upgradede for CWL v1.0
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/repo Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/commit/e56b8021 Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/e56b8021 Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/e56b8021 Branch: refs/heads/cwl-browse Commit: e56b8021080de1b5e1254bc62cb05337801f721e Parents: f2eda87 Author: ThilinaManamgoda <maanafun...@gmail.com> Authored: Thu Aug 4 15:17:36 2016 +0530 Committer: ThilinaManamgoda <maanafun...@gmail.com> Committed: Thu Aug 4 15:17:36 2016 +0530 ---------------------------------------------------------------------- .../ui/serviceprovider/CwlServiceProvider.java | 6 + .../apache/taverna/cwl/utilities/CWLUtil.java | 123 +++++++++++++++---- 2 files changed, 103 insertions(+), 26 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/e56b8021/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/CwlServiceProvider.java ---------------------------------------------------------------------- diff --git a/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/CwlServiceProvider.java b/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/CwlServiceProvider.java index 1d71fe5..a1e2561 100644 --- a/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/CwlServiceProvider.java +++ b/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/CwlServiceProvider.java @@ -105,6 +105,12 @@ public class CwlServiceProvider extends AbstractConfigurableServiceProvider impl } }); + if(stream!=null) + try { + stream.close(); + } catch (IOException e) { + logger.warn("Can't close Stream !"); + } callBack.finished(); } http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/e56b8021/taverna-cwl-utilities/src/main/java/org/apache/taverna/cwl/utilities/CWLUtil.java ---------------------------------------------------------------------- diff --git a/taverna-cwl-utilities/src/main/java/org/apache/taverna/cwl/utilities/CWLUtil.java b/taverna-cwl-utilities/src/main/java/org/apache/taverna/cwl/utilities/CWLUtil.java index aafe81c..49d85a9 100644 --- a/taverna-cwl-utilities/src/main/java/org/apache/taverna/cwl/utilities/CWLUtil.java +++ b/taverna-cwl-utilities/src/main/java/org/apache/taverna/cwl/utilities/CWLUtil.java @@ -19,10 +19,13 @@ package org.apache.taverna.cwl.utilities; import java.util.ArrayList; import java.util.HashMap; import java.util.Iterator; +import java.util.LinkedHashMap; import java.util.Map; +import java.util.Map.Entry; import java.util.regex.Matcher; import java.util.regex.Pattern; +import com.fasterxml.jackson.core.JsonProcessingException; import com.fasterxml.jackson.databind.JsonNode; import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.node.ArrayNode; @@ -105,6 +108,9 @@ public class CWLUtil { Map<String, Integer> result = new HashMap<>(); + if (inputs == null) + return result; + if (inputs.getClass() == ArrayNode.class) { Iterator<JsonNode> iterator = inputs.iterator(); @@ -118,17 +124,31 @@ public class CWLUtil { typeConfigurations = input.get(TYPE); // if type :single argument if (typeConfigurations.getClass() == TextNode.class) { - if(isValidArrayType(typeConfigurations.asText())) + // inputs: + // -id: input_1 + // type: int[] + if (isValidArrayType(typeConfigurations.asText())) result.put(currentInputId, DEPTH_1); + // inputs: + // -id: input_1 + // type: int or int? else - result.put(currentInputId, DEPTH_0); + result.put(currentInputId, DEPTH_0); // type : defined as another map which contains type: } else if (typeConfigurations.getClass() == ObjectNode.class) { + // inputs: + // -id: input_1 + // type: + // type: array or int[] String inputType = typeConfigurations.get(TYPE).asText(); - if (inputType.equals(ARRAY)) { + if (inputType.equals(ARRAY)||isValidArrayType(inputType)) { result.put(currentInputId, DEPTH_1); } + // inputs: + // -id: input_1 + // type: + // type: ["null",int] } else if (typeConfigurations.getClass() == ArrayNode.class) { if (isValidDataType(typeConfigurations)) { result.put(currentInputId, DEPTH_0); @@ -143,9 +163,44 @@ public class CWLUtil { } } else if (inputs.getClass() == ObjectNode.class) { - for (JsonNode parameter : inputs) { - if (parameter.asText().startsWith("$")) - System.out.println("Exception"); + + Iterator<Entry<String, JsonNode>> iterator = inputs.fields(); + + while (iterator.hasNext()) { + Entry<String, JsonNode> entry = iterator.next(); + String currentInputId = entry.getKey(); + JsonNode typeConfigurations = entry.getValue(); + + + if (typeConfigurations.getClass() == TextNode.class) { + if (typeConfigurations.asText().startsWith("$")){ + System.out.println("Exception"); + } + // inputs: + // input_1: int[] + else if (isValidArrayType(typeConfigurations.asText())) + result.put(currentInputId, DEPTH_1); + // inputs: + // input_1: int + else + result.put(currentInputId, DEPTH_0); + + } else if (typeConfigurations.getClass() == ObjectNode.class) { + + if (typeConfigurations.has(TYPE)) { + String inputType = typeConfigurations.get(TYPE).asText(); + // inputs: + // input_1: + // type: array or int[] + if (inputType.equals(ARRAY) || isValidArrayType(inputType)) + result.put(currentInputId, DEPTH_1); + // inputs: + // input_1: + // type: int or int? + else + result.put(currentInputId, DEPTH_0); + } + } } } @@ -171,23 +226,32 @@ public class CWLUtil { PortDetail detail = new PortDetail(); String currentInputId = input.get(ID).asText(); - extractDescription(input, detail); - - extractFormat(input, detail); - - extractLabel(input, detail); - result.put(currentInputId, detail); + getParamDetails(result, input, detail, currentInputId); } } else if (inputs.getClass() == ObjectNode.class) { - for (JsonNode parameter : inputs) { - if (parameter.asText().startsWith("$")) - System.out.println("Exception"); + ObjectMapper mapper = new ObjectMapper(); + JsonNode inputs_json=mapper.valueToTree(inputs); + Iterator<Entry<String, JsonNode>> iterator = inputs_json.fields(); + while(iterator.hasNext()){ + PortDetail detail = new PortDetail(); + Entry<String, JsonNode> s=iterator.next(); + getParamDetails(result, s.getValue(), detail, s.getKey()); } } return result; } + private void getParamDetails(Map<String, PortDetail> result, JsonNode input, PortDetail detail, + String currentInputId) { + extractDescription(input, detail); + + extractFormat(input, detail); + + extractLabel(input, detail); + result.put(currentInputId, detail); + } + /** * This method is used for extracting the Label of a CWL input or Output * @@ -291,7 +355,8 @@ public class CWLUtil { * @return */ public boolean isValidDataType(JsonNode typeConfigurations) { - if(typeConfigurations==null) return false; + if (typeConfigurations == null) + return false; for (JsonNode type : typeConfigurations) { if (!(type.asText().equals(FLOAT) || type.asText().equals(NULL) || type.asText().equals(BOOLEAN) || type.asText().equals(INT) || type.asText().equals(STRING) || type.asText().equals(DOUBLE) @@ -300,23 +365,29 @@ public class CWLUtil { } return true; } - + /** * * This method is for figure out whether the parameter is an array or not. - * As from CWL document v1.0, array can be defined as "TYPE[]". For Example : int[] - * This method will look for "[]" sequence of characters in the end of the type and is provided type is a valid CWL TYPE or not - * @param type type of the CWL parameter + * As from CWL document v1.0, array can be defined as "TYPE[]". For Example + * : int[] This method will look for "[]" sequence of characters in the end + * of the type and is provided type is a valid CWL TYPE or not + * + * @param type + * type of the CWL parameter * @return */ - public boolean isValidArrayType(String type){ - if(type==null) return false; - Pattern pattern= Pattern.compile(ARRAY_SIGNATURE_BRACKETS); + public boolean isValidArrayType(String type) { + if (type == null) + return false; + Pattern pattern = Pattern.compile(ARRAY_SIGNATURE_BRACKETS); Matcher matcher = pattern.matcher(type); ObjectMapper mapper = new ObjectMapper(); - ArrayNode node =mapper.createArrayNode(); + ArrayNode node = mapper.createArrayNode(); node.add(type.split(ARRAY_SPLIT_BRACKETS)[0]); - if(matcher.find() && isValidDataType(node))return true; - else return false; + if (matcher.find() && isValidDataType(node)) + return true; + else + return false; } }
