Examples with TautomersModelBuilder ambit2.rest.task.tautomers.TautomersModelBuilder used on opensource projects

Example 1 with TautomersModelBuilder

use of ambit2.rest.task.tautomers.TautomersModelBuilder in project ambit-mirror by ideaconsult.

the class AllAlgorithmsResource method createCallable.

@Override
protected ICallableTask createCallable(Form form, Algorithm<String> algorithm, ModelURIReporter<IQueryRetrieval<ModelQueryResults>> modelReporter, AlgorithmURIReporter algReporter, Object token) throws ResourceException {
    try {
        if (algorithm.hasType(AlgorithmType.Expert)) {
            String userName = "guest";
            try {
                userName = getRequest().getClientInfo().getUser().getIdentifier();
            } catch (Exception x) {
                userName = "guest";
            }
            Object datasetURI = OpenTox.params.dataset_uri.getFirstValue(form);
            return new CallableSimpleModelCreator(form, getContext(), algorithm, false, new ExpertModelBuilder(datasetURI == null ? null : datasetURI.toString(), userName, getRequest().getRootRef(), modelReporter, algReporter, getRequest().getResourceRef().toString()), token, getRequest().getResourceRef().toString(), getClientInfo());
        } else if (algorithm.hasType(AlgorithmType.SuperService)) {
            return new CallablePOST(form, getRequest().getRootRef(), token, getRequest().getResourceRef().toString());
        } else if (algorithm.hasType(AlgorithmType.SuperBuilder)) {
            return new CallableBuilder(form, getRequest().getRootRef(), token, getRequest().getResourceRef().toString());
        } else if (algorithm.hasType(AlgorithmType.Mockup)) {
            return new CallableMockup(form, token);
        } else if (algorithm.hasType(AlgorithmType.ExternalModels))
            return new CallableSimpleModelCreator(form, getRequest().getRootRef(), getContext(), algorithm, modelReporter, algReporter, false, token, getRequest().getResourceRef().toString(), getClientInfo());
        else if (algorithm.hasType(AlgorithmType.Rules))
            return new CallableSimpleModelCreator(form, getRequest().getRootRef(), getContext(), algorithm, modelReporter, algReporter, false, token, getRequest().getResourceRef().toString(), getClientInfo());
        else if (algorithm.hasType(AlgorithmType.Finder)) {
            return new CallableFinder(form, getRequest().getRootRef(), getContext(), algorithm, token, getRequest().getResourceRef().toString(), getClientInfo());
        } else if (algorithm.hasType(AlgorithmType.Structure)) {
            return new CallableSimpleModelCreator(form, getContext(), algorithm, false, new OptimizerModelBuilder(getRequest().getRootRef(), form, modelReporter, algReporter, false, getRequest().getResourceRef().toString()), token, getRequest().getResourceRef().toString(), getClientInfo());
        } else if (algorithm.hasType(AlgorithmType.Structure2D)) {
            try {
                CallableSimpleModelCreator modelCreator = new CallableSimpleModelCreator(form, getContext(), algorithm, false, new Structure2DModelBuilder(getRequest().getRootRef(), modelReporter, algReporter, false, getRequest().getResourceRef().toString()), token, getRequest().getResourceRef().toString(), getClientInfo());
                TaskResult modelRef = modelCreator.call();
                ModelQueryResults model = modelCreator.getModel();
                Structure2DProcessor predictor = new Structure2DProcessor(getRequest().getRootRef(), model, new ModelURIReporter<IQueryRetrieval<ModelQueryResults>>(getRequest()), new PropertyURIReporter(getRequest()), null);
                return new CallableStructureOptimizer(form, getRequest().getRootRef(), getContext(), (Structure2DProcessor) predictor, token, getRequest().getResourceRef().toString(), getClientInfo());
            } catch (ResourceException x) {
                throw x;
            } catch (Exception x) {
                getLogger().log(Level.WARNING, x.getMessage(), x);
                throw new ResourceException(Status.SERVER_ERROR_INTERNAL, x.getMessage(), x);
            }
        } else if (algorithm.hasType(AlgorithmType.TautomerGenerator)) {
