Ejemplo n.º 1
0
  @Override
  public Response saveGraph(
      final String graphSeed, final String username, final String timeStamp, final String graph) {
    if (requireAuthentication && (authenticatorHelper.getUsername() == null)) {
      // The user needs to be authenticated.
      logger.error("User must be logged in to save a graph.");
      return Response.status(200).entity("Unable to save, you must be logged in. ").build();
    } else {
      String authenticatedUsername = username;
      try {
        if (ValidationUtils.isValid(authenticatorHelper.getUsername())) {
          authenticatedUsername = authenticatorHelper.getUsername();
          // final G_User byUsername =
          // userDataAccess.getByUsername(authenticatedUsername);
          // byUsername.getId();

        } else {
          logger.debug("User was not authenticated");
        }
      } catch (final Exception e) {
        logger.error("Error getting user information during rest call: ", e);
        // e.printStackTrace();
      }

      final G_PersistedGraph pg = new G_PersistedGraph();
      pg.setCreated(DateTime.now().getMillis());
      pg.setModified(DateTime.now().getMillis());
      pg.setGraphSeed(graphSeed);
      pg.setUserName(authenticatedUsername);
      pg.setGraphJSONdata(graph);
      logger.debug("seed: " + graphSeed);
      logger.debug("json: " + graph);
      final G_PersistedGraph saveGraph = wdao.saveGraph(pg);
      if (saveGraph != null) {
        return Response.status(200)
            .entity("Saved " + graphSeed + " as " + saveGraph.getId())
            .build();
      } else {
        return Response.status(200).entity("Unable to save " + graphSeed).build();
      }
    }
  }
Ejemplo n.º 2
0
 public static ArrayList<File> getFilesRecursively(final String path, final String ext)
     throws IOException {
   final File folder = new File(path);
   final File[] listOfFiles = folder.listFiles();
   final ArrayList<File> theFiles = new ArrayList<File>();
   for (final File currentFile : listOfFiles) {
     final String name = currentFile.getName();
     if (currentFile.isDirectory()) {
       // logger.debug("Directory name is " +
       // currentFile.getAbsolutePath());
       theFiles.addAll(getFilesRecursively(currentFile.getAbsolutePath(), ext));
     } else {
       // logger.debug("File name is " + currentFile.getName());
       if (ValidationUtils.isValid(ext)) {
         // it's a file and we care about the extension
         if (name.contains(".")) {
           if (name.startsWith(".")) {
             // ignore these temp files
             logger.debug("Ignoring file " + name);
           } else {
             final String currentExt = getFileExtension(name);
             logger.debug("current Ext is " + currentExt);
             if (("." + ext).equalsIgnoreCase(currentExt)) {
               logger.debug("Adding file " + name);
               theFiles.add(currentFile);
             }
           }
         } else {
           // what do do with files that have no period?
           logger.debug("Ignoring file " + name);
         }
       } else {
         // Just add the file
         logger.debug("Adding file " + name);
         theFiles.add(currentFile);
       }
     }
   }
   return theFiles;
 }
Ejemplo n.º 3
0
  @Override
  public V_CSGraph getProperties(
      final String type,
      final String[] value,
      final String maxDegree,
      final String maxNodes,
      final String maxEdgesPerNode,
      final boolean bipartite,
      final boolean leafNodes,
      final boolean showNameNodes,
      final boolean showIcons,
      final boolean useSaved) {
    logger.debug("-------");
    logger.debug("get property graph for type " + type);
    logger.debug("Value     " + StringUtils.toString(value));
    logger.debug("Degrees   " + maxDegree);
    logger.debug("LeafNodes " + leafNodes);
    logger.debug("Max Nodes " + maxNodes);
    logger.debug("Max Edges " + maxEdgesPerNode);
    logger.debug("LeafNodes " + leafNodes);
    logger.debug("Bipartite " + bipartite);
    logger.debug("showNameNodes " + showNameNodes);
    logger.debug("useSaved " + useSaved);

    final int maxDegreeInt = FastNumberUtils.parseIntWithCheck(maxDegree, 6);
    final int maxNodesInt = FastNumberUtils.parseIntWithCheck(maxNodes, 1000);
    final int maxEdgesPerNodeInt = FastNumberUtils.parseIntWithCheck(maxEdgesPerNode, 100);

