Jbrowse2 service

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

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+package org.apidb.apicommon.service.services.jbrowse;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStreamReader;
+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 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 String VDI_DATASET_DIR_KEY = "VDI_DATASETS_DIRECTORY";
+    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";
+
+    /*
+    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 trackSets) throws IOException, WdkException {
+
+        // get static json config, for this organism and set of tracks
+        String staticConfigJsonString = getStaticConfigJsonString(publicOrganismAbbrev, trackSets);
+        JSONObject staticConfigJson = new JSONObject(staticConfigJsonString);
+
+        // get similar from user datasets
+        JSONArray udTracks = getUserDatasetTracks(publicOrganismAbbrev, trackSets);
+
+        // 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 trackSets) 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(trackSets);
+
+        return stringFromCommand(command);
+    }
+
+    JSONArray getUserDatasetTracks(String publicOrganismAbbrev, String tracksString) throws WdkModelException {
+        String buildNumber = getWdkModel().getBuildNumber();
+        String projectId = getWdkModel().getProjectId();
+        Long userId = getRequestingUser().getUserId();
+        String vdiDatasetsDir = getWdkModel().getProperties().get(VDI_DATASET_DIR_KEY);
+        String vdiDatasetsSchema = getWdkModel().getProperties().get(VDI_DATASET_SCHEMA_KEY);
+        String vdiControlSchema = getWdkModel().getProperties().get(VDI_CONTROL_SCHEMA_KEY);
+
+        String udDataPathString = String.join("/", vdiDatasetsDir, vdiDatasetsSchema, "build-" + buildNumber, projectId);
+        JSONArray udTracks = new JSONArray();
+        List<String> trackSetList = Arrays.asList(tracksString.split(","));
+
+        // 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 = 'BigWig') " +
+                "and ((is_public = 1 and is_owner = 1) or user_id = " + userId + ") " +
+                "and dd.dataset_id = aud.dataset_id " +
+                " 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);
+                    List<String> fileNames = getBigwigFileNames(udDataPathString + "/" +datasetId);
+                    for (String fileName : fileNames) {
+                        rnaSeqUdTracks.put(createBigwigTrackJson(datasetId, name, fileName, publicOrganismAbbrev, udDataPathString));
+                    }
+                }
+                return rnaSeqUdTracks;
+            });
+        }
+        catch (SQLRunnerException e) {
+            throw new WdkModelException("Unable to query VDI tables for RNA seq datasets", 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 fileName, String organismAbbrev, String userDatasetsFilePath) {
+        JSONObject track = new JSONObject();
+        track.put("assemblyNames", new JSONArray().put(organismAbbrev));
+        track.put("trackId", vdiId);
+        track.put("name", vdiName);
+        JSONObject display = new JSONObject();
+        display.put("displayId", "wiggle_ApiCommonModel::Model::JBrowseTrackConfig::MultiBigWigTrackConfig::XY=HASH(0x2249320)");
+        display.put("maxScore", 1);
+        display.put("maxScore", 1000);
+        display.put("defaultRendering", "multirowxy");
+        display.put("type", "MultiLinearWiggleDisplay");
+        display.put("scaleType", "log");
+        JSONArray displays = new JSONArray().put(display);
+        track.put("displays", displays);
+        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 track;
+    }
+
+    String stringFromCommand(List<String> command) throws IOException {
+        Process p = processFromCommand(command);
+        BufferedReader reader =
+                new BufferedReader(new InputStreamReader(p.getInputStream()));
+        StringBuilder builder = new StringBuilder();
+        String line;
+        while ( (line = reader.readLine()) != null) {
+            builder.append(line);
+            builder.append(System.lineSeparator());
+        }
+        return builder.toString();
+    }
+
+    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();
+    }
+}