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Jbrowse2 service #258

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aa022a7
initial draft
steve-fischer-200 Feb 21, 2025
831ab21
wip
steve-fischer-200 Feb 22, 2025
b107127
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steve-fischer-200 Feb 22, 2025
077e2ac
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steve-fischer-200 Feb 22, 2025
f19b132
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steve-fischer-200 Feb 24, 2025
161b896
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steve-fischer-200 Feb 24, 2025
ce925ca
Merge branch 'master' into jbrowse2-service
ryanrdoherty Feb 25, 2025
e676d61
wip
steve-fischer-200 Feb 26, 2025
fd08416
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steve-fischer-200 Feb 26, 2025
faa7bba
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steve-fischer-200 Feb 27, 2025
775cdb7
Merge branch 'master' into jbrowse2-service
steve-fischer-200 Feb 27, 2025
2f19f58
wip
steve-fischer-200 Feb 27, 2025
25a2dab
correct UD dir paths
steve-fischer-200 Mar 6, 2025
c43a334
debug
steve-fischer-200 Mar 6, 2025
1bdb8b1
Merge branch 'master' into jbrowse2-service
ryanrdoherty Jun 26, 2025
f4270d5
draft of Jbrowse2ConfigReporter
steve-fischer-200 Sep 18, 2025
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193 changes: 193 additions & 0 deletions Model/src/main/java/org/apidb/apicommon/model/report/Jbrowse2ConfigReporter.java
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Original file line number Diff line number Diff line change
@@ -0,0 +1,193 @@
package org.gusdb.wdk.model.report.reporter;

import java.io.IOException;
import java.io.OutputStream;
import java.io.OutputStreamWriter;
import java.sql.SQLException;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;

import org.apache.log4j.Logger;
import org.gusdb.wdk.model.WdkModelException;
import org.gusdb.wdk.model.WdkUserException;
import org.gusdb.wdk.model.answer.AnswerValue;
import org.gusdb.wdk.model.answer.stream.RecordStream;
import org.gusdb.wdk.model.answer.stream.RecordStreamFactory;
import org.gusdb.wdk.model.record.RecordInstance;
import org.gusdb.wdk.model.record.TableField;
import org.gusdb.wdk.model.record.TableValue;
import org.gusdb.wdk.model.record.TableValueRow;
import org.gusdb.wdk.model.record.attribute.AttributeField;
import org.gusdb.wdk.model.record.attribute.AttributeValue;
import org.gusdb.wdk.model.report.AbstractReporter;
import org.gusdb.wdk.model.report.PropertiesProvider;
import org.gusdb.wdk.model.report.Reporter;
import org.gusdb.wdk.model.report.ReporterConfigException;
import org.gusdb.wdk.model.report.util.TableCache;
import org.json.JSONException;
import org.json.JSONObject;
import org.json.JSONWriter;

/**
* @author Steve
*
*/
public class Jbrowse2ConfigReporter extends AbstractReporter {

private static final Logger LOG = Logger.getLogger(Jbrowse2ConfigReporter.class);

private TableCache _tableCache;

@Override
public Jbrowse2ConfigReporter setProperties(PropertiesProvider reporterRef) throws WdkModelException {
super.setProperties(reporterRef);
String cacheTableName = TableCache.getCacheTableName(_properties);
if (cacheTableName != null) {
_tableCache = new TableCache(getQuestion().getRecordClass(), _wdkModel.getAppDb(), cacheTableName);
}
return this;
}

@Override
public Reporter configure(JSONObject config) throws ReporterConfigException, WdkModelException {
return null;
}

@Override
public String getHttpContentType() {
return "application/json";
}

@Override
public String getDownloadFileName() {
return getQuestion().getName() + "_detail.json";
}

@Override
public void write(OutputStream out) throws WdkModelException {

Map<String, AttributeField> attrFieldMap = getQuestion().getAttributeFieldMap();
if (!attrFieldMap.containsKey("short_display_name")) throw new WdkModelException();
AttributeField af = attrFieldMap.get("short_display_name");
Set<AttributeField> afs = new HashSet<>();
afs.add(af);

Map<String, TableField> tblFieldMap = getQuestion().;
if (!tblFieldMap.containsKey("short_display_name")) throw new WdkModelException();
TableField tf = tblFieldMap.get("short_display_name");
Set<AttributeField> afs = new HashSet<>();
afs.add(af);