    V_CSGraph m = null;
    if (requireAuthentication && (authenticatorHelper.getUsername() == null)) {
      // The user needs to be authenticated.
      m = new V_CSGraph();
      m.setIntStatus(1);
      final String errorMessage = "You must be authenticated in order to get the graph.";
      m.setStrStatus(errorMessage);
      m.setUserId("Unknown");
      m.setUserName("Unknown");
    } else {
      // Either we don't need authentication or the user is
      // authenticated.

      String userId = null;
      String username = authenticatorHelper.getUsername();
      if (requireAuthentication) {
        if (ValidationUtils.isValid(username)) {
          try {
            final G_User byUsername = userDataAccess.getByUsername(username);
            userId = byUsername.getId();
          } catch (final Exception e) {
            logger.error("Error getting user information during rest call: ", e);
            // e.printStackTrace();
          }
        } else {
          logger.debug("User was not authenticated");
        }
      }
      if (ValidationUtils.isValid(value) && !"null".equals(value[0])) {
        final String firstValue = value[0];
        final G_GraphViewEvent gve = new G_GraphViewEvent();
        gve.setReportId(firstValue);
        gve.setUserId(userId);
        gve.setUserName(username);
        gve.setTimeInitiated(DateTime.now().getMillis());
        if (useSaved) {
          try {
            // TODO: fix which key is going to be used as the seed
            final G_PersistedGraph existingGraph =
                wdao.getExistingGraph(firstValue, userId, username);
            final ObjectMapper mapper = new ObjectMapper();
            if (existingGraph != null) {
              m = mapper.readValue(existingGraph.getGraphJSONdata(), V_CSGraph.class);
              if (m == null) {
                logger.error(
                    "Could not parse existing graph from a previous save, will regenerate.");
              } else {
                gve.setReportType("Existing");
                loggingDao.recordGraphViewEvent(gve);
                m.setStrStatus(
                    "This graph was previously saved on "
                        + DataFormatConstants.formatDate(existingGraph.getModified()));
                m.createPositionMapping(); // necessary for
                // preset layout in
                // Cytoscape 3.2.9
              }
            } else {
              logger.info("Could not find previously saved graph, will regenerate");
            }

          } catch (final Exception e) {
            logger.error("Error building graph at rest service: ", e);
          }
        }
        // If pulling from cache didn't work, get a new graph
        if (m == null) {
          V_GenericGraph g = null;
          try {
            final V_GraphQuery q = new V_GraphQuery();
            for (final String v : value) {
              q.addSearchIds(StringUtils.split(v, ','));
            }
            q.setDirected(false);
            q.setMaxNodes(maxNodesInt);
            q.setMaxEdgesPerNode(maxEdgesPerNodeInt);
            q.setMaxHops(maxDegreeInt);
            q.setUserId(userId);
            q.setUsername(username);
            gve.setQueryObject(q);
            gve.setReportType("New");
            loggingDao.recordGraphViewEvent(gve);
            g = propertyGraphBuilder.buildFromSubGraphs(q);
            // g = propertyGraphBuilder.makeGraphResponse(q);
            g.setUserId(userId);
            g.setUsername(username);
            m = new V_CSGraph(g, true);

          } catch (final Exception e) {
            logger.error("Error building graph at rest service: ", e);
          }
        }

      } else {
        m = new V_CSGraph();
        String errorMessage;
        m.setUserId(userId);
        m.setUserName(username);
        if (useSaved) {
          errorMessage =
              "Tried to recover an existing graph, but no valid id was provided to the server: ["
                  + StringUtils.toString(value)
                  + "]";
        } else {
          errorMessage =
              "Tried to generate a new graph, but no valid id was provided to the server: ["
                  + StringUtils.toString(value)
                  + "]";
        }
        logger.error(errorMessage);
        m.setIntStatus(1);
        m.setStrStatus(errorMessage);
      }
    }
    return m;
  }