Jbrowse2 service

Service/src/main/java/org/apidb/apicommon/service/ApiWebServiceApplication.java

@@ -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;
@@ -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)

Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/JBrowse2Service.java

@@ -0,0 +1,257 @@
+package org.apidb.apicommon.service.services.jbrowse;
+
+import java.io.*;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Map;
+
+import javax.sql.DataSource;
+import javax.ws.rs.*;
+import javax.ws.rs.core.MediaType;
+import javax.ws.rs.core.Response;
+import javax.ws.rs.BadRequestException;
+
+import org.apache.log4j.Logger;
+import org.gusdb.fgputil.db.runner.SQLRunner;
+import org.gusdb.fgputil.db.runner.SQLRunnerException;
+import org.gusdb.wdk.model.WdkException;
+import org.gusdb.wdk.model.WdkModelException;
+import org.gusdb.wdk.model.WdkRuntimeException;
+import org.gusdb.wdk.service.service.AbstractWdkService;
+import org.json.JSONArray;
+import org.json.JSONObject;
+
+@Path("/jbrowse2")
+public class JBrowse2Service extends AbstractWdkService {
+
+    private static final Logger LOG = Logger.getLogger(JBrowse2Service.class);
+
+    private static final String VDI_CONTROL_SCHEMA_KEY ="VDI_CONTROL_SCHEMA";
+    private static final String VDI_DATASET_SCHEMA_KEY ="VDI_DATASETS_SCHEMA";
+    private static final String WEB_SVC_DIR_KEY ="WEBSERVICEMIRROR";
+
+    private static final String USER_DATASETS_DIR = "./userDatasetsData";  // hard-coded mount point in the jbrowse2 service
+    /*
+    Get config for a single organism.  Assumes JSON will easily fit in memory.
+     */
+    @GET
+    @Path("orgview/{publicOrganismAbbrev}/config.json")
+    @Produces(MediaType.APPLICATION_JSON)
+    public Response getJbrowseSingleOrgTracks(@PathParam("publicOrganismAbbrev") String publicOrganismAbbrev,
+                                     @QueryParam("trackSets") String trackSetsString) throws IOException, WdkException {
+
+        String errMsg = "Must provide a comma delimited list of tracks in a 'trackSets' query param";
+        if (trackSetsString == null) throw new BadRequestException(errMsg);
+        List<String> trackSetsList = Arrays.asList(trackSetsString.split(","));
+        if (trackSetsList.isEmpty()) throw new BadRequestException(errMsg);
+
+        // get static json config, for this organism and set of tracks
+        String staticConfigJsonString = getStaticConfigJsonString(publicOrganismAbbrev, trackSetsString);
+        JSONObject staticConfigJson = new JSONObject(staticConfigJsonString);
+
+        // get similar from user datasets
+        JSONArray udTracks = getUserDatasetTracks(publicOrganismAbbrev, trackSetsList);
+
+        // merge UD tracks into static
+        staticConfigJson.getJSONArray("tracks").putAll(udTracks);
+
+        // send response
+        String jsonString = staticConfigJson.toString();
+        return Response.ok(jsonString, MediaType.APPLICATION_JSON).build();
+    }
+
+    // call out to perl code to produce static config json
+    String getStaticConfigJsonString(String publicOrganismAbbrev, String trackSetsString) throws IOException {
+
+        String gusHome = getWdkModel().getGusHome();
+        String projectId = getWdkModel().getProjectId();
+        String buildNumber = getWdkModel().getBuildNumber();
+
+        List<String> command = new ArrayList<>();
+        command.add(gusHome + "/bin/jbrowse2Config");
+        command.add("--orgAbbrev");
+        command.add(publicOrganismAbbrev);
+        command.add("--projectId");
+        command.add(projectId);
+        command.add("--buildNumber");
+        command.add(buildNumber);
+        command.add("--webSvcDir");
+        command.add(getWdkModel().getProperties().get(WEB_SVC_DIR_KEY));
+        command.add("--trackSets");
+        command.add(trackSetsString);
+
+        return stringFromCommand(command);
+    }
+
+    JSONArray getUserDatasetTracks(String publicOrganismAbbrev, List<String> trackSetList) throws WdkModelException {
+        String buildNumber = getWdkModel().getBuildNumber();
+        String projectId = getWdkModel().getProjectId();
+        Long userId = getRequestingUser().getUserId();
+        String vdiDatasetsSchema = getWdkModel().getProperties().get(VDI_DATASET_SCHEMA_KEY);
+        String vdiControlSchema = getWdkModel().getProperties().get(VDI_CONTROL_SCHEMA_KEY);
+
+        String udDataPathString = String.join("/", USER_DATASETS_DIR, vdiDatasetsSchema, "build-" + buildNumber, projectId);
+        JSONArray udTracks = new JSONArray();
+
+        // for now we only have rnaseq UD tracks
+        if (trackSetList.contains("rnaseq")) {
+            udTracks.put(getRnaSeqUdTracks(publicOrganismAbbrev, projectId, vdiControlSchema,
+                    udDataPathString, userId));
+        }
+        return udTracks;
+    }
+
+    JSONArray getRnaSeqUdTracks(String publicOrganismAbbrev, String projectId, String vdiControlSchema,
+                      String udDataPathString, Long userId) throws WdkModelException {
+
+        DataSource appDs = getWdkModel().getAppDb().getDataSource();
+        String sql = "select distinct user_dataset_id, name " +
+                "from " + vdiControlSchema + ".AvailableUserDatasets aud, " +
+                vdiControlSchema + ".dataset_dependency dd " +
+                "where project_id = '" + projectId + "' " +
+                "and (type = 'rnaseq' or type = 'bigwigfiles') " +
