into from
Jun 29, 2022
Merged

Pipeline update #32

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e0f351f
https://github.com/databio/bedstat/issues/31
xuebingjie1990 Jan 14, 2022
38fed38
update trackhub file path with endpoint url: https://github.com/datab…
xuebingjie1990 Jan 15, 2022
8987977
rename endpoint https://github.com/databio/bedhost-ui/issues/6
xuebingjie1990 Jan 19, 2022
caefad5
rename endpoint https://github.com/databio/bedhost-ui/issues/6
xuebingjie1990 Jan 19, 2022
3172655
rename endpoint https://github.com/databio/bedhost-ui/issues/6
xuebingjie1990 Jan 19, 2022
c2ccec4
fix endpoint url
xuebingjie1990 Jan 21, 2022
c89f929
hide iGD download
xuebingjie1990 May 16, 2022
a05f0ee
update dist score calculation
xuebingjie1990 Jun 9, 2022
140dddf
select and add BED files to create BED set cart
xuebingjie1990 Jun 13, 2022
5a0572c
download BED files in BED set cart
xuebingjie1990 Jun 15, 2022
900392a
download myBEDSet file paths https://github.com/databio/bedbase/issue…
xuebingjie1990 Jun 22, 2022
61b57f1
add alert after submit bedset
xuebingjie1990 Jun 23, 2022
1d46e0f
fix bug
xuebingjie1990 Jun 23, 2022
d7e8f7f
hide myBEDSet submit btn, styling
xuebingjie1990 Jun 29, 2022
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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}</>
)}
Expand Down
30 changes: 17 additions & 13 deletions src/bedSetSplash.jsx
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Original file line number Diff line number Diff line change
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={{
Expand Down
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({
Expand Down
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
Expand Down
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