@weng-lab/genomebrowser-ui 0.1.9 → 0.1.10

package/dist/lib.d.ts

@@ -1,8 +1,6 @@
 import { default as TrackSelect, TrackSelectProps } from './TrackSelect/TrackSelect';
 import { createSelectionStore, SelectionStoreInstance } from './TrackSelect/store.ts';
-import { rowById } from './TrackSelect/consts.ts';
 import { RowInfo } from './TrackSelect/types.ts';
 export { TrackSelect, TrackSelectProps };
 export { createSelectionStore, SelectionStoreInstance };
-export { rowById };
 export { RowInfo };

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@weng-lab/genomebrowser-ui",
   "private": false,
-  "version": "0.1.9",
+  "version": "0.1.10",
   "license": "MIT",
   "type": "module",
   "publishConfig": {
@@ -22,7 +22,7 @@
     "@mui/x-data-grid-premium": "^8.19.0",
     "react": "^19.0.0",
     "react-dom": "^19.0.0",
-    "@weng-lab/genomebrowser": "1.7.2-beta.4"
+    "@weng-lab/genomebrowser": "1.7.3"
   },
   "devDependencies": {
     "@eslint/js": "^9.34.0",

package/src/TrackSelect/Data/formatBiosamples.go

@@ -0,0 +1,254 @@
+package main
+
+import (
+	"encoding/json"
+	"fmt"
+	"os"
+	"path"
+	"strings"
+)
+
+type RNASeqTrack struct {
+	ID                        string `json:"id"`
+	Title                     string `json:"title"`
+	URL                       string `json:"url"`
+	RNASeqExperimentAccession string `json:"rnaseq_experiment_accession"`
+	RNASeqFileAccession       string `json:"rnaseq_file_accession"`
+}
+
+type OldBiosample struct {
+	Name                       string        `json:"name"`
+	Ontology                   string        `json:"ontology"`
+	LifeStage                  string        `json:"lifeStage"`
+	SampleType                 string        `json:"sampleType"`
+	DisplayName                string        `json:"displayname"`
+	DNaseExperimentAccession   *string       `json:"dnase_experiment_accession"`
+	H3K4Me3ExperimentAccession *string       `json:"h3k4me3_experiment_accession"`
+	H3K27AcExperimentAccession *string       `json:"h3k27ac_experiment_accession"`
+	CTCFExperimentAccession    *string       `json:"ctcf_experiment_accession"`
+	ATACExperimentAccession    *string       `json:"atac_experiment_accession"`
+	DNaseFileAccession         *string       `json:"dnase_file_accession"`
+	H3K4Me3FileAccession       *string       `json:"h3k4me3_file_accession"`
+	H3K27AcFileAccession       *string       `json:"h3k27ac_file_accession"`
+	CTCFFileAccession          *string       `json:"ctcf_file_accession"`
+	ATACFileAccession          *string       `json:"atac_file_accession"`
+	DNaseSignalURL             string        `json:"dnase_signal_url,omitempty"`
+	H3K4Me3SignalURL           string        `json:"h3k4me3_signal_url,omitempty"`
+	H3K27AcSignalURL           string        `json:"h3k27ac_signal_url,omitempty"`
+	CTCFSignalURL              string        `json:"ctcf_signal_url,omitempty"`
+	ATACSignalURL              string        `json:"atac_signal_url,omitempty"`
+	ChromHMM                   string        `json:"chromhmm,omitempty"`
+	ChromHMMURL                string        `json:"chromhmm_url,omitempty"`
+	RNASeqTracks               []RNASeqTrack `json:"rna_seq_tracks"`
+	BigBedURL                  string        `json:"bigbedurl,omitempty"`
+}
+
+type Assay struct {