            return new CallableSimpleModelCreator(form, getContext(), algorithm, false, new TautomersModelBuilder(getRequest().getRootRef(), modelReporter, algReporter, false, getRequest().getResourceRef().toString()), token, getRequest().getResourceRef().toString(), getClientInfo());
        } else if (algorithm.hasType(AlgorithmType.PreferredStructure)) {
            return new CallableFixPreferredStructure(form, getRequest().getRootRef(), getContext(), null, token, getRequest().getResourceRef().toString(), getClientInfo());
        } else if (algorithm.hasType(AlgorithmType.DescriptorCalculation)) {
            try {
                CallableSimpleModelCreator modelCreator = new CallableSimpleModelCreator(form, getRequest().getRootRef(), getContext(), algorithm, modelReporter, algReporter, true, token, getRequest().getResourceRef().toString(), getClientInfo());
                TaskResult modelRef = modelCreator.call();
                ModelQueryResults model = modelCreator.getModel();
                if (algorithm.getParameters() != null) {
                    StringBuilder b = new StringBuilder();
                    for (Parameter prm : algorithm.getParameters()) // b.append(String.format("-%s\t'%s'\t",
                    // prm.getName(),prm.getValue()));
                    b.append(String.format("-%s\t'%s'\t", prm.getName(), prm.getValue()));
                    // this is wrong, the parameters should be stored in the
                    // model already (and in the database!)
                    model.setParameters(b.toString().split("\t"));
                }
                DescriptorPredictor predictor = new DescriptorPredictor(getRequest().getRootRef(), model, modelReporter, new PropertyURIReporter(getRequest()), null);
                return new CallableDescriptorCalculator(form, getRequest().getRootRef(), getContext(), predictor, token, getRequest().getResourceRef().toString(), getClientInfo());
            } catch (ResourceException x) {
                throw x;
            } catch (Exception x) {
                getLogger().log(Level.WARNING, x.getMessage(), x);
                throw new ResourceException(Status.SERVER_ERROR_INTERNAL, x.getMessage(), x);
            }
        } else if (algorithm.hasType(AlgorithmType.AppDomain)) {
            switch(algorithm.getRequirement()) {
                case structure:
                    {
                        return new CallableFingerprintsModelCreator(form, getRequest().getRootRef(), getContext(), algorithm, modelReporter, algReporter, token, getRequest().getResourceRef().toString(), getClientInfo());
                    }
                case property:
                    {
                        return new CallableNumericalModelCreator(form, getRequest().getRootRef(), getContext(), algorithm, modelReporter, algReporter, token, getRequest().getResourceRef().toString(), getClientInfo());
                    }
                default:
                    {
                        throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, algorithm.toString());
                    }
            }
        } else if (algorithm.hasType(AlgorithmType.Fingerprints.toString())) {
            return new CallableFingerprintsCalculator(form, getRequest().getRootRef(), getContext(), algorithm, token, getRequest().getResourceRef().toString(), getClientInfo());
        /*
				 * } else if
				 * (AlgorithmFormat.WAFFLES_JSON.equals(algorithm.getFormat()))
				 * { return new CallableWafflesModelCreator(form,
				 * getRequest().getRootRef(), getContext(), algorithm,
				 * modelReporter, algReporter,
				 * token,getRequest().getResourceRef().toString());
				 */
        } else {
            return new CallableWekaModelCreator(form, getRequest().getRootRef(), getContext(), algorithm, modelReporter, algReporter, token, getRequest().getResourceRef().toString(), getClientInfo());
        }
    } catch (ResourceException x) {
        throw x;
    } catch (Exception x) {
        throw new ResourceException(Status.SERVER_ERROR_INTERNAL);
    } finally {
    // try { connection.close(); } catch (Exception x) {}
    }
}