--- /dev/null
+package jalview.ws2.client.slivka;
+
+import static java.util.Objects.requireNonNullElse;
+
+import java.io.File;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+import java.util.Map;
+
+import com.stevesoft.pat.NotImplementedError;
+
+import jalview.bin.Cache;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.ParamDatastoreI;
+import jalview.ws.params.ParamManager;
+import jalview.ws.params.WsParamSetI;
+import jalview.ws.params.simple.BooleanOption;
+import jalview.ws.params.simple.DoubleParameter;
+import jalview.ws.params.simple.IntegerParameter;
+import jalview.ws.params.simple.Option;
+import jalview.ws.params.simple.StringParameter;
+import jalview.ws2.params.SimpleParamDatastore;
+import jalview.ws2.params.SimpleParamSet;
+import uk.ac.dundee.compbio.slivkaclient.Parameter;
+import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
+
+class SlivkaParamStoreFactory
+{
+ private final SlivkaService service;
+ private final ParamManager manager;
+
+ SlivkaParamStoreFactory(SlivkaService service, ParamManager manager)
+ {
+ this.service = service;
+ this.manager = manager;
+ }
+
+ ParamDatastoreI createParamDatastore()
+ {
+ URL url = null;
+ try
+ {
+ url = service.getUrl().toURL();
+ } catch (MalformedURLException e)
+ {
+ Cache.log.warn("Invalid service url " + service.getUrl(), e);
+ }
+ List<WsParamSetI> presets = new ArrayList<>(service.getPresets().size());
+ for (var preset : service.getPresets())
+ {
+ presets.add(createPreset(preset));
+ }
+ List<ArgumentI> arguments = createPresetArguments(Collections.emptyMap());
+ return new SimpleParamDatastore(url, arguments, presets, manager);
+ }
+
+ WsParamSetI createPreset(SlivkaService.Preset preset)
+ {
+ var builder = SimpleParamSet.newBuilder();
+ builder.name(preset.name);
+ builder.description(preset.description);
+ builder.url(service.getUrl().toString());
+ builder.modifiable(false);
+ builder.arguments(createPresetArguments(preset.values));
+ return builder.build();
+ }
+
+ List<ArgumentI> createPresetArguments(Map<String, Object> values)
+ {
+ var args = new ArrayList<ArgumentI>();
+ for (Parameter param : service.getParameters())
+ {
+ if (param instanceof Parameter.IntegerParameter)
+ {
+ args.add(createOption((Parameter.IntegerParameter) param,
+ (Integer) values.get(param.getId())));
+ }
+ else if (param instanceof Parameter.DecimalParameter)
+ {
+ args.add(createOption((Parameter.DecimalParameter) param,
+ (Double) values.get(param.getId())));
+ }
+ else if (param instanceof Parameter.TextParameter)
+ {
+ args.add(createOption((Parameter.TextParameter) param,
+ (String) values.get(param.getId())));
+ }
+ else if (param instanceof Parameter.FlagParameter)
+ {
+ args.add(createOption((Parameter.FlagParameter) param,
+ (Boolean) values.get(param.getId())));
+ }
+ else if (param instanceof Parameter.ChoiceParameter)
+ {
+ Object ovalue = values.get(param.getId());
+ List<String> lvalue = null;
+ if (param.isArray())
+ lvalue = (List<String>) ovalue;
+ else if (ovalue != null)
+ lvalue = List.of((String) ovalue);
+ args.addAll(createChoiceOptions((Parameter.ChoiceParameter) param, lvalue));
+ }
+ else if (param instanceof Parameter.FileParameter)
+ {
+ // args.add(createOption((Parameter.FileParameter) param, null));
+ }
+ else
+ {
+ args.add(createOption(param, values.get(param.getId())));
+ }
+ }
+ return args;
+ }
+
+ private Option createOption(Parameter.IntegerParameter param, Integer value)
+ {
+ var builder = IntegerParameter.newBuilder();
+ setCommonProperties(param, builder);
+ builder.setDefaultValue((Integer) param.getDefault());
+ builder.setValue(value);
+ builder.setBounds(param.getMin(), param.getMax());
+ return builder.build();
+ }
+
+ private Option createOption(Parameter.DecimalParameter param, Double value)
+ {
+ var builder = DoubleParameter.newBuilder();
+ setCommonProperties(param, builder);
+ builder.setDefaultValue((Double) param.getDefault());
+ builder.setValue(value);
+ builder.setBounds(param.getMin(), param.getMax());
+ return builder.build();
+ }
+
+ private Option createOption(Parameter.TextParameter param, String value)
+ {
+ var builder = StringParameter.newBuilder();
+ setCommonProperties(param, builder);
+ builder.setDefaultValue((String) param.getDefault());
+ builder.setValue(value);
+ return builder.build();
+ }
+
+ private Option createOption(Parameter.FlagParameter param, Boolean value)
+ {
+ var builder = BooleanOption.newBuilder();
+ setCommonProperties(param, builder);
+ builder.setDefaultValue((Boolean) param.getDefault());
+ builder.setValue(value);
+ return builder.build();
+ }
+
+ private List<Option> createChoiceOptions(Parameter.ChoiceParameter param, List<String> value)
+ {
+ value = requireNonNullElse(value, Collections.emptyList());
+ if (param.isArray())
+ {
+ /*
+ * Array parameter means that multiple values can be provided.
+ * Use multiple boolean checkboxes to represent the value.
+ */
+ List<Option> options = new ArrayList<>();
+ List<?> selected = requireNonNullElse(
+ (List<?>) param.getDefault(), Collections.emptyList());
+ int i = 0;
+ var builder = BooleanOption.newBuilder();
+ setCommonProperties(param, builder);
+ for (String choice : param.getChoices())
+ {
+ builder.setName(String.format("%s$%d", param.getId(), i++));
+ builder.setLabel(choice);
+ builder.setDefaultValue(selected.contains(choice));
+ builder.setValue(value.contains(choice));
+ builder.setReprValue(choice);
+ options.add(builder.build());
+ }
+ return options;
+ }
+ else
+ {
+ /*
+ * Single value parameter means a single string with limited possible
+ * values can be used.
+ */
+ var builder = StringParameter.newBuilder();
+ setCommonProperties(param, builder);
+ builder.setDefaultValue((String) param.getDefault());
+ if (value.size() > 0)
+ builder.setValue(value.get(0));
+ builder.setPossibleValues(param.getChoices());
+ return List.of(builder.build());
+ }
+ }
+
+ private Option createOption(Parameter.FileParameter param, File value)
+ {
+ throw new NotImplementedError("file paramters are not implemented for slivka");
+ }
+
+ private Option createOption(Parameter param, Object value)
+ {
+ var builder = StringParameter.newBuilder();
+ setCommonProperties(param, builder);
+ if (param.getDefault() != null)
+ builder.setDefaultValue(param.getDefault().toString());
+ if (value != null)
+ builder.setValue(value.toString());
+ return builder.build();
+ }
+
+ private void setCommonProperties(Parameter param, Option.Builder builder)
+ {
+ builder.setName(param.getId());
+ builder.setLabel(param.getName());
+ builder.setDescription(param.getDescription());
+ builder.setRequired(param.isRequired());
+ try
+ {
+ builder.setDetailsUrl(service.getUrl().toURL());
+ } catch (MalformedURLException e)
+ {
+ Cache.log.warn("invalid service url " + service.getUrl(), e);
+ }
+ }
+}
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git://source.jalview.org / jalview.git / blobdiff