Release v0.10.4

bedhost/_version.py

@@ -1 +1 @@
-__version__ = "0.10.3"
+__version__ = "0.10.4"

bedhost/const.py

@@ -9,5 +9,7 @@
 EXAMPLE_BED = "bbad85f21962bb8d972444f7f9a3a932"
 EXAMPLE_BEDSET = "gse218680"
 
-# how often to save usage data (in days)
-USAGE_SAVE_DAYS = 7
+# how often to save usage data (in hours)
+USAGE_SAVE_HOURS = 1
+# For how many days record usage data (every month this will be reset)
+USAGE_RECORD_DAYS = 30

bedhost/main.py

@@ -18,7 +18,7 @@
 from . import _LOGGER
 from ._version import __version__ as bedhost_version
 from .cli import build_parser
-from .const import PKG_NAME, STATIC_PATH, USAGE_SAVE_DAYS
+from .const import PKG_NAME, STATIC_PATH, USAGE_SAVE_HOURS, USAGE_RECORD_DAYS
 from .helpers import attach_routers, configure, drs_response, init_model_usage
 from apscheduler.schedulers.background import BackgroundScheduler
 
@@ -173,7 +173,9 @@ def upload_usage():
             """
 
             print("Running uploading of the usage")
-            usage_data.date_to = datetime.datetime.now()
+            usage_data.date_to = datetime.datetime.now() + datetime.timedelta(
+                days=USAGE_RECORD_DAYS
+            )
             bbagent.add_usage(usage_data)
 
             usage_data.bed_meta = {}
@@ -184,7 +186,7 @@ def upload_usage():
             usage_data.date_from = datetime.datetime.now()
             usage_data.date_to = None
 
-        scheduler.add_job(upload_usage, "interval", days=USAGE_SAVE_DAYS)
+        scheduler.add_job(upload_usage, "interval", hours=USAGE_SAVE_HOURS)
         scheduler.start()
 
         attach_routers(app)

bedhost/routers/base_api.py

@@ -7,7 +7,7 @@
 from platform import python_version
 
 from bbconf import __version__ as bbconf_version
-from bbconf.models.base_models import StatsReturn, FileStats
+from bbconf.models.base_models import StatsReturn, FileStats, UsageStats
 from fastapi import APIRouter, Request
 from geniml import __version__ as geniml_version
 
@@ -46,11 +46,25 @@ async def get_bedbase_db_stats():
     summary="Get detailed statistics for BEDbase platform, including number of files for each genome",
     response_model=FileStats,
 )
-async def get_detailed_stats():
+async def get_detailed_stats(
+    concise: bool = False,
+):
     """
     Returns detailed statistics
     """
-    return bbagent.get_detailed_stats()
+    return bbagent.get_detailed_stats(concise=concise)
+
+
+@router.get(
+    "/detailed-usage",
+    summary="Get detailed usage statistics for BEDbase platform",
+    response_model=UsageStats,
+)
+async def get_detailed_usage():
+    """
+    Returns detailed usage statistics
+    """
+    return bbagent.get_detailed_usage()
 
 
 @router.get(

requirements/requirements-all.txt

@@ -1,5 +1,5 @@
 # bbconf @ git+https://github.com/databio/bbconf.git@dev#egg=bbconf
-bbconf>=0.11.2
+bbconf>=0.11.3
 fastapi>=0.103.0
 logmuse>=0.2.7
 markdown