+	ID                  string `json:"id"`
+	Assay               string `json:"assay"`
+	URL                 string `json:"url"`
+	ExperimentAccession string `json:"experimentAccession"`
+	FileAccession       string `json:"fileAccession"`
+}
+
+type NewBiosample struct {
+	Name        string  `json:"name"`
+	Ontology    string  `json:"ontology"`
+	LifeStage   string  `json:"lifeStage"`
+	SampleType  string  `json:"sampleType"`
+	DisplayName string  `json:"displayname"`
+	Assays      []Assay `json:"assays"`
+}
+
+func main() {
+	if len(os.Args) < 3 {
+		fmt.Println("Usage: go run format.go <input.json> <output.json>")
+		os.Exit(1)
+	}
+
+	inputFile := os.Args[1]
+	outputFile := os.Args[2]
+
+	data, err := os.ReadFile(inputFile)
+	if err != nil {
+		fmt.Printf("Error reading input file: %v\n", err)
+		os.Exit(1)
+	}
+
+	var inputWrapper struct {
+		Data struct {
+			CCREBiosampleQuery struct {
+				Biosamples []OldBiosample `json:"biosamples"`
+			} `json:"ccREBiosampleQuery"`
+		} `json:"data"`
+	}
+	if err := json.Unmarshal(data, &inputWrapper); err != nil {
+		fmt.Printf("Error parsing JSON: %v\n", err)
+		os.Exit(1)
+	}
+	oldSamples := inputWrapper.Data.CCREBiosampleQuery.Biosamples
+
+	var newSamples []NewBiosample
+	for _, old := range oldSamples {
+		newSample := NewBiosample{
+			Name:        old.Name,
+			Ontology:    old.Ontology,
+			LifeStage:   old.LifeStage,
+			SampleType:  old.SampleType,
+			DisplayName: old.DisplayName,
+			Assays:      []Assay{},
+		}
+
+		// Add DNase assay if present
+		if old.DNaseFileAccession != nil {
+			url := old.DNaseSignalURL
+			if url == "" {
+				url = "https://downloads.wenglab.org/Registry-V4/" + *old.DNaseFileAccession + ".bigWig"
+			}
+			newSample.Assays = append(newSample.Assays, Assay{
+				ID:                  "dnase-" + *old.DNaseFileAccession,
+				Assay:               "dnase",
+				URL:                 url,
+				ExperimentAccession: ptrToString(old.DNaseExperimentAccession),
+				FileAccession:       *old.DNaseFileAccession,
+			})
+		}
+
+		// Add H3K4me3 assay if present
+		if old.H3K4Me3FileAccession != nil {
+			url := old.H3K4Me3SignalURL
+			if url == "" {
+				url = "https://downloads.wenglab.org/Registry-V4/" + *old.H3K4Me3FileAccession + ".bigWig"
+			}
+			newSample.Assays = append(newSample.Assays, Assay{
+				ID:                  "h3k4me3-" + *old.H3K4Me3FileAccession,
+				Assay:               "h3k4me3",
+				URL:                 url,
+				ExperimentAccession: ptrToString(old.H3K4Me3ExperimentAccession),
+				FileAccession:       *old.H3K4Me3FileAccession,
+			})
+		}
+
+		// Add H3K27ac assay if present
+		if old.H3K27AcFileAccession != nil {
+			url := old.H3K27AcSignalURL
+			if url == "" {
+				url = "https://downloads.wenglab.org/Registry-V4/" + *old.H3K27AcFileAccession + ".bigWig"
+			}
+			newSample.Assays = append(newSample.Assays, Assay{
+				ID:                  "h3k27ac-" + *old.H3K27AcFileAccession,
+				Assay:               "h3k27ac",
+				URL:                 url,
+				ExperimentAccession: ptrToString(old.H3K27AcExperimentAccession),
+				FileAccession:       *old.H3K27AcFileAccession,
+			})
+		}
+
+		// Add CTCF assay if present
+		if old.CTCFFileAccession != nil {
+			url := old.CTCFSignalURL
+			if url == "" {
