format is stable and custom tool is updated
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/cabca1dd Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/cabca1dd Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/cabca1dd Branch: refs/heads/cwl-browse Commit: cabca1ddb32ed3ce7fc47995dec3cec4cb551493 Parents: a76e71b Author: ThilinaManamgoda <[email protected]> Authored: Mon Jun 20 21:26:24 2016 +0530 Committer: ThilinaManamgoda <[email protected]> Committed: Mon Jun 20 21:26:24 2016 +0530 ---------------------------------------------------------------------- .../CWLFiles/customtool1.cwl | 5 +- .../taverna/cwl/ui/view/CwlContextualView.java | 19 ++++- .../org/apache/taverna/cwl/CwlDumyActivity.java | 86 ++++++++++++++------ 3 files changed, 82 insertions(+), 28 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/cabca1dd/taverna-cwl-activity-ui/CWLFiles/customtool1.cwl ---------------------------------------------------------------------- diff --git a/taverna-cwl-activity-ui/CWLFiles/customtool1.cwl b/taverna-cwl-activity-ui/CWLFiles/customtool1.cwl index 20939e7..5d580fd 100644 --- a/taverna-cwl-activity-ui/CWLFiles/customtool1.cwl +++ b/taverna-cwl-activity-ui/CWLFiles/customtool1.cwl @@ -37,17 +37,20 @@ inputs: items: int label: input 2 testing label description: this is a short description of input 2 - + format: $expression + - id: input_3 type: String label: input 3 testing label description: this is a short description of input 3 + format: noNameSpace:testing outputs: - id: output_1 type: int label: output 1 testing label description: this is a short description of output 1 + format: just a string - id: ouput_2 type: String http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/cabca1dd/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/view/CwlContextualView.java ---------------------------------------------------------------------- diff --git a/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/view/CwlContextualView.java b/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/view/CwlContextualView.java index 2a036c7..0eb4484 100644 --- a/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/view/CwlContextualView.java +++ b/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/view/CwlContextualView.java @@ -44,7 +44,6 @@ public class CwlContextualView extends HTMLBasedActivityContextualView<CwlActivi private static final String TABLE_WIDTH = "100%"; private static final String TABLE_CELL_PADDING = "5%"; - private static final String FORMAT = "format"; private final CwlActivityConfigurationBean configurationBean; private final CwlDumyActivity activity; @@ -130,16 +129,25 @@ public class CwlContextualView extends HTMLBasedActivityContextualView<CwlActivi HashMap<String, PortDetail> inputs = activity.getProcessedInputs(); if (inputs != null && !inputs.isEmpty()) for (String id : inputs.keySet()) { + PortDetail detail = inputs.get(id); + summery += "<tr align='left'><td> ID: " + id + " </td><td>Depth: " + detail.getDepth() + "</td></tr>"; + if (detail.getLabel() != null) { summery += "<tr><td align ='left' colspan ='2'>Label: " + detail.getLabel() + "</td></tr>"; } + if (detail.getDescription() != null) { summery = paragraphToHtml(summery, detail.getDescription()); } + + if (detail.getFormat() != null) { + summery += "<tr><td align ='left' colspan ='2'>Format: " + detail.getFormat() + "</td></tr>"; + } + // putting a space summery += "<tr></tr>"; } @@ -150,14 +158,23 @@ public class CwlContextualView extends HTMLBasedActivityContextualView<CwlActivi if (outPuts != null && !outPuts.isEmpty()) for (String id : outPuts.keySet()) { + PortDetail detail = outPuts.get(id); + summery += "<tr align='left'><td> ID: " + id + " </td><td>Depth: " + detail.getDepth() + "</td></tr>"; + if (detail.getLabel() != null) { summery += "<tr><td align ='left' colspan ='2'>Label: " + detail.getLabel() + "</td></tr>"; } + if (detail.getDescription() != null) { summery = paragraphToHtml(summery, detail.getDescription()); } + + if (detail.getFormat() != null) { + summery += "<tr><td align ='left' colspan ='2'>Format: " + detail.getFormat() + "</td></tr>"; + } + summery += "<tr></tr>"; } summery += "</table>"; http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/cabca1dd/taverna-cwl-activity/src/main/java/org/apache/taverna/cwl/CwlDumyActivity.java ---------------------------------------------------------------------- diff --git a/taverna-cwl-activity/src/main/java/org/apache/taverna/cwl/CwlDumyActivity.java b/taverna-cwl-activity/src/main/java/org/apache/taverna/cwl/CwlDumyActivity.java index 9b189ac..40f4f9f 100644 --- a/taverna-cwl-activity/src/main/java/org/apache/taverna/cwl/CwlDumyActivity.java +++ b/taverna-cwl-activity/src/main/java/org/apache/taverna/cwl/CwlDumyActivity.java @@ -40,7 +40,8 @@ public class CwlDumyActivity extends AbstractAsynchronousActivity<CwlActivityCon private static final int DEPTH_1 = 1; private static final int DEPTH_2 = 2; private static final String LABEL = "label"; - + private static final String EXPRESSSION = "$"; + private static final String COLON = ":"; private static final String NAMESPACES = "$namespaces"; // datatypes private static final String FLOAT = "float"; @@ -140,31 +141,14 @@ public class CwlDumyActivity extends AbstractAsynchronousActivity<CwlActivityCon PortDetail detail = new PortDetail(); String currentInputId = (String) input.get(ID); + + extractDescription(input, detail); + + extractFormat(input, detail); + + extractLabel(input, detail); + Object typeConfigurations; - // get the parameter description - if (input.containsKey(DESCRIPTION)) { - detail.setDescription((String) input.get(DESCRIPTION)); - } else { - detail.setDescription(null); - } - // get the parameter label - if (input.containsKey(LABEL)) { - detail.setLabel((String) input.get(LABEL)); - } else { - detail.setLabel(null); - } - // getting the format info - if (input.containsKey(FORMAT)) { - - String format[] = input.get(FORMAT).toString().split(":"); - String namespaceKey = format[0]; - String urlAppednd = format[1]; - if (!nameSpace.isEmpty()) { - detail.setFormat(nameSpace.get(namespaceKey) + urlAppednd); - } else { - detail.setFormat(null); - } - } try { typeConfigurations = input.get(TYPE); @@ -196,13 +180,63 @@ public class CwlDumyActivity extends AbstractAsynchronousActivity<CwlActivityCon } } else if (inputs.getClass() == LinkedHashMap.class) { for (Object parameter : ((Map) inputs).keySet()) { - if (parameter.toString().startsWith("$")) + if (parameter.toString().startsWith(EXPRESSSION)) System.out.println("Exception"); } } return result; } + private void extractLabel(Map input, PortDetail detail) { + if (input != null) + if (input.containsKey(LABEL)) { + detail.setLabel((String) input.get(LABEL)); + } else { + detail.setLabel(null); + } + } + + private void extractDescription(Map input, PortDetail detail) { + if (input != null) + if (input.containsKey(DESCRIPTION)) { + detail.setDescription((String) input.get(DESCRIPTION)); + } else { + detail.setDescription(null); + } + } + + private void extractFormat(Map input, PortDetail detail) { + if (input != null) + if (input.containsKey(FORMAT)) { + String formatInfo = input.get(FORMAT).toString(); + + if (formatInfo.startsWith(EXPRESSSION)) { + + detail.setFormat(formatInfo); + } else if (formatInfo.contains(COLON)) { + + String format[] = formatInfo.split(COLON); + String namespaceKey = format[0]; + String urlAppned = format[1]; + + if (!nameSpace.isEmpty()) { + if (nameSpace.containsKey(namespaceKey)) + detail.setFormat(nameSpace.get(namespaceKey) + urlAppned); + else + //Can't figure out the format defined + detail.setFormat(formatInfo); + } else { + //Can't figure out the format defined + detail.setFormat(formatInfo); + } + } else { + //Can't figure out the format defined + detail.setFormat(formatInfo); + } + + } + } + @Override public void executeAsynch(Map<String, T2Reference> arg0, AsynchronousActivityCallback arg1) { }