ui/bedbase-types.d.ts

@@ -704,7 +704,7 @@ export interface paths {
          * Create Bedset
          * @description Create a new bedset by providing registry path to the PEPhub project
          */
-        post: operations["create_bedset_v1_bedset_create__post"];
+        post: operations["create_bedset_v1_bedset_create_post"];
         delete?: never;
         options?: never;
         head?: never;
@@ -939,6 +939,11 @@ export interface components {
              */
             license_id: string | null;
             annotation?: components["schemas"]["StandardMeta"] | null;
+            /**
+             * Processed
+             * @default true
+             */
+            processed: boolean | null;
             stats?: components["schemas"]["BedStatsModel"] | null;
             plots?: components["schemas"]["BedPlots"] | null;
             files?: components["schemas"]["BedFiles"] | null;
@@ -1000,6 +1005,11 @@ export interface components {
              */
             license_id: string | null;
             annotation?: components["schemas"]["StandardMeta"] | null;
+            /**
+             * Processed
+             * @default true
+             */
+            processed: boolean | null;
         };
         /** BedPEPHub */
         BedPEPHub: {
@@ -1034,11 +1044,11 @@ export interface components {
              */
             cell_line: string;
             /**
-             * Exp Protocol
+             * Assay
              * @description Experimental protocol (e.g. ChIP-seq)
              * @default
              */
-            exp_protocol: string;
+            assay: string;
             /**
              * Library Source
              * @description Library source (e.g. genomic, transcriptomic)
@@ -1129,11 +1139,11 @@ export interface components {
              */
             cell_line: string;
             /**
-             * Exp Protocol
+             * Assay
              * @description Experimental protocol (e.g. ChIP-seq)
              * @default
              */
-            exp_protocol: string;
+            assay: string;
             /**
              * Library Source
              * @description Library source (e.g. genomic, transcriptomic)
@@ -1392,18 +1402,22 @@ export interface components {
         };
         /** FileStats */
         FileStats: {
-            /** File Type */
-            file_type: {
+            /** Bed Compliance */
+            bed_compliance: {
                 [key: string]: number;
             };
-            /** File Format */
-            file_format: {
+            /** Data Format */
+            data_format: {
                 [key: string]: number;
             };
             /** File Genome */
             file_genome: {
                 [key: string]: number;
             };
+            /** File Organism */
+            file_organism: {
+                [key: string]: number;
+            };
         };
         /** HTTPValidationError */
         HTTPValidationError: {
@@ -1537,7 +1551,7 @@ export interface components {
              */
             library_source: string;
             /**
-             * Exp Protocol
+             * Assay
              * @description Experimental protocol (e.g. ChIP-seq)
              * @default
              */
@@ -1565,13 +1579,13 @@ export interface components {
              * @description Global sample identifier. e.g. GSM000
              * @default
              */
-            global_sample_id: string[];
+            global_sample_id: string[] | null;
             /**
              * Global Experiment Id
              * @description Global experiment identifier. e.g. GSE000
              * @default
              */
-            global_experiment_id: string[];
+            global_experiment_id: string[] | null;
             /**
              * Original File Name
              * @description Original file name
@@ -1850,7 +1864,7 @@ export interface operations {
                 /** @description filter by genome of the bed file. e.g. 'hg38' */
                 genome?: string;
                 /** @description filter by bed type. e.g. 'bed6+4' */
-                bed_type?: string;
+                bed_compliance?: string;
             };
             header?: never;
             path?: never;
@@ -2682,7 +2696,7 @@ export interface operations {
             };
         };
     };
-    create_bedset_v1_bedset_create__post: {
+    create_bedset_v1_bedset_create_post: {
         parameters: {
             query?: never;
             header?: never;

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

@@ -4,7 +4,7 @@ import { Fragment, useState } from 'react';
 import { components } from '../../../bedbase-types';
 import { useCopyToClipboard } from '@uidotdev/usehooks';
 import { bytesToSize, formatDateTime } from '../../utils';
-import { Dropdown, OverlayTrigger } from 'react-bootstrap';
+import { Dropdown, OverlayTrigger, Tooltip } from 'react-bootstrap';
 import { RefGenomeModal } from './refgenome-modal';
 