+				url = "https://downloads.wenglab.org/Registry-V4/" + *old.CTCFFileAccession + ".bigWig"
+			}
+			newSample.Assays = append(newSample.Assays, Assay{
+				ID:                  "ctcf-" + *old.CTCFFileAccession,
+				Assay:               "ctcf",
+				URL:                 url,
+				ExperimentAccession: ptrToString(old.CTCFExperimentAccession),
+				FileAccession:       *old.CTCFFileAccession,
+			})
+		}
+
+		// Add ATAC assay if present
+		if old.ATACFileAccession != nil {
+			url := old.ATACSignalURL
+			if url == "" {
+				url = "https://downloads.wenglab.org/Registry-V4/" + *old.ATACFileAccession + ".bigWig"
+			}
+			newSample.Assays = append(newSample.Assays, Assay{
+				ID:                  "atac-" + *old.ATACFileAccession,
+				Assay:               "atac",
+				URL:                 url,
+				ExperimentAccession: ptrToString(old.ATACExperimentAccession),
+				FileAccession:       *old.ATACFileAccession,
+			})
+		}
+
+		// Add ChromHMM assay if present
+		if old.ChromHMMURL != "" {
+			chromhmmAccession := extractAccessionFromURL(old.ChromHMMURL)
+			newSample.Assays = append(newSample.Assays, Assay{
+				ID:            "chromhmm-" + chromhmmAccession,
+				Assay:         "chromhmm",
+				URL:           old.ChromHMMURL,
+				FileAccession: chromhmmAccession,
+			})
+		}
+
+		// Add RNA-seq tracks
+		for _, rna := range old.RNASeqTracks {
+			url := rna.URL
+			if url == "" {
+				url = "https://downloads.wenglab.org/Registry-V4/" + rna.RNASeqFileAccession + ".bigWig"
+			}
+			newSample.Assays = append(newSample.Assays, Assay{
+				ID:                  "rnaseq-" + rna.RNASeqFileAccession,
+				Assay:               "rnaseq",
+				URL:                 url,
+				ExperimentAccession: rna.RNASeqExperimentAccession,
+				FileAccession:       rna.RNASeqFileAccession,
+			})
+		}
+
+		// Add cCRE bigBed as an assay
+		if old.BigBedURL != "" {
+			ccreAccession := extractAccessionFromURL(old.BigBedURL)
+			newSample.Assays = append(newSample.Assays, Assay{
+				ID:            "ccre-" + ccreAccession,
+				Assay:         "ccre",
+				URL:           old.BigBedURL,
+				FileAccession: ccreAccession,
+			})
+		}
+
+		newSamples = append(newSamples, newSample)
+	}
+
+	// Wrap in object with "tracks" key to match expected format
+	wrapper := struct {
+		Tracks []NewBiosample `json:"tracks"`
+	}{
+		Tracks: newSamples,
+	}
+
+	output, err := json.MarshalIndent(wrapper, "", "  ")
+	if err != nil {
+		fmt.Printf("Error marshaling JSON: %v\n", err)
+		os.Exit(1)
+	}
+
+	if err := os.WriteFile(outputFile, output, 0644); err != nil {
+		fmt.Printf("Error writing output file: %v\n", err)
+		os.Exit(1)
+	}
+
+	fmt.Printf("Successfully converted %d biosamples to %s\n", len(newSamples), outputFile)
+}
+
+func ptrToString(s *string) string {
+	if s == nil {
+		return ""
+	}
+	return *s
+}
+
+// extractAccessionFromURL extracts the file accession from a URL
+// e.g., "https://downloads.wenglab.org/Registry-V4/ENCFF170YYM.bigBed" -> "ENCFF170YYM"
+// e.g., "https://downloads.wenglab.org/Registry-V4/ENCFF606INL_ENCFF501ILD.bigBed" -> "ENCFF606INL_ENCFF501ILD"
+func extractAccessionFromURL(url string) string {
+	// Get the filename from the URL
+	filename := path.Base(url)
+	// Remove the extension
+	ext := path.Ext(filename)
+	return strings.TrimSuffix(filename, ext)
+}