Package uk.ac.bbsrc.tgac.miso.integration.util

Examples of uk.ac.bbsrc.tgac.miso.integration.util.IntegrationException

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      JSONArray r = JSONArray.fromObject(response);
      if (!r.isEmpty()) {
        if (r.size() == 1 && r.getJSONObject(0).has("error")) {
          String error = r.getJSONObject(0).getString("error");
          log.error(error);
          throw new IntegrationException("Analysis query returned an error: " + error);
        }

        return JSONArray.fromObject(response);
      }
    }
    throw new IntegrationException("No such task.");
  }
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      JSONArray r = JSONArray.fromObject(response);
      if (!r.isEmpty()) {
        if (r.size() == 1 && r.getJSONObject(0).has("error")) {
          String error = r.getJSONObject(0).getString("error");
          log.error(error);
          throw new IntegrationException("Analysis query returned an error: " + error);
        }

        return JSONArray.fromObject(response);
      }
    }
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      JSONArray r = JSONArray.fromObject(response);
      if (!r.isEmpty()) {
        if (r.size() == 1 && r.getJSONObject(0).has("error")) {
          String error = r.getJSONObject(0).getString("error");
          log.error(error);
          throw new IntegrationException("Analysis query returned an error: " + error);
        }
        else {
          JSONArray n = new JSONArray();
          for (JSONObject task : (Iterable<JSONObject>)r) {
            if (!task.getString("statusMessage").contains("Failed")) {
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      JSONArray r = JSONArray.fromObject(response);
      if (!r.isEmpty()) {
        if (r.size() == 1 && r.getJSONObject(0).has("error")) {
          String error = r.getJSONObject(0).getString("error");
          log.error(error);
          throw new IntegrationException("Analysis query returned an error: " + error);
        }
        else {
          JSONArray n = new JSONArray();
          for (JSONObject task : (Iterable<JSONObject>)r) {
            if (task.getString("statusMessage").contains("Failed")) {
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      JSONArray r = JSONArray.fromObject(response);
      if (!r.isEmpty()) {
        if (r.size() == 1 && r.getJSONObject(0).has("error")) {
          String error = r.getJSONObject(0).getString("error");
          log.error(error);
          throw new IntegrationException("Analysis query returned an error: " + error);
        }

        return JSONArray.fromObject(response);
      }
    }
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      JSONArray r = JSONArray.fromObject(response);
      if (!r.isEmpty()) {
        if (r.size() == 1 && r.getJSONObject(0).has("error")) {
          String error = r.getJSONObject(0).getString("error");
          log.error(error);
          throw new IntegrationException("Analysis query returned an error: " + error);
        }

        return JSONArray.fromObject(response);
      }
    }
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      JSONObject r = JSONObject.fromObject(response);
      if (!r.isEmpty()) {
        if (r.has("error")) {
          String error = r.getString("error");
          log.error(error);
          throw new IntegrationException("Analysis query returned an error: " + error);
        }

        return r;
      }
    }
    throw new IntegrationException("No such pipeline.");
  }
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      JSONArray r = JSONArray.fromObject(response);
      if (!r.isEmpty()) {
        if (r.size() == 1 && r.getJSONObject(0).has("error")) {
          String error = r.getJSONObject(0).getString("error");
          log.error(error);
          throw new IntegrationException("Analysis query returned an error: " + error);
        }

        return JSONArray.fromObject(response);
      }
    }
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    if (!"".equals(response)) {
      JSONObject r = JSONObject.fromObject(response);
      if (r.has("error")) {
        String error = r.getString("error");
        log.error(error);
        throw new IntegrationException("Analysis query returned an error: " + error);
      }
      return r;
    }
    throw new IntegrationException("Cannot submit task.");
  }
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          for (Dilution d : p.getDilutions()) {
            if ("RNA-Seq".equals(d.getLibrary().getLibraryStrategyType().getName())) naType = "rna";
          }
        }
        else {
          throw new IntegrationException("Cannot start analysis pipelines on a run with no pools on any lanes.");
        }
      }
      map.put("lane-value", laneValue);
      map.put("nucleic-acid-type", naType);
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Related Classes of uk.ac.bbsrc.tgac.miso.integration.util.IntegrationException

  • uk.ac.bbsrc.tgac.miso.integration.AnalysisQueryService
  • uk.ac.bbsrc.tgac.miso.webapp.controller.task.AnalysisController
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