 const API_BASE = import.meta.env.VITE_API_BASE || '';
@@ -51,14 +51,34 @@ export const BedSplashHeader = (props: Props) => {
             </button>
           </h4>
         </div>
+        {!metadata?.processed && (
+          <p
+            className="text-warning text-nowrap me-1 btn btn-outline btn-sm transparent-btn"
+          >
+            <OverlayTrigger
+              placement="top"
+              overlay={
+                <Tooltip id="tooltip-top">
+                  This file has not been processed by the BedBoss pipeline yet.
+                </Tooltip>
+              }
+            >
+    <span>
+      <i className="bi bi-exclamation-triangle-fill me-1"></i>
+      Not Processed
+    </span>
+            </OverlayTrigger>
+          </p>
+        )}
+
         <div className="d-flex flex-col align-items-center gap-1 flex-shrink-0">
           <a href={`${API_BASE}/bed/${record_identifier}/metadata?full=true`}>
             <button className="btn btn-outline-primary btn-sm">
-              <i className="bi bi-info-circle me-1"/>
+              <i className="bi bi-info-circle me-1" />
               API
             </button>
           </a>
-          {!addedToCart && cart.includes(record_identifier || '') ? (
+          {!addedToCart && cart[record_identifier || ''] ? (
             <button
               className="btn btn-outline-danger btn-sm"
               onClick={() => {
@@ -79,21 +99,34 @@ export const BedSplashHeader = (props: Props) => {
               disabled={addedToCart}
               className="btn btn-primary btn-sm"
               onClick={() => {
-                if (record_identifier == undefined) {
+                if (record_identifier == undefined || metadata === undefined) {
                   toast.error(
                     'This bed file does not have a record identifier... please contact the administrator to fix this issue.',
                   );
                   return;
                 }
-                addBedToCart(record_identifier);
+
+                // Create the bed item object with all required fields
+                const bedItem = {
+                  id: record_identifier,
+                  name: metadata.name || 'No name',
+                  genome: metadata.genome_alias || 'N/A',
+                  tissue: metadata.annotation?.tissue || 'N/A',
+                  cell_line: metadata.annotation?.cell_line || 'N/A',
+                  cell_type: metadata.annotation?.cell_type || 'N/A',
+                  description: metadata.description || '',
+                  assay: metadata.annotation?.assay || 'N/A',
+                };
+
+                addBedToCart(bedItem);
                 setAddedToCart(true);
                 setTimeout(() => {
                   setAddedToCart(false);
                 }, 500);
               }}
             >
               <i className="bi bi-cart-fill me-1" />
-              {addedToCart ? 'Added to cart!' : 'Add to cart'}
+              {addedToCart ? 'Adding...' : 'Add to cart'}
             </button>
           )}
           <Dropdown>
@@ -104,11 +137,11 @@ export const BedSplashHeader = (props: Props) => {
             {
               // If there are no files to download, disable the dropdown
               noFilesToDownload ? (
-                <Dropdown.Menu className='border border-light-subtle shadow-sm'>
+                <Dropdown.Menu className="border border-light-subtle shadow-sm">
                   <Dropdown.Item disabled>There are no files to download</Dropdown.Item>
                 </Dropdown.Menu>
               ) : (
-                <Dropdown.Menu className='border border-light-subtle shadow-sm'>
+                <Dropdown.Menu className="border border-light-subtle shadow-sm">
                   {metadata.files?.bed_file && (
                     <Fragment>
                       {(metadata.files?.bed_file?.access_methods || []).map((method) => {
@@ -149,7 +182,8 @@ export const BedSplashHeader = (props: Props) => {
         <h5 className="fw-semibold mb-1">{metadata.name}</h5>
         <p className="text-body-secondary fst-italic">{metadata?.description || 'No description available'}</p>
       </div>
-      <div className="d-flex flex-column flex-xl-row align-items-start align-items-xl-end justify-content-xl-between mt-2 overflow-x-auto">
+      <div
+        className="d-flex flex-column flex-xl-row align-items-start align-items-xl-end justify-content-xl-between mt-2 overflow-x-auto">
         <div className="d-md-flex flex-row gap-1 text-lg mb-2 mb-xl-0">
           <div className="d-flex flex-row">
             <div className="mb-0">
@@ -164,8 +198,10 @@ export const BedSplashHeader = (props: Props) => {
               >
                 {metadata?.genome_digest ? (
                   <>
-                    <a href={`http://refgenomes.databio.org/v3/genomes/splash/${metadata.genome_digest}`} target="_blank">
-                      <div className={genomeStats?.compared_genome ? "badge bg-primary rounded-end-0" : "badge bg-primary"}>
+                    <a href={`http://refgenomes.databio.org/v3/genomes/splash/${metadata.genome_digest}`}
+                       target="_blank">
+                      <div
+                        className={genomeStats?.compared_genome ? 'badge bg-primary rounded-end-0' : 'badge bg-primary'}>
                         <i className="bi bi-database-fill me-2" />
                         {metadata.genome_alias || 'No assembly available'}
                       </div>
@@ -190,7 +226,7 @@ export const BedSplashHeader = (props: Props) => {
                     </div>
                   }
                 >
-                  <div 
+                  <div
                     className="badge bg-primary border-start border-light rounded-start-0"
                     role="button"
                     onClick={() => {
@@ -285,7 +321,8 @@ export const BedSplashHeader = (props: Props) => {
             </div>
           )}
         </div>
-        <div className="d-flex flex-column flex-md-row justify-content-xl-between align-items-start align-items-xl-end text-sm">
+        <div
+          className="d-flex flex-column flex-md-row justify-content-xl-between align-items-start align-items-xl-end text-sm">
           <div className="d-flex flex-row text-muted">
             <i className="bi bi-calendar4-event me-1" />
             <p className="mb-0">