Added get bedset pep and genome browser to ui and api

bedhost/routers/bedset_api.py

@@ -12,6 +12,7 @@
 
 from ..main import bbagent
 from ..const import PKG_NAME, EXAMPLE_BEDSET
+from ..utils import zip_pep
 
 
 router = APIRouter(prefix="/v1/bedset", tags=["bedset"])
@@ -63,6 +64,20 @@ async def get_bedset_metadata(
         raise HTTPException(status_code=404, detail="No records found")
 
 
+@router.get(
+    "/{bedset_id}/pep",
+    summary="Download PEP project for a single BEDset record",
+    description=f"Example\n bed_id: {EXAMPLE_BEDSET}",
+)
+async def get_bedset_pep(
+    bedset_id: str,
+):
+    try:
+        return zip_pep(bbagent.bedset.get_bedset_pep(bedset_id))
+    except BedSetNotFoundError as _:
+        raise HTTPException(status_code=404, detail="No records found")
+
+
 @router.get(
     "/{bedset_id}/metadata/plots",
     response_model=BedSetPlots,

bedhost/utils.py

@@ -0,0 +1,80 @@
+import io
+import zipfile
+from datetime import date
+from typing import Any, Dict
+
+import pandas as pd
+import yaml
+from fastapi import Response
+from peppy.const import (
+    CFG_SAMPLE_TABLE_KEY,
+    CFG_SUBSAMPLE_TABLE_KEY,
+    CONFIG_KEY,
+    NAME_KEY,
+    SAMPLE_RAW_DICT_KEY,
+    SUBSAMPLE_RAW_LIST_KEY,
+)
+
+
+def zip_conv_result(conv_result: dict, filename: str = "project.zip") -> Response:
+    """
+    Given a dictionary of converted results, zip them up and return a response
+
+    ## Copied from pephub/helpers.py
+
+    :param conv_result: dictionary of converted results
+    :param filename: name of the zip
+    return Response: response object
+    """
+    mf = io.BytesIO()
+
+    with zipfile.ZipFile(mf, mode="w", compression=zipfile.ZIP_DEFLATED) as zf:
+        for name, res in conv_result.items():
+            # Add file, at correct path
+            zf.writestr(name, str.encode(res))
+
+    # Grab ZIP file from in-memory, make response with correct MIME-type
+    resp = Response(
+        mf.getvalue(),
+        media_type="application/x-zip-compressed",
+        headers={"Content-Disposition": f"attachment;filename={filename}"},
+    )
+
+    return resp
+
+
+def zip_pep(project: Dict[str, Any]) -> Response:
+    """
+    Zip a project up to download
+    ## Copied from pephub/helpers.py
+
+    :param project: peppy project to zip
+    """
+
+    content_to_zip = {}
+    config = project[CONFIG_KEY]
+    project_name = config[NAME_KEY]
+
+    if project[SAMPLE_RAW_DICT_KEY] is not None:
+        config[CFG_SAMPLE_TABLE_KEY] = ["sample_table.csv"]
+        content_to_zip["sample_table.csv"] = pd.DataFrame(
+            project[SAMPLE_RAW_DICT_KEY]
+        ).to_csv(index=False)
+
+    if project[SUBSAMPLE_RAW_LIST_KEY] is not None:
+        if not isinstance(project[SUBSAMPLE_RAW_LIST_KEY], list):
+            config[CFG_SUBSAMPLE_TABLE_KEY] = ["subsample_table1.csv"]
+            content_to_zip["subsample_table1.csv"] = pd.DataFrame(
+                project[SUBSAMPLE_RAW_LIST_KEY]
+            ).to_csv(index=False)
+        else:
+            config[CFG_SUBSAMPLE_TABLE_KEY] = []
+            for number, file in enumerate(project[SUBSAMPLE_RAW_LIST_KEY]):
+                file_name = f"subsample_table{number + 1}.csv"
+                config[CFG_SUBSAMPLE_TABLE_KEY].append(file_name)
+                content_to_zip[file_name] = pd.DataFrame(file).to_csv(index=False)
+
+    content_to_zip[f"{project_name}_config.yaml"] = yaml.dump(config, indent=4)
+
+    zip_filename = project_name or f"downloaded_pep_{date.today()}"
+    return zip_conv_result(content_to_zip, filename=zip_filename)

ui/src/components/bedset-splash-components/header.tsx

@@ -43,6 +43,23 @@ export const BedsetSplashHeader = (props: Props) => {
           <p className="mb-0">{metadata?.description || 'No description available'}</p>
         </div>
         <div className="d-flex flex-row align-items-center gap-1">
+
+          {/*  TODO: change hg38 on correct genome */}
+          {/*<a href={`https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hubUrl=https://api-dev.bedbase.org/v1/bedset/${metadata.id}/track_hub`}>*/}
+          <a href={`https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hubUrl=${API_BASE}/bedset/${metadata.id}/track_hub`}>
+            <button className="btn btn-outline-primary btn-sm">
+              <i className="bi bi-distribute-vertical me-1" />
+              Genome Browser
+            </button>
+          </a>
+
+          <a href={`${API_BASE}/bedset/${metadata.id}/pep`}>
+            <button className="btn btn-outline-primary btn-sm">
+              <i className="bi bi-download me-1" />
+              Download PEP
+            </button>
+          </a>
+
           <a href={`${API_BASE}/bedset/${metadata.id}/metadata?full=true`}>
             <button className="btn btn-outline-primary btn-sm">
               <i className="bi bi-info-circle me-1" />
@@ -65,12 +82,12 @@ export const BedsetSplashHeader = (props: Props) => {
                   metadata.bed_ids?.length === 0
                     ? undefined
                     : () => {
-                        addMultipleBedsToCart(metadata.bed_ids || []);
-                        setAddedToCart(true);
-                        setTimeout(() => {
-                          setAddedToCart(false);
-                        }, 500);
-                      }
+                      addMultipleBedsToCart(metadata.bed_ids || []);
+                      setAddedToCart(true);
+                      setTimeout(() => {
+                        setAddedToCart(false);
+                      }, 500);
+                    }
                 }
                 disabled={metadata.bed_ids?.length === 0 || addedToCart}
                 className="btn btn-primary btn-sm"