TASK-6442 - Add Resources Management functionality

opencga-analysis/src/main/java/org/opencb/opencga/analysis/AnalysisUtils.java

@@ -1,15 +1,21 @@
 package org.opencb.opencga.analysis;
 
+import org.apache.commons.collections4.CollectionUtils;
 import org.opencb.commons.datastore.core.Query;
 import org.opencb.commons.datastore.core.QueryOptions;
 import org.opencb.opencga.catalog.db.api.FileDBAdaptor;
+import org.opencb.opencga.catalog.db.api.ProjectDBAdaptor;
 import org.opencb.opencga.catalog.exceptions.CatalogException;
+import org.opencb.opencga.catalog.managers.CatalogManager;
 import org.opencb.opencga.catalog.managers.FileManager;
 import org.opencb.opencga.catalog.managers.JobManager;
+import org.opencb.opencga.catalog.utils.CatalogFqn;
 import org.opencb.opencga.core.exceptions.ToolException;
+import org.opencb.opencga.core.models.JwtPayload;
 import org.opencb.opencga.core.models.common.Enums;
 import org.opencb.opencga.core.models.file.File;
 import org.opencb.opencga.core.models.job.Job;
+import org.opencb.opencga.core.models.project.Project;
 import org.opencb.opencga.core.response.OpenCGAResult;
 
 import java.io.BufferedReader;
@@ -20,6 +26,13 @@
 
 public class AnalysisUtils {
 
+    public static String REFERENCE_GENOME_GRCH38_FA = "REFERENCE_GENOME_GRCH38_FA";
+    public static String REFERENCE_GENOME_GRCH38_FAI= "REFERENCE_GENOME_GRCH38_FAI";
+    public static String REFERENCE_GENOME_GRCH38_GZI = "REFERENCE_GENOME_GRCH38_GZI";
+    public static String REFERENCE_GENOME_GRCH37_FA= "REFERENCE_GENOME_GRCH37_FA";
+    public static String REFERENCE_GENOME_GRCH37_FAI = "REFERENCE_GENOME_GRCH37_FAI";
+    public static String REFERENCE_GENOME_GRCH37_GZI= "REFERENCE_GENOME_GRCH37_GZI";
+
     public static boolean isSupportedCommand(String commands) {
         Set<String> commandSet = new HashSet<>(Arrays.asList(commands.replace(" ", "").split(",")));
         if (!commandSet.contains(commands)) {
@@ -193,4 +206,22 @@ public static String getJobFileRelativePath(String path) {
         }
         return path.substring(index + 5);
     }
+
+    public static String getAssembly(CatalogManager catalogManager, String studyId, String sessionId) throws CatalogException {
+        String assembly = "";
+        OpenCGAResult<Project> projectQueryResult;
+
+        JwtPayload jwtPayload = catalogManager.getUserManager().validateToken(sessionId);
+        CatalogFqn studyFqn = CatalogFqn.extractFqnFromStudy(studyId, jwtPayload);
+        String organizationId = studyFqn.getOrganizationId();
+
+        projectQueryResult = catalogManager.getProjectManager().search(organizationId, new Query(ProjectDBAdaptor.QueryParams.STUDY.key(), studyId),
+                new QueryOptions(QueryOptions.INCLUDE, ProjectDBAdaptor.QueryParams.ORGANISM.key()), sessionId);
+        if (CollectionUtils.isNotEmpty(projectQueryResult.getResults())
+                && projectQueryResult.first().getOrganism() != null
+                && projectQueryResult.first().getOrganism().getAssembly() != null) {
+            assembly = projectQueryResult.first().getOrganism().getAssembly();
+        }
+        return assembly;
+    }
 }

opencga-analysis/src/main/java/org/opencb/opencga/analysis/ConfigurationUtils.java

@@ -21,6 +21,7 @@
 import org.opencb.commons.utils.FileUtils;
 import org.opencb.opencga.core.config.AnalysisTool;
 import org.opencb.opencga.core.config.Configuration;
+import org.opencb.opencga.core.config.ResourceFile;
 import org.opencb.opencga.core.config.storage.StorageConfiguration;
 import org.opencb.opencga.core.exceptions.ToolException;
 import org.slf4j.Logger;
@@ -121,4 +122,39 @@ public static String getToolDefaultVersion(String toolId, Configuration configur
         }
         return defaultVersion;
     }
+
+
+    public static AnalysisTool getAnalysisTool(String toolId, String version, Configuration configuration) throws ToolException {
+        for (AnalysisTool tool : configuration.getAnalysis().getTools()) {
+            if (toolId.equals(tool.getId())) {
+                if (StringUtils.isEmpty(version) || version.equals(tool.getVersion())) {
+                    return tool;
+                }
+            }
+        }
+        throw new ToolException("Missing analysis tool (ID = " + toolId + ", version = " + version + ") in configuration file");
+    }
+
+    public static Path getToolResourcePath(String resourceId, Configuration configuration) throws ToolException {
+        // Get resources from the configuration file
+        for (ResourceFile resourceFile : configuration.getAnalysis().getResource().getFiles()) {
+            if (resourceFile.getId().equalsIgnoreCase(resourceId)) {
+                Path resourcePath = configuration.getAnalysis().getResource().getBasePath().resolve(resourceFile.getPath());
+                if (!Files.exists(resourcePath)) {
+                    throw new ToolException("Error getting resource '" + resourceId + "': it is not installed (i.e., missing file '"
+                            + resourcePath + "')");
+                }
+                return resourcePath;
+            }
+        }
+        throw new ToolException("Error getting resource '" + resourceId + "': it does not exist in the configuration file");
+    }
+
+    public static void checkAnalysisResources(String toolId, String version, Configuration configuration) throws ToolException {
+        AnalysisTool analysisTool = getAnalysisTool(toolId, version, configuration);
+        for (String resourceId : analysisTool.getResources()) {
+            getToolResourcePath(resourceId, configuration);
+        }
+
+    }
 }