+                "and ((is_public = 1 and is_owner = 1) or user_id = " + userId + ") " +
+                "and dd.dataset_id = aud.user_dataset_id " +
+                "and dd.identifier = '" + publicOrganismAbbrev + "'";
+        try {
+            return new SQLRunner(appDs, sql).executeQuery(rs -> {
+                JSONArray rnaSeqUdTracks = new JSONArray();
+                while (rs.next()) {
+                    String datasetId = rs.getString(1);
+                    String name = rs.getString(2);
+                    JSONObject track = createBigwigTrackJson(datasetId, name, publicOrganismAbbrev);
+                    List<String> fileNames = getBigwigFileNames(udDataPathString + "/" +datasetId);
+                    for (String fileName : fileNames) {
+                        track.getJSONObject("adapter")
+                                .getJSONArray("subadapters")
+                                .put(createBigwigSubadapterJson(datasetId, fileName, udDataPathString));
+                    }
+                }
+                return rnaSeqUdTracks;
+            });
+        }
+        catch (SQLRunnerException e) {
+          throw new WdkModelException("Unable to query VDI tables for RNA seq datasets. " + e.getMessage(), e.getCause());
+        }
+    }
+
+    // boilerplate method written by copilot
+    public static List<String> getBigwigFileNames(String directoryPath) throws SQLRunnerException {
+        List<String> bwFiles = new ArrayList<>();
+        File directory = new File(directoryPath);
+
+        if (directory.isDirectory()) {
+            File[] files = directory.listFiles();
+            if (files != null) {
+                for (File file : files) {
+                    if (file.isFile() && file.getName().endsWith(".bw")) {
+                        bwFiles.add(file.getName());
+                    }
+                }
+            }
+        } else {
+            throw new SQLRunnerException("User Dataset directory not found for path: " + directoryPath);
+        }
+
+        return bwFiles;
+    }
+
+/*
+    MULTI BIGWIG TRACK EXAMPLE
+    {
+      "assemblyNames": [
+        "ORG_ABBREV"
+      ],
+      "trackId": "VDI_ID",
+      "name": "VDI_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": "FILE_NAME",
+            "type": "BigWigAdapter",
+            "bigWigLocation": {
+              "locationType": "UriLocation",
+              "uri": "USER_DATASET_PATH/VDI_ID/FILE_NAME"
+            }
+          }
+        }
+      }
+ */
+    JSONObject createBigwigTrackJson(String vdiId, String vdiName, String organismAbbrev) {
+        return new JSONObject()
+            .put("assemblyNames", new JSONArray().put(organismAbbrev))
+            .put("trackId", vdiId)
+            .put("name", vdiName)
+            .put("displays", new JSONArray()
+                .put(new JSONObject()
+                    .put("displayId", "wiggle_ApiCommonModel::Model::JBrowseTrackConfig::MultiBigWigTrackConfig::XY=HASH(0x2249320)")
+                    .put("maxScore", 1)
+                    .put("maxScore", 1000)
+                    .put("defaultRendering", "multirowxy")
+                    .put("type", "MultiLinearWiggleDisplay")
+                    .put("scaleType", "log")
+                    )
+                )
+            .put("adapter", new JSONObject()
+                    .put("subadapters", new JSONArray())
+            );
+    }
+
+    JSONObject createBigwigSubadapterJson(String vdiId, String fileName, String userDatasetsFilePath) {
+        JSONObject subAdapter = new JSONObject();
+        subAdapter.put("color1", "grey");
+        subAdapter.put("name", fileName);
+        subAdapter.put("type", "BigWigAdapter");
+        JSONObject location = new JSONObject().put("locationType", "UriLocation");
+        location.put("uri", String.join("/", userDatasetsFilePath, vdiId, fileName));
+        subAdapter.put("bigWigLocation", location);
+        return subAdapter;
+    }
+
+    String stringFromCommand(List<String> command) throws IOException {
+      LOG.debug("Running command: " + String.join(" ", command));
+        try {
+            Process p = processFromCommand(command);
+
+            ByteArrayOutputStream stringBuffer = new ByteArrayOutputStream();
+            p.getErrorStream().transferTo(stringBuffer);
+            String errors = stringBuffer.toString();
+
+            stringBuffer.reset();
+            p.getInputStream().transferTo(stringBuffer);
+
+            if (p.waitFor() != 0) {
+                throw new RuntimeException("Subprocess from [" + String.join(" ", command) + "] returned non-zero.  Errors:\n" + errors);
+            }
+
+            return stringBuffer.toString();
+        }
+        catch (InterruptedException e) {
+            throw new RuntimeException("Subprocess from [" + String.join(" ", command) + "] was interrupted befor it could complete.");
+        }
+    }
+    Process processFromCommand (List<String> command) throws IOException {
+        for (int i = 0; i < command.size(); i++) {
+            if (command.get(i) == null)
+                throw new WdkRuntimeException(
+                        "Command part at index " + i + " is null.  Could be due to unchecked user input.");
+        }
+        ProcessBuilder pb = new ProcessBuilder(command);
+        Map<String, String> env = pb.environment();
+        env.put("GUS_HOME", getWdkModel().getGusHome());
+        pb.redirectErrorStream(true);
+        return pb.start();
+    }
+}