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Posted to commits@taverna.apache.org by st...@apache.org on 2016/06/22 16:39:24 UTC
[05/11] incubator-taverna-common-activities git commit: format and
[null, int] resolving
format and [null,int] resolving
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/2d28ba83
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/2d28ba83
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/2d28ba83
Branch: refs/heads/cwl-browse
Commit: 2d28ba8300608a86c699691e278ced087e93cb7c
Parents: 7b75067
Author: ThilinaManamgoda <ma...@gmail.com>
Authored: Mon Jun 20 03:46:01 2016 +0530
Committer: ThilinaManamgoda <ma...@gmail.com>
Committed: Mon Jun 20 03:46:01 2016 +0530
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.../taverna/cwl/ui/serviceprovider/Testing.java | 6 ++-
.../taverna/cwl/ui/view/CwlContextualView.java | 1 +
.../org/apache/taverna/cwl/CwlDumyActivity.java | 55 +++++++++++++++++++-
.../java/org/apache/taverna/cwl/PortDetail.java | 7 +++
4 files changed, 65 insertions(+), 4 deletions(-)
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http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/2d28ba83/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/Testing.java
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diff --git a/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/Testing.java b/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/Testing.java
index 50d8063..c509d11 100644
--- a/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/Testing.java
+++ b/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/Testing.java
@@ -81,9 +81,11 @@ public static void main(String[] args) {
for(File file:cwlFiles)
try {
Yaml cwlReader = new Yaml();
- System.out.println(file.getName());
+ // System.out.println(file.getName());
Map cwlFile = (Map) cwlReader.load(new FileInputStream(file));
- processInputs(cwlFile);
+ //processInputs(cwlFile);
+ if(file.getName().equals("bedtool-genomecov.cwl"))System.out.println(((String)(( ArrayList<Map>)cwlFile.get(INPUTS)).get(0).get("format")).split(":")[0]);
+ if(file.getName().equals("bedtool-genomecov.cwl"))System.out.println(((Map)(cwlFile.get("$namespaces"))).get("edam"));
}catch(Exception e){
System.out.println(e.getMessage());
}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/2d28ba83/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 ddc5d4d..2a036c7 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
@@ -44,6 +44,7 @@ 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;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/2d28ba83/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 e8023f1..9b189ac 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
@@ -40,8 +40,21 @@ 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 NAMESPACES = "$namespaces";
+ // datatypes
+ private static final String FLOAT = "float";
+ private static final String NULL = "null";
+ private static final String BOOLEAN = "boolean";
+ private static final String INT = "int";
+ private static final String DOUBLE = "double";
+ private static final String STRING = "string";
+ private static final String FILE = "file";
+ private static final String FORMAT = "format";
+
private HashMap<String, PortDetail> processedInputs;
private HashMap<String, PortDetail> processedOutputs;
+ private LinkedHashMap nameSpace;
public HashMap<String, PortDetail> getProcessedInputs() {
return processedInputs;
@@ -59,12 +72,22 @@ public class CwlDumyActivity extends AbstractAsynchronousActivity<CwlActivityCon
this.processedOutputs = processedOutputs;
}
+ public void processNameSpace(Map cwlFile) {
+
+ if (cwlFile.containsKey(NAMESPACES)) {
+ nameSpace = (LinkedHashMap) cwlFile.get(NAMESPACES);
+ }
+
+ }
+
@Override
public void configure(CwlActivityConfigurationBean configurationBean) throws ActivityConfigurationException {
removeInputs();
removeOutputs();
Map cwlFile = configurationBean.getCwlConfigurations();
+ processNameSpace(cwlFile);
+
if (cwlFile != null) {
processedInputs = processInputs(cwlFile);
@@ -97,6 +120,16 @@ public class CwlDumyActivity extends AbstractAsynchronousActivity<CwlActivityCon
return process(cwlFile.get(INPUTS));
}
+ public boolean isValidDataType(ArrayList typeConfigurations) {
+ for (Object type : typeConfigurations) {
+ if (!(((String) type).equals(FLOAT) || ((String) type).equals(NULL)) || (((String) type).equals(BOOLEAN))
+ || (((String) type).equals(INT) || (((String) type).equals(DOUBLE)))
+ || (((String) type).equals(STRING)) || (((String) type).equals(FILE)))
+ return false;
+ }
+ return true;
+ }
+
private HashMap<String, PortDetail> process(Object inputs) {
HashMap<String, PortDetail> result = new HashMap<>();
@@ -108,18 +141,30 @@ public class CwlDumyActivity extends AbstractAsynchronousActivity<CwlActivityCon
String currentInputId = (String) input.get(ID);
Object typeConfigurations;
- //get the parameter description
+ // get the parameter description
if (input.containsKey(DESCRIPTION)) {
detail.setDescription((String) input.get(DESCRIPTION));
} else {
detail.setDescription(null);
}
- //get the parameter label
+ // 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);
@@ -135,6 +180,12 @@ public class CwlDumyActivity extends AbstractAsynchronousActivity<CwlActivityCon
detail.setDepth(DEPTH_1);
result.put(currentInputId, detail);
}
+ } else if (typeConfigurations.getClass() == ArrayList.class) {
+ if (isValidDataType((ArrayList) typeConfigurations)) {
+ detail.setDepth(DEPTH_0);
+ result.put(currentInputId, detail);
+ }
+
}
} catch (ClassCastException e) {
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/2d28ba83/taverna-cwl-activity/src/main/java/org/apache/taverna/cwl/PortDetail.java
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diff --git a/taverna-cwl-activity/src/main/java/org/apache/taverna/cwl/PortDetail.java b/taverna-cwl-activity/src/main/java/org/apache/taverna/cwl/PortDetail.java
index 8899344..18ab918 100644
--- a/taverna-cwl-activity/src/main/java/org/apache/taverna/cwl/PortDetail.java
+++ b/taverna-cwl-activity/src/main/java/org/apache/taverna/cwl/PortDetail.java
@@ -23,6 +23,7 @@ public class PortDetail {
private int depth;
private String description;
private String label;
+ private String format;
public int getDepth() {
return depth;
}
@@ -41,6 +42,12 @@ public class PortDetail {
public void setLabel(String label) {
this.label = label;
}
+ public String getFormat() {
+ return format;
+ }
+ public void setFormat(String format) {
+ this.format = format;
+ }
}