// TableField udDependenciesTable = (TableField) fieldMap.get("UdDependencies");

try (RecordStream records = RecordStreamFactory.getRecordStream(_baseAnswer, afs, tables)) {
OutputStreamWriter streamWriter = new OutputStreamWriter(out);
JSONWriter writer = new JSONWriter(streamWriter);

AnswerValue av = _baseAnswer;
writer.object().key("response").object().key("recordset").object().key("id").value(
av.getChecksum()).key("count").value(this.getResultSize()).key("type").value(
av.getAnswerSpec().getQuestion().getRecordClass().getDisplayName()).key("records").array();

if (_tableCache != null) {
_tableCache.open();
}

// get page based answers with a maximum size (defined in PageAnswerIterator)
int recordCount = 0;
for (RecordInstance record : records) {

// get VDI ID
String datasetId = record.getPrimaryKey().getValues().get("dataset_id");
String suffix = "EDAUD_";
if (!datasetId.startsWith(suffix)) throw new WdkUserException();
String vdiId = datasetId.substring(suffix.length());

// get display name
String shortDisplayName = record.getAttributeValue("short_display_name").getValue();

// get organism name for files
TableValue tv = record.getTableValue("UdDependencies");
if (tv.getNumRows() != 1) throw new WdkUserException();
TableValueRow tvr = tv.iterator().next();
if (!tvr.containsKey("identifier")) throw new WdkUserException();
String orgNameForFiles = tvr.get("identifier").getValue();

// count the records processed so far
recordCount++;
writer.endObject();
streamWriter.flush();
}

writer.endArray() // records
.endObject().endObject().endObject();
streamWriter.flush();
LOG.info("Totally " + recordCount + " records dumped");
} catch (WdkUserException | JSONException | SQLException | IOException e) {
throw new WdkModelException("Unable to write JSON report", e);
} finally {
if (_tableCache != null) {
_tableCache.close();
}
}
}

/*
{
"assemblyNames": [
"VDI_ORGANISM_FOR_FILES"
],
"trackId": "UD_VDI_ID",
"name": "SHORT_DISPLAY_NAME",
"displays": [
{
"displayId": "wiggle_ApiCommonModel::Model::JBrowseTrackConfig::MultiBigWigTrackConfig::XY=HASH(0x2249320)",
"maxScore": 1000,
"minScore": 1,
"defaultRendering": "multirowxy",
"type": "MultiLinearWiggleDisplay",
"scaleType": "log"
}
],
"adapter": {
"subadapters": [
{
"color": "grey",
"name": "Unsporulated oocyst (non-unique)",
"type": "BigWigAdapter",
"bigWigLocation": {
"locationType": "UriLocation",
"uri": "ToxoDB/build-68/EtenellaHoughton2021/bigwig/etenHoughton2021_Reid_RNASeq_ebi_rnaSeq_RSRC/1_Unsporulated_oocyst/non_
unique_resultsCombinedReps_unlogged.bw"
}
}
*/


private static void formatAttributes(RecordInstance record, Set<AttributeField> attributes, JSONWriter writer)
throws WdkModelException, WdkUserException {
if (!attributes.isEmpty()) {
writer.key("fields").array();
for (AttributeField field : attributes) {
AttributeValue value = record.getAttributeValue(field.getName());
writer.object().key("name").value(field.getName()).key("value").value(value.getValue()).endObject();
}
writer.endArray();
}
}

/*
- dataset id
-
*/
private Set<AttributeField> getAttributes() {
return null;
}
private Set<TableField> getTables() {
return null;
}

}


2 changes: 2 additions & 0 deletions Service/src/main/java/org/apidb/apicommon/service/ApiWebServiceApplication.java
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@
import org.apidb.apicommon.service.services.comments.AttachmentsService;
import org.apidb.apicommon.service.services.comments.UserCommentsService;
import org.apidb.apicommon.service.services.dataPlotter.ProfileSetService;
import org.apidb.apicommon.service.services.jbrowse.JBrowse2Service;
import org.apidb.apicommon.service.services.jbrowse.JBrowseService;
import org.apidb.apicommon.service.services.jbrowse.JBrowseUserDatasetsService;
import org.eupathdb.common.service.EuPathServiceApplication;
Expand Down Expand Up @@ -46,6 +47,7 @@ public Set<Class<?>> getClasses() {
.add(UserCommentsService.class)
.add(TranscriptToggleService.class)
.add(JBrowseService.class)
.add(JBrowse2Service.class)
.add(JBrowseUserDatasetsService.class)
.add(ProfileSetService.class)
.add(OrganismMetricsService.class)
Expand Down
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